Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005847.1 Corchorus capsularis cultivar CVL-1 contig05865, 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, 730

Length: 1218
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36


Found at i:227 original size:13 final size:13

Alignment explanation


    Indices: 178--234  Score: 51
    Period size: 13  Copynumber: 4.1  Consensus size: 13

        168 TACTAATAAA

                         
        178 TAAAAATATATAT
          1 TAAAAATATATAT

                   *        *
        191 TAAATAGTTACTGATAA
          1 TAAA-A-ATA-T-ATAT

              *          
        208 TATAAATATATAT
          1 TAAAAATATATAT

                         
        221 TAAAAATATATAT
          1 TAAAAATATATAT

             
        234 T
          1 T

        235 GTTAAGTGTT


Statistics
Matches: 34,  Mismatches: 6, Indels: 8
        0.71            0.12        0.17

Matches are distributed among these distances:
  13   20  0.59
  14    2  0.06
  15    4  0.12
  16    2  0.06
  17    6  0.18

ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40


Consensus pattern (13 bp):   
TAAAAATATATAT

Found at i:228 original size:32 final size:31

Alignment explanation


    Indices: 167--224  Score: 91
    Period size: 30  Copynumber: 1.9  Consensus size: 31

        157 CATATATGTT

                                           
        167 TTACTAATAAATAAAAATATATATTAAATAG
          1 TTACTAATAAATAAAAATATATATTAAATAG

                 *       *              
        198 TTACTGAT-AATATAAATATATATTAAA
          1 TTACTAATAAATAAAAATATATATTAAA

        225 AATATATATT


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

Matches are distributed among these distances:
  30   18  0.72
  31    7  0.28

ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38


Consensus pattern (31 bp):   
TTACTAATAAATAAAAATATATATTAAATAG

Found at i:358 original size:2 final size:2

Alignment explanation


    Indices: 351--405  Score: 85
    Period size: 2  Copynumber: 28.0  Consensus size: 2

        341 CGACCCTAAA

                                                                  *  *    
        351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT GT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                
        392 AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT

        406 TTTTTTCTGG


Statistics
Matches: 50,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   49  0.98

ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51


Consensus pattern (2 bp):   
AT

Done.