Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold762

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: 5923
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33


Found at i:1338 original size:48 final size:47

Alignment explanation


    Indices: 1284--1558  Score: 288
    Period size: 48  Copynumber: 5.6  Consensus size: 47

       1274 ACATGCCAAA

                                           *                 
       1284 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTTGGTGCCCAT
          1 GCCATGTCCCAGACATGGTCTTACATGGGA-CTTCTC-TTGGTGCCCAT

                                   * *              *      * *
       1333 G-CATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAAC
          1 GCCATGTCCCAGACATGGTCTTACATGGGA-CT-TC-TCTTGGTGCCCAT

                                           *        *       *
       1382 GCCATGTCCCAGACAT-GTCTTACAT-GGACCTCTCATCTCGTG-CCAA
          1 GCCATGTCCCAGACATGGTCTTACATGGGACTTCTC-T-TGGTGCCCAT

                                           *                
       1428 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTTGGTGCCCAT
          1 GCCATGTCCCAGACATGGTCTTACATGGGACTTCTC-TTGGTGCCCAT

                                     *                        *  
       1476 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTTAAGGATGCCAAT
          1 GCCATGTCCCAGACATGGTCTTACATGGGA-CT-TC-TCTT--GG-TGCCCAT

                                          
       1529 GCCATGTCCCAGACATGGTCTTACATGGGA
          1 GCCATGTCCCAGACATGGTCTTACATGGGA

       1559 TCTCTTTACC


Statistics
Matches: 191,  Mismatches: 21, Indels: 24
        0.81            0.09        0.10

Matches are distributed among these distances:
  45    2  0.01
  46   21  0.11
  47   17  0.09
  48   72  0.38
  49   20  0.10
  50   20  0.10
  51    2  0.01
  52    2  0.01
  53   35  0.18

ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26


Consensus pattern (47 bp):   
GCCATGTCCCAGACATGGTCTTACATGGGACTTCTCTTGGTGCCCAT

Found at i:1447 original size:96 final size:95

Alignment explanation


    Indices: 1277--1563  Score: 328
    Period size: 96  Copynumber: 2.9  Consensus size: 95

       1267 GATAATAACA

                                                  **    *           *        
       1277 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGT-TGGTGCCCATG-CATGTC
          1 TGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGA-CCTCTCATCTGGTG-CCAAGCCATGTC

                           *                   
       1340 CCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
         63 CCAGACATGGTCTTACAGGGGACCTCTCAT-T-GG

                  *                                       *                  
       1375 TGCCAACGCCATGTCCCAGACAT-GTCTTACATGGACCTCTCATCTCGTGCCAAGCCATGTCCCA
          1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGACCTCTCATCTGGTGCCAAGCCATGTCCCA

                          *          *    
       1439 GACATGGTCTTACATGGGACCTCTCGTTGG
         66 GACATGGTCTTACAGGGGACCTCTCATTGG

                * *                          *                               
       1469 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTTAAGGATGCCAATGCCAT
          1 TGCCAAAGCCATGTCCCAGACATGGTCTTACA-TGGACCTCTCATC-T--GG-TGCCAA-GCCAT

                                *    *    
       1534 GTCCCAGACATGGTCTTACATGGGATCTCT
         60 GTCCCAGACATGGTCTTACAGGGGACCTCT

       1564 TTACCCAAAT


Statistics
Matches: 166,  Mismatches: 14, Indels: 15
        0.85            0.07        0.08

Matches are distributed among these distances:
  94   23  0.14
  95   18  0.11
  96   52  0.31
  97   10  0.06
  98   22  0.13
  99    1  0.01
 100    6  0.04
 101   34  0.20

ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26


Consensus pattern (95 bp):   
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGACCTCTCATCTGGTGCCAAGCCATGTCCCA
GACATGGTCTTACAGGGGACCTCTCATTGG

Found at i:1679 original size:13 final size:13

Alignment explanation


    Indices: 1658--1689  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       1648 GCTTGGATCA

                *        
       1658 TCATCAAATAAAT
          1 TCATAAAATAAAT

                         
       1671 TCATAAAATAAAT
          1 TCATAAAATAAAT

                  
       1684 TCATAA
          1 TCATAA

       1690 TTGCTGGAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31


Consensus pattern (13 bp):   
TCATAAAATAAAT
Done.