Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01003724.1 Corchorus olitorius cultivar O-4 contig03734, 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: 1965
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38


Found at i:556 original size:17 final size:17

Alignment explanation


    Indices: 531--585  Score: 52
    Period size: 17  Copynumber: 3.6  Consensus size: 17

        521 TTATGTGTTT

                *            
        531 ATATCTTTATTTTTCGA
          1 ATATATTTATTTTTCGA

                             
        548 ATATATTTA---TT--A
          1 ATATATTTATTTTTCGA

                             
        560 A-ATA-TTATTTTTCGA
          1 ATATATTTATTTTTCGA

                       
        575 ATATATTTATT
          1 ATATATTTATT

        586 AAATGTCATT


Statistics
Matches: 30,  Mismatches: 1, Indels: 14
        0.67            0.02        0.31

Matches are distributed among these distances:
  10    3  0.10
  11    3  0.10
  12    2  0.07
  13    2  0.07
  14    2  0.07
  15    2  0.07
  16    3  0.10
  17   13  0.43

ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58


Consensus pattern (17 bp):   
ATATATTTATTTTTCGA

Found at i:563 original size:13 final size:13

Alignment explanation


    Indices: 547--589  Score: 52
    Period size: 13  Copynumber: 3.2  Consensus size: 13

        537 TTATTTTTCG

                         
        547 AATATATTTATTA
          1 AATATATTTATTA

                          *
        560 AATATTATTT-TTCG
          1 AATA-TATTTATT-A

                         
        574 AATATATTTATTA
          1 AATATATTTATTA

               
        587 AAT
          1 AAT

        590 GTCATTGTTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 6
        0.76            0.06        0.18

Matches are distributed among these distances:
  13   14  0.56
  14   11  0.44

ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53


Consensus pattern (13 bp):   
AATATATTTATTA

Found at i:568 original size:27 final size:27

Alignment explanation


    Indices: 537--589  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        527 GTTTATATCT

                                       
        537 TTATTTTTCGAATATATTTATTAAATA
          1 TTATTTTTCGAATATATTTATTAAATA

                                      
        564 TTATTTTTCGAATATATTTATTAAAT
          1 TTATTTTTCGAATATATTTATTAAAT

        590 GTCATTGTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57


Consensus pattern (27 bp):   
TTATTTTTCGAATATATTTATTAAATA

Found at i:1492 original size:11 final size:11

Alignment explanation


    Indices: 1449--1486  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       1439 TTCCTATATA

                *      
       1449 AAATAAATTAT
          1 AAATTAATTAT

                        
       1460 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       1471 AAATTAATTAT
          1 AAATTAATTAT

                 
       1482 AAATT
          1 AAATT

       1487 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT
Done.