Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005691.1 Corchorus capsularis cultivar CVL-1 contig05709, 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: 4523
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37


Found at i:2096 original size:27 final size:27

Alignment explanation


    Indices: 2066--2127  Score: 99
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       2056 ATGATAATCA

                                        
       2066 AAAATTTAATTACAATT-ATATGATTTC
          1 AAAATTTAATTACAATTGA-ATGATTTC

                                       
       2093 AAAATTTAATTACAATTGAATGATTTC
          1 AAAATTTAATTACAATTGAATGATTTC

                    
       2120 AAATATTT
          1 AAA-ATTT

       2128 GTAGAAATTC


Statistics
Matches: 33,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  27   28  0.85
  28    5  0.15

ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44


Consensus pattern (27 bp):   
AAAATTTAATTACAATTGAATGATTTC

Found at i:3656 original size:31 final size:30

Alignment explanation


    Indices: 3591--3659  Score: 77
    Period size: 31  Copynumber: 2.2  Consensus size: 30

       3581 TCCGTTTAAG

                             *        *    
       3591 GCGGATTTGGATAGTGATATATGGATGCGGA
          1 GCGGATTTGGATAGTGAAATAT-GATCCGGA

                                          * 
       3622 GCGGATTTGGATAGTGAAACTACT-ATCCGTA
          1 GCGGATTTGGATAGTGAAA-TA-TGATCCGGA

                   
       3653 GCGGATT
          1 GCGGATT

       3660 CGGAGCGGTG


Statistics
Matches: 33,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  31   30  0.91
  32    2  0.06
  33    1  0.03

ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29


Consensus pattern (30 bp):   
GCGGATTTGGATAGTGAAATATGATCCGGA

Found at i:3925 original size:6 final size:6

Alignment explanation


    Indices: 3910--3940  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       3900 TATGGTTAGG

                 *                              
       3910 CGGATA CGGATT CGGATT CGGATT CGGATT C
          1 CGGATT CGGATT CGGATT CGGATT CGGATT C

       3941 TAAATGGATA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.19, C:0.19, G:0.32, T:0.29


Consensus pattern (6 bp):   
CGGATT

Done.