Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1597

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: 11643
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:165 original size:14 final size:16

Alignment explanation


    Indices: 133--165  Score: 52
    Period size: 14  Copynumber: 2.2  Consensus size: 16

        123 TCAAATAATT

                            
        133 AACTTAAAATGATTTA
          1 AACTTAAAATGATTTA

                            
        149 AACTT-AAATGA-TTA
          1 AACTTAAAATGATTTA

               
        163 AAC
          1 AAC

        166 CCTATGAATC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    6  0.35
  15    6  0.35
  16    5  0.29

ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33


Consensus pattern (16 bp):   
AACTTAAAATGATTTA

Found at i:8433 original size:31 final size:31

Alignment explanation


    Indices: 8388--8479  Score: 82
    Period size: 31  Copynumber: 3.0  Consensus size: 31

       8378 TTTTAATATA

                 *   *                     
       8388 TTTTAATAATTAAATTTAAATAAAATTTATT
          1 TTTTATTAAATAAATTTAAATAAAATTTATT

                                * *        *
       8419 TTTTATTAAATAAATATTAATTTAAATTTA-A
          1 TTTTATTAAATAAAT-TTAAATAAAATTTATT

              **        *                  
       8450 TTAAATTAAAT-TATTTAAA-AAAATTTATT
          1 TTTTATTAAATAAATTTAAATAAAATTTATT

             
       8479 T
          1 T

       8480 AATTTTTTTA


Statistics
Matches: 48,  Mismatches: 11, Indels: 6
        0.74            0.17        0.09

Matches are distributed among these distances:
  28    7  0.15
  29    5  0.10
  30    2  0.04
  31   22  0.46
  32   12  0.25

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (31 bp):   
TTTTATTAAATAAATTTAAATAAAATTTATT

Found at i:10568 original size:22 final size:23

Alignment explanation


    Indices: 10525--10598  Score: 86
    Period size: 22  Copynumber: 3.3  Consensus size: 23

      10515 ATAATATAAA

                                     
      10525 AAATT-TA-AATATTATATAAATAT
          1 AAATTATATAATATT-T-TAAATAT

                        *          
      10548 AAATTAT-TAATTTTTTAAATAT
          1 AAATTATATAATATTTTAAATAT

                                   
      10570 AAA-TATATAATATTTTAAATAT
          1 AAATTATATAATATTTTAAATAT

                    
      10592 -AATTATA
          1 AAATTATA

      10599 ATATATAAAA


Statistics
Matches: 45,  Mismatches: 2, Indels: 9
        0.80            0.04        0.16

Matches are distributed among these distances:
  21    5  0.11
  22   28  0.62
  23    6  0.13
  24    6  0.13

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (23 bp):   
AAATTATATAATATTTTAAATAT

Found at i:10574 original size:6 final size:6

Alignment explanation


    Indices: 10563--10633  Score: 58
    Period size: 6  Copynumber: 11.5  Consensus size: 6

      10553 ATTAATTTTT

                                               *                    *   
      10563 TAAATA TAAATA TATAATA TTTTAAATA TAATTA TAATATA TAAA-A -ATATA
          1 TAAATA TAAATA TA-AATA ---TAAATA TAAATA TAA-ATA TAAATA TAAATA

                                    
      10614 TAAATA T-AATA TAAATA TAA
          1 TAAATA TAAATA TAAATA TAA

      10634 GATAATTTTG


Statistics
Matches: 53,  Mismatches: 4, Indels: 16
        0.73            0.05        0.22

Matches are distributed among these distances:
   4    2  0.04
   5    7  0.13
   6   29  0.55
   7    9  0.17
   9    4  0.08
  10    2  0.04

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (6 bp):   
TAAATA

Done.