Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009994.1 Corchorus capsularis cultivar CVL-1 contig10015, 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: 3827
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:1716 original size:36 final size:36

Alignment explanation


    Indices: 1597--1730  Score: 103
    Period size: 36  Copynumber: 3.7  Consensus size: 36

       1587 CCGCCATTTC

                      *     *              *   *
       1597 GAACTGAACTAAAGAACGACCACCCTCGATCGTTCC
          1 GAACTGAACTGAAGAAAGACCACCCTCGATCATTCT

                  *     *         *    * * *  *  
       1633 G-ACTCAAACTGGAGAAAGACCGCCCTGGGTTA-ACT
          1 GAACT-GAACTGAAGAAAGACCACCCTCGATCATTCT

               *             *                   
       1668 GAAAT-AAGCTGAAGAACGACCACCCTCGATCATTCT
          1 GAACTGAA-CTGAAGAAAGACCACCCTCGATCATTCT

                                       
       1704 GAACTGAACTGAAGAATAGACCACCCT
          1 GAACTGAACTGAAGAA-AGACCACCCT

       1731 GGGTCATTGA


Statistics
Matches: 71,  Mismatches: 21, Indels: 11
        0.69            0.20        0.11

Matches are distributed among these distances:
  34    2  0.03
  35   23  0.32
  36   35  0.49
  37   11  0.15

ACGTcount: A:0.35, C:0.28, G:0.19, T:0.17


Consensus pattern (36 bp):   
GAACTGAACTGAAGAAAGACCACCCTCGATCATTCT

Found at i:2034 original size:34 final size:34

Alignment explanation


    Indices: 1995--2060  Score: 96
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       1985 TGAAAGCAAC

                               *              
       1995 TGAAGAAAGACCGCCCTGGGTCAATTGAAATTAT
          1 TGAAGAAAGACCGCCCTGGATCAATTGAAATTAT

                  *     *  *                
       2029 TGAAGAGAGACCTCCTTGGATCAATTGAAATT
          1 TGAAGAAAGACCGCCCTGGATCAATTGAAATT

       2061 TACTGAATGG


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   28  1.00

ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26


Consensus pattern (34 bp):   
TGAAGAAAGACCGCCCTGGATCAATTGAAATTAT
Done.