Read alignments to edited mRNA cyb

from to

Legend

The edited mRNA is shown in traditional 5'->3' direction. The mapped putative guide RNAs are shown in 3'->5' direction. The nucleotides of the mapped putative guide RNAs are color coded according to the following scheme:

An example of this with an excerpt of an edited mRNA on top and a single putative guide RNA on the bottom looks like this:
ATTATTTTTTTATGTTTTTGTTTCGTTGTATATTTGTTGGTGTTAGTGGTGTTTTTGTTTTTTTATCTT
   TTTTTTTTTTTTTAATATTGTTAGTATATGATCAACTGCAATTACCACAAAAACATATATA

Putative guide RNAs

    1 GTTAAGAATAATGGTTATAAATTTTATATAAATATGTTTCGTTGTAGATTTTTATTATTTTTTTTATTATTTAGAAATTTGTGTTGTCTTTTAATGTCAGGTTGTTTATATAGAATATATGGGGTAGGTTTTAGTTTAGGATTTTTTATAGCATTGCAAATAATTTGTGGAGTGTGTTTAGCTTGATTATTTTTTAGTTGTTTTATTTGTTCAAATTGATATTTTGTATTATTTTTATGAGATTTTGATTTGGGTTTTGTGATAAGAAGTGTACATATATGTTTTACATCTTTATTATATTTACTATTATATATCCATATATTTAAGTCAATAACGTTAATAATATTGTTTGACACACATATATTAGTATGATTTATAGGTTTTATATTGTTTGTATTTATAATAATAATAGCTTTTATAGGATATGTACTGCCTTGTACAATGATGTCATACTGAGGTTTAACGGTGTTTAGTAATATTATAGCAACAGTACCAATTTTAGGTATATGATTATGTTATTGAATTTGGGGAAGTGAATTTATAAACGATTTTACATTATTAAAGTTACATGTATTACATGTGTTATTACCATTTATATTACTAATAATATTAATTTTACATTTATTTTGTCTACATTATTTTATGAGTTCTGATGCATTTTGTGATAGGTTTGCATTTTATTGTGAAAGATTAAGTTTTTGTATGTGGTTTTATTTGAGAGATATGTTTTTAGCATTTTCAATATTATTATGTATGATGTATGTTATATTTATAAATTGGTATTTTGTATTTCATGAGGAATCTTGAGTTATAGTAGATACACTAAAAACATCAGATAAAATATTACCAGAATGATTTTTTTTGTATTTATTCGGTTTTTTAAAGGCAATCCCAGATAAGTTTATGGGTTTGTTTTTAATGGTTATTTTATTATTCTCATTATTTTTATTTATATTGAATTGTATATTATGATTTGTGTATTGTAGAAGTTCATTATTATGATTAACATATTCGTTAATATTATTTTATAGTATATGAATGAGTGGTTTTTTAGCATTATATGTAGTATTAGCATATCCAATATGAATGGAATTACAATACTGAGTATTATTATTATTTTTGTTGATAGTGTGTAGGTTAGATTAGTTTAGA 1152
                TTTTTTTTTTTTGATGAGTGTCGTACGAGGTGGTATTTGGAGGTAATAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAT
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTNGGATGTAGTGTATCATAAAATACAAC
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAAC
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                                 TTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTGTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                    TTTTTTTTGATGAGTGTCGTACGAGGTGGTATTTGGAGGTAATAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTNGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACTA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTCTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTAGTGTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACTA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                 TTTTTTTTATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGGAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                            TTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                     TTTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAANTACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                     TTTTTTTTTGTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACA
                                                                                                                                                                                                                                                                                                                                                                              TTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                TTTTTTTTTTTCAATAGGNGGGGTAANGAGTNTTTAGATGTAACAGAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                             TTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                     TTTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTANGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                    TTTTTTTCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTATGTAGTGTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACA
                                                                                                                                                                                                                                                                                                                                                                             TTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                            TTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAAC
                                                                                                                                                                                                                                                                                                                                                                     TTTTTTTATGTAGTGTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                          TTTTTTTTTTTTTTTATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TNNTTTTTTTTTTTAATTAAGNGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGATCATAAAATACGACAATATATA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                      TTTTTCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                         NTTTTTTTTTTTTAATTAAGTGTCTAGGNTGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGATCATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGCGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAAGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAAGAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACGA
                                                 TTTTTTTTTTCAATAGGAGGGGTAATGNGTCTTTNGATGTAANNGAAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TTTTTTTTTTTTATTAGTGAATGAAATAGATGTAGNGGCATCAAACAGTATATATA
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTAT
                                                TTTTTTTTCATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATA
                                             TTTTTTTTTTTTATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                           TTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACTAGTA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATC
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCAT
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                           TTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTATTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                           TTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                           TTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTGTCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                           TTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                TTTTTTTTTTTTTATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAAC
                                                                                                                                                                                                                                                                                                                                                                           TTTTTTTTTTTAATNAAGTGTCTAGGATGTAGTGTATCATAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA