Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009722.1 Corchorus capsularis cultivar CVL-1 contig09743, 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: 21038
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:12942 original size:25 final size:25

Alignment explanation


    Indices: 12914--13004  Score: 119
    Period size: 25  Copynumber: 3.6  Consensus size: 25

      12904 CGCTCATGTT

                     *         *  ** 
      12914 CTTGCGTTTGGCAAACGAGTCTACG
          1 CTTGCGTTTAGCAAACGAGCCTGTG

                   *                 
      12939 CTTGCGTATAGCAAACGAGCCTGTG
          1 CTTGCGTTTAGCAAACGAGCCTGTG

                            *        
      12964 CTTGCGTTTAGCAAACAAGCCTGTG
          1 CTTGCGTTTAGCAAACGAGCCTGTG

                       *    
      12989 CTTGCGTTTAGAAAAC
          1 CTTGCGTTTAGCAAAC

      13005 ACATAGGCTG


Statistics
Matches: 58,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   58  1.00

ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27


Consensus pattern (25 bp):   
CTTGCGTTTAGCAAACGAGCCTGTG

Found at i:13751 original size:21 final size:22

Alignment explanation


    Indices: 13726--13775  Score: 68
    Period size: 21  Copynumber: 2.3  Consensus size: 22

      13716 AAAAAATCTT

                                   
      13726 TATTTTAAATAAATA-ATTTT-A
          1 TATTTTAAA-AAATACATTTTGA

                                  
      13747 TATTTTAAAAAATACATTTTGA
          1 TATTTTAAAAAATACATTTTGA

             *     
      13769 TTTTTTA
          1 TATTTTA

      13776 TTTTTTTAAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  20    5  0.19
  21   14  0.54
  22    7  0.27

ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54


Consensus pattern (22 bp):   
TATTTTAAAAAATACATTTTGA

Found at i:17136 original size:35 final size:35

Alignment explanation


    Indices: 17090--17157  Score: 136
    Period size: 35  Copynumber: 1.9  Consensus size: 35

      17080 AGGTTAGTCT

                                               
      17090 CAATATTAGCTTTCCTTAAACTTTATTTTGTTGCA
          1 CAATATTAGCTTTCCTTAAACTTTATTTTGTTGCA

                                             
      17125 CAATATTAGCTTTCCTTAAACTTTATTTTGTTG
          1 CAATATTAGCTTTCCTTAAACTTTATTTTGTTG

      17158 TCATATTCTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   33  1.00

ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50


Consensus pattern (35 bp):   
CAATATTAGCTTTCCTTAAACTTTATTTTGTTGCA

Found at i:17560 original size:6 final size:6

Alignment explanation


    Indices: 17549--17582  Score: 59
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      17539 TTAATAATCT

                                                   
      17549 ATTATA ATTATA ATTATA ATTATA ATTAATA ATT
          1 ATTATA ATTATA ATTATA ATTATA ATT-ATA ATT

      17583 TATTTCTCAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   21  0.78
   7    6  0.22

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


Consensus pattern (6 bp):   
ATTATA

Found at i:19646 original size:60 final size:60

Alignment explanation


    Indices: 19571--19686  Score: 214
    Period size: 60  Copynumber: 1.9  Consensus size: 60

      19561 AACGTTTAAG

                                                    *                   
      19571 CCCAATTTGGTCCTGTTTAAAGGTTTAACCTCAAATTGAATAAATTTGGAAATGTTTAGA
          1 CCCAATTTGGTCCTGTTTAAAGGTTTAACCTCAAATTGAACAAATTTGGAAATGTTTAGA

                                *                                   
      19631 CCCAATTTGGTCCTGTTTAAGGGTTTAACCTCAAATTGAACAAATTTGGAAATGTT
          1 CCCAATTTGGTCCTGTTTAAAGGTTTAACCTCAAATTGAACAAATTTGGAAATGTT

      19687 ACCACTTATA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  60   54  1.00

ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Consensus pattern (60 bp):   
CCCAATTTGGTCCTGTTTAAAGGTTTAACCTCAAATTGAACAAATTTGGAAATGTTTAGA
Done.