Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold226
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: 1170647
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 8
Found at i:256683 original size:26 final size:26
Alignment explanation
Indices: 256653--256708 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
256643 CATGTCATAT
256653 TTATATATTTTTA-AATATTTAAGATA
1 TTATATATTTTTATAAT-TTTAAGATA
*
256679 TTATATATTTTTATTAATTTTAATATA
1 TTATATATTTTTA-TAATTTTAAGATA
256706 TTA
1 TTA
256709 ATAATTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 13 0.48
27 11 0.41
28 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TTATATATTTTTATAATTTTAAGATA
Found at i:256735 original size:32 final size:33
Alignment explanation
Indices: 256653--256757 Score: 108
Period size: 32 Copynumber: 3.2 Consensus size: 33
256643 CATGTCATAT
* *
256653 TTATAT-ATTTTTAA-ATATTTAAGATATTATATA
1 TTATATAAATTTTAATATA-TTAATATATT-TATA
* * *
256686 TTTTTATTAATTTTAATATATTAATA-ATTTATG
1 -TTATATAAATTTTAATATATTAATATATTTATA
*
256719 TTATATAAATTTTAATATATTCATATATTTATA
1 TTATATAAATTTTAATATATTAATATATTTATA
256752 TTATAT
1 TTATAT
256758 TCGTATTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
32 22 0.37
33 15 0.25
34 8 0.13
35 12 0.20
36 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (33 bp):
TTATATAAATTTTAATATATTAATATATTTATA
Found at i:257369 original size:16 final size:16
Alignment explanation
Indices: 257325--257369 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
257315 TAATATGCAC
*
257325 TTTAATTAG-AATATAA
1 TTTAA-TAGTAATTTAA
257341 TTTAATAGTAATTTAA
1 TTTAATAGTAATTTAA
*
257357 TTTTATAGTAATT
1 TTTAATAGTAATT
257370 AAAGAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
TTTAATAGTAATTTAA
Found at i:257788 original size:3 final size:3
Alignment explanation
Indices: 257780--257834 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
257770 CCCGAACATC
257780 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
257828 ATA ATA A
1 ATA ATA A
257835 ATTAAGAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:259550 original size:2 final size:2
Alignment explanation
Indices: 259543--259574 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
259533 GGATCCACAA
*
259543 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
259575 GTTGTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:260273 original size:15 final size:15
Alignment explanation
Indices: 260253--260282 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
260243 GATATTGATA
*
260253 CTACTACTATATTAT
1 CTACTACTACATTAT
260268 CTACTACTACATTAT
1 CTACTACTACATTAT
260283 ATAAATGAAA
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:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
CTACTACTACATTAT
Found at i:260566 original size:3 final size:3
Alignment explanation
Indices: 260553--260595 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
260543 CACTCTATCT
260553 TTC TATC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
260596 ACCAGCAGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:261622 original size:13 final size:13
Alignment explanation
Indices: 261604--261629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
261594 ACCAAGTTTA
261604 ATCTAAATTTAAT
1 ATCTAAATTTAAT
261617 ATCTAAATTTAAT
1 ATCTAAATTTAAT
261630 TAAATTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCTAAATTTAAT
Found at i:262024 original size:17 final size:18
Alignment explanation
Indices: 262004--262045 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
261994 ATAAAATAAT
*
262004 ATAAATTATTT-AATATA
1 ATAAATAATTTAAATATA
262021 ATAAA-AATTTAAATATA
1 ATAAATAATTTAAATATA
262038 A-AAATAAT
1 ATAAATAAT
262046 ATATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATAATTTAAATATA
