Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1638

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: 22825
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32


Found at i:4783 original size:93 final size:93

Alignment explanation


    Indices: 4670--4841  Score: 317
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       4660 CGCCCATAAG

                                         * *                                 
       4670 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                                        
       4735 ACGAGTTCGGATGCCTAGTTACATCTCA
         66 ACGAGTTCGGATGCCTAGTTACATCTCA

                                    *                                        
       4763 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                          
       4828 ACGAGTTCGGATGC
         66 ACGAGTTCGGATGC

       4842 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:4838 original size:46 final size:46

Alignment explanation


    Indices: 4663--4838  Score: 216
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       4653 TGTAACCCGC

                                           *    * *       
       4663 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                                       *   
       4709 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT

                *                                         
       4759 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                             
       4802 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA

       4839 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:12331 original size:93 final size:93

Alignment explanation


    Indices: 12218--12389  Score: 317
    Period size: 93  Copynumber: 1.8  Consensus size: 93

      12208 CCCCCATAAG

                                         * *                                 
      12218 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                                        
      12283 ACGAGTTCGGATGCCTAGTTACATCTCA
         66 ACGAGTTCGGATGCCTAGTTACATCTCA

                                    *                                        
      12311 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                          
      12376 ACGAGTTCGGATGC
         66 ACGAGTTCGGATGC

      12390 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:12386 original size:46 final size:46

Alignment explanation


    Indices: 12211--12386  Score: 216
    Period size: 46  Copynumber: 3.8  Consensus size: 46

      12201 CATGTAACCC

                                           *    * *       
      12211 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                                       *   
      12257 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT

                *                                         
      12307 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                   *                             
      12350 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA

      12387 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.