Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015651.1 Corchorus capsularis cultivar CVL-1 contig15672, 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: 20023
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:5286 original size:32 final size:33

Alignment explanation


    Indices: 5247--5369  Score: 115
    Period size: 32  Copynumber: 3.7  Consensus size: 33

       5237 TTAGTTGGCA

                                             
       5247 AAACGCCCCTATATTGCGGCGTTTTCTATCC-C
          1 AAACGCCCCTATATTGCGGCGTTTTCTATCCAC

                          **        *  *      
       5279 AAACGCCCCTATATCCCGGCGTTTCCTCTCCATC
          1 AAACGCCCCTATATTGCGGCGTTTTCTATCCA-C

                                      ** ***  
       5313 AAACGCCCCTAT-TTGCCGGCGTTTTAAAGAAAC
          1 AAACGCCCCTATATTG-CGGCGTTTTCTATCCAC

                          **        
       5346 AAACGCCCCTATATCCCGGCGTTT
          1 AAACGCCCCTATATTGCGGCGTTT

       5370 ATCTTTACAA


Statistics
Matches: 72,  Mismatches: 15, Indels: 7
        0.77            0.16        0.07

Matches are distributed among these distances:
  32   27  0.38
  33   22  0.31
  34   23  0.32

ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27


Consensus pattern (33 bp):   
AAACGCCCCTATATTGCGGCGTTTTCTATCCAC

Found at i:7841 original size:15 final size:15

Alignment explanation


    Indices: 7821--7850  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       7811 ATCGGTTAAA

                           
       7821 ATATTGTGGATCGTG
          1 ATATTGTGGATCGTG

                    *      
       7836 ATATTGTGTATCGTG
          1 ATATTGTGGATCGTG

       7851 GCAGTCTGAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.20, C:0.07, G:0.30, T:0.43


Consensus pattern (15 bp):   
ATATTGTGGATCGTG

Found at i:9207 original size:6 final size:6

Alignment explanation


    Indices: 9196--9231  Score: 72
    Period size: 6  Copynumber: 6.0  Consensus size: 6

       9186 GCAAAGCAAT

                                                     
       9196 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA
          1 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA

       9232 GCAAATTAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33


Consensus pattern (6 bp):   
TCTAAA

Found at i:9246 original size:13 final size:13

Alignment explanation


    Indices: 9228--9260  Score: 66
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       9218 AATCTAAATC

                         
       9228 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                         
       9241 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                   
       9254 TAAAGCA
          1 TAAAGCA

       9261 CACAATAATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:15118 original size:13 final size:13

Alignment explanation


    Indices: 15100--15127  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      15090 AAAATCAGTT

                         
      15100 TTTTTAGCTCTTC
          1 TTTTTAGCTCTTC

                         
      15113 TTTTTAGCTCTTC
          1 TTTTTAGCTCTTC

              
      15126 TT
          1 TT

      15128 CCTAGTTGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64


Consensus pattern (13 bp):   
TTTTTAGCTCTTC
Done.