Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2500

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: 33343
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36


Found at i:8793 original size:19 final size:20

Alignment explanation


    Indices: 8766--8807  Score: 59
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       8756 ATCATTTTAA

                            *   
       8766 AAATATTTTTTAAATATTTT
          1 AAATATTTTTTAAATAATTT

                         *      
       8786 AAAT-TTTTTTAACTAATTT
          1 AAATATTTTTTAAATAATTT

               
       8805 AAA
          1 AAA

       8808 AATAAAACAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  19   16  0.80
  20    4  0.20

ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55


Consensus pattern (20 bp):   
AAATATTTTTTAAATAATTT

Found at i:12628 original size:19 final size:17

Alignment explanation


    Indices: 12586--12632  Score: 58
    Period size: 19  Copynumber: 2.6  Consensus size: 17

      12576 ATATATTATA

                             
      12586 TATTATATTTAAAATTT
          1 TATTATATTTAAAATTT

              *            *   
      12603 TAATATATTTAATTATTTT
          1 TATTATATTTAA--AATTT

                       
      12622 TATTATATTTA
          1 TATTATATTTA

      12633 TATTTATAAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  17   11  0.44
  19   14  0.56

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (17 bp):   
TATTATATTTAAAATTT

Found at i:16201 original size:17 final size:17

Alignment explanation


    Indices: 16179--16211  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      16169 AAAAAGTTAA

                      *      
      16179 ATATTTTATATTTAAAT
          1 ATATTTTATAATTAAAT

                            
      16196 ATATTTTATAATTAAA
          1 ATATTTTATAATTAAA

      16212 AATAAATAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (17 bp):   
ATATTTTATAATTAAAT

Found at i:20281 original size:29 final size:29

Alignment explanation


    Indices: 20219--20287  Score: 79
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      20209 ATTTTATAAA

                  *                      
      20219 AATTTTTAAAAATAAATATAAATAATTTT
          1 AATTTTAAAAAATAAATATAAATAATTTT

            *                              
      20248 TATTTTAATAAAATAAA-ATAAAATAA-TTT
          1 AATTTTAA-AAAATAAATAT-AAATAATTTT

                  *    
      20277 AATTTTGAAAA
          1 AATTTTAAAAA

      20288 TCATGCAAAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 5
        0.79            0.09        0.12

Matches are distributed among these distances:
  28    3  0.09
  29   17  0.50
  30   14  0.41

ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42


Consensus pattern (29 bp):   
AATTTTAAAAAATAAATATAAATAATTTT

Found at i:21753 original size:15 final size:16

Alignment explanation


    Indices: 21733--21764  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      21723 AAATATGTTC

                            
      21733 AGAATCA-AAACAACA
          1 AGAATCACAAACAACA

                            
      21748 AGAATCACAAACAACA
          1 AGAATCACAAACAACA

             
      21764 A
          1 A

      21765 TCATCAATCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    7  0.44
  16    9  0.56

ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06


Consensus pattern (16 bp):   
AGAATCACAAACAACA

Found at i:22598 original size:102 final size:102

Alignment explanation


    Indices: 22422--22627  Score: 385
    Period size: 102  Copynumber: 2.0  Consensus size: 102

      22412 GATCGCTAAT

                                                          *        *         
      22422 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAATTACCCGATTGAGTGAACT
          1 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTACCCGATCGAGTGAACT

                                                 
      22487 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA
         66 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA

                                                             *               
      22524 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTATCCGATCGAGTGAACT
          1 GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTACCCGATCGAGTGAACT

                                                 
      22589 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA
         66 TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA

              
      22626 GA
          1 GA

      22628 CGTAGTTCTT


Statistics
Matches: 101,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 102  101  1.00

ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26


Consensus pattern (102 bp):   
GAGGCAAACCAGTGCAGTGCTCGAACTAAAGTTTATTGGAGCTGAACTACCCGATCGAGTGAACT
TATCTGACTGAACTTGAGACTATGCGACTGAGCCTTA

Found at i:30468 original size:2 final size:2

Alignment explanation


    Indices: 30463--30493  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      30453 AAAAAAGTTG

                                                *         
      30463 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      30494 ATAAATTTGA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
AT

Done.