Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007007.1 Corchorus olitorius cultivar O-4 contig07032, 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, 817

Length: 1362
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33


Found at i:478 original size:22 final size:22

Alignment explanation


    Indices: 434--485  Score: 70
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        424 GCTTACAAGA

                        *   *     
        434 TTACT-AAAATTTTAATAAAGG
          1 TTACTAAAAATTGTAACAAAGG

                               *  
        455 TTACTAAAAATTGTAACAAGGG
          1 TTACTAAAAATTGTAACAAAGG

                     
        477 TTACTAAAA
          1 TTACTAAAA

        486 CCTTTAGTAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  21    5  0.19
  22   22  0.81

ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33


Consensus pattern (22 bp):   
TTACTAAAAATTGTAACAAAGG

Found at i:818 original size:20 final size:22

Alignment explanation


    Indices: 747--820  Score: 66
    Period size: 21  Copynumber: 3.5  Consensus size: 22

        737 TAATAAAGTT

                *     *  *        
        747 ACTTTATAAGATTTCTAAAAC-
          1 ACTTCATAAGGTTACTAAAACA

                                   
        768 AC-TCAATAAGGTTACTAAAACA
          1 ACTTC-ATAAGGTTACTAAAACA

                              *    
        790 ACCTTCATAAGGTTACTATAA-A
          1 A-CTTCATAAGGTTACTAAAACA

                      
        812 A-TTCATAAG
          1 ACTTCATAAG

        821 TTAACGATAA


Statistics
Matches: 45,  Mismatches: 4, Indels: 9
        0.78            0.07        0.16

Matches are distributed among these distances:
  20    9  0.20
  21   16  0.36
  22    3  0.07
  23   15  0.33
  24    2  0.04

ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31


Consensus pattern (22 bp):   
ACTTCATAAGGTTACTAAAACA

Found at i:830 original size:20 final size:20

Alignment explanation


    Indices: 793--831  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        783 TAAAACAACC

                         *      
        793 TTCATAAGGTTACTATAAAA
          1 TTCATAAGGTTACGATAAAA

                                
        813 TTCATAA-GTTAACGATAAA
          1 TTCATAAGGTT-ACGATAAA

        832 TCTTACAAGG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    3  0.18
  20   14  0.82

ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33


Consensus pattern (20 bp):   
TTCATAAGGTTACGATAAAA

Found at i:1069 original size:85 final size:85

Alignment explanation


    Indices: 894--1063  Score: 299
    Period size: 85  Copynumber: 2.0  Consensus size: 85

        884 TAAGATCACT

                        *                                                    
        894 AAAAATCTTAAATGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT
          1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT

                                
        959 GAAAAATTTATAAGCTTACC
         66 GAAAAATTTATAAGCTTACC

                                                         *     *             
        979 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACT-ATTTAAAA-CTTTTAAGTTTAAT
          1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT

                                
       1042 GAAAAATTTATAAGCTTACC
         66 GAAAAATTTATAAGCTTACC

              
       1062 AA
          1 AA

       1064 GAAAATTTAC


Statistics
Matches: 82,  Mismatches: 3, Indels: 2
        0.94            0.03        0.02

Matches are distributed among these distances:
  83   35  0.43
  84    7  0.09
  85   40  0.49

ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33


Consensus pattern (85 bp):   
AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT
GAAAAATTTATAAGCTTACC

Found at i:1152 original size:21 final size:20

Alignment explanation


    Indices: 1105--1144  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1095 CAATTACAAT

                         *      
       1105 AAAAGTTAAATAGTTTACTA
          1 AAAAGTTAAATAGATTACTA

                                
       1125 AAAAGTTAAATAAGATTACT
          1 AAAAGTTAAAT-AGATTACT

       1145 TGAAAGTTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   11  0.61
  21    7  0.39

ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33


Consensus pattern (20 bp):   
AAAAGTTAAATAGATTACTA
Done.