Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009306.1 Corchorus capsularis cultivar CVL-1 contig09327, 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: 22197
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:823 original size:129 final size:129

Alignment explanation


    Indices: 593--853  Score: 522
    Period size: 129  Copynumber: 2.0  Consensus size: 129

        583 AAGCCTATGA

                                                                             
        593 AAATTCAAGAATTTACAAAGAAAAGCCTAAAACTCTACATGATCAAAGGGTATTGAGAAGATCAT
          1 AAATTCAAGAATTTACAAAGAAAAGCCTAAAACTCTACATGATCAAAGGGTATTGAGAAGATCAT

                                                                            
        658 TCCATGAAGGTCAGAAAGTTTTGTTGTTCAATAGCACAATTAAGCATCATGGAAAGTTAAGGAC
         66 TCCATGAAGGTCAGAAAGTTTTGTTGTTCAATAGCACAATTAAGCATCATGGAAAGTTAAGGAC

                                                                             
        722 AAATTCAAGAATTTACAAAGAAAAGCCTAAAACTCTACATGATCAAAGGGTATTGAGAAGATCAT
          1 AAATTCAAGAATTTACAAAGAAAAGCCTAAAACTCTACATGATCAAAGGGTATTGAGAAGATCAT

                                                                            
        787 TCCATGAAGGTCAGAAAGTTTTGTTGTTCAATAGCACAATTAAGCATCATGGAAAGTTAAGGAC
         66 TCCATGAAGGTCAGAAAGTTTTGTTGTTCAATAGCACAATTAAGCATCATGGAAAGTTAAGGAC

               
        851 AAA
          1 AAA

        854 ATGGAATGGA


Statistics
Matches: 132,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 129  132  1.00

ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25


Consensus pattern (129 bp):   
AAATTCAAGAATTTACAAAGAAAAGCCTAAAACTCTACATGATCAAAGGGTATTGAGAAGATCAT
TCCATGAAGGTCAGAAAGTTTTGTTGTTCAATAGCACAATTAAGCATCATGGAAAGTTAAGGAC

Found at i:1106 original size:6 final size:6

Alignment explanation


    Indices: 1095--1124  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       1085 GAGGCAACCC

                                              
       1095 AATTTT AATTTT AATTTT AATTTT AATTTT
          1 AATTTT AATTTT AATTTT AATTTT AATTTT

       1125 TGTTTTTAGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (6 bp):   
AATTTT

Found at i:10166 original size:17 final size:17

Alignment explanation


    Indices: 10146--10181  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      10136 CTTTTCAGTG

                              
      10146 TTTTTTCTTCTTCTTCCT
          1 TTTTTTC-TCTTCTTCCT

                       *     
      10164 TTTTTTCTCTTTTTCCT
          1 TTTTTTCTCTTCTTCCT

             
      10181 T
          1 T

      10182 CCGCAGATTG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17   10  0.59
  18    7  0.41

ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75


Consensus pattern (17 bp):   
TTTTTTCTCTTCTTCCT

Found at i:18459 original size:33 final size:33

Alignment explanation


    Indices: 18422--18487  Score: 114
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      18412 ATTGAAGTAT

                      *          *           
      18422 TTGATACCAATCGTTGAAGTTTGTGAAGCTCCC
          1 TTGATACCAACCGTTGAAGTTAGTGAAGCTCCC

                                             
      18455 TTGATACCAACCGTTGAAGTTAGTGAAGCTCCC
          1 TTGATACCAACCGTTGAAGTTAGTGAAGCTCCC

      18488 CCTTTGAGTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30


Consensus pattern (33 bp):   
TTGATACCAACCGTTGAAGTTAGTGAAGCTCCC
Done.