Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold797

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: 3100
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35


Found at i:482 original size:24 final size:24

Alignment explanation


    Indices: 433--534  Score: 74
    Period size: 24  Copynumber: 4.3  Consensus size: 24

        423 ATTAAGCATA

                                    
        433 AATATTTATATTTTAATATAATAT
          1 AATATTTATATTTTAATATAATAT

                                     
        457 AATA-TTACTATTTT-A-ATAAT-T
          1 AATATTTA-TATTTTAATATAATAT

                 *                     
        478 AATA-ATA-ATTATTAATATAATGAAT
          1 AATATTTATATT-TTAATATAAT--AT

             *                 *     
        503 ATTATTTATTATTTTAATAGAA-AT
          1 AATATTTA-TATTTTAATATAATAT

             *      
        527 ATTATTTA
          1 AATATTTA

        535 ATATAATAAT


Statistics
Matches: 64,  Mismatches: 4, Indels: 20
        0.73            0.05        0.23

Matches are distributed among these distances:
  19    3  0.05
  20    2  0.03
  21    8  0.12
  22   10  0.16
  23    4  0.06
  24   20  0.31
  25    4  0.06
  26    2  0.03
  27    8  0.12
  28    3  0.05

ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51


Consensus pattern (24 bp):   
AATATTTATATTTTAATATAATAT

Found at i:497 original size:22 final size:22

Alignment explanation


    Indices: 472--513  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        462 TACTATTTTA

                 *                
        472 ATAATTAATAATAATTATTAAT
          1 ATAATGAATAATAATTATTAAT

                      *  *      
        494 ATAATGAATATTATTTATTA
          1 ATAATGAATAATAATTATTA

        514 TTTTAATAGA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (22 bp):   
ATAATGAATAATAATTATTAAT

Found at i:970 original size:30 final size:28

Alignment explanation


    Indices: 936--997  Score: 88
    Period size: 30  Copynumber: 2.1  Consensus size: 28

        926 AAAAATAACA

                            *             
        936 TTTAATAATAATTATATTAATGGAAATAAT
          1 TTTAATAATAATTATAAT-AT-GAAATAAT

                                *       
        966 TTTAATAATAATTATAATATTAAATAAT
          1 TTTAATAATAATTATAATATGAAATAAT

                
        994 TTTA
          1 TTTA

        998 TTATTTTTAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  28   11  0.37
  29    2  0.07
  30   17  0.57

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (28 bp):   
TTTAATAATAATTATAATATGAAATAAT

Found at i:1131 original size:23 final size:23

Alignment explanation


    Indices: 1105--1181  Score: 57
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       1095 TTTTTTTTTT

                                   
       1105 AAGAAAATCTTTACATTTTTCAA
          1 AAGAAAATCTTTACATTTTTCAA

                          ** *      ***
       1128 AAGAAGTATTATC-AAAAATTTTTTTT
          1 AAGAA--A--ATCTTTACATTTTTCAA

                                   
       1154 AAGAAAATCTTTACATTTTTCAA
          1 AAGAAAATCTTTACATTTTTCAA

                 
       1177 AAGAA
          1 AAGAA

       1182 GTATTATCAA


Statistics
Matches: 37,  Mismatches: 12, Indels: 10
        0.63            0.20        0.17

Matches are distributed among these distances:
  22    3  0.08
  23   17  0.46
  24    1  0.03
  25    1  0.03
  26   12  0.32
  27    3  0.08

ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39


Consensus pattern (23 bp):   
AAGAAAATCTTTACATTTTTCAA

Found at i:1151 original size:49 final size:48

Alignment explanation


    Indices: 1097--1197  Score: 193
    Period size: 49  Copynumber: 2.1  Consensus size: 48

       1087 CATCAGATTT

                                                             
       1097 TTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAAAA
          1 TTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATC-AAAA

                                                            
       1146 TTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAAA
          1 TTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAAA

                
       1194 TTTT
          1 TTTT

       1198 GTTGTTCCTC


Statistics
Matches: 52,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  48    8  0.15
  49   44  0.85

ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46


Consensus pattern (48 bp):   
TTTTTTTTAAGAAAATCTTTACATTTTTCAAAAGAAGTATTATCAAAA
Done.