Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019454.1 Corchorus olitorius cultivar O-4 contig19487, 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: 11379
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--33  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

                                                             
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         34 AAATGAGAAG


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

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:771 original size:21 final size:21

Alignment explanation


    Indices: 730--775  Score: 51
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        720 TTCCCTAAGT

                    *       *    
        730 TAAAATTTCATTAAGCTAAAA
          1 TAAAATTTAATTAAGCAAAAA

                                  
        751 TAAAATTTAATTTAAG-AAAAA
          1 TAAAATTTAA-TTAAGCAAAAA

                 
        772 -AAAA
          1 TAAAA

        776 GAAAAAGAGG


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  20    4  0.18
  21   13  0.59
  22    5  0.23

ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30


Consensus pattern (21 bp):   
TAAAATTTAATTAAGCAAAAA

Found at i:1626 original size:21 final size:22

Alignment explanation


    Indices: 1586--1633  Score: 71
    Period size: 21  Copynumber: 2.2  Consensus size: 22

       1576 ATGGAAACAG

                      *    *      
       1586 AAAAACAGAATCAAGGATGTCT
          1 AAAAACAGAAACAAGAATGTCT

                                  
       1608 AAAAACAGAAAC-AGAATGTCT
          1 AAAAACAGAAACAAGAATGTCT

                 
       1629 AAAAA
          1 AAAAA

       1634 TAGTTTAAAC


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

Matches are distributed among these distances:
  21   13  0.54
  22   11  0.46

ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15


Consensus pattern (22 bp):   
AAAAACAGAAACAAGAATGTCT

Found at i:2980 original size:24 final size:24

Alignment explanation


    Indices: 2930--2987  Score: 62
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       2920 TTAGGTTAGG

                 *           **     
       2930 TATAACTATATATATTTTCTGAAT
          1 TATAAATATATATATTTAATGAAT

                                * * 
       2954 TATAAATATATATATTTAATTATT
          1 TATAAATATATATATTTAATGAAT

                *     
       2978 TATATATATA
          1 TATAAATATA

       2988 ATAAAACTAA


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   28  1.00

ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52


Consensus pattern (24 bp):   
TATAAATATATATATTTAATGAAT

Found at i:4536 original size:2 final size:2

Alignment explanation


    Indices: 4523--4569  Score: 78
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       4513 TATTCAAATA

                                                                           
       4523 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                   
       4566 -T AT A
          1 AT AT A

       4570 GTTAAAGCTT


Statistics
Matches: 43,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   1    1  0.02
   2   40  0.93
   3    2  0.05

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:5082 original size:12 final size:13

Alignment explanation


    Indices: 5045--5083  Score: 53
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       5035 ACTCAACACT

                     *    
       5045 AACTGACTAAAAAA
          1 AACTGACT-CAAAA

                         
       5059 AACTGACTCAAAA
          1 AACTGACTCAAAA

                         
       5072 AACTGAC-CAAAA
          1 AACTGACTCAAAA

       5084 CCTGACCGAT


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

Matches are distributed among these distances:
  12    5  0.21
  13   11  0.46
  14    8  0.33

ACGTcount: A:0.59, C:0.21, G:0.08, T:0.13


Consensus pattern (13 bp):   
AACTGACTCAAAA
Done.