Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005685.1 Corchorus capsularis cultivar CVL-1 contig05703, 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: 1907
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 5--56  Score: 104
    Period size: 2  Copynumber: 26.0  Consensus size: 2

          1 CTCA

                                                                          
          5 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                          
         47 TC TC TC TC TC
          1 TC TC TC TC TC

         57 CTCAATTTGA


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   50  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:238 original size:16 final size:17

Alignment explanation


    Indices: 219--256  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

        209 GAAAAAGATA

                             
        219 GGAAAAAGAAA-AAAAG
          1 GGAAAAAGAAATAAAAG

                  *          
        235 GGAAAAGGAAATAAAAG
          1 GGAAAAAGAAATAAAAG

            *    
        252 TGAAA
          1 GGAAA

        257 TTTTTGGATA


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

Matches are distributed among these distances:
  16   10  0.53
  17    9  0.47

ACGTcount: A:0.68, C:0.00, G:0.26, T:0.05


Consensus pattern (17 bp):   
GGAAAAAGAAATAAAAG

Found at i:1264 original size:24 final size:24

Alignment explanation


    Indices: 1237--1282  Score: 56
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       1227 CTTGGTTTTG

                   *   *            
       1237 GATTGATTATCTTGATTTTACTAT
          1 GATTGATGATCCTGATTTTACTAT

                *         *       
       1261 GATTTATGATCCTGGTTTTACT
          1 GATTGATGATCCTGATTTTACT

       1283 GATTTTCCCT


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   18  1.00

ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52


Consensus pattern (24 bp):   
GATTGATGATCCTGATTTTACTAT
Done.