Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01029.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: 4752
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Found at i:1315 original size:13 final size:13

Alignment explanation


    Indices: 1299--1323  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1289 CTTTGATTAA

                         
       1299 ATAGTTTGTTTGC
          1 ATAGTTTGTTTGC

                        
       1312 ATAGTTTGTTTG
          1 ATAGTTTGTTTG

       1324 AATCCATGTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.04, G:0.24, T:0.56


Consensus pattern (13 bp):   
ATAGTTTGTTTGC

Found at i:2264 original size:174 final size:173

Alignment explanation


    Indices: 1975--2313  Score: 617
    Period size: 174  Copynumber: 2.0  Consensus size: 173

       1965 AATTAAGTTC

                                                                             
       1975 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATCAAATGTAAAATAAC
          1 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATCAAATGTAAAATAAC

                                                                             
       2040 TTCTCCTACTACTTTAGCTCCCGTCTTCAATTCGTAACAAGAGCCTTTTATAATTCAGACTT-TT
         66 TTCTCCTACTACTTTAGCTCCCGTCTTCAATTCGTAACAAGAGCCTTTTATAATTCAGACTTCTT

                                      *                 
       2104 CGTTTCTCTGAACCTCTATAAAGAAATGCACATATGATAAAATG
        131 -GTTTCTCTGAACCTCTATAAAGAAACGCACATATGATAAAATG

                                                                             
       2148 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATCAAAATGTAAAATAA
          1 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATC-AAATGTAAAATAA

                                             *                  *            
       2213 CTTCTCCTACTACTTTAGCTCCCGTCTTCAATTTGTAACAAGAGCCTTTTATCATTCAGACTTCT
         65 CTTCTCCTACTACTTTAGCTCCCGTCTTCAATTCGTAACAAGAGCCTTTTATAATTCAGACTTCT

                             *                  
       2278 TGTTTCTCTGAACCTCTGTAAAGAAACGCACATATG
        130 TGTTTCTCTGAACCTCTATAAAGAAACGCACATATG

       2314 GTTAATGACT


Statistics
Matches: 160,  Mismatches: 4, Indels: 3
        0.96            0.02        0.02

Matches are distributed among these distances:
 173   51  0.32
 174  107  0.67
 175    2  0.01

ACGTcount: A:0.34, C:0.19, G:0.09, T:0.37


Consensus pattern (173 bp):   
CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATCAAATGTAAAATAAC
TTCTCCTACTACTTTAGCTCCCGTCTTCAATTCGTAACAAGAGCCTTTTATAATTCAGACTTCTT
GTTTCTCTGAACCTCTATAAAGAAACGCACATATGATAAAATG

Found at i:3533 original size:17 final size:17

Alignment explanation


    Indices: 3496--3548  Score: 56
    Period size: 17  Copynumber: 3.1  Consensus size: 17

       3486 GCTCGTAGTG

                      *      
       3496 TTGGTAAGCTAGCA-AT
          1 TTGGTAAGCTCGCACAT

                               
       3512 CTTGGTAAG-TGCGCACAT
          1 -TTGGTAAGCT-CGCACAT

                 *           
       3530 TTGGTGAGCTCGCACAT
          1 TTGGTAAGCTCGCACAT

              
       3547 TT
          1 TT

       3549 TGGTGAGCTT


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

Matches are distributed among these distances:
  16    1  0.03
  17   27  0.87
  18    3  0.10

ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32


Consensus pattern (17 bp):   
TTGGTAAGCTCGCACAT

Found at i:3552 original size:18 final size:17

Alignment explanation


    Indices: 3523--3557  Score: 61
    Period size: 18  Copynumber: 2.0  Consensus size: 17

       3513 TTGGTAAGTG

                             
       3523 CGCACATTTGGTGAGCT
          1 CGCACATTTGGTGAGCT

                              
       3540 CGCACATTTTGGTGAGCT
          1 CGCACA-TTTGGTGAGCT

       3558 TACAGTTCAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31


Consensus pattern (17 bp):   
CGCACATTTGGTGAGCT
Done.