Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold794

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: 6430
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1182 original size:16 final size:16

Alignment explanation


    Indices: 1157--1191  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1147 CCGTATGCAA

                            
       1157 TTTTTTTTCAAT-TTT
          1 TTTTTTTTCAATATTT

                             
       1172 TTTTCTTTTCAATATTT
          1 TTTT-TTTTCAATATTT

               
       1189 TTT
          1 TTT

       1192 GATTTTTTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  15    4  0.22
  16    8  0.44
  17    6  0.33

ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77


Consensus pattern (16 bp):   
TTTTTTTTCAATATTT

Found at i:1211 original size:22 final size:22

Alignment explanation


    Indices: 1172--1213  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1162 TTTCAATTTT

                                  
       1172 TTTTCTTTTCAATATTTTTTGA
          1 TTTTCTTTTCAATATTTTTTGA

                          *      
       1194 TTTT-TTTTCGAATTTTTTTT
          1 TTTTCTTTTC-AATATTTTTT

       1214 TGAAACTACA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    5  0.28
  22   13  0.72

ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74


Consensus pattern (22 bp):   
TTTTCTTTTCAATATTTTTTGA

Found at i:3118 original size:18 final size:17

Alignment explanation


    Indices: 3095--3149  Score: 65
    Period size: 18  Copynumber: 3.1  Consensus size: 17

       3085 AGCAACTCAT

                              
       3095 TTATTAAGCTAAGATGAG
          1 TTATTAA-CTAAGATGAG

                             *
       3113 TTATTAACTAAGATGAAC
          1 TTATTAACTAAGATG-AG

                         *    
       3131 TTAATTAACTAAGTTGAG
          1 TT-ATTAACTAAGATGAG

             
       3149 T
          1 T

       3150 AATTTATTCA


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  17    8  0.25
  18   12  0.38
  19   12  0.38

ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36


Consensus pattern (17 bp):   
TTATTAACTAAGATGAG

Found at i:4075 original size:66 final size:67

Alignment explanation


    Indices: 3977--4110  Score: 245
    Period size: 66  Copynumber: 2.0  Consensus size: 67

       3967 CAAAGTGCTG

                                                                             
       3977 ACCCAAGACGTATACGTCACTTAAGGTGGACCTTGACCCACTAACTAGGAAGTTAGGAACCAAAG
          1 ACCCAAGACGTATACGTCACTTAAGGTGGACCTTGACCCACTAACTAGGAAGTTAGGAACCAAAG

              
       4042 GT
         66 GT

                                                                             
       4044 ACCCAAGACG-ATACCGTC-CTTAAGGTGGACCTTGACCCACTAACTAGGAAGTTAGGAACCAAA
          1 ACCCAAGACGTATA-CGTCACTTAAGGTGGACCTTGACCCACTAACTAGGAAGTTAGGAACCAAA

               
       4107 GGT
         65 GGT

             
       4110 A
          1 A

       4111 TATTTTGGAG


Statistics
Matches: 66,  Mismatches: 0, Indels: 3
        0.96            0.00        0.04

Matches are distributed among these distances:
  66   52  0.79
  67   14  0.21

ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19


Consensus pattern (67 bp):   
ACCCAAGACGTATACGTCACTTAAGGTGGACCTTGACCCACTAACTAGGAAGTTAGGAACCAAAG
GT

Found at i:6055 original size:20 final size:20

Alignment explanation


    Indices: 6006--6062  Score: 78
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       5996 AGTTTATGCT

                     *     *   *
       6006 AAGTAAATGAAATGGAAAGT
          1 AAGTAAATGGAATGGTAAGA

                                
       6026 AAGTAAATGGAATGGTAAGA
          1 AAGTAAATGGAATGGTAAGA

                       *     
       6046 AAGTAAATGGAGTGGTA
          1 AAGTAAATGGAATGGTA

       6063 CATAGTTTAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21


Consensus pattern (20 bp):   
AAGTAAATGGAATGGTAAGA
Done.