Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2213

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: 14759
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31


Found at i:1490 original size:38 final size:40

Alignment explanation


    Indices: 1432--1548  Score: 175
    Period size: 38  Copynumber: 3.0  Consensus size: 40

       1422 CGGATGTAAC

                *    *   *                          
       1432 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
          1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT

                                                     
       1472 AA-CCGCACGAA-ACCTTCGGGACTTAACCCGGTTATAAAT
          1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTAT-AAT

                         *                        
       1511 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA
          1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATA

       1549 TTTTTTTTCC


Statistics
Matches: 70,  Mismatches: 4, Indels: 6
        0.88            0.05        0.08

Matches are distributed among these distances:
  38   23  0.33
  39   12  0.17
  40   12  0.17
  41   23  0.33

ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21


Consensus pattern (40 bp):   
AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT

Found at i:1541 original size:41 final size:41

Alignment explanation


    Indices: 1432--1548  Score: 186
    Period size: 41  Copynumber: 2.9  Consensus size: 41

       1422 CGGATGTAAC

                *    *                               
       1432 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTAT-AAT
          1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAAT

                         *                           
       1472 AA-CCGCACGAA-ACCTTCGGGACTTAACCCGGTTATAAAT
          1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAAT

                                                  
       1511 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA
          1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATA

       1549 TTTTTTTTCC


Statistics
Matches: 70,  Mismatches: 4, Indels: 5
        0.89            0.05        0.06

Matches are distributed among these distances:
  38   23  0.33
  39   12  0.17
  40   11  0.16
  41   24  0.34

ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21


Consensus pattern (41 bp):   
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAAT

Found at i:6590 original size:28 final size:28

Alignment explanation


    Indices: 6550--6607  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       6540 TTCAGACAGT

                                        
       6550 CTCGGGCAATCCTTGATAAAGTGGTCAG
          1 CTCGGGCAATCCTTGATAAAGTGGTCAG

                                        
       6578 CTCGGGCAATCCTTGATAAAGTGGTCAG
          1 CTCGGGCAATCCTTGATAAAGTGGTCAG

              
       6606 CT
          1 CT

       6608 GATCCGCACT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26


Consensus pattern (28 bp):   
CTCGGGCAATCCTTGATAAAGTGGTCAG

Found at i:9341 original size:40 final size:40

Alignment explanation


    Indices: 9297--9425  Score: 116
    Period size: 40  Copynumber: 3.2  Consensus size: 40

       9287 CGGAATTTGG

                   *          *                     
       9297 CTCGGATGTAACAACCAGTACAAATGCCTTCGGGACTTAA
          1 CTCGGATATAACAACCAGCACAAATGCCTTCGGGACTTAA

                 *     *    *    *                  
       9337 CTCGGTTATAATAACCCGCACGAATGCCTTCGGGACTTAA
          1 CTCGGATATAACAACCAGCACAAATGCCTTCGGGACTTAA

             *   *    **    *    **                 
       9377 CCCGGTTATAGTAACCCGCACGGATGCCTTC-GGACTTAA
          1 CTCGGATATAACAACCAGCACAAATGCCTTCGGGACTTAA

             *   *    
       9416 CCCGGTTATA
          1 CTCGGATATA

       9426 TTTTTTTCCA


Statistics
Matches: 80,  Mismatches: 9, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  39   18  0.22
  40   62  0.77

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24


Consensus pattern (40 bp):   
CTCGGATATAACAACCAGCACAAATGCCTTCGGGACTTAA

Found at i:9423 original size:39 final size:40

Alignment explanation


    Indices: 9319--9425  Score: 180
    Period size: 40  Copynumber: 2.7  Consensus size: 40

       9309 AACCAGTACA

                               *                    
       9319 AATGCCTTCGGGACTTAACTCGGTTATAATAACCCGCACG
          1 AATGCCTTCGGGACTTAACCCGGTTATAATAACCCGCACG

                                        *           
       9359 AATGCCTTCGGGACTTAACCCGGTTATAGTAACCCGCACG
          1 AATGCCTTCGGGACTTAACCCGGTTATAATAACCCGCACG

            *                           
       9399 GATGCCTTC-GGACTTAACCCGGTTATA
          1 AATGCCTTCGGGACTTAACCCGGTTATA

       9426 TTTTTTTCCA


Statistics
Matches: 64,  Mismatches: 3, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  39   18  0.28
  40   46  0.72

ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGTTATAATAACCCGCACG

Found at i:14646 original size:44 final size:45

Alignment explanation


    Indices: 14585--14681  Score: 110
    Period size: 44  Copynumber: 2.2  Consensus size: 45

      14575 ACTGCTTAAG

                        *     **  **                      
      14585 GAGATAAGATCTTCAATCTTCAGTCTGCT-TCCTTGCTACCTCAG-
          1 GAGATAAGATCTACAATCGCCAACCTGCTCT-CTTGCTACCTCAGA

                                                          
      14629 GAAGATAAGA-CTACAATCGCCAACCTGCTCTCTTGCTACCTCAGA
          1 G-AGATAAGATCTACAATCGCCAACCTGCTCTCTTGCTACCTCAGA

                    
      14674 GAGATAAG
          1 GAGATAAG

      14682 GCTAATGGCT


Statistics
Matches: 45,  Mismatches: 5, Indels: 6
        0.80            0.09        0.11

Matches are distributed among these distances:
  44   35  0.78
  45   10  0.22

ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27


Consensus pattern (45 bp):   
GAGATAAGATCTACAATCGCCAACCTGCTCTCTTGCTACCTCAGA
Done.