Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3559

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: 11210
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29


Found at i:1619 original size:40 final size:40

Alignment explanation


    Indices: 1399--1619  Score: 251
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       1389 GCTCCTCGTT

                            *        *              
       1399 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                               *       *            
       1439 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                               *       *            
       1479 CAAATGCCTTCGGG-CTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                     *        *      
       1518 C-AATGCCTTC-GGATCTTAG-CC-AAT-TAGTATCTCGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCGCA

                                 *        *  *    *   
       1554 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA

                                      
       1595 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

       1620 CATCATTCAA


Statistics
Matches: 160,  Mismatches: 13, Indels: 16
        0.85            0.07        0.08

Matches are distributed among these distances:
  36   12  0.08
  37   22  0.14
  38   13  0.08
  39   32  0.20
  40   70  0.44
  41   11  0.07

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


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

Found at i:9456 original size:79 final size:82

Alignment explanation


    Indices: 9345--9529  Score: 247
    Period size: 79  Copynumber: 2.3  Consensus size: 82

       9335 GCTACTCGTT

                            *         *                                      
       9345 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC

                *         *   
       9408 GGATTTAGTAAC-TCGCA
         65 GGATATAGTAACTTAGCA

                                                                        **   
       9425 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG

                 *  *        
       9488 GATATGGTCACTTAGCA
         66 GATATAGTAACTTAGCA

                                      
       9505 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

       9530 CATCATTCAA


Statistics
Matches: 93,  Mismatches: 8, Indels: 8
        0.85            0.07        0.07

Matches are distributed among these distances:
  78    3  0.03
  79   56  0.60
  80   34  0.37

ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24


Consensus pattern (82 bp):   
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA

Found at i:9529 original size:40 final size:40

Alignment explanation


    Indices: 9326--9529  Score: 247
    Period size: 40  Copynumber: 5.1  Consensus size: 40

       9316 CGGAATTTAA

                              **                *    
       9326 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
          1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC

                *                                 * 
       9366 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                  *                                 
       9406 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                                                     *
       9445 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
          1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC

                    *  *    *                        
       9485 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
          1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC

                 
       9525 CCGGA
          1 CCGGA

       9530 CATCATTCAA


Statistics
Matches: 143,  Mismatches: 14, Indels: 14
        0.84            0.08        0.08

Matches are distributed among these distances:
  38    2  0.01
  39   34  0.24
  40   95  0.66
  41   12  0.08

ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25


Consensus pattern (40 bp):   
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.