Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00993.P2

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: 4452
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36


Found at i:2163 original size:43 final size:43

Alignment explanation


    Indices: 2102--2263  Score: 270
    Period size: 43  Copynumber: 3.8  Consensus size: 43

       2092 ATGAAACTTG

                                *                     *
       2102 GTGAAATAATATCGGGCTTCAAGCCTAGCAGGCTATAATGCCT
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

                                     *                 
       2145 GTGAAATAATATCGGGCTTCGAGCCGAGCAGGCTATAATGCCA
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

                             *                        *
       2188 GTGAAATAATATCGGGCCTCGAGCCTAGCAGGCTATAATGCCG
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

                        *                    
       2231 GTGAAATAATATTGGGCTTCGAGCCTAGCAGGC
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGC

       2264 GAAATGCAGG


Statistics
Matches: 111,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  43  111  1.00

ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23


Consensus pattern (43 bp):   
GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

Found at i:2872 original size:16 final size:18

Alignment explanation


    Indices: 2841--2873  Score: 52
    Period size: 16  Copynumber: 1.9  Consensus size: 18

       2831 AACTCATCAC

                              
       2841 ACTATCTATCGTTTTGGT
          1 ACTATCTATCGTTTTGGT

                             
       2859 ACTAT-TAT-GTTTTGG
          1 ACTATCTATCGTTTTGG

       2874 AATTCGTATG


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    7  0.47
  17    3  0.20
  18    5  0.33

ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52


Consensus pattern (18 bp):   
ACTATCTATCGTTTTGGT

Found at i:3156 original size:16 final size:16

Alignment explanation


    Indices: 3137--3186  Score: 51
    Period size: 16  Copynumber: 3.6  Consensus size: 16

       3127 ATTGTTTTGC

                            
       3137 TTAAATGTTGTTTAAA
          1 TTAAATGTTGTTTAAA

                            
       3153 TTAAA---TGTTT--A
          1 TTAAATGTTGTTTAAA

                            
       3164 TT--ATGTTGTTTAAA
          1 TTAAATGTTGTTTAAA

                     
       3178 TTAAATGTT
          1 TTAAATGTT

       3187 TATTATGTTG


Statistics
Matches: 27,  Mismatches: 0, Indels: 14
        0.66            0.00        0.34

Matches are distributed among these distances:
   9    1  0.04
  11    3  0.11
  12    5  0.19
  13    5  0.19
  14    3  0.11
  16   10  0.37

ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54


Consensus pattern (16 bp):   
TTAAATGTTGTTTAAA

Found at i:3169 original size:25 final size:25

Alignment explanation


    Indices: 3141--3199  Score: 118
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       3131 TTTTGCTTAA

                                     
       3141 ATGTTGTTTAAATTAAATGTTTATT
          1 ATGTTGTTTAAATTAAATGTTTATT

                                     
       3166 ATGTTGTTTAAATTAAATGTTTATT
          1 ATGTTGTTTAAATTAAATGTTTATT

                     
       3191 ATGTTGTTT
          1 ATGTTGTTT

       3200 TGATGTAAAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   34  1.00

ACGTcount: A:0.29, C:0.00, G:0.14, T:0.58


Consensus pattern (25 bp):   
ATGTTGTTTAAATTAAATGTTTATT
Done.