Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015625.1 Corchorus capsularis cultivar CVL-1 contig15646, 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: 33629
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:1724 original size:5 final size:5

Alignment explanation


    Indices: 1714--1749  Score: 72
    Period size: 5  Copynumber: 7.2  Consensus size: 5

       1704 ATCTGAGAAC

                                                       
       1714 TTGAT TTGAT TTGAT TTGAT TTGAT TTGAT TTGAT T
          1 TTGAT TTGAT TTGAT TTGAT TTGAT TTGAT TTGAT T

       1750 CAAGGGTCGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   31  1.00

ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61


Consensus pattern (5 bp):   
TTGAT

Found at i:2746 original size:22 final size:22

Alignment explanation


    Indices: 2719--2763  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2709 CCCCCCAATT

                                  
       2719 TTTTTTTTCCAAGTTAGCCCTA
          1 TTTTTTTTCCAAGTTAGCCCTA

                                  
       2741 TTTTTTTTCCAAGTTAGCCCTA
          1 TTTTTTTTCCAAGTTAGCCCTA

             
       2763 T
          1 T

       2764 GATAATATTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51


Consensus pattern (22 bp):   
TTTTTTTTCCAAGTTAGCCCTA

Found at i:13714 original size:41 final size:37

Alignment explanation


    Indices: 13630--13715  Score: 91
    Period size: 41  Copynumber: 2.2  Consensus size: 37

      13620 GTACCATTAT

                          *                    **
      13630 TATTTACTTTTTTTTGTATCAAAAATTATTATTTACT
          1 TATTTACTTTTTTTAGTATCAAAAATTATTATTTAAA

             *                      *                
      13667 TTTTTACTTTTTTGTAAGTATACATAAATTAATTATTTAAA
          1 TATTTACTTTTTT-T-AGTAT-CAAAAATT-ATTATTTAAA

                    
      13708 TATTTACT
          1 TATTTACT

      13716 CTCAATAAAT


Statistics
Matches: 39,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  37   12  0.31
  38    1  0.03
  39    4  0.10
  40    7  0.18
  41   15  0.38

ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57


Consensus pattern (37 bp):   
TATTTACTTTTTTTAGTATCAAAAATTATTATTTAAA

Found at i:18974 original size:3 final size:3

Alignment explanation


    Indices: 18962--19001  Score: 71
    Period size: 3  Copynumber: 13.3  Consensus size: 3

      18952 AAATCAGGAG

                  *                                              
      18962 GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G

      19002 GAGAGAGAGA


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:32236 original size:14 final size:14

Alignment explanation


    Indices: 32217--32251  Score: 61
    Period size: 14  Copynumber: 2.5  Consensus size: 14

      32207 CCCTAGCCGC

                          
      32217 TCCTCTCCCCTTCT
          1 TCCTCTCCCCTTCT

                          
      32231 TCCTCTCCCCTTCT
          1 TCCTCTCCCCTTCT

            *      
      32245 CCCTCTC
          1 TCCTCTC

      32252 TAGTTCTAGT


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

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40


Consensus pattern (14 bp):   
TCCTCTCCCCTTCT

Found at i:32416 original size:26 final size:27

Alignment explanation


    Indices: 32379--32433  Score: 78
    Period size: 26  Copynumber: 2.1  Consensus size: 27

      32369 TTTATTTGAG

                        *              
      32379 TTTTTTTTAGTCGGTTT-GAGTC-AGT
          1 TTTTTTTTAGTCAGTTTCGAGTCTAGT

                                        
      32404 TTTTGTTTTAGTCAGTTTCGAGTCTAGT
          1 TTTT-TTTTAGTCAGTTTCGAGTCTAGT

              
      32432 TT
          1 TT

      32434 CAGTTCTTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  25    4  0.15
  26   12  0.46
  27    5  0.19
  28    5  0.19

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


Consensus pattern (27 bp):   
TTTTTTTTAGTCAGTTTCGAGTCTAGT

Done.