Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010577.1 Corchorus capsularis cultivar CVL-1 contig10598, 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: 6544
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30


Found at i:1722 original size:48 final size:49

Alignment explanation


    Indices: 1664--1767  Score: 147
    Period size: 48  Copynumber: 2.1  Consensus size: 49

       1654 TAAATAAAAA

                 *         **                                
       1664 TTAATTCTTGGTGGTTTTATTTTCAAATGGGTAGTTTTTATTTTTG-TT
          1 TTAATCCTTGGTGGTCATATTTTCAAATGGGTAGTTTTTATTTTTGCTT

                        *          *                          
       1712 TTAATCCTTGGTTGTCATATTTTGAAATGGGTAGTTTTTATTTTTGCTTT
          1 TTAATCCTTGGTGGTCATATTTTCAAATGGGTAGTTTTTATTTTTGC-TT

                  
       1762 TTAATC
          1 TTAATC

       1768 TTTTAAAAAT


Statistics
Matches: 49,  Mismatches: 5, Indels: 2
        0.88            0.09        0.04

Matches are distributed among these distances:
  48   41  0.84
  50    8  0.16

ACGTcount: A:0.18, C:0.07, G:0.17, T:0.58


Consensus pattern (49 bp):   
TTAATCCTTGGTGGTCATATTTTCAAATGGGTAGTTTTTATTTTTGCTT

Found at i:3153 original size:41 final size:42

Alignment explanation


    Indices: 3096--3179  Score: 152
    Period size: 41  Copynumber: 2.0  Consensus size: 42

       3086 CGTGCGGTTG

                                                  *   
       3096 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
          1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAAAAA

                                                      
       3137 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAAAAA
          1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAAAAA

             
       3179 T
          1 T

       3180 GAGATTTTGT


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  41   24  0.59
  42   17  0.41

ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46


Consensus pattern (42 bp):   
TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAAAAA

Found at i:3187 original size:42 final size:41

Alignment explanation


    Indices: 3100--3187  Score: 131
    Period size: 42  Copynumber: 2.1  Consensus size: 41

       3090 CGGTTGTTTT

                                             *    ***
       3100 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATTTT
          1 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAAAAATGAG

                                                      
       3141 ATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAAAAATGAG
          1 ATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAAAAATGAG

                 
       3183 ATTTT
          1 ATTTT

       3188 GTTGTGAAAT


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  41   20  0.48
  42   22  0.52

ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44


Consensus pattern (41 bp):   
ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAAAAATGAG

Found at i:3570 original size:17 final size:17

Alignment explanation


    Indices: 3548--3582  Score: 61
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3538 ACAATAACTT

                             
       3548 AATGGGATTACATTCAC
          1 AATGGGATTACATTCAC

                      *      
       3565 AATGGGATTATATTCAC
          1 AATGGGATTACATTCAC

             
       3582 A
          1 A

       3583 TAGCTATATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31


Consensus pattern (17 bp):   
AATGGGATTACATTCAC

Found at i:3691 original size:21 final size:21

Alignment explanation


    Indices: 3667--3709  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3657 TTAGGCTTGG

                 *               
       3667 TCAATCAATTACTTTGATTGC
          1 TCAATAAATTACTTTGATTGC

                                 
       3688 TCAATAAATTACTTTGATTGC
          1 TCAATAAATTACTTTGATTGC

             
       3709 T
          1 T

       3710 ATTGTCTTCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44


Consensus pattern (21 bp):   
TCAATAAATTACTTTGATTGC
Done.