Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_2625

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: 22491
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:9367 original size:6 final size:6

Alignment explanation


    Indices: 9346--9404  Score: 50
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       9336 TTCTTTTTTG

                                         *          *                  
       9346 TTTTAT ATTTTA- -TTTAT TTTTAT CTTTAT TTTTGT TTTTCAT TGCTTTAT
          1 TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT-AT T--TTTAT

                      
       9396 TTTTAT TTT
          1 TTTTAT TTT

       9405 CTTAGACTTA


Statistics
Matches: 43,  Mismatches: 4, Indels: 11
        0.74            0.07        0.19

Matches are distributed among these distances:
   4    4  0.09
   6   26  0.60
   7    7  0.16
   8    3  0.07
   9    3  0.07

ACGTcount: A:0.15, C:0.05, G:0.03, T:0.76


Consensus pattern (6 bp):   
TTTTAT

Found at i:9383 original size:17 final size:18

Alignment explanation


    Indices: 9340--9383  Score: 56
    Period size: 17  Copynumber: 2.6  Consensus size: 18

       9330 TTTCTTTTCT

                         *    
       9340 TTTTTGTTTTATATTTTA
          1 TTTTTGTTTTATACTTTA

               *              
       9358 TTTAT-TTTTAT-CTTTA
          1 TTTTTGTTTTATACTTTA

                      
       9374 TTTTTGTTTT
          1 TTTTTGTTTT

       9384 TCATTGCTTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  16    8  0.36
  17   10  0.45
  18    4  0.18

ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80


Consensus pattern (18 bp):   
TTTTTGTTTTATACTTTA

Found at i:10388 original size:8 final size:7

Alignment explanation


    Indices: 10353--10387  Score: 61
    Period size: 7  Copynumber: 4.9  Consensus size: 7

      10343 TTTCTCTTGT

                    
      10353 AAAAAAGG
          1 AAAAAA-G

                   
      10361 AAAAAAG
          1 AAAAAAG

                   
      10368 AAAAAAG
          1 AAAAAAG

                   
      10375 AAAAAAG
          1 AAAAAAG

                  
      10382 AAAAAA
          1 AAAAAA

      10388 AATAATGATT


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   7   21  0.78
   8    6  0.22

ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00


Consensus pattern (7 bp):   
AAAAAAG
Done.