Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005195.1 Corchorus capsularis cultivar CVL-1 contig05213, 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: 2706
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30


Found at i:106 original size:31 final size:32

Alignment explanation


    Indices: 66--128  Score: 101
    Period size: 31  Copynumber: 2.0  Consensus size: 32

         56 GCGACCCCCC

                          *                 
         66 TTTTCGCTATGCGCTAAGGGGGTAA-CCCCTT
          1 TTTTCGCTATGCGCCAAGGGGGTAATCCCCTT

                *                           
         97 TTTTGGCTATGCGCCAAGGGGGTAATCCCCTT
          1 TTTTCGCTATGCGCCAAGGGGGTAATCCCCTT

        129 GCCATGCGCA


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  31   23  0.79
  32    6  0.21

ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32


Consensus pattern (32 bp):   
TTTTCGCTATGCGCCAAGGGGGTAATCCCCTT

Found at i:151 original size:90 final size:87

Alignment explanation


    Indices: 4--176  Score: 292
    Period size: 90  Copynumber: 2.0  Consensus size: 87

          1 TAA

                                                                             
          4 CCCTTTTTTGCTATGCGCCAAGGGATAATCCCCTTGCCATGCGCAAAGAGGGGCGACCCCCCTTT
          1 CCCTTTTTTGCTATGCGCCAAGGGATAATCCCCTTGCCATGCGCAAAGAGGGGCGACCCCCCTTT

                          *        
         69 TCGCTATGCGCTAAGGGGGTAAC
         66 TCGCTATGCG-TAAAGGGGTAAC

                                      *                                      
         92 CCCTTTTTTGGCTATGCGCCAAGGGGGTAATCCCCTTGCCATGCGCAAAGAGGGGCGACCCCCCT
          1 CCCTTTTTT-GCTATGCGCCAA-GGGATAATCCCCTTGCCATGCGCAAAGAGGGGCGACCCCCCT

               *                
        157 TTTTGCTATGCGTAAAGGGG
         64 TTTCGCTATGCGTAAAGGGG

        177 AGCGATCCCC


Statistics
Matches: 80,  Mismatches: 3, Indels: 3
        0.93            0.03        0.03

Matches are distributed among these distances:
  88    9  0.11
  89   19  0.24
  90   52  0.65

ACGTcount: A:0.18, C:0.29, G:0.28, T:0.24


Consensus pattern (87 bp):   
CCCTTTTTTGCTATGCGCCAAGGGATAATCCCCTTGCCATGCGCAAAGAGGGGCGACCCCCCTTT
TCGCTATGCGTAAAGGGGTAAC

Found at i:973 original size:35 final size:35

Alignment explanation


    Indices: 776--974  Score: 154
    Period size: 35  Copynumber: 5.6  Consensus size: 35

        766 GGTGTCACGC

                             *  *       * *      
        776 CCCCTTATCACAATTTAGTTAGGGAGGCGTGACGCCT
          1 CCCCTT-T-ACAATTTAATTGGGGAGGCATTACGCCT

                  **      *    *                
        813 ACCCCTCAACAATTCAATTTGGGAGGCATTACGCCT
          1 -CCCCTTTACAATTTAATTGGGGAGGCATTACGCCT

                  * *    *    *                
        849 CCCCTTGAAAATTAAATTAGGGAGGCATTACG-C-
          1 CCCCTTTACAATTTAATTGGGGAGGCATTACGCCT

                  *     *          *  * *      
        882 CCCCTTCACAATCTAATTGGGGAAGCGTAACGCCT
          1 CCCCTTTACAATTTAATTGGGGAGGCATTACGCCT

                                                 
        917 -CCC-TTATCAATTTAATCTGGGGAGGCATTACGCCT
          1 CCCCTTTA-CAATTTAAT-TGGGGAGGCATTACGCCT

                              *    
        952 CCCCTTTAGCAATTTAATGGGGG
          1 CCCCTTTA-CAATTTAATTGGGG

        975 TGGAGGTATT


Statistics
Matches: 128,  Mismatches: 27, Indels: 14
        0.76            0.16        0.08

Matches are distributed among these distances:
  33   26  0.20
  34   13  0.10
  35   42  0.33
  36   30  0.23
  37   12  0.09
  38    5  0.04

ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27


Consensus pattern (35 bp):   
CCCCTTTACAATTTAATTGGGGAGGCATTACGCCT

Found at i:1600 original size:31 final size:31

Alignment explanation


    Indices: 1558--1676  Score: 202
    Period size: 31  Copynumber: 3.8  Consensus size: 31

       1548 CATGATTACT

                                       *    
       1558 CACCAAAAGGTATACCGTAAATACTCCCTACC
          1 CACC-AAAGGTATACCGTAAATACTCCATACC

                                           
       1590 CACCAAAGGTATACCGTAAATACTCCATACC
          1 CACCAAAGGTATACCGTAAATACTCCATACC

                  *                        
       1621 CACCAAGGGTATACCGTAAATACTCCATACC
          1 CACCAAAGGTATACCGTAAATACTCCATACC

                                *    
       1652 CACCAAAGGTATACCGTAAACACTC
          1 CACCAAAGGTATACCGTAAATACTC

       1677 ACCAAGTATT


Statistics
Matches: 83,  Mismatches: 4, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
  31   79  0.95
  32    4  0.05

ACGTcount: A:0.38, C:0.33, G:0.11, T:0.18


Consensus pattern (31 bp):   
CACCAAAGGTATACCGTAAATACTCCATACC
Done.