Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold846

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: 26697
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30


Found at i:4248 original size:40 final size:40

Alignment explanation


    Indices: 4203--4470  Score: 439
    Period size: 40  Copynumber: 6.7  Consensus size: 40

       4193 GCAAACACAT

                                   *                
       4203 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                          *         
       4243 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                        *                 *         
       4283 TTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                         *              * *         
       4323 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                         *                           
       4363 TTGCCTTCGGGTCATAGCCCGGATATATCAATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAA-CTCGCATAA

                                                    
       4404 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                         *              
       4444 TTGCCTTC-GGTCATAGCCCGGATATAT
          1 TTGCCTTCGGGTCTTAGCCCGGATATAT

       4471 TCCAATGCTC


Statistics
Matches: 217,  Mismatches: 10, Indels: 3
        0.94            0.04        0.01

Matches are distributed among these distances:
  39   18  0.08
  40  160  0.74
  41   39  0.18

ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31


Consensus pattern (40 bp):   
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

Found at i:12800 original size:40 final size:40

Alignment explanation


    Indices: 12755--13020  Score: 455
    Period size: 40  Copynumber: 6.7  Consensus size: 40

      12745 GCAAACACAT

                                   *      *         
      12755 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA

                                                    
      12795 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA

                                                    
      12835 TTGCCTTCGGG--TTAGCCCGGATATATCATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA

                         *              *           
      12873 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA

                         *                          
      12913 TTGCCTTCGGGTCATAGCCCGGATATATCATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA

                                          *         
      12953 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA

                         *              
      12993 TTGCCTTCGGGTCATAGCCCGGATATAT
          1 TTGCCTTCGGGTCTTAGCCCGGATATAT

      13021 TCCAATGCTC


Statistics
Matches: 216,  Mismatches: 8, Indels: 4
        0.95            0.04        0.02

Matches are distributed among these distances:
  38   38  0.18
  40  178  0.82

ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31


Consensus pattern (40 bp):   
TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA

Found at i:18896 original size:17 final size:17

Alignment explanation


    Indices: 18870--18910  Score: 73
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      18860 GAGTAGACCT

                 *           
      18870 CAACCAATACTCAACCA
          1 CAACCGATACTCAACCA

                             
      18887 CAACCGATACTCAACCA
          1 CAACCGATACTCAACCA

                   
      18904 CAACCGA
          1 CAACCGA

      18911 ATTACCAAGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.44, C:0.41, G:0.05, T:0.10


Consensus pattern (17 bp):   
CAACCGATACTCAACCA

Found at i:19644 original size:29 final size:29

Alignment explanation


    Indices: 19610--19683  Score: 96
    Period size: 29  Copynumber: 2.6  Consensus size: 29

      19600 TAATCAACCG

                              *           
      19610 CGCACACTTAGTGCCATGTACTTT-AAACT
          1 CGCACACTTAGTGCCATGCA-TTTCAAACT

                                      ** 
      19639 CGCACACTTAGTGCCATGCATTTCAAGTT
          1 CGCACACTTAGTGCCATGCATTTCAAACT

                   *        
      19668 CGCACACCTAGTGCCA
          1 CGCACACTTAGTGCCA

      19684 ATCTCACAAC


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  28    3  0.08
  29   37  0.93

ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27


Consensus pattern (29 bp):   
CGCACACTTAGTGCCATGCATTTCAAACT
Done.