Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1699

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, 833

Length: 1389
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23


Found at i:447 original size:10 final size:10

Alignment explanation


    Indices: 434--466  Score: 57
    Period size: 10  Copynumber: 3.3  Consensus size: 10

        424 AAAATCTCAA

                      
        434 AAAAAAATAT
          1 AAAAAAATAT

                     *
        444 AAAAAAATAC
          1 AAAAAAATAT

                      
        454 AAAAAAATAT
          1 AAAAAAATAT

               
        464 AAA
          1 AAA

        467 TTACATTTTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  10   21  1.00

ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15


Consensus pattern (10 bp):   
AAAAAAATAT

Found at i:520 original size:50 final size:51

Alignment explanation


    Indices: 436--536  Score: 195
    Period size: 50  Copynumber: 2.0  Consensus size: 51

        426 AATCTCAAAA

                                                               
        436 AAAAATATAAAAAAATACAAAAAAATATAAATTACATTTTAACCCCTCTAC
          1 AAAAATATAAAAAAATACAAAAAAATATAAATTACATTTTAACCCCTCTAC

                                                               
        487 AAAAATATAAAAAAATAC-AAAAAATATAAATTACATTTTAACCCCTCTAC
          1 AAAAATATAAAAAAATACAAAAAAATATAAATTACATTTTAACCCCTCTAC

        537 TTTTTAAAAT


Statistics
Matches: 50,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  50   32  0.64
  51   18  0.36

ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26


Consensus pattern (51 bp):   
AAAAATATAAAAAAATACAAAAAAATATAAATTACATTTTAACCCCTCTAC

Found at i:650 original size:29 final size:29

Alignment explanation


    Indices: 618--682  Score: 78
    Period size: 29  Copynumber: 2.2  Consensus size: 29

        608 ACAGTCGGGC

                                          
        618 CCCCAAACTTTCC-AGAAATTACATTTTAG
          1 CCCCAAACTTTCCTA-AAATTACATTTTAG

                 * *              *    * 
        647 CCCCATATTTTCCTAAAATTACGTTTTTG
          1 CCCCAAACTTTCCTAAAATTACATTTTAG

                   
        676 CCCCAAA
          1 CCCCAAA

        683 AACTTTGCAC


Statistics
Matches: 30,  Mismatches: 5, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  29   29  0.97
  30    1  0.03

ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34


Consensus pattern (29 bp):   
CCCCAAACTTTCCTAAAATTACATTTTAG

Found at i:945 original size:21 final size:21

Alignment explanation


    Indices: 896--936  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        886 CGGCAACCAA

                 *               
        896 AGAAACAA-AAAAAATAGCAG
          1 AGAAAAAAGAAAAAATAGCAG

                                 
        916 AGAAAAAAGAAAAAATAGCAG
          1 AGAAAAAAGAAAAAATAGCAG

        937 CAAGCAAAGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    7  0.37
  21   12  0.63

ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05


Consensus pattern (21 bp):   
AGAAAAAAGAAAAAATAGCAG

Found at i:1298 original size:27 final size:26

Alignment explanation


    Indices: 1247--1298  Score: 61
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       1237 GAAAGGAGAG

                                *     
       1247 AAAAAAAATAGAAAAAGAAAGAAAAT
          1 AAAAAAAATAGAAAAAGAAACAAAAT

                              *        
       1273 AAAATAAAATA-AAAAGATAAACAAAA
          1 AAAA-AAAATAGAAAA-AGAAACAAAA

       1299 AAATATCAGT


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  26    8  0.36
  27   14  0.64

ACGTcount: A:0.81, C:0.02, G:0.08, T:0.10


Consensus pattern (26 bp):   
AAAAAAAATAGAAAAAGAAACAAAAT
Done.