Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002847.1 Corchorus olitorius cultivar O-4 contig02849, 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, 660

Length: 1101
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37


Found at i:491 original size:23 final size:22

Alignment explanation


    Indices: 448--494  Score: 71
    Period size: 20  Copynumber: 2.2  Consensus size: 22

        438 TATTATTATT

                                  
        448 TAAATATATATAAACGGAATAA
          1 TAAATATATATAAACGGAATAA

                          *       
        470 TAAATA-ATATAAATGG-ATAA
          1 TAAATATATATAAACGGAATAA

                 
        490 TAAAT
          1 TAAAT

        495 TTAAATATAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  20    9  0.38
  21    9  0.38
  22    6  0.25

ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30


Consensus pattern (22 bp):   
TAAATATATATAAACGGAATAA

Found at i:543 original size:29 final size:28

Alignment explanation


    Indices: 501--557  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 28

        491 AAATTTAAAT

                     *                   
        501 ATATATGTACTAATTGTAATAGTAATTAA
          1 ATATATGTAATAATTGTAATAGT-ATTAA

                                        
        530 ATATATGTAATAATTGTAATAGTATTAA
          1 ATATATGTAATAATTGTAATAGTATTAA

        558 TAATAATAGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  28    5  0.19
  29   22  0.81

ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42


Consensus pattern (28 bp):   
ATATATGTAATAATTGTAATAGTATTAA

Found at i:624 original size:21 final size:19

Alignment explanation


    Indices: 600--641  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        590 TATTTATATA

                             *   
        600 ATTAATATAATAATATAGAAT
          1 ATTAATAT-ATAA-ATAAAAT

                               
        621 ATTAATATATAAATAAAAT
          1 ATTAATATATAAATAAAAT

              
        640 AT
          1 AT

        642 GCATTATATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    8  0.40
  20    4  0.20
  21    8  0.40

ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38


Consensus pattern (19 bp):   
ATTAATATATAAATAAAAT

Found at i:662 original size:52 final size:51

Alignment explanation


    Indices: 555--662  Score: 114
    Period size: 51  Copynumber: 2.1  Consensus size: 51

        545 GTAATAGTAT

                         *     *          *                   * 
        555 TAATAATAATAGAGTATTATTCATATAAATGAATATATTTATATAATTAATA
          1 TAATAATAATAGAATATTAATCATATAAATAAATATATTTATATAA-TAACA

                                                                   
        607 TAATAAT-ATAGAATATTAAT-ATATAAATAAAATATGCATTATATATAA-AACA
          1 TAATAATAATAGAATATTAATCATATAAAT-AAATAT--ATT-TATATAATAACA

                
        659 TAAT
          1 TAAT

        663 TAATTATATA


Statistics
Matches: 48,  Mismatches: 4, Indels: 8
        0.80            0.07        0.13

Matches are distributed among these distances:
  50    8  0.17
  51   16  0.33
  52   14  0.29
  53    3  0.06
  54    7  0.15

ACGTcount: A:0.54, C:0.03, G:0.05, T:0.39


Consensus pattern (51 bp):   
TAATAATAATAGAATATTAATCATATAAATAAATATATTTATATAATAACA
Done.