Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 19
Found at i:261362 original size:20 final size:20
Alignment explanation
Indices: 261339--261390 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
261329 TTAAGTTACC
261339 TAATATATAATT-AATAGTAA
1 TAATATATAATTAAATA-TAA
* *
261359 TAATATTTTATTAAATATAA
1 TAATATATAATTAAATATAA
261379 -AAGTATATAATT
1 TAA-TATATAATT
261391 CTATTTATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
TAATATATAATTAAATATAA
Found at i:261431 original size:3 final size:3
Alignment explanation
Indices: 261423--261451 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
261413 TAAATGAAAA
261423 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
261452 ATACTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:262058 original size:2 final size:2
Alignment explanation
Indices: 262053--262085 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
262043 TGTGTGTATG
*
262053 TA TA TA TA TA TA TG TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
262086 GGTGAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:262066 original size:14 final size:14
Alignment explanation
Indices: 262049--262079 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
262039 ATAGTGTGTG
262049 TATGTATATATATA
1 TATGTATATATATA
262063 TATGTATATATATA
1 TATGTATATATATA
262077 TAT
1 TAT
262080 ATTATAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:272401 original size:6 final size:6
Alignment explanation
Indices: 272392--272526 Score: 67
Period size: 6 Copynumber: 23.0 Consensus size: 6
272382 TAAATTTAAA
*
272392 TATACT TATATT TATA-T TATATT TATATAAT T-T-TT TATATTAT TATATAT
1 TATATT TATATT TATATT TATATT TATAT--T TATATT TATA-T-T TATAT-T
* *
272442 TATA-T TATATT T-T-TT TATA-T TATATT TATATAA TATAAT TATA-T
1 TATATT TATATT TATATT TATATT TATATT TATAT-T TATATT TATATT
* * *
272486 CATATT TA-ATAT TATAATT T-TATT TATTTT TGTA-T TATATT
1 TATATT TATAT-T TAT-ATT TATATT TATATT TATATT TATATT
272527 ATAAGTGACG
Statistics
Matches: 101, Mismatches: 10, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
4 5 0.05
5 32 0.32
6 40 0.40
7 15 0.15
8 9 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:272413 original size:5 final size:5
Alignment explanation
Indices: 272392--272529 Score: 78
Period size: 5 Copynumber: 27.8 Consensus size: 5
272382 TAAATTTAAA
*
272392 TATACT TATATT TATAT TATAT T-TA- TATAAT T-TTT TATAT TAT-T
1 TATA-T TATA-T TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT
* * *
272436 ATATAT TATAT TATAT TTTTT TATAT TATAT T-TA- TATAA TATAAT TATAT
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT
* * *
272486 CATATT TAATAT TATAAT TTTAT T-TAT T-T-T TGTAT TATAT TATA
1 TATA-T T-ATAT TAT-AT TATAT TATAT TATAT TATAT TATAT TATA
272530 AGTGACGGCT
Statistics
Matches: 106, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
3 4 0.04
4 16 0.15
5 61 0.58
6 22 0.21
7 3 0.03
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:272505 original size:13 final size:12
Alignment explanation
Indices: 272397--272501 Score: 66
Period size: 11 Copynumber: 9.4 Consensus size: 12
272387 TTAAATATAC
272397 TTATATTT-ATA
1 TTATATTTAATA
272408 TTATATTT-ATA
1 TTATATTTAATA
* * *
272419 TAATTTTTTATA
1 TTATATTTAATA
*
272431 TTAT-TAT-ATA
1 TTATATTTAATA
272441 TTATA-TT-ATA
1 TTATATTTAATA
*
272451 TT-T-TTTTATA
1 TTATATTTAATA
272461 TTATATTTATATA
1 TTATATTTA-ATA
* *
272474 ATATAATT-ATA
1 TTATATTTAATA
*
272485 TCATATTTAATA
1 TTATATTTAATA
272497 TTATA
1 TTATA
272502 ATTTTATTTA
Statistics
Matches: 74, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
9 3 0.04
10 18 0.24
11 28 0.38
12 16 0.22
13 9 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATTTAATA
Found at i:272512 original size:53 final size:54
Alignment explanation
Indices: 272400--272512 Score: 144
Period size: 53 Copynumber: 2.1 Consensus size: 54
272390 AATATACTTA
** * *
272400 TATTTATATTATATTTATATAATTTTTTATATTATTATATATTATATTATATTT
1 TATTTATATTATATTTATATAATTAATTATATCATTATATATAATATTATATTT
272454 T-TTTATATTATATTTATATAATATAATTATATCA-TAT-T-TAATATTATAATTT
1 TATTTATATTATATTTATATAAT-TAATTATATCATTATATATAATATTAT-ATTT
272506 TATTTAT
1 TATTTAT
272513 TTTTGTATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
51 8 0.15
52 6 0.12
53 29 0.56
54 9 0.17
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (54 bp):
TATTTATATTATATTTATATAATTAATTATATCATTATATATAATATTATATTT
Found at i:274793 original size:21 final size:21
Alignment explanation
Indices: 274740--274798 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
274730 TTTGAGTTTG
*
274740 ATTAA-TTAAAATTTATAAAC
1 ATTAATTTAAAATTTTTAAAC
**
274760 ATT-ATTTAAAAATTTTTAATT
1 ATTAATTT-AAAATTTTTAAAC
274781 ATTAATTTAAAATTTTTA
1 ATTAATTTAAAATTTTTA
274799 TATTTAAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 23 0.70
22 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAATTTAAAATTTTTAAAC
Found at i:276513 original size:16 final size:16
Alignment explanation
Indices: 276492--276529 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
276482 TATTCAACCT
*
276492 TTTTTTTATAT-TTAAA
1 TTTTTTTAAATATT-AA
276508 TTTTTTTAAATATTAA
1 TTTTTTTAAATATTAA
276524 TTTTTT
1 TTTTTT
276530 CAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTAAATATTAA
Found at i:277422 original size:29 final size:27
Alignment explanation
Indices: 277360--277424 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
277350 TATTTTTATT
277360 TAAATTTAATATATATTAAAATAACAA
1 TAAATTTAATATATATTAAAATAACAA
*
277387 TAAAAATTTAATATTATTTTCAATAATAA-AA
1 T--AAATTTAATA-TATATT-AA-AATAACAA
277418 TAAATTT
1 TAAATTT
277425 TTGAATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
27 1 0.03
29 16 0.50
30 5 0.16
31 5 0.16
32 5 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATTTAATATATATTAAAATAACAA
Found at i:277756 original size:2 final size:2
Alignment explanation
Indices: 277751--277775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
277741 TTATCTTTAA
277751 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
277776 ATTCTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:278355 original size:31 final size:30
Alignment explanation
Indices: 278285--278341 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
278275 TCTATTCATG
*
278285 ATATTTAAAATATTTATTTTATTATTTTAA
1 ATATTTAAAATATATATTTTATTATTTTAA
278315 ATATATTAAAATA-ATATTTTA-TATTTT
1 ATAT-TTAAAATATATATTTTATTATTTT
278342 TATATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 11 0.44
31 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATATTTAAAATATATATTTTATTATTTTAA
Found at i:278996 original size:6 final size:6
Alignment explanation
Indices: 278980--279013 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
278970 TATTCGAATT
278980 TTTATTA TTTATA TTTATA TTTAATA TTTATA TT
1 TTTA-TA TTTATA TTTATA TTT-ATA TTTATA TT
279014 AAATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.62
7 10 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:279006 original size:13 final size:13
Alignment explanation
Indices: 278980--279019 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
278970 TATTCGAATT
278980 TTTATTATTT-ATA
