Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002587.1 Corchorus olitorius cultivar O-4 contig02588, 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, 750

Length: 1250
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:63 original size:21 final size:21

Alignment explanation


    Indices: 37--149  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

         27 TGCTAGAAGT

                                 
         37 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                                 
         58 TCATTGGAGCAAGTTCCAAGC
          1 TCATTGGAGCAAGTTCCAAGC

                       *        *
         79 TCATTGGAGCAGGTTCCAAGA
          1 TCATTGGAGCAAGTTCCAAGC

                                 *
        100 TCATTGGAG-AAGGTTCCAAGA
          1 TCATTGGAGCAA-GTTCCAAGC

                            *     
        121 TCATTGGAG-AAGGTTTCAAGC
          1 TCATTGGAGCAA-GTTCCAAGC

                    
        142 TCATTGGA
          1 TCATTGGA

        150 AATGCCTAAG


Statistics
Matches: 86,  Mismatches: 5, Indels: 2
        0.92            0.05        0.02

Matches are distributed among these distances:
  20    1  0.01
  21   85  0.99

ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGCAAGTTCCAAGC

Found at i:1237 original size:154 final size:154

Alignment explanation


    Indices: 949--1250  Score: 421
    Period size: 154  Copynumber: 2.0  Consensus size: 154

        939 GATTCGTATC

                    *                                         *   *          
        949 AGTTAGGCTATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGATGACGATTCAAAACG
          1 AGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACG

            *                                            *            *      
       1014 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAATC
         66 AAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAATC

                                    
       1079 GACTAATCTCACCAAAATAATTAT
        131 GACTAATCTCACCAAAATAATTAT

                                                           *                 
       1103 AGTTAGGCCATAAACAACTT-AAAGAAAAGC-TTCGAGGATTT-CCATATCGAAGACAATTCAAA
          1 AGTTAGGCCATAAACAA-TTGAAAGAAAAGCATT-GAGG-TTTGCCAAATCGAAGACAATTCAAA

                    *       *      *                           *   *         
       1165 ACGAAACTTATGGGCCTCGATAGTCCCAAAATAACAAGTGTTCCAAATGAGTTAATAACTTAACA
         63 ACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACA

            * *         *        
       1230 GTGGACTAATCTGACCAAAAT
        128 ATCGACTAATCTCACCAAAAT


Statistics
Matches: 130,  Mismatches: 15, Indels: 6
        0.86            0.10        0.04

Matches are distributed among these distances:
 153    2  0.02
 154  123  0.95
 155    5  0.04

ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23


Consensus pattern (154 bp):   
AGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACAATTCAAAACG
AAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTAACAATC
GACTAATCTCACCAAAATAATTAT
Done.