Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005472.1 Corchorus capsularis cultivar CVL-1 contig05490, 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: 3299
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Found at i:606 original size:32 final size:30

Alignment explanation


    Indices: 570--646  Score: 84
    Period size: 32  Copynumber: 2.5  Consensus size: 30

        560 TTTTAAAAGG

                                             
        570 GAAATTTCTTTGATTAAGTACCA-AAGAAAGAA
          1 GAAATTTCTTTGATTAAGTA-CATAA-AAA-AA

                       **  **             
        602 GAAATTTCTTTTTTTTGGTACATAAAAAAA
          1 GAAATTTCTTTGATTAAGTACATAAAAAAA

                           
        632 GAAATTTCTTTGATT
          1 GAAATTTCTTTGATT

        647 GTTTTTTTTT


Statistics
Matches: 38,  Mismatches: 6, Indels: 4
        0.79            0.12        0.08

Matches are distributed among these distances:
  30   15  0.39
  31    5  0.13
  32   18  0.47

ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39


Consensus pattern (30 bp):   
GAAATTTCTTTGATTAAGTACATAAAAAAA

Found at i:2858 original size:141 final size:142

Alignment explanation


    Indices: 2603--2885  Score: 541
    Period size: 141  Copynumber: 2.0  Consensus size: 142

       2593 TTGGTTAAAA

                                                                             
       2603 ATGTCATTTATCTAAAGAAAAAAAGCTTGTGAAACATTCATAATGTACAAACTTTGTTTCCATCA
          1 ATGTCATTTATCTAAAGAAAAAAAGCTTGTGAAACATTCATAATGTACAAACTTTGTTTCCATCA

                                                                             
       2668 CAACAAAGTTATACCCTTTTTATTTTAGGGGATTACTAAATACTGCCTCCTTTTACTAGGCACCC
         66 CAACAAAGTTATACCCTTTTTATTTTAGGGGATTACTAAATACTGCCTCCTTTTACTAGGCACCC

                        
       2733 CCCCTCCCCCCC
        131 CCCCTCCCCCCC

                                                                             
       2745 ATGTCATTTATCTAAAG-AAAAAAGCTTGTGAAACATTCATAATGTACAAACTTTGTTTCCATCA
          1 ATGTCATTTATCTAAAGAAAAAAAGCTTGTGAAACATTCATAATGTACAAACTTTGTTTCCATCA

                          *                       *                          
       2809 CAACAAAGTTATACTCTTTTTATTTTAGGGGATTACTAGATACTGCCTCCTTTTACTAGGCACCC
         66 CAACAAAGTTATACCCTTTTTATTTTAGGGGATTACTAAATACTGCCTCCTTTTACTAGGCACCC

                        
       2874 CCCCTCCCCCCC
        131 CCCCTCCCCCCC

       2886 GCGCGGGACT


Statistics
Matches: 139,  Mismatches: 2, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
 141  122  0.88
 142   17  0.12

ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33


Consensus pattern (142 bp):   
ATGTCATTTATCTAAAGAAAAAAAGCTTGTGAAACATTCATAATGTACAAACTTTGTTTCCATCA
CAACAAAGTTATACCCTTTTTATTTTAGGGGATTACTAAATACTGCCTCCTTTTACTAGGCACCC
CCCCTCCCCCCC
Done.