Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2046

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: 24822
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:720 original size:23 final size:22

Alignment explanation


    Indices: 690--755  Score: 75
    Period size: 23  Copynumber: 3.1  Consensus size: 22

        680 ATTTTATATA

                        *          
        690 ATATATTTAAAATTTTAAAATTT
          1 ATATATTTAAAAATTT-AAATTT

                             *    
        713 ATATATTTAAAAATTTATATTT
          1 ATATATTTAAAAATTTAAATTT

                       *          
        735 -TATATTT--ATATTTAAATTT
          1 ATATATTTAAAAATTTAAATTT

              
        754 AT
          1 AT

        756 GTTAAGCATA


Statistics
Matches: 38,  Mismatches: 4, Indels: 5
        0.81            0.09        0.11

Matches are distributed among these distances:
  19   10  0.26
  20    1  0.03
  21    7  0.18
  22    5  0.13
  23   15  0.39

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (22 bp):   
ATATATTTAAAAATTTAAATTT

Found at i:721 original size:15 final size:14

Alignment explanation


    Indices: 701--755  Score: 62
    Period size: 16  Copynumber: 4.0  Consensus size: 14

        691 TATATTTAAA

                          
        701 ATTTTAAAATTTAT
          1 ATTTTAAAATTTAT

                            
        715 ATATTTAAAAATTTAT
          1 AT-TTT-AAAATTTAT

                   *      
        731 ATTTT-ATATTTAT
          1 ATTTTAAAATTTAT

                          
        744 A-TTT-AAATTTAT
          1 ATTTTAAAATTTAT

        756 GTTAAGCATA


Statistics
Matches: 37,  Mismatches: 2, Indels: 6
        0.82            0.04        0.13

Matches are distributed among these distances:
  12   10  0.27
  13    8  0.22
  14    2  0.05
  15    6  0.16
  16   11  0.30

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (14 bp):   
ATTTTAAAATTTAT

Found at i:3125 original size:2 final size:2

Alignment explanation


    Indices: 3118--3142  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3108 TTCAATGGTT

                                                 
       3118 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       3143 TTAATATCTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:3227 original size:13 final size:14

Alignment explanation


    Indices: 3209--3237  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       3199 CAAATAATTC

                          
       3209 ATTAAA-AGGTTCA
          1 ATTAAAGAGGTTCA

                          
       3222 ATTAAAGAGGTTCA
          1 ATTAAAGAGGTTCA

              
       3236 AT
          1 AT

       3238 AAATTTATTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.40
  14    9  0.60

ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31


Consensus pattern (14 bp):   
ATTAAAGAGGTTCA

Found at i:9388 original size:20 final size:20

Alignment explanation


    Indices: 9365--9422  Score: 50
    Period size: 20  Copynumber: 3.0  Consensus size: 20

       9355 TTATTATAAA

                *       *       
       9365 ATAATATAATAAGATAAATT
          1 ATAAAATAATAAAATAAATT

                   *           *
       9385 ATAAAATTATAAAATAAA-A
          1 ATAAAATAATAAAATAAATT

                                 
       9404 ATAAAA-ATATAAAA-AAATT
          1 ATAAAATA-ATAAAATAAATT

       9423 GGGGTTGGCT


Statistics
Matches: 30,  Mismatches: 6, Indels: 5
        0.73            0.15        0.12

Matches are distributed among these distances:
  18    3  0.10
  19   12  0.40
  20   15  0.50

ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29


Consensus pattern (20 bp):   
ATAAAATAATAAAATAAATT

Found at i:16857 original size:22 final size:22

Alignment explanation


    Indices: 16815--16860  Score: 58
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      16805 TGGGACGATT

                         *        
      16815 AAAAAATACGAAAGGGAAAAAG
          1 AAAAAATACGAAAAGGAAAAAG

                                    
      16837 AAAAAATA-GATAAAGGTAAAAAG
          1 AAAAAATACGA-AAAGG-AAAAAG

             
      16860 A
          1 A

      16861 TCAAAACTGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  21    2  0.10
  22   12  0.57
  23    7  0.33

ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09


Consensus pattern (22 bp):   
AAAAAATACGAAAAGGAAAAAG
Done.