Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2586
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: 24516
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:310 original size:10 final size:10
Alignment explanation
Indices: 280--304 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
270 TAATAAAAAT
280 GAAAATAATA
1 GAAAATAATA
290 GAAAATAATA
1 GAAAATAATA
300 GAAAA
1 GAAAA
305 ATATAGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (10 bp):
GAAAATAATA
Found at i:3976 original size:19 final size:19
Alignment explanation
Indices: 3947--3991 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
3937 TATTAGAATA
3947 TATTCATTCT-ATATATAGTC
1 TATT-ATTCTAAT-TATAGTC
*
3967 TATTATTCTAATTCTAGTC
1 TATTATTCTAATTATAGTC
3986 TATTAT
1 TATTAT
3992 ATTAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (19 bp):
TATTATTCTAATTATAGTC
Found at i:3994 original size:5 final size:5
Alignment explanation
Indices: 3986--4088 Score: 53
Period size: 5 Copynumber: 21.8 Consensus size: 5
3976 AATTCTAGTC
* * * *
3986 TATTA TATTA -A-TA TATTC TATTC TATTA -ATTC TATTA -ATTC TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* * *
4032 TATTA -A-TA TATTC TATTC TATTA -ATTC TATTA TTATATA TATTA CTA-TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TAT-TA TATTA -TATTA
4081 TA-TA TATT
1 TATTA TATT
4089 CTAATTTAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
3 4 0.05
4 19 0.25
5 44 0.57
6 8 0.10
7 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:4005 original size:23 final size:23
Alignment explanation
Indices: 3977--4054 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
3967 TATTATTCTA
*
3977 ATTCTAGTCTATTATATTAATAT
1 ATTCTATTCTATTATATTAATAT
*
4000 ATTCTATTCTATTA-A-T--TCT
1 ATTCTATTCTATTATATTAATAT
*
4019 ATT-AATTCTATTATATTAATAT
1 ATTCTATTCTATTATATTAATAT
4041 ATTCTATTCTATTA
1 ATTCTATTCTATTA
4055 ATTCTATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 9 0.20
19 6 0.13
20 1 0.02
21 1 0.02
22 6 0.13
23 22 0.49
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.55
Consensus pattern (23 bp):
ATTCTATTCTATTATATTAATAT
Found at i:4007 original size:18 final size:18
Alignment explanation
Indices: 3984--4056 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 18
3974 CTAATTCTAG
3984 TCTATTATATTAATATAT
1 TCTATTATATTAATATAT
*
4002 TCTATTCTATTAATTCTATTAAT
1 TCTATTATATTAA---TA-T-AT
4025 TCTATTATATTAATATAT
1 TCTATTATATTAATATAT
*
4043 TCTATTCTATTAAT
1 TCTATTATATTAAT
4057 TCTATTATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 27 0.57
19 1 0.02
20 2 0.04
21 2 0.04
22 1 0.02
23 14 0.30
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTATTATATTAATATAT
Found at i:4019 original size:9 final size:9
Alignment explanation
Indices: 4005--4063 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
3995 AATATATTCT
4005 ATTCTATTA
1 ATTCTATTA
4014 ATTCTATTA
1 ATTCTATTA
4023 ATTCTATT-
1 ATTCTATTA
4031 A---TATTA
1 ATTCTATTA
* *
4037 A-TATATTCT
1 ATTCTATT-A
4046 ATTCTATTA
1 ATTCTATTA
4055 ATTCTATTA
1 ATTCTATTA
4064 TTATATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
8 5 0.12
9 27 0.64
10 5 0.12
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTCTATTA
Found at i:4029 original size:41 final size:40
Alignment explanation
Indices: 3984--4091 Score: 164
Period size: 41 Copynumber: 2.7 Consensus size: 40
3974 CTAATTCTAG
3984 TCTATTATATTAATATATTCTATTCTATTAATTCTATTAAT
1 TCTATTATATTAATATATTCTATTCTATTAATTCTATT-AT
4025 TCTATTATATTAATATATTCTATTCTATTAATTCTATTAT
1 TCTATTATATTAATATATTCTATTCTATTAATTCTATTAT
* * *
4065 TATA-TATATTACTATATATATATTCTA
1 TCTATTATATTAATATAT-TCTATTCTA
