Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014232.1 Corchorus capsularis cultivar CVL-1 contig14253, 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: 13114
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:138 original size:2 final size:2

Alignment explanation


    Indices: 131--167  Score: 65
    Period size: 2  Copynumber: 18.0  Consensus size: 2

        121 AGTGTACCAA

                                                                  
        131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT

        168 TATTTTTAAC


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   32  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:889 original size:22 final size:21

Alignment explanation


    Indices: 864--923  Score: 68
    Period size: 22  Copynumber: 2.8  Consensus size: 21

        854 TCGTGAGCTG

                                  
        864 TTCGAGCTCGACTCGAGAAAAA
          1 TTCGAGCTCGACTCGAG-AAAA

                  *   *          
        886 TTCGAGTTCGGCTCG-GAAAA
          1 TTCGAGCTCGACTCGAGAAAA

             *                
        906 TCCGAGCTCGAGCTCGAG
          1 TTCGAGCTCGA-CTCGAG

        924 CTACTCAAGT


Statistics
Matches: 31,  Mismatches: 5, Indels: 4
        0.77            0.12        0.10

Matches are distributed among these distances:
  20   12  0.39
  21    5  0.16
  22   14  0.45

ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20


Consensus pattern (21 bp):   
TTCGAGCTCGACTCGAGAAAA

Found at i:911 original size:20 final size:21

Alignment explanation


    Indices: 866--921  Score: 62
    Period size: 20  Copynumber: 2.7  Consensus size: 21

        856 GTGAGCTGTT

                                  *
        866 CGAGCTCGA-CTCGAGAAAAATT
          1 CGAGCTCGAGCTCG-G-AAAATC

                *                
        888 CGAGTTCG-GCTCGGAAAATC
          1 CGAGCTCGAGCTCGGAAAATC

                          
        908 CGAGCTCGAGCTCG
          1 CGAGCTCGAGCTCG

        922 AGCTACTCAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  20   12  0.41
  21    6  0.21
  22   11  0.38

ACGTcount: A:0.27, C:0.27, G:0.29, T:0.18


Consensus pattern (21 bp):   
CGAGCTCGAGCTCGGAAAATC

Found at i:3339 original size:24 final size:23

Alignment explanation


    Indices: 3288--3332  Score: 65
    Period size: 24  Copynumber: 2.0  Consensus size: 23

       3278 CTAGGATATG

                *                   
       3288 TTTTCTACCTTAATGACATGTTTT
          1 TTTTATACCTTAATGA-ATGTTTT

                                  
       3312 TTTTATACCTTAATG-ATGTTT
          1 TTTTATACCTTAATGAATGTTT

       3333 AGTTTTTTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  22    6  0.30
  24   14  0.70

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (23 bp):   
TTTTATACCTTAATGAATGTTTT

Found at i:5101 original size:18 final size:18

Alignment explanation


    Indices: 5047--5104  Score: 53
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       5037 AGGTGATCAG

                           *  
       5047 AAATTACTGGTAATTCTA
          1 AAATTACTGGTAATTTTA

               *  *       *      
       5065 ATAGTAAACATGGTGATTTTA
          1 A-AAT-TAC-TGGTAATTTTA

                              
       5086 AAATTACTGGTAATTTTA
          1 AAATTACTGGTAATTTTA

             
       5104 A
          1 A

       5105 TCGTCAAACC


Statistics
Matches: 30,  Mismatches: 7, Indels: 6
        0.70            0.16        0.14

Matches are distributed among these distances:
  18   12  0.40
  19    4  0.13
  20    4  0.13
  21   10  0.33

ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40


Consensus pattern (18 bp):   
AAATTACTGGTAATTTTA

Found at i:6098 original size:78 final size:78

Alignment explanation


    Indices: 5945--6100  Score: 197
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       5935 CAGGAGGCAA

                                      *  *                              *    
       5945 GTCGACAATAGAAAGCCAAGGGTGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGT
          1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT

             *           
       6010 TTGCAGAAATCCT
         66 TCGCAGAAATCCT

                              *              **     *           *            
       6023 GTCGACAATAGAAAGCCAGGGGTGGAAATAGCTTGTGGTGGCCCTATTGAAAGACCTG-AACATG
          1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAAC-TG

                * *       
       6087 TTCGTATAAATCCT
         65 TTCGCAGAAATCCT

       6101 ATCTATGATA


Statistics
Matches: 66,  Mismatches: 11, Indels: 2
        0.84            0.14        0.03

Matches are distributed among these distances:
  77    2  0.03
  78   64  0.97

ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24


Consensus pattern (78 bp):   
GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
TCGCAGAAATCCT
Done.