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
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTATCTAGGATGTAGTGATCATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATAT
                                            TTTTTTTTTTTTTATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                   TTTTTTTTTGATAAGAGTCGTNTAGGGTGGTNTTTGNGAGTAATAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
               TTTTTTTTTTTTTGATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTATGTAGTGTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TNTTTTTTTTTTTTTAATTAAGNGTCTAGGATGTAGTGTATCATAANATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                          TTTTTTTTTTTTTTTATCAATNGGNGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAAAA
                                            TTTTTTTTTTTTTATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAA
                      TTTTTTTATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                 TTTTTTTTTTTGATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                TTTTTTTTTTTTTATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                    TTTTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTATCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTGGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAAC
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                              TTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAGCAATATATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                TTTTTTTTTTTTGATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                     TTTTGTGTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                 NTTTTTTTTTTTTTAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                              TTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                             TTTTTTTTTTTTTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                TTTTTTTTTTTTTATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAA
              TTTTTTTTTTTTTTGATAAGAGTCGTATAGGGTGGTATTTGAGAGTGATAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                       TTTTTTAAGGGATCTCTCATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                         TTTTTTTTTTTCTCTCATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                       TTTTTTTTTTTTGTCGTATAGGGTGGTATTTGAGAGTAATAAAA
                                                                                                                                                                                                                                                                                                                                                                       TTTGTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                              TTTTTTTTAATTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                           TTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
               TTTTTTTTTTTTTGATAAGAGTCGTATAGGGTGGTATTTGAGAGTAATAAAAAAAAAA
                                             TTTTTTTTTTTTATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                            TTTTTTTTTTAGTTAAGTGTCTAGGATGTAGTGTACATAAAATACAACAATATATA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAN
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAN
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTGAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
            TTTTTTTTTTTTTTATGATGAGTGTCGTACGAGGTGGTATTTGGAGGTAATAAAAAAANNA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                              TTTTATCTCTCATCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAA
                                                                                                                                                                                                                                                                                                                                                                       TTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACNN
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                          TTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGNGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                             TTTTTTTTTTTTTTCAATAGGAGGGGTAATGAGTCTTTAGATGTAACAGAAAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            TTTTTTTTTTTTTTAAAATGTAATAATTTCAATGTNCATAATGTACACAATAATGGTAAATATA
                 TTTTTTTTTTTGATGAGTGTCGTACGAGGTGGTANTNGGAGGTAATAAAAAAAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAAC
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAA
                                                                                                                                                                                                                                                                                                                                                                      TTTTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTGTATCATAAAATACAACA
                                                                                                                                                                                                                                                                                                                                                                         TTTTTTTTTTTTTAATTAAGTGTCTAGGATGTNGTGTATCATAAAATACAACAA
                                                                                                                                                                                                                                                                                                                                                                        TTTTTTTTTTTTTTAATTAAGTGTCTAGGATGTAGTNTATCATAAAATACNA