Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014832.1 Corchorus capsularis cultivar CVL-1 contig14853, 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: 6187
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32


Found at i:4809 original size:76 final size:78

Alignment explanation


    Indices: 4616--4810  Score: 211
    Period size: 80  Copynumber: 2.5  Consensus size: 78

       4606 TTTAAAAGTC

                      *                     *            *                   
       4616 AAAGTAAAACAAAGTAATCAGAAAGATGGTAACCAAGAGAAGTAATCAGTAAAGGAAGTAATCAG
          1 AAAGTAAAA-GAAGTAATCAGAAA-ATGGTAATCAAGAGAAGTAACCAGTAAAGGAAGTAATCAG

                            
       4681 TTTAAGTGAAAGATCA
         64 -TTAAGTGAAAGATCA

                    *    *                                *                  
       4697 AAAGTAAAGGAAGCAATCAGAAAAATGGTAATCAAGAGAAGTAACCCGTAGAA-GAAGTAATCAG
          1 AAAGTAAAAGAAGTAATCAG-AAAATGGTAATCAAGAGAAGTAACCAGTA-AAGGAAGTAATCAG

                     *     *
       4761 -TAAGATG-GAG-T-G
         64 TTAAG-TGAAAGATCA

                              *                   
       4773 AAAGTAAAAGAAGTAATCGGTAAAATGGTAATCAAGAG
          1 AAAGTAAAAGAAGTAATCAG-AAAATGGTAATCAAGAG

       4811 TGAAAGTAAA


Statistics
Matches: 99,  Mismatches: 12, Indels: 11
        0.81            0.10        0.09

Matches are distributed among these distances:
  76   34  0.34
  77    1  0.01
  78    6  0.06
  79    2  0.02
  80   43  0.43
  81   13  0.13

ACGTcount: A:0.51, C:0.08, G:0.24, T:0.17


Consensus pattern (78 bp):   
AAAGTAAAAGAAGTAATCAGAAAATGGTAATCAAGAGAAGTAACCAGTAAAGGAAGTAATCAGTT
AAGTGAAAGATCA

Found at i:4886 original size:40 final size:40

Alignment explanation


    Indices: 4768--4878  Score: 168
    Period size: 43  Copynumber: 2.7  Consensus size: 40

       4758 CAGTAAGATG

                                   *                
       4768 GAGTGAAAGTAAAAGAAGTAATCGGTAAAATGGTAATCAA
          1 GAGTGAAAGTAAAAGAAGTAATCAGTAAAATGGTAATCAA

                                                    *  
       4808 GAGTGAAAGTAAAAAAGGAAGTAATCAGTAAAATGGTAATTAA
          1 GAGTGAAAGT--AAAA-GAAGTAATCAGTAAAATGGTAATCAA

                *                       
       4851 GAGTAAAAGTAAAAGAAGTAATCAGTAA
          1 GAGTGAAAGTAAAAGAAGTAATCAGTAA

       4879 GTCGGTAAAG


Statistics
Matches: 65,  Mismatches: 3, Indels: 6
        0.88            0.04        0.08

Matches are distributed among these distances:
  40   24  0.37
  41    4  0.06
  42    4  0.06
  43   33  0.51

ACGTcount: A:0.53, C:0.04, G:0.23, T:0.20


Consensus pattern (40 bp):   
GAGTGAAAGTAAAAGAAGTAATCAGTAAAATGGTAATCAA

Found at i:4991 original size:32 final size:33

Alignment explanation


    Indices: 4921--4984  Score: 96
    Period size: 32  Copynumber: 2.0  Consensus size: 33

       4911 GAGTAATCAG

                                             
       4921 TAAAGAGTAAAATGGTAAAATGGTAATTAAATC
          1 TAAAGAGTAAAATGGTAAAATGGTAATTAAATC

                                     *       
       4954 TAAAGAGTAAAAT-G-ACAAATGGTGATTAAAT
          1 TAAAGAGTAAAATGGTA-AAATGGTAATTAAAT

       4985 TCAAAGAATG


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  31    1  0.03
  32   15  0.52
  33   13  0.45

ACGTcount: A:0.52, C:0.03, G:0.19, T:0.27


Consensus pattern (33 bp):   
TAAAGAGTAAAATGGTAAAATGGTAATTAAATC

Found at i:4999 original size:26 final size:27

Alignment explanation


    Indices: 4964--5014  Score: 68
    Period size: 26  Copynumber: 1.9  Consensus size: 27

       4954 TAAAGAGTAA

                      *  *             
       4964 AATGACAAATGGTGATTAAATTCAAAG
          1 AATGACAAATAGTAATTAAATTCAAAG

                               *     
       4991 AATGA-AAATAGTAATTAAGTTCAA
          1 AATGACAAATAGTAATTAAATTCAA

       5015 GAGGGTAAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  26   16  0.76
  27    5  0.24

ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27


Consensus pattern (27 bp):   
AATGACAAATAGTAATTAAATTCAAAG
Done.