Found at i:262516 original size:33 final size:32
Alignment explanation
Indices: 262479--262545 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 32
262469 TTACTTCATT
262479 TAAATAATTATTAATATTT-TTGTTATATTCAAA
1 TAAA-AATTATTAATATTTATT-TTATATTCAAA
*
262512 T--AAATTATTAATATTTAATTTTATATTTAAA
1 TAAAAATTATTAATATTT-ATTTTATATTCAAA
262543 TAA
1 TAA
262546 GTTATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
30 14 0.48
31 12 0.41
32 2 0.07
33 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (32 bp):
TAAAAATTATTAATATTTATTTTATATTCAAA
Found at i:262519 original size:30 final size:29
Alignment explanation
Indices: 262478--262586 Score: 115
Period size: 31 Copynumber: 3.9 Consensus size: 29
262468 ATTACTTCAT
262478 TTAAAT-AATTATTAATATTT-TTGTTATA
1 TTAAATAAATTATTAATATTTATT-TTATA
262506 TTCAAATAAATTATTAATATTTAATTTTATA
1 TT-AAATAAATTATTAATATTT-ATTTTATA
* *
262537 TTTAAATAAGTTATT--T-TTTAATTTATA
1 -TTAAATAAATTATTAATATTTATTTTATA
262564 TTAAATAAATTATT-AT-TTTATTT
1 TTAAATAAATTATTAATATTTATTT
262587 AAAATAAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 13
0.81 0.05 0.15
Matches are distributed among these distances:
26 13 0.18
27 14 0.20
28 5 0.07
29 5 0.07
30 14 0.20
31 16 0.23
32 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (29 bp):
TTAAATAAATTATTAATATTTATTTTATA
Found at i:262571 original size:26 final size:27
Alignment explanation
Indices: 262501--262587 Score: 106
Period size: 26 Copynumber: 3.1 Consensus size: 27
262491 AATATTTTTG
262501 TTATATTCAAATAAATTATTAATATTTAATT
1 TTATATT-AAATAAATTATT-AT-TTTAA-T
*
262532 TTATATTTAAATAAGTTATT-TTTTAAT
1 TTATA-TTAAATAAATTATTATTTTAAT
262559 TTATATTAAATAAATTATTATTTT-AT
1 TTATATTAAATAAATTATTATTTTAAT
262585 TTA
1 TTA
262588 AAATAAAAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
26 18 0.35
27 10 0.19
28 5 0.10
29 1 0.02
31 16 0.31
32 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
TTATATTAAATAAATTATTATTTTAAT
Found at i:262594 original size:26 final size:26
Alignment explanation
Indices: 262539--262594 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
262529 ATTTTATATT
* * *
262539 TAAATAAGTTATTTTTTAATTTATAT
1 TAAATAAATTATTTTTTAATTTAAAA
262565 TAAATAAATTATTATTTT-ATTTAAAA
1 TAAATAAATTATT-TTTTAATTTAAAA
262591 TAAA
1 TAAA
262595 AACCCTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TAAATAAATTATTTTTTAATTTAAAA
Found at i:263332 original size:2 final size:2
Alignment explanation
Indices: 263325--263368 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
263315 TGACATATGC
263325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
263366 AT A
1 AT A
263369 GAGTAATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 36 0.92
3 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:264434 original size:17 final size:17
Alignment explanation
Indices: 264390--264447 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
264380 ATGATATTAA
*
264390 AAATAATTTTTA-TATT
1 AAATTATTTTTATTATT
*
264406 AATATTTATATTTTTTTAATT
1 AA-A-TTAT-TTTTATT-ATT
264427 AAATTATTTTTATTATT
1 AAATTATTTTTATTATT
264444 AAAT
1 AAAT
264448 AATAATTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
18 9 0.26
19 8 0.24
20 2 0.06
21 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATTATTTTTATTATT
Found at i:265351 original size:17 final size:14
Alignment explanation
Indices: 265314--265342 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
265304 TTCAGAGATC
265314 GGACAAATAATTTA
1 GGACAAATAATTTA
265328 GGACAAATAATTTA
1 GGACAAATAATTTA
265342 G
1 G
265343 TTTGACAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (14 bp):
GGACAAATAATTTA
Found at i:268948 original size:9 final size:9
Alignment explanation
Indices: 268928--268961 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
