Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011507.1 Corchorus capsularis cultivar CVL-1 contig11528, 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: 11634
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31


Found at i:18 original size:2 final size:2

Alignment explanation


    Indices: 12--46  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

          2 TTTGATTTAT

                                                                   
         12 TA TA TA TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         47 TAAGTTTAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   29  0.94

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:34 original size:14 final size:12

Alignment explanation


    Indices: 12--46  Score: 56
    Period size: 11  Copynumber: 3.1  Consensus size: 12

          2 TTTGATTTAT

                        
         12 TATATATATATA
          1 TATATATATATA

                        
         24 -ATATA-ATATA
          1 TATATATATATA

                        
         34 TATATATATATA
          1 TATATATATATA

             
         46 T
          1 T

         47 TAAGTTTAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  10    5  0.24
  11   10  0.48
  12    6  0.29

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (12 bp):   
TATATATATATA

Found at i:9416 original size:12 final size:12

Alignment explanation


    Indices: 9399--9427  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       9389 TAAACTTTAT

                        
       9399 AAAGCCATGATC
          1 AAAGCCATGATC

                        
       9411 AAAGCCATGATC
          1 AAAGCCATGATC

                 
       9423 AAAGC
          1 AAAGC

       9428 AAAAATATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14


Consensus pattern (12 bp):   
AAAGCCATGATC

Found at i:9691 original size:134 final size:135

Alignment explanation


    Indices: 9442--9691  Score: 357
    Period size: 136  Copynumber: 1.8  Consensus size: 135

       9432 ATATTTCACG

                                             *                               
       9442 ATAAAAATTGGAAAATTCTTTCTTTCTTTCTTTCTTTTTTTAGTTTTTATTTCAAGACTTGGTTA
          1 ATAAAAATTGGAAAATTCTTTCTTTC-TTCTTTATTTTTTTAGTTTTTATTTCAAGACTTGGTTA

                                       *      *          *                   
       9507 GACTTCTCAAATAAATGAGGGTTGTGTGTGGATGTTGGACTATGTCAATGTGGAAAATTACTTCC
         65 GACTTCTCAAATAAATGAGGGTTGTGTATGGATGATGGA--ATGTAAATGTGGAAAATTACTTCC

                    
       9572 AAATCATA
        128 AAATCATA

                                                                             
       9580 ATAAAAATTGGAAAATTCTTTCTTTC-T-TTTATTTTTTT-GTTTTTATTTCAAGACTTGGTTAT
          1 ATAAAAATTGGAAAATTCTTTCTTTCTTCTTTATTTTTTTAGTTTTTATTTCAAGACTTGG-T-T

                                             *                  
       9642 AGACTTCTCAAATAAATGAGGGTTGTGTACATGTAT-ATGG-ATGTAAATGT
         64 AGACTTCTCAAATAAATGAGGGTTGTGT--ATGGATGATGGAATGTAAATGT

       9692 TGGACTATGT


Statistics
Matches: 103,  Mismatches: 5, Indels: 12
        0.86            0.04        0.10

Matches are distributed among these distances:
 134   29  0.28
 135   11  0.11
 136   30  0.29
 137    3  0.03
 138   30  0.29

ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45


Consensus pattern (135 bp):   
ATAAAAATTGGAAAATTCTTTCTTTCTTCTTTATTTTTTTAGTTTTTATTTCAAGACTTGGTTAG
ACTTCTCAAATAAATGAGGGTTGTGTATGGATGATGGAATGTAAATGTGGAAAATTACTTCCAAA
TCATA
Done.