Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00120.M6

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: 6715
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33


Found at i:1031 original size:78 final size:78

Alignment explanation


    Indices: 942--1176  Score: 380
    Period size: 78  Copynumber: 3.0  Consensus size: 78

        932 GTCAGGCAGA

                                    *    **                                  
        942 GCCAACTAGTGTGACTCAGAAAACCAATTTAACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

                         
       1007 CGGCTTTCTGGAC
         66 CGGCTTTCTGGAC

                                                              *              
       1020 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTATTGAGTCAGAGGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

                         
       1085 CGGCTTTCTGGAC
         66 CGGCTTTCTGGAC

            *                              *           *             *  *    
       1098 ACCAACTAGTGTGACTCAGAAAACAAATTCGGCTCGTCCTAATCAAGCTACTGAGTCGGAAGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

             *           
       1163 CAGCTTTCTGGAC
         66 CGGCTTTCTGGAC

             
       1176 G
          1 G

       1177 GCATGTCCGT


Statistics
Matches: 145,  Mismatches: 12, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  78  145  1.00

ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23


Consensus pattern (78 bp):   
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC

Found at i:2282 original size:192 final size:189

Alignment explanation


    Indices: 1955--2330  Score: 515
    Period size: 192  Copynumber: 2.0  Consensus size: 189

       1945 AGTTTTTTGG

                                                                    *        
       1955 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATTTTCACTGA
          1 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA

                          * *                  *      *                      
       2020 TATTCTGTCAATTTTGGGCTGGTATTGCAATTTGACTTGCCATTTTTGCTTGCATTGTGGTTTTA
         66 TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA

                    *  **                                                 
       2085 TTATTTGGGGTTGTGCCGTAGTTTAATTTCCATACCATAGTAAAAAGCTTCTTTATTGTAGC
        131 TTATTT--AGTCATGCCGTAGTTTAATTTCCATACCATAGT-AAAAGCTTCTTTATTGTAGC

                                    *                                        
       2147 AATTAAAAAGATGTT-GG-TTATTGTTGTATAGCAAGGGTTTTACTTCAGGTTTTTATATTCACT
          1 AATT-AAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGG-TTTTATATTCACT

                       *       *           *          *            *         
       2210 GATATTCTGTCTATTTCGATCTGGTATTGCATTTTGAATTGCTACTTTTGCTTG-TTTCGTGGTT
         64 GATATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATT-GTGGTT

                                      *       **       *             
       2274 TTATTATTTAGTCATGCCGTAGTTTATTTTCCATTTCATAGTAGAAGCTTCTTTATT
        128 TTATTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATT

       2331 ATATATAATC


Statistics
Matches: 163,  Mismatches: 18, Indels: 9
        0.86            0.09        0.05

Matches are distributed among these distances:
 189   14  0.09
 190   27  0.17
 191   33  0.20
 192   79  0.48
 193   10  0.06

ACGTcount: A:0.23, C:0.12, G:0.19, T:0.47


Consensus pattern (189 bp):   
AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
TTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATTGTAGC

Found at i:3771 original size:31 final size:31

Alignment explanation


    Indices: 3736--3807  Score: 92
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       3726 TGCAAAATTT

                      *          *          
       3736 TTATTGAGTTTTTTGAAAGTTTTCA-TTTAAA
          1 TTATTGAGTTATTTGAAAGTTAT-ATTTTAAA

                   *                      *
       3767 TTATTGAATTATTTGAAAGTTATATTTTAAG
          1 TTATTGAGTTATTTGAAAGTTATATTTTAAA

                      
       3798 TTATTGAGTT
          1 TTATTGAGTT

       3808 GTTAAGTTAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  30    1  0.03
  31   34  0.97

ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54


Consensus pattern (31 bp):   
TTATTGAGTTATTTGAAAGTTATATTTTAAA

Found at i:4197 original size:41 final size:41

Alignment explanation


    Indices: 4151--4276  Score: 185
    Period size: 35  Copynumber: 3.2  Consensus size: 41

       4141 ACTAAATCAT

                                               *     
       4151 AATATCTCATATAATACACTTAGATTTGTATGCTTCTGATA
          1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

                                                     
       4192 AATATCTC-----ATA-ACTTAGATTTGTATGCTTGTGATA
          1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

                                  *                  
       4227 AATATCTCATATAATACACTTATATTTGTATGCTTGT-ATA
          1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

                      
       4267 AATATCTCAT
          1 AATATCTCAT

       4277 TTAGTAAGAA


Statistics
Matches: 77,  Mismatches: 2, Indels: 13
        0.84            0.02        0.14

Matches are distributed among these distances:
  35   31  0.40
  36    3  0.04
  40   16  0.21
  41   27  0.35

ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43


Consensus pattern (41 bp):   
AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

Done.