Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1629

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: 25135
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33


Found at i:11085 original size:256 final size:254

Alignment explanation


    Indices: 10632--11128  Score: 976
    Period size: 256  Copynumber: 1.9  Consensus size: 254

      10622 GGACTTCAAT

                                                                             
      10632 TTACTTTCTTGCTGTTCATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTT
          1 TTACTTTCTTGCTGTTCATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTT

                                                                             
      10697 GTTTATTCTTCTTGTGAATTTCTAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCT
         66 GTTTATTCTTCTTGTGAATTTCTAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCT

                                                                             
      10762 TGGTAGCCAAATTCGACTAAACTTATCTTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAA
        131 TGGTAGCCAAATTCGACTAAACTTATCTTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAA

                                                                       
      10827 CTGACTGTTTTAGGTTGCTGAAATTTTGGGAAAAATCAAGTTGCTGTTCATTCTTCCAA
        196 CTGACTGTTTTAGGTTGCTGAAATTTTGGGAAAAATCAAGTTGCTGTTCATTCTTCCAA

                                                                             
      10886 TTACTTTCTTGCTGTTCATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAAACT
          1 TTACTTTCTTGCTGTTCATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCT-AACT

                                                                             
      10951 TGTTTATTCTTCTTGTGAATTTCTAGCCATCTTTATTACTCAAAAAGATCGATCGGGTACTCATT
         65 TGTTTATTCTTCTTGTGAATTTCTAGCCATCTTTATTACTCAAAAAGATCGATC-GGTACTCATT

                                                                             
      11016 CTTGGTAGCCAAATTCGACTAAACTTATCTTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAA
        129 CTTGGTAGCCAAATTCGACTAAACTTATCTTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAA

                                                            
      11081 AACTGACTGTTTTAGGTTGCTGAAATTTTGGGAAAAATCAAGTTGCTG
        194 AACTGACTGTTTTAGGTTGCTGAAATTTTGGGAAAAATCAAGTTGCTG

      11129 GAATTTGGGG


Statistics
Matches: 241,  Mismatches: 0, Indels: 2
        0.99            0.00        0.01

Matches are distributed among these distances:
 254   60  0.25
 255   58  0.24
 256  123  0.51

ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45


Consensus pattern (254 bp):   
TTACTTTCTTGCTGTTCATTCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTT
GTTTATTCTTCTTGTGAATTTCTAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCT
TGGTAGCCAAATTCGACTAAACTTATCTTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAA
CTGACTGTTTTAGGTTGCTGAAATTTTGGGAAAAATCAAGTTGCTGTTCATTCTTCCAA

Found at i:14491 original size:19 final size:19

Alignment explanation


    Indices: 14430--14493  Score: 67
    Period size: 19  Copynumber: 3.3  Consensus size: 19

      14420 TTTTTGAGAG

                                  
      14430 AAAAAGAAAAGAGCGAAAAT-A
          1 AAAAAGAAAAGA---AAAATCA

            *                * 
      14451 CAAAAGAAAAGAAAAATGA
          1 AAAAAGAAAAGAAAAATCA

                           *   
      14470 AAAAAGAAAAGAAAATTCA
          1 AAAAAGAAAAGAAAAATCA

                 
      14489 AAAAA
          1 AAAAA

      14494 AGAGAATGAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  18    5  0.13
  19   22  0.58
  21   11  0.29

ACGTcount: A:0.75, C:0.05, G:0.14, T:0.06


Consensus pattern (19 bp):   
AAAAAGAAAAGAAAAATCA

Found at i:18561 original size:22 final size:22

Alignment explanation


    Indices: 18533--18576  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      18523 TTTTGAACCA

                                  
      18533 TTACCATTTCGTACCAAATCCC
          1 TTACCATTTCGTACCAAATCCC

                             *    
      18555 TTACCATTTCGTACCAATTCCC
          1 TTACCATTTCGTACCAAATCCC

      18577 AAATACCAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34


Consensus pattern (22 bp):   
TTACCATTTCGTACCAAATCCC

Found at i:18903 original size:13 final size:13

Alignment explanation


    Indices: 18872--18913  Score: 57
    Period size: 13  Copynumber: 3.0  Consensus size: 13

      18862 ATAGGTACGT

                            
      18872 AAAAAAAAAGAGTTCG
          1 AAAAAAAAA-A-TT-G

                         
      18888 AAAAAAAAAATTG
          1 AAAAAAAAAATTG

                         
      18901 AAAAAAAAAATTG
          1 AAAAAAAAAATTG

      18914 CATACGGTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  13   14  0.54
  14    2  0.08
  15    1  0.04
  16    9  0.35

ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14


Consensus pattern (13 bp):   
AAAAAAAAAATTG

Found at i:21161 original size:17 final size:17

Alignment explanation


    Indices: 21116--21169  Score: 63
    Period size: 17  Copynumber: 3.2  Consensus size: 17

      21106 AGAAAAGAGC

                  *     *    
      21116 GAAAATACAAAAGAAAA
          1 GAAAATTCAAAAAAAAA

                 * *         
      21133 GAAAAATGAAAAAAAAA
          1 GAAAATTCAAAAAAAAA

                           * 
      21150 GAAAATTCAAAAAAAGA
          1 GAAAATTCAAAAAAAAA

               
      21167 GAA
          1 GAA

      21170 TGAAAAGAGA


Statistics
Matches: 30,  Mismatches: 7, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  17   30  1.00

ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07


Consensus pattern (17 bp):   
GAAAATTCAAAAAAAAA
Done.