Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold168

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1096678
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.29

Warning! 140106 characters in sequence are not A, C, G, or T


File 4 of 3

Found at i:1060888 original size:21 final size:21

Alignment explanation


    Indices: 1060862--1060911  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

    1060852 AGCCCTATCC

                  *            * 
    1060862 TATCCTGTATCCAGTATCCTG
          1 TATCCTATATCCAGTATCCAG

                        *        
    1060883 TATCCTATATCCTGTATCCAG
          1 TATCCTATATCCAGTATCCAG

               *    
    1060904 TATTCTAT
          1 TATCCTAT

    1060912 TCTATTTATT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42


Consensus pattern (21 bp):   
TATCCTATATCCAGTATCCAG

Found at i:1072026 original size:9 final size:9

Alignment explanation


    Indices: 1072012--1072038  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

    1072002 GATGGATGCA

                     
    1072012 GGATAGGAT
          1 GGATAGGAT

                     
    1072021 GGATAGGAT
          1 GGATAGGAT

                     
    1072030 GGATAGGAT
          1 GGATAGGAT

    1072039 TGAAAGCGTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.33, C:0.00, G:0.44, T:0.22


Consensus pattern (9 bp):   
GGATAGGAT

Found at i:1072073 original size:14 final size:14

Alignment explanation


    Indices: 1072054--1072095  Score: 57
    Period size: 14  Copynumber: 3.0  Consensus size: 14

    1072044 GCGTTTCTAT

                  *     * 
    1072054 TCTATCATGTATTC
          1 TCTATCCTGTATCC

                          
    1072068 TCTATCCTGTATCC
          1 TCTATCCTGTATCC

             *            
    1072082 TATATCCTGTATCC
          1 TCTATCCTGTATCC

    1072096 AGCATCCTAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  14   25  1.00

ACGTcount: A:0.19, C:0.29, G:0.07, T:0.45


Consensus pattern (14 bp):   
TCTATCCTGTATCC

Found at i:1087847 original size:28 final size:24

Alignment explanation


    Indices: 1087793--1087841  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

    1087783 AAAAAATCGT

                                    
    1087793 ATTTATTTTCATCAGTCAATACAA
          1 ATTTATTTTCATCAGTCAATACAA

                                    
    1087817 ATTTATTTTCATCAGTCAATACAA
          1 ATTTATTTTCATCAGTCAATACAA

             
    1087841 A
          1 A

    1087842 GAAATTCAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41


Consensus pattern (24 bp):   
ATTTATTTTCATCAGTCAATACAA

Found at i:1089263 original size:2 final size:2

Alignment explanation


    Indices: 1089258--1089286  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

    1089248 AACTATTACT

                                                       
    1089258 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 T

    1089287 GTTTAAATAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
TC


Done.