Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011255.1 Corchorus capsularis cultivar CVL-1 contig11276, 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: 22928
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:851 original size:33 final size:34

Alignment explanation


    Indices: 788--874  Score: 83
    Period size: 33  Copynumber: 2.6  Consensus size: 34

        778 CTTTTACACT

                *        *  *                *
        788 GAGCTTCCCCACTAGGACGGC-TCAGCCACGGCG
          1 GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA

                                      *       
        821 GAGCCTCCCCACTGGGGCGGCTTC-GTCACGGCA
          1 GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA

                 *                 
        854 G-GCCGCCCTCA-TGGGGCGGCT
          1 GAGCCTCCC-CACTGGGGCGGCT

        875 AGACCAAAAT


Statistics
Matches: 46,  Mismatches: 6, Indels: 5
        0.81            0.11        0.09

Matches are distributed among these distances:
  32   16  0.35
  33   28  0.61
  34    2  0.04

ACGTcount: A:0.13, C:0.39, G:0.34, T:0.14


Consensus pattern (34 bp):   
GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA

Found at i:977 original size:32 final size:33

Alignment explanation


    Indices: 941--1014  Score: 89
    Period size: 33  Copynumber: 2.3  Consensus size: 33

        931 CCGCCCCACC

                                          *   
        941 GGGGCGGC-CTGCAC-TGGCTAAGCCACCCCAGT
          1 GGGGCGGCTCTGC-CGTGGCTAAGCCACCCAAGT

                              * *    *       
        973 GGGGCGGCTCTGCCGTGGTTGAGCCTCCCAAGT
          1 GGGGCGGCTCTGCCGTGGCTAAGCCACCCAAGT

                     
       1006 GGGGCGGCT
          1 GGGGCGGCT

       1015 TCGCCACGGT


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  32    9  0.25
  33   27  0.75

ACGTcount: A:0.11, C:0.32, G:0.41, T:0.16


Consensus pattern (33 bp):   
GGGGCGGCTCTGCCGTGGCTAAGCCACCCAAGT

Found at i:9595 original size:15 final size:17

Alignment explanation


    Indices: 9575--9611  Score: 51
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       9565 CTAAAAATAT

                             
       9575 TTTTTGTT-GGT-TTCA
          1 TTTTTGTTAGGTCTTCA

                      *      
       9590 TTTTTGTTAGTTCTTCA
          1 TTTTTGTTAGGTCTTCA

                 
       9607 TTTTT
          1 TTTTT

       9612 TTCCCCTTCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  15    8  0.42
  16    2  0.11
  17    9  0.47

ACGTcount: A:0.08, C:0.08, G:0.14, T:0.70


Consensus pattern (17 bp):   
TTTTTGTTAGGTCTTCA

Found at i:12315 original size:20 final size:19

Alignment explanation


    Indices: 12291--12352  Score: 115
    Period size: 19  Copynumber: 3.2  Consensus size: 19

      12281 TTTTTATAAA

                               
      12291 AAAAAAAAATTAATTTTAT
          1 AAAAAAAAATTAATTTTAT

                               
      12310 AAAAAAAAATTAATTTTAT
          1 AAAAAAAAATTAATTTTAT

                                
      12329 AAAAAAAAATTAATTTTTAT
          1 AAAAAAAAATTAA-TTTTAT

                
      12349 AAAA
          1 AAAA

      12353 GAGAGAGAAA


Statistics
Matches: 42,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  19   32  0.76
  20   10  0.24

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (19 bp):   
AAAAAAAAATTAATTTTAT

Found at i:14157 original size:26 final size:26

Alignment explanation


    Indices: 14126--14194  Score: 138
    Period size: 26  Copynumber: 2.7  Consensus size: 26

      14116 GCTTAATCTT

                                      
      14126 AGGTTCTCTGTATTTTTTTTGAAGAA
          1 AGGTTCTCTGTATTTTTTTTGAAGAA

                                      
      14152 AGGTTCTCTGTATTTTTTTTGAAGAA
          1 AGGTTCTCTGTATTTTTTTTGAAGAA

                             
      14178 AGGTTCTCTGTATTTTT
          1 AGGTTCTCTGTATTTTT

      14195 ATATGCTTTA


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   43  1.00

ACGTcount: A:0.20, C:0.09, G:0.19, T:0.52


Consensus pattern (26 bp):   
AGGTTCTCTGTATTTTTTTTGAAGAA
Done.