Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002116.1 Corchorus olitorius cultivar O-4 contig02116, 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: 7165
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:504 original size:2 final size:2

Alignment explanation


    Indices: 497--523  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

        487 AAAATTTAAG

                                                    
        497 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 A

        524 CACACACACA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:4707 original size:14 final size:13

Alignment explanation


    Indices: 4690--4732  Score: 52
    Period size: 12  Copynumber: 3.3  Consensus size: 13

       4680 TTGTTATTTG

                          
       4690 TTTTTCATTTTCCT
          1 TTTTTCATTTT-CT

                 *   *   
       4704 TTTTTTATTCTC-
          1 TTTTTCATTTTCT

                         
       4716 TTTTTCATTTTCT
          1 TTTTTCATTTTCT

                
       4729 TTTT
          1 TTTT

       4733 CGTCTTTTAC


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  12   10  0.42
  13    5  0.21
  14    9  0.38

ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77


Consensus pattern (13 bp):   
TTTTTCATTTTCT

Found at i:4711 original size:25 final size:26

Alignment explanation


    Indices: 4677--4732  Score: 80
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       4667 TGACGTGGCT

                         *             
       4677 TTTTTGTTATT-TGTTTTTCATTTTCC
          1 TTTTTGTTATTCTCTTTTTCATTTT-C

                                      
       4703 TTTTT-TTATTCTCTTTTTCATTTTC
          1 TTTTTGTTATTCTCTTTTTCATTTTC

                 
       4728 TTTTT
          1 TTTTT

       4733 CGTCTTTTAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  25   11  0.39
  26   17  0.61

ACGTcount: A:0.07, C:0.12, G:0.04, T:0.77


Consensus pattern (26 bp):   
TTTTTGTTATTCTCTTTTTCATTTTC

Found at i:4726 original size:20 final size:21

Alignment explanation


    Indices: 4697--4740  Score: 56
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       4687 TTGTTTTTCA

                 *                
       4697 TTTTCCTTTT-TTTATTC-TCT
          1 TTTTCATTTTCTTT-TTCGTCT

                                 
       4717 TTTTCATTTTCTTTTTCGTCT
          1 TTTTCATTTTCTTTTTCGTCT

               
       4738 TTT
          1 TTT

       4741 ACCTTCTTTC


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  20   12  0.57
  21    9  0.43

ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75


Consensus pattern (21 bp):   
TTTTCATTTTCTTTTTCGTCT

Found at i:5211 original size:36 final size:36

Alignment explanation


    Indices: 5154--5223  Score: 106
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       5144 GCAGTTTAAT

                                                
       5154 TTCGATGTAAAGTTTCAAATTGATTTGGGGTTTTGG
          1 TTCGATGTAAAGTTTCAAATTGATTTGGGGTTTTGG

                  *          *                 
       5190 TTCGATTTAAA-TATTCGAATTGATTTGGGGTTTT
          1 TTCGATGTAAAGT-TTCAAATTGATTTGGGGTTTT

       5224 CGAAGGGTGA


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  35    1  0.03
  36   30  0.97

ACGTcount: A:0.23, C:0.06, G:0.24, T:0.47


Consensus pattern (36 bp):   
TTCGATGTAAAGTTTCAAATTGATTTGGGGTTTTGG
Done.