Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006908.1 Corchorus capsularis cultivar CVL-1 contig06929, 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: 29323
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32


Found at i:1218 original size:24 final size:24

Alignment explanation


    Indices: 1177--1224  Score: 62
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       1167 GCAAAAAGCA

                                     
       1177 TTTTTTTTTAAAGGAAAACACAAAT
          1 TTTTTTTTTAAA-GAAAACACAAAT

                               *    
       1202 TTTTTTTTTAGAA-AAAACGCAAA
          1 TTTTTTTTTA-AAGAAAACACAAA

       1225 AACAAAACTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  24    9  0.43
  25   10  0.48
  26    2  0.10

ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40


Consensus pattern (24 bp):   
TTTTTTTTTAAAGAAAACACAAAT

Found at i:2745 original size:10 final size:10

Alignment explanation


    Indices: 2730--2754  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       2720 TAACTCCAAT

                      
       2730 TATGGACTTA
          1 TATGGACTTA

                      
       2740 TATGGACTTA
          1 TATGGACTTA

                 
       2750 TATGG
          1 TATGG

       2755 GCTGAATATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40


Consensus pattern (10 bp):   
TATGGACTTA

Found at i:6518 original size:24 final size:24

Alignment explanation


    Indices: 6473--6518  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       6463 TCGCAAAAAG

                             *      
       6473 CAATTTTTTTTTTAAAGGAAAACA
          1 CAATTTTTTTTTTAAAGAAAAACA

                         **       
       6497 CAATTTTTTTTTTTTAGAAAAA
          1 CAATTTTTTTTTTAAAGAAAAA

       6519 ACGCAAAAAC


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48


Consensus pattern (24 bp):   
CAATTTTTTTTTTAAAGAAAAACA

Found at i:9745 original size:55 final size:55

Alignment explanation


    Indices: 9699--9879  Score: 183
    Period size: 55  Copynumber: 3.3  Consensus size: 55

       9689 GATAAATAGC

                                     *                      *      
       9699 TTGATCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAA
          1 TTGATCCTGATGGTGTTGCCTTCAAATTATCATTCAGATCATCTGGACTAAAAAA

               *                 *   *             *      *       *   
       9754 TTGGTCCTGATGGTGTTGTCAATTAAAAATTA-C--TCAAATCATCGGGACTAATAAA
          1 TTGATCCTGATGGTGTTG-C-CTT-CAAATTATCATTCAGATCATCTGGACTAAAAAA

                               *      *                              
       9809 TTGATCCCT-ATGGTGTTGTCTTCAATTTATCATTCAGATCATCTGGA-TCAAAAAA
          1 TTGAT-CCTGATGGTGTTGCCTTCAAATTATCATTCAGATCATCTGGACT-AAAAAA

               *            
       9864 TTGTTCCTGATGGTGT
          1 TTGATCCTGATGGTGT

       9880 AATATTTAAT


Statistics
Matches: 100,  Mismatches: 17, Indels: 18
        0.74            0.13        0.13

Matches are distributed among these distances:
  52    5  0.05
  53    3  0.03
  54    4  0.04
  55   76  0.76
  56    4  0.04
  57    3  0.03
  58    5  0.05

ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36


Consensus pattern (55 bp):   
TTGATCCTGATGGTGTTGCCTTCAAATTATCATTCAGATCATCTGGACTAAAAAA

Found at i:27287 original size:2 final size:2

Alignment explanation


    Indices: 27280--27308  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      27270 TTGTCGGTTT

                                                       
      27280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      27309 GAGGTTTTGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:29042 original size:12 final size:13

Alignment explanation


    Indices: 29019--29051  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

      29009 CGTGGATTTT

                         
      29019 ATAAAA-AAAATA
          1 ATAAAATAAAATA

                         
      29031 A-AAAATAAAATA
          1 ATAAAATAAAATA

                     
      29043 ATAAAATAA
          1 ATAAAATAA

      29052 TCATTCTTTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  11    4  0.21
  12    8  0.42
  13    7  0.37

ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18


Consensus pattern (13 bp):   
ATAAAATAAAATA

Found at i:29097 original size:31 final size:31

Alignment explanation


    Indices: 29059--29160  Score: 109
    Period size: 31  Copynumber: 3.3  Consensus size: 31

      29049 TAATCATTCT

                     *              **      
      29059 TTATATCCTGAAATGATCGCTTT-TTGAAACG
          1 TTATATCCTAAAATGATCG-TTTCCAGAAACG

                                           
      29090 TTATATCCTAAAATGATCGTTTCCAGAAACG
          1 TTATATCCTAAAATGATCGTTTCCAGAAACG

                    *   *        **         
      29121 TTATATCCCAAATTGATCG-TGGCAGCAAACG
          1 TTATATCCTAAAATGATCGTTTCCAG-AAACG

                     
      29152 TTATATCCT
          1 TTATATCCT

      29161 GAATTGGTTA


Statistics
Matches: 61,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  30    7  0.11
  31   54  0.89

ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34


Consensus pattern (31 bp):   
TTATATCCTAAAATGATCGTTTCCAGAAACG

Done.