Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004907.1 Corchorus capsularis cultivar CVL-1 contig04925, 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: 10049
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33


Found at i:3418 original size:34 final size:34

Alignment explanation


    Indices: 3380--3447  Score: 136
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       3370 TCCAGGAGTC

                                              
       3380 ATGATACTTGCAATACTCCTTGCCTCGTAACTCA
          1 ATGATACTTGCAATACTCCTTGCCTCGTAACTCA

                                              
       3414 ATGATACTTGCAATACTCCTTGCCTCGTAACTCA
          1 ATGATACTTGCAATACTCCTTGCCTCGTAACTCA

       3448 TCAGCATGTG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32


Consensus pattern (34 bp):   
ATGATACTTGCAATACTCCTTGCCTCGTAACTCA

Found at i:5013 original size:90 final size:90

Alignment explanation


    Indices: 4860--5041  Score: 355
    Period size: 90  Copynumber: 2.0  Consensus size: 90

       4850 CATTAAACTC

                                                                             
       4860 ATTTTTGACCTCGTCAAGAGAAATGAGCGTTTCTTGAGACTGATCATCTCCATCAACTCCACTTC
          1 ATTTTTGACCTCGTCAAGAGAAATGAGCGTTTCTTGAGACTGATCATCTCCATCAACTCCACTTC

                     *               
       4925 CACCAGAACTTGACCGTAAGTTCAT
         66 CACCAGAACCTGACCGTAAGTTCAT

                                                                             
       4950 ATTTTTGACCTCGTCAAGAGAAATGAGCGTTTCTTGAGACTGATCATCTCCATCAACTCCACTTC
          1 ATTTTTGACCTCGTCAAGAGAAATGAGCGTTTCTTGAGACTGATCATCTCCATCAACTCCACTTC

                                     
       5015 CACCAGAACCTGACCGTAAGTTCAT
         66 CACCAGAACCTGACCGTAAGTTCAT

              
       5040 AT
          1 AT

       5042 GGTGTTGATT


Statistics
Matches: 91,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  90   91  1.00

ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30


Consensus pattern (90 bp):   
ATTTTTGACCTCGTCAAGAGAAATGAGCGTTTCTTGAGACTGATCATCTCCATCAACTCCACTTC
CACCAGAACCTGACCGTAAGTTCAT

Found at i:5149 original size:17 final size:18

Alignment explanation


    Indices: 5117--5151  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       5107 AGGTAGAAGA

                              
       5117 GTGGCGTGAAAGCCAAAT
          1 GTGGCGTGAAAGCCAAAT

                     *        
       5135 GTGGCGT-AGAGCCAAAT
          1 GTGGCGTGAAAGCCAAAT

       5152 AAAACAAAAA


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

Matches are distributed among these distances:
  17    9  0.56
  18    7  0.44

ACGTcount: A:0.31, C:0.17, G:0.34, T:0.17


Consensus pattern (18 bp):   
GTGGCGTGAAAGCCAAAT

Found at i:9310 original size:18 final size:18

Alignment explanation


    Indices: 9276--9310  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       9266 CTGCCACATC

                       **     
       9276 ATATTTTTTAATTAAAAA
          1 ATATTTTTTAAAAAAAAA

                             
       9294 ATATTTTTTAAAAAAAA
          1 ATATTTTTTAAAAAAAA

       9311 TGAGTCAGGG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (18 bp):   
ATATTTTTTAAAAAAAAA
Done.