Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013569.1 Corchorus capsularis cultivar CVL-1 contig13590, 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: 6499
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:877 original size:164 final size:165

Alignment explanation


    Indices: 703--1026  Score: 440
    Period size: 164  Copynumber: 2.0  Consensus size: 165

        693 TTCCATTGAT

                                                                             
        703 CTCCAAAACTCTTAT-T-ATTTATCTTGCTTATCAGATTCTATCTCAGGTTGAAGCTTCTGATA-
          1 CTCCAAAACTCTT-TCTCA-TTATCTTGCTTATCAGATTCTATCTCAGGTTGAAGCTTCTG-TAC

                   * *           *                 **     *   *    *         
        765 AGGTTTTGTCTTTGTCCTTAGGAGCTACATTTT-TTTACTTCTGTTTTGTTTATGTACCATTTAA
         63 AGGTTTTCTATTTGTCCTTAGAAGCTACATTTTGTTTACCCCTGTTCTGTCTATGAACCATTTAA

                 *         *     *   *            
        829 ATGCTTTGTGCTTTGGAAATCTATGTTTCTTTTTGTAC
        128 ATGCTATGTGCTTTGAAAATCCATGCTTCTTTTTGTAC

                                         *         *      *                  
        867 CTCCAAAACTCTTTCTCATTATCTTGCTTCTCAGATTCTGTCTCAGTTTGAAGCTTCTGTACAGG
          1 CTCCAAAACTCTTTCTCATTATCTTGCTTATCAGATTCTATCTCAGGTTGAAGCTTCTGTACAGG

                                    *                                        
        932 TTTTCTATTTGTCCTTAGAAGCTATATTTTGTTTACCCCTGTTCTGTCTATGAACCATTTAAATG
         66 TTTTCTATTTGTCCTTAGAAGCTACATTTTGTTTACCCCTGTTCTGTCTATGAACCATTTAAATG

            *                             
        997 GTATGTGCTTTGAAAATCCATGCTTCTTTT
        131 CTATGTGCTTTGAAAATCCATGCTTCTTTT

       1027 AGTATATATG


Statistics
Matches: 139,  Mismatches: 17, Indels: 7
        0.85            0.10        0.04

Matches are distributed among these distances:
 163    3  0.02
 164   81  0.58
 165   55  0.40

ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47


Consensus pattern (165 bp):   
CTCCAAAACTCTTTCTCATTATCTTGCTTATCAGATTCTATCTCAGGTTGAAGCTTCTGTACAGG
TTTTCTATTTGTCCTTAGAAGCTACATTTTGTTTACCCCTGTTCTGTCTATGAACCATTTAAATG
CTATGTGCTTTGAAAATCCATGCTTCTTTTTGTAC

Found at i:6076 original size:12 final size:13

Alignment explanation


    Indices: 6035--6079  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       6025 AGTTATCGTT

                         
       6035 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
       6048 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       6061 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       6073 TGCTTTA
          1 TGCTTTA

       6080 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC
Done.