Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold699

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: 5942
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32


Found at i:172 original size:49 final size:49

Alignment explanation


    Indices: 113--231  Score: 150
    Period size: 49  Copynumber: 2.4  Consensus size: 49

        103 ATATCTAAGT

                                              *          *    
        113 CGATGCCATGTCCCAGACAGGTCTTACACTAACTTTCATATATC-ATGGC
          1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGT-GC

                       *    *             **       *        *
        162 CGATGCCATGTTCCAGGCAGGTCTTACACTGGCTCTCATCTATCGGTGT
          1 CGATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGC

                                 
        211 CGATGCCATGTCCCAGACAGG
          1 CGATGCCATGTCCCAGACAGG

        232 CCAGTGTCTG


Statistics
Matches: 59,  Mismatches: 10, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  49   58  0.98
  50    1  0.02

ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27


Consensus pattern (49 bp):   
CGATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGC

Found at i:1020 original size:20 final size:19

Alignment explanation


    Indices: 985--1033  Score: 55
    Period size: 20  Copynumber: 2.5  Consensus size: 19

        975 ATAGCACCTG

                  *            
        985 ACATTTTCAATTATTTCAC
          1 ACATTTACAATTATTTCAC

                             *  
       1004 ACATTTACAACTTATTTTAC
          1 ACATTTACAA-TTATTTCAC

                       
       1024 A-ACTTTACAA
          1 ACA-TTTACAA

       1034 AATAGCCCTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  19   10  0.38
  20   16  0.62

ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43


Consensus pattern (19 bp):   
ACATTTACAATTATTTCAC

Found at i:4242 original size:39 final size:40

Alignment explanation


    Indices: 4184--4326  Score: 175
    Period size: 39  Copynumber: 3.6  Consensus size: 40

       4174 CTCGCACAAG

                     *    *         *   *      *    
       4184 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
          1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT

                                                    
       4224 GCCTTC-GGACTTAGCCCGGATATAGTCGCTAGCACAAAT
          1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT

                             *     *                 *
       4263 GCCTTC-GGATCTTAG-TCGGATGTAGTCGCTTAGCACAAAA
          1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT

                                    
       4303 GCCTTCGGGACTTAGCCCGGATAT
          1 GCCTTCGGGACTTAGCCCGGATAT

       4327 CATTCGAGTA


Statistics
Matches: 89,  Mismatches: 10, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
  39   49  0.55
  40   31  0.35
  41    9  0.10

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


Consensus pattern (40 bp):   
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT

Found at i:5549 original size:38 final size:38

Alignment explanation


    Indices: 5507--5582  Score: 134
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       5497 CAAGAACTCC

                      *                           
       5507 TTCCTCCTTCTTTAGAATTTTCGGCCAAAAGAAATGAA
          1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA

                                 *                
       5545 TTCCTCCTTCCTTAGAATTTTTGGCCAAAAGAAATGAA
          1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA

       5583 AAAGGATGAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   36  1.00

ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34


Consensus pattern (38 bp):   
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Done.