Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2486

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: 6229
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32


Found at i:4889 original size:92 final size:92

Alignment explanation


    Indices: 4778--4947  Score: 313
    Period size: 92  Copynumber: 1.8  Consensus size: 92

       4768 GCCCCTAAGT

                                        * *                                  
       4778 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                       
       4843 CGAGTTCGGATGCCTAGTTACATTCAC
         66 CGAGTTCGGATGCCTAGTTACATTCAC

                                   *                                         
       4870 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                         
       4935 CGAGTTCGGATGC
         66 CGAGTTCGGATGC

       4948 TCAACCATCC


Statistics
Matches: 75,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  92   75  1.00

ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21


Consensus pattern (92 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTCAC

Found at i:4944 original size:46 final size:46

Alignment explanation


    Indices: 4773--4944  Score: 217
    Period size: 46  Copynumber: 3.7  Consensus size: 46

       4763 AACCCGCCCC

                                        *    * *          
       4773 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA

                                                 *        *  
       4819 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCA

              *  *                                         
       4865 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
          1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA

                                              
       4911 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

       4945 TGCTCAACCA


Statistics
Matches: 108,  Mismatches: 10, Indels: 16
        0.81            0.07        0.12

Matches are distributed among these distances:
  43    1  0.01
  44    3  0.03
  45    2  0.02
  46   95  0.88
  47    2  0.02
  48    4  0.04
  49    1  0.01

ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22


Consensus pattern (46 bp):   
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA

Found at i:4963 original size:46 final size:46

Alignment explanation


    Indices: 4775--4963  Score: 151
    Period size: 46  Copynumber: 4.1  Consensus size: 46

       4765 CCCGCCCCTA

                                      *    ** *    *       
       4775 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCAT
          1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T

                                                            *  
       4820 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTC-
          1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCT

              *                                * *  *      *
       4868 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
          1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCT

                                                          
       4913 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
          1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT

                 
       4959 AGTGA
          1 AGTGA

       4964 CATGTCACTT


Statistics
Matches: 116,  Mismatches: 13, Indels: 28
        0.74            0.08        0.18

Matches are distributed among these distances:
  44    9  0.08
  45    2  0.02
  46   95  0.82
  47    1  0.01
  48    4  0.03
  49    1  0.01
  50    4  0.03

ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22


Consensus pattern (46 bp):   
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT

Found at i:5401 original size:30 final size:30

Alignment explanation


    Indices: 5367--5426  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       5357 ATTTAATACG

                                          
       5367 AACTTTGGAAAAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

                  * * *                   
       5397 AACTTTTGCATAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

       5427 GGCTCGGGAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37


Consensus pattern (30 bp):   
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.