Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005297.1 Corchorus capsularis cultivar CVL-1 contig05315, 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: 10587
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:375 original size:4 final size:4

Alignment explanation


    Indices: 362--407  Score: 85
    Period size: 4  Copynumber: 11.8  Consensus size: 4

        352 TTATTATTAT

                                                                      
        362 TATC -ATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
          1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT

        408 ATATATATAT


Statistics
Matches: 41,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   3    3  0.07
   4   38  0.93

ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50


Consensus pattern (4 bp):   
TATC

Found at i:461 original size:2 final size:2

Alignment explanation


    Indices: 405--441  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

        395 TCTATCTATC

                                                                   
        405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        442 GAGAAGAAAT


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

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:469 original size:40 final size:40

Alignment explanation


    Indices: 414--495  Score: 128
    Period size: 40  Copynumber: 2.0  Consensus size: 40

        404 CTATATATAT

                             * * *   *              
        414 ATATATATATATATATATATATATATATGAGAAGAAATGC
          1 ATATATATATATATATAAAAACATAAATGAGAAGAAATGC

                                                    
        454 ATATATATATATATATAAAAACATAAATGAGAAGAAATGC
          1 ATATATATATATATATAAAAACATAAATGAGAAGAAATGC

              
        494 AT
          1 AT

        496 TATTTTGATC


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  40   38  1.00

ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33


Consensus pattern (40 bp):   
ATATATATATATATATAAAAACATAAATGAGAAGAAATGC

Found at i:8598 original size:18 final size:18

Alignment explanation


    Indices: 8577--8645  Score: 57
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       8567 GGCGCAGCCT

                              
       8577 CCACCATACCCTCCACGA
          1 CCACCATACCCTCCACGA

                 *     *  *  *
       8595 CCACCGTACCCACCGCGC
          1 CCACCATACCCTCCACGA

              *     *  *     *
       8613 CCTCCATAGCCGCCACGG
          1 CCACCATACCCTCCACGA

                 *         
       8631 CCACCGTACCCTCCA
          1 CCACCATACCCTCCA

       8646 TAACCTCCAC


Statistics
Matches: 37,  Mismatches: 14, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
  18   37  1.00

ACGTcount: A:0.20, C:0.57, G:0.13, T:0.10


Consensus pattern (18 bp):   
CCACCATACCCTCCACGA

Found at i:8634 original size:27 final size:27

Alignment explanation


    Indices: 8612--8677  Score: 105
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       8602 ACCCACCGCG

                     *                 
       8612 CCCTCCATAGCCGCCACGGCCACCGTA
          1 CCCTCCATAACCGCCACGGCCACCGTA

                        *     *        
       8639 CCCTCCATAACCTCCACGTCCACCGTA
          1 CCCTCCATAACCGCCACGGCCACCGTA

                        
       8666 CCCTCCATAACC
          1 CCCTCCATAACC

       8678 CCCTTGGTTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   36  1.00

ACGTcount: A:0.21, C:0.53, G:0.11, T:0.15


Consensus pattern (27 bp):   
CCCTCCATAACCGCCACGGCCACCGTA

Found at i:9875 original size:2 final size:2

Alignment explanation


    Indices: 9868--9895  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       9858 TAACAATGAA

                                                     
       9868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9896 TGTCACGCCC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Done.