Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00993.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: 10250
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33


Found at i:3833 original size:26 final size:26

Alignment explanation


    Indices: 3774--3908  Score: 227
    Period size: 26  Copynumber: 5.2  Consensus size: 26

       3764 TGATACAAAT

                                      
       3774 TGATAATAGGTTAGGTAAATGTT-CA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
       3799 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                                      
       3825 TGATAATAGGTTAGGTAAATGTTCCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
       3851 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                   *               *  
       3877 TGATAATGGGTTAGGTAAATGTTTCA
          1 TGATAATAGGTTAGGTAAATGTTCCA

                  
       3903 TGATAA
          1 TGATAA

       3909 GAATTCATGT


Statistics
Matches: 107,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
  25   23  0.21
  26   84  0.79

ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36


Consensus pattern (26 bp):   
TGATAATAGGTTAGGTAAATGTTCCA

Found at i:5420 original size:25 final size:25

Alignment explanation


    Indices: 5392--5442  Score: 68
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       5382 TTTACAGTTT

                                      
       5392 TACCCCTAGAGATAAATT-ACCGAAA
          1 TACCCCTAG-GATAAATTGACCGAAA

                      *          *   
       5417 TACCCCTAGGTTAAATTGACCTAAA
          1 TACCCCTAGGATAAATTGACCGAAA

             
       5442 T
          1 T

       5443 GCATGTTTGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  24    7  0.30
  25   16  0.70

ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25


Consensus pattern (25 bp):   
TACCCCTAGGATAAATTGACCGAAA

Found at i:7961 original size:43 final size:43

Alignment explanation


    Indices: 7900--8061  Score: 270
    Period size: 43  Copynumber: 3.8  Consensus size: 43

       7890 ATGAAACTTG

                                *                     *
       7900 GTGAAATAATATCGGGCTTCAAGCCTAGCAGGCTATAATGCCT
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

                                     *                 
       7943 GTGAAATAATATCGGGCTTCGAGCCGAGCAGGCTATAATGCCA
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

                             *                        *
       7986 GTGAAATAATATCGGGCCTCGAGCCTAGCAGGCTATAATGCCG
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

                        *                    
       8029 GTGAAATAATATTGGGCTTCGAGCCTAGCAGGC
          1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGC

       8062 GAAATGCAGG


Statistics
Matches: 111,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  43  111  1.00

ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23


Consensus pattern (43 bp):   
GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA

Found at i:8670 original size:16 final size:18

Alignment explanation


    Indices: 8639--8671  Score: 52
    Period size: 16  Copynumber: 1.9  Consensus size: 18

       8629 AACTCATCAC

                              
       8639 ACTATCTATCGTTTTGGT
          1 ACTATCTATCGTTTTGGT

                             
       8657 ACTAT-TAT-GTTTTGG
          1 ACTATCTATCGTTTTGG

       8672 AATTCGTATG


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    7  0.47
  17    3  0.20
  18    5  0.33

ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52


Consensus pattern (18 bp):   
ACTATCTATCGTTTTGGT

Found at i:8954 original size:16 final size:16

Alignment explanation


    Indices: 8935--8984  Score: 51
    Period size: 16  Copynumber: 3.6  Consensus size: 16

       8925 ATTGTTTTGC

                            
       8935 TTAAATGTTGTTTAAA
          1 TTAAATGTTGTTTAAA

                            
       8951 TTAAA---TGTTT--A
          1 TTAAATGTTGTTTAAA

                            
       8962 TT--ATGTTGTTTAAA
          1 TTAAATGTTGTTTAAA

                     
       8976 TTAAATGTT
          1 TTAAATGTT

       8985 TATTATGTTG


Statistics
Matches: 27,  Mismatches: 0, Indels: 14
        0.66            0.00        0.34

Matches are distributed among these distances:
   9    1  0.04
  11    3  0.11
  12    5  0.19
  13    5  0.19
  14    3  0.11
  16   10  0.37

ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54


Consensus pattern (16 bp):   
TTAAATGTTGTTTAAA

Found at i:8967 original size:25 final size:25

Alignment explanation


    Indices: 8939--8997  Score: 118
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       8929 TTTTGCTTAA

                                     
       8939 ATGTTGTTTAAATTAAATGTTTATT
          1 ATGTTGTTTAAATTAAATGTTTATT

                                     
       8964 ATGTTGTTTAAATTAAATGTTTATT
          1 ATGTTGTTTAAATTAAATGTTTATT

                     
       8989 ATGTTGTTT
          1 ATGTTGTTT

       8998 TGATGTAAAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   34  1.00

ACGTcount: A:0.29, C:0.00, G:0.14, T:0.58


Consensus pattern (25 bp):   
ATGTTGTTTAAATTAAATGTTTATT
Done.