Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold11994.1

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: 2462
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37


Found at i:1089 original size:18 final size:18

Alignment explanation


    Indices: 1068--1102  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1058 TTTTTCTTTT

                               
       1068 TCAATTT-TTTTCTCAATC
          1 TCAATTTCTTTT-TCAATC

                             
       1086 TCAATTTCTTTTTCAAT
          1 TCAATTTCTTTTTCAAT

       1103 TTTCTTTTCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   12  0.75
  19    4  0.25

ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57


Consensus pattern (18 bp):   
TCAATTTCTTTTTCAATC

Found at i:2097 original size:13 final size:13

Alignment explanation


    Indices: 2081--2155  Score: 62
    Period size: 14  Copynumber: 5.5  Consensus size: 13

       2071 TTTTGCTCGA

                       *  
       2081 TTTTTTTTCACTTT
          1 TTTTTTTTCA-ATT

                    *     
       2095 TTTTTTTTGAATTT
          1 TTTTTTTTCAA-TT

                            
       2109 TTTTTTTCAATCAATT
          1 TTTTTTT---TCAATT

                       * 
       2125 TTTTTTTTCAAAT
          1 TTTTTTTTCAATT

                     *   
       2138 TTTTTTTT-GATT
          1 TTTTTTTTCAATT

                  
       2150 TTTTTT
          1 TTTTTT

       2156 GTTACTCCAA


Statistics
Matches: 51,  Mismatches: 6, Indels: 10
        0.76            0.09        0.15

Matches are distributed among these distances:
  12    8  0.16
  13   13  0.25
  14   18  0.35
  16    9  0.18
  17    3  0.06

ACGTcount: A:0.15, C:0.07, G:0.03, T:0.76


Consensus pattern (13 bp):   
TTTTTTTTCAATT

Found at i:2098 original size:14 final size:14

Alignment explanation


    Indices: 2081--2145  Score: 69
    Period size: 13  Copynumber: 4.4  Consensus size: 14

       2071 TTTTGCTCGA

                      *   
       2081 TTTTTTTTCACTTT
          1 TTTTTTTTCAATTT

                    *     
       2095 TTTTTTTTGAA-TT
          1 TTTTTTTTCAATTT

                             
       2108 TTTTTTTTCAATCAATT
          1 TTTTTTTTCAAT---TT

                           
       2125 TTTTTTTTCAAATTT
          1 TTTTTTTTC-AATTT

                  
       2140 TTTTTT
          1 TTTTTT

       2146 GATTTTTTTT


Statistics
Matches: 43,  Mismatches: 3, Indels: 9
        0.78            0.05        0.16

Matches are distributed among these distances:
  13   12  0.28
  14    9  0.21
  15    8  0.19
  17   11  0.26
  18    3  0.07

ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75


Consensus pattern (14 bp):   
TTTTTTTTCAATTT
Done.