Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007389.1 Corchorus capsularis cultivar CVL-1 contig07410, 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: 17357
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--70  Score: 140
    Period size: 2  Copynumber: 35.0  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                     
         43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC

         71 GTTTGAATAG


Statistics
Matches: 68,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   68  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:1466 original size:31 final size:31

Alignment explanation


    Indices: 1431--1496  Score: 80
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1421 GTATGTTGAC

                        *                   
       1431 GTGGCATGCCACGTGGCAATTATT-GACTGAT
          1 GTGGCATGCCACATGGCAATT-TTCGACTGAT

                    *  *             *     
       1462 GTGGCATGTCATATGGCAATTTTCGGCTGAT
          1 GTGGCATGCCACATGGCAATTTTCGACTGAT

                
       1493 GTGG
          1 GTGG

       1497 ACGTGGCATG


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  30    2  0.07
  31   28  0.93

ACGTcount: A:0.20, C:0.17, G:0.32, T:0.32


Consensus pattern (31 bp):   
GTGGCATGCCACATGGCAATTTTCGACTGAT

Found at i:1613 original size:29 final size:29

Alignment explanation


    Indices: 1578--1675  Score: 85
    Period size: 29  Copynumber: 3.3  Consensus size: 29

       1568 AAAATGTACC

                                         
       1578 CAAAATAAAACATTATGGTGCAATATAAT
          1 CAAAATAAAACATTATGGTGCAATATAAT

                           * *   *    *    **
       1607 CAAAATAAAA-A--AAGTTGAGAATTTTGCACC
          1 CAAAATAAAACATTATGGTG-CAA-TAT--AAT

                                         
       1637 CAAAATAAAACATTATGGTGCAATATAAT
          1 CAAAATAAAACATTATGGTGCAATATAAT

                      
       1666 CAAAATAAAA
          1 CAAAATAAAA

       1676 AAAGTTGAGT


Statistics
Matches: 50,  Mismatches: 12, Indels: 14
        0.66            0.16        0.18

Matches are distributed among these distances:
  26    4  0.08
  27    2  0.04
  28    3  0.06
  29   21  0.42
  30   11  0.22
  31    3  0.06
  32    2  0.04
  33    4  0.08

ACGTcount: A:0.54, C:0.11, G:0.10, T:0.24


Consensus pattern (29 bp):   
CAAAATAAAACATTATGGTGCAATATAAT

Found at i:2030 original size:3 final size:3

Alignment explanation


    Indices: 2022--2059  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       2012 GTTAGTAGCA

                                                              
       2022 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

       2060 ACCATAATAG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:4652 original size:34 final size:34

Alignment explanation


    Indices: 4613--4678  Score: 132
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       4603 ACTAATCATT

                                              
       4613 CCATTAATTGTAATTTCTTACAAGTTTAGATTTC
          1 CCATTAATTGTAATTTCTTACAAGTTTAGATTTC

                                            
       4647 CCATTAATTGTAATTTCTTACAAGTTTAGATT
          1 CCATTAATTGTAATTTCTTACAAGTTTAGATT

       4679 GCATATACGT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   32  1.00

ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47


Consensus pattern (34 bp):   
CCATTAATTGTAATTTCTTACAAGTTTAGATTTC

Done.