Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold9624.1

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: 4315
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36


Found at i:2422 original size:34 final size:33

Alignment explanation


    Indices: 2350--2449  Score: 164
    Period size: 34  Copynumber: 3.0  Consensus size: 33

       2340 GTAAACTTCG

                                   *    *    
       2350 ATTTAGTTGTCACTGTGTTGACCGAAAAGTTCA
          1 ATTTAGTTGTCACTGTGTTGACCAAAAATTTCA

                                              
       2383 ATTTAGTTGTCACTGTGTTGACCAAAAAATTTCA
          1 ATTTAGTTGTCACTGTGTTGACC-AAAAATTTCA

                                             
       2417 ATTTAGTTGTCACTGTGTTGACCGAAAAATTTC
          1 ATTTAGTTGTCACTGTGTTGACC-AAAAATTTC

       2450 GTTGGCCGAA


Statistics
Matches: 63,  Mismatches: 3, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  33   23  0.37
  34   40  0.63

ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38


Consensus pattern (33 bp):   
ATTTAGTTGTCACTGTGTTGACCAAAAATTTCA

Found at i:2469 original size:16 final size:16

Alignment explanation


    Indices: 2432--2476  Score: 54
    Period size: 17  Copynumber: 2.8  Consensus size: 16

       2422 GTTGTCACTG

                            
       2432 TGTTGACCGAAAAATT
          1 TGTTGACCGAAAAATT

                  *       *  
       2448 TCGTTGGCCGAAAACTT
          1 T-GTTGACCGAAAAATT

                 *      
       2465 TGTTGCCCGAAA
          1 TGTTGACCGAAA

       2477 TTTTTATCAC


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  16   11  0.44
  17   14  0.56

ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Consensus pattern (16 bp):   
TGTTGACCGAAAAATT

Found at i:2567 original size:18 final size:18

Alignment explanation


    Indices: 2518--2594  Score: 82
    Period size: 18  Copynumber: 4.1  Consensus size: 18

       2508 CGTCGAATTA

                         *    
       2518 GTTGGCACTATGTTGCCC
          1 GTTGGCACTATGTCGCCC

                     *  *   *    
       2536 GAAATTGGCTCTTTGTTGCCC
          1 G---TTGGCACTATGTCGCCC

                     *        
       2557 GTTGGCACTTTGTCGCCC
          1 GTTGGCACTATGTCGCCC

                              
       2575 GTTGGCACTATGTCGCCC
          1 GTTGGCACTATGTCGCCC

              
       2593 GT
          1 GT

       2595 AATTTTTGAC


Statistics
Matches: 51,  Mismatches: 5, Indels: 6
        0.82            0.08        0.10

Matches are distributed among these distances:
  18   35  0.69
  21   16  0.31

ACGTcount: A:0.10, C:0.29, G:0.27, T:0.34


Consensus pattern (18 bp):   
GTTGGCACTATGTCGCCC
Done.