Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021300.1 Corchorus olitorius cultivar O-4 contig21333, 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: 3988
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39


Found at i:1347 original size:204 final size:206

Alignment explanation


    Indices: 996--1398  Score: 670
    Period size: 204  Copynumber: 2.0  Consensus size: 206

        986 CTTTATGAAT

                   *                                     *                   
        996 ATGTTATTAATTTTTTAAGTCTACAATTACTAACAAAGTTGTAGTTAATAAGATACAACACACTA
          1 ATGTTATAAATTTTTTAAGTCTACAATTACTAACAAAGTTGTAGTGAATAAGATACAACACACTA

            *              *                                                 
       1061 TTATTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAAT
         66 CTATTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAAT

                                                                             
       1126 TAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-A-AAAGATATTAAAGATCCGATTTATT
        131 TAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAGATATT-AAGATCCGATTTATT

                        
       1189 TATCAATGGTGA
        195 TATCAATGGTGA

                                                                           * 
       1201 ATGTTATAAATTTTTTAAGTCTA-AGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATT
          1 ATGTTATAAATTTTTTAAGTCTACA-ATTACTAACAAAGTTGTAGTGAATAAGATACAACACACT

                                              *        *                     
       1265 ACTATTA-TATATATAGAACTATACCAAAAAAAATTAGTTGAATATTAGTGGTTGATTTATTAAA
         65 ACTATTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAA

                                                                      *      
       1329 TTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAATTAAAGATATTAAGATCTGATTTA
        130 TTAAATTAGATCAATGTCAAACAAAATTTCAAAATTAT-AA-TAAAGATATTAAGATCCGATTTA

                 
       1394 TTTAT
        193 TTTAT

       1399 TATTAAGGAA


Statistics
Matches: 185,  Mismatches: 8, Indels: 8
        0.92            0.04        0.04

Matches are distributed among these distances:
 204   93  0.50
 205   65  0.35
 206    1  0.01
 207   17  0.09
 208    9  0.05

ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37


Consensus pattern (206 bp):   
ATGTTATAAATTTTTTAAGTCTACAATTACTAACAAAGTTGTAGTGAATAAGATACAACACACTA
CTATTATTATATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAAT
TAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAAAGATATTAAGATCCGATTTATTT
ATCAATGGTGA

Found at i:2596 original size:35 final size:36

Alignment explanation


    Indices: 2548--2615  Score: 129
    Period size: 35  Copynumber: 1.9  Consensus size: 36

       2538 AGCAATTTTT

                                                
       2548 TTTTTTTGTTTTTTTTGTTTCCCTCCTAGAAATCCA
          1 TTTTTTTGTTTTTTTTGTTTCCCTCCTAGAAATCCA

                                             
       2584 TTTTTTTG-TTTTTTTGTTTCCCTCCTAGAAAT
          1 TTTTTTTGTTTTTTTTGTTTCCCTCCTAGAAAT

       2616 ATTTTGTTTC


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  35   24  0.75
  36    8  0.25

ACGTcount: A:0.13, C:0.18, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTTTTTTGTTTTTTTTGTTTCCCTCCTAGAAATCCA

Found at i:2623 original size:22 final size:22

Alignment explanation


    Indices: 2595--2642  Score: 87
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       2585 TTTTTTGTTT

                                  
       2595 TTTTGTTTCCCTCCTAGAAATA
          1 TTTTGTTTCCCTCCTAGAAATA

                                 *
       2617 TTTTGTTTCCCTCCTAGAAATC
          1 TTTTGTTTCCCTCCTAGAAATA

                
       2639 TTTT
          1 TTTT

       2643 TTTTTTGTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.19, C:0.23, G:0.08, T:0.50


Consensus pattern (22 bp):   
TTTTGTTTCCCTCCTAGAAATA

Found at i:2629 original size:57 final size:58

Alignment explanation


    Indices: 2560--2675  Score: 198
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       2550 TTTTTGTTTT

                                                                      
       2560 TTTTGTTTCCCTCCTAGAAATC-CATTTTTTTGTTTTTTTGTTTCCCTCCTAGAAATA
          1 TTTTGTTTCCCTCCTAGAAATCTCATTTTTTTGTTTTTTTGTTTCCCTCCTAGAAATA

                                   **                        *        
       2617 TTTTGTTTCCCTCCTAGAAATCTTTTTTTTTTGTTTTTTTGTTTCCCTCTTAGAAATA
          1 TTTTGTTTCCCTCCTAGAAATCTCATTTTTTTGTTTTTTTGTTTCCCTCCTAGAAATA

             
       2675 T
          1 T

       2676 ACAAAATAAT


Statistics
Matches: 55,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  57   22  0.40
  58   33  0.60

ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56


Consensus pattern (58 bp):   
TTTTGTTTCCCTCCTAGAAATCTCATTTTTTTGTTTTTTTGTTTCCCTCCTAGAAATA

Done.