Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011839.1 Corchorus capsularis cultivar CVL-1 contig11860, 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: 7324
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32


Found at i:1716 original size:75 final size:75

Alignment explanation


    Indices: 1538--1722  Score: 194
    Period size: 75  Copynumber: 2.4  Consensus size: 75

       1528 GAATACCCCC

                 *      *                  *            *      *     *       
       1538 TGAAAATTACTAAAGATTCCCATCAACTTTTCACGTGGGAGAACTTTTTCGTTCCGTGTTTTGGT
          1 TGAAATTTACTATAGA-TCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCTCCG-ATTTTGGT

                       *
       1603 CTTTTCTCACTC
         64 CTTTTCTCACTA

              * *      *    *    *                                           
       1615 TGGATTTTACCAATAGCTCCCTTCAACTTTTAACGTGGGA-AAGCCTTTTCGCTCC-ATTTTGGT
          1 TGAAATTTA-CTATAGATCCCATCAACTTTTAACGTGGGAGAA-CCTTTTCGCTCCGATTTTGGT

                     *  
       1678 CTTTTCTCATTA
         64 CTTTTCTCACTA

                                             
       1690 TGAAATTTACTGATAGATCCCATCAACTTTTAA
          1 TGAAATTTACT-ATAGATCCCATCAACTTTTAA

       1723 TTTTGGAGAT


Statistics
Matches: 87,  Mismatches: 18, Indels: 8
        0.77            0.16        0.07

Matches are distributed among these distances:
  74    1  0.01
  75   43  0.49
  76    2  0.02
  77   37  0.43
  78    4  0.05

ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40


Consensus pattern (75 bp):   
TGAAATTTACTATAGATCCCATCAACTTTTAACGTGGGAGAACCTTTTCGCTCCGATTTTGGTCT
TTTCTCACTA

Found at i:3067 original size:30 final size:29

Alignment explanation


    Indices: 3033--3090  Score: 91
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       3023 GTACTGATTG

                                           
       3033 TTTTC-CTACATATATGCCTTATATCATATT
          1 TTTTCGCTACATA-ATGCCTTATAT-ATATT

                                        
       3063 TTTTCGCTACATAATGCCTTATATATAT
          1 TTTTCGCTACATAATGCCTTATATATAT

       3091 ATATATATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  29    4  0.15
  30   16  0.59
  31    7  0.26

ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48


Consensus pattern (29 bp):   
TTTTCGCTACATAATGCCTTATATATATT

Found at i:3089 original size:2 final size:2

Alignment explanation


    Indices: 3082--3113  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       3072 CATAATGCCT

                                                             
       3082 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3114 TGTTGTAATC


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

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


Consensus pattern (2 bp):   
TA

Found at i:6772 original size:70 final size:70

Alignment explanation


    Indices: 6647--6779  Score: 171
    Period size: 70  Copynumber: 1.9  Consensus size: 70

       6637 AATGCATTGC

                                  *       *             **  * *              
       6647 CTTTATATGTAATTTTAGCATTTGGATGTAGTTAATGGTGTCCTTGCCGTTTTTTTCTTTAGTGC
          1 CTTTATATGTAATTTTAGCATTCGGATGTAATTAATGGTGTCCTCACCATATTTTTCTTTAGTGC

                 
       6712 TTTTT
         66 TTTTT

                                              *                              
       6717 CTTTATATGTAATTTTAGCA-TCGAGATGTAATTGATGGTGTTCC-CACCATATTTTTCTTTAGT
          1 CTTTATATGTAATTTTAGCATTCG-GATGTAATTAATGGTG-TCCTCACCATATTTTTCTTTAGT

       6780 TATTAGGTTT


Statistics
Matches: 54,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  69    2  0.04
  70   49  0.91
  71    3  0.06

ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50


Consensus pattern (70 bp):   
CTTTATATGTAATTTTAGCATTCGGATGTAATTAATGGTGTCCTCACCATATTTTTCTTTAGTGC
TTTTT
Done.