Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000747.1 Corchorus capsularis cultivar CVL-1 contig00747, 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: 8354
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:52 original size:33 final size:33

Alignment explanation


    Indices: 5--79  Score: 116
    Period size: 33  Copynumber: 2.3  Consensus size: 33

          1 CCCC

                                 *            
          5 AGTGGGGAGGCTCCGCCGTGGTTGAGCC-TCCCT
          1 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGT-CCT

                *                            
         38 AGTGAGGAGGCTCCGCCGTGGCTGAGCCGTCCT
          1 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT

                     
         71 AGTGGGGAG
          1 AGTGGGGAG

         80 ACTCAGTGTA


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

Matches are distributed among these distances:
  33   37  0.97
  34    1  0.03

ACGTcount: A:0.12, C:0.27, G:0.43, T:0.19


Consensus pattern (33 bp):   
AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT

Found at i:1037 original size:25 final size:25

Alignment explanation


    Indices: 1003--1052  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        993 TCAGCTTGCA

                                     
       1003 ATCTTTCTCAATCCGCAATTGAGTC
          1 ATCTTTCTCAATCCGCAATTGAGTC

                                     
       1028 ATCTTTCTCAATCCGCAATTGAGTC
          1 ATCTTTCTCAATCCGCAATTGAGTC

       1053 GATTTCGAAT


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

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36


Consensus pattern (25 bp):   
ATCTTTCTCAATCCGCAATTGAGTC

Found at i:2589 original size:45 final size:45

Alignment explanation


    Indices: 2538--2630  Score: 177
    Period size: 45  Copynumber: 2.1  Consensus size: 45

       2528 AGATCTATAC

                                        *                
       2538 ACCGTTACGTGATTAGTCGTATTACTATGCTAACCCAACAAAAAA
          1 ACCGTTACGTGATTAGTCGTATTACTATACTAACCCAACAAAAAA

                                                         
       2583 ACCGTTACGTGATTAGTCGTATTACTATACTAACCCAACAAAAAA
          1 ACCGTTACGTGATTAGTCGTATTACTATACTAACCCAACAAAAAA

               
       2628 ACC
          1 ACC

       2631 CAGTGAAATC


Statistics
Matches: 47,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   47  1.00

ACGTcount: A:0.39, C:0.24, G:0.12, T:0.26


Consensus pattern (45 bp):   
ACCGTTACGTGATTAGTCGTATTACTATACTAACCCAACAAAAAA

Found at i:3618 original size:7 final size:7

Alignment explanation


    Indices: 3606--3639  Score: 59
    Period size: 7  Copynumber: 4.9  Consensus size: 7

       3596 ATTGTCCATG

                  *
       3606 TTATATC
          1 TTATATA

                   
       3613 TTATATA
          1 TTATATA

                   
       3620 TTATATA
          1 TTATATA

                   
       3627 TTATATA
          1 TTATATA

                  
       3634 TTATAT
          1 TTATAT

       3640 GTGACCCAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   7   26  1.00

ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59


Consensus pattern (7 bp):   
TTATATA

Found at i:5589 original size:19 final size:19

Alignment explanation


    Indices: 5552--5589  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       5542 AAATGCTATG

                         **    
       5552 TCAAAATTGGATTTTTTTT
          1 TCAAAATTGGATTGATTTT

                               
       5571 TCAAAATTGGATTGATTTT
          1 TCAAAATTGGATTGATTTT

       5590 ATTGCTTTCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53


Consensus pattern (19 bp):   
TCAAAATTGGATTGATTTT
Done.