Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011471.1 Corchorus capsularis cultivar CVL-1 contig11492, 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: 14595
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29


Found at i:1441 original size:156 final size:154

Alignment explanation


    Indices: 1204--1566  Score: 367
    Period size: 155  Copynumber: 2.3  Consensus size: 154

       1194 GAGCTTCTCA

                                     *                 *        *  *         
       1204 CCTCAAACTGTCCTTAAATGAAAAATTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
          1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTCAACGAGCTG-AA

                      *            *       *                          ** *   
       1269 TTTTGCCAAGGGACTTAGAATATCCACATAAGACTATGGAAAAAATTATAAGTAAAACTGAGCTC
         65 TTTTGCCAAGAGACTTAGAATATACACATAAAACTATGG-AAAAATTATAAGTAAAACCAAACT-

                *    * *            *  
       1334 CTCTTG-ATGGTGAACTAGGTTTCTCT
        128 CTCTAGCATAGAGAACTAGGTTTCACT

                 * **                               *                        
       1360 CC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTACATACTAAGTC-CAACGAAGCTG-
          1 CCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTCAACG-AGCTGA

                           *       *     *             *      *   *          
       1422 ATTTT-CCACCAGTATACTTAGATTATACTCATAAAACTATGGGAAAATTCTAATTAAAACCAAA
         64 ATTTTGCCA--AG-AGACTTAGAATATACACATAAAACTATGGAAAAATTATAAGTAAAACCAAA

                             * *     *   
       1486 CTCTCTAGCATAGAGAAGTTGGTTTGACT
        126 CTCTCTAGCATAGAGAACTAGGTTTCACT

                             *                                  
       1515 CCTCAAACTGTCCTTAATTGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
          1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCT

       1567 GTTTGAGATG


Statistics
Matches: 167,  Mismatches: 32, Indels: 16
        0.78            0.15        0.07

Matches are distributed among these distances:
 153    3  0.02
 154   10  0.06
 155   82  0.49
 156   72  0.43

ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31


Consensus pattern (154 bp):   
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTCTCAACGAGCTGAAT
TTTGCCAAGAGACTTAGAATATACACATAAAACTATGGAAAAATTATAAGTAAAACCAAACTCTC
TAGCATAGAGAACTAGGTTTCACT

Found at i:14473 original size:112 final size:114

Alignment explanation


    Indices: 14336--14554  Score: 311
    Period size: 113  Copynumber: 1.9  Consensus size: 114

      14326 CTCTGGAGCT

                                                             * *             
      14336 AAAAAAAAATTGCAAAGAGTGTTGCACCTTAGAG-TTTAGTCGCATCT-TGGGAAATATTTCCTG
          1 AAAAAAAAATTGCAAAGAGTGTTGCACCTTAGAGTTTTAGTCGCATCTCAGAG-AATATTTCCTG

                 *            *            *                  
      14399 AGTATTGCACTTTAAACTTGGGTCGCACCT-TAAGAAAATATTATCCTGC
         65 AGTATCGCACTTTAAACTAGGGTCGCACCTCAAAGAAAATATTATCCTGC

                                                   *  *                      
      14448 AAAAAAAAATTGC-AAGAAGTGTTGCACCTTAGAGTTTTGGTTGCATCTCAGAGAATATTTCCTG
          1 AAAAAAAAATTGCAAAG-AGTGTTGCACCTTAGAGTTTTAGTCGCATCTCAGAGAATATTTCCTG

               *                   *                   
      14512 AGTGTCGCACTTTAAACTAGGGTTGCACCTCAAAGAAAATATT
         65 AGTATCGCACTTTAAACTAGGGTCGCACCTCAAAGAAAATATT

      14555 TTCTTCCATT


Statistics
Matches: 94,  Mismatches: 9, Indels: 6
        0.86            0.08        0.06

Matches are distributed among these distances:
 111    3  0.03
 112   30  0.32
 113   48  0.51
 114   13  0.14

ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Consensus pattern (114 bp):   
AAAAAAAAATTGCAAAGAGTGTTGCACCTTAGAGTTTTAGTCGCATCTCAGAGAATATTTCCTGA
GTATCGCACTTTAAACTAGGGTCGCACCTCAAAGAAAATATTATCCTGC

Done.