Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012010.1 Corchorus capsularis cultivar CVL-1 contig12031, 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: 25708
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:1001 original size:15 final size:15

Alignment explanation


    Indices: 981--1014  Score: 68
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        971 TCCTAAACAA

                           
        981 CCAAAACCCATATAC
          1 CCAAAACCCATATAC

                           
        996 CCAAAACCCATATAC
          1 CCAAAACCCATATAC

                
       1011 CCAA
          1 CCAA

       1015 CATACTCAGC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12


Consensus pattern (15 bp):   
CCAAAACCCATATAC

Found at i:7128 original size:12 final size:12

Alignment explanation


    Indices: 7111--7135  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       7101 CCTCCTATAA

                        
       7111 TAGTTTCTGGTT
          1 TAGTTTCTGGTT

                        
       7123 TAGTTTCTGGTT
          1 TAGTTTCTGGTT

             
       7135 T
          1 T

       7136 GCTCTCAAAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60


Consensus pattern (12 bp):   
TAGTTTCTGGTT

Found at i:8530 original size:22 final size:22

Alignment explanation


    Indices: 8505--8547  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       8495 ACCCGACATC

                                   
       8505 ACCGAACCGAACAA-ACCGAAAA
          1 ACCGAACCG-ACAAGACCGAAAA

                **               
       8527 ACCGCCCCGACAAGACCGAAA
          1 ACCGAACCGACAAGACCGAAA

       8548 TTGGTCGGTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    4  0.22
  22   14  0.78

ACGTcount: A:0.47, C:0.37, G:0.16, T:0.00


Consensus pattern (22 bp):   
ACCGAACCGACAAGACCGAAAA

Found at i:23152 original size:2 final size:2

Alignment explanation


    Indices: 23139--23188  Score: 82
    Period size: 2  Copynumber: 24.0  Consensus size: 2

      23129 GTTAAAAATA

                                                                            
      23139 AT AT AT AGT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
      23183 AT AT AT
          1 AT AT AT

      23189 TACTAACTTT


Statistics
Matches: 46,  Mismatches: 0, Indels: 4
        0.92            0.00        0.08

Matches are distributed among these distances:
   2   42  0.91
   3    4  0.09

ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48


Consensus pattern (2 bp):   
AT

Done.