268918 TTTATGCACG
268928 TAATTAAAAT
1 TAATT-AAAT
268938 TAATTAAAT
1 TAATTAAAT
*
268947 TAATTTAAT
1 TAATTAAAT
268956 TAATTA
1 TAATTA
268962 TGAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTAAAT
Found at i:269762 original size:2 final size:2
Alignment explanation
Indices: 269757--269783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
269747 AAAAAAAAGA
269757 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 A
269784 GATTGAGTCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:270099 original size:14 final size:14
Alignment explanation
Indices: 270068--270109 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
270058 AAAAAATATA
270068 TTTAATATTTAAAT
1 TTTAATATTTAAAT
*
270082 TTTAA-ATTTTAAT
1 TTTAATATTTAAAT
270095 ATTT-ATATTTAAAT
1 -TTTAATATTTAAAT
270109 T
1 T
270110 GAGATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAATATTTAAAT
Found at i:270105 original size:20 final size:19
Alignment explanation
Indices: 270067--270122 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
270057 AAAAAAATAT
*
270067 ATTTAATATTTAAATTTTAA
1 ATTTAATATTTATA-TTTAA
270087 ATTTTAATATTTATATTTAA
1 A-TTTAATATTTATATTTAA
*
270107 ATTGAGATATTTATAT
1 ATTTA-ATATTTATAT
270123 ATATAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.09
20 17 0.53
21 12 0.38
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
ATTTAATATTTATATTTAA
Found at i:270302 original size:10 final size:11
Alignment explanation
Indices: 270285--270346 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 11
270275 AAAAATTTTA
270285 TAAATTTAAAT
1 TAAATTTAAAT
270296 T-AATTT-AAT
1 TAAATTTAAAT
270305 TAAATTTAAAT
1 TAAATTTAAAT
* *
270316 AAAAAATTAAAT
1 -TAAATTTAAAT
*
270328 T--TTTTAAAT
1 TAAATTTAAAT
270337 TATAATTTAA
1 TA-AATTTAA
270347 TGTTGCTGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
9 11 0.28
10 10 0.26
11 4 0.10
12 14 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:271371 original size:22 final size:21
Alignment explanation
Indices: 271341--271381 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
271331 ATTTTTTATT
271341 TAAATTTAATTATAA-AATATA
1 TAAATTTAA-TATAACAATATA
271362 TAAATATTAATATAACAATA
1 TAAAT-TTAATATAACAATA
271382 ATTTTTGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTTAATATAACAATATA
Found at i:271587 original size:24 final size:23
Alignment explanation
Indices: 271560--271646 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 23
271550 ATTATTGTTT
*
271560 ATTTGATAAAAATAATTTTTTAAA
1 ATTT-ATAAAAATAATATTTTAAA
* *
271584 ATTTAATTAGAAA-AATATATTAAA
1 ATTT-A-TAAAAATAATATTTTAAA
271608 ATTAATATAAAAATAATATTTT-AA
1 ATT--TATAAAAATAATATTTTAAA
*
271632 ATTTTTAAATAATAA
1 ATTTATAAA-AATAA
271647 AATAAATTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
22 5 0.10
23 5 0.10
24 27 0.53
25 13 0.25
26 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTATAAAAATAATATTTTAAA
Found at i:273500 original size:2 final size:2
Alignment explanation
Indices: 273495--273519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
273485 TTTTTGACTT
273495 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 T
273520 GACTTTTGGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:273990 original size:19 final size:18
Alignment explanation
Indices: 273966--274009 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
273956 TTATTACTTT
273966 TTAAATACTAAAAAATATA
1 TTAAATA-TAAAAAATATA
**
273985 TTAAAT-TATTAAATATA
1 TTAAATATAAAAAATATA
274002 TTAAATAT
1 TTAAATAT
274010 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAATATAAAAAATATA
Found at i:273996 original size:8 final size:8
Alignment explanation
Indices: 273978--274031 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
273968 AAATACTAAA
273978 AAATATATT
1 AAAT-TATT
