Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2808

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: 34124
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:4713 original size:40 final size:39

Alignment explanation


    Indices: 4495--4713  Score: 256
    Period size: 40  Copynumber: 5.7  Consensus size: 39

       4485 GCTACTCGTT

                            *        *              
       4495 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA

                               *                    
       4535 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA

                                                   
       4575 CAAATGCCTTCGGG-CTTA-CCCGGATTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA

                                 *                  
       4612 CAAATGCCTTC---ATCTTAGTCCGGATTAGT-ACTCGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAGTAACTCGCA

                                 *        *  *    *   
       4648 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA

                                      
       4689 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

       4714 CATCATTCAA


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

Matches are distributed among these distances:
  36   22  0.14
  37   34  0.21
  38   20  0.12
  39    7  0.04
  40   67  0.41
  41   12  0.07

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


Consensus pattern (39 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA

Found at i:10384 original size:13 final size:13

Alignment explanation


    Indices: 10368--10402  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      10358 TAGTAAAAAA

                   *     
      10368 AAATAAGGATAAT
          1 AAATAAGAATAAT

                *        
      10381 AAATTAGAATAAT
          1 AAATAAGAATAAT

                     
      10394 AAATAAGAA
          1 AAATAAGAA

      10403 ATCAAATCAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23


Consensus pattern (13 bp):   
AAATAAGAATAAT

Found at i:10726 original size:22 final size:23

Alignment explanation


    Indices: 10682--10726  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      10672 TTTTTAAAAT

                   *               
      10682 TAAAATTTAATTATAAAAGTATA
          1 TAAAATTCAATTATAAAAGTATA

                                    
      10705 TAAAATATCAATTA-AAAA-TATA
          1 TAAAAT-TCAATTATAAAAGTATA

      10727 AAATACAATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  22    4  0.20
  23   10  0.50
  24    6  0.30

ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36


Consensus pattern (23 bp):   
TAAAATTCAATTATAAAAGTATA

Found at i:13378 original size:45 final size:45

Alignment explanation


    Indices: 13328--13415  Score: 167
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      13318 GCAAAACATG

                                                         
      13328 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTTATA
          1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTTATA

                     *                                 
      13373 TGTCACATATATCATGAACTCAGACCACAACTCAATGAGTTTA
          1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTTA

      13416 GATCACATAA


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27


Consensus pattern (45 bp):   
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTTATA

Found at i:26344 original size:15 final size:15

Alignment explanation


    Indices: 26324--26353  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      26314 CAACACTTGT

                           
      26324 GCCGAAACCACAAAA
          1 GCCGAAACCACAAAA

                     *     
      26339 GCCGAAACCTCAAAA
          1 GCCGAAACCACAAAA

      26354 AATACATTAG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03


Consensus pattern (15 bp):   
GCCGAAACCACAAAA
Done.