Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014250.1 Corchorus capsularis cultivar CVL-1 contig14271, 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: 3632
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31


Found at i:1643 original size:29 final size:29

Alignment explanation


    Indices: 1609--1682  Score: 121
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       1599 GCAAAACGTC

                                         
       1609 CCAAAATTGAAGTTCAGGAGACAAAATAT
          1 CCAAAATTGAAGTTCAGGAGACAAAATAT

                    *         *        * 
       1638 CCAAAATTAAAGTTCAGGGGACAAAATCT
          1 CCAAAATTGAAGTTCAGGAGACAAAATAT

                            
       1667 CCAAAATTGAAGTTCA
          1 CCAAAATTGAAGTTCA

       1683 TGGGAAAAAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  29   41  1.00

ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22


Consensus pattern (29 bp):   
CCAAAATTGAAGTTCAGGAGACAAAATAT

Found at i:1687 original size:29 final size:28

Alignment explanation


    Indices: 1609--1700  Score: 114
    Period size: 29  Copynumber: 3.2  Consensus size: 28

       1599 GCAAAACGTC

                                       * 
       1609 CCAAAATTGAAGTTCAGGAGACAAAATAT
          1 CCAAAATTGAAGTTCAGG-GACAAAATCT

                    *                    
       1638 CCAAAATTAAAGTTCAGGGGACAAAATCT
          1 CCAAAATTGAAGTTCA-GGGACAAAATCT

                                      *   
       1667 CCAAAATTGAAGTTCATGGGA-AAAAACGT
          1 CCAAAATTGAAGTTCA-GGGACAAAATC-T

                 
       1696 CCAAA
          1 CCAAA

       1701 TGCTACAAGT


Statistics
Matches: 56,  Mismatches: 5, Indels: 4
        0.86            0.08        0.06

Matches are distributed among these distances:
  28    5  0.09
  29   49  0.88
  30    2  0.04

ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20


Consensus pattern (28 bp):   
CCAAAATTGAAGTTCAGGGACAAAATCT

Found at i:2326 original size:32 final size:33

Alignment explanation


    Indices: 2221--2327  Score: 116
    Period size: 32  Copynumber: 3.4  Consensus size: 33

       2211 GACCACACAC

                          *   *   *       *  
       2221 AGGG-GCGGCCTTGGCA-AGCAAGCCGCACTCT
          1 AGGGTGCGGCCTTGCCACGGCAGGCCGCACCCT

                *      *                     
       2252 -GGGGGCGGCCGTGCCACGGCAGGCCGCACCCT
          1 AGGGTGCGGCCTTGCCACGGCAGGCCGCACCCT

            *                                
       2284 GGGGT-CGGCCTTGCCACGGCAGGCCGC-CCCT
          1 AGGGTGCGGCCTTGCCACGGCAGGCCGCACCCT

                         
       2315 AGGGTGCGGCCTT
          1 AGGGTGCGGCCTT

       2328 TCAATGGCTG


Statistics
Matches: 64,  Mismatches: 8, Indels: 7
        0.81            0.10        0.09

Matches are distributed among these distances:
  30    3  0.05
  31   18  0.28
  32   40  0.62
  33    3  0.05

ACGTcount: A:0.11, C:0.36, G:0.40, T:0.12


Consensus pattern (33 bp):   
AGGGTGCGGCCTTGCCACGGCAGGCCGCACCCT

Found at i:2407 original size:24 final size:25

Alignment explanation


    Indices: 2362--2414  Score: 65
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       2352 GGCGGCCAGC

                     *   *           
       2362 TATTTTTTTTGTTTTTTCTT-AAAT
          1 TATTTTTTTGGTTATTTCTTAAAAT

                                      
       2386 TATTTTTTATGGTTATTT-TTAAAAT
          1 TATTTTTT-TGGTTATTTCTTAAAAT

                
       2411 TATT
          1 TATT

       2415 AGTTTTAATA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  24   10  0.40
  25   15  0.60

ACGTcount: A:0.23, C:0.02, G:0.06, T:0.70


Consensus pattern (25 bp):   
TATTTTTTTGGTTATTTCTTAAAAT
Done.