Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023394.1 Corchorus olitorius cultivar O-4 contig23427, 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: 11365
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35


Found at i:102 original size:13 final size:13

Alignment explanation


    Indices: 81--112  Score: 57
    Period size: 12  Copynumber: 2.5  Consensus size: 13

         71 CTAAACCTAT

                         
         81 TTATTTTTTTAA-
          1 TTATTTTTTTAAC

                         
         93 TTATTTTTTTAAC
          1 TTATTTTTTTAAC

                   
        106 TTATTTT
          1 TTATTTT

        113 CCTATTTATC


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

Matches are distributed among these distances:
  12   12  0.63
  13    7  0.37

ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75


Consensus pattern (13 bp):   
TTATTTTTTTAAC

Found at i:3515 original size:11 final size:9

Alignment explanation


    Indices: 3508--3574  Score: 66
    Period size: 10  Copynumber: 7.0  Consensus size: 9

       3498 TTTGAAGACT

                     
       3508 TATTGAAGA
          1 TATTGAAGA

                       
       3517 TAATTTGAAGA
          1 T-A-TTGAAGA

                     
       3528 T-TTGAAGA
          1 TATTGAAGA

                      
       3536 CTATTGAAGA
          1 -TATTGAAGA

                       
       3546 TAATTTGAAGA
          1 T-A-TTGAAGA

                     
       3557 T-TTGAAGA
          1 TATTGAAGA

                      
       3565 CTATTGAAGA
          1 -TATTGAAGA

       3575 ATTATCTCAA


Statistics
Matches: 50,  Mismatches: 0, Indels: 15
        0.77            0.00        0.23

Matches are distributed among these distances:
   8   14  0.28
   9    4  0.08
  10   16  0.32
  11   16  0.32

ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34


Consensus pattern (9 bp):   
TATTGAAGA

Found at i:3544 original size:18 final size:18

Alignment explanation


    Indices: 3521--3574  Score: 59
    Period size: 18  Copynumber: 3.4  Consensus size: 18

       3511 TGAAGATAAT

                              
       3521 TTGAAGATTTGAAGACTA
          1 TTGAAGATTTGAAGACTA

                              
       3539 TTGAAGA--T--A-A-T-
          1 TTGAAGATTTGAAGACTA

                              
       3550 TTGAAGATTTGAAGACTA
          1 TTGAAGATTTGAAGACTA

                   
       3568 TTGAAGA
          1 TTGAAGA

       3575 ATTATCTCAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 14
        0.67            0.00        0.33

Matches are distributed among these distances:
  11    7  0.24
  12    1  0.03
  13    2  0.07
  14    1  0.03
  15    1  0.03
  16    2  0.07
  17    1  0.03
  18   14  0.48

ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATTTGAAGACTA

Found at i:3546 original size:29 final size:29

Alignment explanation


    Indices: 3498--3574  Score: 145
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       3488 GAAGTTCGTG

                                          
       3498 TTTGAAGACTTATTGAAGATAATTTGAAGA
          1 TTTGAAGAC-TATTGAAGATAATTTGAAGA

                                         
       3528 TTTGAAGACTATTGAAGATAATTTGAAGA
          1 TTTGAAGACTATTGAAGATAATTTGAAGA

                              
       3557 TTTGAAGACTATTGAAGA
          1 TTTGAAGACTATTGAAGA

       3575 ATTATCTCAA


Statistics
Matches: 47,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  29   38  0.81
  30    9  0.19

ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35


Consensus pattern (29 bp):   
TTTGAAGACTATTGAAGATAATTTGAAGA
Done.