Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024893.1 Corchorus olitorius cultivar O-4 contig24926, 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: 2215
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34


Found at i:302 original size:17 final size:17

Alignment explanation


    Indices: 280--312  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        270 TTTTATTGAT

                              
        280 ATTTAT-ATTATTAATTA
          1 ATTTATAATT-TTAATTA

                            
        297 ATTTATAATTTTAATT
          1 ATTTATAATTTTAATT

        313 GATGTAATGA


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

Matches are distributed among these distances:
  17   12  0.80
  18    3  0.20

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (17 bp):   
ATTTATAATTTTAATTA

Found at i:1319 original size:130 final size:131

Alignment explanation


    Indices: 1130--1393  Score: 399
    Period size: 130  Copynumber: 2.0  Consensus size: 131

       1120 GTCATTTAAG

                      *                                   *                  
       1130 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTTAATTAAATTAGTAAAATGGTAAAAAT
          1 AAATATATTTAAAAAATTCTAATATA-CTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT

                                      *         *                 *       *  
       1195 AAAATAGGTATAAAGATATTAGATTTTA-TACAATAGAAATAGAGTTTTTAATTGAGTAAAATTA
         65 AAAATAGGTATAAAGATATTAGATTTAATTA-AATAAAAATAGAGTTTTTAATTAAGTAAAACTA

               
       1259 TAA
        129 TAA

                                                                             
       1262 AAATATA-TTAAAAAATTCTAATATA-TAAGTGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
          1 AAATATATTTAAAAAATTCTAATATACTAAGT-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT

                   *     *                                    *              
       1325 AAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTAT
         65 AAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTAAGTAAAACTAT

              
       1390 AA
        130 AA

              
       1392 AA
          1 AA

       1394 GTTTAAATGA


Statistics
Matches: 121,  Mismatches: 9, Indels: 6
        0.89            0.07        0.04

Matches are distributed among these distances:
 129    5  0.04
 130   90  0.74
 131   19  0.16
 132    7  0.06

ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38


Consensus pattern (131 bp):   
AAATATATTTAAAAAATTCTAATATACTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATA
AAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTAAGTAAAACTATA
A
Done.