Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1942

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: 14926
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Found at i:3418 original size:32 final size:31

Alignment explanation


    Indices: 3335--3419  Score: 77
    Period size: 36  Copynumber: 2.6  Consensus size: 31

       3325 ATATATTAAC

                                            
       3335 ATATATATTTT-TAT-AATAAATTTAAATAAA
          1 ATATATATTTTATATAAATAAATTTAAAT-AA

             *                                   
       3365 AAATATATTTTACATAGATAAATAATAATTTAAAT-A
          1 ATATATATTTT--AT--ATAAAT-A-AATTTAAATAA

                               
       3401 ATATATATTTTATATAAAT
          1 ATATATATTTTATATAAAT

       3420 GTGTCGTAAC


Statistics
Matches: 45,  Mismatches: 2, Indels: 14
        0.74            0.03        0.23

Matches are distributed among these distances:
  30   10  0.22
  32    6  0.13
  33    1  0.02
  34    2  0.04
  35    2  0.04
  36   14  0.31
  37    1  0.02
  38    9  0.20

ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45


Consensus pattern (31 bp):   
ATATATATTTTATATAAATAAATTTAAATAA

Found at i:6595 original size:13 final size:13

Alignment explanation


    Indices: 6557--6596  Score: 62
    Period size: 13  Copynumber: 3.1  Consensus size: 13

       6547 ATACAATGAT

                   *    *
       6557 AATGTATTGATAT
          1 AATGTATCGATAC

                         
       6570 AATGTATCGATAC
          1 AATGTATCGATAC

                         
       6583 AATGTATCGATAC
          1 AATGTATCGATAC

             
       6596 A
          1 A

       6597 TTCATTAATG


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  13   25  1.00

ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35


Consensus pattern (13 bp):   
AATGTATCGATAC

Found at i:7392 original size:28 final size:24

Alignment explanation


    Indices: 7361--7432  Score: 69
    Period size: 24  Copynumber: 2.9  Consensus size: 24

       7351 TTTTTATAGT

                                        
       7361 AAATTTTTATATTTTTATTATATTAAAA
          1 AAATTTTTATA--TTTA-TAT-TTAAAA

                                    *
       7389 AAATATTTT-TATTTATATTTAAAT
          1 AAAT-TTTTATATTTATATTTAAAA

                                  
       7413 AAATTTTTAT-TTTA-ATTTAA
          1 AAATTTTTATATTTATATTTAA

       7433 GATTGATTTA


Statistics
Matches: 41,  Mismatches: 1, Indels: 10
        0.79            0.02        0.19

Matches are distributed among these distances:
  22    6  0.15
  23    8  0.20
  24   10  0.24
  25    3  0.07
  26    4  0.10
  28    6  0.15
  29    4  0.10

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (24 bp):   
AAATTTTTATATTTATATTTAAAA

Found at i:7426 original size:23 final size:23

Alignment explanation


    Indices: 7369--7432  Score: 80
    Period size: 22  Copynumber: 2.9  Consensus size: 23

       7359 GTAAATTTTT

                             *     
       7369 ATATTTTTA-TTATATTAAAAAA
          1 ATATTTTTATTTATATTTAAAAA

                                 * 
       7391 ATATTTTTATTTATATTTAAATA
          1 ATATTTTTATTTATATTTAAAAA

                                 
       7414 A-ATTTTTATTT-TAATTTAA
          1 ATATTTTTATTTAT-ATTTAA

       7433 GATTGATTTA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  21    1  0.03
  22   25  0.66
  23   12  0.32

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (23 bp):   
ATATTTTTATTTATATTTAAAAA

Found at i:8347 original size:14 final size:15

Alignment explanation


    Indices: 8328--8356  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       8318 CGATAAAAAT

                           
       8328 TATATTTATT-ATTA
          1 TATATTTATTGATTA

                           
       8342 TATATTTATTGATTA
          1 TATATTTATTGATTA

       8357 AAATTTTTTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62


Consensus pattern (15 bp):   
TATATTTATTGATTA

Found at i:9520 original size:23 final size:23

Alignment explanation


    Indices: 9490--9534  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       9480 TAGTTTAAAT

                     *             
       9490 TAAATAAATTTATTTACGAATAC
          1 TAAATAAATATATTTACGAATAC

                            *     
       9513 TAAATAAATATATTTATGAATA
          1 TAAATAAATATATTTACGAATA

       9535 TATAATTGAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40


Consensus pattern (23 bp):   
TAAATAAATATATTTACGAATAC

Found at i:11497 original size:55 final size:55

Alignment explanation


    Indices: 11421--11531  Score: 222
    Period size: 55  Copynumber: 2.0  Consensus size: 55

      11411 ATCATTCATT

                                                                   
      11421 TAAAGAAATTGAGCAAACACCACTCTCTCAACTTTGCCAACAAAAAAATTTAAAA
          1 TAAAGAAATTGAGCAAACACCACTCTCTCAACTTTGCCAACAAAAAAATTTAAAA

                                                                   
      11476 TAAAGAAATTGAGCAAACACCACTCTCTCAACTTTGCCAACAAAAAAATTTAAAA
          1 TAAAGAAATTGAGCAAACACCACTCTCTCAACTTTGCCAACAAAAAAATTTAAAA

             
      11531 T
          1 T

      11532 CACATCGCTC


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   56  1.00

ACGTcount: A:0.49, C:0.22, G:0.07, T:0.23


Consensus pattern (55 bp):   
TAAAGAAATTGAGCAAACACCACTCTCTCAACTTTGCCAACAAAAAAATTTAAAA
Done.