Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010406.1 Corchorus capsularis cultivar CVL-1 contig10427, 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: 4074
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:323 original size:13 final size:13

Alignment explanation


    Indices: 305--334  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

        295 CACTTCTAAG

                         
        305 TTCAGAGTTGCCT
          1 TTCAGAGTTGCCT

                         
        318 TTCAGAGTTGCCT
          1 TTCAGAGTTGCCT

                
        331 TTCA
          1 TTCA

        335 ATTTGTAGTG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40


Consensus pattern (13 bp):   
TTCAGAGTTGCCT

Found at i:1152 original size:3 final size:3

Alignment explanation


    Indices: 1144--1169  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       1134 GCATGATTAA

                                              
       1144 AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AA

       1170 AAGTTAATCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Found at i:4023 original size:30 final size:31

Alignment explanation


    Indices: 3961--4035  Score: 91
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       3951 AAAAATGGTG

                              *            
       3961 AGGGACCCAATTGCTCAATTAACTCAACTTC
          1 AGGGACCCAATTGCTCAACTAACTCAACTTC

                  *                *        
       3992 AGGGACTCAATTGCTC-ACTAAGTTC-ACTTC
          1 AGGGACCCAATTGCTCAACTAA-CTCAACTTC

                     *    
       4022 AGGGACCCATTTGC
          1 AGGGACCCAATTGC

       4036 ACATTTACCC


Statistics
Matches: 38,  Mismatches: 5, Indels: 3
        0.83            0.11        0.07

Matches are distributed among these distances:
  30   21  0.55
  31   17  0.45

ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27


Consensus pattern (31 bp):   
AGGGACCCAATTGCTCAACTAACTCAACTTC
Done.