sallet_2.scaffold.fasta.s102.2.7.7.80.10.50.500.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: C7511

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1056
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37


Found at i:583 original size:11 final size:10

Alignment explanation


    Indices: 562--594  Score: 52
    Period size: 9  Copynumber: 3.5  Consensus size: 10

        552 CTTATATATT

                      
        562 TATATAAATA
          1 TATATAAATA

                      
        572 TATATAAA-A
          1 TATATAAATA

                      
        581 TATATAAAT-
          1 TATATAAATA

                 
        590 TATAT
          1 TATAT

        595 TATTTGAACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
   9   14  0.64
  10    8  0.36

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (10 bp):   
TATATAAATA

Left flanking sequence: Indices 62 -- 561
GCAACTGCTGGCACATGCATTGGTTAGGACTCTTACATATTTATATCATTATTATAAATAAGCTG
AAGTTTATAGTTATCCTTTTATAATTACTTTTATATATTTAAAAATATATAAACAATCATTTATA
AAAATGATTTAATATTATATACTTCTCGTAGATTGCTTGATCAGTCGTTAGACCATTGTCAAAGA
TTCCTCACTGCTGCTCCTAATAAGAGTACCCCTATGGGGCATGTGATCGTTGTGACGTTAATCAT
CGATTCCAGTTCTACAGCTAGATAATTATATCTAATACCTACATCTGAAAACATATTTTCATATG
TTTTATCACTCACCAGTACGCTAAAATATTTATATATTAACTCGCATGTGTTATGCATCTACAAA
GCATTTGATCTGAACCAACATCATGTTCTCATTAATTTTATTTTATTTTTTATTTTATAAATATA
AATATTTTATATTTATTTATTTCTCACCTATATATCTTATATATT


Right flanking sequence: Indices 595 -- 1056
TATTTGAACTACTCAGAATTGAACTGAGATAGATCCATTATGAGTGGATTGCTCTACCATTGAGC
TATAATTCATTTAATATACCTACATTTTATGTAGGTATATATAATTTATTTAATATACCTACATT
TTATGTAGGTATGATAAAATTGCAGCAGATAGATTCGAACTACCATAACAAGGTCATGAGCCTGG
TATGTTACCTATTACATTATACTGCATATCATATAATACTTACCTATAAAACAACGAATATATAT
AATAAAGAAGAAGCATCTCATAAGAAATCAATAGCTCAATTAGGGAAGAAACCTAAGAAAATAGT
AGGAATAATTAATGCTAACATTAAGAATGATTCTCTATTAGTACAATCAGCTGTTAAATTAATAT
AAGGAGTTTTAACTCCACCTGTTAATCTATTAGTTAATTTCATTTGATAACAAGCTGATAATAAA
ACAGAAA



Found at i:714 original size:39 final size:40

Alignment explanation


    Indices: 660--745  Score: 147
    Period size: 39  Copynumber: 2.2  Consensus size: 40

        650 ACCATTGAGC

                                                    
        660 TATAATTCATTTAATATACCTACATTTTATGTAGGTAT-A
          1 TATAATTCATTTAATATACCTACATTTTATGTAGGTATGA

                   *                                
        699 TATAATTTATTTAATATACCTACATTTTATGTAGGTATGA
          1 TATAATTCATTTAATATACCTACATTTTATGTAGGTATGA

              *    
        739 TAAAATT
          1 TATAATT

        746 GCAGCAGATA


Statistics
Matches: 44,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  39   37  0.84
  40    7  0.16

ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47


Consensus pattern (40 bp):   
TATAATTCATTTAATATACCTACATTTTATGTAGGTATGA

Left flanking sequence: Indices 160 -- 659
TATATTTAAAAATATATAAACAATCATTTATAAAAATGATTTAATATTATATACTTCTCGTAGAT
TGCTTGATCAGTCGTTAGACCATTGTCAAAGATTCCTCACTGCTGCTCCTAATAAGAGTACCCCT
ATGGGGCATGTGATCGTTGTGACGTTAATCATCGATTCCAGTTCTACAGCTAGATAATTATATCT
AATACCTACATCTGAAAACATATTTTCATATGTTTTATCACTCACCAGTACGCTAAAATATTTAT
ATATTAACTCGCATGTGTTATGCATCTACAAAGCATTTGATCTGAACCAACATCATGTTCTCATT
AATTTTATTTTATTTTTTATTTTATAAATATAAATATTTTATATTTATTTATTTCTCACCTATAT
ATCTTATATATTTATATAAATATATATAAAATATATAAATTATATTATTTGAACTACTCAGAATT
GAACTGAGATAGATCCATTATGAGTGGATTGCTCTACCATTGAGC


Right flanking sequence: Indices 746 -- 1056
GCAGCAGATAGATTCGAACTACCATAACAAGGTCATGAGCCTGGTATGTTACCTATTACATTATA
CTGCATATCATATAATACTTACCTATAAAACAACGAATATATATAATAAAGAAGAAGCATCTCAT
AAGAAATCAATAGCTCAATTAGGGAAGAAACCTAAGAAAATAGTAGGAATAATTAATGCTAACAT
TAAGAATGATTCTCTATTAGTACAATCAGCTGTTAAATTAATATAAGGAGTTTTAACTCCACCTG
TTAATCTATTAGTTAATTTCATTTGATAACAAGCTGATAATAAAACAGAAA


Done.