Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1534

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: 8161
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:4021 original size:13 final size:13

Alignment explanation


    Indices: 4003--4029  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       3993 TACAATTTTT

                         
       4003 TTGTATCGATACA
          1 TTGTATCGATACA

                         
       4016 TTGTATCGATACA
          1 TTGTATCGATACA

             
       4029 T
          1 T

       4030 ACTTGCTGTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41


Consensus pattern (13 bp):   
TTGTATCGATACA

Found at i:4115 original size:20 final size:20

Alignment explanation


    Indices: 4090--4162  Score: 101
    Period size: 20  Copynumber: 3.6  Consensus size: 20

       4080 ATCTTTTTTT

                                
       4090 ATGTATCGATACATTGCAAC
          1 ATGTATCGATACATTGCAAC

                            **** 
       4110 ATGTATCGATACATCTTTTTC
          1 ATGTATCGATACAT-TGCAAC

                                
       4131 ATGTATCGATACATTGCAAC
          1 ATGTATCGATACATTGCAAC

                        
       4151 ATGTATCGATAC
          1 ATGTATCGATAC

       4163 TTTGAGTTGT


Statistics
Matches: 44,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  20   28  0.64
  21   16  0.36

ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36


Consensus pattern (20 bp):   
ATGTATCGATACATTGCAAC

Found at i:4141 original size:41 final size:42

Alignment explanation


    Indices: 4068--4162  Score: 174
    Period size: 41  Copynumber: 2.3  Consensus size: 42

       4058 CTGCCAAGAA

                                 *                    
       4068 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
          1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC

                                                      
       4110 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
          1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC

                        
       4151 ATGTATCGATAC
          1 ATGTATCGATAC

       4163 TTTGAGTTGT


Statistics
Matches: 52,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  41   37  0.71
  42   15  0.29

ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40


Consensus pattern (42 bp):   
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC

Found at i:4793 original size:15 final size:15

Alignment explanation


    Indices: 4763--4806  Score: 54
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       4753 TTCTCCTTTG

                             
       4763 TCTCCCCCGTTTAAAAA
          1 TCTCCCCC--TTAAAAA

                            
       4780 TCTCCCCCTTAAAAAA
          1 TCTCCCCCTT-AAAAA

                        
       4796 TCT-CCCCTTAA
          1 TCTCCCCCTTAA

       4807 TCAAGTAATT


Statistics
Matches: 26,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  14    2  0.08
  15    8  0.31
  16    8  0.31
  17    8  0.31

ACGTcount: A:0.30, C:0.39, G:0.02, T:0.30


Consensus pattern (15 bp):   
TCTCCCCCTTAAAAA

Found at i:4794 original size:16 final size:16

Alignment explanation


    Indices: 4763--4806  Score: 63
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       4753 TTCTCCTTTG

                       *     
       4763 TCTCCCCCGTTTAAAAA
          1 TCTCCCCC-TTAAAAAA

                            
       4780 TCTCCCCCTTAAAAAA
          1 TCTCCCCCTTAAAAAA

                        
       4796 TCT-CCCCTTAA
          1 TCTCCCCCTTAA

       4807 TCAAGTAATT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  15    8  0.31
  16   10  0.38
  17    8  0.31

ACGTcount: A:0.30, C:0.39, G:0.02, T:0.30


Consensus pattern (16 bp):   
TCTCCCCCTTAAAAAA

Found at i:6617 original size:13 final size:13

Alignment explanation


    Indices: 6599--6637  Score: 69
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       6589 ATAATCACCC

                        *
       6599 TGTATCGATACAG
          1 TGTATCGATACAA

                         
       6612 TGTATCGATACAA
          1 TGTATCGATACAA

                         
       6625 TGTATCGATACAA
          1 TGTATCGATACAA

       6638 CAAAAAATGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  13   25  1.00

ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Consensus pattern (13 bp):   
TGTATCGATACAA
Done.