Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009818.1 Corchorus olitorius cultivar O-4 contig09850, 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: 5962
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--27  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

                                                    
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

         28 GATAAACACA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:324 original size:35 final size:35

Alignment explanation


    Indices: 278--347  Score: 140
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        268 TATCTGTACC

                                               
        278 CCTATAAATGCACACGTGCTTCAATTATATATTGA
          1 CCTATAAATGCACACGTGCTTCAATTATATATTGA

                                               
        313 CCTATAAATGCACACGTGCTTCAATTATATATTGA
          1 CCTATAAATGCACACGTGCTTCAATTATATATTGA

        348 GCAAATGATA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   35  1.00

ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34


Consensus pattern (35 bp):   
CCTATAAATGCACACGTGCTTCAATTATATATTGA

Found at i:572 original size:19 final size:19

Alignment explanation


    Indices: 552--588  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        542 AATTAATTAT

                               
        552 TTTA-ATATTAAATTTTTA
          1 TTTATATATTAAATTTTTA

                       *       
        570 TTTATATATTATATTTTTA
          1 TTTATATATTAAATTTTTA

        589 CTTAAAAATT


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

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (19 bp):   
TTTATATATTAAATTTTTA

Found at i:4451 original size:12 final size:13

Alignment explanation


    Indices: 4432--4477  Score: 58
    Period size: 12  Copynumber: 3.4  Consensus size: 13

       4422 TATATAATAT

                         
       4432 ATATAAATTATAA
          1 ATATAAATTATAA

                         
       4445 A-ATAAATTATAA
          1 ATATAAATTATAA

                           
       4457 ATATAAAATCTATAA
          1 ATAT-AAAT-TATAA

                  
       4472 TATATA
          1 -ATATA

       4478 TATATATACT


Statistics
Matches: 29,  Mismatches: 0, Indels: 6
        0.83            0.00        0.17

Matches are distributed among these distances:
  12   12  0.41
  13    3  0.10
  14    4  0.14
  15    6  0.21
  16    4  0.14

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37


Consensus pattern (13 bp):   
ATATAAATTATAA

Found at i:4478 original size:18 final size:18

Alignment explanation


    Indices: 4421--4479  Score: 59
    Period size: 18  Copynumber: 3.4  Consensus size: 18

       4411 TGGCGCAACA

                    *         
       4421 ATATATAATATATATAA-
          1 ATATATAAAATATATAAT

                        *  *  
       4438 AT-TATAAAATAAATTAT
          1 ATATATAAAATATATAAT

             *         *      
       4455 AAATATAAAATCTATAAT
          1 ATATATAAAATATATAAT

                   
       4473 ATATATA
          1 ATATATA

       4480 TATATACTAG


Statistics
Matches: 32,  Mismatches: 8, Indels: 3
        0.74            0.19        0.07

Matches are distributed among these distances:
  16   11  0.34
  17    3  0.09
  18   18  0.56

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39


Consensus pattern (18 bp):   
ATATATAAAATATATAAT
Done.