1 TTTA-TATTTAATA
278993 TTTATATTTAATA
1 TTTATATTTAATA
*
279006 TTTATATTAAATA
1 TTTATATTTAATA
279019 T
1 T
279020 GTATTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATATTTAATA
Found at i:279310 original size:22 final size:22
Alignment explanation
Indices: 279268--279312 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
279258 GTCCATAAAT
*
279268 AAATTTGTAAAAATTATATATA
1 AAATTTGTAAAAATTAAATATA
*
279290 AAATTT-TAAAATTTAAAATATA
1 AAATTTGTAAAAATT-AAATATA
279312 A
1 A
279313 TTCCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTTGTAAAAATTAAATATA
Found at i:281362 original size:27 final size:27
Alignment explanation
Indices: 281332--281440 Score: 62
Period size: 28 Copynumber: 3.9 Consensus size: 27
281322 ATTCACCTTC
281332 ATTAAAATTAATAATTTATATATTTAT
1 ATTAAAATTAATAATTTATATATTTAT
* * *
281359 ATT-ATATTTATAAATTT-TATTATATCAT
1 ATTAAAATTAAT-AATTTATA-TAT-TTAT
* * * *
281387 AATAATATTTATAATATTTTATATTTAT
1 ATTAAAATTAATAAT-TTATATATTTAT
* *
281415 A-TAAATTTTAAAATATTTATATATTT
1 ATTAAA-ATTAATA-ATTTATATATTT
281441 TAATTTTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
26 8 0.12
27 14 0.22
28 25 0.39
29 15 0.23
30 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTAAAATTAATAATTTATATATTTAT
Found at i:281970 original size:14 final size:14
Alignment explanation
Indices: 281907--281976 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
281897 ATATTCAATT
*
281907 TATTTAAATAATTAA
1 TATTTAAAT-TTTAA
* * *
281922 TTTTTAAAATATAA
1 TATTTAAATTTTAA
*
281936 TATTTTATAAATTTAA
1 TA-TTTA-AATTTTAA
*
281952 CATTTAAATTTTAA
1 TATTTAAATTTTAA
281966 TATTT-AATTTT
1 TATTTAAATTTT
281977 TTTATTTCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
13 6 0.14
14 15 0.34
15 15 0.34
16 8 0.18
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTTAAATTTTAA
Found at i:283222 original size:17 final size:17
Alignment explanation
Indices: 283200--283234 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
283190 TTTAAAATTT
283200 ATATTTTAATATTTGTA
1 ATATTTTAATATTTGTA
**
283217 ATATTTTTTTATTTGTA
1 ATATTTTAATATTTGTA
283234 A
1 A
283235 ATTGTTGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (17 bp):
ATATTTTAATATTTGTA
Found at i:284197 original size:2 final size:2
Alignment explanation
Indices: 284192--284226 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
284182 AATGTGTGTG
284192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
284227 TAGAGGGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:286745 original size:22 final size:24
Alignment explanation
Indices: 286718--286763 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
286708 AAATTTTTTT
286718 ATAAA-TAAAATTATAA-AATTTA
1 ATAAACTAAAATTATAATAATTTA
*
286740 ATAAATCTAAATTTATAATAATTT
1 ATAAA-CTAAAATTATAATAATTT
286764 GCAGGTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAAACTAAAATTATAATAATTTA
Found at i:289062 original size:21 final size:23
Alignment explanation
Indices: 289038--289086 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
289028 AATATGACAC
* *
289038 ATTTATTAAT-AAA-TTTATTAT
1 ATTTATGAATAAAATTTTAATAT
289059 ATTTATGAATAAAATTTTAATAT
1 ATTTATGAATAAAATTTTAATAT
289082 ATTTA
1 ATTTA
289087 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTATGAATAAAATTTTAATAT
Found at i:289106 original size:19 final size:20
Alignment explanation
Indices: 289073--289111 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
289063 ATGAATAAAA
289073 TTTTAATATATTTAATATTT
1 TTTTAATATATTTAATATTT
*
289093 TTTTATTATA-TTAATATTT
1 TTTTAATATATTTAATATTT
289112 AGGTTAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATATATTTAATATTT
Found at i:290188 original size:46 final size:47
Alignment explanation
Indices: 290098--290188 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 47
290088 TAATTAACTT
* * *
290098 ATAATTTTTATATGAAAAAAAGTTATAAACTATTCAACACATAATTA
1 ATAATTTTTACATGAAAAAAAGCTATAAACTATTCAACAAATAATTA
* * * *
290145 ATAATTTTTGCATG-AAAGAAGCTATAAACTTTTCAATAAATAAT
1 ATAATTTTTACATGAAAAAAAGCTATAAACTATTCAACAAATAAT
290189 CCATAGCTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 25 0.68
47 12 0.32
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (47 bp):
ATAATTTTTACATGAAAAAAAGCTATAAACTATTCAACAAATAATTA
Found at i:291329 original size:20 final size:20
Alignment explanation
Indices: 291306--291371 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
291296 TGTATGCGTG
291306 AATTTAAATTAAATTTAATT
1 AATTTAAATTAAATTTAATT
*
291326 AATTTATATTAAA--T-ATT
1 AATTTAAATTAAATTTAATT
* *
291343 -A-TTAAAATAATATTTAATA
1 AATTTAAATTAA-ATTTAATT
291362 AATTTAAATT
1 AATTTAAATT
291372 TTAAAATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
15 7 0.20
16 2 0.06
17 3 0.09
18 2 0.06
19 2 0.06
20 13 0.37
21 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTAAATTAAATTTAATT
Found at i:291892 original size:20 final size:20
Alignment explanation
Indices: 291845--291892 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
291835 ATATTAATTC
*
291845 TTTTAAAATTTTAAAAAAAT
1 TTTTATAATTTTAAAAAAAT
** **
291865 TTAAATAATTTTAAATTAAT
1 TTTTATAATTTTAAAAAAAT
291885 TTTTATAA
1 TTTTATAA
291893 ACACTTGTTA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTATAATTTTAAAAAAAT
Found at i:294110 original size:22 final size:22
Alignment explanation
Indices: 294082--294123 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
294072 TTAAAAAAAT
* *
294082 TATTTTTATATTAATATTTATA
1 TATTTTTATAATAAAATTTATA
294104 TATTTTTATAATAAAATTTA
1 TATTTTTATAATAAAATTTA
294124 AATAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAATAAAATTTATA
Found at i:295047 original size:22 final size:21
Alignment explanation
Indices: 294984--295047 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 21
294974 AAATATAAAA
294984 ATAATAA-A-TAAATTATTTTT
1 ATAATAATATTAAA-TATTTTT
**
295004 ATAATAATATT-AATATAATT
1 ATAATAATATTAAATATTTTT
295024 ATAATTAA-ATTTAAATATTTTT
1 ATAA-TAATA-TTAAATATTTTT
295046 AT
1 AT
295048 TTTTTATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 17 0.49
21 8 0.23
22 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATAATATTAAATATTTTT
Found at i:295863 original size:5 final size:5
Alignment explanation
Indices: 295853--295880 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
295843 TAATCATTCA
295853 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
295881 TTAAATAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:296257 original size:20 final size:21
Alignment explanation
Indices: 296222--296333 Score: 78
Period size: 20 Copynumber: 5.5 Consensus size: 21
296212 TATTTATTCG
296222 TATATTTTATTATATTATA-AT
1 TATATTTTA-TATATTATATAT
296243 TATATTTTATATATT-TATAT
1 TATATTTTATATATTATATAT
* * *
296263 AATATTTAATATATTAAATA-
1 TATATTTTATATATTATATAT
*
296283 AAT-TTTTAAAATATATT-TATAT
1 TATATTTT---ATATATTATATAT
*
296305 TATATTTTA-ATTATTCTAT-T
1 TATATTTTATA-TATTATATAT
296325 TA-ATTTTAT
1 TATATTTTAT
296334 TAAGTGTATA
Statistics
Matches: 75, Mismatches: 6, Indels: 21
0.74 0.06 0.21
Matches are distributed among these distances:
19 12 0.16
20 32 0.43
21 18 0.24
22 9 0.12
23 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATTTTATATATTATATAT
