Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01029.C1

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: 4810
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Found at i:1373 original size:13 final size:13

Alignment explanation


    Indices: 1357--1381  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1347 CTTTGATTAA

                         
       1357 ATAGTTTGTTTGC
          1 ATAGTTTGTTTGC

                        
       1370 ATAGTTTGTTTG
          1 ATAGTTTGTTTG

       1382 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:2322 original size:174 final size:173

Alignment explanation


    Indices: 2033--2371  Score: 617
    Period size: 174  Copynumber: 2.0  Consensus size: 173

       2023 AATTAAGTTC

                                                                             
       2033 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATCAAATGTAAAATAAC
          1 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATCAAATGTAAAATAAC

                                                                             
       2098 TTCTCCTACTACTTTAGCTCCCGTCTTCAATTCGTAACAAGAGCCTTTTATAATTCAGACTT-TT
         66 TTCTCCTACTACTTTAGCTCCCGTCTTCAATTCGTAACAAGAGCCTTTTATAATTCAGACTTCTT

                                      *                 
       2162 CGTTTCTCTGAACCTCTATAAAGAAATGCACATATGATAAAATG
        131 -GTTTCTCTGAACCTCTATAAAGAAACGCACATATGATAAAATG

                                                                             
       2206 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATCAAAATGTAAAATAA
          1 CTCTTAAAATGAGTTACATAAGACTTTTAATATAATTTTCTTAAAATTATC-AAATGTAAAATAA

                                             *                  *            
       2271 CTTCTCCTACTACTTTAGCTCCCGTCTTCAATTTGTAACAAGAGCCTTTTATCATTCAGACTTCT
         65 CTTCTCCTACTACTTTAGCTCCCGTCTTCAATTCGTAACAAGAGCCTTTTATAATTCAGACTTCT

                             *                  
       2336 TGTTTCTCTGAACCTCTGTAAAGAAACGCACATATG
        130 TGTTTCTCTGAACCTCTATAAAGAAACGCACATATG

       2372 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:3591 original size:17 final size:17

Alignment explanation


    Indices: 3554--3606  Score: 56
    Period size: 17  Copynumber: 3.1  Consensus size: 17

       3544 GCTCGTAGTG

                      *      
       3554 TTGGTAAGCTAGCA-AT
          1 TTGGTAAGCTCGCACAT

                               
       3570 CTTGGTAAG-TGCGCACAT
          1 -TTGGTAAGCT-CGCACAT

                 *           
       3588 TTGGTGAGCTCGCACAT
          1 TTGGTAAGCTCGCACAT

              
       3605 TT
          1 TT

       3607 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:3610 original size:18 final size:17

Alignment explanation


    Indices: 3581--3615  Score: 61
    Period size: 18  Copynumber: 2.0  Consensus size: 17

       3571 TTGGTAAGTG

                             
       3581 CGCACATTTGGTGAGCT
          1 CGCACATTTGGTGAGCT

                              
       3598 CGCACATTTTGGTGAGCT
          1 CGCACA-TTTGGTGAGCT

       3616 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.