Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold885

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: 41514
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:1445 original size:46 final size:45

Alignment explanation


    Indices: 1395--1563  Score: 180
    Period size: 46  Copynumber: 3.6  Consensus size: 45

       1385 TGGTTGAGCA

                                                          
       1395 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G

                                          *   *    *     * *  
       1441 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTAGGGCA-
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAAG

                                                     *    
       1489 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G

            *    *   *                   
       1535 CCCGAGCTCATTGAGTTGAGTCCGAGTTC
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC

       1564 CCTTTGGGCG


Statistics
Matches: 101,  Mismatches: 14, Indels: 16
        0.77            0.11        0.12

Matches are distributed among these distances:
  44    2  0.02
  45    2  0.02
  46   56  0.55
  47    6  0.06
  48   30  0.30
  49    2  0.02
  50    3  0.03

ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28


Consensus pattern (45 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG

Found at i:1553 original size:94 final size:94

Alignment explanation


    Indices: 1392--1563  Score: 299
    Period size: 94  Copynumber: 1.8  Consensus size: 94

       1382 GGATGGTTGA

                                                        *  * *        *      
       1392 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT

                                         
       1457 TGAGTCCGAGTTCGTGAAATGTAACTAGG
         66 TGAGTCCGAGTTCGTGAAATGTAACTAGG

                                                                  *          
       1486 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCATTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT

                         
       1551 TGAGTCCGAGTTC
         66 TGAGTCCGAGTTC

       1564 CCTTTGGGCG


Statistics
Matches: 73,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  94   73  1.00

ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28


Consensus pattern (94 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAGG

Found at i:13511 original size:20 final size:20

Alignment explanation


    Indices: 13472--13512  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      13462 TACCAACTAG

                *          *    
      13472 CAACTTACCATAATCTTTCA
          1 CAACATACCATAATCATTCA

                        *       
      13492 CAACATACCATAGTCATTCA
          1 CAACATACCATAATCATTCA

             
      13512 C
          1 C

      13513 GACTTAAACT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29


Consensus pattern (20 bp):   
CAACATACCATAATCATTCA

Found at i:16558 original size:45 final size:45

Alignment explanation


    Indices: 16422--16591  Score: 189
    Period size: 45  Copynumber: 3.7  Consensus size: 45

      16412 CGATGCTGAT

                  *  *            **         *       *    
      16422 GTCCTAGACATGGTCTTACAC-GTAACTACATAGATCGATGACAAC
          1 GTCCTAAACGTGGTCTTACACAAAAAC-ACATATATCGATGCCAAC

                *   *     *   *                            
      16467 GTCCCAAATGTGGTATTATACAAAAACACAAATATATCGATGCCAAC
          1 GTCCTAAACGTGGTCTTACACAAAAACAC--ATATATCGATGCCAAC

            *     *                                      
      16514 ATCCTAGACGTGGTCTTACACAAAAACACATATATCGATGCCAAC
          1 GTCCTAAACGTGGTCTTACACAAAAACACATATATCGATGCCAAC

                                 *           
      16559 GTCCTAAACGTGGTCTTACACGAAAACACATAT
          1 GTCCTAAACGTGGTCTTACACAAAAACACATAT

      16592 CAAAATCCTG


Statistics
Matches: 103,  Mismatches: 19, Indels: 6
        0.80            0.15        0.05

Matches are distributed among these distances:
  45   63  0.61
  46    3  0.03
  47   37  0.36

ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24


Consensus pattern (45 bp):   
GTCCTAAACGTGGTCTTACACAAAAACACATATATCGATGCCAAC

Found at i:29741 original size:23 final size:22

Alignment explanation


    Indices: 29715--29767  Score: 56
    Period size: 23  Copynumber: 2.4  Consensus size: 22

      29705 TTAAGAGTGA

                                   *
      29715 AAAAGAAATT-GAAGAAAGAAGAG
          1 AAAAGAAATTAGAA-AAAGAA-AC

                                   
      29738 AAAATG-AATTAGAAAAAGAAAC
          1 AAAA-GAAATTAGAAAAAGAAAC

                    
      29760 AAAAGAAA
          1 AAAAGAAA

      29768 AAGACGTGGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    1  0.04
  22    7  0.27
  23   14  0.54
  24    4  0.15

ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09


Consensus pattern (22 bp):   
AAAAGAAATTAGAAAAAGAAAC
Done.