Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015810.1 Corchorus capsularis cultivar CVL-1 contig15831, 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: 5322
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:644 original size:16 final size:17

Alignment explanation


    Indices: 623--656  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        613 TAAGTTACAG

                             
        623 ATTTTTCAAAAAATAAT
          1 ATTTTTCAAAAAATAAT

                       *     
        640 ATTTTTCAAAAGATAAT
          1 ATTTTTCAAAAAATAAT

        657 TGACGGGAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41


Consensus pattern (17 bp):   
ATTTTTCAAAAAATAAT

Found at i:1250 original size:167 final size:164

Alignment explanation


    Indices: 817--1251  Score: 527
    Period size: 167  Copynumber: 2.6  Consensus size: 164

        807 TGAGTCATTT

                                        *        *                           
        817 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAGTTCA-CTCAAGAATCAAAAGTTAGGACA
          1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTA-ATCACCTCAAGAATCAAAAGTTAGGACA

                        *         *     *      *  *  * *         ** *   *    
        881 TTTAAGTAATTTACCAAGTAGGTAAAGAGGAAAAAGATTAGTTTTCTAACTCATCATCAATCCTT
         64 TTTAAGTAA-TTGCCAAGTAGGAAAAGACGAAAAAAATAAGCTCTCTAACTCAAAAGCAAGCCTT

                           *                  *  
        946 GATGTGGATCTTTTATTAATTCCACTACTCTATTCAA
        128 GATGTGGATCTTTTAGTAATTCCACTACTCTATTAAA

                                    *   *                                    
        983 GTTC-ATTGAGAAATGACCAAAAAATTACTTATTTAATC-CTCTCAAGAATCAAAAGTTAGGACA
          1 G-TCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCAC-CTCAAGAATCAAAAGTTAGGACA

                                          *                                  
       1046 TTTAAGTAATCTGCCAAGTAGGAAAAGACCAAAAAAAATAAGCTCTCTAACTCCAAAAGCAAGCC
         64 TTTAAGTAAT-TGCCAAGTAGGAAAAGA-CGAAAAAAATAAGCTCTCTAACT-CAAAAGCAAGCC

               *                                    
       1111 TTGGTAG-GGATCTTTTAGTAATTCCACTACTCTATTAAA
        126 TTGAT-GTGGATCTTTTAGTAATTCCACTACTCTATTAAA

                                                                         *   
       1150 GTCAATTGAGAAATGACCAAAAAGTCTAATTATTTAATCACCTCAAGAATCAAAAGTTAGGGCAT
          1 GTCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCACCTCAAGAATCAAAAGTTAGGACAT

                        *     *      * *         
       1215 TTAAGTAATTGGTCAAGTGGGAAAATATGAAAAAAAT
         65 TTAAGTAATT-GCCAAGTAGGAAAAGACGAAAAAAAT

       1252 TAGTTCTCGC


Statistics
Matches: 232,  Mismatches: 26, Indels: 21
        0.83            0.09        0.08

Matches are distributed among these distances:
 164    3  0.01
 165   57  0.25
 166   39  0.17
 167   74  0.32
 168   58  0.25
 169    1  0.00

ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30


Consensus pattern (164 bp):   
GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCACCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATTGCCAAGTAGGAAAAGACGAAAAAAATAAGCTCTCTAACTCAAAAGCAAGCCTTGAT
GTGGATCTTTTAGTAATTCCACTACTCTATTAAA

Found at i:3126 original size:14 final size:14

Alignment explanation


    Indices: 3107--3135  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       3097 GAGTGCTTAA

                          
       3107 GGCCGACGAAAGAG
          1 GGCCGACGAAAGAG

                          
       3121 GGCCGACGAAAGAG
          1 GGCCGACGAAAGAG

             
       3135 G
          1 G

       3136 AGGGATAGCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.34, C:0.21, G:0.45, T:0.00


Consensus pattern (14 bp):   
GGCCGACGAAAGAG
Done.