Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3494

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: 21722
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:379 original size:19 final size:19

Alignment explanation


    Indices: 355--393  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        345 AATTATTTTT

                               
        355 CACATTTGATTTGAAATGA
          1 CACATTTGATTTGAAATGA

                               
        374 CACATTTGATTTGAAATGA
          1 CACATTTGATTTGAAATGA

             
        393 C
          1 C

        394 TAAAAGAAGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Consensus pattern (19 bp):   
CACATTTGATTTGAAATGA

Found at i:9515 original size:24 final size:24

Alignment explanation


    Indices: 9454--9569  Score: 155
    Period size: 24  Copynumber: 4.9  Consensus size: 24

       9444 TACTTAGACA

                *             *     
       9454 ATTTGCCGTCAATTCATCATTTAC
          1 ATTTTCCGTCAATTCATCCTTTAC

                *     *             
       9478 A-TTACCGTCGATTCATCCTTTAC
          1 ATTTTCCGTCAATTCATCCTTTAC

                           *  *     
       9501 ATTTTCCGTCAATTCCTCATTTAC
          1 ATTTTCCGTCAATTCATCCTTTAC

                 *                  
       9525 ATTTTTCGTCAATTCATCCTTTAC
          1 ATTTTCCGTCAATTCATCCTTTAC

                                  
       9549 A-TTTCCGTCAATTCATCCTTT
          1 ATTTTCCGTCAATTCATCCTTT

       9570 CCCAATAATG


Statistics
Matches: 80,  Mismatches: 11, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  23   39  0.49
  24   41  0.51

ACGTcount: A:0.22, C:0.28, G:0.06, T:0.45


Consensus pattern (24 bp):   
ATTTTCCGTCAATTCATCCTTTAC

Found at i:9554 original size:47 final size:46

Alignment explanation


    Indices: 9454--9565  Score: 161
    Period size: 47  Copynumber: 2.4  Consensus size: 46

       9444 TACTTAGACA

                                             *             
       9454 ATTTGCCGTCAATTCATCATTTACATTACCGTCGATTCATCCTTTAC
          1 ATTT-CCGTCAATTCATCATTTACATTACCGTCAATTCATCCTTTAC

                           *            **                  
       9501 ATTTTCCGTCAATTCCTCATTTACATTTTTCGTCAATTCATCCTTTAC
          1 A-TTTCCGTCAATTCATCATTTACA-TTACCGTCAATTCATCCTTTAC

                             
       9549 ATTTCCGTCAATTCATC
          1 ATTTCCGTCAATTCATC

       9566 CTTTCCCAAT


Statistics
Matches: 58,  Mismatches: 5, Indels: 4
        0.87            0.07        0.06

Matches are distributed among these distances:
  47   35  0.60
  48   23  0.40

ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44


Consensus pattern (46 bp):   
ATTTCCGTCAATTCATCATTTACATTACCGTCAATTCATCCTTTAC

Found at i:16581 original size:21 final size:21

Alignment explanation


    Indices: 16555--16595  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      16545 AGACGAGCAA

                   * *           
      16555 TACTCCACAGCAGGTGGAGTG
          1 TACTCCAAAACAGGTGGAGTG

                                
      16576 TACTCCAAAACAGGTGGAGT
          1 TACTCCAAAACAGGTGGAGT

      16596 TTGAGCAGAT


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20


Consensus pattern (21 bp):   
TACTCCAAAACAGGTGGAGTG
Done.