Found at i:296308 original size:11 final size:11
Alignment explanation
Indices: 296222--296311 Score: 59
Period size: 11 Copynumber: 8.6 Consensus size: 11
296212 TATTTATTCG
296222 TATATTT-TAT
1 TATATTTATAT
296232 TATA-TTATAAT
1 TATATTTAT-AT
296243 TATATTT-TA-
1 TATATTTATAT
296252 TATATTTATAT
1 TATATTTATAT
*
296263 AATATTTA-A-
1 TATATTTATAT
*
296272 TATA-TTAAAT
1 TATATTTATAT
* * * *
296282 AAATTTTTAAAA
1 -TATATTTATAT
296294 TATATTTATAT
1 TATATTTATAT
296305 TATATTT
1 TATATTT
296312 TAATTATTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
8 3 0.05
9 13 0.21
10 9 0.15
11 30 0.48
12 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATATTTATAT
Found at i:297447 original size:18 final size:18
Alignment explanation
Indices: 297416--297459 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
297406 TTAGAATATT
* * *
297416 TTATTTAAATTTAAATTA
1 TTATTAAAAATTAAAATA
297434 TTATTAAAAATTAAAATA
1 TTATTAAAAATTAAAATA
297452 TT-TTAAAA
1 TTATTAAAA
297460 TATTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTAAAAATTAAAATA
Found at i:298466 original size:15 final size:15
Alignment explanation
Indices: 298448--298477 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
298438 TATTCAGTTT
*
298448 TAATCCGATTTTTAA
1 TAATCCAATTTTTAA
298463 TAATCCAATTTTTAA
1 TAATCCAATTTTTAA
298478 AAATTCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (15 bp):
TAATCCAATTTTTAA
Found at i:303748 original size:22 final size:22
Alignment explanation
Indices: 303723--303771 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
303713 AATTTATATT
* *
303723 ATATAAATATAAAATATTTTAA
1 ATATAAATATAAAATAATTAAA
* *
303745 ATATAATTATAATATAATTAAA
1 ATATAAATATAAAATAATTAAA
303767 ATATA
1 ATATA
303772 TGAATTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAAATATAAAATAATTAAA
Found at i:307930 original size:28 final size:26
Alignment explanation
Indices: 307871--307932 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
307861 TTTTTTTATA
307871 TTAA-TTAAATTTAAATAAAAATTTT
1 TTAATTTAAATTTAAATAAAAATTTT
307896 TAATAATTTAAA-TTAAATTAAATTAATTTT
1 T--TAATTTAAATTTAAA-TAAA--AATTTT
307926 TTAATTT
1 TTAATTT
307933 TTAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
25 1 0.03
27 8 0.26
28 15 0.48
30 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAATTTAAATTTAAATAAAAATTTT
Found at i:307960 original size:38 final size:38
Alignment explanation
Indices: 307924--308004 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
307914 TAAATTAATT
307924 TTTTAATTTTTAAATA-A-TA-AAAAATATTTTATTTAA
1 TTTTAA-TTTTAAATATATTATAAAAATATTTTATTTAA
307960 TTTTAATTTTAAATATTATTATAAAAATA-TTT-TTTAA
1 TTTTAATTTTAAATA-TATTATAAAAATATTTTATTTAA
307997 CTTTTAAT
1 -TTTTAAT
308005 ATCATTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
35 9 0.22
36 6 0.15
37 6 0.15
38 12 0.30
39 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (38 bp):
TTTTAATTTTAAATATATTATAAAAATATTTTATTTAA
Found at i:311844 original size:31 final size:30
Alignment explanation
Indices: 311807--311914 Score: 97
Period size: 26 Copynumber: 3.8 Consensus size: 30
311797 TTCGATAATT
311807 TATATTTATATTATATTATTATTAAATTTAA
1 TATATTTATATTATATTATTATT-AATTTAA
* * * *
311838 AATATTTATA-TAAATT-TTAATATTTTAA
1 TATATTTATATTATATTATTATTAATTTAA
*
311866 TA-ATTTATATTATATAATT-TTAA---AA
1 TATATTTATATTATATTATTATTAATTTAA
*
311891 TATTTTTATATTATATTA-TATTAA
1 TATATTTATATTATATTATTATTAA
311915 ATTTTTTAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
25 5 0.08
26 17 0.27
27 7 0.11
28 13 0.21
29 6 0.10
30 5 0.08
31 9 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TATATTTATATTATATTATTATTAATTTAA
Found at i:311859 original size:18 final size:18
Alignment explanation
Indices: 311825--311888 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
311815 TATTATATTA
*
311825 TTAT-TAAATTTAAAATAT
1 TTATATAAATTT-TAATAT
311843 TTATATAAATTTTAATAT
1 TTATATAAATTTTAATAT
311861 TT-TA-ATAA-TTT-ATA-
1 TTATATA-AATTTTAATAT
311875 TTATAT-AATTTTAA
1 TTATATAAATTTTAA
311889 AATATTTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
14 4 0.10
15 8 0.21
16 5 0.13
17 4 0.10
18 11 0.28
19 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATAAATTTTAATAT
Found at i:311905 original size:26 final size:24
Alignment explanation
Indices: 311869--311922 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
311859 ATTTTAATAA
*
311869 TTTATATTATATAATTTTAAAATATT
1 TTTATATTATATAATATT-AAAT-TT
*
311895 TTTATATTATATTATATTAAATTT
1 TTTATATTATATAATATTAAATTT
311919 TTTA
1 TTTA
311923 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 4 0.15
26 16 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATATTATATAATATTAAATTT
Found at i:311918 original size:33 final size:30
Alignment explanation
Indices: 311843--311936 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 30
311833 TTTAAAATAT
*
311843 TTATATAAATTTTAATATTTTAATAATTTATA
1 TTATATAAATTTTAATATTTTTAT-A-TTATA
311875 TTATAT-AATTTTAAAATATTTTTATATTATA
1 TTATATAAATTTT--AATATTTTTATATTATA
311906 TTATATTAAATTTTTTAA-ATTTTT-TATTATA
1 TTATA-TAAA--TTTTAATATTTTTATATTATA
311937 ATCATAGGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
31 23 0.42
32 14 0.25
33 14 0.25
35 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATATAAATTTTAATATTTTTATATTATA
Found at i:316624 original size:29 final size:29
Alignment explanation
Indices: 316587--316648 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
316577 ATTACTTTTA
* *
316587 ATTTTAAAATAAATTGTTAAAATAATATT
1 ATTTCAAAATAAATTATTAAAATAATATT
** *
316616 ATTTCAAAATATTTTATTAAAATATTATT
1 ATTTCAAAATAAATTATTAAAATAATATT
316645 ATTT
1 ATTT
316649 TTTGAGTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
ATTTCAAAATAAATTATTAAAATAATATT
Found at i:316626 original size:13 final size:14
Alignment explanation
Indices: 316610--316646 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
316600 TTGTTAAAAT
316610 AATATTATT-TCAA
1 AATATTATTATCAA
*
316623 AATATT-TTATTAA
1 AATATTATTATCAA
316636 AATATTATTAT
1 AATATTATTAT
316647 TTTTTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 2 0.10
13 15 0.71
14 4 0.19
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTATTATCAA
Found at i:317016 original size:15 final size:15
Alignment explanation
Indices: 316996--317031 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
316986 TAAGTATGAA
316996 TATAATAAATATTAT
1 TATAATAAATATTAT
*
317011 TATAATAAATTTTAT
1 TATAATAAATATTAT
317026 TA-AATA
1 TATAATA
317032 TTAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATAAATATTAT
Found at i:320763 original size:18 final size:16
Alignment explanation
Indices: 320731--320762 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
320721 ATTGATATAA
320731 ATATATTTAATTTTTT
1 ATATATTTAATTTTTT
320747 ATATATTTAATTTTTT
1 ATATATTTAATTTTTT
320763 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATATATTTAATTTTTT
Found at i:320777 original size:14 final size:14
Alignment explanation
Indices: 320760--320793 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
320750 TATTTAATTT
320760 TTTTAAAAATTATA
1 TTTTAAAAATTATA
* *
320774 TTTTTAAATTTATA
