Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016975.1 Corchorus olitorius cultivar O-4 contig17008, 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: 2223
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33


Found at i:219 original size:33 final size:33

Alignment explanation


    Indices: 177--283  Score: 98
    Period size: 33  Copynumber: 3.3  Consensus size: 33

        167 AAAAAAGGGA

                                             
        177 GTTAGTAACCCCTAAATCATGAACACTTCTAAG
          1 GTTAGTAACCCCTAAATCATGAACACTTCTAAG

                      *              *****     
        210 GTTAGTAACCTC-AAA--A-GAA-AAAAAAAAGGG
          1 GTTAGTAACCCCTAAATCATGAACACTTCTAA--G

                                              
        240 AGTTAGTAACCCCTAAATCATGAACACTTCTAAG
          1 -GTTAGTAACCCCTAAATCATGAACACTTCTAAG

                      
        274 GTTAGTAACC
          1 GTTAGTAACC

        284 TTGCTTTCTC


Statistics
Matches: 54,  Mismatches: 12, Indels: 16
        0.66            0.15        0.20

Matches are distributed among these distances:
  28    3  0.06
  29    3  0.06
  30    2  0.04
  31   11  0.20
  32    6  0.11
  33   21  0.39
  34    2  0.04
  35    3  0.06
  36    3  0.06

ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23


Consensus pattern (33 bp):   
GTTAGTAACCCCTAAATCATGAACACTTCTAAG

Found at i:225 original size:63 final size:64

Alignment explanation


    Indices: 147--284  Score: 269
    Period size: 64  Copynumber: 2.2  Consensus size: 64

        137 AAAAATGAGT

                                                                            
        147 GTTAGTAACCTCAAAAG-AAAAAAAAAGGGAGTTAGTAACCCCTAAATCATGAACACTTCTAAG
          1 GTTAGTAACCTCAAAAGAAAAAAAAAAGGGAGTTAGTAACCCCTAAATCATGAACACTTCTAAG

                                                                            
        210 GTTAGTAACCTCAAAAGAAAAAAAAAAGGGAGTTAGTAACCCCTAAATCATGAACACTTCTAAG
          1 GTTAGTAACCTCAAAAGAAAAAAAAAAGGGAGTTAGTAACCCCTAAATCATGAACACTTCTAAG

                       
        274 GTTAGTAACCT
          1 GTTAGTAACCT

        285 TGCTTTCTCA


Statistics
Matches: 74,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  63   17  0.23
  64   57  0.77

ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22


Consensus pattern (64 bp):   
GTTAGTAACCTCAAAAGAAAAAAAAAAGGGAGTTAGTAACCCCTAAATCATGAACACTTCTAAG

Done.