Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3232

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: 32202
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32


Found at i:1386 original size:17 final size:18

Alignment explanation


    Indices: 1360--1393  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       1350 GATAAATCCT

                              
       1360 AATCAAGGA-TTACTCCC
          1 AATCAAGGATTTACTCCC

                 *           
       1377 AATCAGGGATTTACTCC
          1 AATCAAGGATTTACTCC

       1394 TATATTACAG


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    8  0.53
  18    7  0.47

ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26


Consensus pattern (18 bp):   
AATCAAGGATTTACTCCC

Found at i:11163 original size:58 final size:58

Alignment explanation


    Indices: 11098--11211  Score: 210
    Period size: 58  Copynumber: 2.0  Consensus size: 58

      11088 TTCTGATATT

                                                                      
      11098 CAATCACACTATTAAATTGAATACAATGAAACCCTATCAATGGACGGAAACTGGCTGA
          1 CAATCACACTATTAAATTGAATACAATGAAACCCTATCAATGGACGGAAACTGGCTGA

                                                 **                 
      11156 CAATCACACTATTAAATTGAATACAATGAAACCCTATTGATGGACGGAAACTGGCT
          1 CAATCACACTATTAAATTGAATACAATGAAACCCTATCAATGGACGGAAACTGGCT

      11212 AACCTTGAAA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  58   54  1.00

ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24


Consensus pattern (58 bp):   
CAATCACACTATTAAATTGAATACAATGAAACCCTATCAATGGACGGAAACTGGCTGA

Found at i:19004 original size:20 final size:20

Alignment explanation


    Indices: 18967--19004  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      18957 TAAATTTTAA

                         *      
      18967 TTAAATATATAAATTATATT
          1 TTAAATATATAAAATATATT

                               
      18987 TTAAATA-ATCAAAATATA
          1 TTAAATATAT-AAAATATA

      19005 AGCATTGCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  19    2  0.12
  20   14  0.88

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (20 bp):   
TTAAATATATAAAATATATT

Found at i:24277 original size:103 final size:104

Alignment explanation


    Indices: 24033--24298  Score: 419
    Period size: 103  Copynumber: 2.6  Consensus size: 104

      24023 GTTGTACATA

                       **                               *                    
      24033 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
          1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT

            *       **                             
      24098 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
         66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC

            *                                                                
      24137 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
          1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC

                                                    
      24201 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
         65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC

                                          * *                  *       
      24240 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
          1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC

      24299 AATAACGGTT


Statistics
Matches: 149,  Mismatches: 11, Indels: 5
        0.90            0.07        0.03

Matches are distributed among these distances:
 103   83  0.56
 104   66  0.44

ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30


Consensus pattern (104 bp):   
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC

Found at i:31660 original size:101 final size:101

Alignment explanation


    Indices: 31506--31766  Score: 375
    Period size: 101  Copynumber: 2.6  Consensus size: 101

      31496 GTTGTACATA

                       **                               *                    
      31506 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
          1 AAGGGGTTGCTAAGTGCTGATT-CCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT

            *       **                            
      31571 TTGAAATGTGAAAGGGGGTTGCTATGT-CTGATTCCCC
         65 CTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCC

             *                                                               
      31608 -CGAGGGTTGCTAAGTGCTGATTCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
          1 AAG-GGGTTGCTAAGTGCTGATTCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC

                                                  
      31671 TCTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCC
         64 TCTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCC

                                         * *                  *       
      31709 AAGGGGTTGCTAAGTGCTGATTCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
          1 AAGGGGTTGCTAAGTGCTGATTCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC

      31767 AATAACGGTT


Statistics
Matches: 143,  Mismatches: 11, Indels: 11
        0.87            0.07        0.07

Matches are distributed among these distances:
 100   18  0.13
 101  106  0.74
 102   19  0.13

ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30


Consensus pattern (101 bp):   
AAGGGGTTGCTAAGTGCTGATTCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTC
TGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCC
Done.