Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013245.1 Corchorus capsularis cultivar CVL-1 contig13266, 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: 8120
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Found at i:172 original size:2 final size:2

Alignment explanation


    Indices: 165--196  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        155 ACTTTTATTT

                                                           
        165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        197 CTAGTTAAAG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1625 original size:29 final size:29

Alignment explanation


    Indices: 1563--1631  Score: 84
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       1553 TAACGTTAGA

                                      *  
       1563 CCCTTATTTGACCAAATTAAAAGATCGGG
          1 CCCTTATTTGACCAAATTAAAAGATCAGG

                      *         *    *   
       1592 CCCTTATTTGGCCAAATTAAGAGATTAGG
          1 CCCTTATTTGACCAAATTAAAAGATCAGG

            *    *     
       1621 TCCTTGTTTGA
          1 CCCTTATTTGA

       1632 GCATTTTATC


Statistics
Matches: 33,  Mismatches: 7, Indels: 0
        0.82            0.17        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33


Consensus pattern (29 bp):   
CCCTTATTTGACCAAATTAAAAGATCAGG

Found at i:7896 original size:159 final size:157

Alignment explanation


    Indices: 7452--7899  Score: 610
    Period size: 165  Copynumber: 2.8  Consensus size: 157

       7442 ATTCTCAATT

                           *    *          *                 *  *         *  
       7452 TTTTCAGCTTTTGCAATCTTTCCGACATATAAAATGGAAAAATACTCAAAAGATCCTCGCATTTT
          1 TTTTCAGCTTTTGCAGTCTTCCCGACATATAGAATGGAAAAATACTCAATAGTTCCT-GCA-GTT

                                                      *                      
       7517 TCAACCTCAAGATGTTCTAAATTGCAATAGCTATGATCTGTAACTTGTTGGTCATCCCATATTCG
         64 TCAACCTCAAGATGTTCTAAATTGCAATAGC--T-ATCTGTAGCTTGTTGGTCATCCCATATTCG

              *                           * 
       7582 CTTCAAGCACCTGAGGTCTCTTAGTTTCAATG
        126 CTCCAAGCACCTGAGGTCTCTTAGTTTCAAAG

                              *  *                              *            
       7614 TTTTCAGCTTTTGCAGTCCTCGCGACATATAGAATATTGCTGGAAAAATACTAAATAGTTCCGTG
          1 TTTTCAGCTTTTGCAGTCTTCCCGACATATAG-A-A----TGGAAAAATACTCAATAGTTCC-TG

                                            *          *                     
       7679 CAGTTTCTAACCTCAAGATGTTCTAAATTGCAGTAGCTATCTGCAGCTTGTTGGTCATCCCATAT
         59 CAGTTTC-AACCTCAAGATGTTCTAAATTGCAATAGCTATCTGTAGCTTGTTGGTCATCCCATAT

                                                
       7744 TCGCTCCAAGCACCTGAGGTCTCTTA-TTTCCAAAG
        123 TCGCTCCAAGCACCTGAGGTCTCTTAGTTT-CAAAG

                                                                   *         
       7779 TTTTCAGCTTTTGCAGTCTTCCCGACATATAGAATGGAAAAATACTCAATAGTTTGCTGCAGTTT
          1 TTTTCAGCTTTTGCAGTCTTCCCGACATATAGAATGGAAAAATACTCAATAG-TTCCTGCAGTTT

                                                                    
       7844 ACAACCTCAAGATGTTCTAAATTGCAATAGCTATCTGTAGCTTGTTGGTCATCCCA
         65 -CAACCTCAAGATGTTCTAAATTGCAATAGCTATCTGTAGCTTGTTGGTCATCCCA

       7900 AATCCCTTTT


Statistics
Matches: 255,  Mismatches: 20, Indels: 25
        0.85            0.07        0.08

Matches are distributed among these distances:
 159   77  0.30
 160    4  0.02
 162   27  0.11
 163    2  0.01
 164    5  0.02
 165   84  0.33
 166    1  0.00
 167    4  0.02
 168   50  0.20
 169    1  0.00

ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34


Consensus pattern (157 bp):   
TTTTCAGCTTTTGCAGTCTTCCCGACATATAGAATGGAAAAATACTCAATAGTTCCTGCAGTTTC
AACCTCAAGATGTTCTAAATTGCAATAGCTATCTGTAGCTTGTTGGTCATCCCATATTCGCTCCA
AGCACCTGAGGTCTCTTAGTTTCAAAG

Done.