Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7231.1

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: 7683
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33


Found at i:916 original size:37 final size:37

Alignment explanation


    Indices: 865--935  Score: 101
    Period size: 37  Copynumber: 1.9  Consensus size: 37

        855 CATTCTTGTA

                                                  
        865 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
          1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC

                                    *          
        902 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
          1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA

        936 GAGAGGCAAG


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  37   28  0.90
  38    3  0.10

ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03


Consensus pattern (37 bp):   
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC

Found at i:935 original size:6 final size:6

Alignment explanation


    Indices: 875--924  Score: 50
    Period size: 6  Copynumber: 8.2  Consensus size: 6

        865 AAGAGAAAAC

                                                                  *   
        875 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
          1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA

             
        924 A
          1 A

        925 TAAAAAGAAA


Statistics
Matches: 40,  Mismatches: 1, Indels: 7
        0.83            0.02        0.15

Matches are distributed among these distances:
   5    9  0.22
   6   22  0.55
   7    3  0.08
   8    3  0.08
   9    3  0.08

ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02


Consensus pattern (6 bp):   
AAAGAA

Found at i:1017 original size:11 final size:12

Alignment explanation


    Indices: 985--1015  Score: 62
    Period size: 12  Copynumber: 2.6  Consensus size: 12

        975 TTGAGAGAAC

                        
        985 TTGAAAAAGCCT
          1 TTGAAAAAGCCT

                        
        997 TTGAAAAAGCCT
          1 TTGAAAAAGCCT

                   
       1009 TTGAAAA
          1 TTGAAAA

       1016 GCAAAAAGAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26


Consensus pattern (12 bp):   
TTGAAAAAGCCT

Found at i:3185 original size:22 final size:20

Alignment explanation


    Indices: 3153--3201  Score: 53
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       3143 GCCGAATTTA

                                   
       3153 TGAACTATTTTAATACATTAGTG
          1 TGAAC-ATTTTAAT-CATT-GTG

                      *  *      
       3176 TGAACATTTTTATTATTGTG
          1 TGAACATTTTAATCATTGTG

                  
       3196 TGAACA
          1 TGAACA

       3202 CCTAGATGCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  20    9  0.38
  21    3  0.12
  22    7  0.29
  23    5  0.21

ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45


Consensus pattern (20 bp):   
TGAACATTTTAATCATTGTG

Found at i:3324 original size:22 final size:20

Alignment explanation


    Indices: 3292--3340  Score: 53
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       3282 GCCGAATTTA

                                   
       3292 TGAACTATTTTAATACATTAGTG
          1 TGAAC-ATTTTAAT-CATT-GTG

                      *  *      
       3315 TGAACATTTTTATTATTGTG
          1 TGAACATTTTAATCATTGTG

                  
       3335 TGAACA
          1 TGAACA

       3341 CCTAAATGCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  20    9  0.38
  21    3  0.12
  22    7  0.29
  23    5  0.21

ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45


Consensus pattern (20 bp):   
TGAACATTTTAATCATTGTG

Found at i:3324 original size:139 final size:139

Alignment explanation


    Indices: 3074--3350  Score: 536
    Period size: 139  Copynumber: 2.0  Consensus size: 139

       3064 TGAAGCCTTT

                                                                             
       3074 CTTTATGACTAAGCATTCATGCACAAACTAAGGGGGAAGAAAGTGTCCATTCAGCTAGTGCATGA
          1 CTTTATGACTAAGCATTCATGCACAAACTAAGGGGGAAGAAAGTGTCCATTCAGCTAGTGCATGA

                                                                             
       3139 ATCTGCCGAATTTATGAACTATTTTAATACATTAGTGTGAACATTTTTATTATTGTGTGAACACC
         66 ATCTGCCGAATTTATGAACTATTTTAATACATTAGTGTGAACATTTTTATTATTGTGTGAACACC

              *      
       3204 TAGATGCCG
        131 TAAATGCCG

                                                                            *
       3213 CTTTATGACTAAGCATTCATGCACAAACTAAGGGGGAAGAAAGTGTCCATTCAGCTAGTGCATGG
          1 CTTTATGACTAAGCATTCATGCACAAACTAAGGGGGAAGAAAGTGTCCATTCAGCTAGTGCATGA

                                                                             
       3278 ATCTGCCGAATTTATGAACTATTTTAATACATTAGTGTGAACATTTTTATTATTGTGTGAACACC
         66 ATCTGCCGAATTTATGAACTATTTTAATACATTAGTGTGAACATTTTTATTATTGTGTGAACACC

                    
       3343 TAAATGCC
        131 TAAATGCC

       3351 AAATTTGAAT


Statistics
Matches: 136,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 139  136  1.00

ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Consensus pattern (139 bp):   
CTTTATGACTAAGCATTCATGCACAAACTAAGGGGGAAGAAAGTGTCCATTCAGCTAGTGCATGA
ATCTGCCGAATTTATGAACTATTTTAATACATTAGTGTGAACATTTTTATTATTGTGTGAACACC
TAAATGCCG
Done.