Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011252.1 Corchorus capsularis cultivar CVL-1 contig11273, 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: 7809
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29


Found at i:133 original size:29 final size:29

Alignment explanation


    Indices: 101--175  Score: 91
    Period size: 29  Copynumber: 2.6  Consensus size: 29

         91 ATCACAAATG

                *              *          
        101 TGTGCACCTCCCACACACAGTAATGCTT-T
          1 TGTGAACCTCCCACACACAATAATG-TTCT

                        *                 
        130 TGTGAACCTCCCGCACACAATAATGTTCGT
          1 TGTGAACCTCCCACACACAATAATGTTC-T

                             
        160 T-TGAACCTCCCACACA
          1 TGTGAACCTCCCACACA

        176 TATGAGTTAT


Statistics
Matches: 40,  Mismatches: 4, Indels: 4
        0.83            0.08        0.08

Matches are distributed among these distances:
  28    2  0.05
  29   36  0.90
  30    2  0.05

ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25


Consensus pattern (29 bp):   
TGTGAACCTCCCACACACAATAATGTTCT

Found at i:3487 original size:19 final size:19

Alignment explanation


    Indices: 3460--3503  Score: 79
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       3450 AAGGCTACAG

                *              
       3460 AATGCCAGATACGATCTCA
          1 AATGTCAGATACGATCTCA

                               
       3479 AATGTCAGATACGATCTCA
          1 AATGTCAGATACGATCTCA

                  
       3498 AATGTC
          1 AATGTC

       3504 CCCAAGCACG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25


Consensus pattern (19 bp):   
AATGTCAGATACGATCTCA

Found at i:3540 original size:13 final size:13

Alignment explanation


    Indices: 3522--3548  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       3512 CGTTAAATTG

                         
       3522 AAAAAAAAAACAA
          1 AAAAAAAAAACAA

                         
       3535 AAAAAAAAAACAA
          1 AAAAAAAAAACAA

             
       3548 A
          1 A

       3549 GTGGAACAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAACAA

Found at i:7719 original size:51 final size:52

Alignment explanation


    Indices: 7601--7736  Score: 179
    Period size: 51  Copynumber: 2.7  Consensus size: 52

       7591 AATTTCATTT

                              *                  *            * *
       7601 GCACCATTACACCTTTAATTATGTAATAGGAATGCATCATATGACTTCAATTT
          1 GCACCATTACACCTTT-ACTATGTAATAGGAATGCATAATATGACTTCAACTG

               *                                                
       7654 GCATCATTACACCTTTACTATGTAATAGGAATGCATAATA-GACTTCAACTG
          1 GCACCATTACACCTTTACTATGTAATAGGAATGCATAATATGACTTCAACTG

                     *       *                
       7705 GCACCATTATACCTTTAGTA-G-AATAGGAATGC
          1 GCACCATTACACCTTTACTATGTAATAGGAATGC

       7737 CTTATATCTT


Statistics
Matches: 75,  Mismatches: 8, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  49   11  0.15
  50    1  0.01
  51   26  0.35
  52   22  0.29
  53   15  0.20

ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32


Consensus pattern (52 bp):   
GCACCATTACACCTTTACTATGTAATAGGAATGCATAATATGACTTCAACTG
Done.