Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013766.1 Corchorus olitorius cultivar O-4 contig13799, 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: 7760
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:894 original size:2 final size:2

Alignment explanation


    Indices: 887--950  Score: 83
    Period size: 2  Copynumber: 32.0  Consensus size: 2

        877 TATGTAAAGA

                                                 *  *  *                  
        887 AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                   *    *                   
        929 AT AT AC AT GT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT

        951 TAATAAAATT


Statistics
Matches: 56,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   56  1.00

ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44


Consensus pattern (2 bp):   
AT

Found at i:3503 original size:19 final size:19

Alignment explanation


    Indices: 3453--3503  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       3443 TGTGGGATTT

                               
       3453 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       3471 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       3490 TTAATAATTAATTA
          1 TTAATAATTAATTA

       3504 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:3875 original size:13 final size:13

Alignment explanation


    Indices: 3857--3882  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3847 AAGGTAGCAA

                         
       3857 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
       3870 CAAAAATCATCAC
          1 CAAAAATCATCAC

       3883 TCATGCCAAG


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:5453 original size:22 final size:22

Alignment explanation


    Indices: 5404--5454  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       5394 GAATATTACC

                         *   **   
       5404 ATAATTATTTTTGGCAGCCATA
          1 ATAATTATTTTTGCCAGAAATA

                                   
       5426 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGCC-AGAAATA

                   
       5449 A-AATTA
          1 ATAATTA

       5455 GGGAATAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22   19  0.76
  23    6  0.24

ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGCCAGAAATA
Done.