Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012032.1 Corchorus capsularis cultivar CVL-1 contig12053, 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: 7758
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:933 original size:12 final size:13

Alignment explanation


    Indices: 889--933  Score: 65
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        879 AATTATTGTT

                         
        889 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
        902 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
        915 TGCTTTA-TAATC
          1 TGCTTTATTAATC

              *    
        927 TGTTTTA
          1 TGCTTTA

        934 GATTTAGATT


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  12   10  0.34
  13   19  0.66

ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:941 original size:6 final size:6

Alignment explanation


    Indices: 930--956  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

        920 TATAATCTGT

                                           
        930 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

        957 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:1251 original size:22 final size:22

Alignment explanation


    Indices: 1163--1558  Score: 175
    Period size: 22  Copynumber: 18.2  Consensus size: 22

       1153 GACACGATCA

                               * *
       1163 GTTATCAAAATTTCATA-GTAT
          1 GTTATCAAAATTTCATAGGGAG

               *                   
       1184 GTAGATCAAAATTTCATAGGGAG
          1 GT-TATCAAAATTTCATAGGGAG

            *   *            **   
       1207 ATTAACAAAATTTCATAATGAG
          1 GTTATCAAAATTTCATAGGGAG

                      **          
       1229 GTTATCAAAAAATCATAGGGAG
          1 GTTATCAAAATTTCATAGGGAG

                  *            *  
       1251 GTTATCGAAA-TT--T--GTA-
          1 GTTATCAAAATTTCATAGGGAG

                    *        *** *
       1267 GTTATCAAGATTTCATAAAAAA
          1 GTTATCAAAATTTCATAGGGAG

                         *        
       1289 GTTATCAAAATTTTATAGGGAG
          1 GTTATCAAAATTTCATAGGGAG

                               *   
       1311 GTTTATCAAAATTTCATAGCGAG
          1 G-TTATCAAAATTTCATAGGGAG

                   *          * * 
       1334 GTTATCACAATTTCATAGTGTG
          1 GTTATCAAAATTTCATAGGGAG

            *              *  * * 
       1356 ATTATCAAAATTTCAGAGTGTG
          1 GTTATCAAAATTTCATAGGGAG

            *              *   *    
       1378 ATTA-CTAACAA-TTGATATGGAG
          1 GTTATC-AA-AATTTCATAGGGAG

               * *   *       ** * 
       1400 GTTTTTAAATTTTCATAACGTG
          1 GTTATCAAAATTTCATAGGGAG

                    *  *     *    
       1422 GTTATCAATATATCATATGGAG
          1 GTTATCAAAATTTCATAGGGAG

                *   *  *        ** 
       1444 GTTACCAACATCTCATAGTGTTG
          1 GTTATCAAAATTTCATAG-GGAG

                            *    *
       1467 GTTATCAAAATTTCATTGGGAA
          1 GTTATCAAAATTTCATAGGGAG

                       *     ***  
       1489 GTTATCAAAATATCATATTAAG
          1 GTTATCAAAATTTCATAGGGAG

                         * *       
       1511 GTCT-TCAAAATTCCTTAGGGAG
          1 GT-TATCAAAATTTCATAGGGAG

                 *            * *  
       1533 GTTA-AAAGAATTTCATAAGAAG
          1 GTTATCAA-AATTTCATAGGGAG

                
       1555 GTTA
          1 GTTA

       1559 AAAAAATTAA


Statistics
Matches: 272,  Mismatches: 86, Indels: 33
        0.70            0.22        0.08

Matches are distributed among these distances:
  16    8  0.03
  17    4  0.01
  19    2  0.01
  21    9  0.03
  22  207  0.76
  23   42  0.15

ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35


Consensus pattern (22 bp):   
GTTATCAAAATTTCATAGGGAG

Done.