Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020772.1 Corchorus olitorius cultivar O-4 contig20805, 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: 16067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:885 original size:31 final size:29

Alignment explanation


    Indices: 775--890  Score: 96
    Period size: 29  Copynumber: 3.9  Consensus size: 29

        765 GTACAGGTCT

                           *               
        775 CTCTACTTACAAAA-AGATCAATTTG-GTCC
          1 CTCTACTTACAAAATTG-TCAA-TTGAGTCC

              *                            
        804 CTTTACTATA-AAAATTGTCAATTTG-GTCC
          1 CTCTACT-TACAAAATTGTCAA-TTGAGTCC

                        **                 
        833 CTCTACTTACAATTTGGTGTCAATTGAGTCC
          1 CTCTACTTACAAAAT--TGTCAATTGAGTCC

                                       
        864 CTCTACTTAACAAAATCTGTCAATTGA
          1 CTCTACTT-ACAAAAT-TGTCAATTGA

        891 TTATATATTT


Statistics
Matches: 72,  Mismatches: 8, Indels: 12
        0.78            0.09        0.13

Matches are distributed among these distances:
  28    2  0.03
  29   31  0.43
  30    6  0.08
  31   28  0.39
  32    5  0.07

ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36


Consensus pattern (29 bp):   
CTCTACTTACAAAATTGTCAATTGAGTCC

Found at i:1200 original size:31 final size:30

Alignment explanation


    Indices: 1128--1201  Score: 78
    Period size: 29  Copynumber: 2.5  Consensus size: 30

       1118 CACCAAATTA

                          *   *    *    * 
       1128 TAAGTAGAGGGACCGAATTGACAGTTTTTG
          1 TAAGTAGAGGGACCAAATCGACACTTTTGG

                   *               *       
       1158 T-AGTAGGGGGACCAAATCGATCCCTTTTGG
          1 TAAGTAGAGGGACCAAATCGA-CACTTTTGG

                          
       1188 TAAGTAGAGGGACC
          1 TAAGTAGAGGGACC

       1202 TGTACGGTAT


Statistics
Matches: 35,  Mismatches: 7, Indels: 3
        0.78            0.16        0.07

Matches are distributed among these distances:
  29   16  0.46
  30    8  0.23
  31   11  0.31

ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26


Consensus pattern (30 bp):   
TAAGTAGAGGGACCAAATCGACACTTTTGG

Found at i:15096 original size:6 final size:6

Alignment explanation


    Indices: 15081--15116  Score: 54
    Period size: 6  Copynumber: 5.8  Consensus size: 6

      15071 CAAAACTCTT

                 *                                   
      15081 AAAAAA AAAAAC AAAAAC AAAAAC AAAAAC ACAAAA
          1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC A-AAAA

      15117 TGCTAAACTG


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
   6   24  0.86
   7    4  0.14

ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00


Consensus pattern (6 bp):   
AAAAAC

Done.