Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01372.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: 9850
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:1631 original size:5 final size:5

Alignment explanation


    Indices: 1621--1645  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

       1611 CCTCAAGCGG

                                         
       1621 GAAAA GAAAA GAAAA GAAAA GAAAA
          1 GAAAA GAAAA GAAAA GAAAA GAAAA

       1646 TATGAAAAAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00


Consensus pattern (5 bp):   
GAAAA

Found at i:3823 original size:197 final size:197

Alignment explanation


    Indices: 3488--3872  Score: 648
    Period size: 197  Copynumber: 2.0  Consensus size: 197

       3478 AAGGAATATT

                                                                             
       3488 CATGTATTGACTTACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATTGTAAG
          1 CATGTATTGACTTACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATTGTAAG

                                *           *                                
       3553 GTACCAACAACTTTTCCATATAGATGCAATCTGAAAATAGTTGACCATCAATAACATAGAGTTTA
         66 GTACCAACAACTTTTCCATACAGATGCAATCTAAAAATAGTTGACCATCAATAACATAGAGTTTA

                                   *                   *      *              
       3618 GGCCATAAAAGGCCTCAAGTATGGAAAACAATTTTTGAGCATTTAAAGGCCTCAAGTAAGTCAAT
        131 GGCCATAAAAGGCCTCAAGTATGAAAAACAATTTTTGAGCATTAAAAGGCATCAAGTAAGTCAAT

              
       3683 AG
        196 AG

                          *                                                * 
       3685 CATGTATTGACTTATTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATTGTAGG
          1 CATGTATTGACTTACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATTGTAAG

                                                  *               *          
       3750 GTACCAACAACTTTTCCATACAGATGCAATCTAAAAATGGTTG-CCAATCAATAGCAGT-GAGTT
         66 GTACCAACAACTTTTCCATACAGATGCAATCTAAAAATAGTTGACC-ATCAATAACA-TAGAGTT

                           *                                            
       3813 TAGGCCATAAAAGGCTTCAAGTATGAAAAACAATTTTTGAGCATTAAAAGGCATCAAGTA
        129 TAGGCCATAAAAGGCCTCAAGTATGAAAAACAATTTTTGAGCATTAAAAGGCATCAAGTA

       3873 TGGAAAACAG


Statistics
Matches: 176,  Mismatches: 10, Indels: 4
        0.93            0.05        0.02

Matches are distributed among these distances:
 196    2  0.01
 197  173  0.98
 198    1  0.01

ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30


Consensus pattern (197 bp):   
CATGTATTGACTTACTTTGTTCACTGTAAGAAATATCTAGTCTGGTAAGACAAACATATTGTAAG
GTACCAACAACTTTTCCATACAGATGCAATCTAAAAATAGTTGACCATCAATAACATAGAGTTTA
GGCCATAAAAGGCCTCAAGTATGAAAAACAATTTTTGAGCATTAAAAGGCATCAAGTAAGTCAAT
AG

Found at i:4831 original size:43 final size:44

Alignment explanation


    Indices: 4765--4852  Score: 142
    Period size: 43  Copynumber: 2.0  Consensus size: 44

       4755 ATTCTATACA

                           *                 *          
       4765 ATCTTTATCTTTTTAGGATTTATACTATTTACCGTGAAAACTCT
          1 ATCTTTATCTTTTTAAGATTTATACTATTTACCCTGAAAACTCT

                                                *       
       4809 ATCTTTATC-TTTTAAGATTTATACTATTTACCCTGGAAACTCT
          1 ATCTTTATCTTTTTAAGATTTATACTATTTACCCTGAAAACTCT

             
       4852 A
          1 A

       4853 GTTTTACTAG


Statistics
Matches: 41,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  43   32  0.78
  44    9  0.22

ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47


Consensus pattern (44 bp):   
ATCTTTATCTTTTTAAGATTTATACTATTTACCCTGAAAACTCT

Found at i:7166 original size:21 final size:21

Alignment explanation


    Indices: 7142--7183  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7132 ATGTTTCACA

                                 
       7142 TTTGTTTCTTTATGTTCTTCT
          1 TTTGTTTCTTTATGTTCTTCT

                       *         
       7163 TTTGTTTCTTTGTGTTCTTCT
          1 TTTGTTTCTTTATGTTCTTCT

       7184 ATACGTTTCC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.02, C:0.14, G:0.12, T:0.71


Consensus pattern (21 bp):   
TTTGTTTCTTTATGTTCTTCT
Done.