Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2608

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: 16574
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33


Found at i:1286 original size:45 final size:45

Alignment explanation


    Indices: 1222--1393  Score: 224
    Period size: 45  Copynumber: 3.8  Consensus size: 45

       1212 TGTAACCCGC

                                           *     *       
       1222 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT

                   *                               *      
       1267 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-AT

            *     *                                         
       1311 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT

                   *                            
       1358 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG

       1394 ATGCTCAACC


Statistics
Matches: 109,  Mismatches: 11, Indels: 13
        0.82            0.08        0.10

Matches are distributed among these distances:
  43    1  0.01
  44    6  0.06
  45   64  0.59
  46   30  0.28
  47    7  0.06
  48    1  0.01

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


Consensus pattern (45 bp):   
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT

Found at i:1383 original size:91 final size:90

Alignment explanation


    Indices: 1229--1397  Score: 311
    Period size: 91  Copynumber: 1.9  Consensus size: 90

       1219 CGCCCATAAG

                                          *                                  
       1229 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                     
       1294 CGAGTTCGGATGCCTATACATCTCA
         66 CGAGTTCGGATGCCTATACATCTCA

                                    *                                        
       1319 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                          
       1384 ACGAGTTCGGATGC
         65 ACGAGTTCGGATGC

       1398 TCAACCATCC


Statistics
Matches: 76,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  90   28  0.37
  91   48  0.63

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


Consensus pattern (90 bp):   
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTATACATCTCA

Found at i:8793 original size:93 final size:93

Alignment explanation


    Indices: 8680--8851  Score: 317
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       8670 CGCCCATAAG

                                         * *                                 
       8680 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                                        
       8745 ACGAGTTCGGATGCCTAGTTACATCTCA
         66 ACGAGTTCGGATGCCTAGTTACATCTCA

                                    *                                        
       8773 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                          
       8838 ACGAGTTCGGATGC
         66 ACGAGTTCGGATGC

       8852 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:8848 original size:46 final size:46

Alignment explanation


    Indices: 8673--8848  Score: 216
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       8663 TGTAACCCGC

                                           *    * *       
       8673 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                                       *   
       8719 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT

                *                                         
       8769 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                             
       8812 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA

       8849 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

Done.