Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold725

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: 10430
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29


Found at i:1473 original size:79 final size:81

Alignment explanation


    Indices: 1349--1532  Score: 227
    Period size: 79  Copynumber: 2.3  Consensus size: 81

       1339 GCTACTCGTT

                            *         *                                      
       1349 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG

               *         *   
       1412 GATTTAGTAAC-TCGCA
         65 GATATAGTAACTTAGCA

                                              *                         **   
       1428 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG

                 *  *        
       1491 GATATGGTCACTTAGCA
         65 GATATAGTAACTTAGCA

                                      
       1508 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

       1533 CATCATTCAA


Statistics
Matches: 91,  Mismatches: 9, Indels: 9
        0.83            0.08        0.08

Matches are distributed among these distances:
  78   24  0.26
  79   48  0.53
  80   19  0.21

ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24


Consensus pattern (81 bp):   
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA

Found at i:1532 original size:40 final size:40

Alignment explanation


    Indices: 1330--1532  Score: 229
    Period size: 39  Copynumber: 5.1  Consensus size: 40

       1320 CGGAATTTAA

                              **                *    
       1330 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
          1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC

                *                                 * 
       1370 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                  *                                 
       1409 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                         *                           *
       1448 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
          1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC

                    *  *    *                        
       1488 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
          1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC

                 
       1528 CCGGA
          1 CCGGA

       1533 CATCATTCAA


Statistics
Matches: 139,  Mismatches: 16, Indels: 16
        0.81            0.09        0.09

Matches are distributed among these distances:
  38    2  0.01
  39   68  0.49
  40   57  0.41
  41   12  0.09

ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25


Consensus pattern (40 bp):   
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

Found at i:8998 original size:39 final size:39

Alignment explanation


    Indices: 8914--9055  Score: 139
    Period size: 39  Copynumber: 3.6  Consensus size: 39

       8904 AACTCGTTCA

                          *                    *    
       8914 AAATGCCTTCGGACATAGCCC-G-TTATAGTAACTCGCAC
          1 AAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTTGCAC

              *               *                     
       8952 AATTGCCTTCGGGACTTAACCCGGATTTAGT-ACTTGCAC
          1 AAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTTGCAC

                               *      * *  *         
       8991 AAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCAC
          1 AAATGCCTTCGGA-CTTAGCCCGGATTTAGTAACTT-GCAC

                                     
       9032 AAA-GCCTTCGGGACTTAGCCCGGA
          1 AAATGCCTTC-GGACTTAGCCCGGA

       9056 CATCATTCAA


Statistics
Matches: 87,  Mismatches: 10, Indels: 12
        0.80            0.09        0.11

Matches are distributed among these distances:
  38   12  0.14
  39   38  0.44
  40   25  0.29
  41   12  0.14

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


Consensus pattern (39 bp):   
AAATGCCTTCGGACTTAGCCCGGATTTAGTAACTTGCAC
Done.