1 TTTTAAAAATTATA
320788 TTTTAA
1 TTTTAA
320794 TATATATAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTAAAAATTATA
Found at i:324348 original size:18 final size:18
Alignment explanation
Indices: 324325--324362 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
324315 CTCTAGCATG
324325 CAAATTATGTATCTTTCT
1 CAAATTATGTATCTTTCT
324343 CAAATTATGTATCTTTCT
1 CAAATTATGTATCTTTCT
324361 CA
1 CA
324363 TTGTTCTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (18 bp):
CAAATTATGTATCTTTCT
Found at i:324457 original size:14 final size:14
Alignment explanation
Indices: 324440--324478 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
324430 TTTTCCATTG
324440 AAAAAAAAGGAAAA
1 AAAAAAAAGGAAAA
324454 AAAAAAAA-GAAAA
1 AAAAAAAAGGAAAA
* *
324467 AGAAAAGAGGAA
1 AAAAAAAAGGAA
324479 TGCCCTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGGAAAA
Found at i:326110 original size:2 final size:2
Alignment explanation
Indices: 326103--326135 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
326093 ATTTTATCTG
326103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
326136 TCTTTGCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:334906 original size:2 final size:2
Alignment explanation
Indices: 334901--334930 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
334891 TAGTATACGA
334901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
334931 TGTTCATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:337345 original size:58 final size:58
Alignment explanation
Indices: 337268--337382 Score: 212
Period size: 58 Copynumber: 2.0 Consensus size: 58
337258 ATATATTTAC
*
337268 GATTAATTACTACTGTATCATAATTATAAATTGTTTTATTTAAAACTTATAAATATAT
1 GATTAATTACTACTATATCATAATTATAAATTGTTTTATTTAAAACTTATAAATATAT
*
337326 GATTAATTATTACTATATCATAATTATAAATTGTTTTATTTAAAACTTATAAATATA
1 GATTAATTACTACTATATCATAATTATAAATTGTTTTATTTAAAACTTATAAATATA
337383 AATAAGAGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (58 bp):
GATTAATTACTACTATATCATAATTATAAATTGTTTTATTTAAAACTTATAAATATAT
Found at i:337377 original size:29 final size:29
Alignment explanation
Indices: 337287--337385 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
337277 CTACTGTATC
*
337287 ATAATTATAAATTGTTTTATTTAAAACTT
1 ATAAATATAAATTGTTTTATTTAAAACTT
* * **
337316 ATAAATAT--A-TG-ATTAATTATTACTAT
1 ATAAATATAAATTGTTTTATTTAAAACT-T
337342 ATCATAATTATAAATTGTTTTATTTAAAACTT
1 AT-A-AA-TATAAATTGTTTTATTTAAAACTT
337374 ATAAATATAAAT
1 ATAAATATAAAT
337386 AAGAGTAATC
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
25 9 0.17
26 5 0.09
27 2 0.04
28 2 0.04
29 17 0.32
30 2 0.04
31 2 0.04
32 5 0.09
33 9 0.17
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (29 bp):
ATAAATATAAATTGTTTTATTTAAAACTT
Found at i:337466 original size:9 final size:9
Alignment explanation
Indices: 337445--337480 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
337435 GAAAGAGAAT
337445 TAAAATAAAA
1 TAAAAT-AAA
337455 TAAAATAAA
1 TAAAATAAA
*
337464 TAAAGTAAA
1 TAAAATAAA
337473 TAAAATAA
1 TAAAATAA
337481 TAGCATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
TAAAATAAA
Found at i:337763 original size:2 final size:2
Alignment explanation
Indices: 337756--337794 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
337746 AAACATTTGA
337756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
337795 AAGGGGAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:340882 original size:8 final size:8
Alignment explanation
Indices: 340857--340933 Score: 52
Period size: 8 Copynumber: 9.5 Consensus size: 8
340847 ATATAAATAT
340857 TATATAAA
1 TATATAAA
*
340865 TACATAAA
1 TATATAAA
*
340873 TATATCAA
1 TATATAAA
340881 TATAT-AA
1 TATATAAA
*
340888 TATA-AAT
1 TATATAAA
*
340895 TAT-TTAA
1 TATATAAA
340902 TATATTAAAA
1 TATA-T-AAA
*
340912 TTTATATAA
1 TATATA-AA
340921 TATTATAAA
1 TA-TATAAA
340930 TATA
1 TATA
340934 ATTATAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
7 14 0.26
8 21 0.40
9 9 0.17
10 9 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (8 bp):
TATATAAA
Found at i:343421 original size:11 final size:9
Alignment explanation
Indices: 343397--343502 Score: 58
Period size: 9 Copynumber: 11.3 Consensus size: 9
343387 TATAATATAA
343397 ATAAATATT
1 ATAAATATT
*
343406 ATAAATATG
1 ATAAATATT
343415 ATATAA-ATT
1 ATA-AATATT
*
343424 ATTAATATT
1 ATAAATATT
*
343433 ATAAATTTT
1 ATAAATATT
343442 ATATAA-ATAT
1 ATA-AATAT-T
*
343452 AAAATATATT
1 ATAA-ATATT
*
343462 TTAAATACGATT
1 ATAAAT---ATT
*
343474 AT-AATATG
1 ATAAATATT
343482 ATAAA-ATTT
1 ATAAATA-TT
343491 ATAAATATT
1 ATAAATATT
343500 ATA
1 ATA
343503 TAAATATATG
Statistics
Matches: 73, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
8 7 0.10
9 45 0.62
10 12 0.16
11 5 0.07
12 4 0.05
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (9 bp):
ATAAATATT
Found at i:343516 original size:27 final size:28
Alignment explanation
Indices: 343369--343511 Score: 114
Period size: 29 Copynumber: 5.0 Consensus size: 28
343359 CTAAGAATAC
* * *
343369 TAAATATTAT-TATACGAATATAATATAAA
1 TAAATATTATAAATATG-ATATAA-ATATA
343398 TAAATATTATAAATATGATATAAAT-TA
1 TAAATATTATAAATATGATATAAATATA
* * *
343425 TTAATATTATAAATTTTATATAAATATA
1 TAAATATTATAAATATGATATAAATATA
* * *
343453 AAATATATTTTAAATACGAT-TATAATATGA
1 TAA-ATATTATAAATATGATATA-AATAT-A
*
343483 TAAA-ATTTATAAATATTATATAAATATA
1 TAAATA-TTATAAATATGATATAAATATA
343511 T
1 T
343512 GAATTATCGA
Statistics
Matches: 91, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
27 23 0.25
28 10 0.11
29 49 0.54
30 9 0.10
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
TAAATATTATAAATATGATATAAATATA
Found at i:343700 original size:2 final size:2
Alignment explanation
Indices: 343688--343723 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
343678 TAATTAAGAT
*
343688 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
343724 ACTCATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:343806 original size:22 final size:23
Alignment explanation
Indices: 343776--343823 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
343766 TGGAGTTTAT
343776 AAAAGGT-AAGAA-AAAAAACTTA
1 AAAAGGTAAAGAATAAAAAA-TTA
* *
343798 AAAATGTAAAGAATCAAAAATTA
1 AAAAGGTAAAGAATAAAAAATTA
343821 AAA
1 AAA
343824 TATATAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (23 bp):
AAAAGGTAAAGAATAAAAAATTA
Found at i:345315 original size:15 final size:16
Alignment explanation
Indices: 345290--345319 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
345280 GTAATAGTTA
345290 ATAATTTTATTTATTT
1 ATAATTTTATTTATTT
345306 ATAA-TTTATTTATT
1 ATAATTTTATTTATT
345320 ATTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATAATTTTATTTATTT
Found at i:345323 original size:18 final size:19
Alignment explanation
Indices: 345295--345333 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
345285 AGTTAATAAT
*
345295 TTTATTTATTTATAATTTA
1 TTTATTTATTTATAATATA
*
345314 TTTA-TTATTTTTAATATA
1 TTTATTTATTTATAATATA
345332 TT
1 TT
345334 CAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTTATTTATAATATA
Found at i:345982 original size:10 final size:10
Alignment explanation
Indices: 345967--346042 Score: 57
