Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013379.1 Corchorus capsularis cultivar CVL-1 contig13400, 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: 7275
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 5--37  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

          1 GATG

                                                             
          5 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         38 GGAGTAGGAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1707 original size:22 final size:23

Alignment explanation


    Indices: 1682--1727  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1672 TTCTCTGTTT

                       *           
       1682 TTTTAG-AACTTCTTTGTGAGAG
          1 TTTTAGAAACTCCTTTGTGAGAG

                *                  
       1704 TTTTTGAAACTCCTTTGTGAGAG
          1 TTTTAGAAACTCCTTTGTGAGAG

             
       1727 T
          1 T

       1728 ATTTTCTATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  22    5  0.24
  23   16  0.76

ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46


Consensus pattern (23 bp):   
TTTTAGAAACTCCTTTGTGAGAG

Found at i:1714 original size:23 final size:24

Alignment explanation


    Indices: 1688--1732  Score: 74
    Period size: 23  Copynumber: 1.9  Consensus size: 24

       1678 GTTTTTTTAG

                *                   
       1688 AACTTCTTTGTGAGAGT-TTTTGA
          1 AACTCCTTTGTGAGAGTATTTTGA

                                  
       1711 AACTCCTTTGTGAGAGTATTTT
          1 AACTCCTTTGTGAGAGTATTTT

       1733 CTATTGTCTT


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

Matches are distributed among these distances:
  23   16  0.80
  24    4  0.20

ACGTcount: A:0.22, C:0.11, G:0.20, T:0.47


Consensus pattern (24 bp):   
AACTCCTTTGTGAGAGTATTTTGA

Found at i:3612 original size:6 final size:6

Alignment explanation


    Indices: 3597--3628  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       3587 AAAACAAAGC

                                                  
       3597 AAAT-T AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       3629 GCAGATTATA


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

Matches are distributed among these distances:
   5    4  0.15
   6   22  0.85

ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31


Consensus pattern (6 bp):   
AAATCT

Found at i:3640 original size:12 final size:13

Alignment explanation


    Indices: 3625--3658  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       3615 AATCTAAATC

                   *     
       3625 TAAAGCAGATT-A
          1 TAAAGCAAATTAA

                         
       3637 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       3650 TAAAGCAAA
          1 TAAAGCAAA

       3659 CAATAATTAA


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

Matches are distributed among these distances:
  12   10  0.50
  13   10  0.50

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


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:5184 original size:12 final size:11

Alignment explanation


    Indices: 5130--5188  Score: 50
    Period size: 12  Copynumber: 5.4  Consensus size: 11

       5120 AAATACTTAC

                   *   
       5130 AAAATAGGATA
          1 AAAATAGTATA

                *  *    
       5141 AAAACACATATA
          1 AAAATA-GTATA

                       
       5153 AAAATAGTA-A
          1 AAAATAGTATA

               *       
       5163 AAAGTA-TATA
          1 AAAATAGTATA

                        
       5173 AAAATAGCTATA
          1 AAAATAG-TATA

                
       5185 AAAA
          1 AAAA

       5189 CATGCATAAT


Statistics
Matches: 37,  Mismatches: 7, Indels: 7
        0.73            0.14        0.14

Matches are distributed among these distances:
   9    2  0.05
  10   12  0.32
  11    7  0.19
  12   16  0.43

ACGTcount: A:0.66, C:0.05, G:0.08, T:0.20


Consensus pattern (11 bp):   
AAAATAGTATA
Done.