Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014255.1 Corchorus capsularis cultivar CVL-1 contig14276, 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: 17508
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:6729 original size:30 final size:29

Alignment explanation


    Indices: 6661--6729  Score: 84
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       6651 TACACAAGAT

                                 *   ** *
       6661 AGTCAAATAAGCCCCTGAACTTTTATTAC
          1 AGTCAAATAAGCCCCTGAACTCTTAGAAA

              *                          
       6690 AGCCAAATAAGCCCCTGAACTCTTAGAAA
          1 AGTCAAATAAGCCCCTGAACTCTTAGAAA

                       
       6719 ATGTCAAATAA
          1 A-GTCAAATAA

       6730 ACCATTTTTC


Statistics
Matches: 33,  Mismatches: 6, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  29   25  0.76
  30    8  0.24

ACGTcount: A:0.41, C:0.23, G:0.12, T:0.25


Consensus pattern (29 bp):   
AGTCAAATAAGCCCCTGAACTCTTAGAAA

Found at i:7989 original size:29 final size:30

Alignment explanation


    Indices: 7933--8002  Score: 99
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       7923 GTTAGAAAAA

                           **             
       7933 GGGCTTATTTGGCTTTTTCTAAGAGTTCAG
          1 GGGCTTATTTGGCTTAATCTAAGAGTTCAG

                                           
       7963 GGGCTTATTTGGCTGTAAT-TAA-AGTTCAG
          1 GGGCTTATTTGGCT-TAATCTAAGAGTTCAG

                       
       7992 GGGCTTATTTG
          1 GGGCTTATTTG

       8003 ATCGTCTTGT


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  29   18  0.49
  30   17  0.46
  31    2  0.05

ACGTcount: A:0.19, C:0.11, G:0.29, T:0.41


Consensus pattern (30 bp):   
GGGCTTATTTGGCTTAATCTAAGAGTTCAG

Found at i:8612 original size:2 final size:2

Alignment explanation


    Indices: 8605--8642  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       8595 TGAGAGGTAA

                                                    *  *            
       8605 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       8643 GACATGACAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:11034 original size:97 final size:97

Alignment explanation


    Indices: 10912--11107  Score: 374
    Period size: 97  Copynumber: 2.0  Consensus size: 97

      10902 GATGGAAAGT

                                                                             
      10912 CATTCTATTAATCTCATGGGTCAAGGAGCTGGAAAGAAACTCAAGCCTAAGACCAAGAAGTTTAA
          1 CATTCTATTAATCTCATGGGTCAAGGAGCTGGAAAGAAACTCAAGCCTAAGACCAAGAAGTTTAA

                                            
      10977 GAAGAAAAAGATGTCTGATAATGCACCTCAGA
         66 GAAGAAAAAGATGTCTGATAATGCACCTCAGA

                                                *        *                   
      11009 CATTCTATTAATCTCATGGGTCAAGGAGCTGGAAAGGAACTCAAGTCTAAGACCAAGAAGTTTAA
          1 CATTCTATTAATCTCATGGGTCAAGGAGCTGGAAAGAAACTCAAGCCTAAGACCAAGAAGTTTAA

                                            
      11074 GAAGAAAAAGATGTCTGATAATGCACCTCAGA
         66 GAAGAAAAAGATGTCTGATAATGCACCTCAGA

              
      11106 CA
          1 CA

      11108 GCTCAGAAGA


Statistics
Matches: 97,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  97   97  1.00

ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22


Consensus pattern (97 bp):   
CATTCTATTAATCTCATGGGTCAAGGAGCTGGAAAGAAACTCAAGCCTAAGACCAAGAAGTTTAA
GAAGAAAAAGATGTCTGATAATGCACCTCAGA

Found at i:17485 original size:13 final size:13

Alignment explanation


    Indices: 17467--17493  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      17457 GCAGACTCCA

                         
      17467 TATATGGGTGTAG
          1 TATATGGGTGTAG

                         
      17480 TATATGGGTGTAG
          1 TATATGGGTGTAG

             
      17493 T
          1 T

      17494 TATTACAACC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41


Consensus pattern (13 bp):   
TATATGGGTGTAG
Done.