Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2030

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: 21420
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32


Found at i:1429 original size:46 final size:45

Alignment explanation


    Indices: 1379--1554  Score: 212
    Period size: 46  Copynumber: 3.8  Consensus size: 45

       1369 ATGGTTGGCA

                                                          
       1379 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G

                                           ***    *       *  
       1425 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG

                 *                                        
       1472 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G

            *    *                               
       1518 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

       1555 GCGGGTTACA


Statistics
Matches: 111,  Mismatches: 12, Indels: 14
        0.81            0.09        0.10

Matches are distributed among these distances:
  43    1  0.01
  44    3  0.03
  45    1  0.01
  46   69  0.62
  47   32  0.29
  48    1  0.01
  49    3  0.03
  50    1  0.01

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


Consensus pattern (45 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG

Found at i:1534 original size:93 final size:93

Alignment explanation


    Indices: 1375--1546  Score: 308
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       1365 TAGGATGGTT

                                                            * *              
       1375 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG

                                        
       1440 TTGAGTCCGAGTTCGAGAGATGTAACTA
         66 TTGAGTCCGAGTTCGAGAGATGTAACTA

                     *                                             *         
       1468 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG

                          
       1533 TTGAGTCCGAGTTC
         66 TTGAGTCCGAGTTC

       1547 ACTTATGGGC


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

Matches are distributed among these distances:
  93   75  1.00

ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27


Consensus pattern (93 bp):   
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA

Found at i:4476 original size:15 final size:15

Alignment explanation


    Indices: 4456--4519  Score: 89
    Period size: 15  Copynumber: 4.4  Consensus size: 15

       4446 GTATCTTGGG

                           
       4456 TTTCTTTATTCTGGA
          1 TTTCTTTATTCTGGA

                           
       4471 TTTCTTTATTCTGGA
          1 TTTCTTTATTCTGGA

                 *          
       4486 TTTCTCTA-TCTTGGA
          1 TTTCTTTATTC-TGGA

                           
       4501 TTTCTTTATTC-GG-
          1 TTTCTTTATTCTGGA

                  
       4514 TTTCTT
          1 TTTCTT

       4520 GTTATCTTTG


Statistics
Matches: 45,  Mismatches: 2, Indels: 6
        0.85            0.04        0.11

Matches are distributed among these distances:
  13    6  0.13
  14    4  0.09
  15   33  0.73
  16    2  0.04

ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61


Consensus pattern (15 bp):   
TTTCTTTATTCTGGA

Found at i:9470 original size:28 final size:29

Alignment explanation


    Indices: 9405--9503  Score: 125
    Period size: 28  Copynumber: 3.5  Consensus size: 29

       9395 CATGAGATTG

                                 *   *    
       9405 GCACTAAGTGTGCG-GGTTCAAATTGTATA
          1 GCACTAAGTGTGCGAGGTTC-GATTATATA

                                         
       9434 GCACTAAGTGTGCGAGGTT-GATTATATA
          1 GCACTAAGTGTGCGAGGTTCGATTATATA

                                  *       
       9462 GCACTAAGTGTGCGA-GTTCGACTAT-TAA
          1 GCACTAAGTGTGCGAGGTTCGATTATAT-A

                          
       9490 GCACTAAGTGTGCG
          1 GCACTAAGTGTGCG

       9504 GGCTTATTAT


Statistics
Matches: 64,  Mismatches: 3, Indels: 7
        0.86            0.04        0.09

Matches are distributed among these distances:
  27    4  0.06
  28   42  0.66
  29   14  0.22
  30    4  0.06

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29


Consensus pattern (29 bp):   
GCACTAAGTGTGCGAGGTTCGATTATATA

Found at i:17473 original size:27 final size:28

Alignment explanation


    Indices: 17410--17507  Score: 128
    Period size: 27  Copynumber: 3.5  Consensus size: 28

      17400 CATGAGATTG

                          *     *   *    
      17410 GCACTAAGTGTGCGGGTTCAAATTGTATA
          1 GCACTAAGTGTGCGAGTTC-GATTATATA

                                        
      17439 GCACTAAGTGTGCGAGTT-GATTATATA
          1 GCACTAAGTGTGCGAGTTCGATTATATA

                                 *       
      17466 GCACTAAGTGTGCGAGTTCGACTAT-TAA
          1 GCACTAAGTGTGCGAGTTCGATTATAT-A

                          
      17494 GCACTAAGTGTGCG
          1 GCACTAAGTGTGCG

      17508 GGCTTATTAT


Statistics
Matches: 63,  Mismatches: 4, Indels: 5
        0.88            0.06        0.07

Matches are distributed among these distances:
  27   26  0.41
  28   20  0.32
  29   17  0.27

ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30


Consensus pattern (28 bp):   
GCACTAAGTGTGCGAGTTCGATTATATA
Done.