Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3637

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: 15151
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30


Found at i:594 original size:18 final size:18

Alignment explanation


    Indices: 567--656  Score: 105
    Period size: 18  Copynumber: 5.2  Consensus size: 18

        557 TACGACCGTT

                              
        567 TACGGTACTATTCACGTA
          1 TACGGTACTATTCACGTA

                 *         *  
        585 TACGGCACTATTCACATA
          1 TACGGTACTATTCACGTA

            *                 
        603 CAC-GTACTATT--CGTA
          1 TACGGTACTATTCACGTA

              *  *            
        618 TATGGCACTATTCACGTA
          1 TACGGTACTATTCACGTA

                     *        
        636 TACGGTACTGTTCACGTA
          1 TACGGTACTATTCACGTA

               
        654 TAC
          1 TAC

        657 AGTAGTTGGG


Statistics
Matches: 58,  Mismatches: 11, Indels: 6
        0.77            0.15        0.08

Matches are distributed among these distances:
  15    4  0.07
  16    7  0.12
  17    7  0.12
  18   40  0.69

ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32


Consensus pattern (18 bp):   
TACGGTACTATTCACGTA

Found at i:5294 original size:18 final size:18

Alignment explanation


    Indices: 5267--5359  Score: 105
    Period size: 18  Copynumber: 5.2  Consensus size: 18

       5257 TACGACTGTT

                              
       5267 TACGGTACTATTCACGTA
          1 TACGGTACTATTCACGTA

                 *      *  *  
       5285 TACGGCACTATTTACATA
          1 TACGGTACTATTCACGTA

            *             *   
       5303 CACGGTACTATTCATGTA
          1 TACGGTACTATTCACGTA

              *  *        *   
       5321 TATGGCACTATTCATGTA
          1 TACGGTACTATTCACGTA

                     *        
       5339 TACGGTACTGTTCACGTA
          1 TACGGTACTATTCACGTA

               
       5357 TAC
          1 TAC

       5360 AGTAGTTGGG


Statistics
Matches: 60,  Mismatches: 15, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  18   60  1.00

ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34


Consensus pattern (18 bp):   
TACGGTACTATTCACGTA

Found at i:5315 original size:36 final size:36

Alignment explanation


    Indices: 5268--5359  Score: 121
    Period size: 36  Copynumber: 2.6  Consensus size: 36

       5258 ACGACTGTTT

                                         *      
       5268 ACGGTACTATTCACGTATACGGCACTATTTACATAC
          1 ACGGTACTATTCACGTATACGGCACTATTCACATAC

                         *     *           **  *
       5304 ACGGTACTATTCATGTATATGGCACTATTCATGTAT
          1 ACGGTACTATTCACGTATACGGCACTATTCACATAC

                    *           
       5340 ACGGTACTGTTCACGTATAC
          1 ACGGTACTATTCACGTATAC

       5360 AGTAGTTGGG


Statistics
Matches: 47,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  36   47  1.00

ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34


Consensus pattern (36 bp):   
ACGGTACTATTCACGTATACGGCACTATTCACATAC

Found at i:12739 original size:36 final size:35

Alignment explanation


    Indices: 12693--12765  Score: 128
    Period size: 36  Copynumber: 2.1  Consensus size: 35

      12683 CTGCCAGATT

                           *                   
      12693 AAAAATGTTATACTTGGGTGAATAATGGTAATAAG
          1 AAAAATGTTATACTTAGGTGAATAATGGTAATAAG

                                                
      12728 AAAAACTGTTATACTTAGGTGAATAATGGTAATAAG
          1 AAAAA-TGTTATACTTAGGTGAATAATGGTAATAAG

              
      12764 AA
          1 AA

      12766 TGATACTAAA


Statistics
Matches: 36,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  35    5  0.14
  36   31  0.86

ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30


Consensus pattern (35 bp):   
AAAAATGTTATACTTAGGTGAATAATGGTAATAAG
Done.