Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012519.1 Corchorus capsularis cultivar CVL-1 contig12540, 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: 55481
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:6860 original size:29 final size:29

Alignment explanation


    Indices: 6813--6936  Score: 130
    Period size: 29  Copynumber: 4.3  Consensus size: 29

       6803 ATCTTGGATA

                     *                    
       6813 TATGCCTTTGGAAGATTTT-TCCTAGGCTG
          1 TATGCCTTTAGAA-ATTTTATCCTAGGCTG

                               * *      * 
       6842 TATGCCTTTAGAAACTTTTGTAC-AGGCCG
          1 TATGCCTTTAGAAA-TTTTATCCTAGGCTG

                                          
       6871 TATGCCTTTAGAAATTTT-TACCTAGGCTG
          1 TATGCCTTTAGAAATTTTAT-CCTAGGCTG

                     *             *    *
       6900 TATGCCTTTGGAAATTTTAT-CTGGGCTA
          1 TATGCCTTTAGAAATTTTATCCTAGGCTG

                     
       6928 TATGCCTTT
          1 TATGCCTTT

       6937 GGGTAGGTTG


Statistics
Matches: 82,  Mismatches: 8, Indels: 11
        0.81            0.08        0.11

Matches are distributed among these distances:
  27    1  0.01
  28   21  0.26
  29   57  0.70
  30    3  0.04

ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41


Consensus pattern (29 bp):   
TATGCCTTTAGAAATTTTATCCTAGGCTG

Found at i:22913 original size:27 final size:26

Alignment explanation


    Indices: 22875--22927  Score: 97
    Period size: 27  Copynumber: 2.0  Consensus size: 26

      22865 AGAGCGAGTG

                                       
      22875 TGGTCGGCACAAAATTGCAAAAGCAAA
          1 TGGTCGGCACAAAATTGC-AAAGCAAA

                                      
      22902 TGGTCGGCACAAAATTGCAAAGCAAA
          1 TGGTCGGCACAAAATTGCAAAGCAAA

      22928 ACAAGAAAGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  26    8  0.31
  27   18  0.69

ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15


Consensus pattern (26 bp):   
TGGTCGGCACAAAATTGCAAAGCAAA

Found at i:47030 original size:13 final size:13

Alignment explanation


    Indices: 47012--47036  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      47002 AGATTTAGCC

                         
      47012 ATGTTAATATTGA
          1 ATGTTAATATTGA

                        
      47025 ATGTTAATATTG
          1 ATGTTAATATTG

      47037 TTTGCTTGGC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48


Consensus pattern (13 bp):   
ATGTTAATATTGA

Found at i:47873 original size:30 final size:30

Alignment explanation


    Indices: 47827--47933  Score: 178
    Period size: 30  Copynumber: 3.6  Consensus size: 30

      47817 ATGAAGTAGT

                *    *            *       
      47827 AGTGAAAGACAACAATGGAAACCAGCAGCA
          1 AGTGGAAGATAACAATGGAAACGAGCAGCA

             *                            
      47857 AATGGAAGATAACAATGGAAACGAGCAGCA
          1 AGTGGAAGATAACAATGGAAACGAGCAGCA

                                          
      47887 AGTGGAAGATAACAATGGAAACGAGCAGCA
          1 AGTGGAAGATAACAATGGAAACGAGCAGCA

                             
      47917 AGTGGAAGATAACAATG
          1 AGTGGAAGATAACAATG

      47934 TTGGAGAGGG


Statistics
Matches: 72,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  30   72  1.00

ACGTcount: A:0.49, C:0.14, G:0.27, T:0.10


Consensus pattern (30 bp):   
AGTGGAAGATAACAATGGAAACGAGCAGCA

Found at i:51527 original size:6 final size:6

Alignment explanation


    Indices: 51516--51542  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      51506 ATTAATCTGC

                                           
      51516 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

      51543 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:51834 original size:6 final size:6

Alignment explanation


    Indices: 51823--51852  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      51813 CCAAGAATTA

                                              
      51823 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
          1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT

      51853 TCTAAAAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83


Consensus pattern (6 bp):   
GTTTTT

Found at i:54048 original size:15 final size:14

Alignment explanation


    Indices: 54021--54068  Score: 69
    Period size: 15  Copynumber: 3.3  Consensus size: 14

      54011 AAGTACAAGA

                          
      54021 AACACCCACTGCCC
          1 AACACCCACTGCCC

                          *
      54035 AACACCCTACTGCCT
          1 AACACCC-ACTGCCC

                           
      54050 AACACCCCACTGCCC
          1 AACA-CCCACTGCCC

                
      54065 AACA
          1 AACA

      54069 ATCATCAGCC


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  14    7  0.23
  15   20  0.67
  16    3  0.10

ACGTcount: A:0.31, C:0.52, G:0.06, T:0.10


Consensus pattern (14 bp):   
AACACCCACTGCCC
Done.