Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009559.1 Corchorus capsularis cultivar CVL-1 contig09580, 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: 20831
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:113 original size:27 final size:27

Alignment explanation


    Indices: 70--145  Score: 95
    Period size: 27  Copynumber: 2.8  Consensus size: 27

         60 TAGGGAATTA

                                        
         70 ACTTTGAATGG-GAAACTGACTTGACT-
          1 ACTTTGAATGGAG-AACTGACTTGACTG

                                        
         96 AGCTTTGAATGGAGAACTGACTTGACTG
          1 A-CTTTGAATGGAGAACTGACTTGACTG

                *                  
        124 ACTTGGAAT-GAGAGACTGACTT
          1 ACTTTGAATGGAGA-ACTGACTT

        146 TGAATAATCC


Statistics
Matches: 45,  Mismatches: 1, Indels: 7
        0.85            0.02        0.13

Matches are distributed among these distances:
  26    5  0.11
  27   38  0.84
  28    2  0.04

ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29


Consensus pattern (27 bp):   
ACTTTGAATGGAGAACTGACTTGACTG

Found at i:5661 original size:21 final size:21

Alignment explanation


    Indices: 5635--5700  Score: 105
    Period size: 21  Copynumber: 3.1  Consensus size: 21

       5625 TAATCCTATG

                                 
       5635 TTGGAGGTTTCTTATTTATAT
          1 TTGGAGGTTTCTTATTTATAT

                                 
       5656 TTGGAGGTTTCTTATTTATAT
          1 TTGGAGGTTTCTTATTTATAT

                 **               
       5677 TTAGGTTGTTTCTTATTTATAT
          1 TT-GGAGGTTTCTTATTTATAT

              
       5699 TT
          1 TT

       5701 AGGTTTTCTT


Statistics
Matches: 42,  Mismatches: 2, Indels: 1
        0.93            0.04        0.02

Matches are distributed among these distances:
  21   23  0.55
  22   19  0.45

ACGTcount: A:0.18, C:0.05, G:0.17, T:0.61


Consensus pattern (21 bp):   
TTGGAGGTTTCTTATTTATAT

Found at i:5690 original size:22 final size:22

Alignment explanation


    Indices: 5641--5705  Score: 105
    Period size: 22  Copynumber: 3.0  Consensus size: 22

       5631 TATGTTGGAG

                                **
       5641 GTTTCTTATTTATATTT-GGAG
          1 GTTTCTTATTTATATTTAGGTT

                                  
       5662 GTTTCTTATTTATATTTAGGTT
          1 GTTTCTTATTTATATTTAGGTT

                                  
       5684 GTTTCTTATTTATATTTAGGTT
          1 GTTTCTTATTTATATTTAGGTT

       5706 TTCTTTATAA


Statistics
Matches: 41,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  21   17  0.41
  22   24  0.59

ACGTcount: A:0.18, C:0.05, G:0.15, T:0.62


Consensus pattern (22 bp):   
GTTTCTTATTTATATTTAGGTT

Found at i:11146 original size:27 final size:27

Alignment explanation


    Indices: 11116--11168  Score: 97
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      11106 CTACCTCCAT

                                       
      11116 TTTGGATGAGGATGCTAACAGGTGATC
          1 TTTGGATGAGGATGCTAACAGGTGATC

                              *       
      11143 TTTGGATGAGGATGCTAATAGGTGAT
          1 TTTGGATGAGGATGCTAACAGGTGAT

      11169 TGTGAAAGGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32


Consensus pattern (27 bp):   
TTTGGATGAGGATGCTAACAGGTGATC

Found at i:13962 original size:17 final size:19

Alignment explanation


    Indices: 13925--13962  Score: 53
    Period size: 20  Copynumber: 2.1  Consensus size: 19

      13915 CCATTCAGAG

                                
      13925 TCTTGTTCAATTTTGTTAAT
          1 TCTTGTTC-ATTTTGTTAAT

                               
      13945 TCTTGTTC-TTTT-TTAAT
          1 TCTTGTTCATTTTGTTAAT

             
      13962 T
          1 T

      13963 TTGAGAAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  17    6  0.33
  18    4  0.22
  20    8  0.44

ACGTcount: A:0.16, C:0.11, G:0.08, T:0.66


Consensus pattern (19 bp):   
TCTTGTTCATTTTGTTAAT
Done.