Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002625.1 Corchorus capsularis cultivar CVL-1 contig02633, 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: 1770
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37


Found at i:188 original size:25 final size:25

Alignment explanation


    Indices: 160--218  Score: 86
    Period size: 25  Copynumber: 2.4  Consensus size: 25

        150 CCTGTAATTA

                                  *   
        160 TTCTTTTGGCCGA-AGTATGTATTGT
          1 TTCTTTTGGCCGAGAGTATGTACT-T

                                     
        185 TTCTTTTGG-CGAGAGTATGTACTT
          1 TTCTTTTGGCCGAGAGTATGTACTT

                      
        209 TTCTTTTGGC
          1 TTCTTTTGGC

        219 TAGTGCCAAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  24   13  0.42
  25   18  0.58

ACGTcount: A:0.14, C:0.14, G:0.24, T:0.49


Consensus pattern (25 bp):   
TTCTTTTGGCCGAGAGTATGTACTT

Found at i:1281 original size:33 final size:33

Alignment explanation


    Indices: 1181--1285  Score: 131
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       1171 TTGAAAAGAG

                    *               *        
       1181 TGTTTTAGATGTTGTTTGCGATGATACTAAATC
          1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

             **                 *    *        
       1214 TAATTT-GAGTGTTGTTTGCAATGACACTAAATC
          1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC

                              *              
       1247 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
          1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

                  
       1280 TGTTTT
          1 TGTTTT

       1286 GGATGCTAAT


Statistics
Matches: 60,  Mismatches: 10, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    1  0.02
  33   58  0.97
  34    1  0.02

ACGTcount: A:0.25, C:0.09, G:0.21, T:0.46


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC

Found at i:1299 original size:33 final size:32

Alignment explanation


    Indices: 1234--1321  Score: 97
    Period size: 33  Copynumber: 2.7  Consensus size: 32

       1224 GTTGTTTGCA

                *                   * **     
       1234 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTG
          1 ATGAAACTAAATCTGTTTT-GGTGCTAATTGTG

                                             
       1267 ATGAAACTAAATCTGTTTTGGATGCTAATTGTG
          1 ATGAAACTAAATCTGTTTTGG-TGCTAATTGTG

                       *           
       1300 ATGAAAAC-AATTCTGTTTTGGT
          1 ATG-AAACTAAATCTGTTTTGGT

       1322 TGAACATAGC


Statistics
Matches: 48,  Mismatches: 5, Indels: 5
        0.83            0.09        0.09

Matches are distributed among these distances:
  32    3  0.06
  33   41  0.85
  34    4  0.08

ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42


Consensus pattern (32 bp):   
ATGAAACTAAATCTGTTTTGGTGCTAATTGTG

Found at i:1390 original size:33 final size:31

Alignment explanation


    Indices: 1301--1421  Score: 111
    Period size: 33  Copynumber: 3.8  Consensus size: 31

       1291 CTAATTGTGA

                  *                          
       1301 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
          1 TGAAAATAA-TCTGTTTTGGTTG-ACATAGCAT

             *         * *    *              
       1334 TAAAAATAATTTTATTTTAGTTGATCATAGCAT
          1 TGAAAATAA-TCTGTTTTGGTTGA-CATAGCAT

              *                             
       1367 TGCAAATAATCCTGTTTTGGTTG--ATAGCAT
          1 TGAAAATAAT-CTGTTTTGGTTGACATAGCAT

                                *    
       1397 TGAAAATAAATCTGTTTTGGGTGAC
          1 TGAAAAT-AATCTGTTTTGGTTGAC

       1422 GAGAAAGAGA


Statistics
Matches: 71,  Mismatches: 12, Indels: 11
        0.76            0.13        0.12

Matches are distributed among these distances:
  30   24  0.34
  31    3  0.04
  32    2  0.03
  33   42  0.59

ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40


Consensus pattern (31 bp):   
TGAAAATAATCTGTTTTGGTTGACATAGCAT

Done.