Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00001.P4

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: 10791
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39


Found at i:1378 original size:39 final size:39

Alignment explanation


    Indices: 1324--1406  Score: 132
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       1314 GGTGGTGACG

                                                *   
       1324 GGTGGACCGATGGTGACTA-CCTGACTGGTGAACGATGAT
          1 GGTGGACCGATGGTGAC-AGCCTGACTGGTGAACGACGAT

                     *                             
       1363 GGTGGACCGGTGGTGACAGCCTGACTGGTGAACGACGAT
          1 GGTGGACCGATGGTGACAGCCTGACTGGTGAACGACGAT

                 
       1402 GGTGG
          1 GGTGG

       1407 TGGCCAGTGG


Statistics
Matches: 41,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  38    1  0.02
  39   40  0.98

ACGTcount: A:0.20, C:0.18, G:0.41, T:0.20


Consensus pattern (39 bp):   
GGTGGACCGATGGTGACAGCCTGACTGGTGAACGACGAT

Found at i:3557 original size:31 final size:31

Alignment explanation


    Indices: 3521--3583  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       3511 TTCCTTATTT

                                           
       3521 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

                                           
       3552 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

             
       3583 C
          1 C

       3584 TTCTCGTACT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57


Consensus pattern (31 bp):   
CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

Found at i:8383 original size:116 final size:117

Alignment explanation


    Indices: 8226--8439  Score: 367
    Period size: 116  Copynumber: 1.8  Consensus size: 117

       8216 CTGTAATGTG

                                     *                               *       
       8226 TTTTATTTTATTTTTTCTGATTGTTTGTTTCCCTTTGTATTTAACGACATTTTCTTGTAAATATT
          1 TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATATT

                                  *                             
       8291 TGAATAATTGAATCCCATTAATTAGATTTTATATTGCCTGTTATGTGTTTTA
         66 TGAATAATTGAATCCCATTAATGAGATTTTATATTGCCTGTTATGTGTTTTA

                                                                          *  
       8343 TTTTATTTTATTTTTT-TGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATCTT
          1 TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATATT

                 *                   *       
       8407 TGAATGATTGAATCCCATTAATGAGGTTTTATA
         66 TGAATAATTGAATCCCATTAATGAGATTTTATA

       8440 GCGAAGATAT


Statistics
Matches: 91,  Mismatches: 6, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
 116   75  0.82
 117   16  0.18

ACGTcount: A:0.23, C:0.11, G:0.12, T:0.54


Consensus pattern (117 bp):   
TTTTATTTTATTTTTTCTGATTGTTAGTTTCCCTTTGTATTTAACGACATTTTCTTGCAAATATT
TGAATAATTGAATCCCATTAATGAGATTTTATATTGCCTGTTATGTGTTTTA

Found at i:8583 original size:42 final size:42

Alignment explanation


    Indices: 8537--8630  Score: 120
    Period size: 42  Copynumber: 2.3  Consensus size: 42

       8527 GTAAATACCG

                            *        *         *       
       8537 CTCATATCCCAC-CTTGGAATAATCTATTCCAGGGTTATCCCT
          1 CTCATATCCCACTCTTAGAATAATCAATTCC-GGGATATCCCT

                 *                                    
       8579 CTCATTTCCC-CTCTTAGAATAATCAATTCCGGGATATCCCT
          1 CTCATATCCCACTCTTAGAATAATCAATTCCGGGATATCCCT

              *        
       8620 CTGATATCCCA
          1 CTCATATCCCA

       8631 TCCCGGTTCG


Statistics
Matches: 44,  Mismatches: 6, Indels: 4
        0.81            0.11        0.07

Matches are distributed among these distances:
  41   19  0.43
  42   25  0.57

ACGTcount: A:0.24, C:0.32, G:0.11, T:0.33


Consensus pattern (42 bp):   
CTCATATCCCACTCTTAGAATAATCAATTCCGGGATATCCCT

Found at i:8770 original size:16 final size:16

Alignment explanation


    Indices: 8751--8804  Score: 74
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       8741 CATTCCGAGG

                            
       8751 ATATCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                    **      
       8767 ATATCCCGAATTAGG-
          1 ATATCCCGGCTTAGGT

               *            
       8782 ATAGCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                   
       8798 ATATCCC
          1 ATATCCC

       8805 ACTTGCGGAT


Statistics
Matches: 31,  Mismatches: 6, Indels: 2
        0.79            0.15        0.05

Matches are distributed among these distances:
  15   12  0.39
  16   19  0.61

ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28


Consensus pattern (16 bp):   
ATATCCCGGCTTAGGT

Found at i:8815 original size:31 final size:31

Alignment explanation


    Indices: 8748--8830  Score: 105
    Period size: 31  Copynumber: 2.7  Consensus size: 31

       8738 TCCCATTCCG

                                           
       8748 AGGATATCCCGGCTTAGGTATATCCCGAATT
          1 AGGATATCCCGGCTTAGGTATATCCCGAATT

                  *                     *  
       8779 AGGATAGCCCGGCTTAGGTATATCCC-ACTT
          1 AGGATATCCCGGCTTAGGTATATCCCGAATT

             *           *  *     
       8809 GCGGATATCCCGGTTTCGGTAT
          1 -AGGATATCCCGGCTTAGGTAT

       8831 TAATTACCAT


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  30    3  0.07
  31   42  0.93

ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29


Consensus pattern (31 bp):   
AGGATATCCCGGCTTAGGTATATCCCGAATT
Done.