Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006394.1 Corchorus capsularis cultivar CVL-1 contig06415, 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: 15224
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:1128 original size:14 final size:15

Alignment explanation


    Indices: 1101--1133  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       1091 AAGGAGGACT

                     *     
       1101 AAAAATAAAGAAAAG
          1 AAAAATAAAAAAAAG

                           
       1116 AAAAA-AAAAAAAAG
          1 AAAAATAAAAAAAAG

                
       1130 AAAA
          1 AAAA

       1134 CTGGAAGTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14   12  0.71
  15    5  0.29

ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03


Consensus pattern (15 bp):   
AAAAATAAAAAAAAG

Found at i:7261 original size:12 final size:13

Alignment explanation


    Indices: 7236--7269  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       7226 ATAATTATTG

                         
       7236 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
       7249 TTTGCTTTA-TAA
          1 TTTGCTTTATTAA

             *       
       7261 TCTGCTTTA
          1 TTTGCTTTA

       7270 GATTTAGATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   11  0.55
  13    9  0.45

ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:7618 original size:35 final size:35

Alignment explanation


    Indices: 7570--7640  Score: 106
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       7560 TTCAAGAATT

                   **        *        *        
       7570 AGTTTTTTGTTTTTCCGTTTTTTCTATAAAAAAAA
          1 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA

                                               
       7605 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA
          1 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA

             
       7640 A
          1 A

       7641 TTTGCTTTTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  35   32  1.00

ACGTcount: A:0.32, C:0.11, G:0.07, T:0.49


Consensus pattern (35 bp):   
AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA

Found at i:14417 original size:12 final size:13

Alignment explanation


    Indices: 14392--14425  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

      14382 ATAATTATTG

                         
      14392 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
      14405 TTTGCTTTA-TAA
          1 TTTGCTTTATTAA

             *       
      14417 TCTGCTTTA
          1 TTTGCTTTA

      14426 GATTTAGATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   11  0.55
  13    9  0.45

ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59


Consensus pattern (13 bp):   
TTTGCTTTATTAA
Done.