Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2191

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: 23270
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:4235 original size:15 final size:16

Alignment explanation


    Indices: 4217--4251  Score: 63
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       4207 AATAGTAACA

                            
       4217 ATAATAATAAATAAT-
          1 ATAATAATAAATAATG

                            
       4232 ATAATAATAAATAATG
          1 ATAATAATAAATAATG

                
       4248 ATAA
          1 ATAA

       4252 ATATTTAAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   15  0.79
  16    4  0.21

ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31


Consensus pattern (16 bp):   
ATAATAATAAATAATG

Found at i:6506 original size:14 final size:14

Alignment explanation


    Indices: 6480--6510  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       6470 TTAATTTAGA

                          
       6480 AAATTTAATTAATT
          1 AAATTTAATTAATT

                          
       6494 AAATTTAATTAATT
          1 AAATTTAATTAATT

               
       6508 AAA
          1 AAA

       6511 AAATCATTTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

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


Consensus pattern (14 bp):   
AAATTTAATTAATT

Found at i:6724 original size:13 final size:14

Alignment explanation


    Indices: 6708--6736  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

       6698 TAAAAATTTT

                          
       6708 AAAAATTA-ATTAA
          1 AAAAATTATATTAA

                          
       6721 AAAAATTATATTAA
          1 AAAAATTATATTAA

              
       6735 AA
          1 AA

       6737 TTAAATGAAT


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

Matches are distributed among these distances:
  13    8  0.53
  14    7  0.47

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (14 bp):   
AAAAATTATATTAA

Found at i:9177 original size:16 final size:16

Alignment explanation


    Indices: 9156--9188  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9146 GAAATTCAAT

                            
       9156 AAAAAAACAAAAAGAA
          1 AAAAAAACAAAAAGAA

                   *        
       9172 AAAAAAAGAAAAAGAA
          1 AAAAAAACAAAAAGAA

             
       9188 A
          1 A

       9189 CCATAAGCTT


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00


Consensus pattern (16 bp):   
AAAAAAACAAAAAGAA

Found at i:21036 original size:14 final size:15

Alignment explanation


    Indices: 21008--21045  Score: 55
    Period size: 14  Copynumber: 2.7  Consensus size: 15

      20998 GTTTTCCAGT

                           
      21008 AAAAT-ATTTTCTGG
          1 AAAATGATTTTCTGG

                           
      21022 AAAATGATTTT-TGG
          1 AAAATGATTTTCTGG

                       
      21036 AAAATG-TTTT
          1 AAAATGATTTT

      21046 ACTTTTCTGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  13    4  0.17
  14   14  0.61
  15    5  0.22

ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45


Consensus pattern (15 bp):   
AAAATGATTTTCTGG

Found at i:22471 original size:32 final size:32

Alignment explanation


    Indices: 22426--22518  Score: 161
    Period size: 32  Copynumber: 2.9  Consensus size: 32

      22416 TGTCAATCAT

                    *                       
      22426 TTCAATATCCAACAAGCTTAAAACATAATAAA
          1 TTCAATATTCAACAAGCTTAAAACATAATAAA

                                            
      22458 TTCAATATTCAACAAGCTTAAAACATAATAAA
          1 TTCAATATTCAACAAGCTTAAAACATAATAAA

                                          
      22490 TTCAATA-TCTAACAAGCTTAAAACATAAT
          1 TTCAATATTC-AACAAGCTTAAAACATAAT

      22519 CAATATCTAT


Statistics
Matches: 59,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  31    2  0.03
  32   57  0.97

ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28


Consensus pattern (32 bp):   
TTCAATATTCAACAAGCTTAAAACATAATAAA
Done.