Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022786.1 Corchorus olitorius cultivar O-4 contig22819, 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: 1676
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36


Found at i:314 original size:124 final size:126

Alignment explanation


    Indices: 98--353  Score: 419
    Period size: 124  Copynumber: 2.0  Consensus size: 126

         88 ATTTAAGAAA

                                                                             
         98 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
          1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT---AATAAAA

                                                                       *     
        163 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
         63 T--GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA

             
        228 G
        126 G

                                                                             
        229 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-
          1 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAATAAAATG

                 *                                                        
        291 TATAATGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
         65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

             
        353 T
          1 T

        354 TTAAACAATG


Statistics
Matches: 122,  Mismatches: 2, Indels: 9
        0.92            0.02        0.07

Matches are distributed among these distances:
 124   61  0.50
 127    5  0.04
 128    1  0.01
 131   29  0.24
 132   26  0.21

ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38


Consensus pattern (126 bp):   
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAATAAAATGT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG

Found at i:1296 original size:2 final size:2

Alignment explanation


    Indices: 1289--1359  Score: 92
    Period size: 2  Copynumber: 34.5  Consensus size: 2

       1279 AATAATAATC

                                                                            
       1289 AT AT AT AT CAT AT CAT AT A- AT AT AT AT AT AT A- AT AT AT AT AT
          1 AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                                      
       1331 AT CAT AT AT CAT AT AT AT AT AT AT AT AT A
          1 AT -AT AT AT -AT AT AT AT AT AT AT AT AT A

       1360 ATGATAACAA


Statistics
Matches: 63,  Mismatches: 0, Indels: 12
        0.84            0.00        0.16

Matches are distributed among these distances:
   1    2  0.03
   2   53  0.84
   3    8  0.13

ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Done.