Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006095.1 Corchorus capsularis cultivar CVL-1 contig06113, 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: 26294
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:235 original size:23 final size:22

Alignment explanation


    Indices: 205--248  Score: 79
    Period size: 23  Copynumber: 2.0  Consensus size: 22

        195 CTTAAAAAGC

                                   
        205 TGTTATAAAATTTGATTGAGAAT
          1 TGTTATAAAATTTGATT-AGAAT

                                 
        228 TGTTATAAAATTTGATTAGAA
          1 TGTTATAAAATTTGATTAGAA

        249 GACACTTCTG


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

Matches are distributed among these distances:
  22    4  0.19
  23   17  0.81

ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43


Consensus pattern (22 bp):   
TGTTATAAAATTTGATTAGAAT

Found at i:4397 original size:12 final size:12

Alignment explanation


    Indices: 4380--4404  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       4370 GCAAATCTTT

                        
       4380 TTTGGAAAGGAG
          1 TTTGGAAAGGAG

                        
       4392 TTTGGAAAGGAG
          1 TTTGGAAAGGAG

             
       4404 T
          1 T

       4405 ATGTAAAGTC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28


Consensus pattern (12 bp):   
TTTGGAAAGGAG

Found at i:9856 original size:33 final size:33

Alignment explanation


    Indices: 9814--9881  Score: 136
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       9804 ATAATAAGTA

                                             
       9814 TAATATTTGTTTTTATGATTGGGGTCAACTAGT
          1 TAATATTTGTTTTTATGATTGGGGTCAACTAGT

                                             
       9847 TAATATTTGTTTTTATGATTGGGGTCAACTAGT
          1 TAATATTTGTTTTTATGATTGGGGTCAACTAGT

              
       9880 TA
          1 TA

       9882 TTTACTCTTG


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

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.25, C:0.06, G:0.21, T:0.49


Consensus pattern (33 bp):   
TAATATTTGTTTTTATGATTGGGGTCAACTAGT

Found at i:15758 original size:13 final size:13

Alignment explanation


    Indices: 15740--15767  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      15730 CTAATCTCTC

                         
      15740 TTCTTTTTCTTTT
          1 TTCTTTTTCTTTT

                         
      15753 TTCTTTTTCTTTT
          1 TTCTTTTTCTTTT

              
      15766 TT
          1 TT

      15768 TCTACTTAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (13 bp):   
TTCTTTTTCTTTT

Found at i:17943 original size:28 final size:27

Alignment explanation


    Indices: 17888--17944  Score: 71
    Period size: 28  Copynumber: 2.0  Consensus size: 27

      17878 TGTTATTTAT

                                *       
      17888 ATAAAAAGAGGGTTTTTTGGCAAAAAAA
          1 ATAAAAAGAGGGTTTTTT-GAAAAAAAA

                                         
      17916 ATAAAAAGAGGGTTTTATT-AAAATAAAA
          1 ATAAAAAGAGGGTTTT-TTGAAAA-AAAA

             
      17944 A
          1 A

      17945 GAATTAGTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
  27    3  0.12
  28   21  0.81
  29    2  0.08

ACGTcount: A:0.54, C:0.02, G:0.18, T:0.26


Consensus pattern (27 bp):   
ATAAAAAGAGGGTTTTTTGAAAAAAAA

Found at i:18900 original size:29 final size:32

Alignment explanation


    Indices: 18859--18917  Score: 97
    Period size: 29  Copynumber: 1.9  Consensus size: 32

      18849 ATTTTGCCTT

                                            
      18859 TTTTTTTTTAAGA-G-A-AAATTTTGGGCAGA
          1 TTTTTTTTTAAGAGGAAGAAATTTTGGGCAGA

                                          
      18888 TTTTTTTTTAAGAGGAAGAAATTTTGGGCA
          1 TTTTTTTTTAAGAGGAAGAAATTTTGGGCA

      18918 AATGGGCCTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  29   13  0.48
  30    1  0.04
  31    1  0.04
  32   12  0.44

ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44


Consensus pattern (32 bp):   
TTTTTTTTTAAGAGGAAGAAATTTTGGGCAGA

Found at i:19109 original size:22 final size:23

Alignment explanation


    Indices: 19078--19129  Score: 79
    Period size: 22  Copynumber: 2.3  Consensus size: 23

      19068 GGGCAGTGGG

                 *                 
      19078 TTAATGTTTATTTACTTTCT-AA
          1 TTAATTTTTATTTACTTTCTCAA

                              *    
      19100 TTAATTTTTATTTACTTTTTCAA
          1 TTAATTTTTATTTACTTTCTCAA

                   
      19123 TTAATTT
          1 TTAATTT

      19130 CTTAATTTCA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  22   18  0.67
  23    9  0.33

ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63


Consensus pattern (23 bp):   
TTAATTTTTATTTACTTTCTCAA
Done.