Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018582.1 Corchorus olitorius cultivar O-4 contig18615, 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: 3562
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36


Found at i:848 original size:2 final size:2

Alignment explanation


    Indices: 837--872  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

        827 AGTTTAGACT

                                 *                                 
        837 TA TA TA -A TA TA TA GA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        873 TGAGAATAAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:1462 original size:135 final size:134

Alignment explanation


    Indices: 1218--1470  Score: 402
    Period size: 135  Copynumber: 1.9  Consensus size: 134

       1208 TAATTTTACT

                                                                  *          
       1218 CAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
          1 CAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACTATTTCATTTTTACCA

                        *  *           *                                     
       1283 TTTTACTAATTTTATTAAAAAAACTTATATATATTAGAATTTTTTTTAAAATATACTTTTATAGG
         66 TTTTACTAATTTAATAAAAAAAACTTAGATATATTAGAA--TTTTTTAAAATATACTTTTATAGG

                  
       1348 TTGACC
        129 TTGACC

                                                    **     *                 
       1354 CAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATTTTTATACCTATTTCATTTTTACCA
          1 CAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACTATTTCATTTTTACCA

                                                                  
       1418 TTTTACTAATTTAAATAAAAAAAACTTAGATATATTAGAA-TTTTTAAAATATA
         66 TTTTACTAATTT-AATAAAAAAAACTTAGATATATTAGAATTTTTTAAAATATA

       1471 TTTCTTAAAT


Statistics
Matches: 109,  Mismatches: 7, Indels: 5
        0.90            0.06        0.04

Matches are distributed among these distances:
 133   13  0.12
 135   57  0.52
 136   39  0.36

ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47


Consensus pattern (134 bp):   
CAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACTATTTCATTTTTACCA
TTTTACTAATTTAATAAAAAAAACTTAGATATATTAGAATTTTTTAAAATATACTTTTATAGGTT
GACC

Done.