Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014800.1 Corchorus capsularis cultivar CVL-1 contig14821, 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: 4477
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35


Found at i:3556 original size:12 final size:13

Alignment explanation


    Indices: 3515--3560  Score: 67
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       3505 AATTATTGTT

                         
       3515 TGCTTTAGTAATC
          1 TGCTTTAGTAATC

                   *    *
       3528 TGCTTTATTAATT
          1 TGCTTTAGTAATC

                         
       3541 TGCTTTA-TAATC
          1 TGCTTTAGTAATC

                    
       3553 TGCTTTAG
          1 TGCTTTAG

       3561 ATTTAGATTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  12   11  0.38
  13   18  0.62

ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52


Consensus pattern (13 bp):   
TGCTTTAGTAATC

Found at i:3567 original size:6 final size:6

Alignment explanation


    Indices: 3556--3582  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       3546 TATAATCTGC

                                           
       3556 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       3583 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:3631 original size:14 final size:15

Alignment explanation


    Indices: 3603--3635  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3593 ATTTTTAGTT

                    *      
       3603 TAATTGTTTTCTTCA
          1 TAATTGTTATCTTCA

                           
       3618 TAATTGTTAT-TTCA
          1 TAATTGTTATCTTCA

                
       3632 TAAT
          1 TAAT

       3636 CCCTGTTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58


Consensus pattern (15 bp):   
TAATTGTTATCTTCA

Found at i:4063 original size:40 final size:42

Alignment explanation


    Indices: 3986--4063  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 42

       3976 GATTTTTATT

                     *         *          *           
       3986 TAAAAAAAATTAATTTTTCTTTTTCCGTTTTTCCTTTTTAAA
          1 TAAAAAAAAATAATTTTTCATTTTCCGTTTCTCCTTTTTAAA

                                     *      *     
       4028 TAAAAAAAAAT-ATTTTT-ATTTTCTGTTTCTGCTTTT
          1 TAAAAAAAAATAATTTTTCATTTTCCGTTTCTCCTTTT

       4064 AATTTTTTTA


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  40   15  0.48
  41    6  0.19
  42   10  0.32

ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55


Consensus pattern (42 bp):   
TAAAAAAAAATAATTTTTCATTTTCCGTTTCTCCTTTTTAAA
Done.