Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020508.1 Corchorus olitorius cultivar O-4 contig20541, 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: 6816
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:327 original size:23 final size:23

Alignment explanation


    Indices: 284--328  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        274 TTTTTTTTAT

                      *    *       
        284 AAAAATAAAATTAAGGTGATAGA
          1 AAAAATAAAACTAAGATGATAGA

                                   
        307 AAAAATAAAACT-AGATAGATAG
          1 AAAAATAAAACTAAGAT-GATAG

        329 TTTATTAATG


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22    3  0.16
  23   16  0.84

ACGTcount: A:0.62, C:0.02, G:0.16, T:0.20


Consensus pattern (23 bp):   
AAAAATAAAACTAAGATGATAGA

Found at i:691 original size:16 final size:15

Alignment explanation


    Indices: 653--694  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        643 ACAGAGATTG

                   *       
        653 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
        668 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        683 ACTAGAAAACAA
          1 AC-AGAAAACAA

        695 AGCAAAGTTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3596 original size:22 final size:22

Alignment explanation


    Indices: 3552--3596  Score: 54
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3542 TAACAAATCC

                   *     * *      
       3552 AAGGACTTAATTGCACACAATT
          1 AAGGACTCAATTGAAAACAATT

                              *   
       3574 AAGGACTCAATTGAAAACCATT
          1 AAGGACTCAATTGAAAACAATT

             
       3596 A
          1 A

       3597 GAAACCTTAC


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24


Consensus pattern (22 bp):   
AAGGACTCAATTGAAAACAATT

Found at i:6360 original size:30 final size:32

Alignment explanation


    Indices: 6322--6394  Score: 114
    Period size: 30  Copynumber: 2.3  Consensus size: 32

       6312 CAATCGAATC

                                            
       6322 TATTTTTGTAAAGTG-AAAATGTAAAT-CTAT
          1 TATTTTTGTAAAGTGAAAAATGTAAATACTAT

             *                               
       6352 TTTTTTTGTAAAGTGAAAAATGTAAATGACTAT
          1 TATTTTTGTAAAGTGAAAAATGTAAAT-ACTAT

                      
       6385 TATTTTTGTA
          1 TATTTTTGTA

       6395 TTTTTTGGGA


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  30   14  0.37
  31   11  0.29
  33   13  0.34

ACGTcount: A:0.37, C:0.03, G:0.14, T:0.47


Consensus pattern (32 bp):   
TATTTTTGTAAAGTGAAAAATGTAAATACTAT

Done.