Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2573

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: 12060
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34


Found at i:1984 original size:40 final size:39

Alignment explanation


    Indices: 1929--2095  Score: 190
    Period size: 39  Copynumber: 4.2  Consensus size: 39

       1919 ATTTGATGTG

                                                    
       1929 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
          1 TATCCGGGCTT-AAGACCCGCAGGCTATATGCTGGAATTA

                                                    
       1969 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
          1 TATCCGGGCTT-AAGACCCGCAGGCTATATGCTGGAATTA

              *    *      **           *           
       2009 TACCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
          1 TATCCGGGCTTAAGACCCGCAGGCTATATGCTGGAATTA

              *  * *      **           **       *  
       2048 TAACCAGACTTAAGGTCCGCAGGCTATGCGCTGGAAATA
          1 TATCCGGGCTTAAGACCCGCAGGCTATATGCTGGAATTA

             *       
       2087 TGTCCGGGC
          1 TATCCGGGC

       2096 AAAAGTCCCA


Statistics
Matches: 114,  Mismatches: 13, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  39   65  0.57
  40   49  0.43

ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24


Consensus pattern (39 bp):   
TATCCGGGCTTAAGACCCGCAGGCTATATGCTGGAATTA

Found at i:4514 original size:21 final size:21

Alignment explanation


    Indices: 4490--4550  Score: 68
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       4480 GACACATAAA

                        **       
       4490 GTGCCTAAAACGGTACACGAG
          1 GTGCCTAAAACGACACACGAG

                  * *            
       4511 GTGCCTGATACGACACACGAG
          1 GTGCCTAAAACGACACACGAG

                               
       4532 GTGCCTGAAATACGACACA
          1 GTGCCT-AAA-ACGACACA

       4551 TAAAGTGCCT


Statistics
Matches: 32,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  21   23  0.72
  22    1  0.03
  23    8  0.25

ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15


Consensus pattern (21 bp):   
GTGCCTAAAACGACACACGAG

Found at i:4548 original size:23 final size:21

Alignment explanation


    Indices: 4504--4550  Score: 76
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4494 CTAAAACGGT

                                 
       4504 ACACGAGGTGCCTGATACGAC
          1 ACACGAGGTGCCTGATACGAC

                                   
       4525 ACACGAGGTGCCTGAAATACGAC
          1 ACACGAGGTGCCTG--ATACGAC

               
       4548 ACA
          1 ACA

       4551 TAAAGTGCCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  21   14  0.58
  23   10  0.42

ACGTcount: A:0.34, C:0.28, G:0.26, T:0.13


Consensus pattern (21 bp):   
ACACGAGGTGCCTGATACGAC

Found at i:4875 original size:15 final size:15

Alignment explanation


    Indices: 4850--4907  Score: 89
    Period size: 15  Copynumber: 3.8  Consensus size: 15

       4840 TCATATATAT

                            
       4850 TATATAATTCAATCAA
          1 TATA-AATTCAATCAA

                           
       4866 TATAAATTCAATCAA
          1 TATAAATTCAATCAA

            *    *         
       4881 AATAATTTCAATCAA
          1 TATAAATTCAATCAA

                        
       4896 TATAAATTCAAT
          1 TATAAATTCAAT

       4908 AAATTCATCG


Statistics
Matches: 38,  Mismatches: 4, Indels: 1
        0.88            0.09        0.02

Matches are distributed among these distances:
  15   34  0.89
  16    4  0.11

ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36


Consensus pattern (15 bp):   
TATAAATTCAATCAA

Found at i:5268 original size:42 final size:42

Alignment explanation


    Indices: 5205--5286  Score: 107
    Period size: 43  Copynumber: 2.0  Consensus size: 42

       5195 TTCTTTTGTT

                                        *              
       5205 TCTTTAGTTTATATAATATAAT-ATA-ATTAAAACATAAAATA
          1 TCTTTAGTTTATATAATATAATAATATACT-AAACATAAAATA

                                                      
       5246 TCTTTA-TTATATAATAATATAATAATATACTAAACATAAAA
          1 TCTTTAGTT-TAT-ATAATATAATAATATACTAAACATAAAA

       5287 AAAATCTTAG


Statistics
Matches: 36,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
  40    2  0.06
  41    9  0.25
  42   10  0.28
  43   13  0.36
  44    2  0.06

ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40


Consensus pattern (42 bp):   
TCTTTAGTTTATATAATATAATAATATACTAAACATAAAATA

Found at i:10662 original size:21 final size:21

Alignment explanation


    Indices: 10636--10681  Score: 74
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      10626 TGTTAGGTTT

                   *             
      10636 TTTTTTTTAAATTCTAGCTAG
          1 TTTTTTTAAAATTCTAGCTAG

                               * 
      10657 TTTTTTTAAAATTCTAGCTTG
          1 TTTTTTTAAAATTCTAGCTAG

                
      10678 TTTT
          1 TTTT

      10682 AGGTTAATCA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61


Consensus pattern (21 bp):   
TTTTTTTAAAATTCTAGCTAG
Done.