Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007278.1 Corchorus capsularis cultivar CVL-1 contig07299, 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: 19647
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:1831 original size:27 final size:27

Alignment explanation


    Indices: 1770--1852  Score: 121
    Period size: 27  Copynumber: 3.0  Consensus size: 27

       1760 AAAAGTGGAC

                       *                 
       1770 TAAAAATGACCGAAATGCCCCCTTGAATG
          1 TAAAAATGACCAAAATG-CCCC-TGAATG

            *          *               
       1799 CAAAAATGACCTAAATGCCCCTGAATG
          1 TAAAAATGACCAAAATGCCCCTGAATG

                                       
       1826 TAAAAATGACCAAAATGCCCCTGAATG
          1 TAAAAATGACCAAAATGCCCCTGAATG

       1853 ACCTTGATGC


Statistics
Matches: 50,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  27   31  0.62
  28    4  0.08
  29   15  0.30

ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19


Consensus pattern (27 bp):   
TAAAAATGACCAAAATGCCCCTGAATG

Found at i:2828 original size:33 final size:30

Alignment explanation


    Indices: 2756--2855  Score: 119
    Period size: 33  Copynumber: 3.2  Consensus size: 30

       2746 GCCACGGAAC

                                    *    *  
       2756 ACCGGCCACATGACCGGCCATCGCATGGGGCA
          1 ACCGGCCACA--ACCGGCCATCGCTTGGGCCA

                                             
       2788 ACCGGCCACAACCGGCCATCGCTTGGCGCACCA
          1 ACCGGCCACAACCGGCCATCGCTTGG-G--CCA

                                 *        
       2821 ACCGGCCACAACCGGCCATCGATTGGGCCA
          1 ACCGGCCACAACCGGCCATCGCTTGGGCCA

            *    
       2851 TCCGG
          1 ACCGG

       2856 GCAAGACCGG


Statistics
Matches: 61,  Mismatches: 4, Indels: 8
        0.84            0.05        0.11

Matches are distributed among these distances:
  30   22  0.36
  31    1  0.02
  32   11  0.18
  33   27  0.44

ACGTcount: A:0.21, C:0.41, G:0.28, T:0.10


Consensus pattern (30 bp):   
ACCGGCCACAACCGGCCATCGCTTGGGCCA

Found at i:4068 original size:21 final size:21

Alignment explanation


    Indices: 4032--4091  Score: 77
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       4022 AGTCTCTGAG

                    **           
       4032 GAAGAAGAAAAAGAAGAAAGT
          1 GAAGAAGAGGAAGAAGAAAGT

                             *    
       4053 G-AGAACGAGGAAGAAGGAAGT
          1 GAAGAA-GAGGAAGAAGAAAGT

                              
       4074 GAAGAAGAGGAAGAAGAA
          1 GAAGAAGAGGAAGAAGAA

       4092 GAAGGACCTG


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  20    4  0.12
  21   25  0.76
  22    4  0.12

ACGTcount: A:0.58, C:0.02, G:0.37, T:0.03


Consensus pattern (21 bp):   
GAAGAAGAGGAAGAAGAAAGT

Found at i:9028 original size:15 final size:16

Alignment explanation


    Indices: 8996--9029  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       8986 AAAGAAGAAT

                 *          
       8996 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       9012 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       9027 TAA
          1 TAA

       9030 GAAAGCAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC

Found at i:13729 original size:13 final size:13

Alignment explanation


    Indices: 13711--13736  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      13701 TATAAAAATT

                         
      13711 CAAAAATTAAAAA
          1 CAAAAATTAAAAA

                         
      13724 CAAAAATTAAAAA
          1 CAAAAATTAAAAA

      13737 TTGGGTTGCC


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:0.77, C:0.08, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATTAAAAA
Done.