273987 AAATTATT
1 AAATTATT
273995 AAATATATT
1 AAAT-TATT
274004 AAA-TATTT
1 AAATTA-TT
*
274012 AAATTTTT
1 AAATTATT
*
274020 AAATTTTT
1 AAATTATT
274028 AAAT
1 AAAT
274032 ATAATATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
7 2 0.05
8 27 0.66
9 12 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATTATT
Found at i:274000 original size:17 final size:17
Alignment explanation
Indices: 273978--274034 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
273968 AAATACTAAA
273978 AAATATATTAAATTATT
1 AAATATATTAAATTATT
273995 AAATATATTAAA-TATTT
1 AAATATATTAAATTA-TT
* *
274012 AAAT-TTTTAAATTTTT
1 AAATATATTAAATTATT
274028 AAATATA
1 AAATATA
274035 ATATTATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 14 0.41
17 20 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATATTAAATTATT
Found at i:274602 original size:2 final size:2
Alignment explanation
Indices: 274595--274627 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
274585 ACATAATGAA
*
274595 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
274628 CACATTAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:274833 original size:24 final size:25
Alignment explanation
Indices: 274800--274869 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 25
274790 CATCGATAAG
*
274800 AATATGATATATTTAATA-AACATA
1 AATATAATATATTTAATATAACATA
* * *
274824 AATATAATATAATAAAAATAACATA
1 AATATAATATATTTAATATAACATA
*
274849 ATATATAATAAATTTAATATA
1 A-ATATAATATATTTAATATA
274870 TACTATATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 14 0.39
25 7 0.19
26 15 0.42
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (25 bp):
AATATAATATATTTAATATAACATA
Found at i:274868 original size:16 final size:16
Alignment explanation
Indices: 274847--274899 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
274837 AAAAATAACA
274847 TAATATATAATAAATT
1 TAATATATAATAAATT
* *
274863 TAATATATACTATATT
1 TAATATATAATAAATT
*
274879 T-ATAT-TTA-AAATT
1 TAATATATAATAAATT
274892 TAATATAT
1 TAATATAT
274900 TTAATAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 5 0.17
14 5 0.17
15 5 0.17
16 15 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATATAATAAATT
Found at i:274876 original size:21 final size:20
Alignment explanation
Indices: 274806--274860 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
274796 TAAGAATATG
* *
274806 ATATATTTAATAAACATAA-
1 ATATATATAATAAAAATAAC
274825 ATATAATATAATAAAAATAAC
1 ATAT-ATATAATAAAAATAAC
274846 ATAATATATAATAAA
1 AT-ATATATAATAAA
274861 TTTAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.13
20 13 0.42
21 12 0.39
22 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATATATAATAAAAATAAC
Found at i:274900 original size:16 final size:19
Alignment explanation
Indices: 274873--274921 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
274863 TAATATATAC
274873 TATATTTATATTTAA-AATT
1 TATA-TTATATTTAATAATT
274892 TA-A-TATATTTAATAATT
1 TATATTATATTTAATAATT
274909 TATATTATATTTA
1 TATATTATATTTA
274922 TATTTACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 2 0.07
19 10 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTTAATAATT
Found at i:275368 original size:18 final size:17
Alignment explanation
Indices: 275345--275384 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
275335 GCCTTATTTT
*
275345 AAAATGTTTAAAAATAAA
1 AAAATGATT-AAAATAAA
*
275363 AAAATGATTGAAATAAA
1 AAAATGATTAAAATAAA
275380 AAAAT
1 AAAAT
275385 CATATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (17 bp):
AAAATGATTAAAATAAA
Found at i:276151 original size:3 final size:3
Alignment explanation
Indices: 276143--276188 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
276133 CAGCCCAAAT
*
276143 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
