Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_2464

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: 23235
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34


Found at i:2056 original size:30 final size:30

Alignment explanation


    Indices: 2022--2082  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2012 TCCTTAACTC

                                          
       2022 AAACTTTGGAAAAATTACAATTTTGCCCCT
          1 AAACTTTGGAAAAATTACAATTTTGCCCCT

                   * * * *     *          
       2052 AAACTTTTGCATATTTACACTTTTGCCCCT
          1 AAACTTTGGAAAAATTACAATTTTGCCCCT

             
       2082 A
          1 A

       2083 GGCTCGGGAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38


Consensus pattern (30 bp):   
AAACTTTGGAAAAATTACAATTTTGCCCCT

Found at i:4438 original size:68 final size:67

Alignment explanation


    Indices: 4366--4515  Score: 171
    Period size: 67  Copynumber: 2.2  Consensus size: 67

       4356 CATCATGTGT

                                                      *        *     * *     
       4366 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
          1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC

                  
       4428 ATGTAG
         62 ATGTAG

                          **                           * *                   
       4434 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
          1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT

              
       4499 AG
         66 AG

                           
       4501 ACAAGAGAGCTACGA
          1 ACAAGAGAGCTACGA

       4516 GATAAACTGG


Statistics
Matches: 70,  Mismatches: 9, Indels: 7
        0.81            0.10        0.08

Matches are distributed among these distances:
  64   20  0.29
  65    7  0.10
  66    4  0.06
  67   26  0.37
  68   13  0.19

ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21


Consensus pattern (67 bp):   
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG

Found at i:4471 original size:64 final size:64

Alignment explanation


    Indices: 4390--4573  Score: 194
    Period size: 67  Copynumber: 2.8  Consensus size: 64

       4380 AGACATTATG

                                                                      *    *
       4390 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
          1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA

                              *    * * *     * *                             
       4454 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
          1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT

              
       4519 AA
         63 AA

                          *        *     *    *                     
       4521 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
          1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC

       4574 CGAACTATAT


Statistics
Matches: 98,  Mismatches: 17, Indels: 11
        0.78            0.13        0.09

Matches are distributed among these distances:
  62    1  0.01
  63   19  0.19
  64   21  0.21
  65    8  0.08
  66   16  0.16
  67   31  0.32
  68    2  0.02

ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23


Consensus pattern (64 bp):   
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA

Found at i:6589 original size:41 final size:40

Alignment explanation


    Indices: 6482--6589  Score: 121
    Period size: 41  Copynumber: 2.6  Consensus size: 40

       6472 CTAAGACACC

                                     * *          *  
       6482 TGTAAGACCATATCTGGGATATGGCGTCGATATAGATTTCA
          1 TGTAAGACCATATCTGGGATAT-GCATAGATATAGATTACA

                        *                              
       6523 TGTAAGACCATAGCT--GACTATTGCATAGATATGAGATTACA
          1 TGTAAGACCATATCTGGGA-TA-TGCATAGATAT-AGATTACA

                 *                    
       6564 TGTAATACCATATCTGGGATATGCAT
          1 TGTAAGACCATATCTGGGATATGCAT

       6590 TGGTATGGTA


Statistics
Matches: 56,  Mismatches: 6, Indels: 10
        0.78            0.08        0.14

Matches are distributed among these distances:
  39    2  0.04
  40   10  0.18
  41   40  0.71
  42    2  0.04
  43    2  0.04

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31


Consensus pattern (40 bp):   
TGTAAGACCATATCTGGGATATGCATAGATATAGATTACA

Found at i:22115 original size:12 final size:13

Alignment explanation


    Indices: 22086--22118  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

      22076 GCAAATGTTA

                  *      
      22086 AGTTTTTATGCAT
          1 AGTTTTGATGCAT

                         
      22099 AGTTTTGATGCAT
          1 AGTTTTGATGCAT

                    
      22112 -GTTTTGA
          1 AGTTTTGA

      22119 GATGTGTTAT


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

Matches are distributed among these distances:
  12    7  0.37
  13   12  0.63

ACGTcount: A:0.21, C:0.06, G:0.21, T:0.52


Consensus pattern (13 bp):   
AGTTTTGATGCAT
Done.