Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold843

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: 10868
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32


Found at i:1364 original size:93 final size:93

Alignment explanation


    Indices: 1252--1423  Score: 317
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       1242 CGCCCATAAG

                                         * *                                 
       1252 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                                        
       1317 ACGAGTTCGGATGCCTAGTTACATCTCA
         66 ACGAGTTCGGATGCCTAGTTACATCTCA

                                    *                                        
       1345 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                          
       1410 ACGAGTTCGGATGC
         66 ACGAGTTCGGATGC

       1424 TCAACCATCC


Statistics
Matches: 76,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  93   76  1.00

ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21


Consensus pattern (93 bp):   
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA

Found at i:1420 original size:46 final size:46

Alignment explanation


    Indices: 1245--1420  Score: 216
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       1235 TGTAACCCGC

                                           *    * *       
       1245 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                                       *   
       1291 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT

                *                                         
       1341 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                             
       1384 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA

       1421 TGCTCAACCA


Statistics
Matches: 111,  Mismatches: 10, Indels: 18
        0.80            0.07        0.13

Matches are distributed among these distances:
  42    2  0.02
  43    4  0.04
  44    2  0.02
  45    2  0.02
  46   63  0.57
  47   29  0.26
  48    2  0.02
  49    2  0.02
  50    3  0.03
  51    2  0.02

ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20


Consensus pattern (46 bp):   
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

Found at i:4425 original size:13 final size:13

Alignment explanation


    Indices: 4407--4437  Score: 62
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       4397 TTTCACCATA

                         
       4407 CAAATAATGTCGC
          1 CAAATAATGTCGC

                         
       4420 CAAATAATGTCGC
          1 CAAATAATGTCGC

                 
       4433 CAAAT
          1 CAAAT

       4438 TTCAAAGCAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23


Consensus pattern (13 bp):   
CAAATAATGTCGC

Found at i:8868 original size:91 final size:91

Alignment explanation


    Indices: 8759--8928  Score: 304
    Period size: 91  Copynumber: 1.9  Consensus size: 91

       8749 CGCCCATAAG

                                         * *                                 
       8759 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                                      
       8824 ACGAGCTCGGATGCCTAGTTACTTCA
         66 ACGAGCTCGGATGCCTAGTTACTTCA

                                    *                                        
       8850 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                 *        
       8915 ACGAGTTCGGATGC
         66 ACGAGCTCGGATGC

       8929 TCAACCATCC


Statistics
Matches: 75,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  91   75  1.00

ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21


Consensus pattern (91 bp):   
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACTTCA

Found at i:8925 original size:46 final size:46

Alignment explanation


    Indices: 8752--8925  Score: 203
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       8742 TGTAACCCGC

                                                * *       
       8752 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

                   *                                *        
       8798 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T

            * * *                          *              
       8844 ACTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

                   *                       *     
       8889 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA

       8926 TGCTCAACCA


Statistics
Matches: 108,  Mismatches: 13, Indels: 14
        0.80            0.10        0.10

Matches are distributed among these distances:
  43    1  0.01
  44    3  0.03
  45   31  0.29
  46   68  0.63
  47    4  0.04
  48    1  0.01

ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20


Consensus pattern (46 bp):   
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

Done.