Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005359.1 Corchorus capsularis cultivar CVL-1 contig05377, 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: 8197
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28


Found at i:1011 original size:27 final size:26

Alignment explanation


    Indices: 981--1081  Score: 87
    Period size: 27  Copynumber: 3.7  Consensus size: 26

        971 TTTTGGAAGT

                                       
        981 AAAATTGATATATTTATTTATTCTAAA
          1 AAAATTGATATATTTATTTATT-TAAA

                       *   *      **   
       1008 AAAATTGATATTTTTTTTTGA-GGAAA
          1 AAAATTGATATATTTATTT-ATTTAAA

                            *      *      
       1034 AAAATTGATATATTTTTTTTGAAGTTATAA
          1 AAAATTGATATA-TTTATTT--ATTTA-AA

                              
       1064 AAAATTGATATATTTATT
          1 AAAATTGATATATTTATT

       1082 ATAGCGTAAA


Statistics
Matches: 60,  Mismatches: 9, Indels: 8
        0.78            0.12        0.10

Matches are distributed among these distances:
  26   14  0.23
  27   24  0.40
  28    2  0.03
  29    6  0.10
  30   14  0.23

ACGTcount: A:0.42, C:0.01, G:0.09, T:0.49


Consensus pattern (26 bp):   
AAAATTGATATATTTATTTATTTAAA

Found at i:1034 original size:26 final size:29

Alignment explanation


    Indices: 1005--1078  Score: 109
    Period size: 30  Copynumber: 2.6  Consensus size: 29

        995 TATTTATTCT

                                         
       1005 AAAAAAATTGATAT-TTTTTTTTG-AG-G
          1 AAAAAAATTGATATATTTTTTTTGAAGTG

                                        *
       1031 AAAAAAATTGATATATTTTTTTTGAAGTT
          1 AAAAAAATTGATATATTTTTTTTGAAGTG

                               
       1060 ATAAAAAATTGATATATTT
          1 A-AAAAAATTGATATATTT

       1079 ATTATAGCGT


Statistics
Matches: 43,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  26   14  0.33
  27    9  0.21
  28    2  0.05
  29    1  0.02
  30   17  0.40

ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46


Consensus pattern (29 bp):   
AAAAAAATTGATATATTTTTTTTGAAGTG

Found at i:8014 original size:21 final size:21

Alignment explanation


    Indices: 7971--8014  Score: 70
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       7961 AAAAAAGGGG

                            * *  
       7971 TTGCTAAATACCGCCCTAGTT
          1 TTGCTAAATACCGCCCCACTT

                                 
       7992 TTGCTAAATACCGCCCCACTT
          1 TTGCTAAATACCGCCCCACTT

              
       8013 TT
          1 TT

       8015 CACATTTTTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34


Consensus pattern (21 bp):   
TTGCTAAATACCGCCCCACTT

Found at i:8164 original size:32 final size:32

Alignment explanation


    Indices: 8066--8190  Score: 128
    Period size: 33  Copynumber: 3.8  Consensus size: 32

       8056 CATTGAGCCT

                   *  *            *         *
       8066 CCCCACTAGGACGGC-TCAGCCACGGCAGAGCCT
          1 CCCCACTGGGGCGGCTTCA-CCAAGGCAG-GCCG

                                   *         
       8099 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
          1 CCCCACTGGGGCGGCTTCACCA-AGGCAGGCCG

                  *                         
       8132 CCCCACCGGGGCGGCTTCACCAAGGCAGGCCG
          1 CCCCACTGGGGCGGCTTCACCAAGGCAGGCCG

                               *   *    
       8164 CCCTCA-TGGGGCGGCTTCGCCACGGCA
          1 CCC-CACTGGGGCGGCTTCACCAAGGCA

       8191 AACCGCC


Statistics
Matches: 80,  Mismatches: 9, Indels: 7
        0.83            0.09        0.07

Matches are distributed among these distances:
  32   30  0.38
  33   42  0.52
  34    8  0.10

ACGTcount: A:0.15, C:0.42, G:0.33, T:0.10


Consensus pattern (32 bp):   
CCCCACTGGGGCGGCTTCACCAAGGCAGGCCG
Done.