Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold570
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: 38408
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:13619 original size:56 final size:51
Alignment explanation
Indices: 13547--13787 Score: 202
Period size: 50 Copynumber: 4.7 Consensus size: 51
13537 GGAATGAGAC
* * *
13547 CCCATGTAAGACCATGTCTGGGAGATGGCATTGGCATTATTGAGATTATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA--ACTGAG---ATGAGAGGT
* *
13603 CCCACGTAAGACCATGTTTGAGACATGGCATTGGC-ACTGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACTGAGATGAGAGGT
* * * * * **
13653 CCCCCGTAAGACCATGTCTAGGACATGGCATGGGC-ACCGATATGAGAACT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACTGAGATGAGAGGT
* * * * * * **
13703 CCCATGTAAGACCATATCTGGGATATGGCATTGGCAA-T-ACAGGAAACAT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACTGAGATGAGAGGT
* * *
13752 ACCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
13788 TGTTATTATC
Statistics
Matches: 154, Mismatches: 30, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
49 38 0.25
50 79 0.51
51 1 0.01
53 5 0.03
56 31 0.20
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (51 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACTGAGATGAGAGGT
Found at i:14013 original size:20 final size:20
Alignment explanation
Indices: 13988--14027 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13978 ATGAGTTATT
13988 CAAGTAAGTA-AGTAAGTAAA
1 CAAGTAAG-AGAGTAAGTAAA
14008 CAAGTAAGAGAGTAAGTAAA
1 CAAGTAAGAGAGTAAGTAAA
14028 GATCATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.17
Consensus pattern (20 bp):
CAAGTAAGAGAGTAAGTAAA
Found at i:15217 original size:13 final size:13
Alignment explanation
Indices: 15199--15223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15189 TCGTGATTGA
15199 CTCCGGCAACGGT
1 CTCCGGCAACGGT
15212 CTCCGGCAACGG
1 CTCCGGCAACGG
15224 AGTATCAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.32, T:0.12
Consensus pattern (13 bp):
CTCCGGCAACGGT
Found at i:17786 original size:205 final size:205
Alignment explanation
Indices: 17434--17844 Score: 705
Period size: 205 Copynumber: 2.0 Consensus size: 205
17424 TGGTTAGATT
* *
17434 TGATTGAGTGCAATTCAACCCTAGGATTGACAACCCTAGGAAGTTATTTATGTAGGAATTAACCC
1 TGATTGAGTGCAATTAAACCCTAGGATTGACAACCCTAGGAAGTTATTTAGGTAGGAATTAACCC
* *
17499 AAGATCAATATTGCCTACCAAGCATCACTTTACAAATTAGTGGTTAGGGAAGGAAGAACGTAAAC
66 AAAATCAATATTGCCTACCAAGCATCACTTTACAAATTAGTGGCTAGGGAAGGAAGAACGTAAAC
* * *
17564 CCTAGGATTGACAATCCTAGGAAGTCATATAGGTGTGAATTAACCTAAAATCAGTATTGCCTATC
131 CCCAGGATTAACAATCCTAGGAAGCCATATAGGTGTGAATTAACCTAAAATCAGTATTGCCTATC
17629 CTTGAAAACC
196 CTTGAAAACC
* *
17639 TGATTGATTGCAATTAAACCCTCGGATTGACAACCCTAGGAAGTTATTTAGGTAGGAATTAACCC
1 TGATTGAGTGCAATTAAACCCTAGGATTGACAACCCTAGGAAGTTATTTAGGTAGGAATTAACCC
* * *
17704 AAAATCAGTATTGCCTACCAAGCATCACTTTGCAAATTAGTGGCTAGGGAAGGAAGAATGTAAAC
66 AAAATCAATATTGCCTACCAAGCATCACTTTACAAATTAGTGGCTAGGGAAGGAAGAACGTAAAC
*
17769 CCCAGGATTAACAATCCTAGGAAGCCATATAGGTGTGAATTAACCTGAAATCAGTATTGCCTATC
131 CCCAGGATTAACAATCCTAGGAAGCCATATAGGTGTGAATTAACCTAAAATCAGTATTGCCTATC
17834 CTTGAAAACC
196 CTTGAAAACC
17844 T
1 T
17845 TACCCTACCT
Statistics
Matches: 193, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
205 193 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (205 bp):
TGATTGAGTGCAATTAAACCCTAGGATTGACAACCCTAGGAAGTTATTTAGGTAGGAATTAACCC
AAAATCAATATTGCCTACCAAGCATCACTTTACAAATTAGTGGCTAGGGAAGGAAGAACGTAAAC
CCCAGGATTAACAATCCTAGGAAGCCATATAGGTGTGAATTAACCTAAAATCAGTATTGCCTATC
CTTGAAAACC
Found at i:22370 original size:20 final size:20
Alignment explanation
Indices: 22345--22385 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
22335 CCAAGTAAGA
22345 ATGTTTGATGATGCTATATG
1 ATGTTTGATGATGCTATATG
22365 ATGTTTGATGATGCTATATG
1 ATGTTTGATGATGCTATATG
22385 A
1 A
22386 GATATAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (20 bp):
ATGTTTGATGATGCTATATG
Found at i:24946 original size:21 final size:21
Alignment explanation
Indices: 24921--24961 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24911 GGATCTACCC
24921 AAGAAA-AGAAGGAGAGAGAAG
1 AAGAAAGAGAAGGAG-GAGAAG
*
24942 AAGAAAGAGGAGGAGGAGAA
1 AAGAAAGAGAAGGAGGAGAA
24962 TTTGCGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (21 bp):
AAGAAAGAGAAGGAGGAGAAG
Found at i:26890 original size:15 final size:16
Alignment explanation
Indices: 26870--26900 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
26860 GCCCAGCACC
26870 TCATAACCATC-CTTT
1 TCATAACCATCACTTT
26885 TCATAACCATCACTTT
1 TCATAACCATCACTTT
26901 CATTTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (16 bp):
TCATAACCATCACTTT
Done.