Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2404

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: 23635
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30


Found at i:1335 original size:40 final size:40

Alignment explanation


    Indices: 1273--1397  Score: 166
    Period size: 40  Copynumber: 3.1  Consensus size: 40

       1263 AAACCAAGTA

                     *    *                   *      
       1273 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
          1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG

                                                    
       1312 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                       *   *         
       1352 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG

                  
       1392 CCTTCG
          1 CCTTCG

       1398 TTATCATCCG


Statistics
Matches: 78,  Mismatches: 5, Indels: 5
        0.89            0.06        0.06

Matches are distributed among these distances:
  39   14  0.18
  40   64  0.82

ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

Found at i:8978 original size:39 final size:40

Alignment explanation


    Indices: 8880--9062  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       8870 GAATGATGTC

                                        *   *   *    *
       8880 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATC
          1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TA

               *                                     
       8920 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTA
          1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTA

                                  *              * *
       8960 CGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATC
          1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTA

                *                                 * 
       8999 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAA
          1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTA

                    *                
       9038 TCGGGCTATGTCCCGAAGGCATTTG
          1 -CGGGCTAAGTCCCGAAGGCATTTG

       9063 AACTAGTAGC


Statistics
Matches: 121,  Mismatches: 16, Indels: 12
        0.81            0.11        0.08

Matches are distributed among these distances:
  39   35  0.29
  40   76  0.63
  41   10  0.08

ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26


Consensus pattern (40 bp):   
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTA
Done.