Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005312.1 Corchorus capsularis cultivar CVL-1 contig05330, 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: 6299
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36


Found at i:301 original size:23 final size:23

Alignment explanation


    Indices: 252--302  Score: 59
    Period size: 23  Copynumber: 2.2  Consensus size: 23

        242 TTATACAGTT

                             * *   
        252 AAAAAGGAAAAAAAATGTACCAA
          1 AAAAAGGAAAAAAAATGAAACAA

                     *             
        275 AAAAAGGAAGAAAAA-GAAACAA
          1 AAAAAGGAAAAAAAATGAAACAA

                  
        297 GAAAAA
          1 -AAAAA

        303 ATAAGTACTA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22    5  0.21
  23   19  0.79

ACGTcount: A:0.75, C:0.06, G:0.16, T:0.04


Consensus pattern (23 bp):   
AAAAAGGAAAAAAAATGAAACAA

Found at i:1554 original size:22 final size:22

Alignment explanation


    Indices: 1528--1574  Score: 85
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1518 ATTTATTCAT

                                  
       1528 TATTAATTAACTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

                     *            
       1550 TATTAATTAGCTATTAATTAGA
          1 TATTAATTAACTATTAATTAGA

               
       1572 TAT
          1 TAT

       1575 AGTATAATAG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47


Consensus pattern (22 bp):   
TATTAATTAACTATTAATTAGA

Found at i:1570 original size:11 final size:11

Alignment explanation


    Indices: 1528--1570  Score: 68
    Period size: 11  Copynumber: 3.9  Consensus size: 11

       1518 ATTTATTCAT

                     * 
       1528 TATTAATTAAC
          1 TATTAATTAGC

                      *
       1539 TATTAATTAGA
          1 TATTAATTAGC

                       
       1550 TATTAATTAGC
          1 TATTAATTAGC

                      
       1561 TATTAATTAG
          1 TATTAATTAG

       1571 ATATAGTATA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  11   29  1.00

ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47


Consensus pattern (11 bp):   
TATTAATTAGC

Found at i:1813 original size:2 final size:2

Alignment explanation


    Indices: 1806--1849  Score: 61
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       1796 GAAATATACA

                                                 *                          
       1806 AT AT AT AT AT AT AT AT AT AT AT AT AA AT CAT AT AT AT GAT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT

       1850 CATTTTTTTT


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
   2   34  0.89
   3    4  0.11

ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:3313 original size:14 final size:14

Alignment explanation


    Indices: 3294--3323  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       3284 ATGAGGAATA

                          
       3294 TATTTATATAAATT
          1 TATTTATATAAATT

                          
       3308 TATTTATATAAATT
          1 TATTTATATAAATT

              
       3322 TA
          1 TA

       3324 AAAATAACCC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (14 bp):   
TATTTATATAAATT

Found at i:4799 original size:27 final size:27

Alignment explanation


    Indices: 4767--4830  Score: 110
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       4757 ATTTCTGAAA

                                     * 
       4767 AACAAGGGAAATGGACAATTAAAAAGG
          1 AACAAGGGAAATGGACAATTAAAAAAG

                                       
       4794 AACAAGGGAAATGGACAATTAAAAAAG
          1 AACAAGGGAAATGGACAATTAAAAAAG

                      
       4821 AACAGAGGGA
          1 AACA-AGGGA

       4831 GTATTATTTA


Statistics
Matches: 35,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  27   30  0.86
  28    5  0.14

ACGTcount: A:0.56, C:0.08, G:0.27, T:0.09


Consensus pattern (27 bp):   
AACAAGGGAAATGGACAATTAAAAAAG
Done.