Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4061

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, 357

Length: 595
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55


Found at i:210 original size:104 final size:104

Alignment explanation


    Indices: 15--275  Score: 286
    Period size: 109  Copynumber: 2.5  Consensus size: 104

          5 AAATTGTTGT

                     *                 **                         *          
         15 GTTTTGTGAGTTTTTAGTAATGTAAAAAATTTTTAAAAAT-AAT-TT-TA--TAGTTATTTTGTT
          1 GTTTTGTGATTTTTTAGTAATGT--AATTTTTTTAAAAATAAATGTTATAGTTATTTATTTTGTT

                *          *                      * *
         75 AATAGTTTATGATTATGTTATAAATTGTTAG-T-GTTTTGT
         64 AATAATTTATGATTAGGTTATAAATTGTTAGTTAGTTTAGG

                   *                                                         
        114 GTTTTGTTATTTTTTAGTAATGTAATTTCTTTT-AAAATAAATGTTATAGTTATTTATTTTGTTA
          1 GTTTTGTGATTTTTTAGTAATGTAATTT-TTTTAAAAATAAATGTTATAGTTATTTATTTTGTTA

            *                                            
        178 GTAATTTATGGGATTAGGTTATAAATTGTTAGTATTTAGTTTAGG
         65 ATAATTTAT--GATTAGGTTATAAATTGTTAG---TTAGTTTAGG

                                                  *   *          
        223 GTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAATTAATTTTATAGTTAT
          1 GTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAATAAATGTTATAGTTAT

        276 ATAAATTTTT


Statistics
Matches: 135,  Mismatches: 13, Indels: 18
        0.81            0.08        0.11

Matches are distributed among these distances:
  97    8  0.06
  98    7  0.05
  99   23  0.17
 100    2  0.01
 102   20  0.15
 104   20  0.15
 108    5  0.04
 109   50  0.37

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55


Consensus pattern (104 bp):   
GTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAATAAATGTTATAGTTATTTATTTTGTTAA
TAATTTATGATTAGGTTATAAATTGTTAGTTAGTTTAGG

Found at i:336 original size:77 final size:78

Alignment explanation


    Indices: 197--352  Score: 217
    Period size: 77  Copynumber: 2.0  Consensus size: 78

        187 GGGATTAGGT

                                                                    **     * 
        197 TATAAATTGTTAGTATTTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAATT
          1 TATAAATTGTTAGTATTTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTTAAAAAAAAT

                         
        262 AATTTTATAGTTA
         66 AATTTTATAGTTA

                    *     *         * *                       *              
        275 TATAAATTTTTAGTGTTTAG-TTATGTTTTTGTGATTTTTTAGTAATGT-CTTTTTAAAAAAAAA
          1 TATAAATTGTTAGTATTTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTT-AAAAAAAA

                          
        338 TAATTTTATAGTTA
         65 TAATTTTATAGTTA

             
        352 T
          1 T

        353 TTTGTTAGTA


Statistics
Matches: 69,  Mismatches: 8, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  76    5  0.07
  77   46  0.67
  78   18  0.26

ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55


Consensus pattern (78 bp):   
TATAAATTGTTAGTATTTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTTAAAAAAAAT
AATTTTATAGTTA

Found at i:406 original size:44 final size:45

Alignment explanation


    Indices: 348--439  Score: 141
    Period size: 44  Copynumber: 2.1  Consensus size: 45

        338 TAATTTTATA

                     *           *                *      
        348 GTTATTTTGTTAGTAATTTATTATTAGGTTATATAAATTATTAGT
          1 GTTATTTTGGTAGTAATTTATGATTAGGTTATATAAATGATTAGT

                                                   *     
        393 GTTA-TTTGGTAGTAATTTATGATTAGGTTATATAAATGGTTAGT
          1 GTTATTTTGGTAGTAATTTATGATTAGGTTATATAAATGATTAGT

               
        437 GTT
          1 GTT

        440 TAGTTTAGTG


Statistics
Matches: 43,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  44   39  0.91
  45    4  0.09

ACGTcount: A:0.29, C:0.00, G:0.18, T:0.52


Consensus pattern (45 bp):   
GTTATTTTGGTAGTAATTTATGATTAGGTTATATAAATGATTAGT
Done.