Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012075.1 Corchorus capsularis cultivar CVL-1 contig12096, 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: 5777
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35


Found at i:2473 original size:17 final size:17

Alignment explanation


    Indices: 2453--2486  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       2443 TATATATTAA

                 *           
       2453 TTTGTTTTATTATTTAT
          1 TTTGTATTATTATTTAT

                             
       2470 TTTGTATTATTATTTAT
          1 TTTGTATTATTATTTAT

       2487 AATATATAGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74


Consensus pattern (17 bp):   
TTTGTATTATTATTTAT

Found at i:3067 original size:16 final size:16

Alignment explanation


    Indices: 3046--3076  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       3036 ATCGTTTTTA

                            
       3046 AAAAAATATATATACC
          1 AAAAAATATATATACC

                           
       3062 AAAAAATATATATAC
          1 AAAAAATATATATAC

       3077 TATTATATAA


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

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26


Consensus pattern (16 bp):   
AAAAAATATATATACC

Found at i:3979 original size:17 final size:17

Alignment explanation


    Indices: 3957--3991  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3947 TTGGTTTGAC

                              
       3957 ATTTTT-TTTTTTTCAAA
          1 ATTTTTATTTTTTT-AAA

                             
       3974 ATTTTTATTTTTTTAAA
          1 ATTTTTATTTTTTTAAA

             
       3991 A
          1 A

       3992 AATCATTATA


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

Matches are distributed among these distances:
  17   10  0.59
  18    7  0.41

ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69


Consensus pattern (17 bp):   
ATTTTTATTTTTTTAAA

Found at i:3994 original size:19 final size:17

Alignment explanation


    Indices: 3957--3992  Score: 54
    Period size: 18  Copynumber: 2.1  Consensus size: 17

       3947 TTGGTTTGAC

                         *   
       3957 ATTTTTTTTTTTTCAAA
          1 ATTTTTTTTTTTTAAAA

                              
       3974 ATTTTTATTTTTTTAAAA
          1 ATTTTT-TTTTTTTAAAA

             
       3992 A
          1 A

       3993 ATCATTATAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67


Consensus pattern (17 bp):   
ATTTTTTTTTTTTAAAA
Done.