Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008940.1 Corchorus capsularis cultivar CVL-1 contig08961, 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: 22007
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:5454 original size:3 final size:3

Alignment explanation


    Indices: 5446--5478  Score: 57
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       5436 TAGGTTGTGT

                                                       
       5446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT

       5479 TATATTGATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3   26  0.90
   4    3  0.10

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:6880 original size:13 final size:13

Alignment explanation


    Indices: 6862--6894  Score: 50
    Period size: 12  Copynumber: 2.5  Consensus size: 13

       6852 CTCAAAAATT

                         
       6862 AAGAAAAAAGAAG
          1 AAGAAAAAAGAAG

                         
       6875 AAG-AAAAAGAAG
          1 AAGAAAAAAGAAG

                    
       6887 AGAGAAAA
          1 A-AGAAAA

       6895 TGTAGTATTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  12   10  0.56
  13    5  0.28
  14    3  0.17

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (13 bp):   
AAGAAAAAAGAAG

Found at i:6881 original size:12 final size:13

Alignment explanation


    Indices: 6866--6894  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       6856 AAAATTAAGA

                         
       6866 AAAAAGAAGA-AG
          1 AAAAAGAAGAGAG

                         
       6878 AAAAAGAAGAGAG
          1 AAAAAGAAGAGAG

                
       6891 AAAA
          1 AAAA

       6895 TGTAGTATTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   10  0.62
  13    6  0.38

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (13 bp):   
AAAAAGAAGAGAG

Found at i:8302 original size:40 final size:40

Alignment explanation


    Indices: 8241--8445  Score: 249
    Period size: 40  Copynumber: 5.0  Consensus size: 40

       8231 AATCAAAAGA

                                                     
       8241 AAGTCTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
          1 AAGT-TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC

                           *                    *    
       8282 AAGTGTTTTT-AAAGATTTCAATTTAGGGAAAGATCTCATC
          1 AAGT-TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC

                                                       
       8322 AAGTTTTTTTTCCAAAGTTTTCAATTTAGGGAAAGATCCCATC
          1 AAG--TTTTTT-CAAAGTTTTCAATTTAGGGAAAGATCCCATC

                                                 *  
       8365 AAG-TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCGTC
          1 AAGTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC

                          *          *         *       
       8404 -AGCTTTGGTTT--TAGTTTTCAATCTAGGGAAAGTTCCCATC
          1 AAG-TTT--TTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC

              
       8444 AA
          1 AA

       8446 AAAGTTTTTT


Statistics
Matches: 145,  Mismatches: 10, Indels: 18
        0.84            0.06        0.10

Matches are distributed among these distances:
  38    2  0.01
  39   30  0.21
  40   63  0.43
  41   15  0.10
  42    4  0.03
  43   31  0.21

ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38


Consensus pattern (40 bp):   
AAGTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC

Found at i:8343 original size:83 final size:81

Alignment explanation


    Indices: 8246--8445  Score: 273
    Period size: 82  Copynumber: 2.5  Consensus size: 81

       8236 AAAGAAAGTC

                                                         *                   
       8246 TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTGTTTTTAAAGATTTCAATTTAGGGA
          1 TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGT-TTTTCAAAGATTTCAATTTAGGGA

                             
       8311 AAGATCTCATCAAGTTT
         65 AAGATCTCATCAAGTTT

                                                              *              
       8328 TTTTTCCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTCAAAGTTTTCAATTTAGGGA
          1 TTTTT-CAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTCAAAGATTTCAATTTAGGGA

                  * *         
       8393 AAGATCCCGTC-AGCTTT
         65 AAGATCTCATCAAG-TTT

             *                 *         *         
       8410 GGTTTT---AGTTTTCAATCTAGGGAAAGTTCCCATCAA
          1 -TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAA

       8446 AAAGTTTTTT


Statistics
Matches: 108,  Mismatches: 7, Indels: 9
        0.87            0.06        0.07

Matches are distributed among these distances:
  79   28  0.26
  81    2  0.02
  82   39  0.36
  83   39  0.36

ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38


Consensus pattern (81 bp):   
TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTCAAAGATTTCAATTTAGGGAA
AGATCTCATCAAGTTT

Found at i:20835 original size:1 final size:1

Alignment explanation


    Indices: 20829--20867  Score: 60
    Period size: 1  Copynumber: 39.0  Consensus size: 1

      20819 TCATGTAAGG

                                     **            
      20829 TTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      20868 GGGACAATAG


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95


Consensus pattern (1 bp):   
T

Done.