Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008630.1 Corchorus capsularis cultivar CVL-1 contig08651, 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: 33642
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:434 original size:34 final size:35

Alignment explanation


    Indices: 367--441  Score: 98
    Period size: 40  Copynumber: 2.0  Consensus size: 35

        357 GACTTTCCGA

                                                    
        367 TACTGAATTCAGGTGAATTGCCTTTTTTTTTTTTTCCTGT
          1 TACTGAATTCAGGTGAATTGCC-----TTTTTTTTCCTGT

                                               
        407 TACTGAATTCAGGTGAATTGCCTTTTTTTT-CTGT
          1 TACTGAATTCAGGTGAATTGCCTTTTTTTTCCTGT

             
        441 T
          1 T

        442 TTCATTTCAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
  34    5  0.14
  35    8  0.23
  40   22  0.63

ACGTcount: A:0.16, C:0.15, G:0.16, T:0.53


Consensus pattern (35 bp):   
TACTGAATTCAGGTGAATTGCCTTTTTTTTCCTGT

Found at i:3403 original size:2 final size:2

Alignment explanation


    Indices: 3396--3447  Score: 95
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       3386 ACAAATTATG

                                        *                                 
       3396 AT AT AT AT AT AT AT AT AT AC 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 AT AT AT AT AT AT AT

                          
       3438 AT AT AT AT AT
          1 AT AT AT AT AT

       3448 CATAACAATT


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   48  1.00

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:10206 original size:13 final size:13

Alignment explanation


    Indices: 10190--10222  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      10180 TTAATGAGTT

                         
      10190 AAATTAATAAAAG
          1 AAATTAATAAAAG

                *        
      10203 AAATGAATAAAAG
          1 AAATTAATAAAAG

                   
      10216 AAATTAA
          1 AAATTAA

      10223 ATTAAATTAA


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

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21


Consensus pattern (13 bp):   
AAATTAATAAAAG

Found at i:12649 original size:27 final size:27

Alignment explanation


    Indices: 12611--12672  Score: 97
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      12601 CCTTTTGTCC

                           *  *        
      12611 CAAACCCAACAACTTTAATACCCCTCT
          1 CAAACCCAACAACTTAAAAACCCCTCT

                                       
      12638 CAAACCCAACAACTTAAAAACCCCTCT
          1 CAAACCCAACAACTTAAAAACCCCTCT

            *       
      12665 TAAACCCA
          1 CAAACCCA

      12673 GAAATTCTCC


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   32  1.00

ACGTcount: A:0.42, C:0.40, G:0.00, T:0.18


Consensus pattern (27 bp):   
CAAACCCAACAACTTAAAAACCCCTCT

Found at i:12956 original size:49 final size:49

Alignment explanation


    Indices: 12884--12982  Score: 135
    Period size: 49  Copynumber: 2.0  Consensus size: 49

      12874 ATTTCAGAAA

                        **                *         *        
      12884 ACACTTACCTCTTTATTGTAATGAAAAAAGCAAAATGCATGGCCAGCTT
          1 ACACTTACCTCTCCATTGTAATGAAAAAAGAAAAATGCATAGCCAGCTT

                  *                   *                  *   
      12933 ACACTTGCCTCTCCATTGTAATGAAAGAAGAAAAATGCATAGCCATCTT
          1 ACACTTACCTCTCCATTGTAATGAAAAAAGAAAAATGCATAGCCAGCTT

             
      12982 A
          1 A

      12983 GCTCTCCCAA


Statistics
Matches: 43,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  49   43  1.00

ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27


Consensus pattern (49 bp):   
ACACTTACCTCTCCATTGTAATGAAAAAAGAAAAATGCATAGCCAGCTT

Found at i:25916 original size:1 final size:1

Alignment explanation


    Indices: 25910--25939  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

      25900 CTCTGGCCCC

                                          
      25910 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      25940 CTTGTGTTTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:29310 original size:2 final size:2

Alignment explanation


    Indices: 29291--29329  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      29281 ATATATGCGC

                   *        *                                         
      29291 AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      29330 GTTTTCACTT


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44


Consensus pattern (2 bp):   
AT

Done.