Period size: 10 Copynumber: 7.7 Consensus size: 10
345957 AGCCAAAATT
345967 ATATATTAAA
1 ATATATTAAA
345977 ATATATTAAA
1 ATATATTAAA
* *
345987 GTATTTTAAA
1 ATATATTAAA
* *
345997 AAATATTTAA
1 ATATATTAAA
* *
346007 AT-TAATAAT
1 ATATATTAAA
346016 ATATATTATAA
1 ATATATTA-AA
* *
346027 TTAAATTAAA
1 ATATATTAAA
346037 A-ATATT
1 ATATATT
346043 TATTATTTAT
Statistics
Matches: 48, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
9 10 0.21
10 31 0.65
11 7 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (10 bp):
ATATATTAAA
Found at i:346031 original size:24 final size:25
Alignment explanation
Indices: 346003--346057 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
345993 TAAAAAATAT
*
346003 TTAAATTAATAATATATATTA-TAA
1 TTAAATTAAAAATATATATTATTAA
* *
346027 TTAAATTAAAAATATTTATTATTTA
1 TTAAATTAAAAATATATATTATTAA
346052 TTAAAT
1 TTAAAT
346058 ATTAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAAATTAAAAATATATATTATTAA
Found at i:346472 original size:22 final size:22
Alignment explanation
Indices: 346442--346485 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
346432 CCCTTACGTT
* * *
346442 ATAATATAAGAGATTATTAAAA
1 ATAAAATAAGAAATGATTAAAA
346464 ATAAAATAAGAAATGATTAAAA
1 ATAAAATAAGAAATGATTAAAA
346486 TATATTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (22 bp):
ATAAAATAAGAAATGATTAAAA
Found at i:346666 original size:29 final size:29
Alignment explanation
Indices: 346598--346666 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
346588 AATTTTAGAG
346598 AATAATTATTAAGATAATTTTTTATATCTAA
1 AATAATTA--AAGATAATTTTTTATATCTAA
** * *
346629 AATTTTTAAAGATAATTTTTTCTCT-TAA
1 AATAATTAAAGATAATTTTTTATATCTAA
346657 ACATAATTAA
1 A-ATAATTAA
346667 TTGTCCTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 4 0.13
29 21 0.68
31 6 0.19
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (29 bp):
AATAATTAAAGATAATTTTTTATATCTAA
Found at i:347839 original size:20 final size:18
Alignment explanation
Indices: 347814--347858 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
347804 ACCAATTATT
*
347814 AATTATTATATTTAATATAA
1 AATTATTAT-TATAA-ATAA
347834 AATTATTATTATAAATAA
1 AATTATTATTATAAATAA
347852 AA-TATTA
1 AATTATTA
347859 ATTAATCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 4 0.17
20 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTATTATTATAAATAA
Found at i:347862 original size:18 final size:20
Alignment explanation
Indices: 347814--347862 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
347804 ACCAATTATT
347814 AATTATTATATT-TAATATAA
1 AATTATTA-ATTATAATATAA
347834 AATTATT-ATTATAA-ATAA
1 AATTATTAATTATAATATAA
347852 AA-TATTAATTA
1 AATTATTAATTA
347863 ATCTTAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.15
18 13 0.48
19 3 0.11
20 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTATTAATTATAATATAA
Found at i:348483 original size:17 final size:17
Alignment explanation
Indices: 348463--348512 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 17
348453 AAAATAATTT
348463 ATATTTAATAAATTTTA
1 ATATTTAATAAATTTTA
348480 ATATATTAAT-AA-TTTA
1 ATAT-TTAATAAATTTTA
*
348496 AT-TAT-ATAAATTTTA
1 ATATTTAATAAATTTTA
348511 AT
1 AT
348513 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 7 0.24
16 6 0.21
17 6 0.21
18 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTTAATAAATTTTA
Found at i:348531 original size:20 final size:20
Alignment explanation
Indices: 348473--348531 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 20
348463 ATATTTAATA
*
348473 AATTTTAATATATTAATAATTT
1 AATTTTAAT-TA-TATTAATTT
*
348495 AATTATATAA--ATTTTAATTT
1 AATT-T-TAATTATATTAATTT
348515 AATTTTAATTATATTAA
1 AATTTTAATTATATTAA
348532 ATAATTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 17 0.57
21 1 0.03
22 4 0.13
23 1 0.03
24 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTTAATTATATTAATTT
Found at i:353378 original size:21 final size:22
Alignment explanation
Indices: 353353--353394 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
353343 GCTCTTCTAG
*
353353 TTATT-TCTTAGGATTTTTTAA
1 TTATTATCTTAAGATTTTTTAA
*
353374 TTATTATTTTAAGATTTTTTA
1 TTATTATCTTAAGATTTTTTA
353395 TATTTAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (22 bp):
TTATTATCTTAAGATTTTTTAA
Found at i:353798 original size:2 final size:2
Alignment explanation
Indices: 353791--353830 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
353781 AAAGTTAGTG
353791 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
353831 AAAGTGACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:355076 original size:41 final size:44
Alignment explanation
Indices: 355027--355122 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 44
355017 TTATTTTTAA
355027 TATT-TTATTTTAAAATA-AT-TTTTAAAAATAATATTTAAT-T
1 TATTATTATTTTAAAATATATATTTTAAAAATAATATTTAATAT
* * *
355067 TATTATTA--TTAAATTATATATTTTAAAATTTATATTTAATAT
1 TATTATTATTTTAAAATATATATTTTAAAAATAATATTTAATAT
355109 TATTAAATTATTTT
1 TATT--ATTATTTT
355123 CTTATTTCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
39 7 0.16
40 6 0.13
41 21 0.47
42 5 0.11
44 4 0.09
46 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (44 bp):
TATTATTATTTTAAAATATATATTTTAAAAATAATATTTAATAT
Found at i:356007 original size:18 final size:18
Alignment explanation
Indices: 355980--356025 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
355970 TAAATTTTAT
*
355980 TTAA-AATATTTTATAT-
1 TTAATAATATTTAATATG
355996 TTATATAATATTTAATATG
1 TTA-ATAATATTTAATATG
356015 TTAATAATATT
1 TTAATAATATT
356026 ACATTCGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 19 0.73
19 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTAATAATATTTAATATG
Found at i:356294 original size:3 final size:3
Alignment explanation
Indices: 356286--356320 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
356276 TTCCAGGCAG
*
356286 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT ATT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
356321 GATTCTAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:358558 original size:2 final size:2
Alignment explanation
Indices: 358551--358586 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
358541 AAGTTTCTTC
358551 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
358587 GGAGAGACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:358841 original size:2 final size:2
Alignment explanation
Indices: 358834--358867 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
358824 GTCGATGTTT
358834 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
358868 CAAAGTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:359087 original size:2 final size:2
Alignment explanation
Indices: 359080--359140 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
359070 CAATGAGCAC
* * *
359080 AT AT AT AT AT AT AT AT A- AT AT AT GT AT AT AT GT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
359121 AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT
359141 CCATGCCTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:359423 original size:19 final size:20
Alignment explanation
Indices: 359401--359445 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
