Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015537.1 Corchorus capsularis cultivar CVL-1 contig15558, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2863
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40


Found at i:903 original size:170 final size:170

Alignment explanation


    Indices: 570--876  Score: 465
    Period size: 170  Copynumber: 1.8  Consensus size: 170

        560 ATTGATAAAG

                                *               *               **           
        570 TTAGTCGTTAATCAACTTTGTCAATCAAAGTTATAATTGATTGATGATTATTTGATTTTGCCATA
          1 TTAGTCGTTAATCAACTTTGCCAATCAAAGTTATAACTGATTGATGATTATTACATTTTGCCATA

                                                    *       *                
        635 AATAAATGAATCAATTAGTAATTATGTTAGCAAAAAAATAGATTGATTGAACATACTAAATAAAT
         66 AATAAATGAATCAATTAGTAATTATGTTAGCAAAAAAATAAATTGATTCAACATACTAAATAAAT

            * *    *            *                   
        700 TAGTGAATCAAATTAGTCGATAATTAATTGCCAAAAAAAA
        131 AAATGAACCAAATTAGTCGACAATTAATTGCCAAAAAAAA

                        *                              *                     
        740 TTAGTCGTTAATTAACTTTGCCAATCAAAGTTATAACTGATTGGTGATTATTACA-TTTGCCATA
          1 TTAGTCGTTAATCAACTTTGCCAATCAAAGTTATAACTGATTGATGATTATTACATTTTGCCATA

                                            *           *         *          
        804 AATAAATGAATCAATTAGTAATTATGTTAGC-CAAAAATAAATTTATTCAACATGCTAAATAAAT
         66 AATAAATGAATCAATTAGTAATTATGTTAGCAAAAAAATAAATTGATTCAACATACTAAATAAAT

                     
        868 AAATGAACC
        131 AAATGAACC

        877 GAGATAGTCC


Statistics
Matches: 123,  Mismatches: 14, Indels: 2
        0.88            0.10        0.01

Matches are distributed among these distances:
 168   34  0.28
 169   40  0.33
 170   49  0.40

ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35


Consensus pattern (170 bp):   
TTAGTCGTTAATCAACTTTGCCAATCAAAGTTATAACTGATTGATGATTATTACATTTTGCCATA
AATAAATGAATCAATTAGTAATTATGTTAGCAAAAAAATAAATTGATTCAACATACTAAATAAAT
AAATGAACCAAATTAGTCGACAATTAATTGCCAAAAAAAA

Found at i:1182 original size:140 final size:141

Alignment explanation


    Indices: 1019--1348  Score: 509
    Period size: 141  Copynumber: 2.3  Consensus size: 141

       1009 TTAGTGATCG

                                    *             *     *                    
       1019 TTAGTTAATTTTGCCAATCAAAGTCGTAATTGATTGATAATTATTTAATTTTACCAT-AAATCGC
          1 TTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAATCGC

            *                *              *                                
       1083 TACCAAAAAAAGTAACATAAAGAAATAAATCATTTAGTAATTATGTTACCAAAAAAATAAATTAT
         66 CACCAAAAAAAGTAACACAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTAT

                       
       1148 TGAACATGTCA
        131 TGAACATGTCA

                         *    *                                              
       1159 TTAGTTAATTTTGTCAATTAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAATCGC
          1 TTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAATCGC

                       *  *      *                                           
       1224 CACCAAAAAAATTACCACAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTAT
         66 CACCAAAAAAAGTAACACAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTAT

                *     *
       1289 TGAATATGTCG
        131 TGAACATGTCA

              *                      *                  *    
       1300 TTTGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGATTATGTAAT
          1 TTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAAT

       1349 CAAAGTTGTA


Statistics
Matches: 171,  Mismatches: 18, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
 140   52  0.30
 141  119  0.70

ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37


Consensus pattern (141 bp):   
TTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAATCGC
CACCAAAAAAAGTAACACAAAGAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTAT
TGAACATGTCA

Found at i:2814 original size:2 final size:2

Alignment explanation


    Indices: 2807--2863  Score: 114
    Period size: 2  Copynumber: 28.5  Consensus size: 2

       2797 TATTGCAGAC

                                                                          
       2807 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                  
       2849 AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG A


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   55  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.