Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3767

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, 398

Length: 664
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35


Found at i:182 original size:23 final size:23

Alignment explanation


    Indices: 156--199  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        146 ATGACTGAAG

                *        *         
        156 CACATGTAACCCTGTGTATTTAA
          1 CACACGTAACCCTATGTATTTAA

                                 
        179 CACACGTAACCCTATGTATTT
          1 CACACGTAACCCTATGTATTT

        200 TGATACGTAG


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34


Consensus pattern (23 bp):   
CACACGTAACCCTATGTATTTAA

Found at i:593 original size:176 final size:176

Alignment explanation


    Indices: 260--598  Score: 416
    Period size: 176  Copynumber: 1.9  Consensus size: 176

        250 TGTATCGAAT

                     *                                         *          *  
        260 TTTTGCGATTTTTTACGGAAAATCGATGACTTTTCGGAATTAGAATCGGGTTTGCTCCATCCGAG
          1 TTTTGCGATATTTTACGGAAAATCGATGACTTTTCGGAATTAGAATCGGGTCTGCTCCATCCAAG

                    *                           *              *  *    *     
        325 ATCGGAGATATGTACCCAACATGATTGGAGCACATCGACTCTTACGTATTTTTATACGTGGAATC
         66 ATCGGAGAAATGTACCCAACATGATTGGAGCACATCAACTCTTACGTATTTCTACACGTAGAATC

            *              *    *                         
        390 GATATATAACCTCGATAAGTCGATATATCGATCAATTGTAATTGAA
        131 AATATATAACCTCGACAAGTAGATATATCGATCAATTGTAATTGAA

                          *              *        *                      *   
        436 TTTTGCGATATTTTGCGGAAAATCGATG-GTTTATCGGGATT-GAGATCGGTGTCT-CTCCGTCC
          1 TTTTGCGATATTTTACGGAAAATCGATGACTTT-TCGGAATTAGA-ATCGG-GTCTGCTCCATCC

                                **                   *                       
        498 AAGATCGGAGAAATGTACCCTTCATGATTGGAGCACATCAATTCTTACGTATTTCTACACGTAGA
         63 AAGATCGGAGAAATGTACCCAACATGATTGGAGCACATCAACTCTTACGTATTTCTACACGTAGA

                    *     *     *           *    
        563 ATCAAT-TTTAAACGTCGACGAGTAGATATATTGATC
        128 ATCAATATAT-AACCTCGACAAGTAGATATATCGATC

        599 TGGATATATC


Statistics
Matches: 137,  Mismatches: 22, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
 175    7  0.05
 176  127  0.93
 177    3  0.02

ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Consensus pattern (176 bp):   
TTTTGCGATATTTTACGGAAAATCGATGACTTTTCGGAATTAGAATCGGGTCTGCTCCATCCAAG
ATCGGAGAAATGTACCCAACATGATTGGAGCACATCAACTCTTACGTATTTCTACACGTAGAATC
AATATATAACCTCGACAAGTAGATATATCGATCAATTGTAATTGAA
Done.