Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015706.1 Corchorus capsularis cultivar CVL-1 contig15727, 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: 26857
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:7211 original size:20 final size:20

Alignment explanation


    Indices: 7186--7224  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       7176 AATATTATCA

                    *     *     
       7186 TGGTGATCTGATCATCAACT
          1 TGGTGATCAGATCACCAACT

                               
       7206 TGGTGATCAGATCACCAAC
          1 TGGTGATCAGATCACCAAC

       7225 GTGATTTAAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28


Consensus pattern (20 bp):   
TGGTGATCAGATCACCAACT

Found at i:24205 original size:21 final size:21

Alignment explanation


    Indices: 24179--24220  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      24169 ATAGGCAAAA

                                 
      24179 CAGACATAGCAGAATCAAGTT
          1 CAGACATAGCAGAATCAAGTT

                         *       
      24200 CAGACATAGCAGATTCAAGTT
          1 CAGACATAGCAGAATCAAGTT

      24221 GCATTACAGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21


Consensus pattern (21 bp):   
CAGACATAGCAGAATCAAGTT

Found at i:26645 original size:22 final size:21

Alignment explanation


    Indices: 26601--26644  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      26591 GATGACTGGA

                                 
      26601 TTGCTAAACACCGCCCCCCTT
          1 TTGCTAAACACCGCCCCCCTT

                    *            
      26622 TTGCTAAATACCGCCCCCCTT
          1 TTGCTAAACACCGCCCCCCTT

              
      26643 TT
          1 TT

      26645 TACACTTTTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.18, C:0.43, G:0.09, T:0.30


Consensus pattern (21 bp):   
TTGCTAAACACCGCCCCCCTT

Found at i:26740 original size:22 final size:24

Alignment explanation


    Indices: 26715--26770  Score: 91
    Period size: 22  Copynumber: 2.5  Consensus size: 24

      26705 TTCAAACCCT

                                    
      26715 AAACTTCATTTCTAAC-AA-CTTC
          1 AAACTTCATTTCTAACAAATCTTC

                                    
      26737 AAACTTCATTTCTAACAAATCTTC
          1 AAACTTCATTTCTAACAAATCTTC

                       
      26761 AAA-TTCATTT
          1 AAACTTCATTT

      26771 TCCTTCATTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  22   16  0.50
  23    9  0.28
  24    7  0.22

ACGTcount: A:0.38, C:0.23, G:0.00, T:0.39


Consensus pattern (24 bp):   
AAACTTCATTTCTAACAAATCTTC

Found at i:26831 original size:11 final size:10

Alignment explanation


    Indices: 26800--26830  Score: 62
    Period size: 10  Copynumber: 3.1  Consensus size: 10

      26790 ACTAATTAAT

                      
      26800 ATTAAAAAAA
          1 ATTAAAAAAA

                      
      26810 ATTAAAAAAA
          1 ATTAAAAAAA

                      
      26820 ATTAAAAAAA
          1 ATTAAAAAAA

             
      26830 A
          1 A

      26831 AGAAAGAAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   21  1.00

ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19


Consensus pattern (10 bp):   
ATTAAAAAAA

Found at i:26840 original size:20 final size:20

Alignment explanation


    Indices: 26800--26841  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      26790 ACTAATTAAT

                       **       
      26800 ATTAAAAAAAATTAAAAAAA
          1 ATTAAAAAAAAAGAAAAAAA

                            *   
      26820 ATTAAAAAAAAAGAAAGAAA
          1 ATTAAAAAAAAAGAAAAAAA

              
      26840 AT
          1 AT

      26842 GGCCGAGCCG


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17


Consensus pattern (20 bp):   
ATTAAAAAAAAAGAAAAAAA
Done.