Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010660.1 Corchorus capsularis cultivar CVL-1 contig10681, 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: 9354
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28


Found at i:2882 original size:10 final size:10

Alignment explanation


    Indices: 2867--2904  Score: 58
    Period size: 10  Copynumber: 3.7  Consensus size: 10

       2857 ATAAAATAAT

                     *
       2867 AAAAAAGAAA
          1 AAAAAAGAAG

                       
       2877 AAAAAAGAGAG
          1 AAAAAAGA-AG

                      
       2888 AAAAAAGAAG
          1 AAAAAAGAAG

                   
       2898 AAAAAAG
          1 AAAAAAG

       2905 CACTCGGGAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  10   17  0.65
  11    9  0.35

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (10 bp):   
AAAAAAGAAG

Found at i:3688 original size:10 final size:10

Alignment explanation


    Indices: 3675--3719  Score: 58
    Period size: 10  Copynumber: 4.7  Consensus size: 10

       3665 AGAGAAAAAG

                      
       3675 AAAAAAG-AA
          1 AAAAAAGAAA

                   *  
       3684 AAAAAA-CAA
          1 AAAAAAGAAA

                     *
       3693 AAAAAAGAAG
          1 AAAAAAGAAA

                      
       3703 AAAAAAGAAA
          1 AAAAAAGAAA

                   
       3713 AAAAAAG
          1 AAAAAAG

       3720 TAGCTCTAGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
   9   14  0.45
  10   17  0.55

ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00


Consensus pattern (10 bp):   
AAAAAAGAAA

Found at i:3696 original size:18 final size:19

Alignment explanation


    Indices: 3658--3717  Score: 72
    Period size: 19  Copynumber: 3.3  Consensus size: 19

       3648 TCAAGTGCAT

                       *      *
       3658 AAAAAAG-AGAGAAAA-AG
          1 AAAAAAGAAGAAAAAACAA

                               
       3675 AAAAAAGAA-AAAAAACAA
          1 AAAAAAGAAGAAAAAACAA

                            *  
       3693 AAAAAAGAAGAAAAAAGAA
          1 AAAAAAGAAGAAAAAACAA

                  
       3712 AAAAAA
          1 AAAAAA

       3718 AGTAGCTCTA


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  17   12  0.32
  18   11  0.30
  19   14  0.38

ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00


Consensus pattern (19 bp):   
AAAAAAGAAGAAAAAACAA

Found at i:4850 original size:35 final size:35

Alignment explanation


    Indices: 4785--4851  Score: 98
    Period size: 35  Copynumber: 1.9  Consensus size: 35

       4775 AGTTACTCGA

                        *       *    *         
       4785 TCCAGGGCGATCTTTCTTCAGTTAATTTCAATTGG
          1 TCCAGGGCGATCATTCTTCAATTAACTTCAATTGG

                                   *        
       4820 TCCAGGGCGATCATTCTTCAATTTACTTCAAT
          1 TCCAGGGCGATCATTCTTCAATTAACTTCAAT

       4852 GATCCAGAGT


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  35   28  1.00

ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39


Consensus pattern (35 bp):   
TCCAGGGCGATCATTCTTCAATTAACTTCAATTGG

Found at i:5008 original size:61 final size:61

Alignment explanation


    Indices: 4899--5021  Score: 142
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       4889 AATGCTTCAA

                                                   *           *  *      
       4899 TGACCCAGGGTGGTCTTTTCTTCAGTTAGTCCGAAAGGATCGAGGGTGGTCGTTTTTCAGT
          1 TGACCCAGGGTGGTCTTTTCTTCAGTTAGTCCGAAAGGAACGAGGGTGGTCATTCTTCAGT

                                   *   *       *  *      *                 
       4960 TGACCCAGGGTGGTC-TTTCTTCGGTTTG-CGTCGGAATGAACGATGGTGGTCATTCTTCAGT
          1 TGACCCAGGGTGGTCTTTTCTTCAGTTAGTC--CGAAAGGAACGAGGGTGGTCATTCTTCAGT

             
       5021 T
          1 T

       5022 TAGTTTGGAA


Statistics
Matches: 52,  Mismatches: 8, Indels: 4
        0.81            0.12        0.06

Matches are distributed among these distances:
  59    1  0.02
  60   11  0.21
  61   40  0.77

ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35


Consensus pattern (61 bp):   
TGACCCAGGGTGGTCTTTTCTTCAGTTAGTCCGAAAGGAACGAGGGTGGTCATTCTTCAGT

Found at i:6826 original size:30 final size:33

Alignment explanation


    Indices: 6753--6831  Score: 103
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       6743 TCCGGATGGC

                *                            
       6753 CCAATCGATGGCCGGTTGTGGTCGGTTGGTGCG
          1 CCAAGCGATGGCCGGTTGTGGTCGGTTGGTGCG

                                              
       6786 CCAAGCGATGGCCGGTTGTGG-CTGGTT-GT-C-
          1 CCAAGCGATGGCCGGTTGTGGTC-GGTTGGTGCG

               *            
       6816 CCATGCGATGGCCGGT
          1 CCAAGCGATGGCCGGT

       6832 CATGTGGCCG


Statistics
Matches: 43,  Mismatches: 2, Indels: 5
        0.86            0.04        0.10

Matches are distributed among these distances:
  30   15  0.35
  31    1  0.02
  32    3  0.07
  33   24  0.56

ACGTcount: A:0.10, C:0.24, G:0.41, T:0.25


Consensus pattern (33 bp):   
CCAAGCGATGGCCGGTTGTGGTCGGTTGGTGCG
Done.