Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1407

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: 13569
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37


Found at i:44 original size:2 final size:2

Alignment explanation


    Indices: 37--71  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

         27 AGAAATTTAA

                                                                
         37 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         72 GTGAGCTGTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:4046 original size:3 final size:3

Alignment explanation


    Indices: 4038--4071  Score: 68
    Period size: 3  Copynumber: 11.3  Consensus size: 3

       4028 ATTAATTAAC

                                                         
       4038 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T

       4072 TAATCAATTC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:4326 original size:10 final size:10

Alignment explanation


    Indices: 4311--4336  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       4301 AATATTAATA

                      
       4311 TAAATATTTT
          1 TAAATATTTT

                      
       4321 TAAATATTTT
          1 TAAATATTTT

                  
       4331 TAAATA
          1 TAAATA

       4337 AAATTAAATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (10 bp):   
TAAATATTTT

Found at i:4862 original size:20 final size:20

Alignment explanation


    Indices: 4839--4878  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       4829 AAATTCAAAG

                                
       4839 ATTATGATTTATTTTTTAAA
          1 ATTATGATTTATTTTTTAAA

                 **             
       4859 ATTATTTTTTATTTTTTAAA
          1 ATTATGATTTATTTTTTAAA

       4879 TATACTTTAA


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

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65


Consensus pattern (20 bp):   
ATTATGATTTATTTTTTAAA

Found at i:10309 original size:2 final size:2

Alignment explanation


    Indices: 10304--10351  Score: 78
    Period size: 2  Copynumber: 24.0  Consensus size: 2

      10294 ACACACACAC

                                                                  *     * 
      10304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
      10346 AT AT AT
          1 AT AT AT

      10352 GTATCATGGA


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:11239 original size:12 final size:12

Alignment explanation


    Indices: 11224--11249  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      11214 TTTTTTTATT

                        
      11224 AATTATTTTTAA
          1 AATTATTTTTAA

                        
      11236 AATTATTTTTAA
          1 AATTATTTTTAA

              
      11248 AA
          1 AA

      11250 GATAAATTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (12 bp):   
AATTATTTTTAA

Found at i:12349 original size:23 final size:24

Alignment explanation


    Indices: 12313--12357  Score: 74
    Period size: 23  Copynumber: 1.9  Consensus size: 24

      12303 CAAATTTGAC

                     *              
      12313 TATGTGGATTTTTAAAATTTTTTT
          1 TATGTGGATATTTAAAATTTTTTT

                                  
      12337 TATGTGGA-ATTTAAAATTTTT
          1 TATGTGGATATTTAAAATTTTT

      12358 AAAATAATTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  23   12  0.60
  24    8  0.40

ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58


Consensus pattern (24 bp):   
TATGTGGATATTTAAAATTTTTTT

Found at i:13296 original size:14 final size:14

Alignment explanation


    Indices: 13277--13333  Score: 53
    Period size: 14  Copynumber: 4.0  Consensus size: 14

      13267 TTATTATTTT

                          
      13277 TTATATAATATAAA
          1 TTATATAATATAAA

                  *        
      13291 TTATATTATATAATA
          1 TTATATAATATAA-A

              * *       *  
      13306 TACAAATAATATGAA
          1 T-TATATAATATAAA

                          
      13321 TTATATAAT-TAAA
          1 TTATATAATATAAA

      13334 AAGTAAGTTG


Statistics
Matches: 33,  Mismatches: 8, Indels: 5
        0.72            0.17        0.11

Matches are distributed among these distances:
  13    3  0.09
  14   18  0.55
  15    4  0.12
  16    8  0.24

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42


Consensus pattern (14 bp):   
TTATATAATATAAA
Done.