Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020004.1 Corchorus olitorius cultivar O-4 contig20037, 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: 3763
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37


Found at i:435 original size:203 final size:206

Alignment explanation


    Indices: 83--496  Score: 748
    Period size: 203  Copynumber: 2.0  Consensus size: 206

         73 GCTTAATAAT

                                                      *                      
         83 TTTATCAATGGTGAATGTTATTAAATTTTTTTAAGATCTAAGTTTACTAACAAAGTCGTTAGTGA
          1 TTTATCAATGGTGAATGTTATTAAATTTTTTTAAGATCTAAGATTACTAACAAAGTCGTTAGTGA

                              *                                              
        148 ATAAGATACAACACATTATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTG
         66 ATAAGATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTG

                                                                             
        213 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
        131 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA

                       
        278 GATCCGATTTA
        196 GATCCGATTTA

                                                                    *        
        289 TTTATCAATGGTGAATGTTATT-AA-TTTTTTAAG-TCTAAGATTACTAACAAAGTTG-TAGTGA
          1 TTTATCAATGGTGAATGTTATTAAATTTTTTTAAGATCTAAGATTACTAACAAAGTCGTTAGTGA

                                                                             
        350 ATAAGATACAACACATTACTATTATATATATAGAACTATACC-AAAAAAATTAGTTGAACATTAG
         66 ATAAGATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAATTAGTTGAACATTAG

                                                                             
        414 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA
        129 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA

                         
        479 AAGATCCGATTTA
        194 AAGATCCGATTTA

                 
        492 TTTAT
          1 TTTAT

        497 TATTAAGGAA


Statistics
Matches: 203,  Mismatches: 3, Indels: 7
        0.95            0.01        0.03

Matches are distributed among these distances:
 202   35  0.17
 203  126  0.62
 204   18  0.09
 205    2  0.01
 206   22  0.11

ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37


Consensus pattern (206 bp):   
TTTATCAATGGTGAATGTTATTAAATTTTTTTAAGATCTAAGATTACTAACAAAGTCGTTAGTGA
ATAAGATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTG
GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
GATCCGATTTA

Found at i:605 original size:25 final size:24

Alignment explanation


    Indices: 571--617  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        561 ACGTTTGCAC

                                     
        571 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
        596 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

        618 TGTAAGTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:662 original size:39 final size:40

Alignment explanation


    Indices: 608--688  Score: 130
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        598 ATACCTAAGA

                                              *      
        608 ATTTAATTAATGTAAGTAT-TTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATATT-AGTTATTATATATATTAC

                                                    
        647 ATTTAATTAATGTAAGTATATTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATATTAGTTATTATATATATTAC

              
        687 AT
          1 AT

        689 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 1, Indels: 3
        0.91            0.02        0.07

Matches are distributed among these distances:
  39   29  0.74
  40   10  0.26

ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATATTAGTTATTATATATATTAC

Found at i:1424 original size:36 final size:37

Alignment explanation


    Indices: 1354--1427  Score: 141
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       1344 GTTAGGGGGT

                                                 
       1354 TGGGTAATTGGGTAGGGCCGTAGGGGTGGGGAGTGGG
          1 TGGGTAATTGGGTAGGGCCGTAGGGGTGGGGAGTGGG

                                                 
       1391 TGGGTAATTGGGTAGGGCCGTA-GGGTGGGGAGTGGG
          1 TGGGTAATTGGGTAGGGCCGTAGGGGTGGGGAGTGGG

             
       1427 T
          1 T

       1428 AGAACTGGCA


Statistics
Matches: 37,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  36   15  0.41
  37   22  0.59

ACGTcount: A:0.14, C:0.05, G:0.58, T:0.23


Consensus pattern (37 bp):   
TGGGTAATTGGGTAGGGCCGTAGGGGTGGGGAGTGGG

Found at i:1569 original size:17 final size:17

Alignment explanation


    Indices: 1547--1594  Score: 55
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       1537 TGTCGGGTTA

                             
       1547 TTTGGGTTCGGGTCAAT
          1 TTTGGGTTCGGGTCAAT

                           * 
       1564 TTTGGGTT-GGGTC-GT
          1 TTTGGGTTCGGGTCAAT

                  *         
       1579 TTTCGGTTTCGGGTCA
          1 TTT-GGGTTCGGGTCA

       1595 TACGGTTCGG


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  15    4  0.15
  16    9  0.35
  17   13  0.50

ACGTcount: A:0.06, C:0.12, G:0.38, T:0.44


Consensus pattern (17 bp):   
TTTGGGTTCGGGTCAAT
Done.