Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006997.1 Corchorus capsularis cultivar CVL-1 contig07018, 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: 5737
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32


Found at i:809 original size:31 final size:34

Alignment explanation


    Indices: 774--841  Score: 88
    Period size: 36  Copynumber: 2.0  Consensus size: 34

        764 TAAAATAAAT

                                   *          
        774 AACTGGA-GAA-AA-ACCACCCTGGATCATTCCG
          1 AACTGGACGAAGAAGACCACCCTCGATCATTCCG

                                                
        805 AACTGGACTGAAGAATGACCACCCTCGATCATTCCG
          1 AACTGGAC-GAAGAA-GACCACCCTCGATCATTCCG

             
        841 A
          1 A

        842 CGCAATCCGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 5
        0.84            0.03        0.14

Matches are distributed among these distances:
  31    7  0.23
  33    3  0.10
  34    2  0.06
  36   19  0.61

ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18


Consensus pattern (34 bp):   
AACTGGACGAAGAAGACCACCCTCGATCATTCCG

Found at i:1008 original size:34 final size:35

Alignment explanation


    Indices: 965--1058  Score: 118
    Period size: 35  Copynumber: 2.7  Consensus size: 35

        955 ATAATTGGAG

                         *                  *  
        965 AATTGAAGAAAGACCACCCTGGATC-ATTGAAGTA
          1 AATTGAAGAAAGATCACCCTGGATCAATTGAAATA

                      *    *       *          *
        999 AATTGAAGAACGATCGCCCTGGACCAATTGAAATT
          1 AATTGAAGAAAGATCACCCTGGATCAATTGAAATA

              *                      
       1034 AACTGAAGAAAGATCACCCTGGATC
          1 AATTGAAGAAAGATCACCCTGGATC

       1059 GAGTAACTGA


Statistics
Matches: 49,  Mismatches: 10, Indels: 1
        0.82            0.17        0.02

Matches are distributed among these distances:
  34   21  0.43
  35   28  0.57

ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20


Consensus pattern (35 bp):   
AATTGAAGAAAGATCACCCTGGATCAATTGAAATA

Found at i:3149 original size:20 final size:20

Alignment explanation


    Indices: 3104--3141  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3094 GCCCCGAGTG

                                
       3104 CTTTTTCTTCTTCTTTTTTT
          1 CTTTTTCTTCTTCTTTTTTT

                               
       3124 CTTTTTCTTC-TCTTTTTT
          1 CTTTTTCTTCTTCTTTTTT

       3142 ATTATTTTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    8  0.44
  20   10  0.56

ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79


Consensus pattern (20 bp):   
CTTTTTCTTCTTCTTTTTTT
Done.