Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7290.1

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: 7442
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29


Found at i:3065 original size:63 final size:63

Alignment explanation


    Indices: 2962--3080  Score: 204
    Period size: 63  Copynumber: 1.9  Consensus size: 63

       2952 TACGAACCGA

                                                                           
       2962 TCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAATACCGCAGGGGCATTGAATCGG
          1 TCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAATACCGCAGGGGCATTGAATCGG

                                                *        *           
       3025 TCCAAATACT-GTCTGAAGATCCGATTCATCAAATCTATAAATACTGCAGGGGCATT
          1 TCCAAATA-TGGTCTGAAGATCCGATTCATCAAATCCATAAATACCGCAGGGGCATT

       3081 AGTGAGCCCA


Statistics
Matches: 53,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
  63   52  0.98
  64    1  0.02

ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26


Consensus pattern (63 bp):   
TCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAATACCGCAGGGGCATTGAATCGG

Found at i:4214 original size:43 final size:43

Alignment explanation


    Indices: 4149--4233  Score: 127
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       4139 CATCTCTAGA

                                    *                   
       4149 TCCTCTCTGACCACCACCAGCATTGCCCGTATTTCC-AGATGGG
          1 TCCTCTCTGACCACCACCAGCATTACCCGTA-TTCCTAGATGGG

                        *    *                        
       4192 TCCTCTCTGACCGCCACTAGCATTACCCGTATTCCTAGATGG
          1 TCCTCTCTGACCACCACCAGCATTACCCGTATTCCTAGATGG

       4234 TCTACCCCGA


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  42    4  0.11
  43   34  0.89

ACGTcount: A:0.19, C:0.36, G:0.18, T:0.27


Consensus pattern (43 bp):   
TCCTCTCTGACCACCACCAGCATTACCCGTATTCCTAGATGGG

Found at i:5331 original size:45 final size:45

Alignment explanation


    Indices: 5273--5362  Score: 162
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       5263 ATCATCGCTG

                    *                                    
       5273 TCCGTAGCTTTAAATTCAGTAGCCCCATGTTTTCGGATTCTGTCA
          1 TCCGTAGCCTTAAATTCAGTAGCCCCATGTTTTCGGATTCTGTCA

                                      *                  
       5318 TCCGTAGCCTTAAATTCAGTAGCCCCGTGTTTTCGGATTCTGTCA
          1 TCCGTAGCCTTAAATTCAGTAGCCCCATGTTTTCGGATTCTGTCA

       5363 ACTAGGGGCT


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   43  1.00

ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37


Consensus pattern (45 bp):   
TCCGTAGCCTTAAATTCAGTAGCCCCATGTTTTCGGATTCTGTCA

Found at i:5817 original size:71 final size:70

Alignment explanation


    Indices: 5695--5835  Score: 246
    Period size: 71  Copynumber: 2.0  Consensus size: 70

       5685 TAATCACATA

                                     *                            *          
       5695 AAATGGCATGTATAGCTAGACCCAATGCATTACGGTAGTCCTAGAATCGACTAAGCCGTAGCTCT
          1 AAATGGCATGTATAGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTCT

                 
       5760 GATAC
         66 GATAC

                                        *                                    
       5765 AAATGGCATGTATAGCTAGACCCACACGTATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTC
          1 AAATGGCATGTATAGCTAGACCCA-ACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTC

                  
       5830 TGATAC
         65 TGATAC

       5836 CAATAAAATT


Statistics
Matches: 67,  Mismatches: 3, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  70   24  0.36
  71   43  0.64

ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24


Consensus pattern (70 bp):   
AAATGGCATGTATAGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTCT
GATAC

Found at i:7359 original size:150 final size:150

Alignment explanation


    Indices: 7088--7391  Score: 599
    Period size: 150  Copynumber: 2.0  Consensus size: 150

       7078 CTAATTGTAA

                                                                             
       7088 GGGATCAACTAAATCAATGCATATACGAGACATACCTCATTGCTGGGACTTTACGAGCATATTAA
          1 GGGATCAACTAAATCAATGCATATACGAGACATACCTCATTGCTGGGACTTTACGAGCATATTAA

                                                                             
       7153 TTGAAACTATTACAGCAAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACTGGATATA
         66 TTGAAACTATTACAGCAAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACTGGATATA

                                
       7218 GCTACTTCCTCAATGCCTTC
        131 GCTACTTCCTCAATGCCTTC

                                                            *                
       7238 GGGATCAACTAAATCAATGCATATACGAGACATACCTCATTGCTGGGATTTTACGAGCATATTAA
          1 GGGATCAACTAAATCAATGCATATACGAGACATACCTCATTGCTGGGACTTTACGAGCATATTAA

                                                                             
       7303 TTGAAACTATTACAGCAAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACTGGATATA
         66 TTGAAACTATTACAGCAAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACTGGATATA

                                
       7368 GCTACTTCCTCAATGCCTTC
        131 GCTACTTCCTCAATGCCTTC

                
       7388 GGGA
          1 GGGA

       7392 CATAGCCCGG


Statistics
Matches: 153,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 150  153  1.00

ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28


Consensus pattern (150 bp):   
GGGATCAACTAAATCAATGCATATACGAGACATACCTCATTGCTGGGACTTTACGAGCATATTAA
TTGAAACTATTACAGCAAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACTGGATATA
GCTACTTCCTCAATGCCTTC
Done.