Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020684.1 Corchorus olitorius cultivar O-4 contig20717, 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: 30471
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:6354 original size:21 final size:21

Alignment explanation


    Indices: 6324--6363  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       6314 TGCCAGTTTG

                                  
       6324 CCACTAATTTCTT-CAAAAAAA
          1 CCACTAATTT-TTGCAAAAAAA

                 *             
       6345 CCACTTATTTTTGCAAAAA
          1 CCACTAATTTTTGCAAAAA

       6364 CATGTTTTCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    2  0.12
  21   15  0.88

ACGTcount: A:0.42, C:0.23, G:0.03, T:0.33


Consensus pattern (21 bp):   
CCACTAATTTTTGCAAAAAAA

Found at i:8189 original size:63 final size:63

Alignment explanation


    Indices: 8090--8214  Score: 232
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       8080 GTGCTGACAA

                       *             *                                     
       8090 TTTCAACTCCTTTATTAATTCCTTTTCAATTTTTCCATTTCTTCTCCTTGGGTCAAAAACAGT
          1 TTTCAACTCCTCTATTAATTCCTTTACAATTTTTCCATTTCTTCTCCTTGGGTCAAAAACAGT

                                                                          
       8153 TTTCAACTCCTCTATTAATTCCTTTACAATTTTTCCATTTCTTCTCCTTGGGTCAAAAACAG
          1 TTTCAACTCCTCTATTAATTCCTTTACAATTTTTCCATTTCTTCTCCTTGGGTCAAAAACAG

       8215 GTAGGAAGAG


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  63   60  1.00

ACGTcount: A:0.23, C:0.25, G:0.06, T:0.46


Consensus pattern (63 bp):   
TTTCAACTCCTCTATTAATTCCTTTACAATTTTTCCATTTCTTCTCCTTGGGTCAAAAACAGT

Found at i:14091 original size:30 final size:30

Alignment explanation


    Indices: 14055--14138  Score: 168
    Period size: 30  Copynumber: 2.8  Consensus size: 30

      14045 GTTAATAAGC

                                          
      14055 CATTAAAATTTGAGGGTATAAGAGAAAAAT
          1 CATTAAAATTTGAGGGTATAAGAGAAAAAT

                                          
      14085 CATTAAAATTTGAGGGTATAAGAGAAAAAT
          1 CATTAAAATTTGAGGGTATAAGAGAAAAAT

                                    
      14115 CATTAAAATTTGAGGGTATAAGAG
          1 CATTAAAATTTGAGGGTATAAGAG

      14139 GAAAGTCAAG


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   54  1.00

ACGTcount: A:0.48, C:0.04, G:0.21, T:0.27


Consensus pattern (30 bp):   
CATTAAAATTTGAGGGTATAAGAGAAAAAT

Found at i:15561 original size:45 final size:42

Alignment explanation


    Indices: 15510--15603  Score: 127
    Period size: 45  Copynumber: 2.2  Consensus size: 42

      15500 AGCAATATTT

                    *                 *                  
      15510 AATATTAGTTTTATTTTAATGAATTATCTAGAGATAGAGGAGTAG
          1 AATATTAGCTTTATTTTAATGAATTACCTAGAGAT---GGAGTAG

                             *                        
      15555 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
          1 AATATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGTAG

                    
      15597 AAT-TTAG
          1 AATATTAG

      15604 GTAATGCACT


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  41    4  0.09
  42   10  0.22
  45   32  0.70

ACGTcount: A:0.36, C:0.04, G:0.20, T:0.39


Consensus pattern (42 bp):   
AATATTAGCTTTATTTTAATGAATTACCTAGAGATGGAGTAG

Found at i:17987 original size:27 final size:24

Alignment explanation


    Indices: 17944--17993  Score: 64
    Period size: 27  Copynumber: 2.0  Consensus size: 24

      17934 TGGAACAATT

                             *      
      17944 ATAAAGAAAATAATTAATCTAAAA
          1 ATAAAGAAAATAATTAAACTAAAA

                                      
      17968 ATAAAGCAAAACTAAATTAAACTAAA
          1 ATAAAG-AAAA-T-AATTAAACTAAA

      17994 TCTATGACAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  24    6  0.27
  25    4  0.18
  26    1  0.05
  27   11  0.50

ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22


Consensus pattern (24 bp):   
ATAAAGAAAATAATTAAACTAAAA

Found at i:18778 original size:19 final size:19

Alignment explanation


    Indices: 18740--18776  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      18730 AATTTTTAAG

                               
      18740 TAAAAATATAATATATAAA
          1 TAAAAATATAATATATAAA

                               
      18759 TAAAAATATAATAT-TAAA
          1 TAAAAATATAATATATAAA

      18777 ATCATTAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA

Found at i:21990 original size:25 final size:27

Alignment explanation


    Indices: 21962--22012  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      21952 ATTTTAATGT

                                        
      21962 TTAAATT-TTATT-T-TTTATTAAAAAA
          1 TTAAATTATTATTATATTT-TTAAAAAA

                                      
      21987 TTAAATTATTATTATATTTTTAAAAA
          1 TTAAATTATTATTATATTTTTAAAAA

      22013 TAAATATAGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  25    7  0.30
  26    5  0.22
  27    8  0.35
  28    3  0.13

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (27 bp):   
TTAAATTATTATTATATTTTTAAAAAA
Done.