Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004273.1 Corchorus capsularis cultivar CVL-1 contig04281, 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, 716

Length: 1194
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31


Found at i:259 original size:32 final size:32

Alignment explanation


    Indices: 170--260  Score: 157
    Period size: 32  Copynumber: 2.8  Consensus size: 32

        160 GGACACCCTT

                                     *      
        170 CGTCGGCATTCTCCGATGGCACTTGACCTTGG
          1 CGTCGGCATTCTCCGATGGCACTTGGCCTTGG

                                             
        202 CGTCGGCATTCTCCGATGG-ATCTTGGCCTTGG
          1 CGTCGGCATTCTCCGATGGCA-CTTGGCCTTGG

                                       
        234 CGTCGGCATTCTCCGATGGCACTTGGC
          1 CGTCGGCATTCTCCGATGGCACTTGGC

        261 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:260 original size:26 final size:26

Alignment explanation


    Indices: 248--304  Score: 114
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        238 GGCATTCTCC

                                      
        248 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                                      
        274 GATGGCACTTGGCATCGGCACTTGCT
          1 GATGGCACTTGGCATCGGCACTTGCT

                 
        300 GATGG
          1 GATGG

        305 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:267 original size:13 final size:13

Alignment explanation


    Indices: 251--297  Score: 62
    Period size: 13  Copynumber: 3.6  Consensus size: 13

        241 ATTCTCCGAT

                         
        251 GGCACTTGGCATC
          1 GGCACTTGGCATC

                           
        264 GGCACTT-GCTGAT-
          1 GGCACTTGGC--ATC

                         
        277 GGCACTTGGCATC
          1 GGCACTTGGCATC

                    
        290 GGCACTTG
          1 GGCACTTG

        298 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.