Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012629.1 Corchorus olitorius cultivar O-4 contig12662, 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: 18974
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32


Found at i:5352 original size:19 final size:19

Alignment explanation


    Indices: 5302--5352  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       5292 TGTAGGGTTT

                               
       5302 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       5320 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       5339 TTAATAATTAATTA
          1 TTAATAATTAATTA

       5353 ATTTCAGCCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:5724 original size:13 final size:13

Alignment explanation


    Indices: 5706--5731  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       5696 AAGGTAACAA

                         
       5706 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
       5719 CAAAAATCATCAC
          1 CAAAAATCATCAC

       5732 TCATGCCAAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATCATCAC

Found at i:7294 original size:22 final size:22

Alignment explanation


    Indices: 7245--7295  Score: 68
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       7235 AAATATTGCC

                         *    *   
       7245 ATAATTATTTTTGGCAGACATA
          1 ATAATTATTTTTGCCAGAAATA

                                   
       7267 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGCC-AGAAATA

                   
       7290 A-AATTA
          1 ATAATTA

       7296 GGGAATAATT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  22   19  0.73
  23    7  0.27

ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGCCAGAAATA
Done.