Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006411.1 Corchorus capsularis cultivar CVL-1 contig06432, 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: 13664
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:694 original size:17 final size:17

Alignment explanation


    Indices: 672--705  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        662 TTAGTTTTAA

                             
        672 TTTAGAATTCCTAAAAG
          1 TTTAGAATTCCTAAAAG

                             
        689 TTTAGAATTCCTAAAAG
          1 TTTAGAATTCCTAAAAG

        706 CTCATCTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35


Consensus pattern (17 bp):   
TTTAGAATTCCTAAAAG

Found at i:10968 original size:15 final size:15

Alignment explanation


    Indices: 10941--10973  Score: 50
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      10931 TGTTTAAAAA

                           
      10941 ATAATAATAATATAT
          1 ATAATAATAATATAT

                            
      10956 ATAA-AATATATATAT
          1 ATAATAATA-ATATAT

               
      10971 ATA
          1 ATA

      10974 TATATAATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    4  0.24
  15   13  0.76

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (15 bp):   
ATAATAATAATATAT

Found at i:10974 original size:21 final size:20

Alignment explanation


    Indices: 10938--10980  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 20

      10928 TTCTGTTTAA

                                
      10938 AAAATAATAATAATATATAT
          1 AAAATAATAATAATATATAT

                                  
      10958 AAAAT-ATATATATATATATAT
          1 AAAATAATA-ATA-ATATATAT

              
      10979 AA
          1 AA

      10981 TTTCCACTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  19    3  0.14
  20    8  0.38
  21   10  0.48

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (20 bp):   
AAAATAATAATAATATATAT

Found at i:11098 original size:26 final size:26

Alignment explanation


    Indices: 11069--11122  Score: 65
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      11059 AAGTATTGTC

                *             *        
      11069 CCTCTAGA-AAAAATGAGTGTTAGTAA
          1 CCTCAAGAGAAAAA-GAGCGTTAGTAA

                           *          
      11095 CCTCAAGAGAAAAAGGGCGTTAGTAA
          1 CCTCAAGAGAAAAAGAGCGTTAGTAA

              
      11121 CC
          1 CC

      11123 CCTAAATCAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  26   19  0.79
  27    5  0.21

ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20


Consensus pattern (26 bp):   
CCTCAAGAGAAAAAGAGCGTTAGTAA
Done.