Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008572.1 Corchorus capsularis cultivar CVL-1 contig08593, 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, 948

Length: 1580
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:159 original size:31 final size:30

Alignment explanation


    Indices: 124--234  Score: 105
    Period size: 31  Copynumber: 3.9  Consensus size: 30

        114 GGCATGCCAC

                                          
        124 GTGTCACTTTTTGGTACACGTGGCGTGACA
          1 GTGTCACTTTTTGGTACACGTGGCGTGACA

                               *           
        154 TGTGTCACTTTTTGGTACATGTGGC---AC-
          1 -GTGTCACTTTTTGGTACACGTGGCGTGACA

                        *     *             
        181 --G--ACTTTTTTGTACATGTGGCGTGCCACA
          1 GTGTCACTTTTTGGTACACGTGGCGTG--ACA

                                       
        209 -TGTCACTTTTTGGTACACGTGGCGTG
          1 GTGTCACTTTTTGGTACACGTGGCGTG

        235 CCAAGTCGGA


Statistics
Matches: 67,  Mismatches: 4, Indels: 18
        0.75            0.04        0.20

Matches are distributed among these distances:
  22   18  0.27
  24    1  0.01
  27    2  0.03
  28    2  0.03
  29    1  0.01
  31   43  0.64

ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37


Consensus pattern (30 bp):   
GTGTCACTTTTTGGTACACGTGGCGTGACA

Found at i:194 original size:53 final size:53

Alignment explanation


    Indices: 129--231  Score: 152
    Period size: 53  Copynumber: 1.9  Consensus size: 53

        119 GCCACGTGTC

                                     **                 *        
        129 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
          1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG

                   *     *        *                           
        182 ACTTTTTTGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
          1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC

        232 GTGCCAAGTC


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  53   44  1.00

ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37


Consensus pattern (53 bp):   
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG

Found at i:638 original size:21 final size:22

Alignment explanation


    Indices: 612--656  Score: 65
    Period size: 21  Copynumber: 2.1  Consensus size: 22

        602 CTTGTTGATT

                        *         
        612 ATTTTGGAATCAGCACA-TGAG
          1 ATTTTGGAATCAACACATTGAG

                   *              
        633 ATTTTGGCATCAACACATTGAG
          1 ATTTTGGAATCAACACATTGAG

              
        655 AT
          1 AT

        657 ACGCAATTTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   15  0.71
  22    6  0.29

ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31


Consensus pattern (22 bp):   
ATTTTGGAATCAACACATTGAG

Found at i:1185 original size:2 final size:2

Alignment explanation


    Indices: 1178--1217  Score: 62
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       1168 AAGGTATAAA

                                                   *                   
       1178 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A

       1218 AAAGTACGAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   2   33  0.94
   3    2  0.06

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:1281 original size:31 final size:31

Alignment explanation


    Indices: 1246--1311  Score: 80
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1236 AACTTTATGT

                 *        *             *   
       1246 TTTCCGATAGTA-CTCTTATTTTTAAAATATA
          1 TTTCCAATAGTATCCCTT-TTTTTAAAACATA

                    *                      
       1277 TTTCCAATTGTATCCCTTTTTTTAAAACATA
          1 TTTCCAATAGTATCCCTTTTTTTAAAACATA

                
       1308 TTTC
          1 TTTC

       1312 TAAATTGCCA


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

Matches are distributed among these distances:
  31   26  0.87
  32    4  0.13

ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50


Consensus pattern (31 bp):   
TTTCCAATAGTATCCCTTTTTTTAAAACATA
Done.