Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011532.1 Corchorus capsularis cultivar CVL-1 contig11553, 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: 9132
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30


Found at i:4446 original size:18 final size:18

Alignment explanation


    Indices: 4422--4470  Score: 53
    Period size: 22  Copynumber: 2.5  Consensus size: 18

       4412 GCTTTGGATC

                              
       4422 ATTGGTTTGGATATTGCT
          1 ATTGGTTTGGATATTGCT

            *                     
       4440 GTTGGTTGATTTGGATATTGCT
          1 ATT-G--G-TTTGGATATTGCT

                     
       4462 ATTGGTTTG
          1 ATTGGTTTG

       4471 TTGTCTGTGG


Statistics
Matches: 25,  Mismatches: 2, Indels: 8
        0.71            0.06        0.23

Matches are distributed among these distances:
  18    6  0.24
  19    2  0.08
  21    2  0.08
  22   15  0.60

ACGTcount: A:0.14, C:0.04, G:0.31, T:0.51


Consensus pattern (18 bp):   
ATTGGTTTGGATATTGCT

Found at i:4452 original size:22 final size:22

Alignment explanation


    Indices: 4427--4468  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4417 GGATCATTGG

                         *        
       4427 TTTGGATATTGCTGTTGGTTGA
          1 TTTGGATATTGCTATTGGTTGA

                                
       4449 TTTGGATATTGCTATTGGTT
          1 TTTGGATATTGCTATTGGTT

       4469 TGTTGTCTGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.14, C:0.05, G:0.29, T:0.52


Consensus pattern (22 bp):   
TTTGGATATTGCTATTGGTTGA

Found at i:4576 original size:29 final size:29

Alignment explanation


    Indices: 4543--4601  Score: 118
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       4533 ACAATTTCTT

                                         
       4543 TTTGTAATAAACGGTTAATTAATTAATAC
          1 TTTGTAATAAACGGTTAATTAATTAATAC

                                         
       4572 TTTGTAATAAACGGTTAATTAATTAATAC
          1 TTTGTAATAAACGGTTAATTAATTAATAC

             
       4601 T
          1 T

       4602 AATAGAACCT


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

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42


Consensus pattern (29 bp):   
TTTGTAATAAACGGTTAATTAATTAATAC

Done.