Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1590
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: 5192
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Found at i:2241 original size:1 final size:1
Alignment explanation
Indices: 2230--2331 Score: 96
Period size: 1 Copynumber: 102.0 Consensus size: 1
2220 TGGCAATTGG
* * * ** * * * **
2230 AAAAGAAAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAAAACAAAACAAAAAAAGG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2295 AAAAAGAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2332 GTGAAGATTT
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:2282 original size:36 final size:36
Alignment explanation
Indices: 2229--2330 Score: 154
Period size: 36 Copynumber: 2.8 Consensus size: 36
2219 ATGGCAATTG
2229 GAAAAGAAAAAAAAACAAAACAAAAAAAAAGGAAAAA
1 GAAAA-AAAAAAAAACAAAACAAAAAAAAAGGAAAAA
2266 GAAAAAAAAAAAAACAAAAC--AAAAAAAGGAAAAA
1 GAAAAAAAAAAAAACAAAACAAAAAAAAAGGAAAAA
*
2300 GAAAAAAAAAAAAAAAAAAAACAAAAAAAAA
1 G--AAAAAAAAAAAAACAAAACAAAAAAAAA
2331 AGTGAAGATT
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
34 15 0.25
36 33 0.55
37 5 0.08
38 7 0.12
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (36 bp):
GAAAAAAAAAAAAACAAAACAAAAAAAAAGGAAAAA
Found at i:2299 original size:41 final size:40
Alignment explanation
Indices: 2230--2331 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 40
2220 TGGCAATTGG
* * *
2230 AAAAGAAAAA-AAAACAAAACAAAAAAAAAGGAAAAAGAAA
1 AAAAAAAAAACAAAACAAAA-AAAAAAAAAGAAAAAAAAAA
*
2270 AAAAAAAAAACAAAACAAAAAAAGGAAAAAGAAAAAAAAAA
1 AAAAAAAAAACAAAACAAAAAAA-AAAAAAGAAAAAAAAAA
2311 AAAAAAAAAACAAAA-AAAAAA
1 AAAAAAAAAACAAAACAAAAAA
2332 GTGAAGATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 18 0.32
41 38 0.68
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (40 bp):
AAAAAAAAAACAAAACAAAAAAAAAAAAAGAAAAAAAAAA
Found at i:4696 original size:79 final size:80
Alignment explanation
Indices: 4533--4739 Score: 217
Period size: 79 Copynumber: 2.6 Consensus size: 80
4523 GTTCAATCCC
* * * * *
4533 GTTTTTACTTCTAAAACACT-GAATTTTTCATCTCTGAGGATATTCCAACCTCATAATCTTTGAG
1 GTTTTTACTTCTAAAACACTAGAATTTTTCATCTCTGAGGATACTCCAACCCCACAATATCTGAG
* *
4597 GGACACTCGAACCCT
66 GGACACTCCAACCAT
* * * * *
4612 ATTTTTATTTCTAAAATA-TAGAATTTTTCATCTCTG-TGATACTCCAACCCCACCATATCTGAG
1 GTTTTTACTTCTAAAACACTAGAATTTTTCATCTCTGAGGATACTCCAACCCCACAATATCTGA-
* *
4675 GGGATATTCCAACCAT
65 GGGACACTCCAACCAT
* *
4691 GTTTTTACTTCTAAAACACTA-AAATTTTCATCT-TCAAGGATACTCCAAC
1 GTTTTTACTTCTAAAACACTAGAATTTTTCATCTCT-GAGGATACTCCAAC
4740 TCCTCCATCT
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
78 21 0.20
79 69 0.67
80 13 0.13
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (80 bp):
GTTTTTACTTCTAAAACACTAGAATTTTTCATCTCTGAGGATACTCCAACCCCACAATATCTGAG
GGACACTCCAACCAT
Found at i:4748 original size:26 final size:28
Alignment explanation
Indices: 4719--4791 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
4709 CTAAAATTTT
4719 CATCTTC-A-AGGATACTCCAACTCC-TC
1 CATCTTCAAGAGGATACTCCAAC-CCTTC
* * *
4745 CATCTTCGAGGGGATACTCTAACCCTTC
1 CATCTTCAAGAGGATACTCCAACCCTTC
*
4773 CATCTCCAAGAGGATACTC
1 CATCTTCAAGAGGATACTC
4792 TAATCCCTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 7 0.18
27 3 0.08
28 29 0.74
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (28 bp):
CATCTTCAAGAGGATACTCCAACCCTTC
Found at i:4757 original size:80 final size:78
Alignment explanation
