Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012353.1 Corchorus capsularis cultivar CVL-1 contig12374, 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: 5539
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34


Found at i:2954 original size:36 final size:36

Alignment explanation


    Indices: 2907--2983  Score: 136
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       2897 ATCACAAACT

                           *                    
       2907 TAAATGATTAGCCAATGTCTTGAGACATTGATGAAA
          1 TAAATGATTAGCCAAGGTCTTGAGACATTGATGAAA

                                 *              
       2943 TAAATGATTAGCCAAGGTCTTTAGACATTGATGAAA
          1 TAAATGATTAGCCAAGGTCTTGAGACATTGATGAAA

                 
       2979 TAAAT
          1 TAAAT

       2984 TAGAGAAAAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  36   39  1.00

ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31


Consensus pattern (36 bp):   
TAAATGATTAGCCAAGGTCTTGAGACATTGATGAAA

Found at i:4499 original size:27 final size:27

Alignment explanation


    Indices: 4469--4608  Score: 187
    Period size: 27  Copynumber: 5.3  Consensus size: 27

       4459 TAGTGATTTT

                      * *              
       4469 TACTTATACTCATACCGATGATACCGA
          1 TACTTATACTAAAACCGATGATACCGA

                *       *   * * *      
       4496 TACTAATACTAATACCAAGGGTACCGA
          1 TACTTATACTAAAACCGATGATACCGA

                                       
       4523 TACTTATACTAAAACCGATGATACCGA
          1 TACTTATACTAAAACCGATGATACCGA

                                       
       4550 TACTTATACTAAAACCGATGATACCGA
          1 TACTTATACTAAAACCGATGATACCGA

                                        
       4577 TACTTATACTAAAACCCGA-G--ACCGA
          1 TACTTATACTAAAA-CCGATGATACCGA

                   
       4602 TACTTAT
          1 TACTTAT

       4609 CTCGAAGTGG


Statistics
Matches: 102,  Mismatches: 10, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
  25   12  0.12
  27   86  0.84
  28    4  0.04

ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26


Consensus pattern (27 bp):   
TACTTATACTAAAACCGATGATACCGA

Done.