Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009879.1 Corchorus capsularis cultivar CVL-1 contig09900, 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: 17232
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1388 original size:21 final size:22

Alignment explanation


    Indices: 1339--1388  Score: 59
    Period size: 21  Copynumber: 2.3  Consensus size: 22

       1329 CTATGAGATC

                       *           
       1339 TATTATTTACCTTAGGTTAATTT
          1 TATT-TTTACCGTAGGTTAATTT

              *                   
       1362 T-CTTTTACCGT-GGTTAATTT
          1 TATTTTTACCGTAGGTTAATTT

                   
       1382 TATTTTT
          1 TATTTTT

       1389 TACTGTTTTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  20   10  0.43
  21   11  0.48
  22    1  0.04
  23    1  0.04

ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60


Consensus pattern (22 bp):   
TATTTTTACCGTAGGTTAATTT

Found at i:5534 original size:15 final size:15

Alignment explanation


    Indices: 5514--5547  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       5504 TAATTGTAGA

                           
       5514 ATAATTTCTAAATTG
          1 ATAATTTCTAAATTG

                           
       5529 ATAATTTCTAAATTG
          1 ATAATTTCTAAATTG

                
       5544 ATAA
          1 ATAA

       5548 AATGTTATTG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44


Consensus pattern (15 bp):   
ATAATTTCTAAATTG

Found at i:7227 original size:1 final size:1

Alignment explanation


    Indices: 7221--7249  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

       7211 TTCCTCTTCC

                                         
       7221 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       7250 GTAAAAATAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:9906 original size:19 final size:20

Alignment explanation


    Indices: 9882--9920  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       9872 TAAAGGTTTT

                                 
       9882 TTAATTTGTTT-TT-TAAAAA
          1 TTAATTT-TTTATTCTAAAAA

                                
       9901 TTAATTTTTTATTCTAAAAA
          1 TTAATTTTTTATTCTAAAAA

       9921 ACGTGCATGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    3  0.17
  19    9  0.50
  20    6  0.33

ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56


Consensus pattern (20 bp):   
TTAATTTTTTATTCTAAAAA

Found at i:10792 original size:86 final size:86

Alignment explanation


    Indices: 10679--10847  Score: 320
    Period size: 86  Copynumber: 2.0  Consensus size: 86

      10669 ATTCTCTTCA

                            *                                   *            
      10679 TTTTCAATTTACTCCTGGTTCAACTATGAAATCAGTTGAATGTTATTTTAAATTAGTGATAATGA
          1 TTTTCAATTTACTCCTAGTTCAACTATGAAATCAGTTGAATGTTATTTTAAACTAGTGATAATGA

                                 
      10744 AATTAGCATTAATTGAAGTCG
         66 AATTAGCATTAATTGAAGTCG

                                                                             
      10765 TTTTCAATTTACTCCTAGTTCAACTATGAAATCAGTTGAATGTTATTTTAAACTAGTGATAATGA
          1 TTTTCAATTTACTCCTAGTTCAACTATGAAATCAGTTGAATGTTATTTTAAACTAGTGATAATGA

                              
      10830 AATTAGCATTAATTGAAG
         66 AATTAGCATTAATTGAAG

      10848 GAATCAGCTT


Statistics
Matches: 81,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  86   81  1.00

ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40


Consensus pattern (86 bp):   
TTTTCAATTTACTCCTAGTTCAACTATGAAATCAGTTGAATGTTATTTTAAACTAGTGATAATGA
AATTAGCATTAATTGAAGTCG

Found at i:11352 original size:19 final size:19

Alignment explanation


    Indices: 11328--11364  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      11318 ATAATGTTTA

                               
      11328 AAATTAAAATTACAAGCTG
          1 AAATTAAAATTACAAGCTG

                              
      11347 AAATTAAAATTACAAGCT
          1 AAATTAAAATTACAAGCT

      11365 AAACCCTAGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27


Consensus pattern (19 bp):   
AAATTAAAATTACAAGCTG

Found at i:11712 original size:18 final size:18

Alignment explanation


    Indices: 11689--11726  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      11679 AAAATCCAAT

                              
      11689 ATTTCCCAATGAAGATCC
          1 ATTTCCCAATGAAGATCC

                              
      11707 ATTTCCCAATGAAGATCC
          1 ATTTCCCAATGAAGATCC

              
      11725 AT
          1 AT

      11727 CACAGTTAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29


Consensus pattern (18 bp):   
ATTTCCCAATGAAGATCC
Done.