Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1867

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, 741

Length: 1236
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27

Warning! 22 characters in sequence are not A, C, G, or T


Found at i:407 original size:12 final size:11

Alignment explanation


    Indices: 390--431  Score: 59
    Period size: 12  Copynumber: 3.7  Consensus size: 11

        380 TTGTAGTTTC

                        
        390 AAAAAAAATTCG
          1 AAAAAAAA-TCG

                       
        402 AAAAAAAATC-
          1 AAAAAAAATCG

                       
        412 AAAAAAAATCG
          1 AAAAAAAATCG

                     
        423 AAAAGAAAA
          1 AAAA-AAAA

        432 AAAATTGAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  10   10  0.36
  11    6  0.21
  12   12  0.43

ACGTcount: A:0.76, C:0.07, G:0.07, T:0.10


Consensus pattern (11 bp):   
AAAAAAAATCG

Found at i:417 original size:21 final size:22

Alignment explanation


    Indices: 388--431  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        378 AATTGTAGTT

                                   
        388 TCAAAAAAAATTCGAAAA-AAAA
          1 TCAAAAAAAA-TCGAAAAGAAAA

                                  
        410 TCAAAAAAAATCGAAAAGAAAA
          1 TCAAAAAAAATCGAAAAGAAAA

        432 AAAATTGAAA


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

Matches are distributed among these distances:
  21    7  0.33
  22   14  0.67

ACGTcount: A:0.73, C:0.09, G:0.07, T:0.11


Consensus pattern (22 bp):   
TCAAAAAAAATCGAAAAGAAAA

Found at i:442 original size:10 final size:11

Alignment explanation


    Indices: 427--451  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

        417 AAATCGAAAA

                       
        427 GAAAAAAAATT
          1 GAAAAAAAATT

                       
        438 GAAAAAAAATT
          1 GAAAAAAAATT

               
        449 GAA
          1 GAA

        452 TACGGTCTAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16


Consensus pattern (11 bp):   
GAAAAAAAATT

Found at i:443 original size:17 final size:16

Alignment explanation


    Indices: 412--446  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

        402 AAAAAAAATC

                            
        412 AAAAAAAATCGAAAAG
          1 AAAAAAAATCGAAAAG

                     *      
        428 AAAAAAAATTGAAAA-
          1 AAAAAAAATCGAAAAG

                
        443 AAAA
          1 AAAA

        447 TTGAATACGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15    4  0.22
  16   14  0.78

ACGTcount: A:0.80, C:0.03, G:0.09, T:0.09


Consensus pattern (16 bp):   
AAAAAAAATCGAAAAG

Found at i:709 original size:20 final size:21

Alignment explanation


    Indices: 680--720  Score: 66
    Period size: 20  Copynumber: 2.0  Consensus size: 21

        670 CACAAGTGTG

                                 
        680 GATAAATCTAA-GTAGCTTTT
          1 GATAAATCTAAGGTAGCTTTT

                 *               
        700 GATAAGTCTAAGGTAGCTTTT
          1 GATAAATCTAAGGTAGCTTTT

        721 TAGAATATCG


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

Matches are distributed among these distances:
  20   10  0.53
  21    9  0.47

ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39


Consensus pattern (21 bp):   
GATAAATCTAAGGTAGCTTTT

Done.