Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold409

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: 10973
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29


Found at i:1482 original size:80 final size:78

Alignment explanation


    Indices: 1382--1603  Score: 230
    Period size: 80  Copynumber: 2.8  Consensus size: 78

       1372 CTCGTTCAAG

                        *                     **   *                      *  
       1382 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCATTCAATGCCTTCGGGACTTAACCCGGATTTT
          1 TGCCTTCGGGACTTAGCCCGG-TATAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA-ATT

                        *  
       1447 AAAAACTCGCACGAA
         64 AAAAACTCGCACAAA

                           *     *       *   *                               
       1462 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
          1 TGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGGAATT

              *            
       1527 AATAACTCGCACAAA
         64 AAAAACTCGCACAAA

             *               *           *   *                      *      
       1542 TACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
          1 TGCCTTCGGGA-CTTAGCCCGG-TATAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCGGA

       1604 CAGCATTCAA


Statistics
Matches: 117,  Mismatches: 20, Indels: 10
        0.80            0.14        0.07

Matches are distributed among these distances:
  79    4  0.03
  80   85  0.73
  81   28  0.24

ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25


Consensus pattern (78 bp):   
TGCCTTCGGGACTTAGCCCGGTATAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGAATTAA
AAACTCGCACAAA

Found at i:1507 original size:40 final size:40

Alignment explanation


    Indices: 1419--1603  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       1409 TAACTCATTC

                                     *    *         *
       1419 AATGCCTTCGGGACTTAACCCGGATTTTAAAAACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA

                                        *  *        
       1460 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

              *                                     
       1500 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

               *              **          * *    *     
       1540 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
          1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA

                             *      
       1581 AA-GCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAACCCGGA

       1604 CAGCATTCAA


Statistics
Matches: 122,  Mismatches: 17, Indels: 10
        0.82            0.11        0.07

Matches are distributed among these distances:
  39    5  0.04
  40   82  0.67
  41   35  0.29

ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

Found at i:9340 original size:40 final size:43

Alignment explanation


    Indices: 9253--9342  Score: 114
    Period size: 43  Copynumber: 2.2  Consensus size: 43

       9243 TCATTCAATG

                                      *               *
       9253 CCTTCGGGACTTAACCCGCAAATTTAGGAATCTCGCACAAAGG
          1 CCTTCGGGACTTAACCCGCAAATTTAAGAATCTCGCACAAAGA

                               *       *             * 
       9296 CCTTCGGGACTTAACCCG-GAA-TTAATAA-CTCGCACAAATA
          1 CCTTCGGGACTTAACCCGCAAATTTAAGAATCTCGCACAAAGA

                   
       9336 CCTTCGG
          1 CCTTCGG

       9343 ATCTTAGTCC


Statistics
Matches: 42,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  40   17  0.40
  41    5  0.12
  42    2  0.05
  43   18  0.43

ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22


Consensus pattern (43 bp):   
CCTTCGGGACTTAACCCGCAAATTTAAGAATCTCGCACAAAGA
Done.