4092 ATTTAACTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
39 12 0.19
40 13 0.21
41 38 0.60
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (40 bp):
TCTATTATATTAATATATTCTATTCTATTAATTCTATTAT
Found at i:4130 original size:20 final size:22
Alignment explanation
Indices: 4100--4159 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 22
4090 TAATTTAACT
*
4100 AATTTAATTTATTTAT-ATAT-
1 AATTTATTTTATTTATAATATA
*
4120 CATTTATTTTATTTATAATATA
1 AATTTATTTTATTTATAATATA
4142 AATTATAATTTTATTTAT
1 AATT-T-ATTTTATTTAT
4160 TTCATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.42
21 4 0.12
22 3 0.09
23 1 0.03
24 11 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTTATTTTATTTATAATATA
Found at i:13282 original size:11 final size:11
Alignment explanation
Indices: 13268--13304 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
13258 AGGATAATAT
13268 AATAAGTATAA
1 AATAAGTATAA
13279 AATAAGTAT-A
1 AATAAGTATAA
13289 AATAAGTATAA
1 AATAAGTATAA
*
13300 TATAA
1 AATAA
13305 TAAGGAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (11 bp):
AATAAGTATAA
Found at i:13292 original size:21 final size:19
Alignment explanation
Indices: 13240--13306 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
13230 AGATTTACTT
* *
13240 ATAATAGAATAAGTAATAAGG
1 ATAATATAATAAGT-ATAA-A
13261 ATAATATAATAAGTATAAA
1 ATAATATAATAAGTATAAA
*
13280 ATAAGTATAAATAAGTATAAT
1 ATAA-TAT-AATAAGTATAAA
13301 ATAATA
1 ATAATA
13307 AGGAATGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.10
20 9 0.22
21 28 0.68
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (19 bp):
ATAATATAATAAGTATAAA
Found at i:17854 original size:21 final size:21
Alignment explanation
Indices: 17814--17852 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17804 AAATCATGGA
17814 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
17835 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
17853 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:18218 original size:9 final size:8
Alignment explanation
Indices: 18203--18245 Score: 54
Period size: 7 Copynumber: 5.4 Consensus size: 8
18193 GTGTCGTAAG
18203 AAAGAAAT
1 AAAGAAAT
18211 ATAAGAAA-
1 A-AAGAAAT
18219 AAAGAAAT
1 AAAGAAAT
18227 ATAAGAAA-
1 A-AAGAAAT
18235 AAAGAAAT
1 AAAGAAAT
18243 AAA
1 AAA
18246 TAAAAGAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 12 0.39
8 7 0.23
9 12 0.39
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAGAAAT
Found at i:18224 original size:16 final size:16
Alignment explanation
Indices: 18203--18243 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
18193 GTGTCGTAAG
18203 AAAGAAATATAAGAAA
1 AAAGAAATATAAGAAA
18219 AAAGAAATATAAGAAA
1 AAAGAAATATAAGAAA
18235 AAAGAAATA
1 AAAGAAATA
18244 AATAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAGAAATATAAGAAA
Found at i:18225 original size:20 final size:19
Alignment explanation
Indices: 18200--18253 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 19
18190 GTCGTGTCGT
18200 AAGAAAGAAATATAAG--A
1 AAGAAAGAAATATAAGAAA
18217 AA-AAAGAAATATAAGAAAA
1 AAGAAAGAAATATAAG-AAA
* *
18236 AAGAAATAAATAAAAGAA
1 AAGAAAGAAATATAAGAA
18254 TCGAATACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
19 5 0.16
20 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (19 bp):
AAGAAAGAAATATAAGAAA
Found at i:21646 original size:22 final size:22
Alignment explanation
Indices: 21615--21659 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
21605 TCTTATTTAT
*
21615 ATTTATAATTTTTAAATAAAAA
1 ATTTAGAATTTTTAAATAAAAA
21637 ATTTAGAATTTTTAAATAAAAA
1 ATTTAGAATTTTTAAATAAAAA
21659 A
1 A
21660 AAAATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTTAGAATTTTTAAATAAAAA
Done.