Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2309

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: 51500
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:34 original size:15 final size:16

Alignment explanation


    Indices: 14--44  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

          4 ATCTCCATCG

                            
         14 TTAGT-AACATGTACC
          1 TTAGTAAACATGTACC

                            
         29 TTAGTAAACATGTACC
          1 TTAGTAAACATGTACC

         45 AATATGTTGG


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

Matches are distributed among these distances:
  15    5  0.33
  16   10  0.67

ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32


Consensus pattern (16 bp):   
TTAGTAAACATGTACC

Found at i:3027 original size:31 final size:31

Alignment explanation


    Indices: 2992--3050  Score: 82
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       2982 CAAAATAATC

                  *    *   *               
       2992 ATTAAATTATTCAAATGTTTTCATTTAATTT
          1 ATTAAACTATTAAAAAGTTTTCATTTAATTT

                                 *      
       3023 ATTAAACTATTAAAAAGTTTTTATTTAA
          1 ATTAAACTATTAAAAAGTTTTCATTTAA

       3051 ACCACTGGCT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   24  1.00

ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51


Consensus pattern (31 bp):   
ATTAAACTATTAAAAAGTTTTCATTTAATTT

Found at i:3954 original size:18 final size:19

Alignment explanation


    Indices: 3931--3972  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       3921 TTTGGGTATC

                   *           
       3931 TAAAATTGAT-TTCATTAT
          1 TAAAATTAATATTCATTAT

                         *     
       3949 TAAAATTAATATTGATTAT
          1 TAAAATTAATATTCATTAT

                 
       3968 TAAAA
          1 TAAAA

       3973 AGAATTACAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18    9  0.43
  19   12  0.57

ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45


Consensus pattern (19 bp):   
TAAAATTAATATTCATTAT

Found at i:4137 original size:6 final size:6

Alignment explanation


    Indices: 4126--4167  Score: 84
    Period size: 6  Copynumber: 7.0  Consensus size: 6

       4116 ACGGGAGGGA

                                                            
       4126 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
          1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG

       4168 AACGAAGCTG


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   36  1.00

ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00


Consensus pattern (6 bp):   
GAGAGG

Found at i:8984 original size:29 final size:29

Alignment explanation


    Indices: 8942--8999  Score: 116
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       8932 TTTTCCTCCC

                                         
       8942 TTTTTGTGGCCATCAAAGCTCATAGTTTG
          1 TTTTTGTGGCCATCAAAGCTCATAGTTTG

                                         
       8971 TTTTTGTGGCCATCAAAGCTCATAGTTTG
          1 TTTTTGTGGCCATCAAAGCTCATAGTTTG

       9000 GTAGACTTTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41


Consensus pattern (29 bp):   
TTTTTGTGGCCATCAAAGCTCATAGTTTG

Found at i:10026 original size:31 final size:31

Alignment explanation


    Indices: 9988--10051  Score: 119
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       9978 AGCCTTCCTT

                               *           
       9988 TGTCATACCTCTATGCCTTCGCTCATCATAG
          1 TGTCATACCTCTATGCCTTAGCTCATCATAG

                                           
      10019 TGTCATACCTCTATGCCTTAGCTCATCATAG
          1 TGTCATACCTCTATGCCTTAGCTCATCATAG

              
      10050 TG
          1 TG

      10052 AGTAAACGTG


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36


Consensus pattern (31 bp):   
TGTCATACCTCTATGCCTTAGCTCATCATAG

Found at i:10252 original size:25 final size:25

Alignment explanation


    Indices: 10224--10274  Score: 102
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      10214 CAAGTGAGTC

                                     
      10224 GATCAGGACTTCCATCAAGCATTGG
          1 GATCAGGACTTCCATCAAGCATTGG

                                     
      10249 GATCAGGACTTCCATCAAGCATTGG
          1 GATCAGGACTTCCATCAAGCATTGG

             
      10274 G
          1 G

      10275 GGCATTAAAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24


Consensus pattern (25 bp):   
GATCAGGACTTCCATCAAGCATTGG

Found at i:17229 original size:2 final size:2

Alignment explanation


    Indices: 17210--17245  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      17200 AAAGAGAAAC

                   *        *                                    
      17210 AG AG AT AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

      17246 GTGCTTCATT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06


Consensus pattern (2 bp):   
AG

Done.