Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010753.1 Corchorus capsularis cultivar CVL-1 contig10774, 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: 31722
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:959 original size:2 final size:2

Alignment explanation


    Indices: 952--981  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        942 TAAATTGCTC

                                                *       
        952 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

        982 TTCTTTTATG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53


Consensus pattern (2 bp):   
CT

Found at i:13773 original size:103 final size:105

Alignment explanation


    Indices: 13585--13795  Score: 315
    Period size: 103  Copynumber: 2.0  Consensus size: 105

      13575 TAGCAGTTCA

                                                               *             
      13585 TTTCATGTATAATTGTAGCTCAAGCGATGAATCAAAACAAAGTCTATTTCTTGATGTCCTAAATA
          1 TTTCATGTATAATTGTAGCTCAAGCGATGAATCAAAACAAAGTCTATTTCTCGATGTCCTAAATA

                *       *                  *        
      13650 ATATGTTGGATTTGATCTTGTGAATTGAGAACATAGA-CT
         66 ATATATTGGATTGGATCTTGTGAATTGAGAAAATAGACCT

                                         *                                   
      13689 TTTCATGTATAATTGTAGCTCAA-CGATGGATCAAAACAAAGTCTATTTCTCGATGTCCTAAATA
          1 TTTCATGTATAATTGTAGCTCAAGCGATGAATCAAAACAAAGTCTATTTCTCGATGTCCTAAATA

                                                       
      13753 ATATATAT-G-TTGGGGA-CTTGTGAATTGAGAAAATAGACCT
         66 ATATAT-TGGATT--GGATCTTGTGAATTGAGAAAATAGACCT

               
      13793 TTT
          1 TTT

      13796 GAGAAAATTT


Statistics
Matches: 98,  Mismatches: 5, Indels: 8
        0.88            0.05        0.07

Matches are distributed among these distances:
 102    2  0.02
 103   65  0.66
 104   31  0.32

ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36


Consensus pattern (105 bp):   
TTTCATGTATAATTGTAGCTCAAGCGATGAATCAAAACAAAGTCTATTTCTCGATGTCCTAAATA
ATATATTGGATTGGATCTTGTGAATTGAGAAAATAGACCT

Found at i:28148 original size:2 final size:2

Alignment explanation


    Indices: 28104--28130  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      28094 GTAGTTCACC

                                                    
      28104 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      28131 AATAATAAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:28224 original size:6 final size:6

Alignment explanation


    Indices: 28215--28243  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      28205 ACACACACAA

                                             
      28215 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA

      28244 AAAGAGTAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Done.