Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010842.1 Corchorus capsularis cultivar CVL-1 contig10863, 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: 4181
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:43 original size:2 final size:2

Alignment explanation


    Indices: 36--83  Score: 51
    Period size: 2  Copynumber: 23.5  Consensus size: 2

         26 TTATGTGATC

                                                       *      *     *  *   
         36 AT AT AT AT AT AT AT AT AT AT AT AGT AT AT CT AT AA AT AG AA AT
          1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT

                   
         79 AT AT A
          1 AT AT A

         84 ATAAAATCAC


Statistics
Matches: 38,  Mismatches: 7, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
   2   36  0.95
   3    2  0.05

ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42


Consensus pattern (2 bp):   
AT

Found at i:281 original size:21 final size:21

Alignment explanation


    Indices: 242--281  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        232 AGGGGGTTGC

                        *        
        242 TAAATACCGTCCTAGTTTTGT
          1 TAAATACCGTCCCAGTTTTGT

                          *    
        263 TAAATACCGTCCCATTTTT
          1 TAAATACCGTCCCAGTTTT

        282 TACACTTTTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42


Consensus pattern (21 bp):   
TAAATACCGTCCCAGTTTTGT

Found at i:403 original size:33 final size:32

Alignment explanation


    Indices: 333--446  Score: 113
    Period size: 33  Copynumber: 3.5  Consensus size: 32

        323 CACTGAGCCT

                   *  *                *     *
        333 CCCCACTAGGACGG-TTCAGCCACGGCGGAGCCT
          1 CCCCACTGGGGCGGCTTCA-CCACGGCAG-GCCG

                                   *         
        366 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
          1 CCCCACTGGGGCGGCTTCACCA-CGGCAGGCCG

                     *        *             
        399 CCCCACTGGAGCGGCTTCGCCACGGCAGGCCG
          1 CCCCACTGGGGCGGCTTCACCACGGCAGGCCG

                **          
        431 CCCCGGTGGGGCGGCT
          1 CCCCACTGGGGCGGCT

        447 AGACCAATTT


Statistics
Matches: 68,  Mismatches: 11, Indels: 5
        0.81            0.13        0.06

Matches are distributed among these distances:
  32   22  0.32
  33   38  0.56
  34    8  0.12

ACGTcount: A:0.12, C:0.40, G:0.36, T:0.11


Consensus pattern (32 bp):   
CCCCACTGGGGCGGCTTCACCACGGCAGGCCG

Found at i:445 original size:32 final size:33

Alignment explanation


    Indices: 366--446  Score: 110
    Period size: 32  Copynumber: 2.5  Consensus size: 33

        356 GGCGGAGCCT

                                   *         
        366 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
          1 CCCCACTGGGGCGGCTTCACCATCGGCAGGCCG

                     *        *              
        399 CCCCACTGGAGCGGCTTCGCCA-CGGCAGGCCG
          1 CCCCACTGGGGCGGCTTCACCATCGGCAGGCCG

                **          
        431 CCCCGGTGGGGCGGCT
          1 CCCCACTGGGGCGGCT

        447 AGACCAATTT


Statistics
Matches: 42,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  32   22  0.52
  33   20  0.48

ACGTcount: A:0.10, C:0.41, G:0.38, T:0.11


Consensus pattern (33 bp):   
CCCCACTGGGGCGGCTTCACCATCGGCAGGCCG
Done.