Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3003

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: 3669
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31


Found at i:1417 original size:40 final size:40

Alignment explanation


    Indices: 1368--1548  Score: 203
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       1358 CTACTCGTTC

                          *                         
       1368 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACA
          1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA

                             *                      *
       1408 AATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACC
          1 AATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACA

                                    *                
       1448 AATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGCACA
          1 AATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACA

                               *    *   *  *    *     
       1487 AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACA
          1 AATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACA

                                   
       1528 AA-GCCTTC-GGACTTAGCCCGG
          1 AATGCCTTCGGGACTTAGCCCGG

       1549 ACATCATTCG


Statistics
Matches: 122,  Mismatches: 12, Indels: 15
        0.82            0.08        0.10

Matches are distributed among these distances:
  38    2  0.02
  39   40  0.33
  40   69  0.57
  41   11  0.09

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


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA

Found at i:1510 original size:79 final size:80

Alignment explanation


    Indices: 1367--1549  Score: 221
    Period size: 79  Copynumber: 2.3  Consensus size: 80

       1357 GCTACTCGTT

                           *         *                                       
       1367 CAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
          1 CAATGCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG

              *         *   
       1431 ATTTAGTAAC-TCGCA
         65 ATATAGTAACTTAGCA

                                                                        **   
       1446 CCAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
          1 -CAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG

                 *  *        
       1509 GATATGGTCACTTAGCA
         64 GATATAGTAACTTAGCA

               *        *           
       1526 CAAAGCCTTCGGACTTAGCCCGGA
          1 CAATGCCTTCGGGCTTAGCCCGGA

       1550 CATCATTCGA


Statistics
Matches: 90,  Mismatches: 10, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
  78    3  0.03
  79   69  0.77
  80   18  0.20

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24


Consensus pattern (80 bp):   
CAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCA
Done.