Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010995.1 Corchorus capsularis cultivar CVL-1 contig11016, 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: 19875
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30


Found at i:7384 original size:33 final size:34

Alignment explanation


    Indices: 7336--7401  Score: 100
    Period size: 33  Copynumber: 2.0  Consensus size: 34

       7326 TTTAAATCGC

                                               
       7336 AAAAATCTTTTTTTTTAAGAAAA-ATCGGAAAAAG
          1 AAAAATCTTTTTTTTTAAGAAAAGA-CGGAAAAAG

                            *                
       7370 AAAAA-CTTTTTTTTTTAGAAAAGACGGAAAAA
          1 AAAAATCTTTTTTTTTAAGAAAAGACGGAAAAA

       7402 AACAAAAACT


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  33   24  0.80
  34    6  0.20

ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32


Consensus pattern (34 bp):   
AAAAATCTTTTTTTTTAAGAAAAGACGGAAAAAG

Found at i:7402 original size:34 final size:34

Alignment explanation


    Indices: 7335--7411  Score: 95
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       7325 TTTTAAATCG

                                               
       7335 CAAAAATCTTTTTTTTTAAGAAAAATCGG-AAAAA
          1 CAAAAA-CTTTTTTTTTAAGAAAAATCGGAAAAAA

            *               *                   
       7369 GAAAAACTTTTTTTTTTAGAAAAGA-CGGAAAAAAA
          1 CAAAAACTTTTTTTTTAAGAAAA-ATCGG-AAAAAA

                    
       7404 CAAAAACT
          1 CAAAAACT

       7412 AATTGTTGAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  33   19  0.51
  34    6  0.16
  35   12  0.32

ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29


Consensus pattern (34 bp):   
CAAAAACTTTTTTTTTAAGAAAAATCGGAAAAAA

Found at i:18056 original size:24 final size:26

Alignment explanation


    Indices: 18008--18061  Score: 76
    Period size: 24  Copynumber: 2.1  Consensus size: 26

      17998 TATAATGCAA

                   *                   
      18008 AAATCAACACTAATAAAAACTTAAAAG
          1 AAATCAAAACTAATAAAAAC-TAAAAG

                                      
      18035 AAATCAAAAC-AATAAAAA-TAAAAG
          1 AAATCAAAACTAATAAAAACTAAAAG

               
      18059 AAA
          1 AAA

      18062 GGATATAGAT


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

Matches are distributed among these distances:
  24    9  0.35
  26    8  0.31
  27    9  0.35

ACGTcount: A:0.70, C:0.11, G:0.04, T:0.15


Consensus pattern (26 bp):   
AAATCAAAACTAATAAAAACTAAAAG
Done.