359391 ATTTAAATTA
* *
359401 ATTTAATTAAAATTAT-TTT
1 ATTTAATAAAAATAATATTT
359420 ATTTAATAAAAATAATATTT
1 ATTTAATAAAAATAATATTT
359440 ATTTAA
1 ATTTAA
359446 ATTTATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAATAAAAATAATATTT
Found at i:359957 original size:50 final size:50
Alignment explanation
Indices: 359898--360184 Score: 450
Period size: 50 Copynumber: 5.8 Consensus size: 50
359888 TATACTTAGA
* * *
359898 GTCAACAATTATGACCACATTTCTCTATTGTCAAAAGTTGGTGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
359948 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
359998 GTCAACAATTATGACCACTTCTCT-TATTGTCAAAGGTTGATGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
360047 GTCAATAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
360097 GTTAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
360147 ATCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGT
360185 ACTTTCCACC
Statistics
Matches: 219, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
49 43 0.20
50 176 0.80
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:360073 original size:99 final size:100
Alignment explanation
Indices: 359898--360184 Score: 461
Period size: 99 Copynumber: 2.9 Consensus size: 100
359888 TATACTTAGA
* *
359898 GTCAACAATTATGACCACATT-TCTCTATTGTCAAAAGTTGGTGAAGAATCGTCAACAATTATGA
1 GTCAACAATTATGACCAC-TTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGG
359962 CCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
65 CCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
* *
359998 GTCAACAATTATGACCACTTCTCT-TATTGTCAAAGGTTGATGAAGAATCGTCAATAATTATGGC
1 GTCAACAATTATGACCACTTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
* *
360062 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
66 CACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
* * * *
360097 GTTAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCATCAACAATTATGGC
1 GTCAACAATTATGACCACTTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
360162 CACCTCTCTCTATTGTCAAAGGT
66 CACCTCTCTCTATTGTCAAAGGT
360185 ACTTTCCACC
Statistics
Matches: 172, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
99 92 0.53
100 80 0.47
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (100 bp):
GTCAACAATTATGACCACTTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGC
CACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
Found at i:364631 original size:50 final size:49
Alignment explanation
Indices: 364574--364729 Score: 188
Period size: 50 Copynumber: 3.1 Consensus size: 49
364564 TAAAGTCGAT
* *
364574 AATTATGGTCACATTTCTCTATTGTCAAAAGTTGGTGAAGAATCGTCAAT
1 AATTATGGTCAC-TTTCTTTATTGTCAAAAGTTGGTGAAGAATCGTCAAC
* *
364624 AATTATGGTCACTTTCTTTTATTGTCAAAGGTTGGTGAAGAATCATCAAC
1 AATTATGGTCACTTTC-TTTATTGTCAAAAGTTGGTGAAGAATCGTCAAC
* * * * *
364674 AATTACGATCACCTCTCTTTATTGTCAAGAA-TTGATGAAAAATCGTCAAC
1 AATTATGGTCA-CTTTCTTTATTGTCAA-AAGTTGGTGAAGAATCGTCAAC
364724 AATTAT
1 AATTAT
364730 TATCATCTCT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
49 4 0.04
50 82 0.90
51 5 0.05
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (49 bp):
AATTATGGTCACTTTCTTTATTGTCAAAAGTTGGTGAAGAATCGTCAAC
Found at i:364740 original size:50 final size:48
Alignment explanation
Indices: 364574--364751 Score: 169
Period size: 50 Copynumber: 3.6 Consensus size: 48
364564 TAAAGTCGAT
* * * *
364574 AATTATGGTCACATTTCTCTATTGTCAAAAGTTGGTGAAGAATCGTCAAT
1 AATTATGATCAC-TCTCTTTATTGTCAAAA-TTGGTGAAGAATCGTCAAC
* * * *
364624 AATTATGGTCACTTTCTTTTATTGTCAAAGGTTGGTGAAGAATCATCAAC
1 AATTATGATCACTCTC-TTTATTGTCAAA-ATTGGTGAAGAATCGTCAAC
* * *
364674 AATTACGATCACCTCTCTTTATTGTCAAGAATTGATGAAAAATCGTCAAC
1 AATTATGATCA-CTCTCTTTATTGTCAA-AATTGGTGAAGAATCGTCAAC
* * *
364724 AATTATTATCA-TCTCTCTATTATCAAAA
1 AATTATGATCACTCTCTTTATTGTCAAAA
364752 ATACTTTTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
47 2 0.02
48 13 0.12
49 4 0.04
50 85 0.78
51 5 0.05
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (48 bp):
AATTATGATCACTCTCTTTATTGTCAAAATTGGTGAAGAATCGTCAAC
Found at i:365624 original size:21 final size:21
Alignment explanation
Indices: 365600--365655 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
365590 GATTCGGATT
*
365600 AAATTAAAAATAATTACAATA
1 AAATTAAAAATAATAACAATA
* * * *
365621 AAATTAAATATTATAATATTA
1 AAATTAAAAATAATAACAATA
*
365642 AAATTAAAATTAAT
1 AAATTAAAAATAAT
365656 GATAATATAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTAAAAATAATAACAATA
Found at i:365677 original size:29 final size:27
Alignment explanation
Indices: 365619--365679 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
365609 ATAATTACAA
*
365619 TAAAATTAAATATTATAATATTAAAAT
1 TAAAATTAAATAATATAATATTAAAAT
*
365646 TAAAATTAATGATAATATACAT-TTAAATT
1 TAAAATTAA--ATAATATA-ATATTAAAAT
365675 TAAAA
1 TAAAA
365680 ATATTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.31
29 18 0.62
30 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAATTAAATAATATAATATTAAAAT
Found at i:366306 original size:16 final size:16
Alignment explanation
Indices: 366266--366310 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
366256 TTTGAATCGG
* *
366266 GTTATTTTAAATTGAA
1 GTTATTTTAATTTTAA
*
366282 ATT-TTTTAATTTTAA
1 GTTATTTTAATTTTAA
366297 GTTATTTTAATTTT
1 GTTATTTTAATTTT
366311 TTTTTATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (16 bp):
GTTATTTTAATTTTAA
Found at i:366514 original size:2 final size:2
Alignment explanation
Indices: 366501--366534 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
366491 AATTCCTCCG
*
366501 TA TA TCA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
366535 GCAGAATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:366933 original size:5 final size:5
Alignment explanation
Indices: 366892--366947 Score: 51
Period size: 5 Copynumber: 10.4 Consensus size: 5
366882 TAAATATTAA
*
366892 AAATT ATAATT -AATT ATTATT AAAATT AAATAAT AAATT AAATT AAATT
1 AAATT A-AATT AAATT A-AATT -AAATT AAAT--T AAATT AAATT AAATT
366941 AAATT AA
1 AAATT AA
366948 TTTTTAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 4 0.09
5 23 0.53
6 10 0.23
7 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AAATT
Found at i:368501 original size:32 final size:31
Alignment explanation
Indices: 368461--368520 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
368451 GCGTACTCTA
**
368461 TTTAATTTTTAAATTGTATAATTTATATATT
1 TTTAATTTTTAAATAATATAATTTATATATT
*
368492 TTTATATTTTTATATAATATAATTTATAT
1 TTTA-ATTTTTAAATAATATAATTTATAT
368521 TATATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTAATTTTTAAATAATATAATTTATATATT
Found at i:368519 original size:14 final size:14
Alignment explanation
Indices: 368500--368538 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
368490 TTTTTATATT
368500 TTTATATAATATAA
1 TTTATATAATATAA
*
368514 TTTATATTATATAA
1 TTTATATAATATAA
**
368528 AATATATAATA
1 TTTATATAATA
368539 ATACATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTATATAATATAA
Found at i:374186 original size:20 final size:20
Alignment explanation
Indices: 374161--374199 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
