Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1580

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: 16697
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:2852 original size:25 final size:25

Alignment explanation


    Indices: 2810--2860  Score: 59
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       2800 GGTTTCTTTT

                *     *       *       
       2810 TTTTTTTAAGTTTGAGAAGAATCTTA
          1 TTTTGTTAAGATTGAGAAAAAT-TTA

                                     
       2836 TTTTGTTAAGATT-AGAAAAATTTA
          1 TTTTGTTAAGATTGAGAAAAATTTA

             
       2860 T
          1 T

       2861 AGATTAATTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  24    4  0.18
  25    7  0.32
  26   11  0.50

ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49


Consensus pattern (25 bp):   
TTTTGTTAAGATTGAGAAAAATTTA

Found at i:3044 original size:20 final size:21

Alignment explanation


    Indices: 3019--3067  Score: 66
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3009 GACTTAACTC

                                  
       3019 AATTATTTTTCA-A-TTATATA
          1 AATTATTTTT-ATATTTATATA

                                 
       3039 AATTATTTTTATATTTATATA
          1 AATTATTTTTATATTTATATA

            *       
       3060 CATTATTT
          1 AATTATTT

       3068 ACTATAATAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  19    1  0.04
  20   11  0.42
  21   14  0.54

ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59


Consensus pattern (21 bp):   
AATTATTTTTATATTTATATA

Found at i:5645 original size:21 final size:23

Alignment explanation


    Indices: 5612--5657  Score: 69
    Period size: 22  Copynumber: 2.1  Consensus size: 23

       5602 AAACGACATA

                    *              
       5612 ATGTCAAACAAAATC-AAATTTT
          1 ATGTCAAAAAAAATCAAAATTTT

                                   
       5634 ATGT-AAAAAAAATCAAAATTTT
          1 ATGTCAAAAAAAATCAAAATTTT

              
       5656 AT
          1 AT

       5658 TTTCAACAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    9  0.41
  22   13  0.59

ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33


Consensus pattern (23 bp):   
ATGTCAAAAAAAATCAAAATTTT

Found at i:6599 original size:37 final size:36

Alignment explanation


    Indices: 6541--6639  Score: 110
    Period size: 37  Copynumber: 2.7  Consensus size: 36

       6531 CGACAAGTAA

                                                  
       6541 TATTTGAGTGGCTTAGT-CAATCCACTATGATTGTCAG
          1 TATTTGAGTGGC--AGTGCAATCCACTATGATTGTCAG

                                              *  
       6578 TATTTGAGTGGCAGTGCCAATCCACTATGATTGTTAG
          1 TATTTGAGTGGCAGTG-CAATCCACTATGATTGTCAG

            *     *    *  *          
       6615 AATTTGGGTGGTAGCGTCAATCCAC
          1 TATTTGAGTGGCAGTG-CAATCCAC

       6640 GGAAAAATAA


Statistics
Matches: 54,  Mismatches: 6, Indels: 4
        0.84            0.09        0.06

Matches are distributed among these distances:
  35    3  0.06
  37   51  0.94

ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34


Consensus pattern (36 bp):   
TATTTGAGTGGCAGTGCAATCCACTATGATTGTCAG

Found at i:12095 original size:25 final size:25

Alignment explanation


    Indices: 12053--12103  Score: 59
    Period size: 26  Copynumber: 2.0  Consensus size: 25

      12043 GTTTCTTTTT

                *     *       *       
      12053 TTTTTTTAAGTTTGAGAAGAATCTTA
          1 TTTTGTTAAGATTGAGAAAAAT-TTA

                                     
      12079 TTTTGTTAAGATT-AGAAAAATTTA
          1 TTTTGTTAAGATTGAGAAAAATTTA

             
      12103 T
          1 T

      12104 AGATTAATTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  24    4  0.18
  25    7  0.32
  26   11  0.50

ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49


Consensus pattern (25 bp):   
TTTTGTTAAGATTGAGAAAAATTTA

Found at i:14910 original size:19 final size:21

Alignment explanation


    Indices: 14872--14910  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 21

      14862 GACATAATGT

                           *     
      14872 TAAACAAAATCAAATTTTATG
          1 TAAACAAAATCAAATATTATG

                                
      14893 TAAA-AAAATC-AATATTAT
          1 TAAACAAAATCAAATATTAT

      14911 TTCCAACAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    7  0.41
  20    6  0.35
  21    4  0.24

ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33


Consensus pattern (21 bp):   
TAAACAAAATCAAATATTATG

Found at i:16344 original size:3 final size:3

Alignment explanation


    Indices: 16336--16378  Score: 86
    Period size: 3  Copynumber: 14.3  Consensus size: 3

      16326 AAAGGAATTG

                                                                     
      16336 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

      16379 CTTGCTATCA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   40  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Done.