Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1090

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: 12108
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30


Found at i:5995 original size:118 final size:119

Alignment explanation


    Indices: 5814--6035  Score: 299
    Period size: 118  Copynumber: 1.9  Consensus size: 119

       5804 TCCTCGTTCA

                                   *                                         
       5814 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
          1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT

            *         *                                            
       5879 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
         66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC

                          *                 *                          **    
       5933 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
          1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG

                *  *                          *      
       5995 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
         64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA

       6036 CATCATTCAA


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

Matches are distributed among these distances:
 117    4  0.04
 118   66  0.73
 119   20  0.22

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


Consensus pattern (119 bp):   
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC

Found at i:6035 original size:40 final size:40

Alignment explanation


    Indices: 5812--6035  Score: 287
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       5802 GCTCCTCGTT

                            *        *              
       5812 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                               *       *            
       5852 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                               *       *            
       5892 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                              *      
       5932 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA

                                 *        *  *    *   
       5970 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA

                                      
       6011 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

       6036 CATCATTCAA


Statistics
Matches: 164,  Mismatches: 13, Indels: 14
        0.86            0.07        0.07

Matches are distributed among these distances:
  38   24  0.15
  39   21  0.13
  40  107  0.65
  41   12  0.07

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


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

Found at i:9396 original size:43 final size:42

Alignment explanation


    Indices: 9316--9427  Score: 152
    Period size: 43  Copynumber: 2.6  Consensus size: 42

       9306 TGAGATTATG

                           *                      **  
       9316 TGTAAGACCATATCTAGGATATGGCATCGATATGAGATTTCA
          1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCCCA

                         *    *                        
       9358 TGTAAGACCATATTTGGGCTAATGGCATCGATATGAGATCCCA
          1 TGTAAGACCATATCTGGGAT-ATGGCATCGATATGAGATCCCA

                 * *                   
       9401 TGTAAAATCATATCTGGGATATGGCAT
          1 TGTAAGACCATATCTGGGATATGGCAT

       9428 TGTTATGATA


Statistics
Matches: 60,  Mismatches: 9, Indels: 2
        0.85            0.13        0.03

Matches are distributed among these distances:
  42   24  0.40
  43   36  0.60

ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30


Consensus pattern (42 bp):   
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATCCCA
Done.