Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold284

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: 15096
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.34


Found at i:484 original size:27 final size:26

Alignment explanation


    Indices: 423--533  Score: 125
    Period size: 27  Copynumber: 4.2  Consensus size: 26

        413 AGCATGGATG

                             **    *  
        423 CCAGAACAGATAATGTGATAGAGTCA
          1 CCAGAACAGATAATGTGGCAGAGCCA

                                        
        449 CC-GATACAGATAATCGTGGCAGAGCCA
          1 CCAGA-ACAGATAAT-GTGGCAGAGCCA

                                       
        476 CCAGAACAGATATATGTGGCAGAGCCA
          1 CCAGAACAGATA-ATGTGGCAGAGCCA

                 *  *            *     
        503 CCAGATCAAATAATTGTGGCATAGCCA
          1 CCAGAACAGATAA-TGTGGCAGAGCCA

                
        530 CCAG
          1 CCAG

        534 GACACTTCCT


Statistics
Matches: 74,  Mismatches: 6, Indels: 9
        0.83            0.07        0.10

Matches are distributed among these distances:
  25    2  0.03
  26   12  0.16
  27   56  0.76
  28    4  0.05

ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17


Consensus pattern (26 bp):   
CCAGAACAGATAATGTGGCAGAGCCA

Found at i:486 original size:53 final size:54

Alignment explanation


    Indices: 423--533  Score: 145
    Period size: 54  Copynumber: 2.1  Consensus size: 54

        413 AGCATGGATG

                               *    *           *                  
        423 CCAGAACAGATA-ATGTGATAGAGTCACC-GATACAGATAATCGTGGCAGAGCCA
          1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAAATAATCGTGGCAGAGCCA

                              *                      *      *     
        476 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCA
          1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAAATAATCGTGGCAGAGCCA

                
        530 CCAG
          1 CCAG

        534 GACACTTCCT


Statistics
Matches: 50,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  53   12  0.24
  54   35  0.70
  55    3  0.06

ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17


Consensus pattern (54 bp):   
CCAGAACAGATATATGTGACAGAGCCACCAGATCAAATAATCGTGGCAGAGCCA

Found at i:2904 original size:39 final size:39

Alignment explanation


    Indices: 2850--2999  Score: 264
    Period size: 39  Copynumber: 3.8  Consensus size: 39

       2840 ACACTGAAAA

                                                   
       2850 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATG
          1 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATG

                                                  *
       2889 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATA
          1 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATG

                     *                             
       2928 TATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATG
          1 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATG

                    *                 *      
       2967 TATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
          1 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG

       3000 ATAATATAAT


Statistics
Matches: 105,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39  105  1.00

ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24


Consensus pattern (39 bp):   
TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATG

Found at i:8896 original size:31 final size:32

Alignment explanation


    Indices: 8858--8923  Score: 125
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       8848 ATGTTGTATA

                                            
       8858 TTAGAATT-AAAATACTTGAGACTAGGTTACC
          1 TTAGAATTAAAAATACTTGAGACTAGGTTACC

                                            
       8889 TTAGAATTAAAAATACTTGAGACTAGGTTACC
          1 TTAGAATTAAAAATACTTGAGACTAGGTTACC

               
       8921 TTA
          1 TTA

       8924 ATAGTGATAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  31    8  0.24
  32   26  0.76

ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33


Consensus pattern (32 bp):   
TTAGAATTAAAAATACTTGAGACTAGGTTACC

Found at i:11827 original size:39 final size:39

Alignment explanation


    Indices: 11746--12060  Score: 490
    Period size: 39  Copynumber: 8.1  Consensus size: 39

      11736 ATGCAAGACA

                              *                    
      11746 CTGGAAATGTATCCGGGCTAAAGTCCC-CAGGCTTCGTG
          1 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

                                      *            
      11784 CTGGAAATGTATCCGGGCCAAAGTCCAGCAGGCTTCGTG
          1 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

                         *    *                    
      11823 CTGGAAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTG
          1 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

                              *                    
      11862 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
          1 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

                    *                 * *          
      11901 CTGGAAATATATCCGGGCCAAAGTCCTGTAGGCTTCGTG
          1 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

                                                    
      11940 CTGGAAATGTATCC-GGCCTAAAGTCCCGCAGGCTTCGTG
          1 CTGGAAATGTATCCGGGCC-AAAGTCCCGCAGGCTTCGTG

                                                   
      11979 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG
          1 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

                             **       **       *   
      12018 CTGGAAATGTATCCGGGTTAAAGTCCTACAGGCTTTGTG
          1 CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

                
      12057 CTGG
          1 CTGG

      12061 TAATATAATT


Statistics
Matches: 256,  Mismatches: 18, Indels: 5
        0.92            0.06        0.02

Matches are distributed among these distances:
  38   29  0.11
  39  223  0.87
  40    4  0.02

ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24


Consensus pattern (39 bp):   
CTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTG

Done.