Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2392

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, 576

Length: 960
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33


Found at i:247 original size:38 final size:37

Alignment explanation


    Indices: 160--261  Score: 120
    Period size: 36  Copynumber: 2.8  Consensus size: 37

        150 GAATTTCTTG

                          *        *   *  *      
        160 TTTTGAAAACACGAGAATTTCAAGACATAATATTTTT
          1 TTTTGAAAACACGAAAATTTCAAAACACAAGATTTTT

                                                   
        197 TTTT-AAAA-ACGAAAATTT-ATGAAACACAAGATTTTT
          1 TTTTGAAAACACGAAAATTTCA--AAACACAAGATTTTT

                                         
        233 TTTTGAAAACACGAAAATTTTCAAAACAC
          1 TTTTGAAAACACGAAAA-TTTCAAAACAC

        262 CGAAATTTTT


Statistics
Matches: 55,  Mismatches: 4, Indels: 11
        0.79            0.06        0.16

Matches are distributed among these distances:
  34    1  0.02
  35    9  0.16
  36   20  0.36
  37    8  0.15
  38   13  0.24
  39    3  0.05
  40    1  0.02

ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34


Consensus pattern (37 bp):   
TTTTGAAAACACGAAAATTTCAAAACACAAGATTTTT

Found at i:414 original size:18 final size:17

Alignment explanation


    Indices: 232--413  Score: 170
    Period size: 18  Copynumber: 10.3  Consensus size: 17

        222 ACAAGATTTT

                             
        232 TTTTTGAAAACACGAAA
          1 TTTTTGAAAACACGAAA

            *    *            
        249 ATTTTCAAAACACCGAAA
          1 TTTTTGAAAACA-CGAAA

                            * 
        267 TTTTTGAAAACACGAGGA
          1 TTTTTGAAAACACGA-AA

                              
        285 TTTTTG-AAACACGAGAA
          1 TTTTTGAAAACACGA-AA

                         *     
        302 TTTTCTGAAAACATGAAAA
          1 TTTT-TGAAAACACG-AAA

            *         ***    *
        321 ATTTTGAAAATTGGAATT
          1 TTTTTGAAAACACGAA-A

                              
        339 TTTTTGAAAACACGAGAA
          1 TTTTTGAAAACACGA-AA

                        *     
        357 TTTTTGAAAACATGAAAA
          1 TTTTTGAAAACACG-AAA

                           *  
        375 TTTTTG-AAACACGGGAA
          1 TTTTTGAAAACAC-GAAA

                             
        392 TTTTTGAAAACACGAAA
          1 TTTTTGAAAACACGAAA

                 
        409 TTTTT
          1 TTTTT

        414 TTTATTTTTT


Statistics
Matches: 134,  Mismatches: 21, Indels: 20
        0.77            0.12        0.11

Matches are distributed among these distances:
  17   50  0.37
  18   70  0.52
  19   13  0.10
  20    1  0.01

ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32


Consensus pattern (17 bp):   
TTTTTGAAAACACGAAA

Found at i:545 original size:22 final size:21

Alignment explanation


    Indices: 518--560  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 21

        508 CGTTACCTTA

                                  
        518 TTTTTGAAAACACGAGAAATTT
          1 TTTTTGAAAACACGA-AAATTT

                    *            
        540 TTTTTGAAGACACGAAAATTT
          1 TTTTTGAAAACACGAAAATTT

        561 CGAAACCCGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  21    6  0.30
  22   14  0.70

ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37


Consensus pattern (21 bp):   
TTTTTGAAAACACGAAAATTT

Found at i:776 original size:14 final size:15

Alignment explanation


    Indices: 757--791  Score: 54
    Period size: 16  Copynumber: 2.3  Consensus size: 15

        747 ATTGAAATTG

                           
        757 AAAATAT-AAATACA
          1 AAAATATAAAATACA

                            
        771 AAAATATAAAAATACA
          1 AAAATAT-AAAATACA

                 
        787 AAAAT
          1 AAAAT

        792 GCATAAAATG


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    7  0.37
  16   12  0.63

ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20


Consensus pattern (15 bp):   
AAAATATAAAATACA
Done.