374151 TATATTTAAT
374161 ATATATTTTAAAAAA-ATTTC
1 ATATA-TTTAAAAAATATTTC
374181 ATATATTTAAAAAATATTT
1 ATATATTTAAAAAATATTT
374200 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATTTAAAAAATATTTC
Found at i:375875 original size:20 final size:18
Alignment explanation
Indices: 375844--375882 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
375834 ATTTTTCAAT
*
375844 AATTTTTTAAATATATAA
1 AATTTTTTAAATAAATAA
375862 AATTTTTTAAAAATAAATAA
1 AATTTTTT--AAATAAATAA
375882 A
1 A
375883 TAAATTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTTTTAAATAAATAA
Found at i:376224 original size:15 final size:15
Alignment explanation
Indices: 376201--376230 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
376191 AGATCAATTT
*
376201 ACCTTAAAAAAAAAA
1 ACCTAAAAAAAAAAA
376216 ACCTAAAAAAAAAAA
1 ACCTAAAAAAAAAAA
376231 GTGTATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (15 bp):
ACCTAAAAAAAAAAA
Found at i:376509 original size:18 final size:18
Alignment explanation
Indices: 376482--376532 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
376472 TCATTCAAAT
376482 TGCCGACTTTCCTTCAAC
1 TGCCGACTTTCCTTCAAC
*
376500 TGCCGGCTTTCCTTCAAC
1 TGCCGACTTTCCTTCAAC
*
376518 GGCCGACTTTCCTTC
1 TGCCGACTTTCCTTC
376533 TGACAAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.12, C:0.39, G:0.16, T:0.33
Consensus pattern (18 bp):
TGCCGACTTTCCTTCAAC
Found at i:392371 original size:23 final size:24
Alignment explanation
Indices: 392340--392384 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
392330 ATTTTTTATT
*
392340 AATTATAAATAATAAATATAAATA
1 AATTATAAATAAAAAATATAAATA
*
392364 AATT-TAAATAAAAAATTTAAA
1 AATTATAAATAAAAAATATAAA
392385 ATTTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTATAAATAAAAAATATAAATA
Found at i:392630 original size:48 final size:48
Alignment explanation
Indices: 392527--392625 Score: 119
Period size: 52 Copynumber: 2.0 Consensus size: 48
392517 ATTCCATCAG
*
392527 ATAAATTTAATTTAAATTATTATTATTTAATAATAAAAAATATTTTAT
1 ATAAATTTAATTTAAATTATTAATATTTAATAATAAAAAATATTTTAT
* *
392575 ATAAATTTAATTATAAAATTATATAAATATTTAA-CATAAAACAATTTTTTA
1 ATAAATTTAATT-T-AAATTAT-T-AATATTTAATAATAAAA-AATATTTTA
392626 AATTTTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
48 12 0.28
49 1 0.02
50 7 0.16
51 7 0.16
52 16 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (48 bp):
ATAAATTTAATTTAAATTATTAATATTTAATAATAAAAAATATTTTAT
Found at i:394445 original size:2 final size:2
Alignment explanation
Indices: 394438--394477 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
394428 CATTAATTTC
394438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394478 ATAAAGGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:394833 original size:2 final size:2
Alignment explanation
Indices: 394826--394865 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
394816 ATACACAAGT
394826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
394866 AAGAAGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:396826 original size:26 final size:28
Alignment explanation
Indices: 396777--396829 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
396767 ATAAAATCTT
396777 AAATAAAAAATTATTAATACTTATACAA
1 AAATAAAAAATTATTAATACTTATACAA
* *
396805 AAATAAAATATT-TTAAT-TTTATACA
1 AAATAAAAAATTATTAATACTTATACA
396830 CTTTAAGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 5 0.22
28 11 0.48
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATAAAAAATTATTAATACTTATACAA
Found at i:399532 original size:20 final size:19
Alignment explanation
Indices: 399508--399559 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
399498 TTAATTTTTA
399508 AAATTTTATTATTA-ATAAT
1 AAATTTTATTATTACAT-AT
399527 ATAA-TTTATATATTACATAT
1 A-AATTTTAT-TATTACATAT
*
399547 AATTTTTATTATT
1 AAATTTTATTATT
399560 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 11 0.39
20 15 0.54
21 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTTTATTATTACATAT
Found at i:399979 original size:25 final size:25
Alignment explanation
Indices: 399923--399979 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
399913 ATCATTTTAT
399923 TATAATTTTTTTAAAATAAATATAA
1 TATAATTTTTTTAAAATAAATATAA
* *
399948 -ATTATTTTTATTTAAAT-AATATAA
1 TATAATTTTT-TTAAAATAAATATAA
399972 TATAATTT
1 TATAATTT
399980 AATTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATAATTTTTTTAAAATAAATATAA
Found at i:402217 original size:17 final size:18
Alignment explanation
Indices: 402167--402217 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
402157 AGTTATTTAA
*
402167 TTATCATTTTAAAT-TTT
1 TTATCATTATAAATATTT
402184 TTATGCATTA-AATATATTT
1 TTAT-CATTATAA-ATATTT
402203 TT-TCATTATAAATAT
1 TTATCATTATAAATAT
402218 CATCTTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 15 0.52
18 9 0.31
19 5 0.17
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (18 bp):
TTATCATTATAAATATTT
Found at i:402947 original size:20 final size:19
Alignment explanation
Indices: 402922--402961 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
402912 ATAACATCAC
* *
402922 TTTTATACTTATATAAAAAA
1 TTTTATAATT-TAAAAAAAA
402942 TTTTATAATTTAAAAAAAA
1 TTTTATAATTTAAAAAAAA
402961 T
1 T
402962 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTATAATTTAAAAAAAA
Found at i:403026 original size:17 final size:14
Alignment explanation
Indices: 402976--403017 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
402966 TTTTATATTT
*
402976 ATATTAACATAT--
1 ATATTAAAATATAA
402988 ATATT-AAATATAA
1 ATATTAAAATATAA
403001 ATATTAAAATATAA
1 ATATTAAAATATAA
403015 ATA
1 ATA
403018 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 5 0.19
12 5 0.19
13 5 0.19
14 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:405119 original size:6 final size:6
Alignment explanation
Indices: 405108--405132 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
405098 ATTACGGATA
405108 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
405133 TTTCTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:405768 original size:2 final size:2
Alignment explanation
Indices: 405761--405787 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
405751 TGAAAATAGC
405761 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
405788 GATAATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:406135 original size:14 final size:15
Alignment explanation
Indices: 406116--406152 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
406106 CCATAATGAA
406116 GACTGACGACTG-CT
1 GACTGACGACTGACT
*
406130 GACTGACTACTGACT
1 GACTGACGACTGACT
406145 -ACTGACGA
1 GACTGACGA
406153 GCTCAACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 18 0.90
15 2 0.10
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (15 bp):
GACTGACGACTGACT
Found at i:407398 original size:39 final size:32
Alignment explanation
Indices: 407362--407425 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
407352 CTTAAATCTC
407362 AAATCTCGTTTCTTAACATCTAAACTAAGAAA
1 AAATCTCGTTTCTTAACATCTAAACTAAGAAA
407394 AAATCTCGTTTCTTAACATCTAAACTAAGAAA
1 AAATCTCGTTTCTTAACATCTAAACTAAGAAA
407426 GTTTCCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (32 bp):
