Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002125.1 Corchorus capsularis cultivar CVL-1 contig02129, 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, 629

Length: 1049
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29


Found at i:452 original size:48 final size:48

Alignment explanation


    Indices: 376--485  Score: 168
    Period size: 48  Copynumber: 2.3  Consensus size: 48

        366 TGGATTTCTA

                                                            
        376 ATTTTGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC
          1 ATTTTGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                          *               *              *   
        424 -TTTTCGGCCAATTGTTGGGTCCGGAACTCTTGATGGTTAACCTATGGC
          1 ATTTT-GGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC

                          
        472 ATTTTTGGCCAATT
          1 A-TTTTGGCCAATT

        486 TTTTGACCCC


Statistics
Matches: 56,  Mismatches: 3, Indels: 5
        0.88            0.05        0.08

Matches are distributed among these distances:
  47    4  0.07
  48   40  0.71
  49    8  0.14
  50    4  0.07

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35


Consensus pattern (48 bp):   
ATTTTGGCCAATTATTGGGTCCGGAACTCATGATGGTTAACCTACGGC

Found at i:897 original size:32 final size:32

Alignment explanation


    Indices: 808--898  Score: 157
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        798 GGACACCCTT

                                     *      
        808 CGTCGGCATTCTCCGATGGCACTTGACCTTGG
          1 CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

                                             
        840 CGTCGGCATTCTCCGATGG-ATCTTGGCCTTGG
          1 CGTCGGCATTCTCCGATGGCA-CTTGGCCTTGG

                                       
        872 CGTCGGCATTCTCCGATGGCACTTGGC
          1 CGTCGGCATTCTCCGATGGCACTTGGC

        899 ATCGGCACTT


Statistics
Matches: 56,  Mismatches: 1, Indels: 4
        0.92            0.02        0.07

Matches are distributed among these distances:
  31    1  0.02
  32   54  0.96
  33    1  0.02

ACGTcount: A:0.11, C:0.31, G:0.30, T:0.29


Consensus pattern (32 bp):   
CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

Found at i:898 original size:26 final size:26

Alignment explanation


    Indices: 886--942  Score: 114
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        876 GGCATTCTCC

                                      
        886 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                                      
        912 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                 
        938 GATGG
          1 GATGG

        943 ATGGCACTTG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   31  1.00

ACGTcount: A:0.16, C:0.25, G:0.33, T:0.26


Consensus pattern (26 bp):   
GATGGCACTTGGCATCGGCACTTGCT

Found at i:905 original size:13 final size:13

Alignment explanation


    Indices: 889--935  Score: 62
    Period size: 13  Copynumber: 3.6  Consensus size: 13

        879 ATTCTCCGAT

                         
        889 GGCACTTGGCATC
          1 GGCACTTGGCATC

                           
        902 GGCACTT-GCTGAT-
          1 GGCACTTGGC--ATC

                         
        915 GGCACTTGGCATC
          1 GGCACTTGGCATC

                    
        928 GGCACTTG
          1 GGCACTTG

        936 CTGATGGATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 8
        0.79            0.00        0.21

Matches are distributed among these distances:
  12    4  0.13
  13   22  0.73
  14    4  0.13

ACGTcount: A:0.15, C:0.28, G:0.32, T:0.26


Consensus pattern (13 bp):   
GGCACTTGGCATC
Done.