Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold735

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: 16911
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:28 original size:2 final size:2

Alignment explanation


    Indices: 21--61  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

         11 ATCCCTCGTT

                                                                         
         21 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         62 TTATTTTAAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:5155 original size:69 final size:69

Alignment explanation


    Indices: 5041--5171  Score: 185
    Period size: 69  Copynumber: 1.9  Consensus size: 69

       5031 CTTTCGGTTG

                     *                              *                        
       5041 TGTCATTTCGGCAAGGTTATTATATCTTCTCTTTGTCAGTGTAGTGATATTATCTGTTATGAACG
          1 TGTCATTTCAGCAAGGTTATTATATCTTCTCTTTGTCAGTCTAGTGATATTATCTGTTATGAACG

                
       5106 ATGA
         66 ATGA

                               *                   *          *             
       5110 TGTCATTTCAGC-AGGATTGTTATATCTGT-TCTTTGTCGGTCTAGTGATGTTATCTGTTATGA
          1 TGTCATTTCAGCAAGG-TTATTATATCT-TCTCTTTGTCAGTCTAGTGATATTATCTGTTATGA

       5172 GTGACGATAA


Statistics
Matches: 55,  Mismatches: 5, Indels: 4
        0.86            0.08        0.06

Matches are distributed among these distances:
  68    3  0.05
  69   51  0.93
  70    1  0.02

ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45


Consensus pattern (69 bp):   
TGTCATTTCAGCAAGGTTATTATATCTTCTCTTTGTCAGTCTAGTGATATTATCTGTTATGAACG
ATGA

Found at i:8237 original size:21 final size:20

Alignment explanation


    Indices: 8211--8249  Score: 60
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       8201 ATAATATAAA

                          *      
       8211 ATATAATATACAATTATTTTT
          1 ATATAATATA-AATAATTTTT

                              
       8232 ATATAATATAAATAATTT
          1 ATATAATATAAATAATTT

       8250 ATTTTTTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    7  0.41
  21   10  0.59

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (20 bp):   
ATATAATATAAATAATTTTT

Found at i:8241 original size:26 final size:24

Alignment explanation


    Indices: 8205--8261  Score: 71
    Period size: 26  Copynumber: 2.3  Consensus size: 24

       8195 TATATTATAA

                                      
       8205 TATAAAATATAATATACAATTATTTT
          1 TATAAAATATAA-ATA-AATTATTTT

                *           *       
       8231 TATATAATATAAATAATTTATTTT
          1 TATAAAATATAAATAAATTATTTT

                    
       8255 T-TAAAAT
          1 TATAAAAT

       8262 TTTAAATTTG


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  23    5  0.18
  24    9  0.32
  25    3  0.11
  26   11  0.39

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (24 bp):   
TATAAAATATAAATAAATTATTTT

Found at i:8421 original size:25 final size:24

Alignment explanation


    Indices: 8381--8437  Score: 71
    Period size: 25  Copynumber: 2.3  Consensus size: 24

       8371 TAAAAATCTT

                                      
       8381 AAAATCGAACCAATCAAACGG-ATAA
          1 AAAATC-AACCAATCAAA-GGAATAA

                       *             
       8406 AATAATCAACCTATCAAAGGAATAA
          1 AA-AATCAACCAATCAAAGGAATAA

                   
       8431 AAAATCA
          1 AAAATCA

       8438 GCAGCAAGAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  24    7  0.24
  25   18  0.62
  26    4  0.14

ACGTcount: A:0.58, C:0.18, G:0.09, T:0.16


Consensus pattern (24 bp):   
AAAATCAACCAATCAAAGGAATAA
Done.