Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold918

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: 4253
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.29

Warning! 426 characters in sequence are not A, C, G, or T


Found at i:1109 original size:27 final size:29

Alignment explanation


    Indices: 1079--1145  Score: 77
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       1069 TTAATATCCA

                 *                       
       1079 AATAAGTAAAAT-AAAAT-AAAATAAAGT
          1 AATAAATAAAATAAAAATAAAAATAAAGT

                      *                 * 
       1106 AATAAATAAAGTAAAAATAAAAATAAAAAT
          1 AATAAATAAAATAAAAATAAAAAT-AAAGT

                       
       1136 AA-AAATAAAA
          1 AATAAATAAAA

       1146 ATTGGGTTGC


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  27   10  0.30
  28    5  0.15
  29   12  0.36
  30    6  0.18

ACGTcount: A:0.76, C:0.00, G:0.04, T:0.19


Consensus pattern (29 bp):   
AATAAATAAAATAAAAATAAAAATAAAGT

Found at i:1114 original size:12 final size:11

Alignment explanation


    Indices: 1078--1138  Score: 65
    Period size: 12  Copynumber: 5.6  Consensus size: 11

       1068 ATTAATATCC

                       
       1078 AAAT-AAGT-A
          1 AAATAAAGTAA

                   *   
       1087 AAATAAAAT-A
          1 AAATAAAGTAA

                       
       1097 AAATAAAGTAA
          1 AAATAAAGTAA

                        
       1108 TAAATAAAGTAA
          1 -AAATAAAGTAA

                    *   
       1120 AAATAAAAATAA
          1 AAAT-AAAGTAA

                   
       1132 AAATAAA
          1 AAATAAA

       1139 AATAAAAATT


Statistics
Matches: 45,  Mismatches: 3, Indels: 6
        0.83            0.06        0.11

Matches are distributed among these distances:
   9    4  0.09
  10   12  0.27
  11    8  0.18
  12   21  0.47

ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20


Consensus pattern (11 bp):   
AAATAAAGTAA

Found at i:1114 original size:17 final size:16

Alignment explanation


    Indices: 1086--1145  Score: 68
    Period size: 17  Copynumber: 3.6  Consensus size: 16

       1076 CCAAATAAGT

                            
       1086 AAAATAAAATAAAATA
          1 AAAATAAAATAAAATA

                           *  
       1102 AAGTAAT-AAATAAAGTA
          1 AA--AATAAAATAAAATA

                              
       1119 AAAATAAAAATAAAAATA
          1 AAAAT-AAAAT-AAAATA

                     
       1137 AAAATAAAA
          1 AAAATAAAA

       1146 ATTGGGTTGC


Statistics
Matches: 37,  Mismatches: 2, Indels: 9
        0.77            0.04        0.19

Matches are distributed among these distances:
  15    3  0.08
  16    2  0.05
  17   19  0.51
  18   13  0.35

ACGTcount: A:0.78, C:0.00, G:0.03, T:0.18


Consensus pattern (16 bp):   
AAAATAAAATAAAATA

Found at i:1128 original size:6 final size:6

Alignment explanation


    Indices: 1086--1147  Score: 69
    Period size: 6  Copynumber: 10.8  Consensus size: 6

       1076 CCAAATAAGT

                                    *              *                
       1086 AAAAT- AAAAT- AAAAT- AAAGTA ATAAAT- AAAGTA AAAATA AAAATA
          1 AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA AAAATA AAAATA

                               
       1131 AAAATA AAAATA AAAAT
          1 AAAATA AAAATA AAAAT

       1148 TGGGTTGCCT


Statistics
Matches: 50,  Mismatches: 4, Indels: 5
        0.85            0.07        0.08

Matches are distributed among these distances:
   5   17  0.34
   6   30  0.60
   7    3  0.06

ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19


Consensus pattern (6 bp):   
AAAATA

Done.