Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009835.1 Corchorus olitorius cultivar O-4 contig09867, 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: 3830
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36


Found at i:3276 original size:25 final size:24

Alignment explanation


    Indices: 3242--3288  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       3232 ACGTTTGCAC

                                     
       3242 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
       3267 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

       3289 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:3343 original size:45 final size:43

Alignment explanation


    Indices: 3279--3362  Score: 123
    Period size: 45  Copynumber: 1.9  Consensus size: 43

       3269 ATACCTAAGA

                                                         
       3279 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-TA-TATTATTAC

                    *     *      *                 
       3324 ATTTAATTTATGTACGTATTTTAGTTATTATATATATTA
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTA

       3363 CATAGGAATT


Statistics
Matches: 36,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  43    5  0.14
  44    2  0.06
  45   29  0.81

ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54


Consensus pattern (43 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTATTAC

Found at i:3375 original size:45 final size:45

Alignment explanation


    Indices: 3281--3376  Score: 106
    Period size: 45  Copynumber: 2.1  Consensus size: 45

       3271 ACCTAAGAAT

                                                   *    *
       3281 TTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTATTACAT
          1 TTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTAATACAA

                  *     *      *                        *  
       3326 TTAATTTATGTACGTATTTTAGTTATTATA-TA-TATTACATAGGAA
          1 TTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTA-ATA-CAA

                  
       3371 TTAATT
          1 TTAATT

       3377 GAAACAAGCA


Statistics
Matches: 43,  Mismatches: 6, Indels: 4
        0.81            0.11        0.08

Matches are distributed among these distances:
  43    5  0.12
  44    4  0.09
  45   34  0.79

ACGTcount: A:0.35, C:0.04, G:0.09, T:0.51


Consensus pattern (45 bp):   
TTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTAATACAA

Found at i:3631 original size:42 final size:43

Alignment explanation


    Indices: 3580--3672  Score: 129
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       3570 AGAGCAATAT

                                     *                  
       3580 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCTCATCTCTAGATAATTCATC-AAATAAAG

              *                                         
       3621 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAATAAAG
          1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAATAAAG

                    
       3665 CTAATATT
          1 CTAATATT

       3673 AATTGTTGCT


Statistics
Matches: 45,  Mismatches: 3, Indels: 5
        0.85            0.06        0.09

Matches are distributed among these distances:
  41    3  0.07
  42    8  0.18
  43    2  0.04
  44   15  0.33
  45   17  0.38

ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35


Consensus pattern (43 bp):   
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAATAAAG
Done.