Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013316.1 Corchorus capsularis cultivar CVL-1 contig13337, 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: 17912
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:9059 original size:3 final size:3

Alignment explanation


    Indices: 9051--9094  Score: 88
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       9041 GTAAGATATA

                                                                      
       9051 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

       9095 CAAGTTATAT


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   41  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:9930 original size:3 final size:3

Alignment explanation


    Indices: 9909--9954  Score: 65
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       9899 GGTAGTTAAA

                          *                                             
       9909 AAT AAT ATAT AGT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

       9955 ATCCAATTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
   3   34  0.87
   4    5  0.13

ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35


Consensus pattern (3 bp):   
AAT

Found at i:10524 original size:32 final size:31

Alignment explanation


    Indices: 10488--10563  Score: 107
    Period size: 32  Copynumber: 2.4  Consensus size: 31

      10478 GCCCCTTTGC

                    *              *        
      10488 CCCCTGAATTTTGCAAATTTAGGTCATATTGT
          1 CCCCTGAACTTTGCAAATTTAGGCCATATT-T

                         *                 
      10520 CCCCTGAACTTTGTAAATTTAGGCCATATTT
          1 CCCCTGAACTTTGCAAATTTAGGCCATATTT

                         
      10551 CCCCATGAACTTT
          1 CCCC-TGAACTTT

      10564 AAATTGTGCC


Statistics
Matches: 40,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  31    5  0.12
  32   35  0.88

ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38


Consensus pattern (31 bp):   
CCCCTGAACTTTGCAAATTTAGGCCATATTT

Found at i:13617 original size:49 final size:49

Alignment explanation


    Indices: 13508--13651  Score: 209
    Period size: 49  Copynumber: 2.9  Consensus size: 49

      13498 GACAACACCG

                          *                     *  *    *    
      13508 AGCTTTCCCAAGCTCA-AACAAGTGCTCCCCGCACTTATCACAAACCTA
          1 AGCTTTCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTA

                                                              
      13556 AGCTTTCCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTA
          1 AGCTTT-CCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTA

                             * *                 *        
      13606 AGCTTTCCCAAGCTTAGGATAAGTGCTCCCCGCACTGTTTACAATC
          1 AGCTTTCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATC

      13652 AAAGATATAG


Statistics
Matches: 87,  Mismatches: 7, Indels: 3
        0.90            0.07        0.03

Matches are distributed among these distances:
  48    6  0.07
  49   46  0.53
  50   35  0.40

ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24


Consensus pattern (49 bp):   
AGCTTTCCCAAGCTTAGAACAAGTGCTCCCCGCACTGATTACAATCCTA
Done.