Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1419

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: 9789
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:2456 original size:18 final size:18

Alignment explanation


    Indices: 2433--2500  Score: 57
    Period size: 18  Copynumber: 3.6  Consensus size: 18

       2423 AACAAGTGAG

                              
       2433 GAAAAAGAAAAAGAGAAT
          1 GAAAAAGAAAAAGAGAAT

                               * 
       2451 GAAAAAGAGCAAAAAGAGATT
          1 G-AAAA-AG-AAAAAGAGAAT

              * **             
       2472 GAGAGTGAAAAAGA-AATT
          1 GAAAAAGAAAAAGAGAA-T

                       
       2490 GAAAAAGAAAA
          1 GAAAAAGAAAA

       2501 GAAGAAGAAA


Statistics
Matches: 38,  Mismatches: 8, Indels: 8
        0.70            0.15        0.15

Matches are distributed among these distances:
  17    1  0.03
  18   17  0.45
  19    5  0.13
  20    4  0.11
  21   11  0.29

ACGTcount: A:0.66, C:0.01, G:0.24, T:0.09


Consensus pattern (18 bp):   
GAAAAAGAAAAAGAGAAT

Found at i:2511 original size:29 final size:28

Alignment explanation


    Indices: 2478--2541  Score: 78
    Period size: 29  Copynumber: 2.3  Consensus size: 28

       2468 GATTGAGAGT

                                    *     
       2478 GAAAAAGAAATT-GAAAAAGAAAAGAAGAA
          1 GAAAAAGAAATTAGAAAAAG-AAACAA-AA

                 *                      
       2507 GAAAATG-AATTAGAAAAAGAAACAAAA
          1 GAAAAAGAAATTAGAAAAAGAAACAAAA

                    
       2534 GAAAAAGA
          1 GAAAAAGA

       2542 CGTGGAAAGG


Statistics
Matches: 30,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  27    8  0.27
  28    9  0.30
  29   13  0.43

ACGTcount: A:0.72, C:0.02, G:0.19, T:0.08


Consensus pattern (28 bp):   
GAAAAAGAAATTAGAAAAAGAAACAAAA

Found at i:4976 original size:32 final size:31

Alignment explanation


    Indices: 4932--4995  Score: 110
    Period size: 32  Copynumber: 2.0  Consensus size: 31

       4922 TCCTTCGGGT

                   *                        
       4932 TAGCTCCTACCCGTTAAGATTTCTTTATGAAG
          1 TAGCTCCAACCCGTTAAGATTTCTTTA-GAAG

                                           
       4964 TAGCTCCAACCCGTTAAGATTTCTTTAGAAG
          1 TAGCTCCAACCCGTTAAGATTTCTTTAGAAG

             
       4995 T
          1 T

       4996 GGGAATGAGT


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  31    5  0.16
  32   26  0.84

ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36


Consensus pattern (31 bp):   
TAGCTCCAACCCGTTAAGATTTCTTTAGAAG

Found at i:7609 original size:24 final size:24

Alignment explanation


    Indices: 7563--7609  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       7553 GTAACTATGG

                       **     *     
       7563 ATATGTTTAAATTTTAAAGTTTTT
          1 ATATGTTTAAAAATTAAACTTTTT

                            *      
       7587 ATATGTTTAAAAATTATACTTTT
          1 ATATGTTTAAAAATTAAACTTTT

       7610 AGATCCATGT


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55


Consensus pattern (24 bp):   
ATATGTTTAAAAATTAAACTTTTT
Done.