Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3482

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: 41563
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:12409 original size:4 final size:4

Alignment explanation


    Indices: 12400--12437  Score: 53
    Period size: 4  Copynumber: 9.8  Consensus size: 4

      12390 TTAAACTAAG

                                                             
      12400 TAAA TAAA TAAA TAAA TAAA T-AA -AAA TAAAA TAAA TAA
          1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAA

      12438 CTTACAACTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
   3    4  0.13
   4   23  0.74
   5    4  0.13

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (4 bp):   
TAAA

Found at i:13795 original size:23 final size:23

Alignment explanation


    Indices: 13769--13812  Score: 63
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      13759 TTCTTTTTGT

                                    
      13769 TTCTTT-TTCTAATTCATTTTCTC
          1 TTCTTTCTTC-AATTCATTTTCTC

                           *     
      13792 TTCTTTCTTCAATTCTTTTTC
          1 TTCTTTCTTCAATTCATTTTC

      13813 ACTCTCAATC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  23   16  0.84
  24    3  0.16

ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66


Consensus pattern (23 bp):   
TTCTTTCTTCAATTCATTTTCTC

Found at i:13855 original size:18 final size:17

Alignment explanation


    Indices: 13754--13856  Score: 57
    Period size: 18  Copynumber: 5.8  Consensus size: 17

      13744 CCTTTCCACG

                          *  
      13754 TCTTTTTCTTTTT-GTT
          1 TCTTTTTCTTTTTCATT

                     **      
      13770 TCTTTTTCTAATTCATT
          1 TCTTTTTCTTTTTCATT

                 *           * 
      13787 T-TCTCTTCTTTCTTCAAT
          1 TCT-TTTTCTTT-TTCATT

                    ** *     *
      13805 TCTTTTTCACTCTCAATC
          1 TCTTTTTCTTTTTC-ATT

                               
      13823 TCTTTTTGCCTTTTTCATT
          1 TCTTTTT--CTTTTTCATT

                           
      13842 CTCTTTTTCTTTTTC
          1 -TCTTTTTCTTTTTC

      13857 CTCACTTGTT


Statistics
Matches: 62,  Mismatches: 17, Indels: 14
        0.67            0.18        0.15

Matches are distributed among these distances:
  16   12  0.19
  17   10  0.16
  18   26  0.42
  19    3  0.05
  20   11  0.18

ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66


Consensus pattern (17 bp):   
TCTTTTTCTTTTTCATT

Found at i:17410 original size:23 final size:22

Alignment explanation


    Indices: 17359--17410  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 22

      17349 CCCTCGTCTT

                   *              
      17359 TTCTTTTGTTTCTTTTTCTAAC
          1 TTCTTTTCTTTCTTTTTCTAAC

                                     
      17381 -TCATTTTCTCTTCTTTCTTC-AAC
          1 TTC-TTTTCT-TTCTTT-TTCTAAC

                   
      17404 TTCTTTT
          1 TTCTTTT

      17411 TCAATTTCTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    2  0.08
  22    5  0.20
  23   13  0.52
  24    5  0.20

ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65


Consensus pattern (22 bp):   
TTCTTTTCTTTCTTTTTCTAAC

Found at i:17419 original size:12 final size:12

Alignment explanation


    Indices: 17368--17423  Score: 53
    Period size: 12  Copynumber: 4.7  Consensus size: 12

      17358 TTTCTTTTGT

                         
      17368 TTCTTTTTCTAAC
          1 TTCTTTTTC-AAC

               *      * 
      17381 -TCATTTTC-TC
          1 TTCTTTTTCAAC

                         
      17391 TTCTTTCTTCAAC
          1 TTCTTT-TTCAAC

                       *
      17404 TTCTTTTTCAAT
          1 TTCTTTTTCAAC

                    
      17416 TTCTTTTT
          1 TTCTTTTT

      17424 TTTCACATTC


Statistics
Matches: 35,  Mismatches: 5, Indels: 7
        0.74            0.11        0.15

Matches are distributed among these distances:
  10    1  0.03
  11    4  0.11
  12   23  0.66
  13    7  0.20

ACGTcount: A:0.12, C:0.23, G:0.00, T:0.64


Consensus pattern (12 bp):   
TTCTTTTTCAAC
Done.