Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007054.1 Corchorus capsularis cultivar CVL-1 contig07075, 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: 10107
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33


Found at i:1533 original size:13 final size:12

Alignment explanation


    Indices: 1515--1557  Score: 54
    Period size: 10  Copynumber: 3.7  Consensus size: 12

       1505 ATGAAACGGA

                         
       1515 AAAATAAAGACAT
          1 AAAATAAAG-CAT

                        
       1528 AAAATAAAG-A-
          1 AAAATAAAGCAT

                        
       1538 AAAATAAAGCAT
          1 AAAATAAAGCAT

               *    
       1550 AAACTAAA
          1 AAAATAAA

       1558 TAGCTAAACC


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  10    9  0.33
  11    2  0.07
  12    7  0.26
  13    9  0.33

ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14


Consensus pattern (12 bp):   
AAAATAAAGCAT

Found at i:1540 original size:22 final size:22

Alignment explanation


    Indices: 1513--1557  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 22

       1503 TAATGAAACG

                                   
       1513 GAAAAATAAAGACATAAAATAAA
          1 GAAAAATAAAG-CATAAAATAAA

                             *    
       1536 GAAAAATAAAGCATAAACTAAA
          1 GAAAAATAAAGCATAAAATAAA

       1558 TAGCTAAACC


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  22   10  0.48
  23   11  0.52

ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13


Consensus pattern (22 bp):   
GAAAAATAAAGCATAAAATAAA

Found at i:8212 original size:11 final size:11

Alignment explanation


    Indices: 8196--8225  Score: 60
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       8186 ATAACACAAA

                       
       8196 TCACATACTTT
          1 TCACATACTTT

                       
       8207 TCACATACTTT
          1 TCACATACTTT

                    
       8218 TCACATAC
          1 TCACATAC

       8226 CACATAATTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40


Consensus pattern (11 bp):   
TCACATACTTT

Found at i:8273 original size:17 final size:17

Alignment explanation


    Indices: 8247--8281  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       8237 CTTTTCTACC

                 *           
       8247 TTTCTTTAGTTTTAGGT
          1 TTTCTCTAGTTTTAGGT

                             
       8264 TTTCTCTAGTTTTAGGT
          1 TTTCTCTAGTTTTAGGT

             
       8281 T
          1 T

       8282 AAGGGTGTCG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63


Consensus pattern (17 bp):   
TTTCTCTAGTTTTAGGT
Done.