Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012800.1 Corchorus capsularis cultivar CVL-1 contig12821, 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: 23535
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:6994 original size:28 final size:28

Alignment explanation


    Indices: 6954--7009  Score: 94
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       6944 CTAATGAACG

                          *             
       6954 CATTAATGGTGGTGTTTGAAAATAGTGT
          1 CATTAATGGTGGTGCTTGAAAATAGTGT

                                *       
       6982 CATTAATGGTGGTGCTTGAAGATAGTGT
          1 CATTAATGGTGGTGCTTGAAAATAGTGT

       7010 GTGATCAAAG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   26  1.00

ACGTcount: A:0.27, C:0.05, G:0.30, T:0.38


Consensus pattern (28 bp):   
CATTAATGGTGGTGCTTGAAAATAGTGT

Found at i:11401 original size:20 final size:21

Alignment explanation


    Indices: 11368--11409  Score: 68
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      11358 TTATAAAGAA

                             *   
      11368 AACTCACAATTCCGTGAGAGT
          1 AACTCACAATTCCGTGAAAGT

                                 
      11389 AACTCAC-ATTCCGTGAAAGT
          1 AACTCACAATTCCGTGAAAGT

             
      11409 A
          1 A

      11410 GAACCCAAGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  20   13  0.65
  21    7  0.35

ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24


Consensus pattern (21 bp):   
AACTCACAATTCCGTGAAAGT

Found at i:17135 original size:34 final size:33

Alignment explanation


    Indices: 17074--17145  Score: 92
    Period size: 34  Copynumber: 2.2  Consensus size: 33

      17064 TGGTGGAGTG

                                        *    
      17074 TTTGAAATAGTGATCAGAGATTCTTTTGGCTCC
          1 TTTGAAATAGTGATCAGAGATTCTTTTGACTCC

                           *                   
      17107 TTTGAATATAGTGATTAGAG-TTCTTTTTGACTCC
          1 TTTGAA-ATAGTGATCAGAGATTC-TTTTGACTCC

            *    
      17141 ATTGA
          1 TTTGA

      17146 TTTAGCAGGT


Statistics
Matches: 34,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  33    9  0.26
  34   25  0.74

ACGTcount: A:0.25, C:0.12, G:0.19, T:0.43


Consensus pattern (33 bp):   
TTTGAAATAGTGATCAGAGATTCTTTTGACTCC

Found at i:23515 original size:2 final size:2

Alignment explanation


    Indices: 23508--23535  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      23498 CGAAAATAAT

                                                     
      23508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.