Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2530

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: 5959
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39


Found at i:939 original size:25 final size:23

Alignment explanation


    Indices: 883--943  Score: 77
    Period size: 24  Copynumber: 2.5  Consensus size: 23

        873 TTAAAATAAT

                             *     
        883 TATGTATTAAAATAAAAGAAGTA
          1 TATGTATTAAAATAAAAAAAGTA

                *                     
        906 TATAATATTAAAATAAAAAATACGTA
          1 TAT-GTATTAAAATAAAAAA-A-GTA

                        
        932 TATGTATTAAAA
          1 TATGTATTAAAA

        944 CTATGTAATA


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  23    3  0.09
  24   14  0.44
  25    9  0.28
  26    6  0.19

ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33


Consensus pattern (23 bp):   
TATGTATTAAAATAAAAAAAGTA

Found at i:992 original size:17 final size:18

Alignment explanation


    Indices: 949--997  Score: 55
    Period size: 17  Copynumber: 2.6  Consensus size: 18

        939 TAAAACTATG

                                
        949 TAATATAAATATTATTATGA
          1 TAATATAAA-ATTATTA-GA

            *                  
        969 AATATATAAAATTATTA-A
          1 TA-ATATAAAATTATTAGA

                       
        987 TAATATAAAAT
          1 TAATATAAAAT

        998 AAATCATAGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  17    9  0.35
  18    2  0.08
  20    8  0.31
  21    7  0.27

ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41


Consensus pattern (18 bp):   
TAATATAAAATTATTAGA

Found at i:1393 original size:24 final size:25

Alignment explanation


    Indices: 1338--1399  Score: 63
    Period size: 24  Copynumber: 2.4  Consensus size: 25

       1328 AATTTCTATC

                                 *    *
       1338 AAAATAAATTTTTTTTTTTATTATATT
          1 AAAATAAA--TTTTTTTTTATAATATA

            *                        
       1365 TAAATAAATTTTTTTTTA-AATATA
          1 AAAATAAATTTTTTTTTATAATATA

                  *    
       1389 AAAATATATTT
          1 AAAATAAATTT

       1400 GAATAAAATG


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

Matches are distributed among these distances:
  24   13  0.43
  25   10  0.33
  27    7  0.23

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (25 bp):   
AAAATAAATTTTTTTTTATAATATA

Found at i:1586 original size:2 final size:2

Alignment explanation


    Indices: 1579--1611  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1569 TAGCTCAGAT

                                                             
       1579 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 T

       1612 ACGTACTGCT


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

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Done.