Indices: 4533--4768 Score: 210
Period size: 79 Copynumber: 3.0 Consensus size: 78
4523 GTTCAATCCC
* * * * *
4533 GTTTTTACTTCTAAAACACTGAATTTTTCATCTCTGAGGATATTCCAACCTCAT-AATCTTTGA-
1 GTTTTTACTTCTAAAACACTAAATTTTTCATCTC--AGGATACTCCAA-CTCCTCCATCTTCGAG
* * *
4596 GGGACACTCGAACCCT
63 GGGATACTCCAACCAT
* * * * * * *
4612 ATTTTTATTTCTAAAATA-TAGAATTTTTCATCTCTGTGATACTCCAACCCCACCAT-ATCTGAG
1 GTTTTTACTTCTAAAACACTA-AATTTTTCATCTCAG-GATACTCCAACTCCTCCATCTTC-GAG
*
4675 GGGATATTCCAACCAT
63 GGGATACTCCAACCAT
*
4691 GTTTTTACTTCTAAAACACTAAAATTTTCATCTTCAAGGATACTCCAACTCCTCCATCTTCGAGG
1 GTTTTTACTTCTAAAACACTAAATTTTTCATC-TC-AGGATACTCCAACTCCTCCATCTTCGAGG
*
4756 GGATACTCTAACC
64 GGATACTCCAACC
4769 CTTCCATCTC
Statistics
Matches: 122, Mismatches: 26, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
77 4 0.03
78 14 0.11
79 65 0.53
80 36 0.30
81 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (78 bp):
GTTTTTACTTCTAAAACACTAAATTTTTCATCTCAGGATACTCCAACTCCTCCATCTTCGAGGGG
ATACTCCAACCAT
Found at i:4788 original size:108 final size:108
Alignment explanation
Indices: 4649--4877 Score: 264
Period size: 108 Copynumber: 2.1 Consensus size: 108
4639 TCATCTCTGT
** * ** * * *
4649 GATACTCCAACCCCACCATATCTGAGGGGATATTCCAA-CCATGTTTTTACTTCTAAAACACTAA
1 GATACTCCAACCCTTCCATCTCCAAGAGGATACTCCAATCCATGTTTTTACTTCCAAAAC-CTAA
* *
4713 AATTTTCATCT-TCAAGGATACTCCAACTCCTCCATCTTCGAGGG
65 AATTTTCATCTCT-AAGGATACTCCAACCCCACCATCTTCGAGGG
* * * * * *
4757 GATACTCTAACCCTTCCATCTCCAAGAGGATACTCTAATCCCTGTTTTTACTTCCACAACGTCAA
1 GATACTCCAACCCTTCCATCTCCAAGAGGATACTCCAATCCATGTTTTTACTTCCAAAACCTAAA
* *
4822 ATTTTCATCTCTAGGGATACTCCAACCCCACCATCTTCGAGTG
66 ATTTTCATCTCTAAGGATACTCCAACCCCACCATCTTCGAGGG
4865 GATACTCCAACCC
1 GATACTCCAACCC
4878 CATTTTTACT
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
108 81 0.81
109 19 0.19
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.29
Consensus pattern (108 bp):
GATACTCCAACCCTTCCATCTCCAAGAGGATACTCCAATCCATGTTTTTACTTCCAAAACCTAAA
ATTTTCATCTCTAAGGATACTCCAACCCCACCATCTTCGAGGG
Found at i:4792 original size:28 final size:28
Alignment explanation
Indices: 4727--4799 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
4717 TTCATCTTCA
* * *
4727 AGGATACTCCAACTCC-TCCATCTTCGAG
1 AGGATACTCTAAC-CCTTCCATCTCCAAG
*
4755 GGGATACTCTAACCCTTCCATCTCCAAG
1 AGGATACTCTAACCCTTCCATCTCCAAG
4783 AGGATACTCTAATCCCT
1 AGGATACTCTAA-CCCT
4800 GTTTTTACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 2 0.05
28 32 0.84
29 4 0.11
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (28 bp):
AGGATACTCTAACCCTTCCATCTCCAAG
Found at i:4907 original size:80 final size:80
Alignment explanation
Indices: 4755--4928 Score: 192
Period size: 80 Copynumber: 2.2 Consensus size: 80
4745 CATCTTCGAG
* ** * ** * *
4755 GGGATACTCTAACCCTTCCATCTCCAAGAGGATACTCTAATCCCTGTTTTTACTTCCACAACGTC
1 GGGATACTCCAACCCCACCATCTCCAAGAGGATACTCCAATCCCCATTTTTACTTCCAAAACCTC
4820 AAATTTTCATCTCTA
66 AAATTTTCATCTCTA
* * *
4835 GGGATACTCCAACCCCACCATCTTCGAGTGGATACTCCAA-CCCCATTTTTACTTCCAAAACACT
1 GGGATACTCCAACCCCACCATCTCCAAGAGGATACTCCAATCCCCATTTTTACTTCCAAAAC-CT
4899 -AAATTTTTCATCTCTA
65 CAAA-TTTTCATCTCTA
* *
4915 -GAACACTCCAACCC
1 GGGATACTCCAACCC
4929 TATTTTTTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
79 33 0.42
80 46 0.58
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (80 bp):
GGGATACTCCAACCCCACCATCTCCAAGAGGATACTCCAATCCCCATTTTTACTTCCAAAACCTC
AAATTTTCATCTCTA
Done.