Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004991.1 Corchorus capsularis cultivar CVL-1 contig05009, 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: 10524
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:4876 original size:25 final size:25

Alignment explanation


    Indices: 4829--4876  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       4819 TCATCAAGTC

                           ** *      
       4829 AAATAGGATTAACTCTTTCAACTCA
          1 AAATAGGATTAACTCACTAAACTCA

                                   
       4854 AAATAGGATTAACTCACTAAACT
          1 AAATAGGATTAACTCACTAAACT

       4877 TCATCTTTAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  25   20  1.00

ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29


Consensus pattern (25 bp):   
AAATAGGATTAACTCACTAAACTCA

Found at i:8521 original size:32 final size:32

Alignment explanation


    Indices: 8472--8566  Score: 102
    Period size: 33  Copynumber: 2.9  Consensus size: 32

       8462 AATTTGGTCT

                                             
       8472 AGCCGCCCCA-TGAGGGCGGCTTGCCGTGGAGA
          1 AGCCGCCCCAGTG-GGGCGGCTTGCCGTGGAGA

                 *              *     *   *  
       8504 AGCCGTCCCAGTGGGGCGGCCTGCCCATGGTGA
          1 AGCCGCCCCAGTGGGGCGGCTTG-CCGTGGAGA

                            *     *       
       8537 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGG
          1 AGCCGCCCCAGTGGGGCGGCT-TGCCGTGG

       8567 TTGAGCCTCC


Statistics
Matches: 51,  Mismatches: 9, Indels: 5
        0.78            0.14        0.08

Matches are distributed among these distances:
  32   18  0.35
  33   32  0.63
  34    1  0.02

ACGTcount: A:0.13, C:0.34, G:0.41, T:0.13


Consensus pattern (32 bp):   
AGCCGCCCCAGTGGGGCGGCTTGCCGTGGAGA

Found at i:8583 original size:33 final size:33

Alignment explanation


    Indices: 8537--8624  Score: 124
    Period size: 33  Copynumber: 2.7  Consensus size: 33

       8527 CCCATGGTGA

                *   *                     *  
       8537 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
          1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG

                                             
       8570 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG
          1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG

                       *           
       8603 AGCCGT-CCTAATGGGGAGGCTC
          1 AGCC-TCCCTAGTGGGGAGGCTC

       8625 AGTGTAAAAA


Statistics
Matches: 50,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  33   49  0.98
  34    1  0.02

ACGTcount: A:0.11, C:0.32, G:0.40, T:0.17


Consensus pattern (33 bp):   
AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG

Found at i:8599 original size:16 final size:16

Alignment explanation


    Indices: 8547--8599  Score: 54
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       8537 AGCCGCCCCA

                            
       8547 GTGGGGAGGCTCCGCC
          1 GTGGGGAGGCTCCGCC

                 *   *       *
       8563 GTGGTTGAGCCTCC-CTA
          1 GTGG-GGAGGCTCCGC-C

                            
       8580 GTGGGGAGGCTCCGCC
          1 GTGGGGAGGCTCCGCC

                
       8596 GTGG
          1 GTGG

       8600 CTGAGCCGTC


Statistics
Matches: 28,  Mismatches: 6, Indels: 6
        0.70            0.15        0.15

Matches are distributed among these distances:
  16   16  0.57
  17   12  0.43

ACGTcount: A:0.08, C:0.28, G:0.45, T:0.19


Consensus pattern (16 bp):   
GTGGGGAGGCTCCGCC

Found at i:9978 original size:14 final size:14

Alignment explanation


    Indices: 9957--9991  Score: 52
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       9947 AATAAAAACT

                    *     
       9957 AAAAAGAATGAAAA
          1 AAAAAGAAAGAAAA

             *            
       9971 ATAAAGAAAGAAAA
          1 AAAAAGAAAGAAAA

                   
       9985 AAAAAGA
          1 AAAAAGA

       9992 CACGTCGGGG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06


Consensus pattern (14 bp):   
AAAAAGAAAGAAAA
Done.