Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01163.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: 5215
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35


Found at i:136 original size:44 final size:42

Alignment explanation


    Indices: 4--417  Score: 354
    Period size: 43  Copynumber: 9.6  Consensus size: 42

          1 TTT

                                                       
          4 CCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGATCTGTTTC
          1 CCTACTGCTTA-GGGGTTAAGATCTTCATCTTCGATCTGTTTC

                            *        *   *    *      * 
         47 CCTACTGCTTAGGGAGATAAGATCTGCA-ATTCGGTCTGTTAC
          1 CCTACTGCTTAGGG-GTTAAGATCTTCATCTTCGATCTGTTTC

                 * *               *    *               
         89 CCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTC
          1 CCTACTGCTTAGGGG-TTAAGA-TCTTCATCTTCGATCTGTTTC

                                       *         *     * 
        133 CCTACTGCTTAGGGGTTAAGATCTGTAAATCTTC-AGCCTGTTAC
          1 CCTACTGCTTAGGGGTTAAGATCT-T-CATCTTCGA-TCTGTTTC

                                  *      *     * *      * 
        177 CCTACTGCTTAGGGGGTTAAG-GCTTGTAAAT-TTGGCT-TGTTAC
          1 CCTACTGCTTA-GGGGTTAAGATC-T-T-CATCTTCGATCTGTTTC

                                  ** *                  
        220 CCTACTGCTTAGGGGGTTAAAGCCCATCATCTTCGATCTGTTTC
          1 CCTACTGCTTA-GGGGTT-AAGATCTTCATCTTCGATCTGTTTC

                                                       
        264 CCTACTGCTTAGAGGGTTAAGATCTTCATCTTCGATCTGTTTC
          1 CCTACTGCTTAG-GGGTTAAGATCTTCATCTTCGATCTGTTTC

                            * *      *   *    *      * 
        307 CCTACTGCTTAGGGAGATGAGATCTGCA-ATTCGGTCTGTTAC
          1 CCTACTGCTTAGGG-GTTAAGATCTTCATCTTCGATCTGTTTC

                 * *               *    *               
        349 CCTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTC
          1 CCTACTGCTTAGGGG-TTAAGA-TCTTCATCTTCGATCTGTTTC

                                     
        393 CCTACTGCTTAGGGGGTTAAGATCT
          1 CCTACTGCTTA-GGGGTTAAGATCT

        418 GTAAATCTTC


Statistics
Matches: 298,  Mismatches: 53, Indels: 40
        0.76            0.14        0.10

Matches are distributed among these distances:
  41    2  0.01
  42   64  0.21
  43  112  0.38
  44   99  0.33
  45   21  0.07

ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35


Consensus pattern (42 bp):   
CCTACTGCTTAGGGGTTAAGATCTTCATCTTCGATCTGTTTC

Found at i:628 original size:66 final size:66

Alignment explanation


    Indices: 522--648  Score: 218
    Period size: 66  Copynumber: 1.9  Consensus size: 66

        512 TCTATGCTTA

                    *                                                        
        522 TGTCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
          1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT

             
        587 G
         66 G

                                     *         *        *                
        588 TGTCAAATAATTAGGATGCTATGATTGAAATGAATGAAATGCTCTTAACTAGATGTGTTAT
          1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT

        649 TATATGAATG


Statistics
Matches: 57,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  66   57  1.00

ACGTcount: A:0.35, C:0.10, G:0.20, T:0.34


Consensus pattern (66 bp):   
TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G

Found at i:1800 original size:23 final size:23

Alignment explanation


    Indices: 1764--1829  Score: 69
    Period size: 24  Copynumber: 2.8  Consensus size: 23

       1754 GGCCTCTCTT

                  *  *             
       1764 TTTTTGCTTCTTTTTTTTTAGAA
          1 TTTTTGTTTTTTTTTTTTTAGAA

                                * **
       1787 TTTTTGTTTTTTTTTGTTTTCGTG
          1 TTTTTGTTTTTTTTT-TTTTAGAA

                   *           
       1811 TTTTTGTGTTTTTTTTTTT
          1 TTTTTGTTTTTTTTTTTTT

       1830 GGCTTTGCCT


Statistics
Matches: 36,  Mismatches: 6, Indels: 2
        0.82            0.14        0.05

Matches are distributed among these distances:
  23   17  0.47
  24   19  0.53

ACGTcount: A:0.05, C:0.05, G:0.12, T:0.79


Consensus pattern (23 bp):   
TTTTTGTTTTTTTTTTTTTAGAA

Found at i:4656 original size:19 final size:20

Alignment explanation


    Indices: 4632--4678  Score: 71
    Period size: 19  Copynumber: 2.5  Consensus size: 20

       4622 AGTGAAAGTT

                                
       4632 TAATGCAAATGT-TGCAATG
          1 TAATGCAAATGTATGCAATG

                           *    
       4651 TAATGCAAATGTATGGAATG
          1 TAATGCAAATGTATGCAATG

                     
       4671 -AATGCAAA
          1 TAATGCAAA

       4679 AGAAATGAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  19   20  0.77
  20    6  0.23

ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28


Consensus pattern (20 bp):   
TAATGCAAATGTATGCAATG
Done.