Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005657.1 Corchorus capsularis cultivar CVL-1 contig05675, 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: 2301
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36


Found at i:791 original size:87 final size:87

Alignment explanation


    Indices: 631--791  Score: 187
    Period size: 87  Copynumber: 1.9  Consensus size: 87

        621 TGCCCCAAAC

                *         *         *            *  *    *          *        
        631 CTTCTTCCAATTTGGTCATGCATTGATATTCCCAACTGAATTGATGGTTCTGGATCGGCTTCTCA
          1 CTTCCTCCAATTTGATCATGCATTAATATTCCCAACTCAAATGATAGTTCTGGATCAGCTTCTCA

            **                    
        696 CCTCAAGAATTATTTCCGAAAT
         66 AATCAAGAATTATTTCCGAAAT

                                          *               *  *        *  *   
        718 CTTCCTCCAATTTGATCATGCATTAATATTTCCAACTCAAATGATATTTTTGGATCAGTTTTTCA
          1 CTTCCTCCAATTTGATCATGCATTAATATTCCCAACTCAAATGATAGTTCTGGATCAGCTTCTCA

               *     
        783 AATTAAGAA
         66 AATCAAGAA

        792 ACTTTCAAAC


Statistics
Matches: 59,  Mismatches: 15, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  87   59  1.00

ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39


Consensus pattern (87 bp):   
CTTCCTCCAATTTGATCATGCATTAATATTCCCAACTCAAATGATAGTTCTGGATCAGCTTCTCA
AATCAAGAATTATTTCCGAAAT

Found at i:1298 original size:12 final size:13

Alignment explanation


    Indices: 1281--1311  Score: 55
    Period size: 12  Copynumber: 2.5  Consensus size: 13

       1271 AAATTCTTTG

                         
       1281 TTTTTCTTTT-TT
          1 TTTTTCTTTTCTT

                         
       1293 TTTTTCTTTTCTT
          1 TTTTTCTTTTCTT

                  
       1306 TTTTTC
          1 TTTTTC

       1312 CTCATTTTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12   10  0.56
  13    8  0.44

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


Consensus pattern (13 bp):   
TTTTTCTTTTCTT

Found at i:1612 original size:14 final size:14

Alignment explanation


    Indices: 1581--1631  Score: 52
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       1571 AAAGGCGATC

                     *     
       1581 TTTTGAAAACTCA-T
          1 TTTTG-AAAGTCATT

                           
       1595 TTTTGAAAGTCATTT
          1 TTTTGAAAGTCA-TT

                          
       1610 TTTTGAAAG-CATT
          1 TTTTGAAAGTCATT

                     
       1623 TTCTTGAAA
          1 TT-TTGAAA

       1632 TTTTTTTCTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
  13   10  0.30
  14   13  0.39
  15   10  0.30

ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47


Consensus pattern (14 bp):   
TTTTGAAAGTCATT

Found at i:1614 original size:15 final size:14

Alignment explanation


    Indices: 1594--1631  Score: 58
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       1584 TGAAAACTCA

                           
       1594 TTTTTGAAAGTCATT
          1 TTTTTGAAAG-CATT

                          
       1609 TTTTTGAAAGCATT
          1 TTTTTGAAAGCATT

              *      
       1623 TTCTTGAAA
          1 TTTTTGAAA

       1632 TTTTTTTCTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   12  0.55
  15   10  0.45

ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50


Consensus pattern (14 bp):   
TTTTTGAAAGCATT
Done.