Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1877

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, 738

Length: 1231
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30


Found at i:1108 original size:26 final size:27

Alignment explanation


    Indices: 1079--1131  Score: 99
    Period size: 26  Copynumber: 2.0  Consensus size: 27

       1069 TATAACTTTT

                                       
       1079 TTTATTTACCAAAATATAT-AAAAAAA
          1 TTTATTTACCAAAATATATCAAAAAAA

                                       
       1105 TTTATTTACCAAAATATATCAAAAAAA
          1 TTTATTTACCAAAATATATCAAAAAAA

       1132 CTGCAAAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  26   19  0.73
  27    7  0.27

ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34


Consensus pattern (27 bp):   
TTTATTTACCAAAATATATCAAAAAAA

Found at i:1138 original size:11 final size:11

Alignment explanation


    Indices: 1124--1152  Score: 51
    Period size: 10  Copynumber: 2.7  Consensus size: 11

       1114 CAAAATATAT

                       
       1124 CAAAAAAACTG
          1 CAAAAAAACTG

                       
       1135 C-AAAAAACTG
          1 CAAAAAAACTG

                    
       1145 CAAAAAAA
          1 CAAAAAAA

       1153 TCAGATCGAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  10   10  0.59
  11    7  0.41

ACGTcount: A:0.69, C:0.17, G:0.07, T:0.07


Consensus pattern (11 bp):   
CAAAAAAACTG

Found at i:1149 original size:9 final size:10

Alignment explanation


    Indices: 1126--1151  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       1116 AAATATATCA

                      
       1126 AAAAAACTGC
          1 AAAAAACTGC

                      
       1136 AAAAAACTGC
          1 AAAAAACTGC

                  
       1146 AAAAAA
          1 AAAAAA

       1152 ATCAGATCGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08


Consensus pattern (10 bp):   
AAAAAACTGC
Done.