Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g02718.F1

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, 938

Length: 1564
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29


Found at i:1071 original size:3 final size:3

Alignment explanation


    Indices: 1063--1093  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       1053 TTCGATGACA

                                            *        
       1063 AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG A
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A

       1094 GGTAACCGAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:1142 original size:21 final size:21

Alignment explanation


    Indices: 1101--1184  Score: 72
    Period size: 18  Copynumber: 4.3  Consensus size: 21

       1091 AGAGGTAACC

                             *   
       1101 GAAGAAGATGAAGT--TGT-T
          1 GAAGAAGATGAAGTACTTTAT

                   *             
       1119 GAAGAAGGTGAAGTACTTTAT
          1 GAAGAAGATGAAGTACTTTAT

                  *    *     *   
       1140 GAAGAAAATGATGT--TGTA-
          1 GAAGAAGATGAAGTACTTTAT

                                 
       1158 GAAGAAGATGAAGTACTTTAT
          1 GAAGAAGATGAAGTACTTTAT

             *    
       1179 GGAGAA
          1 GAAGAA

       1185 AATGGTGTTG


Statistics
Matches: 50,  Mismatches: 10, Indels: 9
        0.72            0.14        0.13

Matches are distributed among these distances:
  18   25  0.50
  19    3  0.06
  20    5  0.10
  21   17  0.34

ACGTcount: A:0.42, C:0.02, G:0.30, T:0.26


Consensus pattern (21 bp):   
GAAGAAGATGAAGTACTTTAT

Found at i:1194 original size:39 final size:39

Alignment explanation


    Indices: 1101--1196  Score: 138
    Period size: 39  Copynumber: 2.5  Consensus size: 39

       1091 AGAGGTAACC

                  *    *     *       *             
       1101 GAAGAAGATGAAGTTGTTGAAGAAGGTGAAGTACTTTAT
          1 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT

                                                   
       1140 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
          1 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT

             *        *       
       1179 GGAGAAAATGGTGTTGTA
          1 GAAGAAAATGATGTTGTA

       1197 CAGGATGAAA


Statistics
Matches: 51,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  39   51  1.00

ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28


Consensus pattern (39 bp):   
GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT

Found at i:1208 original size:21 final size:21

Alignment explanation


    Indices: 1182--1226  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1172 ACTTTATGGA

                   *         *   
       1182 GAAAATGGTGTTGTACAGGAT
          1 GAAAATGATGTTGTACAAGAT

                           *     
       1203 GAAAATGATGTTGTAGAAGAT
          1 GAAAATGATGTTGTACAAGAT

               
       1224 GAA
          1 GAA

       1227 GTACTTTGTG


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.40, C:0.02, G:0.31, T:0.27


Consensus pattern (21 bp):   
GAAAATGATGTTGTACAAGAT
Done.