276189 ATTAAGAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:276543 original size:3 final size:3
Alignment explanation
Indices: 276535--276565 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
276525 CAAACATGCG
*
276535 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
276566 TCAGAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:276683 original size:3 final size:3
Alignment explanation
Indices: 276675--276702 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
276665 AAAAAAGTTA
276675 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
276703 TCAGAAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:276683 original size:137 final size:124
Alignment explanation
Indices: 276538--276800 Score: 373
Period size: 137 Copynumber: 2.0 Consensus size: 124
276528 ACATGCGTAT
276538 TATTATTATCATTATTATTATTATTATTTCAGAAATCCTATGTTTTTTATTATTATTATATATTT
1 TATTATTATCATTATTATTATTATTATTTCAGAAATCCTATGTTTTTTATTATTATT-T-TA--T
276603 AATTAATCATGACATTCAAGCATGATAAAATTTACCCTTTGCCCAACATGCATCTAAATTTCAAA
62 AATTAAT--T-A-A-TCAAG-A--AT-AAATTTACCCTTTGCCCAACATGCATCTAAATTTCAAA
276668 AAAGTTA
118 AAAGTTA
* * *
276675 TATTATTATTATTATTATTATTATTATTTCAGAAATCCTATGTTTTTTTTTATTATTTTATATTT
1 TATTATTATCATTATTATTATTATTATTTCAGAAATCCTATGTTTTTTATTATTATTTTATAATT
*
276740 AATTAATCAAGAATAAATTTACCCTTTGTCCAACATGCATCTAAATTTCAAAAAAGTTA
66 AATTAATCAAGAATAAATTTACCCTTTGCCCAACATGCATCTAAATTTCAAAAAAGTTA
276799 TA
1 TA
276801 ACTTTCCCCA
Statistics
Matches: 122, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
124 46 0.38
125 2 0.02
127 1 0.01
128 5 0.04
129 1 0.01
130 1 0.01
131 1 0.01
133 7 0.06
135 2 0.02
136 1 0.01
137 55 0.45
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (124 bp):
TATTATTATCATTATTATTATTATTATTTCAGAAATCCTATGTTTTTTATTATTATTTTATAATT
AATTAATCAAGAATAAATTTACCCTTTGCCCAACATGCATCTAAATTTCAAAAAAGTTA
Found at i:277153 original size:2 final size:2
Alignment explanation
Indices: 277146--277174 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
277136 GGATCCACAA
277146 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 A
277175 GTTGGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:277757 original size:13 final size:13
Alignment explanation
Indices: 277731--277774 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
277721 CTCTTAAATT
*
277731 TTTTAAAAATATAA
1 TTTT-AAAAGATAA
277745 TTTTAAAAGATAA
1 TTTTAAAAGATAA
* *
277758 TTTTTAAAGATGA
1 TTTTAAAAGATAA
277771 TTTT
1 TTTT
277775 TTTCATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTAAAAGATAA
Found at i:278244 original size:199 final size:198
Alignment explanation
Indices: 277905--278305 Score: 739
Period size: 199 Copynumber: 2.0 Consensus size: 198
277895 TACTACTACA
* *
277905 TGATCTAAATGAAAGAAAATTAAGGAATAAGAAATAGGATTGCGTAGAAAAAAAATTGTAATAAA
1 TGATCTAAATAAAAGAAAATTAAGGAATAAGAAATAGGATTGCCTAGAAAAAAAATTGTAATAAA
*
277970 ATAATGAATAAATAAAAGAATGGAAATATGCGGCCAAAGGTATCATGTGAATGGAGATGTCTTTT
66 ATAATGAATAAATAAAAGAATGGAAACATGCGGCCAAAGGTATCATGTGAATGGAGATGTCTTTT
*
278035 GTCTACCATGCATATCCAAAGGGGTTTCTAAATATGGGTCCACTCATGTGTATTGATATATTGAC
131 GTCTACCATGCATATCCAAAGAGGTTTCTAAATATGGGTCCACTCATGTGTATTGATATATTGAC
278100 CCT
196 CCT
*
278103 TGATCTAAATCAAAAGAAAATTAAGGAATAAGAAATAGGATTGCCTAGAAAAAAATTTGTAATAA
1 TGATCTAAAT-AAAAGAAAATTAAGGAATAAGAAATAGGATTGCCTAGAAAAAAAATTGTAATAA
278168 AATAATGAATAAATAAAAGAATGGAAACATGCGGCCAAAGGTATCATGTGAATGGAGATGTCTTT
65 AATAATGAATAAATAAAAGAATGGAAACATGCGGCCAAAGGTATCATGTGAATGGAGATGTCTTT
*
278233 TGTCTACCATGCATATCCAAAGAGGTTTCTAAATATGGGTCCACTTATGTGTATTGATATATTGA
130 TGTCTACCATGCATATCCAAAGAGGTTTCTAAATATGGGTCCACTCATGTGTATTGATATATTGA
278298 CCCT
195 CCCT
278302 TGAT
1 TGAT
278306 TTTGCTTATT
Statistics
Matches: 196, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
198 10 0.05
