Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009134.1 Corchorus olitorius cultivar O-4 contig09162, 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, 672

Length: 1121
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:972 original size:17 final size:17

Alignment explanation


    Indices: 952--1002  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 17

        942 AACCAATTAA

                             
        952 CAATCTAAATTATATAT
          1 CAATCTAAATTATATAT

                              
        969 CAAT-TCAAA-T-TA-A-
          1 CAATCT-AAATTATATAT

                             
        982 CAATCTAAATTATATAT
          1 CAATCTAAATTATATAT

                
        999 CAAT
          1 CAAT

       1003 TCAAATGATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 12
        0.70            0.00        0.30

Matches are distributed among these distances:
  13    7  0.25
  14    3  0.11
  15    4  0.14
  16    3  0.11
  17   11  0.39

ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37


Consensus pattern (17 bp):   
CAATCTAAATTATATAT

Found at i:980 original size:30 final size:30

Alignment explanation


    Indices: 946--1008  Score: 126
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        936 CTACTAAACC

                                          
        946 AATTAACAATCTAAATTATATATCAATTCA
          1 AATTAACAATCTAAATTATATATCAATTCA

                                          
        976 AATTAACAATCTAAATTATATATCAATTCA
          1 AATTAACAATCTAAATTATATATCAATTCA

               
       1006 AAT
          1 AAT

       1009 GATTATCAAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37


Consensus pattern (30 bp):   
AATTAACAATCTAAATTATATATCAATTCA

Found at i:1008 original size:17 final size:17

Alignment explanation


    Indices: 958--1020  Score: 66
    Period size: 17  Copynumber: 4.0  Consensus size: 17

        948 TTAACAATCT

                             
        958 AAATTATATATCAATTC
          1 AAATTATATATCAATTC

                             
        975 AAA-T-TA-A-CAA-TC
          1 AAATTATATATCAATTC

                              
        987 TAAATTATATATCAATTC
          1 -AAATTATATATCAATTC

                *            
       1005 AAATGAT-TATCAATTC
          1 AAATTATATATCAATTC

       1021 TTACTATATT


Statistics
Matches: 39,  Mismatches: 1, Indels: 13
        0.74            0.02        0.25

Matches are distributed among these distances:
  12    2  0.05
  13    6  0.15
  14    2  0.05
  15    4  0.10
  16   11  0.28
  17   12  0.31
  18    2  0.05

ACGTcount: A:0.48, C:0.13, G:0.02, T:0.38


Consensus pattern (17 bp):   
AAATTATATATCAATTC

Found at i:1033 original size:18 final size:18

Alignment explanation


    Indices: 1010--1045  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1000 AATTCAAATG

                              
       1010 ATTATCAATTCTTACTAT
          1 ATTATCAATTCTTACTAT

                              
       1028 ATTATCAATTCTTACTAT
          1 ATTATCAATTCTTACTAT

       1046 CAATTATTAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50


Consensus pattern (18 bp):   
ATTATCAATTCTTACTAT
Done.