Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016961.1 Corchorus olitorius cultivar O-4 contig16994, 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: 3987
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34


Found at i:402 original size:42 final size:42

Alignment explanation


    Indices: 343--425  Score: 148
    Period size: 42  Copynumber: 2.0  Consensus size: 42

        333 TAGCTAAGTC

                               *                      
        343 TTGAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCA
          1 TTGAAAATTCTCTGTAAATGAAGAAATACTCAACTCAAATCA

                       *                             
        385 TTGAAAATTCTTTGTAAATGAAGAAATACTCAACTCAAATC
          1 TTGAAAATTCTCTGTAAATGAAGAAATACTCAACTCAAATC

        426 CTGATCCTTA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31


Consensus pattern (42 bp):   
TTGAAAATTCTCTGTAAATGAAGAAATACTCAACTCAAATCA

Found at i:581 original size:56 final size:57

Alignment explanation


    Indices: 491--605  Score: 196
    Period size: 56  Copynumber: 2.0  Consensus size: 57

        481 TTTATTTTGT

                                     *                               
        491 AGAATAATTAAGTAGAGATAGGGGATATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGAGATAGGATTTATTATAACATTTATTGTGTGAA

                                    *    *                           
        548 AGAATAATTAAGT-GAGATAGGGGGGATATGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGAGATAGGATTTATTATAACATTTATTGTGTGAA

              
        604 AG
          1 AG

        606 GAAATGGATA


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

Matches are distributed among these distances:
  56   42  0.76
  57   13  0.24

ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35


Consensus pattern (57 bp):   
AGAATAATTAAGTAGAGATAGGGGAGATAGGATTTATTATAACATTTATTGTGTGAA

Found at i:1572 original size:42 final size:42

Alignment explanation


    Indices: 1513--1595  Score: 148
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1503 TAGTTAAGTC

                               *                      
       1513 TTGAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCA
          1 TTGAAAATTCTCTGTAAATGAAGAAATACTCAACTCAAATCA

                       *                             
       1555 TTGAAAATTCTTTGTAAATGAAGAAATACTCAACTCAAATC
          1 TTGAAAATTCTCTGTAAATGAAGAAATACTCAACTCAAATC

       1596 CTGATCCTTA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31


Consensus pattern (42 bp):   
TTGAAAATTCTCTGTAAATGAAGAAATACTCAACTCAAATCA

Found at i:1739 original size:56 final size:57

Alignment explanation


    Indices: 1665--1775  Score: 197
    Period size: 56  Copynumber: 2.0  Consensus size: 57

       1655 TTTTGTAGAA

                                 *                                   
       1665 TAATTAAGTAGAGATAGGGGATATAGGATTTATTATAACATTTATTGTGTGAAAGAC
          1 TAATTAAGTAGAGATAGGGGAGATAGGATTTATTATAACATTTATTGTGTGAAAGAC

                                *                                  
       1722 TAATTAAGT-GAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
          1 TAATTAAGTAGAGATAGGGGAGATAGGATTTATTATAACATTTATTGTGTGAAAG

       1776 GAAACGGATA


Statistics
Matches: 52,  Mismatches: 2, Indels: 1
        0.95            0.04        0.02

Matches are distributed among these distances:
  56   43  0.83
  57    9  0.17

ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35


Consensus pattern (57 bp):   
TAATTAAGTAGAGATAGGGGAGATAGGATTTATTATAACATTTATTGTGTGAAAGAC

Found at i:2771 original size:18 final size:18

Alignment explanation


    Indices: 2748--2803  Score: 64
    Period size: 18  Copynumber: 3.2  Consensus size: 18

       2738 AGTGTTTCAA

                              
       2748 ATAATATGTAGTATATAT
          1 ATAATATGTAGTATATAT

                   *           
       2766 ATAATATATAGTATATAGT
          1 ATAATATGTAGTATATA-T

                             *
       2785 AT-ATA-GTA-TATATAA
          1 ATAATATGTAGTATATAT

                
       2800 ATAA
          1 ATAA

       2804 CCCTATTAAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  15    2  0.06
  16    7  0.21
  17    2  0.06
  18   19  0.58
  19    3  0.09

ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41


Consensus pattern (18 bp):   
ATAATATGTAGTATATAT

Found at i:2774 original size:7 final size:7

Alignment explanation


    Indices: 2756--2796  Score: 61
    Period size: 7  Copynumber: 6.3  Consensus size: 7

       2746 AAATAATATG

                   
       2756 TAGTATA
          1 TAGTATA

                   
       2763 TA-TATA
          1 TAGTATA

                   
       2769 -A-TATA
          1 TAGTATA

                   
       2774 TAGTATA
          1 TAGTATA

                   
       2781 TAGTATA
          1 TAGTATA

                   
       2788 TAGTATA
          1 TAGTATA

              
       2795 TA
          1 TA

       2797 TAAATAACCC


Statistics
Matches: 32,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   5    5  0.16
   6    5  0.16
   7   22  0.69

ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44


Consensus pattern (7 bp):   
TAGTATA

Done.