Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2552

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: 18373
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29


Found at i:1150 original size:27 final size:26

Alignment explanation


    Indices: 1102--1161  Score: 75
    Period size: 27  Copynumber: 2.3  Consensus size: 26

       1092 GGGAGACTGC

                             *         
       1102 CAGATATTGTGACGAAGTCACCAGATA
          1 CAGATATTGTGACGAAGCCACCAGA-A

                       * * *          
       1129 CAGATATTGTGGCTAGGCCACCAGAA
          1 CAGATATTGTGACGAAGCCACCAGAA

                   
       1155 CAGATAT
          1 CAGATAT

       1162 ATATATGTGG


Statistics
Matches: 29,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  26    8  0.28
  27   21  0.72

ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22


Consensus pattern (26 bp):   
CAGATATTGTGACGAAGCCACCAGAA

Found at i:1248 original size:27 final size:26

Alignment explanation


    Indices: 1200--1251  Score: 68
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       1190 GCGAGGCTGC

                             *        
       1200 CAGATATTGTGACGAAGTCACCAGAA
          1 CAGATATTGTGACGAAGCCACCAGAA

                        *   *         
       1226 CAGATATATGTGGCGAGGCCACCAGA
          1 CAGATAT-TGTGACGAAGCCACCAGA

       1252 TTGCAACGAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26    7  0.32
  27   15  0.68

ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17


Consensus pattern (26 bp):   
CAGATATTGTGACGAAGCCACCAGAA

Found at i:10355 original size:40 final size:40

Alignment explanation


    Indices: 10286--10510  Score: 308
    Period size: 40  Copynumber: 5.6  Consensus size: 40

      10276 AAACCAAGTA

                     *             * *              
      10286 CCTTCGGGATTTAG-CCGGATATCGCAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                         *                      *   
      10325 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACACATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                    *           *     *   *         
      10365 CCTTCGGGTCTTAGCCCGGAAATAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                               *      *                
      10405 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAG-TA--ACTCGCACAAATG

                                          *         
      10448 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                   
      10488 CCTTCGGGACTTAGCCCGGATAT
          1 CCTTCGGGACTTAGCCCGGATAT

      10511 CATCCGAATA


Statistics
Matches: 162,  Mismatches: 20, Indels: 7
        0.86            0.11        0.04

Matches are distributed among these distances:
  39   12  0.07
  40  113  0.70
  42    1  0.01
  43   36  0.22

ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

Found at i:10473 original size:83 final size:80

Alignment explanation


    Indices: 10286--10510  Score: 301
    Period size: 83  Copynumber: 2.8  Consensus size: 80

      10276 AAACCAAGTA

                     *             *       *                      *          
      10286 CCTTCGGGATTTAG-CCGGATATCG-CAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATA
          1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA

             *          *   
      10349 GTAACTCGCACACATG
         65 GAAACTCGCACAAATG

                    *           *                                      *     
      10365 CCTTCGGGTCTTAGCCCGGAAATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG
          1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG

                              
      10430 CAACTACTCGCACAAATG
         66 -AA--ACTCGCACAAATG

                                      *   *                                
      10448 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
          1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT

      10511 CATCCGAATA


Statistics
Matches: 127,  Mismatches: 14, Indels: 6
        0.86            0.10        0.04

Matches are distributed among these distances:
  79   12  0.09
  80   43  0.34
  81    2  0.02
  83   70  0.55

ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23


Consensus pattern (80 bp):   
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
AAACTCGCACAAATG
Done.