Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018686.1 Corchorus olitorius cultivar O-4 contig18719, 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: 10948
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34


Found at i:7346 original size:56 final size:53

Alignment explanation


    Indices: 7255--7392  Score: 132
    Period size: 44  Copynumber: 2.7  Consensus size: 53

       7245 ACAATAAGCT

                       *    *    *    *                             
       7255 TTATCAAATTTAATATGCAAGATTACCAAACCTAATATATAAACTAATATAAGAGA
          1 TTATCAAATTTTATATACAA-TTTACTAAA-CTAATAT-TAAACTAATATAAGAGA

                                                                 
       7311 TTATCAAATTTTATATACAATTT--T-AAC------TAAACTAATATAAGAGA
          1 TTATCAAATTTTATATACAATTTACTAAACTAATATTAAACTAATATAAGAGA

                                                  
       7355 TTATCAAATTTTATATACAATTTTAACTAAACTAATAT
          1 TTATCAAATTTTATATACAA-TTT-ACTAAACTAATAT

       7393 GAGGCAAATT


Statistics
Matches: 67,  Mismatches: 4, Indels: 23
        0.71            0.04        0.24

Matches are distributed among these distances:
  44   37  0.55
  45    3  0.04
  48    1  0.01
  49    3  0.04
  51    1  0.01
  52    2  0.03
  55    2  0.03
  56   18  0.27

ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37


Consensus pattern (53 bp):   
TTATCAAATTTTATATACAATTTACTAAACTAATATTAAACTAATATAAGAGA

Found at i:7348 original size:22 final size:22

Alignment explanation


    Indices: 7323--7392  Score: 63
    Period size: 22  Copynumber: 3.2  Consensus size: 22

       7313 ATCAAATTTT

                                  
       7323 ATATACAATTTTAACTAAACTA
          1 ATATACAATTTTAACTAAACTA

                     **   *      * *
       7345 ATATA-AGAGATTATC-AAATTTT
          1 ATATACA-ATTTTAACTAAA-CTA

                                  
       7367 ATATACAATTTTAACTAAACTA
          1 ATATACAATTTTAACTAAACTA

                
       7389 ATAT
          1 ATAT

       7393 GAGGCAAATT


Statistics
Matches: 34,  Mismatches: 10, Indels: 8
        0.65            0.19        0.15

Matches are distributed among these distances:
  21    4  0.12
  22   26  0.76
  23    4  0.12

ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39


Consensus pattern (22 bp):   
ATATACAATTTTAACTAAACTA

Found at i:7357 original size:44 final size:44

Alignment explanation


    Indices: 7294--7392  Score: 198
    Period size: 44  Copynumber: 2.2  Consensus size: 44

       7284 ACCTAATATA

                                                        
       7294 TAAACTAATATAAGAGATTATCAAATTTTATATACAATTTTAAC
          1 TAAACTAATATAAGAGATTATCAAATTTTATATACAATTTTAAC

                                                        
       7338 TAAACTAATATAAGAGATTATCAAATTTTATATACAATTTTAAC
          1 TAAACTAATATAAGAGATTATCAAATTTTATATACAATTTTAAC

                       
       7382 TAAACTAATAT
          1 TAAACTAATAT

       7393 GAGGCAAATT


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   55  1.00

ACGTcount: A:0.48, C:0.09, G:0.04, T:0.38


Consensus pattern (44 bp):   
TAAACTAATATAAGAGATTATCAAATTTTATATACAATTTTAAC

Found at i:7607 original size:40 final size:44

Alignment explanation


    Indices: 7540--7638  Score: 109
    Period size: 42  Copynumber: 2.3  Consensus size: 44

       7530 TAATAGATTT

                                          *              
       7540 ATCAAATTTTATA-AACAAGATTACCAAAATTAATA-T-AGGGTG
          1 ATCAAA-TTTATACAACAAGATTACCAAAACTAATATTGAGGGTG

                                  *               *    *
       7582 ATCAAATTTATACAA-AA-ATTGCCAAAACTAATATTGGGGGTT
          1 ATCAAATTTATACAACAAGATTACCAAAACTAATATTGAGGGTG

                           
       7624 ATCAAATTTCATACA
          1 ATCAAATTT-ATACA

       7639 CAATGATCAC


Statistics
Matches: 49,  Mismatches: 4, Indels: 7
        0.82            0.07        0.12

Matches are distributed among these distances:
  40   14  0.29
  41    9  0.18
  42   21  0.43
  43    5  0.10

ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31


Consensus pattern (44 bp):   
ATCAAATTTATACAACAAGATTACCAAAACTAATATTGAGGGTG

Done.