Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012083.1 Corchorus capsularis cultivar CVL-1 contig12104, 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: 18943
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:127 original size:23 final size:27

Alignment explanation


    Indices: 75--127  Score: 69
    Period size: 24  Copynumber: 2.1  Consensus size: 27

         65 TTTTTTTTCC

                                     * 
         75 TTTTTCTTTCTTGTTCTTTTTTAATGT
          1 TTTTTCTTTCTTGTTCTTTTTTAATAT

                                       
        102 TTTTTC-TTCTT-TT-TTTTTTAA-AT
          1 TTTTTCTTTCTTGTTCTTTTTTAATAT

               
        125 TTT
          1 TTT

        128 CCTTTAATTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  23    4  0.16
  24    8  0.32
  25    2  0.08
  26    5  0.20
  27    6  0.24

ACGTcount: A:0.09, C:0.09, G:0.04, T:0.77


Consensus pattern (27 bp):   
TTTTTCTTTCTTGTTCTTTTTTAATAT

Found at i:2642 original size:1 final size:1

Alignment explanation


    Indices: 2636--2666  Score: 53
    Period size: 1  Copynumber: 31.0  Consensus size: 1

       2626 AGGAAGTAAG

                                   *       
       2636 TTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       2667 GACATTAAGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97


Consensus pattern (1 bp):   
T

Found at i:14184 original size:11 final size:11

Alignment explanation


    Indices: 14141--14178  Score: 58
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      14131 TTCCTATATA

                *      
      14141 AAATAAATTAT
          1 AAATTAATTAT

            *          
      14152 CAATTAATTAT
          1 AAATTAATTAT

                       
      14163 AAATTAATTAT
          1 AAATTAATTAT

                 
      14174 AAATT
          1 AAATT

      14179 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  11   24  1.00

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:14746 original size:28 final size:28

Alignment explanation


    Indices: 14691--14765  Score: 116
    Period size: 28  Copynumber: 2.7  Consensus size: 28

      14681 GGTCATCCAA

                                    *   
      14691 GGGCATTTTGGTCA-TTTTACATTCAAG
          1 GGGCATTTTGGTCATTTTTACATTAAAG

               *               *        
      14718 GGGTATTTTGGTCATTTTTGCATTAAAG
          1 GGGCATTTTGGTCATTTTTACATTAAAG

                                
      14746 GGGCATTTTGGTCATTTTTA
          1 GGGCATTTTGGTCATTTTTA

      14766 GTCCATTTTT


Statistics
Matches: 42,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  27   13  0.31
  28   29  0.69

ACGTcount: A:0.20, C:0.11, G:0.24, T:0.45


Consensus pattern (28 bp):   
GGGCATTTTGGTCATTTTTACATTAAAG
Done.