Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009272.1 Corchorus olitorius cultivar O-4 contig09301, 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, 744

Length: 1241
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29


Found at i:451 original size:11 final size:11

Alignment explanation


    Indices: 435--474  Score: 55
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        425 TATTTAAAAG

                       
        435 TAAATATACGA
          1 TAAATATACGA

                    *  
        446 TAAATATAAG-
          1 TAAATATACGA

                       
        456 TAAATATACGA
          1 TAAATATACGA

            *       
        467 GAAATATA
          1 TAAATATA

        475 AATAATAAAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  10    9  0.36
  11   16  0.64

ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28


Consensus pattern (11 bp):   
TAAATATACGA

Found at i:473 original size:21 final size:21

Alignment explanation


    Indices: 432--475  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        422 CTATATTTAA

                          *      
        432 AAGTAAATATACGATAAATAT
          1 AAGTAAATATACGAGAAATAT

                                 
        453 AAGTAAATATACGAGAAATAT
          1 AAGTAAATATACGAGAAATAT

              
        474 AA
          1 AA

        476 ATAATAAATA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25


Consensus pattern (21 bp):   
AAGTAAATATACGAGAAATAT

Found at i:485 original size:4 final size:4

Alignment explanation


    Indices: 472--512  Score: 54
    Period size: 4  Copynumber: 11.2  Consensus size: 4

        462 TACGAGAAAT

                                                                    
        472 ATAA AT-A ATAA ATAA AT-- ATAA AT-A ATAA ATAA ATAA ATAA A
          1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A

        513 AGGCCACTCC


Statistics
Matches: 33,  Mismatches: 0, Indels: 8
        0.80            0.00        0.20

Matches are distributed among these distances:
   2    2  0.06
   3    6  0.18
   4   25  0.76

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (4 bp):   
ATAA

Found at i:488 original size:17 final size:17

Alignment explanation


    Indices: 468--506  Score: 78
    Period size: 17  Copynumber: 2.3  Consensus size: 17

        458 AATATACGAG

                             
        468 AAATATAAATAATAAAT
          1 AAATATAAATAATAAAT

                             
        485 AAATATAAATAATAAAT
          1 AAATATAAATAATAAAT

                 
        502 AAATA
          1 AAATA

        507 AATAAAAGGC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (17 bp):   
AAATATAAATAATAAAT
Done.