Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016150.1 Corchorus olitorius cultivar O-4 contig16183, 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: 9251
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:893 original size:48 final size:47

Alignment explanation


    Indices: 818--959  Score: 164
    Period size: 49  Copynumber: 3.0  Consensus size: 47

        808 GAGCGTGCCA

                                  *         *        *      
        818 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGA-TGAAAATTAAAAG
          1 ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG

                         *                                   
        865 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-AAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG

            *                                               
        914 TTCAATTTTGT-AGCAAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
          1 ATCAATTTTGTCA--AAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA

        960 TGATTGCTTT


Statistics
Matches: 83,  Mismatches: 6, Indels: 11
        0.83            0.06        0.11

Matches are distributed among these distances:
  47   20  0.24
  48   22  0.27
  49   40  0.48
  50    1  0.01

ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27


Consensus pattern (47 bp):   
ATCAATTTTGTCAAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG

Found at i:7163 original size:32 final size:33

Alignment explanation


    Indices: 7099--7171  Score: 89
    Period size: 32  Copynumber: 2.2  Consensus size: 33

       7089 AAAAGAAAAT

                                       *     
       7099 AATTTTTTTTCTTTTCTAAAAACGCAGGAACAA
          1 AATTTTTTTTCTTTTCTAAAAACGCAGAAACAA

                                               
       7132 GAATTTTTTTT-TTTT-TAGAAAACGCA-AAACAA
          1 -AATTTTTTTTCTTTTCTA-AAAACGCAGAAACAA

                    
       7164 AGATTTTT
          1 A-ATTTTT

       7172 ATGACGCAAA


Statistics
Matches: 36,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
  31    1  0.03
  32   13  0.36
  33   12  0.33
  34   10  0.28

ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42


Consensus pattern (33 bp):   
AATTTTTTTTCTTTTCTAAAAACGCAGAAACAA

Found at i:7558 original size:15 final size:16

Alignment explanation


    Indices: 7538--7577  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       7528 AGAGGTTGAA

                            
       7538 AGAAAACAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       7553 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       7569 AGAAAACAA
          1 AGAAAACAA

       7578 AGCAAAGTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:8381 original size:10 final size:10

Alignment explanation


    Indices: 8366--8401  Score: 56
    Period size: 10  Copynumber: 3.7  Consensus size: 10

       8356 TAAAGAGAAT

                    * 
       8366 TATGTGAATG
          1 TATGTGAAGG

                      
       8376 TATGTGAAGG
          1 TATGTGAAGG

                      
       8386 TATGTG-AGG
          1 TATGTGAAGG

                   
       8395 TATGTGA
          1 TATGTGA

       8402 TTTGTGTTAC


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

Matches are distributed among these distances:
   9    9  0.38
  10   15  0.62

ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36


Consensus pattern (10 bp):   
TATGTGAAGG
Done.