Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3800

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: 24571
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33


Found at i:1242 original size:28 final size:27

Alignment explanation


    Indices: 1186--1238  Score: 81
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       1176 ATCATCATTA

                                        
       1186 TTGCATGCAGTTATAAAGACTTAGAATT
          1 TTGCATGCAG-TATAAAGACTTAGAATT

                                      
       1214 TTGCATGCA-TATCAAAGACTTAGAA
          1 TTGCATGCAGTAT-AAAGACTTAGAA

       1239 ATTTCCACTA


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

Matches are distributed among these distances:
  26    3  0.12
  27   12  0.50
  28    9  0.38

ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32


Consensus pattern (27 bp):   
TTGCATGCAGTATAAAGACTTAGAATT

Found at i:7257 original size:21 final size:21

Alignment explanation


    Indices: 7231--7271  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7221 AGACGAGCAA

                   * *           
       7231 TACTCCACAGCAGGTGGAGTG
          1 TACTCCAAAACAGGTGGAGTG

                                
       7252 TACTCCAAAACAGGTGGAGT
          1 TACTCCAAAACAGGTGGAGT

       7272 TTGAGCAGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20


Consensus pattern (21 bp):   
TACTCCAAAACAGGTGGAGTG

Found at i:13584 original size:28 final size:28

Alignment explanation


    Indices: 13533--13589  Score: 80
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      13523 TGGAATGAGC

                              *          
      13533 CACTTAAAAAATTATTTATAGAAATAGGT
          1 CACTTAAAAAATTATTTACAGAAAT-GGT

                               *        
      13562 CACTTAAAAAA-TATTTACCGAAATGGT
          1 CACTTAAAAAATTATTTACAGAAATGGT

             
      13589 C
          1 C

      13590 CAAAAAACAC


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  27    4  0.15
  28   11  0.42
  29   11  0.42

ACGTcount: A:0.46, C:0.12, G:0.11, T:0.32


Consensus pattern (28 bp):   
CACTTAAAAAATTATTTACAGAAATGGT

Found at i:15326 original size:47 final size:47

Alignment explanation


    Indices: 15257--15354  Score: 196
    Period size: 47  Copynumber: 2.1  Consensus size: 47

      15247 ATTATTCGAG

                                                           
      15257 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
          1 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT

                                                           
      15304 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
          1 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT

                
      15351 TTAT
          1 TTAT

      15355 GTTTTATATT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  47   51  1.00

ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46


Consensus pattern (47 bp):   
TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT

Found at i:15783 original size:20 final size:21

Alignment explanation


    Indices: 15745--15787  Score: 70
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      15735 TTAAAAAAAA

                          *      
      15745 TTTATACTATTTTTTATAATT
          1 TTTATACTATTTTTAATAATT

                                 
      15766 TTTATACT-TTTTTAATAATT
          1 TTTATACTATTTTTAATAATT

              
      15786 TT
          1 TT

      15788 AATTTTTAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20   13  0.62
  21    8  0.38

ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67


Consensus pattern (21 bp):   
TTTATACTATTTTTAATAATT

Found at i:19084 original size:44 final size:44

Alignment explanation


    Indices: 19018--19105  Score: 131
    Period size: 44  Copynumber: 2.0  Consensus size: 44

      19008 TAAAAAAAAT

                   * *               *                  
      19018 CAATTCTCTTATTGTAAAACATTTATAAGAATTTATTCAAGGGA
          1 CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA

                             *                   *      
      19062 CAATTCTATCATTGTAAGACATTTAAAAGAATTTATTTAAGGGA
          1 CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA

      19106 AAGGATGGTA


Statistics
Matches: 39,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  44   39  1.00

ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38


Consensus pattern (44 bp):   
CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA

Found at i:20502 original size:64 final size:64

Alignment explanation


    Indices: 20412--20540  Score: 249
    Period size: 64  Copynumber: 2.0  Consensus size: 64

      20402 AACAAAATGG

                                                                            
      20412 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
          1 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA

                                 *                                          
      20476 TAGCTTCTTTAGGAACAGAAATGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
          1 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA

             
      20540 T
          1 T

      20541 CTTTCTAAGA


Statistics
Matches: 64,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  64   64  1.00

ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22


Consensus pattern (64 bp):   
TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
Done.