Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013286.1 Corchorus capsularis cultivar CVL-1 contig13307, 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: 8469
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:131 original size:13 final size:13

Alignment explanation


    Indices: 113--138  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        103 TATAAAAATT

                         
        113 CAAAAATTAAAAA
          1 CAAAAATTAAAAA

                         
        126 CAAAAATTAAAAA
          1 CAAAAATTAAAAA

        139 TTGGGTTGCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATTAAAAA

Found at i:1475 original size:15 final size:16

Alignment explanation


    Indices: 1443--1476  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1433 AAAGAAGAAT

                 *          
       1443 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       1459 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       1474 TAA
          1 TAA

       1477 GAAAGCAATC


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

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC

Found at i:4486 original size:23 final size:23

Alignment explanation


    Indices: 4456--4501  Score: 74
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4446 TGTTAGTTTG

                              *    
       4456 TAGAGACCGAGCAAGAGTGCTCA
          1 TAGAGACCGAGCAAGAGTACTCA

                        *          
       4479 TAGAGACCGAGCGAGAGTACTCA
          1 TAGAGACCGAGCAAGAGTACTCA

       4502 AGATTGTTTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.35, C:0.22, G:0.30, T:0.13


Consensus pattern (23 bp):   
TAGAGACCGAGCAAGAGTACTCA

Found at i:7855 original size:13 final size:14

Alignment explanation


    Indices: 7832--7862  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

       7822 AGTTATATCG

                          
       7832 AAAAATATAAAAAA
          1 AAAAATATAAAAAA

                          
       7846 AAAAAT-TAAAAAA
          1 AAAAATATAAAAAA

                
       7859 AAAA
          1 AAAA

       7863 TTTCGACCAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.65
  14    6  0.35

ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13


Consensus pattern (14 bp):   
AAAAATATAAAAAA
Done.