Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006716.1 Corchorus capsularis cultivar CVL-1 contig06737, 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: 26649
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34


Found at i:6306 original size:26 final size:26

Alignment explanation


    Indices: 6273--6332  Score: 113
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       6263 AATAAACGAC

                                      
       6273 AAAA-TAAGTAAGTCTTCAAAAACTA
          1 AAAACTAAGTAAGTCTTCAAAAACTA

                                      
       6298 AAAACTAAGTAAGTCTTCAAAAACTA
          1 AAAACTAAGTAAGTCTTCAAAAACTA

                     
       6324 AAAACTAAG
          1 AAAACTAAG

       6333 ACAAGCTCTG


Statistics
Matches: 34,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  25    4  0.12
  26   30  0.88

ACGTcount: A:0.57, C:0.13, G:0.08, T:0.22


Consensus pattern (26 bp):   
AAAACTAAGTAAGTCTTCAAAAACTA

Found at i:9583 original size:19 final size:20

Alignment explanation


    Indices: 9542--9585  Score: 56
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       9532 CCCTTATGTG

                  *             
       9542 TAATTATTTTATTTGACTTA
          1 TAATTAATTTATTTGACTTA

                                 
       9562 TAATTAATTT-TTTG-CTTGA
          1 TAATTAATTTATTTGACTT-A

                 
       9581 TAATT
          1 TAATT

       9586 GTAACTATTG


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

Matches are distributed among these distances:
  18    3  0.14
  19   10  0.45
  20    9  0.41

ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59


Consensus pattern (20 bp):   
TAATTAATTTATTTGACTTA

Found at i:10015 original size:19 final size:20

Alignment explanation


    Indices: 9974--10017  Score: 56
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       9964 CCCCAATGTG

                  *             
       9974 TAATTATTTTATTTGACTTA
          1 TAATTAATTTATTTGACTTA

                                 
       9994 TAATTAATTT-TTTG-CTTGA
          1 TAATTAATTTATTTGACTT-A

                 
      10013 TAATT
          1 TAATT

      10018 GTAACTCTTG


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

Matches are distributed among these distances:
  18    3  0.14
  19   10  0.45
  20    9  0.41

ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59


Consensus pattern (20 bp):   
TAATTAATTTATTTGACTTA

Found at i:10136 original size:16 final size:16

Alignment explanation


    Indices: 10115--10150  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      10105 AAATGGGCTG

                    *       
      10115 GTTAGGTTGGATTTGA
          1 GTTAGGTTAGATTTGA

                      *     
      10131 GTTAGGTTAGTTTTGA
          1 GTTAGGTTAGATTTGA

                
      10147 GTTA
          1 GTTA

      10151 TAAAGGTTCA


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

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.19, C:0.00, G:0.33, T:0.47


Consensus pattern (16 bp):   
GTTAGGTTAGATTTGA

Found at i:12412 original size:2 final size:2

Alignment explanation


    Indices: 12401--12435  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      12391 CTTAGTATCA

                                                          *      
      12401 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      12436 CGACTTAGTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:26225 original size:14 final size:14

Alignment explanation


    Indices: 26198--26243  Score: 60
    Period size: 14  Copynumber: 3.4  Consensus size: 14

      26188 AATGAAAAAA

                          
      26198 TATC-CCTTTTCTC
          1 TATCTCCTTTTCTC

                           
      26211 TATCT-CTTGTTCTC
          1 TATCTCCTT-TTCTC

             *            
      26225 TCTCTCCTTTTCTC
          1 TATCTCCTTTTCTC

                 
      26239 TATCT
          1 TATCT

      26244 TTTCCCTTCC


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  13    7  0.25
  14   18  0.64
  15    3  0.11

ACGTcount: A:0.07, C:0.35, G:0.02, T:0.57


Consensus pattern (14 bp):   
TATCTCCTTTTCTC
Done.