Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008596.1 Corchorus capsularis cultivar CVL-1 contig08617, 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: 4701
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:1397 original size:31 final size:31

Alignment explanation


    Indices: 1360--1419  Score: 111
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       1350 ATAGGTGATA

                            *              
       1360 CCCACGTGGTTACACATGTTATAGGTAATGC
          1 CCCACGTGGTTACACACGTTATAGGTAATGC

                                         
       1391 CCCACGTGGTTACACACGTTATAGGTAAT
          1 CCCACGTGGTTACACACGTTATAGGTAAT

       1420 ACTCTGTAAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28


Consensus pattern (31 bp):   
CCCACGTGGTTACACACGTTATAGGTAATGC

Found at i:1454 original size:16 final size:16

Alignment explanation


    Indices: 1430--1487  Score: 64
    Period size: 16  Copynumber: 3.6  Consensus size: 16

       1420 ACTCTGTAAC

                            
       1430 TGGTAATACATGTTGT
          1 TGGTAATACATGTTGT

              *      *       *
       1446 TGATAATACCT-TGTGAC
          1 TGGTAATACATGT-TG-T

                            
       1463 TGGTAATACATGTTGT
          1 TGGTAATACATGTTGT

                     
       1479 TGGTAATAC
          1 TGGTAATAC

       1488 CTTATGAACT


Statistics
Matches: 33,  Mismatches: 6, Indels: 6
        0.73            0.13        0.13

Matches are distributed among these distances:
  15    1  0.03
  16   20  0.61
  17   11  0.33
  18    1  0.03

ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40


Consensus pattern (16 bp):   
TGGTAATACATGTTGT

Found at i:1465 original size:33 final size:34

Alignment explanation


    Indices: 1427--1499  Score: 121
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       1417 AATACTCTGT

                                           *  
       1427 AACTGGTAATACATGTTGTTGATAATACCTTGTG
          1 AACTGGTAATACATGTTGTTGATAATACCTTATG

                                 *            
       1461 -ACTGGTAATACATGTTGTTGGTAATACCTTATG
          1 AACTGGTAATACATGTTGTTGATAATACCTTATG

                  
       1494 AACTGG
          1 AACTGG

       1500 GAACACTTTA


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  33   31  0.86
  34    5  0.14

ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37


Consensus pattern (34 bp):   
AACTGGTAATACATGTTGTTGATAATACCTTATG

Found at i:2067 original size:46 final size:47

Alignment explanation


    Indices: 1995--2091  Score: 133
    Period size: 46  Copynumber: 2.1  Consensus size: 47

       1985 CCGATGGGAG

                                 *      *      *   *  *    
       1995 TGACGTGGCCTACCCTTACCTTTTCAG-GAAAATATCACTATTACCA
          1 TGACGTGGCCTACCCTTACCTCTTCAGAAAAAATACCACCATCACCA

                     *                                     
       2041 TGACGTGGCTTACCCTTACCTCTTCAGAAAAAATACCACCATCACCA
          1 TGACGTGGCCTACCCTTACCTCTTCAGAAAAAATACCACCATCACCA

                
       2088 TGAC
          1 TGAC

       2092 ATACCCTTAC


Statistics
Matches: 44,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  46   25  0.57
  47   19  0.43

ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27


Consensus pattern (47 bp):   
TGACGTGGCCTACCCTTACCTCTTCAGAAAAAATACCACCATCACCA

Found at i:2906 original size:126 final size:124

Alignment explanation


    Indices: 2695--2937  Score: 346
    Period size: 126  Copynumber: 1.9  Consensus size: 124

       2685 TAATTTAAAA

                                        *               *     **             
       2695 TTTTTAATAAATAATCTAAAACCCTAGTTCTATATATATCAAAATAGGACTTACCCTATAATTTA
          1 TTTTTAATAAATAATCTAAAACCCTAGTCCTATATATATCAAAAAAGGACCAACCCTATAATTTA

                                                                       
       2760 TTTCCTTATATTAATTTGGGGCTAAACCTTATGAAAAACAATATCCTATTTTAAGGAGT
         66 TTTCCTTATATTAATTTGGGGCTAAACCTTATGAAAAACAATATCCTATTTTAAGGAGT

                                                    *        *               
       2819 TTTTTAATAGAA-AATCTAAAACCCTAGTCCTATAAATATTTCAAAAAATGACCAACCCTATAAT
          1 TTTTTAATA-AATAATCTAAAACCCTAGTCCTAT--ATATATCAAAAAAGGACCAACCCTATAAT

              *    *                      *           *             
       2883 TTCTTTCATT-TAATTAATTTGGGGCTAAATCTTATGAAAAATAATATCCTATTTT
         63 TTATTTCCTTAT-ATTAATTTGGGGCTAAACCTTATGAAAAACAATATCCTATTTT

       2938 GTAACAAAAT


Statistics
Matches: 105,  Mismatches: 10, Indels: 6
        0.87            0.08        0.05

Matches are distributed among these distances:
 124   29  0.28
 125    3  0.03
 126   73  0.70

ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39


Consensus pattern (124 bp):   
TTTTTAATAAATAATCTAAAACCCTAGTCCTATATATATCAAAAAAGGACCAACCCTATAATTTA
TTTCCTTATATTAATTTGGGGCTAAACCTTATGAAAAACAATATCCTATTTTAAGGAGT
Done.