Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016454.1 Corchorus capsularis cultivar CVL-1 contig16475, 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: 24124
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:3259 original size:2 final size:2

Alignment explanation


    Indices: 3252--3283  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       3242 ATCATGTTAC

                                                           
       3252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3284 AAACTCATGT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:5784 original size:20 final size:19

Alignment explanation


    Indices: 5731--5781  Score: 57
    Period size: 21  Copynumber: 2.6  Consensus size: 19

       5721 ATCAATTTCC

                               
       5731 AAATTAATTTTAATCCAAA
          1 AAATTAATTTTAATCCAAA

                 *          *    
       5750 AAATCAAACTTTTAATTCAAA
          1 AAAT-TAA-TTTTAATCCAAA

            *          
       5771 GAATTAATTTT
          1 AAATTAATTTT

       5782 TAAATGTCTA


Statistics
Matches: 26,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  19    8  0.31
  20    4  0.15
  21   14  0.54

ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39


Consensus pattern (19 bp):   
AAATTAATTTTAATCCAAA

Found at i:8126 original size:22 final size:23

Alignment explanation


    Indices: 8094--8142  Score: 73
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       8084 TTTTTCTTCG

                  *            *   
       8094 AAAAAATAGAAAA-AAAAGGAGA
          1 AAAAAAAAGAAAAGAAAAGAAGA

                                   
       8116 AAAAAAAAGAAAAGAAAAGAAGA
          1 AAAAAAAAGAAAAGAAAAGAAGA

                
       8139 AAAA
          1 AAAA

       8143 TCAAATTTCA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  22   12  0.50
  23   12  0.50

ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02


Consensus pattern (23 bp):   
AAAAAAAAGAAAAGAAAAGAAGA

Found at i:10867 original size:33 final size:32

Alignment explanation


    Indices: 10824--10924  Score: 94
    Period size: 33  Copynumber: 3.1  Consensus size: 32

      10814 CAAAGAGTGT

                 *     *         *           
      10824 TTTAAATGTTGATTGTGATGATACTAAACCTAA
          1 TTTAAGTGTTGTTTGTGATGAAACTAAACCT-A

                           **    *      *  *
      10857 TTTAAGTGTTGTTTGCAATGACACTAAATCTG
          1 TTTAAGTGTTGTTTGTGATGAAACTAAACCTA

               *                         *   
      10889 TTTTAGATGTTGTTTGTGATGAAACTAAATCTA
          1 TTTAAG-TGTTGTTTGTGATGAAACTAAACCTA

               
      10922 TTT
          1 TTT

      10925 TGGATGCTAA


Statistics
Matches: 55,  Mismatches: 12, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
  32    5  0.09
  33   50  0.91

ACGTcount: A:0.31, C:0.09, G:0.17, T:0.44


Consensus pattern (32 bp):   
TTTAAGTGTTGTTTGTGATGAAACTAAACCTA

Found at i:10939 original size:33 final size:33

Alignment explanation


    Indices: 10874--10945  Score: 90
    Period size: 33  Copynumber: 2.2  Consensus size: 33

      10864 GTTGTTTGCA

                *         *         * **     
      10874 ATGACACTAAATCTGTTTTAGATGTTGTTTGTG
          1 ATGAAACTAAATCTATTTTAGATGCTAATTGTG

                               *             
      10907 ATGAAACTAAATCTATTTTGGATGCTAATTGTG
          1 ATGAAACTAAATCTATTTTAGATGCTAATTGTG

                  
      10940 ATGAAA
          1 ATGAAA

      10946 ACAAATTTGT


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40


Consensus pattern (33 bp):   
ATGAAACTAAATCTATTTTAGATGCTAATTGTG

Found at i:14215 original size:30 final size:30

Alignment explanation


    Indices: 14165--14221  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      14155 CGTTGGCCTT

                           *              
      14165 AATGATGCGCCCAAGGCTTATCATGGAAGG
          1 AATGATGCGCCCAAGACTTATCATGGAAGG

                                  *     
      14195 AATGATGCG-CCAAGAACTTATTATGGA
          1 AATGATGCGCCCAAG-ACTTATCATGGA

      14222 CTCGAAGAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29    5  0.21
  30   19  0.79

ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23


Consensus pattern (30 bp):   
AATGATGCGCCCAAGACTTATCATGGAAGG

Found at i:23330 original size:8 final size:8

Alignment explanation


    Indices: 23317--23350  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

      23307 CACCTTCTTG

                    
      23317 AAAAATTC
          1 AAAAATTC

                    
      23325 AAAAATTC
          1 AAAAATTC

                 *   
      23333 AGAAACTTC
          1 A-AAAATTC

                    
      23342 AAAAATTC
          1 AAAAATTC

             
      23350 A
          1 A

      23351 TAGCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC
Done.