Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002798.1 Corchorus olitorius cultivar O-4 contig02800, 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, 615

Length: 1026
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:294 original size:11 final size:11

Alignment explanation


    Indices: 278--317  Score: 55
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        268 TATTTAAAAG

                       
        278 TAAATATACGA
          1 TAAATATACGA

                    *  
        289 TAAATATAAG-
          1 TAAATATACGA

                       
        299 TAAATATACGA
          1 TAAATATACGA

            *       
        310 GAAATATA
          1 TAAATATA

        318 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:316 original size:21 final size:21

Alignment explanation


    Indices: 275--318  Score: 79
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        265 CTATATTTAA

                          *      
        275 AAGTAAATATACGATAAATAT
          1 AAGTAAATATACGAGAAATAT

                                 
        296 AAGTAAATATACGAGAAATAT
          1 AAGTAAATATACGAGAAATAT

              
        317 AA
          1 AA

        319 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:328 original size:4 final size:4

Alignment explanation


    Indices: 315--355  Score: 54
    Period size: 4  Copynumber: 11.2  Consensus size: 4

        305 TACGAGAAAT

                                                                    
        315 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

        356 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:331 original size:17 final size:17

Alignment explanation


    Indices: 311--349  Score: 78
    Period size: 17  Copynumber: 2.3  Consensus size: 17

        301 AATATACGAG

                             
        311 AAATATAAATAATAAAT
          1 AAATATAAATAATAAAT

                             
        328 AAATATAAATAATAAAT
          1 AAATATAAATAATAAAT

                 
        345 AAATA
          1 AAATA

        350 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

Found at i:768 original size:17 final size:17

Alignment explanation


    Indices: 737--769  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        727 AAGACGACCC

                             
        737 TTTCTATTTTCTATTTT
          1 TTTCTATTTTCTATTTT

                             
        754 TTTCT-TTTTCATATTT
          1 TTTCTATTTTC-TATTT

        770 GAAAAAGGAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76


Consensus pattern (17 bp):   
TTTCTATTTTCTATTTT
Done.