Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01372.P1

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: 8875
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.32


Found at i:1989 original size:23 final size:23

Alignment explanation


    Indices: 1959--2013  Score: 101
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       1949 ATTTTGAACT

                                   
       1959 TCTGATAATTTATACATAAAACA
          1 TCTGATAATTTATACATAAAACA

                                   
       1982 TCTGATAATTTATACATAAAACA
          1 TCTGATAATTTATACATAAAACA

                *    
       2005 TCTGCTAAT
          1 TCTGATAAT

       2014 AAATACTGGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   31  1.00

ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36


Consensus pattern (23 bp):   
TCTGATAATTTATACATAAAACA

Found at i:7283 original size:46 final size:46

Alignment explanation


    Indices: 7214--7385  Score: 181
    Period size: 46  Copynumber: 3.7  Consensus size: 46

       7204 TATGTGTGCT

                                                          
       7214 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC

             *                                       *       
       7260 AATGTAAGACATGTCTGGGACATGCATC-G--ACATTGAGACGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATT---ATGAGAGCC

               *             *              *    *          *
       7306 AGTATAAGACATGTCTGAGACATGCATCGGCCTCGAGATATGCA-AGCT
          1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTATG-AGAGCC

                      *                     
       7354 AGTGTAAGACCTGTCTGGGACATGGCATCGGC
          1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC

       7386 TTGACATGTG


Statistics
Matches: 104,  Mismatches: 12, Indels: 17
        0.78            0.09        0.13

Matches are distributed among these distances:
  43    5  0.05
  45    1  0.01
  46   60  0.58
  47    1  0.01
  48   25  0.24
  49   10  0.10
  50    1  0.01
  51    1  0.01

ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22


Consensus pattern (46 bp):   
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC

Found at i:7406 original size:92 final size:90

Alignment explanation


    Indices: 7208--7508  Score: 272
    Period size: 92  Copynumber: 3.2  Consensus size: 90

       7198 GGGTGATATG

                 *                 *                  *           *        * 
       7208 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAATGTAAGACAT
          1 TGTGCCAGTGTAAGACATGTCTGAGACATGCATCGGCC-CGAATATGAGAG-CAGTGTAAGACCT

                                          
       7272 GTCTGGGACAT-GCATCGACATTGAGACGA
         64 GTCTGGGACATGGCATCGAC-TT-AGAC-A

              *      *                                                       
       7301 -GAGCCAGTATAAGACATGTCTGAGACATGCATCGGCCTCGAGATATGCA-AGCTAGTGTAAGAC
          1 TGTGCCAGTGTAAGACATGTCTGAGACATGCATCGGCC-CGA-ATATG-AGAGC-AGTGTAAGAC

                                *        
       7364 CTGTCTGGGACATGGCATCGGCTT-GACA
         62 CTGTCTGGGACATGGCATCGACTTAGACA

                *           *                  * *        *                  
       7392 TGTGTCAGTGTAAGACCTGTCT-AGGACATGGCATTGACACCGATAGATGAGAGGCAGTGTAAGA
          1 TGTGCCAGTGTAAGACATGTCTGA-GACAT-GCATCGGC-CCGA-ATATGAGA-GCAGTGTAAGA

               *                        * 
       7456 CCTCTCTGGGACATGGCATCGACTTAGATA
         61 CCTGTCTGGGACATGGCATCGACTTAGACA

                                   
       7486 TGTGAGCCAGTGTAAGACCATGT
          1 TGT--GCCAGTGTAAGA-CATGT

       7509 TTGGAACATG


Statistics
Matches: 171,  Mismatches: 22, Indels: 26
        0.78            0.10        0.12

Matches are distributed among these distances:
  91    2  0.01
  92   60  0.35
  93   48  0.28
  94   38  0.22
  95    8  0.05
  96   11  0.06
  97    4  0.02

ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24


Consensus pattern (90 bp):   
TGTGCCAGTGTAAGACATGTCTGAGACATGCATCGGCCCGAATATGAGAGCAGTGTAAGACCTGT
CTGGGACATGGCATCGACTTAGACA
Done.