Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2492

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: 6502
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30


Found at i:155 original size:52 final size:52

Alignment explanation


    Indices: 76--203  Score: 231
    Period size: 52  Copynumber: 2.5  Consensus size: 52

         66 CGAAATATGA

                                                                
         76 AAATTTG-CTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
          1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC

                                   *     *                      
        127 AAATTTGCCTGCATGTATCGATATATTTTGTAGTGTATCGATACATCTGGGC
          1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC

                                     
        179 AAATTTGCCTGCATGTATCGATACA
          1 AAATTTGCCTGCATGTATCGATACA

        204 AAGATCAGTG


Statistics
Matches: 73,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  51    7  0.10
  52   66  0.90

ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37


Consensus pattern (52 bp):   
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC

Found at i:214 original size:52 final size:52

Alignment explanation


    Indices: 76--224  Score: 223
    Period size: 52  Copynumber: 2.9  Consensus size: 52

         66 CGAAATATGA

                                        *                       
         76 AAATTTG-CTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
          1 AAATTTGCCTGCATGTATCGATACATTTGATAGTGTATCGATACATCTGGGC

                                   *                             
        127 AAATTTGCCTGCATGTATCGATATATTTTG-TAGTGTATCGATACATCTGGGC
          1 AAATTTGCCTGCATGTATCGATACA-TTTGATAGTGTATCGATACATCTGGGC

                                      **                   
        179 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
          1 AAATTTGCCTGCATGTATCGATACATTTGAT-AGTGTATCGATACAT

        225 GTATCGATAC


Statistics
Matches: 89,  Mismatches: 5, Indels: 7
        0.88            0.05        0.07

Matches are distributed among these distances:
  50    1  0.01
  51    8  0.09
  52   77  0.87
  53    3  0.03

ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Consensus pattern (52 bp):   
AAATTTGCCTGCATGTATCGATACATTTGATAGTGTATCGATACATCTGGGC

Found at i:226 original size:32 final size:29

Alignment explanation


    Indices: 190--257  Score: 100
    Period size: 32  Copynumber: 2.2  Consensus size: 29

        180 AATTTGCCTG

                                            
        190 CATGTATCGATACAAAGATCAGTGTATCGATA
          1 CATGTATCGATACAAAGATC-G-GTATCG-TA

                                         
        222 CATGTATCGATACAAAGATCGGTATCGTA
          1 CATGTATCGATACAAAGATCGGTATCGTA

                   
        251 CAATGTA
          1 C-ATGTA

        258 CATACATTTG


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
  29    3  0.09
  30   11  0.31
  31    1  0.03
  32   20  0.57

ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28


Consensus pattern (29 bp):   
CATGTATCGATACAAAGATCGGTATCGTA

Found at i:349 original size:31 final size:31

Alignment explanation


    Indices: 306--393  Score: 140
    Period size: 31  Copynumber: 2.8  Consensus size: 31

        296 TAGCTTAAAT

                         *                 
        306 TGTATCGATACAAAACTTATGTATCAATACA
          1 TGTATCGATACAACACTTATGTATCAATACA

                   *                 *     
        337 TGTATCGGTACAACACTTATGTATCGATACA
          1 TGTATCGATACAACACTTATGTATCAATACA

                                      
        368 TGTATCGATACAACACTTTATGTATC
          1 TGTATCGATACAACAC-TTATGTATC

        394 GATATAAATC


Statistics
Matches: 52,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  31   43  0.83
  32    9  0.17

ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34


Consensus pattern (31 bp):   
TGTATCGATACAACACTTATGTATCAATACA

Found at i:372 original size:12 final size:12

Alignment explanation


    Indices: 355--379  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        345 TACAACACTT

                        
        355 ATGTATCGATAC
          1 ATGTATCGATAC

                        
        367 ATGTATCGATAC
          1 ATGTATCGATAC

             
        379 A
          1 A

        380 ACACTTTATG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Consensus pattern (12 bp):   
ATGTATCGATAC

Found at i:1302 original size:3 final size:3

Alignment explanation


    Indices: 1294--1318  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       1284 TGCAGAGGAA

                                             
       1294 GAT GAT GAT GAT GAT GAT GAT GAT G
          1 GAT GAT GAT GAT GAT GAT GAT GAT G

       1319 GTGACTCGGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32


Consensus pattern (3 bp):   
GAT

Done.