AAATCTCGTTTCTTAACATCTAAACTAAGAAA
Found at i:407744 original size:2 final size:2
Alignment explanation
Indices: 407737--407769 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
407727 TACATACATT
407737 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
407770 CACACCCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:408363 original size:2 final size:2
Alignment explanation
Indices: 408356--408387 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
408346 TTGTTTTTGG
408356 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
408388 ACTGTCTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:411126 original size:2 final size:2
Alignment explanation
Indices: 411119--411159 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
411109 ATGCCATTAC
411119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
411160 CAAGCAAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:416324 original size:30 final size:30
Alignment explanation
Indices: 416263--416324 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
416253 ATTATTTATA
* **
416263 TTTATTTAAATTTAAAATATAATTTTAAAT
1 TTTATTTAAATTTAAAATATAAATAAAAAT
*
416293 TTTATTTAAATTT-ATATATAAATAAATAAT
1 TTTATTTAAATTTAAAATATAAATAAA-AAT
416323 TT
1 TT
416325 AAATTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTATTTAAATTTAAAATATAAATAAAAAT
Found at i:416599 original size:13 final size:14
Alignment explanation
Indices: 416565--416623 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 14
416555 CTTAATTTAA
416565 ATAAATTTATTTTTT
1 ATAAATTTA-TTTTT
416580 ATCTAAATTTATTTTT
1 A--TAAATTTATTTTT
416596 -TAAATCTAATATTTTT
1 ATAAAT-T--TATTTTT
416612 ATAAATTT-TTTT
1 ATAAATTTATTTT
416624 ATTCATTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 1 0.03
16 13 0.34
17 13 0.34
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
ATAAATTTATTTTT
Found at i:417628 original size:20 final size:19
Alignment explanation
Indices: 417601--417662 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
417591 ATATGAAAAT
*
417601 TAAATATAAATATAATATAT
1 TAAATATAAA-ATAATATAA
*
417621 TTAATATATAAATAATATAA
1 TAAATATA-AAATAATATAA
*
417641 TAAATATAAAAAAAT-TAA
1 TAAATATAAAATAATATAA
417659 TAAA
1 TAAA
417663 ACATAACTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.19
19 6 0.16
20 22 0.59
21 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATATAAAATAATATAA
Found at i:417638 original size:9 final size:10
Alignment explanation
Indices: 417601--417655 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
417591 ATATGAAAAT
417601 TAAATATAAA
1 TAAATATAAA
**
417611 TATAATATATT
1 TA-AATATAAA
417622 TAATATATAAA
1 TAA-ATATAAA
417633 T-AATAT-AA
1 TAAATATAAA
417641 TAAATATAAA
1 TAAATATAAA
*
417651 AAAAT
1 TAAAT
417656 TAATAAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
8 3 0.08
9 9 0.25
10 10 0.28
11 14 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAATATAAA
Found at i:417977 original size:20 final size:20
Alignment explanation
Indices: 417926--417978 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
417916 TATCTAAGTT
**
417926 ATATT-TATATAT-TTTATT
1 ATATTATATATATATTTAAA
417944 ATATTATA-ATTATATTTAAA
1 ATATTATATA-TATATTTAAA
417964 ATATTATATATATAT
1 ATATTATATATATAT
417979 ATATATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 5 0.17
20 17 0.59
21 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTATATATATATTTAAA
Found at i:418035 original size:41 final size:41
Alignment explanation
Indices: 417924--418043 Score: 120
Period size: 41 Copynumber: 2.9 Consensus size: 41
417914 TTTATCTAAG
*
417924 TTATATT-TATATATTTTATTATATTATAATTATATTTAAAATA
1 TTATATTATATATATTTT-TTATATTTTAA-TA-ATTTAAAATA
* *
417967 TTATATATATATATATATATGTA-ATTTTAATAATTTAATAAT-
1 TTATAT-TATATATAT-TTTTTATATTTTAATAATTTAA-AATA
* *
418009 TTATATTATATAAATTTTTTATATTTTAATTATTT
1 TTATATTATATATATTTTTTATATTTTAATAATTT
418044 TTTATATTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
40 4 0.06
41 20 0.31
42 12 0.18
43 11 0.17
44 7 0.11
45 9 0.14
46 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (41 bp):
TTATATTATATATATTTTTTATATTTTAATAATTTAAAATA
Found at i:418054 original size:41 final size:41
Alignment explanation
Indices: 417924--418066 Score: 112
Period size: 41 Copynumber: 3.4 Consensus size: 41
417914 TTTATCTAAG
* * *
417924 TTATATT-TATATATTTTATTATATTATAATTATATTTAAAATA
1 TTATATTATATAAATTTT-TTATATTTTAATTAT-TTT-ATATA
* * * * *
417967 TTATATATATATATATATATGTA-ATTTTAATAATTTAATA-A
1 TTATAT-TATATAAAT-TTTTTATATTTTAATTATTTTATATA
*
418008 TTTATATTATATAAATTTTTTATATTTTAATTATTTTTTATA
1 -TTATATTATATAAATTTTTTATATTTTAATTATTTTATATA
418050 TTATATTTATGATAAAT
1 TTATA-TTAT-ATAAAT
418067 AAATTTAAAC
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
40 4 0.05
41 28 0.35
42 13 0.16
43 14 0.17
44 10 0.12
45 9 0.11
46 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (41 bp):
TTATATTATATAAATTTTTTATATTTTAATTATTTTATATA
Found at i:418059 original size:18 final size:18
Alignment explanation
Indices: 418008--418059 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
417998 AATTTAATAA
**
418008 TTTATATTATATAAATTT
1 TTTATATTATATTTATTT
* *
418026 TTTATATTTTAATTATTT
1 TTTATATTATATTTATTT
418044 TTTATATTATATTTAT
1 TTTATATTATATTTAT
418060 GATAAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATATTATATTTATTT
Found at i:420172 original size:17 final size:17
Alignment explanation
Indices: 420090--420180 Score: 53
Period size: 17 Copynumber: 5.5 Consensus size: 17
420080 AACGTGAATA
*
420090 TTAAATTTATATTTAAT
1 TTAAATATATATTTAAT
*
420107 AT-AA-ATATATTTAAT
1 TTAAATATATATTTAAT
*** * *
420122 TTTTTTATATTTTTTA-
1 TTAAATATATATTTAAT
* * *
420138 TTATATTTTATATATAAT
1 TTA-AATATATATTTAAT
420156 TTAAATATATATTTAAT
1 TTAAATATATATTTAAT
*
420173 ATAAATAT
1 TTAAATAT
420181 TAATTAAAAA
Statistics
Matches: 53, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
15 11 0.21
16 4 0.08
17 35 0.66
18 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATATATTTAAT
Found at i:420180 original size:13 final size:13
Alignment explanation
Indices: 420097--420181 Score: 59
Period size: 12 Copynumber: 6.5 Consensus size: 13
420087 ATATTAAATT
420097 TATATTTAATATAAA
1 TATATTTAATAT--A
* *
420112 TATATTTAATTTTTT
1 TATATTTAA--TATA
**
420127 TATATTTTTTAT-
1 TATATTTAATATA
*
420139 TATATTTTATATA
1 TATATTTAATATA
420152 TA-ATTTAA-ATA
1 TATATTTAATATA
420163 TATATTTAATATA
1 TATATTTAATATA
*
420176 AATATT
1 TATATT
420182 AATTAAAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
11 5 0.09
12 22 0.39
13 12 0.21
15 16 0.28
17 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATATTTAATATA
Found at i:423122 original size:27 final size:26
Alignment explanation
Indices: 423092--423151 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
423082 ATAGTACATA
* *
423092 ATTATATTTAA-AATATTTTATATTTAT
1 ATTATATTTAATAA-A-TTAATAATTAT
423119 ATTA-ATTTTAATAAATTAATAATTAT
1 ATTATA-TTTAATAAATTAATAATTAT
423145 ATTATAT
1 ATTATAT
423152 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
26 15 0.54
27 11 0.39
28 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTATATTTAATAAATTAATAATTAT
Done.