Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014168.1 Corchorus capsularis cultivar CVL-1 contig14189, 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: 12991
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:176 original size:26 final size:26

Alignment explanation


    Indices: 121--179  Score: 68
    Period size: 27  Copynumber: 2.2  Consensus size: 26

        111 ACCCTCTAAC

                                *      
        121 AAAAAAGTCAGAGTAGTTCCTCAAAGA
          1 AAAAAAGTCAGAGTAGTT-CGCAAAGA

                                        
        148 AAAAAAGTCAGAGTAGATT-GCAATA-A
          1 AAAAAAGTCAGAGTAG-TTCGCAA-AGA

                  
        174 AAAAAA
          1 AAAAAA

        180 TCATATTGTA


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  26   10  0.34
  27   17  0.59
  28    2  0.07

ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17


Consensus pattern (26 bp):   
AAAAAAGTCAGAGTAGTTCGCAAAGA

Found at i:3259 original size:2 final size:2

Alignment explanation


    Indices: 3252--3290  Score: 53
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       3242 ATCTTACTAC

                           *                                   *       
       3252 TA TA TA TA TA CA TA TA TA TA TA TA TA T- TA TA TA AA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3291 AAATCACGAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:3555 original size:14 final size:15

Alignment explanation


    Indices: 3530--3559  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       3520 TAATAATTAT

                           
       3530 TTTTAGATTATAATA
          1 TTTTAGATTATAATA

                           
       3545 TTTTA-ATTATAATA
          1 TTTTAGATTATAATA

             
       3559 T
          1 T

       3560 CATTATTTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   10  0.67
  15    5  0.33

ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57


Consensus pattern (15 bp):   
TTTTAGATTATAATA
Done.