Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2900

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: 12180
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30


Found at i:1436 original size:40 final size:40

Alignment explanation


    Indices: 1391--1582  Score: 226
    Period size: 40  Copynumber: 4.8  Consensus size: 40

       1381 ATAACCACAA

                  *               *     *           
       1391 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC

                                             *      
       1431 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC

                                            * *     *
       1471 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC

               *             *              * *     *
       1511 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC

               *             *              
       1551 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT

       1583 CATTCAAATG


Statistics
Matches: 142,  Mismatches: 9, Indels: 3
        0.92            0.06        0.02

Matches are distributed among these distances:
  39    1  0.01
  40  137  0.96
  41    4  0.03

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24


Consensus pattern (40 bp):   
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC

Found at i:1475 original size:80 final size:80

Alignment explanation


    Indices: 1362--1581  Score: 248
    Period size: 80  Copynumber: 2.8  Consensus size: 80

       1352 ACCCAAGTTT

                  * *            *  *   *       *               *     *   *  
       1362 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAG
          1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG

                 *          
       1425 CAACTCGCACAAATGC
         66 C-ACTAGCACAAATGC

                   *              *       *                                  
       1441 CTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
          1 CTTCGGGACTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA

            *        *      
       1505 TCACTAGCATAAATGC
         65 GCACTAGCACAAATGC

                                             *             *             
       1521 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATA
          1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATA

       1582 TCATTCAAAT


Statistics
Matches: 117,  Mismatches: 20, Indels: 7
        0.81            0.14        0.05

Matches are distributed among these distances:
  79   12  0.10
  80   98  0.84
  81    7  0.06

ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24


Consensus pattern (80 bp):   
CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
CACTAGCACAAATGC

Found at i:10704 original size:39 final size:39

Alignment explanation


    Indices: 10668--10849  Score: 217
    Period size: 40  Copynumber: 4.6  Consensus size: 39

      10658 AGCACTCGTT

                           *                       
      10668 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCA

                               *                     
      10707 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
          1 CAAATGCCTTC-GGACTTAGCCCGG-TTATAGTAACTCGCA

             *           *           *              
      10747 CCAATGCCTTCGGGCTTAGCCCGG-AATTAGTAACTCGCA
          1 CAAATGCCTTCGGACTTAGCCCGGTTA-TAGTAACTCGCA

                                *    *      *    *   
      10786 CAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
          1 CAAATGCCTTCGGA-CTTAGCCCGGTTATAGTAAC-TCGCA

                                    
      10827 CAAA-GCCTTCGGACTTAGCCCGG
          1 CAAATGCCTTCGGACTTAGCCCGG

      10850 ACATCTCGAA


Statistics
Matches: 123,  Mismatches: 13, Indels: 14
        0.82            0.09        0.09

Matches are distributed among these distances:
  39   55  0.45
  40   57  0.46
  41   11  0.09

ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24


Consensus pattern (39 bp):   
CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCA

Found at i:10742 original size:40 final size:39

Alignment explanation


    Indices: 10668--10850  Score: 235
    Period size: 39  Copynumber: 4.6  Consensus size: 39

      10658 AGCACTCGTT

                           *                        
      10668 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCGCA

                               *                    
      10707 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCA

             *           *           *             
      10747 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
          1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA

                                *      *    *    *   
      10786 CAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
          1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA

                                     
      10827 CAAA-GCCTTCGGACTTAGCCCGGA
          1 CAAATGCCTTCGGACTTAGCCCGGA

      10851 CATCTCGAAT


Statistics
Matches: 126,  Mismatches: 14, Indels: 8
        0.85            0.09        0.05

Matches are distributed among these distances:
  39   58  0.46
  40   58  0.46
  41   10  0.08

ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24


Consensus pattern (39 bp):   
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA

Found at i:10792 original size:79 final size:80

Alignment explanation


    Indices: 10670--10850  Score: 235
    Period size: 79  Copynumber: 2.3  Consensus size: 80

      10660 CACTCGTTCA

                         *         *                                         
      10670 AATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
          1 AATGCCTTCGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGA

             *         *     
      10733 TTTAGTAAC-TCGCACC
         65 TATAGTAACTTAGCA-C

                       *                                             **      
      10749 AATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
          1 AATGCCTTCGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT

                 *         
      10813 ATAGTCACTTAGCAC
         66 ATAGTAACTTAGCAC

              *                    
      10828 AAAGCCTTCGGACTTAGCCCGGA
          1 AATGCCTTCGGACTTAGCCCGGA

      10851 CATCTCGAAT


Statistics
Matches: 89,  Mismatches: 10, Indels: 6
        0.85            0.10        0.06

Matches are distributed among these distances:
  78    3  0.03
  79   81  0.91
  80    5  0.06

ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24


Consensus pattern (80 bp):   
AATGCCTTCGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Done.