199 186 0.95
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (198 bp):
TGATCTAAATAAAAGAAAATTAAGGAATAAGAAATAGGATTGCCTAGAAAAAAAATTGTAATAAA
ATAATGAATAAATAAAAGAATGGAAACATGCGGCCAAAGGTATCATGTGAATGGAGATGTCTTTT
GTCTACCATGCATATCCAAAGAGGTTTCTAAATATGGGTCCACTCATGTGTATTGATATATTGAC
CCT
Found at i:279795 original size:17 final size:17
Alignment explanation
Indices: 279773--279833 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 17
279763 TGTGAATATA
*
279773 AAATATCATAAATTATT
1 AAATATAATAAATTATT
279790 AAATATAATAAAAATT-TT
1 AAATATAAT--AAATTATT
*
279808 AAATATAAAATAATATATT
1 AAATATAATA-AAT-TATT
279827 AAATATA
1 AAATATA
279834 TCATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 1 0.03
17 11 0.30
18 11 0.30
19 14 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATAATAAATTATT
Found at i:279809 original size:18 final size:18
Alignment explanation
Indices: 279780--279833 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
279770 ATAAAATATC
279780 ATAAATTATTAAATATAATA
1 ATAAATT-TTAAATATAA-A
279800 A-AAATTTTAAATATAAA
1 ATAAATTTTAAATATAAA
*
279817 ATAATATATTAAATATA
1 ATAA-ATTTTAAATATA
279834 TCATTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 16 0.52
20 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAATTTTAAATATAAA
Found at i:279830 original size:19 final size:18
Alignment explanation
Indices: 279767--279833 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
279757 CAGTTGTGTG
* *
279767 AATATAAAATATCAT-AA
1 AATATTAAATATAATAAA
*
279784 ATTATTAAATATAATAAA
1 AATATTAAATATAATAAA
*
279802 AATTTTAAATATAA-AATA
1 AATATTAAATATAATAA-A
279820 ATATATTAAATATA
1 A-ATATTAAATATA
279834 TCATTTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.34
18 16 0.39
19 11 0.27
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATTAAATATAATAAA
Found at i:280271 original size:31 final size:31
Alignment explanation
Indices: 280236--280354 Score: 113
Period size: 31 Copynumber: 3.9 Consensus size: 31
280226 AAAATCTTAA
* * *
280236 ATTTTATTATTTTATTTAAATAATTTTTTAT
1 ATTTTATTATTATATTTAAATAATTATTGAT
280267 ATTTT-TTATTATATTTAAATAAATTATTGAT
1 ATTTTATTATTATATTTAAAT-AATTATTGAT
* * *
280298 ATTTAATT-TTATATTTAAATATGTTATTAAT
1 ATTTTATTATTATATTTAAATA-ATTATTGAT
*
280329 -TTTTAAT-TTATA-TTAAATAAATTATT
1 ATTTTATTATTATATTTAAAT-AATTATT
280355 TTTATTTAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
29 11 0.15
30 26 0.35
31 36 0.48
32 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
ATTTTATTATTATATTTAAATAATTATTGAT
Found at i:280351 original size:60 final size:61
Alignment explanation
Indices: 280248--280363 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 61
280238 TTTATTATTT
* *
280248 TATTTAAATAATTTTTTATATTTTTTATTATATTTAAATAAATTATTGATATTTAATTTTA
1 TATTTAAATAATTTATTATATTTTTAATTATATTTAAATAAATTATTGATATTTAATTTTA
**
280309 TATTTAAAT-ATGTTATTA-ATTTTTAATT-TATATTAAATAAATTATTTTTATTTAA
1 TATTTAAATAAT-TTATTATATTTTTAATTATAT-TTAAATAAATTATTGATATTTAA
280364 AATAAAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 3 0.06
60 32 0.65
61 14 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (61 bp):
TATTTAAATAATTTATTATATTTTTAATTATATTTAAATAAATTATTGATATTTAATTTTA
Found at i:280830 original size:2 final size:2
Alignment explanation
Indices: 280819--280848 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
280809 TGCTAGCTTA
280819 AT AT -T 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 A
280849 GGCTTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:282179 original size:17 final size:17
Alignment explanation
Indices: 282157--282190 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
282147 AATATTTATA
282157 TATTTTTATAATTAAAT
1 TATTTTTATAATTAAAT
*
282174 TATTTTTATTATTAAAT
1 TATTTTTATAATTAAAT
