Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015758.1 Corchorus capsularis cultivar CVL-1 contig15779, 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: 9968
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:346 original size:13 final size:13

Alignment explanation


    Indices: 328--362  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

        318 TTAATTATTG

                         
        328 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

                         
        341 TTTGCTTTATTAA
          1 TTTGCTTTATTAA

             *       
        354 TCTGCTTTA
          1 TTTGCTTTA

        363 GATTTAGATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60


Consensus pattern (13 bp):   
TTTGCTTTATTAA

Found at i:370 original size:6 final size:6

Alignment explanation


    Indices: 359--391  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

        349 ATTAATCTGC

                                                  
        359 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

        392 GCTTTGCTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55


Consensus pattern (6 bp):   
TTTAGA

Found at i:6713 original size:13 final size:14

Alignment explanation


    Indices: 6689--6718  Score: 53
    Period size: 13  Copynumber: 2.2  Consensus size: 14

       6679 GAATTAGAAT

                          
       6689 TAAATCTAACTAAG
          1 TAAATCTAACTAAG

                          
       6703 TAAAT-TAACTAAG
          1 TAAATCTAACTAAG

               
       6716 TAA
          1 TAA

       6719 GCAATCAAGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.69
  14    5  0.31

ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30


Consensus pattern (14 bp):   
TAAATCTAACTAAG

Found at i:8028 original size:19 final size:18

Alignment explanation


    Indices: 7995--8030  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7985 TTGAAATAAT

                              
       7995 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       8013 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       8031 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:8232 original size:20 final size:21

Alignment explanation


    Indices: 8194--8232  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       8184 TAGAAAATAA

                          *      
       8194 GGTAAAAATGCATATAAAAGT
          1 GGTAAAAATGCATAGAAAAGT

                      *        
       8215 GGTAAAAA-GTATAGAAAA
          1 GGTAAAAATGCATAGAAAA

       8233 ATAGCCATAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    8  0.50
  21    8  0.50

ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21


Consensus pattern (21 bp):   
GGTAAAAATGCATAGAAAAGT

Found at i:8397 original size:18 final size:19

Alignment explanation


    Indices: 8374--8414  Score: 75
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       8364 ATTGATAAGG

                               
       8374 TATAAATTGATCCTCGAT-
          1 TATAAATTGATCCTCGATA

                               
       8392 TATAAATTGATCCTCGATA
          1 TATAAATTGATCCTCGATA

                
       8411 TATA
          1 TATA

       8415 TACACATGAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  18   18  0.82
  19    4  0.18

ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39


Consensus pattern (19 bp):   
TATAAATTGATCCTCGATA
Done.