Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1060

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: 8913
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29


Found at i:1375 original size:39 final size:40

Alignment explanation


    Indices: 1298--1404  Score: 119
    Period size: 40  Copynumber: 2.7  Consensus size: 40

       1288 TAGCTCCTCG

                              *  *            *      
       1298 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
          1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA

                                         *         *
       1338 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
          1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA

            **                          
       1377 CACGAATGCCTTCGGGACTTAACCCGGA
          1 TTC-AATGCCTTCGGGACTTAACCCGGA

       1405 ATTAGTATCT


Statistics
Matches: 58,  Mismatches: 7, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  39   25  0.43
  40   33  0.57

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


Consensus pattern (40 bp):   
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA

Found at i:1472 original size:40 final size:40

Alignment explanation


    Indices: 1341--1471  Score: 176
    Period size: 40  Copynumber: 3.3  Consensus size: 40

       1331 TAACTCATTC

                                     *              *
       1341 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA

                                        *  *        
       1381 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

              *                                      
       1421 AAGGCCTTC-GGACTATAACCCGGAATTAATAACTCGCACA
          1 AATGCCTTCGGGACT-TAACCCGGAATTAATAACTCGCACA

               *       
       1461 AATACCTTCGG
          1 AATGCCTTCGG

       1472 ATCTTAGTCC


Statistics
Matches: 79,  Mismatches: 9, Indels: 5
        0.85            0.10        0.05

Matches are distributed among these distances:
  39    8  0.10
  40   70  0.89
  41    1  0.01

ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

Found at i:8281 original size:39 final size:40

Alignment explanation


    Indices: 8204--8350  Score: 120
    Period size: 40  Copynumber: 3.7  Consensus size: 40

       8194 TAGCTCCTCG

                              *  *            *      
       8204 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
          1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA

                                         *         *
       8244 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
          1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA

            **                          *     * *   *
       8283 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
          1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA

            **    *                     
       8323 CACAAAGGCCTTCGGGACTTAACCCGGA
          1 TTC-AATGCCTTCGGGACTTAACCCGGA

       8351 ATTAATAACT


Statistics
Matches: 92,  Mismatches: 12, Indels: 6
        0.84            0.11        0.05

Matches are distributed among these distances:
  39   27  0.29
  40   65  0.71

ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25


Consensus pattern (40 bp):   
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA

Found at i:8361 original size:80 final size:80

Alignment explanation


    Indices: 8250--8430  Score: 219
    Period size: 80  Copynumber: 2.3  Consensus size: 80

       8240 CTCATTCAAT

                                  *             *   *                        
       8250 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
          1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-

                      *       
       8313 TAGT-A-TCTCGCACAAA
         64 TAGTCACT-TAGCACAAA

                                                                    **       
       8329 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
          1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA

                             
       8393 TAGTCACTTAGCACAAA
         64 TAGTCACTTAGCACAAA

                          *      
       8410 GCCTTCGGGACTTAGCCCGGA
          1 GCCTTCGGGACTTAACCCGGA

       8431 CAGCATTCAA


Statistics
Matches: 89,  Mismatches: 7, Indels: 10
        0.84            0.07        0.09

Matches are distributed among these distances:
  79    7  0.08
  80   71  0.80
  81   10  0.11
  82    1  0.01

ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24


Consensus pattern (80 bp):   
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA

Found at i:8390 original size:40 final size:40

Alignment explanation


    Indices: 8247--8430  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       8237 TAACTCATTC

                                     *              *
       8247 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA

                                        *  *        
       8287 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

              *                                     
       8327 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

               *              **          * *    *     
       8367 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
          1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA

                             *      
       8408 AA-GCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAACCCGGA

       8431 CAGCATTCAA


Statistics
Matches: 122,  Mismatches: 16, Indels: 11
        0.82            0.11        0.07

Matches are distributed among these distances:
  39    8  0.07
  40  103  0.84
  41   11  0.09

ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Done.