Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004272.1 Corchorus capsularis cultivar CVL-1 contig04280, 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, 747

Length: 1245
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26


Found at i:660 original size:146 final size:146

Alignment explanation


    Indices: 362--640  Score: 346
    Period size: 146  Copynumber: 1.9  Consensus size: 146

        352 TATACTTGGA

                                                            *         *      
        362 ATTTTGGGCTGAAATTTTGCAGGGACACCAAGGAATATATAGAGATGGTCCCTGCAAATTTTCAG
          1 ATTTTGGGCTGAAATTTTGCAGGGACACCAAGGAATATATAGAGATGGACCCTGCAAAATTTCAG

            *  *  **       **          * *                     *        *    
        427 GTCCAATGGATGACCGGAACTATACCGGGCCCCCCGGACCGCTCCGAAACATGGAAAATCGTAGA
         66 CTCAAAAAGATGACCCAAACTATACCGAGACCCCCGGACCGCTCCGAAACACGGAAAATCATAGA

                            
        492 AAATAGAAAACATGGC
        131 AAATAGAAAACATGGC

                                       *                      ***            
        508 ATTTTGGGCTGAAATTTTGCAGGGACATCAA-GAATAATATAGAGATGGAGTGTGCAAAATTTCA
          1 ATTTTGGGCTGAAATTTTGCAGGGACACCAAGGAAT-ATATAGAGATGGACCCTGCAAAATTTCA

                                            *   *           **               
        572 GCTCAAAAAGATGACCCAAACTATAACCGAGATCCCGGGACCGCTCCGGTACACGGAAAATCAT-
         65 GCTCAAAAAGATGACCCAAACTAT-ACCGAGACCCCCGGACCGCTCCGAAACACGGAAAATCATA

                 
        636 GAAAA
        129 GAAAA

        641 ATGGAAAATG


Statistics
Matches: 111,  Mismatches: 20, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
 145    4  0.04
 146   76  0.68
 147   31  0.28

ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21


Consensus pattern (146 bp):   
ATTTTGGGCTGAAATTTTGCAGGGACACCAAGGAATATATAGAGATGGACCCTGCAAAATTTCAG
CTCAAAAAGATGACCCAAACTATACCGAGACCCCCGGACCGCTCCGAAACACGGAAAATCATAGA
AAATAGAAAACATGGC

Found at i:808 original size:48 final size:46

Alignment explanation


    Indices: 732--840  Score: 155
    Period size: 48  Copynumber: 2.3  Consensus size: 46

        722 GATTTCTAAA

                         *                                  
        732 TTTTGGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC
          1 TTTT-GGCCAATTTTTGGGTCCGGAACTCATGATGGTTAA-CTACGGC

                                         *             *   
        780 TTTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACTATGGC
          1 TTTT-GGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACTACGGC

            *             
        827 ATTTGGCCAATTTT
          1 TTTTGGCCAATTTT

        841 GCCCCGAAGC


Statistics
Matches: 56,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  46   10  0.18
  47    9  0.16
  48   37  0.66

ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37


Consensus pattern (46 bp):   
TTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACTACGGC

Found at i:906 original size:72 final size:72

Alignment explanation


    Indices: 782--925  Score: 184
    Period size: 72  Copynumber: 2.0  Consensus size: 72

        772 CCTACGGCTT

                                       *    ****                             
        782 TTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACTATGGCATTTGGCCAATTTTGCCCCG
          1 TTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACTATGGCATTTGGCCAATTTTGCCCCG

              *    
        847 AAGCTCA
         66 AAACTCA

                               *                                    *        
        854 TTCGGCC-ATTTTTGGGTCTGGAACTCATGATACAAAACCTAAT-GCATTTGGCCATTTTTGCCC
          1 TTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAA-CT-ATGGCATTTGGCCAATTTTGCCC

                     
        917 CGAAACTCA
         64 CGAAACTCA

        926 GCGAACACCT


Statistics
Matches: 62,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  71   24  0.39
  72   36  0.58
  73    2  0.03

ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33


Consensus pattern (72 bp):   
TTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACTATGGCATTTGGCCAATTTTGCCCCG
AAACTCA

Found at i:1231 original size:32 final size:32

Alignment explanation


    Indices: 1142--1232  Score: 157
    Period size: 32  Copynumber: 2.8  Consensus size: 32

       1132 GGACACCCTT

                                     *      
       1142 CGTCGGCATTCTCCGATGGCACTTGACCTTGG
          1 CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

                                             
       1174 CGTCGGCATTCTCCGATGG-ATCTTGGCCTTGG
          1 CGTCGGCATTCTCCGATGGCA-CTTGGCCTTGG

                                       
       1206 CGTCGGCATTCTCCGATGGCACTTGGC
          1 CGTCGGCATTCTCCGATGGCACTTGGC

       1233 ATCGGCACTT


Statistics
Matches: 56,  Mismatches: 1, Indels: 4
        0.92            0.02        0.07

Matches are distributed among these distances:
  31    1  0.02
  32   54  0.96
  33    1  0.02

ACGTcount: A:0.11, C:0.31, G:0.30, T:0.29


Consensus pattern (32 bp):   
CGTCGGCATTCTCCGATGGCACTTGGCCTTGG
Done.