Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1442

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: 10090
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32


Found at i:7128 original size:51 final size:52

Alignment explanation


    Indices: 7051--7177  Score: 213
    Period size: 51  Copynumber: 2.5  Consensus size: 52

       7041 CGAAATATGA

                  *                         *                   
       7051 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
          1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC

                                        *                       
       7103 AAA-TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
          1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC

                                     
       7154 AAATTTG-CTGCATGTATCGATACA
          1 AAATTTGCCTGCATGTATCGATACA

       7178 AAGATCAGTG


Statistics
Matches: 71,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  51   65  0.92
  52    6  0.08

ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Consensus pattern (52 bp):   
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC

Found at i:7190 original size:51 final size:50

Alignment explanation


    Indices: 7058--7197  Score: 194
    Period size: 51  Copynumber: 2.7  Consensus size: 50

       7048 TGAAAATTTA

                                                               
       7058 CCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTG
          1 CCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTG

                                 *   *                          
       7109 CCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
          1 CCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAA-TTG

                               *                   
       7161 -CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
          1 CCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA

       7198 ATGTATCGAC


Statistics
Matches: 81,  Mismatches: 5, Indels: 6
        0.88            0.05        0.07

Matches are distributed among these distances:
  50    2  0.02
  51   76  0.94
  52    3  0.04

ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Consensus pattern (50 bp):   
CCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTG

Found at i:7288 original size:33 final size:33

Alignment explanation


    Indices: 7251--7317  Score: 89
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       7241 AGTAGCTTAA

                   *                         
       7251 ATTGTATTGATACAAAAAAATATGTATCGATAC
          1 ATTGTATCGATACAAAAAAATATGTATCGATAC

                           * ***             
       7284 ATTGTATCGATACAACACTTTATGTATCGATAC
          1 ATTGTATCGATACAAAAAAATATGTATCGATAC

             
       7317 A
          1 A

       7318 AATCGGTTGA


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34


Consensus pattern (33 bp):   
ATTGTATCGATACAAAAAAATATGTATCGATAC

Found at i:7291 original size:13 final size:13

Alignment explanation


    Indices: 7273--7297  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7263 CAAAAAAATA

                         
       7273 TGTATCGATACAT
          1 TGTATCGATACAT

                        
       7286 TGTATCGATACA
          1 TGTATCGATACA

       7298 ACACTTTATG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

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


Consensus pattern (13 bp):   
TGTATCGATACAT
Done.