Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004294.1 Corchorus capsularis cultivar CVL-1 contig04302, 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: 2240
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:845 original size:34 final size:35

Alignment explanation


    Indices: 802--867  Score: 107
    Period size: 35  Copynumber: 1.9  Consensus size: 35

        792 TGAATCATAA

                                               
        802 TTTTTTTTGG-CACCAAGATGAATCATAATTTTTG
          1 TTTTTTTTGGCCACCAAGATGAATCATAATTTTTG

                         **                 
        836 TTTTTTTTGGCCAGGAAGATGAATCATAATTT
          1 TTTTTTTTGGCCACCAAGATGAATCATAATTT

        868 AGTGTGGAGT


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

Matches are distributed among these distances:
  34   10  0.34
  35   19  0.66

ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45


Consensus pattern (35 bp):   
TTTTTTTTGGCCACCAAGATGAATCATAATTTTTG

Found at i:1293 original size:31 final size:31

Alignment explanation


    Indices: 1258--1438  Score: 285
    Period size: 31  Copynumber: 5.9  Consensus size: 31

       1248 TGTGGTATGC

                                           
       1258 CATGTGTCACTTTTTGGTACACGTGGCGTGA
          1 CATGTGTCACTTTTTGGTACACGTGGCGTGA

                                           
       1289 CATGTGTCACTTTTTGGTACACGTGGCGTGA
          1 CATGTGTCACTTTTTGGTACACGTGGCGTGA

                                           
       1320 CATGTGTCACTTTTTGGTACACGTGGCGTGA
          1 CATGTGTCACTTTTTGGTACACGTGGCGTGA

                           *           *   
       1351 CATGTGTCACTTTTTTGTACACGTGGCATGA
          1 CATGTGTCACTTTTTGGTACACGTGGCGTGA

                   *       *     *          
       1382 CATGTGTTACTTTTTTGTACATGTGGCGTGCA
          1 CATGTGTCACTTTTTGGTACACGTGGCGTG-A

                            *          
       1414 CA--TGTCACTTTTTGTTACACGTGGC
          1 CATGTGTCACTTTTTGGTACACGTGGC

       1439 ATACCACGTC


Statistics
Matches: 140,  Mismatches: 9, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
  30   19  0.14
  31  118  0.84
  32    3  0.02

ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38


Consensus pattern (31 bp):   
CATGTGTCACTTTTTGGTACACGTGGCGTGA

Found at i:1335 original size:93 final size:92

Alignment explanation


    Indices: 1238--1440  Score: 264
    Period size: 93  Copynumber: 2.2  Consensus size: 92

       1228 ACGTGCCACA

                      *    *   *                           *                 
       1238 TTTTGAAACATGTGGTATGCCATGTGTCACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTT
          1 TTTTGAAACACGTGGCATGACATGTGTCACTTTTTGGTACACGTGGCATGACATGTGTCACTTTT

                                         
       1303 TGGTACACGTGGCGTG-ACATGTGTCACT
         66 TGGTACACGTGGCGTGCACA--TGTCACT

                 **         *                  *                      *      
       1331 TTTTGGTACACGTGGCGTGACATGTGTCACTTTTTTGTACACGTGGCATGACATGTGTTACTTTT
          1 TTTTGAAACACGTGGCATGACATGTGTCACTTTTTGGTACACGTGGCATGACATGTGTCACTTTT

             *     *                   
       1396 TTGTACATGTGGCGTGCACATGTCACT
         66 TGGTACACGTGGCGTGCACATGTCACT

                 **           
       1423 TTTTGTTACACGTGGCAT
          1 TTTTGAAACACGTGGCAT

       1441 ACCACGTCAG


Statistics
Matches: 96,  Mismatches: 13, Indels: 3
        0.86            0.12        0.03

Matches are distributed among these distances:
  92   23  0.24
  93   70  0.73
  94    3  0.03

ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38


Consensus pattern (92 bp):   
TTTTGAAACACGTGGCATGACATGTGTCACTTTTTGGTACACGTGGCATGACATGTGTCACTTTT
TGGTACACGTGGCGTGCACATGTCACT

Found at i:2069 original size:159 final size:158

Alignment explanation


    Indices: 1858--2234  Score: 508
    Period size: 159  Copynumber: 2.4  Consensus size: 158

       1848 TCCATCATTT

                  *                     *   *         *                      
       1858 GACAGCTCTGTGC-AAAAACAAAGCTCTTCTTCAAGTCCAAAGCCTCAGCATTGCACGTTTGTGT
          1 GACAGCCCTGTGCAAAAAACAAAGCTCTCCTTGAAG-CCAAATCCTCA-CATTGCACGTTTGTGT

                     **                      *                               
       1922 GCAAAACATTTTTCTTATCGAAAGGCTCATTCCTGAAGCATTTTTTG-GCAACGAGTGCTCAAAA
         64 GCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTTTTTGTGCAACGAGTGCTCAAAA

                   *           **   *    *
       1986 GCCTTGTGTCAGAGTGAGATTAGCTTGTTG
        129 GCCTTGTATCAGAGTGAGAAGAGCCTGTTC

                                                                  **         
       2016 GACAGCCCTGTGCAAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTACATTGTGCGTTTGTGT
          1 GACAGCCCTGTGCAAAAAACAAAGCTCTCCTTGAAG-CCAAATCCTC-ACATTGCACGTTTGTGT

                 *                                                           
       2081 GCAAAGCATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTTTTTGTGCAACGAGTGCTCAAAA
         64 GCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTTTTTGTGCAACGAGTGCTCAAAA

             *        *                   
       2146 GTCTTGTATCGGAGTGAGAAGAGCCTGTTC
        129 GCCTTGTATCAGAGTGAGAAGAGCCTGTTC

                *       *                                          *    
       2176 GACAACCCTGTGAAAAAAACAAAGCTCTCCTTGAAGCCAAAT-CTCAACATTGCATGTTT
          1 GACAGCCCTGTGCAAAAAACAAAGCTCTCCTTGAAGCCAAATCCTC-ACATTGCACGTTT

       2235 CTATGC


Statistics
Matches: 192,  Mismatches: 24, Indels: 6
        0.86            0.11        0.03

Matches are distributed among these distances:
 158   25  0.13
 159   92  0.48
 160   75  0.39

ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28


Consensus pattern (158 bp):   
GACAGCCCTGTGCAAAAAACAAAGCTCTCCTTGAAGCCAAATCCTCACATTGCACGTTTGTGTGC
AAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTTTTTGTGCAACGAGTGCTCAAAAGC
CTTGTATCAGAGTGAGAAGAGCCTGTTC
Done.