Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3011

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: 20634
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33


Found at i:259 original size:107 final size:108

Alignment explanation


    Indices: 72--266  Score: 329
    Period size: 107  Copynumber: 1.8  Consensus size: 108

         62 GAAAAATGCT

                                                                             
         72 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
          1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT

                                                       
        137 CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGAATAAGA
         66 CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGAATAAGA

                           *      *  *                              **       
        180 TGAAAAAGATTATCACAATGGATAAGATGAAA-TTTGTTGAGAGCAAAGCTCTAAATGAACAAAT
          1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT

            *                      
        244 TAATCAAGATAGCAAATTTTGCT
         66 CAATCAAGATAGCAAATTTTGCT

        267 AGAATACAAA


Statistics
Matches: 81,  Mismatches: 6, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
 107   52  0.64
 108   29  0.36

ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25


Consensus pattern (108 bp):   
TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGAATAAGA

Found at i:330 original size:45 final size:43

Alignment explanation


    Indices: 232--332  Score: 112
    Period size: 45  Copynumber: 2.3  Consensus size: 43

        222 GCAAAGCTCT

                   *                          * *      
        232 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATACA
          1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA

                                    *  **                  
        275 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAA
          1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATAC-A

                       
        322 AAATGAATAAA
          1 AAATGAATAAA

        333 ATGGAAATAG


Statistics
Matches: 48,  Mismatches: 6, Indels: 6
        0.80            0.10        0.10

Matches are distributed among these distances:
  43    4  0.08
  45   32  0.67
  46    7  0.15
  47    5  0.10

ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26


Consensus pattern (43 bp):   
AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA

Found at i:2100 original size:62 final size:62

Alignment explanation


    Indices: 1994--2112  Score: 193
    Period size: 62  Copynumber: 1.9  Consensus size: 62

       1984 CTCGACGTAC

                                   *               *                      
       1994 TTTGGATTTTAGGAAATTTACTGTATGCAATGAAACGTAGTGTTGATGCATGAATGCGTATT
          1 TTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATGCGTATT

                                *       *      *                     
       2056 TTTGGATTTTAGGAAATTTATTGCATGCGATGAAATGTAATGTTGATGCATGAATGC
          1 TTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATGC

       2113 AAAAAAAAGA


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  62   52  1.00

ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39


Consensus pattern (62 bp):   
TTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATGCGTATT

Found at i:5693 original size:6 final size:6

Alignment explanation


    Indices: 5682--5719  Score: 67
    Period size: 6  Copynumber: 6.2  Consensus size: 6

       5672 CGTTCCCTCC

                                                        
       5682 TCCCAT TCCCAT TCCCAT TCCCAT TCCCATT TCCCAT T
          1 TCCCAT TCCCAT TCCCAT TCCCAT TCCCA-T TCCCAT T

       5720 ATCAACAATA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   6   25  0.81
   7    6  0.19

ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37


Consensus pattern (6 bp):   
TCCCAT

Found at i:7064 original size:23 final size:23

Alignment explanation


    Indices: 7038--7086  Score: 66
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       7028 ATTATAAAAA

                                     
       7038 TAAT-ATATATTAAAT-CATTAATC
          1 TAATAATA-ATTAAATACATT-ATC

                                   
       7061 TAATAATAATTAAATACATTATC
          1 TAATAATAATTAAATACATTATC

               
       7084 TAA
          1 TAA

       7087 AACCTCAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  23   17  0.71
  24    7  0.29

ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41


Consensus pattern (23 bp):   
TAATAATAATTAAATACATTATC

Found at i:17269 original size:19 final size:20

Alignment explanation


    Indices: 17247--17291  Score: 56
    Period size: 20  Copynumber: 2.3  Consensus size: 20

      17237 ATTTATATAC

                              * 
      17247 ATATCAAACACA-ATTTCGA
          1 ATATCAAACACATATTTCAA

                *  *            
      17266 ATATTAATCACATATTTCAA
          1 ATATCAAACACATATTTCAA

                  
      17286 ATATCA
          1 ATATCA

      17292 CCAATCAAAT


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  19   10  0.48
  20   11  0.52

ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33


Consensus pattern (20 bp):   
ATATCAAACACATATTTCAA
Done.