Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3754

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: 13143
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33


Found at i:1479 original size:93 final size:93

Alignment explanation


    Indices: 1372--1542  Score: 315
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       1362 GCCCCTAAGT

                                        * *                                  
       1372 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                        
       1437 CGAGTTCGGATGCCTAGTTACATCTCAC
         66 CGAGTTCGGATGCCTAGTTACATCTCAC

                                   *                                         
       1465 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                         
       1530 CGAGTTCGGATGC
         66 CGAGTTCGGATGC

       1543 TCAACCATCC


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

Matches are distributed among these distances:
  93   75  1.00

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


Consensus pattern (93 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC

Found at i:1539 original size:46 final size:46

Alignment explanation


    Indices: 1367--1539  Score: 219
    Period size: 46  Copynumber: 3.7  Consensus size: 46

       1357 AACCCGCCCC

                                        *    * *          
       1367 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA

                                                        *      
       1413 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA

             *  *                                         
       1461 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA

                                              
       1506 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

       1540 TGCTCAACCA


Statistics
Matches: 109,  Mismatches: 9, 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   61  0.56
  47   29  0.27
  48    2  0.02
  49    2  0.02
  50    3  0.03
  51    2  0.02

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


Consensus pattern (46 bp):   
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA

Found at i:1996 original size:30 final size:30

Alignment explanation


    Indices: 1962--2021  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1952 ATTTAATACG

                                          
       1962 AACTTTGGAAAAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

                  * * *                   
       1992 AACTTTTGCATAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

       2022 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

Found at i:9438 original size:30 final size:30

Alignment explanation


    Indices: 9404--9460  Score: 87
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       9394 ATTTAATACG

                                          
       9404 AACTTTGGAAAAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

                  * * *                
       9434 AACTTTTGCATAATTACACTTTTGCCC
          1 AACTTTGGAAAAATTACACTTTTGCCC

       9461 TAGGCTCGGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37


Consensus pattern (30 bp):   
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.