Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004695.1 Corchorus capsularis cultivar CVL-1 contig04711, 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, 616

Length: 1028
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29


Found at i:381 original size:48 final size:48

Alignment explanation


    Indices: 305--417  Score: 183
    Period size: 48  Copynumber: 2.4  Consensus size: 48

        295 TGGATTTCTA

                         *                                  
        305 ATTTTGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC
          1 ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                                          *              *   
        353 -TTTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGC
          1 ATTTT-GGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                             
        401 ATTTTGGCCAATTTTTG
          1 ATTTTGGCCAATTTTTG

        418 CCCCCGAAGC


Statistics
Matches: 60,  Mismatches: 3, Indels: 4
        0.90            0.04        0.06

Matches are distributed among these distances:
  47    4  0.07
  48   52  0.87
  49    4  0.07

ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37


Consensus pattern (48 bp):   
ATTTTGGCCAATTTTTGGGTCCGGAACTCATGATGGTTAACCTACGGC

Found at i:481 original size:77 final size:77

Alignment explanation


    Indices: 354--507  Score: 211
    Period size: 77  Copynumber: 2.0  Consensus size: 77

        344 ACCTACGGCT

                                        *    ****                            
        354 TTTCGGCCAATTTTTGGGTCCGGAACTCTTGATGGTTAACCTATGGCATTTTGGCCAATTTTTGC
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTGGCCAATTTTTGC

                   *    
        419 CCCCGAAGCTCA
         66 CCCCGAAACTCA

                     *          *                                     *      
        431 TTTCGGCCATTTTTTGGGTCTGGAACTCATGATACAAAACCTAAT-GCATTTTGGCCATTTTTTG
          1 TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCT-ATGGCATTTTGGCCAATTTTTG

                         
        495 CCCCCGAAACTCA
         65 CCCCCGAAACTCA

        508 GCGAACACCT


Statistics
Matches: 67,  Mismatches: 9, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  77   65  0.97
  78    2  0.03

ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35


Consensus pattern (77 bp):   
TTTCGGCCAATTTTTGGGTCCGGAACTCATGATACAAAACCTATGGCATTTTGGCCAATTTTTGC
CCCCGAAACTCA

Found at i:815 original size:32 final size:32

Alignment explanation


    Indices: 726--816  Score: 157
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        716 GGACACCCTT

                                     *      
        726 CGTCGGCATTCTCCGATGGCACTTGACCTTGG
          1 CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

                                             
        758 CGTCGGCATTCTCCGATGG-ATCTTGGCCTTGG
          1 CGTCGGCATTCTCCGATGGCA-CTTGGCCTTGG

                                       
        790 CGTCGGCATTCTCCGATGGCACTTGGC
          1 CGTCGGCATTCTCCGATGGCACTTGGC

        817 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

Found at i:816 original size:26 final size:26

Alignment explanation


    Indices: 804--860  Score: 114
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        794 GGCATTCTCC

                                      
        804 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                                      
        830 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                 
        856 GATGG
          1 GATGG

        861 ATGGCACTTG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   31  1.00

ACGTcount: A:0.16, C:0.25, G:0.33, T:0.26


Consensus pattern (26 bp):   
GATGGCACTTGGCATCGGCACTTGCT

Found at i:823 original size:13 final size:13

Alignment explanation


    Indices: 807--853  Score: 62
    Period size: 13  Copynumber: 3.6  Consensus size: 13

        797 ATTCTCCGAT

                         
        807 GGCACTTGGCATC
          1 GGCACTTGGCATC

                           
        820 GGCACTT-GCTGAT-
          1 GGCACTTGGC--ATC

                         
        833 GGCACTTGGCATC
          1 GGCACTTGGCATC

                    
        846 GGCACTTG
          1 GGCACTTG

        854 CTGATGGATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 8
        0.79            0.00        0.21

Matches are distributed among these distances:
  12    4  0.13
  13   22  0.73
  14    4  0.13

ACGTcount: A:0.15, C:0.28, G:0.32, T:0.26


Consensus pattern (13 bp):   
GGCACTTGGCATC
Done.