Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007858.1 Corchorus capsularis cultivar CVL-1 contig07879, 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: 4128
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--81  Score: 162
    Period size: 2  Copynumber: 40.5  Consensus size: 2

                                                                          
          1 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

                                                                      
         43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         82 TTTTAATTTT


Statistics
Matches: 79,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   79  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:314 original size:107 final size:107

Alignment explanation


    Indices: 178--466  Score: 395
    Period size: 107  Copynumber: 2.7  Consensus size: 107

        168 GGGTTTTAAT

                 *           *                                               
        178 TATAGAGTTTTAGAAATCAAATATAAAACTAATTTCACTAAGTTTTGCCCCAAATTAAAATTTTA
          1 TATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTTGCCCCAAATTAAAATTTTA

                         *       *           *       *
        243 TTTTTATTTTAAGGGTAAATTTCAAAATTAATACTTTATTGT
         66 TTTTTATTTTAAGAGTAAATTCCAAAATTAATAATTTATTGG

             *                     *                     *               *   
        285 TCTAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATCTTA
          1 TATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTTGCCCCAAATTAAAATTTTA

                                    **                
        350 TTTTTATTTTAAGAGTAAATTCCATGATTAATAATTTATTGG
         66 TTTTTATTTTAAGAGTAAATTCCAAAATTAATAATTTATTGG

                  *                  *                                     **
        392 TATAGGATTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAT--CCCAAATTAAAATTAA
          1 TATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTT-TGCCCCAAATTAAAATTTT

             *           
        454 AATTTTATTTTAA
         65 ATTTTTATTTTAA

        467 AGGTTAGAAA


Statistics
Matches: 160,  Mismatches: 21, Indels: 4
        0.86            0.11        0.02

Matches are distributed among these distances:
 105   25  0.16
 106   12  0.08
 107  123  0.77

ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41


Consensus pattern (107 bp):   
TATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTTGCCCCAAATTAAAATTTTA
TTTTTATTTTAAGAGTAAATTCCAAAATTAATAATTTATTGG

Found at i:1781 original size:14 final size:14

Alignment explanation


    Indices: 1764--1798  Score: 61
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       1754 ACGAGAACTA

                          
       1764 GAGAGAGAGAAAGG
          1 GAGAGAGAGAAAGG

                       *  
       1778 GAGAGAGAGAAGGG
          1 GAGAGAGAGAAAGG

                   
       1792 GAGAGAG
          1 GAGAGAG

       1799 GAGCGGCTAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00


Consensus pattern (14 bp):   
GAGAGAGAGAAAGG
Done.