Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1113

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: 12741
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32


Found at i:213 original size:15 final size:17

Alignment explanation


    Indices: 180--217  Score: 62
    Period size: 17  Copynumber: 2.4  Consensus size: 17

        170 AAATCAATCC

                             
        180 TTTTAAAAAAAGTTAAA
          1 TTTTAAAAAAAGTTAAA

                             
        197 TTTTAAAAAAA-TT-AA
          1 TTTTAAAAAAAGTTAAA

                  
        212 TTTTAA
          1 TTTTAA

        218 TATGTATCCG


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  15    8  0.38
  16    2  0.10
  17   11  0.52

ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42


Consensus pattern (17 bp):   
TTTTAAAAAAAGTTAAA

Found at i:577 original size:28 final size:27

Alignment explanation


    Indices: 527--579  Score: 70
    Period size: 28  Copynumber: 1.9  Consensus size: 27

        517 TTCAAACTAT

                           ** *        
        527 TTGATTTAATTAGTTTTAGTTAATTAC
          1 TTGATTTAATTAGTTCCAATTAATTAC

                                      
        554 TTGATTTTAATTAGTTCCAATTAATT
          1 TTGA-TTTAATTAGTTCCAATTAATT

        580 TAATTAATTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  27    4  0.18
  28   18  0.82

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (27 bp):   
TTGATTTAATTAGTTCCAATTAATTAC

Found at i:2759 original size:15 final size:13

Alignment explanation


    Indices: 2719--2758  Score: 62
    Period size: 13  Copynumber: 3.1  Consensus size: 13

       2709 TAATCTTAAC

                       * 
       2719 AATATATATATGT
          1 AATATATATATAT

                  *      
       2732 AATATAGATATAT
          1 AATATATATATAT

                         
       2745 AATATATATATAT
          1 AATATATATATAT

             
       2758 A
          1 A

       2759 TCTGAATCAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  13   24  1.00

ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42


Consensus pattern (13 bp):   
AATATATATATAT

Found at i:3028 original size:25 final size:24

Alignment explanation


    Indices: 2989--3049  Score: 74
    Period size: 25  Copynumber: 2.6  Consensus size: 24

       2979 TATTTAGATA

                                     
       2989 TAAATTAAAATAAAGTTTATTTATG
          1 TAAATTAAAATAAAGTTT-TTTATG

                                  *  
       3014 TAAATATAAAA-AAAGTTTTTTGTG
          1 TAAAT-TAAAATAAAGTTTTTTATG

                          
       3038 TAAA--AAAATAAA
          1 TAAATTAAAATAAA

       3050 TTAAAGATTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
  21    4  0.12
  22    3  0.09
  24    9  0.27
  25   12  0.36
  26    5  0.15

ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38


Consensus pattern (24 bp):   
TAAATTAAAATAAAGTTTTTTATG

Found at i:3049 original size:26 final size:26

Alignment explanation


    Indices: 2994--3043  Score: 68
    Period size: 24  Copynumber: 2.0  Consensus size: 26

       2984 AGATATAAAT

                                    * 
       2994 TAAAATAAAGTTTATTTATGTAAATA
          1 TAAAATAAAGTTTATTTATGTAAAAA

                             *        
       3020 TAAAA-AAAGTTT-TTTGTGTAAAAA
          1 TAAAATAAAGTTTATTTATGTAAAAA

       3044 AATAAATTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  24   10  0.45
  25    7  0.32
  26    5  0.23

ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40


Consensus pattern (26 bp):   
TAAAATAAAGTTTATTTATGTAAAAA

Found at i:4193 original size:89 final size:85

Alignment explanation


    Indices: 4046--4204  Score: 210
    Period size: 89  Copynumber: 1.8  Consensus size: 85

       4036 ATACACACAT

                                   *       *     *                           
       4046 AATTAAATAACAAAATAAATAATTATATTTTTATAATGATACATACGCATACCACATAAATTACA
          1 AATTAAATAACAAAATAAATAATAATATTTTCATAATAATACATACGCATACCACATAAATTACA

                                
       4111 CAATTATACAATATATACTC
         66 CAATTATACAATATATACTC

                      * *                                    *     * *       
       4131 AATTAAATAATAGAATAAATAATAACAATATTTTGCATAATAATACATATGCATATCGCATAAAT
          1 AATTAAATAACAAAATAAATAAT---AATATTTT-CATAATAATACATACGCATACCACATAAAT

                     
       4196 TACACAATT
         62 TACACAATT

       4205 TTCAATTACA


Statistics
Matches: 62,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  85   21  0.34
  88    7  0.11
  89   34  0.55

ACGTcount: A:0.51, C:0.13, G:0.04, T:0.33


Consensus pattern (85 bp):   
AATTAAATAACAAAATAAATAATAATATTTTCATAATAATACATACGCATACCACATAAATTACA
CAATTATACAATATATACTC
Done.