Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013895.1 Corchorus capsularis cultivar CVL-1 contig13916, 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: 24003
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30


Found at i:769 original size:29 final size:29

Alignment explanation


    Indices: 716--788  Score: 83
    Period size: 29  Copynumber: 2.5  Consensus size: 29

        706 AAGCTGAAGG

                           **        *    
        716 GGCAAAACGTCCCAAAATTGAAGTTTATGA
          1 GGCAAAACGT-CCAATGTTGAAGTTCATGA

              *    *                    *
        746 GGTAAAATGTCCAATGTTGAAGTTCATGT
          1 GGCAAAACGTCCAATGTTGAAGTTCATGA

                          
        775 GGCAAAACGTCCAA
          1 GGCAAAACGTCCAA

        789 ACGCTACAAG


Statistics
Matches: 35,  Mismatches: 8, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  29   27  0.77
  30    8  0.23

ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25


Consensus pattern (29 bp):   
GGCAAAACGTCCAATGTTGAAGTTCATGA

Found at i:4444 original size:13 final size:13

Alignment explanation


    Indices: 4407--4444  Score: 51
    Period size: 12  Copynumber: 3.0  Consensus size: 13

       4397 CAAATGTAAA

                *        
       4407 GGAAAATGTTAAC
          1 GGAAGATGTTAAC

             *           
       4420 GAAAGA-GTTAAC
          1 GGAAGATGTTAAC

                         
       4432 GGAAGATGTTAAC
          1 GGAAGATGTTAAC

       4445 AATGAATACT


Statistics
Matches: 21,  Mismatches: 3, Indels: 2
        0.81            0.12        0.08

Matches are distributed among these distances:
  12   11  0.52
  13   10  0.48

ACGTcount: A:0.45, C:0.08, G:0.26, T:0.21


Consensus pattern (13 bp):   
GGAAGATGTTAAC

Found at i:9205 original size:30 final size:31

Alignment explanation


    Indices: 9156--9240  Score: 118
    Period size: 30  Copynumber: 2.8  Consensus size: 31

       9146 GTATTATCGT

                   *                  **   
       9156 TATATGCTATAACGATAGACCTAAAAGGAAC
          1 TATATGCAATAACGATAGACCTAAAACAAAC

                                           
       9187 TATATGCAATAA-GATAGACCTAAAACAAAC
          1 TATATGCAATAACGATAGACCTAAAACAAAC

                    *   *           
       9217 TATATGCAGTAATGATAGACCTAA
          1 TATATGCAATAACGATAGACCTAA

       9241 GACTATATGC


Statistics
Matches: 49,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  30   27  0.55
  31   22  0.45

ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24


Consensus pattern (31 bp):   
TATATGCAATAACGATAGACCTAAAACAAAC

Found at i:9255 original size:27 final size:26

Alignment explanation


    Indices: 9213--9295  Score: 105
    Period size: 27  Copynumber: 3.1  Consensus size: 26

       9203 GACCTAAAAC

                                      
       9213 AAACTATATGCAGTAATGATAGACCT
          1 AAACTATATGCAGTAATGATAGACCT

                        *            * 
       9239 AAGACTATATGCCGTAATGATAGACTT
          1 AA-ACTATATGCAGTAATGATAGACCT

                                   *    
       9266 AAATCTATATGCTA-TAATGATAAACCT
          1 AAA-CTATATGC-AGTAATGATAGACCT

               
       9293 AAA
          1 AAA

       9296 TCCATATAGT


Statistics
Matches: 49,  Mismatches: 5, Indels: 5
        0.83            0.08        0.08

Matches are distributed among these distances:
  26    3  0.06
  27   46  0.94

ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29


Consensus pattern (26 bp):   
AAACTATATGCAGTAATGATAGACCT

Found at i:9527 original size:31 final size:31

Alignment explanation


    Indices: 9499--9574  Score: 100
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       9489 CGTTATGCTT

                             **   *        
       9499 TAACGATAGACCTAAAAGGAACTATATGCAA
          1 TAACGATAGACCTAAAACAAACCATATGCAA

                                          *
       9530 TAA-GATAGACCTAAAACAAACCATATGCAG
          1 TAACGATAGACCTAAAACAAACCATATGCAA

              *            
       9560 TATCGATAGACCTAA
          1 TAACGATAGACCTAA

       9575 GACTATATGA


Statistics
Matches: 39,  Mismatches: 5, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  30   25  0.64
  31   14  0.36

ACGTcount: A:0.47, C:0.18, G:0.14, T:0.20


Consensus pattern (31 bp):   
TAACGATAGACCTAAAACAAACCATATGCAA

Found at i:19660 original size:4 final size:4

Alignment explanation


    Indices: 19649--19682  Score: 52
    Period size: 4  Copynumber: 8.8  Consensus size: 4

      19639 TGTTTTCTGT

                            *                          
      19649 TTTA -TTA TTTA TATA TTTA TTTA TTTA TTTA TTT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT

      19683 GGCTTTCGTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   3    3  0.11
   4   24  0.89

ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74


Consensus pattern (4 bp):   
TTTA

Done.