Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003555.1 Corchorus capsularis cultivar CVL-1 contig03563, 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: 6615
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32


Found at i:707 original size:14 final size:14

Alignment explanation


    Indices: 696--743  Score: 53
    Period size: 14  Copynumber: 3.5  Consensus size: 14

        686 ATAAATTCTT

                          
        696 TTAAGAAAATTCAG
          1 TTAAGAAAATTCAG

                      ** *
        710 TTAAG-AAATGAAA
          1 TTAAGAAAATTCAG

              *           
        723 TTTAGAAAATTCAG
          1 TTAAGAAAATTCAG

                   
        737 TTAAGAA
          1 TTAAGAA

        744 TTGAAATTTT


Statistics
Matches: 25,  Mismatches: 8, Indels: 2
        0.71            0.23        0.06

Matches are distributed among these distances:
  13    9  0.36
  14   16  0.64

ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29


Consensus pattern (14 bp):   
TTAAGAAAATTCAG

Found at i:729 original size:27 final size:27

Alignment explanation


    Indices: 699--752  Score: 99
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        689 AATTCTTTTA

                                       
        699 AGAAAATTCAGTTAAGAAATGAAATTT
          1 AGAAAATTCAGTTAAGAAATGAAATTT

                              *        
        726 AGAAAATTCAGTTAAGAATTGAAATTT
          1 AGAAAATTCAGTTAAGAAATGAAATTT

        753 TGTTGTGGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31


Consensus pattern (27 bp):   
AGAAAATTCAGTTAAGAAATGAAATTT

Found at i:1071 original size:11 final size:11

Alignment explanation


    Indices: 1057--1094  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       1047 ATTCATAACA

                       
       1057 AATTTATAATT
          1 AATTTATAATT

                       
       1068 AATTTATAATT
          1 AATTTATAATT

                        
       1079 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       1090 TATTT
          1 AATTT

       1095 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:5858 original size:2 final size:2

Alignment explanation


    Indices: 5851--5902  Score: 77
    Period size: 2  Copynumber: 25.5  Consensus size: 2

       5841 ACTTGATACA

                                                   *                 *    
       5851 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT CT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                          
       5893 ACT AT AT AT A
          1 A-T AT AT AT A

       5903 AAAGTACGAA


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   2   43  0.96
   3    2  0.04

ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:5966 original size:31 final size:31

Alignment explanation


    Indices: 5931--5996  Score: 89
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       5921 AACTTTATGT

                 *                      *   
       5931 TTTCCGATTGTACCCTTATT-TTTAAAATATA
          1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA

                                      *    
       5962 TTTCCAATTGTACCCTTTTCTTTAAACCATA
          1 TTTCCAATTGTACCCTTTTCTTTAAAACATA

                
       5993 TTTC
          1 TTTC

       5997 TAAATTGCCA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  30    2  0.06
  31   29  0.94

ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48


Consensus pattern (31 bp):   
TTTCCAATTGTACCCTTTTCTTTAAAACATA

Found at i:6332 original size:19 final size:20

Alignment explanation


    Indices: 6305--6342  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       6295 TACTATTATT

                                 
       6305 TTTTGAA-TTCAATATTTTAC
          1 TTTTGAATTTCAAT-TTTTAC

                               
       6325 TTTT-AATTTCAATTTTTA
          1 TTTTGAATTTCAATTTTTA

       6343 AATGTCAATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    7  0.41
  20   10  0.59

ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61


Consensus pattern (20 bp):   
TTTTGAATTTCAATTTTTAC

Found at i:6494 original size:24 final size:22

Alignment explanation


    Indices: 6445--6521  Score: 66
    Period size: 22  Copynumber: 3.4  Consensus size: 22

       6435 CACTTTGTTC

                                 **
       6445 AAAATTTCATAGCGT-GGTTACC
          1 AAAATTTCATAG-GTAGGTTATT

                                    
       6467 AAAATTTCATAGGATCAGGTTATT
          1 AAAATTTCATAGG-T-AGGTTATT

                 *  *     *       
       6491 AAAATCTCTTAGGTTGGTTATT
          1 AAAATTTCATAGGTAGGTTATT

            *        
       6513 GAAATTTCA
          1 AAAATTTCA

       6522 AAGGGTGGTT


Statistics
Matches: 44,  Mismatches: 8, Indels: 6
        0.76            0.14        0.10

Matches are distributed among these distances:
  21    1  0.02
  22   26  0.59
  23    1  0.02
  24   16  0.36

ACGTcount: A:0.34, C:0.12, G:0.17, T:0.38


Consensus pattern (22 bp):   
AAAATTTCATAGGTAGGTTATT
Done.