Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017139.1 Corchorus olitorius cultivar O-4 contig17172, 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: 2056
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Found at i:869 original size:15 final size:15

Alignment explanation


    Indices: 839--881  Score: 68
    Period size: 15  Copynumber: 2.8  Consensus size: 15

        829 TTACTTTGTT

                            
        839 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                   *       
        855 TTGTTTTATGTTTAA
          1 TTGTTTTCTGTTTAA

                        
        870 TTGTTTTCTGTT
          1 TTGTTTTCTGTT

        882 AATCTCTGTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   17  0.68
  16    8  0.32

ACGTcount: A:0.14, C:0.05, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:1249 original size:50 final size:50

Alignment explanation


    Indices: 1186--1287  Score: 136
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       1176 CCGTTTTTAA

                                             *          *       
       1186 TTTTGAGTCTTGCGTC-TTTGAAAAAAAAAAATTTTTGTTTTGTTTTCTGCG
          1 TTTTGAGTCTTGCGTCTTTTGAAAAAAAAAAA-ATTTGTTTTGTGTT-TGCG

                *                                              
       1237 TTTTTAGT-TTGCGTCTTTTTGAAAAAAAAAAAATTTGTTTTGTGTTTGCG
          1 TTTTGAGTCTTGCGTC-TTTTGAAAAAAAAAAAATTTGTTTTGTGTTTGCG

             
       1287 T
          1 T

       1288 CGTTTTGAAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 5
        0.85            0.06        0.09

Matches are distributed among these distances:
  50   12  0.26
  51   19  0.41
  52   15  0.33

ACGTcount: A:0.25, C:0.08, G:0.18, T:0.50


Consensus pattern (50 bp):   
TTTTGAGTCTTGCGTCTTTTGAAAAAAAAAAAATTTGTTTTGTGTTTGCG

Found at i:1314 original size:40 final size:37

Alignment explanation


    Indices: 1243--1323  Score: 117
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       1233 TGCGTTTTTA

                     *                          *
       1243 GTTTGCGTCTTTTTGAAAAAAAAAAAATTTGTTTTGT
          1 GTTTGCGTCGTTTTGAAAAAAAAAAAATTTGTTTTGC

                                                    
       1280 GTTTGCGTCGTTTTGAAAAAAAAAAAACTTTTTGTTTTGC
          1 GTTTGCGTCGTTTTGAAAAAAAAAAAA---TTTGTTTTGC

                
       1320 GTTT
          1 GTTT

       1324 TTAATTTTTT


Statistics
Matches: 39,  Mismatches: 2, Indels: 3
        0.89            0.05        0.07

Matches are distributed among these distances:
  37   26  0.67
  40   13  0.33

ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46


Consensus pattern (37 bp):   
GTTTGCGTCGTTTTGAAAAAAAAAAAATTTGTTTTGC
Done.