Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1034

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: 18683
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28


Found at i:716 original size:40 final size:40

Alignment explanation


    Indices: 672--859  Score: 333
    Period size: 40  Copynumber: 4.7  Consensus size: 40

        662 GCTACTTGCT

                                                    
        672 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

                         *           *              
        712 CAAATGCCTTCGGTACTTAGCCCGGATATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

                                   *                
        752 CAAATGCCTTCGGGACTTAGCCCAGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

                                     *              
        792 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

                                         
        832 CAAATG-CTTCGGGACTTAGCCCGGTTAT
          1 CAAATGCCTTCGGGACTTAGCCCGGTTAT

        860 CATCCGAATA


Statistics
Matches: 140,  Mismatches: 8, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
  39   21  0.15
  40  119  0.85

ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

Found at i:771 original size:80 final size:80

Alignment explanation


    Indices: 639--859  Score: 358
    Period size: 80  Copynumber: 2.8  Consensus size: 80

        629 AAACCAAGTA

                     *                     *  *                              
        639 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATA
          1 CCTTCGGAACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATA

                            
        702 GTAACTCGCACAAATG
         65 GTAACTCGCACAAATG

                   *                                                 *       
        718 CCTTCGGTACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCAGTTATAG
          1 CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG

                           
        783 TAACTCGCACAAATG
         66 TAACTCGCACAAATG

                   *                                                       
        798 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG-CTTCGGGACTTAGCCCGGTTAT
          1 CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT

        860 CATCCGAATA


Statistics
Matches: 133,  Mismatches: 7, Indels: 4
        0.92            0.05        0.03

Matches are distributed among these distances:
  79   34  0.26
  80   99  0.74

ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26


Consensus pattern (80 bp):   
CCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAATG

Found at i:1719 original size:35 final size:34

Alignment explanation


    Indices: 1673--1744  Score: 135
    Period size: 35  Copynumber: 2.1  Consensus size: 34

       1663 ATTTCTCTTC

                                               
       1673 TACTTCCTACCATGGCCGAATGCATCAAGACACCA
          1 TACTTCCTACCATGGCCGAATGCATCAAGACA-CA

                                              
       1708 TACTTCCTACCATGGCCGAATGCATCAAGACACA
          1 TACTTCCTACCATGGCCGAATGCATCAAGACACA

               
       1742 TAC
          1 TAC

       1745 CATTTCAATT


Statistics
Matches: 37,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  34    5  0.14
  35   32  0.86

ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21


Consensus pattern (34 bp):   
TACTTCCTACCATGGCCGAATGCATCAAGACACA

Found at i:8777 original size:40 final size:40

Alignment explanation


    Indices: 8733--8920  Score: 333
    Period size: 40  Copynumber: 4.7  Consensus size: 40

       8723 GCTACTTGCT

                                                 *  
       8733 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA

                                     *              
       8773 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA

                                                 *  
       8813 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA

                                     *              
       8853 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACT-ACA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA

                                         
       8892 CAAATGCCTTCGGGACTTAGCCCGGTTAT
          1 CAAATGCCTTCGGGACTTAGCCCGGTTAT

       8921 CATCCGAATA


Statistics
Matches: 141,  Mismatches: 7, Indels: 1
        0.95            0.05        0.01

Matches are distributed among these distances:
  39   30  0.21
  40  111  0.79

ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA

Found at i:8832 original size:80 final size:79

Alignment explanation


    Indices: 8733--8920  Score: 367
    Period size: 80  Copynumber: 2.4  Consensus size: 79

       8723 GCTACTTGCT

                                                                             
       8733 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG

                           
       8798 ATATAGTAACTCACA
         66 ATATAGTAACT-ACA

                                                                             
       8813 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG

                          
       8878 ATATAGTAACTACA
         66 ATATAGTAACTACA

                                         
       8892 CAAATGCCTTCGGGACTTAGCCCGGTTAT
          1 CAAATGCCTTCGGGACTTAGCCCGGTTAT

       8921 CATCCGAATA


Statistics
Matches: 108,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  79   32  0.30
  80   76  0.70

ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24


Consensus pattern (79 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATATAGTAACTACA
Done.