Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4181

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: 15692
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30


Found at i:1814 original size:40 final size:40

Alignment explanation


    Indices: 1733--1960  Score: 354
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       1723 TTTCCAAACC

                 *         *                          
       1733 CAAATACCTTCGGGATTTAG-CCGGATATAG-CAACTCA-CA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTCAA-T-AGCA

                   *      *                         
       1772 CAAATGCATTCGGGTCTTAGCCCGGATATAGTCAATAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCA

                *                             *     
       1812 CAAAAGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCA

                                                    
       1852 CAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCA

                                   *                
       1892 CAAATGCCTTCGGGACTTAGCCCAGATATAGTCAATAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCA

                                         
       1932 CAAATGCCTTCGGGACTTAGCCCGGATAT
          1 CAAATGCCTTCGGGACTTAGCCCGGATAT

       1961 CATTCGAATA


Statistics
Matches: 174,  Mismatches: 12, Indels: 5
        0.91            0.06        0.03

Matches are distributed among these distances:
  39   17  0.10
  40  154  0.89
  41    3  0.02

ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCA

Found at i:10035 original size:39 final size:39

Alignment explanation


    Indices: 9891--10090  Score: 262
    Period size: 39  Copynumber: 5.3  Consensus size: 39

       9881 ACCTCGGGAT

                                                    * 
       9891 TTAG-CCGGATATAG-CAACTCA-CACAAATGCCTTCGGGTC
          1 TTAGCCCGGATATAGTCAA-T-AGCACAAATGCCTTC-GGAC

                                                   
       9930 TTAG-CC-GATA-A-TCAATAGCACAAA-GCC-TCGGAC
          1 TTAGCCCGGATATAGTCAATAGCACAAATGCCTTCGGAC

                              *                    
       9963 TTAGCCC-GATATAG-CACTAG-ACAAATGCCTTCGGAC
          1 TTAGCCCGGATATAGTCAATAGCACAAATGCCTTCGGAC

                                                   
       9999 TTAGCCCGGATATAGTCAATAGCACAAATGCCTTCGGAC
          1 TTAGCCCGGATATAGTCAATAGCACAAATGCCTTCGGAC

                                                    
      10038 TTAGCCCGGATATAGTCAATAGCACAAATGCCTTCAGGAC
          1 TTAGCCCGGATATAGTCAATAGCACAAATGCCTTC-GGAC

                         
      10078 TTAGCCCGGATAT
          1 TTAGCCCGGATAT

      10091 CATTCGAATA


Statistics
Matches: 147,  Mismatches: 3, Indels: 21
        0.86            0.02        0.12

Matches are distributed among these distances:
  33    7  0.05
  34   13  0.09
  35   13  0.09
  36   20  0.14
  37   11  0.07
  38    9  0.06
  39   57  0.39
  40   17  0.12

ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23


Consensus pattern (39 bp):   
TTAGCCCGGATATAGTCAATAGCACAAATGCCTTCGGAC

Found at i:11153 original size:24 final size:22

Alignment explanation


    Indices: 11126--11169  Score: 61
    Period size: 24  Copynumber: 1.9  Consensus size: 22

      11116 TCCATAGCTA

                *                   
      11126 CAATGCCGAAAGTTCTAGACATCT
          1 CAATACCGAAA-TTCTA-ACATCT

                                
      11150 CAATACCGAAATTCTAACAT
          1 CAATACCGAAATTCTAACAT

      11170 GGGTTGTCTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22    4  0.21
  23    5  0.26
  24   10  0.53

ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25


Consensus pattern (22 bp):   
CAATACCGAAATTCTAACATCT

Found at i:14421 original size:39 final size:39

Alignment explanation


    Indices: 14257--14439  Score: 179
    Period size: 40  Copynumber: 4.6  Consensus size: 39

      14247 TTGAATGCTG

                  *              *       *   * *  * 
      14257 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
          1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA

                 **                *         *       
      14297 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
          1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA

                                     *         *    
      14337 TCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTTATTAAA
          1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA

                                       *           
      14377 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA

            *     *  *              
      14416 ACCGGGCTATGTCCCGAAGGCATT
          1 TCCGGGTTAAGTCCCGAAGGCATT

      14440 TGAACGAGGA


Statistics
Matches: 121,  Mismatches: 18, Indels: 9
        0.82            0.12        0.06

Matches are distributed among these distances:
  39   37  0.31
  40   75  0.62
  41    9  0.07

ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26


Consensus pattern (39 bp):   
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Done.