Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g03217.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, 1000

Length: 2500
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21


Found at i:1374 original size:27 final size:26

Alignment explanation


    Indices: 1294--1379  Score: 66
    Period size: 27  Copynumber: 3.2  Consensus size: 26

       1284 ATCGTCGTCG

                     *                 
       1294 TCATCTGCAGCAGCACCAACACAATCA
          1 TCATCTGCAACAG-ACCAACACAATCA

            *  *             *     *    
       1321 GCAGCTGCAAC-GACACCACTACCATCA
          1 TCATCTGCAACAGAC-CAAC-ACAATCA

                     *                 
       1348 TCATCTGCACCAGTACCAACACAATCA
          1 TCATCTGCAACAG-ACCAACACAATCA

            *    
       1375 CCATC
          1 TCATC

       1380 ACAATCAGCA


Statistics
Matches: 44,  Mismatches: 11, Indels: 8
        0.70            0.17        0.13

Matches are distributed among these distances:
  25    2  0.05
  26    4  0.09
  27   32  0.73
  28    4  0.09
  29    2  0.05

ACGTcount: A:0.35, C:0.40, G:0.10, T:0.15


Consensus pattern (26 bp):   
TCATCTGCAACAGACCAACACAATCA

Found at i:1413 original size:27 final size:29

Alignment explanation


    Indices: 1335--1413  Score: 74
    Period size: 33  Copynumber: 2.6  Consensus size: 29

       1325 CTGCAACGAC

                              *            
       1335 ACCACTACCATCATCATCTGCACCAGTACCA
          1 ACCA-TACCATCATCATCAGCACCA-TACCA

                                             
       1366 ACACAATCACCATCA-CAATCAGCACC-TA-CA
          1 AC-C-AT-ACCATCATC-ATCAGCACCATACCA

                              
       1396 ACCATACCATCATCATCA
          1 ACCATACCATCATCATCA

       1414 TCTGCAACAA


Statistics
Matches: 42,  Mismatches: 1, Indels: 14
        0.74            0.02        0.25

Matches are distributed among these distances:
  27   11  0.26
  28    3  0.07
  29    1  0.02
  30    4  0.10
  31    4  0.10
  32    3  0.07
  33   16  0.38

ACGTcount: A:0.38, C:0.41, G:0.04, T:0.18


Consensus pattern (29 bp):   
ACCATACCATCATCATCAGCACCATACCA

Found at i:1457 original size:30 final size:30

Alignment explanation


    Indices: 1376--1464  Score: 76
    Period size: 30  Copynumber: 3.0  Consensus size: 30

       1366 ACACAATCAC

                       *  *            *   
       1376 CATCACAATCAGCACCTACAACCAT-ACCAT
          1 CATCACAATCATCAACTACAA-CATCAACAT

                              *             
       1406 CATCATC-ATC-TGCAACAACAACATCAACAT
          1 CATCA-CAATCAT-CAACTACAACATCAACAT

                          *        *     
       1436 CATCACAATCATCATCTACAACAGCAACA
          1 CATCACAATCATCAACTACAACATCAACA

       1465 CCAGCTCCAA


Statistics
Matches: 47,  Mismatches: 7, Indels: 10
        0.73            0.11        0.16

Matches are distributed among these distances:
  29    4  0.09
  30   41  0.87
  31    2  0.04

ACGTcount: A:0.43, C:0.36, G:0.03, T:0.18


Consensus pattern (30 bp):   
CATCACAATCATCAACTACAACATCAACAT

Found at i:1479 original size:36 final size:36

Alignment explanation


    Indices: 1407--1482  Score: 91
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       1397 CCATACCATC

                      *           *        *    
       1407 ATCATCATCTGCAACAACAACATCAACATCATCACA
          1 ATCATCATCTACAACAACAACACCAACATCAACACA

                            *        *           
       1443 ATCATCATCTACAACAGCAACACCAGC-TCCAACACA
          1 ATCATCATCTACAACAACAACACCAACAT-CAACACA

                
       1479 ATCA
          1 ATCA

       1483 GCGGCTACAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  35    1  0.03
  36   33  0.97

ACGTcount: A:0.43, C:0.36, G:0.04, T:0.17


Consensus pattern (36 bp):   
ATCATCATCTACAACAACAACACCAACATCAACACA

Found at i:1780 original size:15 final size:15

Alignment explanation


    Indices: 1760--1791  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1750 TCACCGTCGC

                           
       1760 CATCACCAGCACCAG
          1 CATCACCAGCACCAG

                     *     
       1775 CATCACCAGTACCAG
          1 CATCACCAGCACCAG

              
       1790 CA
          1 CA

       1792 ACGACAACTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.34, C:0.44, G:0.12, T:0.09


Consensus pattern (15 bp):   
CATCACCAGCACCAG
Done.