Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011275.1 Corchorus capsularis cultivar CVL-1 contig11296, 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: 30284
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:2284 original size:15 final size:15

Alignment explanation


    Indices: 2264--2297  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       2254 AAAACAACTT

                            
       2264 ATAAAACAAGTTA-TA
          1 ATAAAACAA-TTAGTA

                           
       2279 ATAAAACAATTAGTA
          1 ATAAAACAATTAGTA

                
       2294 ATAA
          1 ATAA

       2298 TAAATCCAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    3  0.17
  15   15  0.83

ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26


Consensus pattern (15 bp):   
ATAAAACAATTAGTA

Found at i:5070 original size:6 final size:6

Alignment explanation


    Indices: 5059--5087  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       5049 AAGCATTAAA

                                             
       5059 AAACAT AAACAT AAACAT AAACAT AAACA
          1 AAACAT AAACAT AAACAT AAACAT AAACA

       5088 AGTCCTTGGC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14


Consensus pattern (6 bp):   
AAACAT

Found at i:6470 original size:25 final size:26

Alignment explanation


    Indices: 6441--6491  Score: 68
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       6431 AATACCAATT

                               *      
       6441 ATAAAGAAAAAC-AATTAATCTAAAA
          1 ATAAAGAAAAACAAATTAAACTAAAA

                   *                  
       6466 ATAAAGATAAACTAAATTAAACTAAA
          1 ATAAAGAAAAAC-AAATTAAACTAAA

       6492 GTTATGTCAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  25   11  0.50
  27   11  0.50

ACGTcount: A:0.67, C:0.08, G:0.04, T:0.22


Consensus pattern (26 bp):   
ATAAAGAAAAACAAATTAAACTAAAA

Found at i:13147 original size:16 final size:16

Alignment explanation


    Indices: 13126--13158  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      13116 CTATGGTATA

                             
      13126 GTGGACA-AAAGAGATT
          1 GTGGACATAAAGA-ATT

                            
      13142 GTGGACATAAAGAATT
          1 GTGGACATAAAGAATT

             
      13158 G
          1 G

      13159 CACTACTACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   11  0.69
  17    5  0.31

ACGTcount: A:0.42, C:0.06, G:0.30, T:0.21


Consensus pattern (16 bp):   
GTGGACATAAAGAATT

Found at i:24047 original size:20 final size:20

Alignment explanation


    Indices: 24005--24048  Score: 61
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      23995 AATGAATATT

                      *     * * 
      24005 AAAGGATTTTTTTAAAGTTA
          1 AAAGGATTTTATTAAAATGA

                                
      24025 AAAGGATTTTATTAAAATGA
          1 AAAGGATTTTATTAAAATGA

                
      24045 AAAG
          1 AAAG

      24049 CAAGTTGCTA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36


Consensus pattern (20 bp):   
AAAGGATTTTATTAAAATGA

Found at i:29647 original size:16 final size:16

Alignment explanation


    Indices: 29626--29658  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      29616 CTATGGTATA

                             
      29626 GTGGACA-AAAGAGATT
          1 GTGGACATAAAGA-ATT

                            
      29642 GTGGACATAAAGAATT
          1 GTGGACATAAAGAATT

             
      29658 G
          1 G

      29659 CACTACTGCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   11  0.69
  17    5  0.31

ACGTcount: A:0.42, C:0.06, G:0.30, T:0.21


Consensus pattern (16 bp):   
GTGGACATAAAGAATT

Found at i:30264 original size:11 final size:11

Alignment explanation


    Indices: 30248--30282  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      30238 TTGACAACGC

                       
      30248 AACAAAAACAA
          1 AACAAAAACAA

                     * 
      30259 AACAAAAACGA
          1 AACAAAAACAA

                       
      30270 AACAAAAACAA
          1 AACAAAAACAA

              
      30281 AA
          1 AA

      30283 AA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA
Done.