Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3570

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: 29121
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Found at i:8141 original size:18 final size:18

Alignment explanation


    Indices: 8096--8141  Score: 51
    Period size: 18  Copynumber: 2.5  Consensus size: 18

       8086 TAGCTTATCA

                              
       8096 TCTTTTCTTTCTTCAGTC
          1 TCTTTTCTTTCTTCAGTC

                                 
       8114 TCTTTCTCTTT-TTCAATGT-
          1 TCTTT-TCTTTCTTC-A-GTC

                     
       8133 TCTTTTCTT
          1 TCTTTTCTT

       8142 GATCAAATTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  18   12  0.48
  19   11  0.44
  20    2  0.08

ACGTcount: A:0.07, C:0.24, G:0.04, T:0.65


Consensus pattern (18 bp):   
TCTTTTCTTTCTTCAGTC

Found at i:8245 original size:18 final size:17

Alignment explanation


    Indices: 8212--8247  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       8202 TTTCACACTC

                       *     
       8212 TTTTTCTTTCATTTCTT
          1 TTTTTCTTTCAATTCTT

                              
       8229 TTTTTCTTTCAAATTCTT
          1 TTTTTCTTTC-AATTCTT

             
       8247 T
          1 T

       8248 CTCCCATGCT


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

Matches are distributed among these distances:
  17   10  0.59
  18    7  0.41

ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72


Consensus pattern (17 bp):   
TTTTTCTTTCAATTCTT

Found at i:14129 original size:30 final size:30

Alignment explanation


    Indices: 14095--14191  Score: 99
    Period size: 30  Copynumber: 3.2  Consensus size: 30

      14085 TAAACTAAAA

                                          
      14095 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
          1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT

                    *    * *   * *    *    
      14125 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
          1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT

                     *                    
      14155 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
          1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT

                    
      14184 ATGAGCTA
          1 -TGAGCTA

      14192 GGAGTGAGCT


Statistics
Matches: 51,  Mismatches: 13, Indels: 6
        0.73            0.19        0.09

Matches are distributed among these distances:
  29    3  0.06
  30   45  0.88
  31    3  0.06

ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28


Consensus pattern (30 bp):   
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT

Found at i:20218 original size:4 final size:4

Alignment explanation


    Indices: 20209--20236  Score: 56
    Period size: 4  Copynumber: 7.0  Consensus size: 4

      20199 TTAAACTAAG

                                              
      20209 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
          1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA

      20237 AATAAAACTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (4 bp):   
TAAA

Found at i:21633 original size:23 final size:22

Alignment explanation


    Indices: 21581--21633  Score: 56
    Period size: 23  Copynumber: 2.4  Consensus size: 22

      21571 TCCACGTCTT

                    *             
      21581 TTTCTTTTGTTTCTTTTTCTAA
          1 TTTCTTTTCTTTCTTTTTCTAA

                                     
      21603 -TTCATTTTCTCTTCTTTCTTC-AA
          1 TTTC-TTTTCT-TTCTTT-TTCTAA

                    
      21626 TTTCTTTT
          1 TTTCTTTT

      21634 TCACTCTCAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    3  0.12
  22    5  0.19
  23   12  0.46
  24    6  0.23

ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70


Consensus pattern (22 bp):   
TTTCTTTTCTTTCTTTTTCTAA
Done.