Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2063

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: 9349
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38


Found at i:819 original size:32 final size:32

Alignment explanation


    Indices: 783--849  Score: 134
    Period size: 32  Copynumber: 2.1  Consensus size: 32

        773 AATAGCTACG

                                            
        783 AACTACTTTGATATGATAGAAAGCTAAAATCA
          1 AACTACTTTGATATGATAGAAAGCTAAAATCA

                                            
        815 AACTACTTTGATATGATAGAAAGCTAAAATCA
          1 AACTACTTTGATATGATAGAAAGCTAAAATCA

               
        847 AAC
          1 AAC

        850 GATGAAAAAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   35  1.00

ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27


Consensus pattern (32 bp):   
AACTACTTTGATATGATAGAAAGCTAAAATCA

Found at i:1429 original size:20 final size:20

Alignment explanation


    Indices: 1386--1429  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       1376 TTTATATTTT

                       *  * *  *
       1386 TTAAAAACAAATAACAGATT
          1 TTAAAAACAAAGAAAAAATA

                                
       1406 TTAAAAACAAAGAAAAAATA
          1 TTAAAAACAAAGAAAAAATA

                
       1426 TTAA
          1 TTAA

       1430 CTAAACAGAT


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23


Consensus pattern (20 bp):   
TTAAAAACAAAGAAAAAATA

Found at i:4955 original size:12 final size:12

Alignment explanation


    Indices: 4924--4973  Score: 55
    Period size: 12  Copynumber: 4.2  Consensus size: 12

       4914 ATTTTAATTA

                  *     
       4924 TTCTTTACTTTT
          1 TTCTTTTCTTTT

             * *        
       4936 TCCATTTCTTTT
          1 TTCTTTTCTTTT

              *         
       4948 TTTTTTTCTTTT
          1 TTCTTTTCTTTT

                   *    
       4960 TTCTTTTATTTT
          1 TTCTTTTCTTTT

              
       4972 TT
          1 TT

       4974 ACCAAAGAAA


Statistics
Matches: 30,  Mismatches: 8, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  12   30  1.00

ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80


Consensus pattern (12 bp):   
TTCTTTTCTTTT

Found at i:7034 original size:52 final size:52

Alignment explanation


    Indices: 6977--7075  Score: 189
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       6967 AAAAATAAAA

                                                                
       6977 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
          1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT

                                              *            
       7029 ATATTTTTCATATTATGGATATTAATAGACATAAGTTATATAATAGA
          1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGA

       7076 ATATAAATAT


Statistics
Matches: 46,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  52   46  1.00

ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43


Consensus pattern (52 bp):   
ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT

Found at i:8396 original size:13 final size:13

Alignment explanation


    Indices: 8374--8403  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       8364 CAACAATTTT

                         
       8374 AATAAAATGTATA
          1 AATAAAATGTATA

                 *       
       8387 AATAAGATGTATA
          1 AATAAAATGTATA

                
       8400 AATA
          1 AATA

       8404 TATAGACCAA


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

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30


Consensus pattern (13 bp):   
AATAAAATGTATA

Found at i:9327 original size:2 final size:2

Alignment explanation


    Indices: 9308--9345  Score: 53
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       9298 AATTAAAATA

                                                                       
       9308 AT AT A- AT AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A

       9346 AGAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   1    2  0.06
   2   30  0.91
   3    1  0.03

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45


Consensus pattern (2 bp):   
AT

Done.