282191 AATAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTTATAATTAAAT
Found at i:284642 original size:48 final size:48
Alignment explanation
Indices: 284586--284683 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
284576 ATGTCCCTTT
284586 GCTATGATTTAGACAGCCTAATTAACCCACAAACCCACATTTTATTTA
1 GCTATGATTTAGACAGCCTAATTAACCCACAAACCCACATTTTATTTA
284634 GCTATGATTTAGACAGCCTAATTAACCCACAAACCCACATTTTATTTA
1 GCTATGATTTAGACAGCCTAATTAACCCACAAACCCACATTTTATTTA
284682 GC
1 GC
284684 CTCTAAAGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.31
Consensus pattern (48 bp):
GCTATGATTTAGACAGCCTAATTAACCCACAAACCCACATTTTATTTA
Found at i:284871 original size:20 final size:20
Alignment explanation
Indices: 284846--284885 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
284836 ATTATTTTAT
284846 ATATTATA-ATTATATATAAA
1 ATATTATATATT-TATATAAA
284866 ATATTATATATTTATATAAA
1 ATATTATATATTTATATAAA
284886 TTTTAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATATATTTATATAAA
Found at i:285895 original size:2 final size:2
Alignment explanation
Indices: 285888--285918 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
285878 GAAATCATCC
285888 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 A
285919 AAGTTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:292931 original size:2 final size:2
Alignment explanation
Indices: 292924--292954 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
292914 AGAAAAGGGC
292924 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 T
292955 GTAGCGTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:293772 original size:12 final size:12
Alignment explanation
Indices: 293755--293802 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
293745 TAATATCATA
293755 TTTATATTATTT
1 TTTATATTATTT
293767 TTTATATT-TTT
1 TTTATATTATTT
*
293778 TATTTTATTAATTT
1 T-TTATATT-ATTT
293792 TTTAATATTAT
1 TTT-ATATTAT
293803 ATGATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 4 0.13
12 14 0.47
13 4 0.13
14 8 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:293782 original size:16 final size:16
Alignment explanation
Indices: 293761--293795 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
293751 CATATTTATA
293761 TTATTTT-TTATATTTT
1 TTATTTTATTA-ATTTT
293777 TTATTTTATTAATTTT
1 TTATTTTATTAATTTT
293793 TTA
1 TTA
293796 ATATTATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTATTAATTTT
Found at i:293802 original size:17 final size:17
Alignment explanation
Indices: 293772--293825 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
293762 TATTTTTTAT
*
293772 ATTTTTT-ATTTTATTA
1 ATTTTTTAATATTATTA
*
293788 ATTTTTTAATATTATATG
1 ATTTTTTAATATTAT-TA
*
293806 A-TATTTAATATTA-TA
1 ATTTTTTAATATTATTA
293821 ATTTT
1 ATTTT
293826 GTGACAACTG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.07
16 9 0.30
17 17 0.57
18 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTTAATATTATTA
Found at i:293810 original size:24 final size:23
Alignment explanation
Indices: 293737--293810 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
293727 TTTAAAATAT
* *
293737 TTATTTATTAATATCATATTTATA
1 TTATTTTTTAATATTATA-TTATA
* * *
293761 TTATTTTTTATATTTTTTATTTTA
1 TTATTTTTTA-ATATTATATTATA
*
293785 TTAATTTTTTAATATTATATGATA
1 TT-ATTTTTTAATATTATATTATA
293809 TT
1 TT
293811 TAATATTATA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 26 0.67
25 13 0.33
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTTTTTAATATTATATTATA
Found at i:294026 original size:7 final size:8
Alignment explanation
Indices: 293992--294034 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 8
293982 CTATAACTTA
293992 AAAATATAT
1 AAAATAT-T
294001 AAAATATT
1 AAAATATT
294009 ACAAATATT
1 A-AAATATT
294018 AAAAT-TT
1 AAAATATT
294025 -AAATATT
1 AAAATATT
294032 AAA
1 AAA
294035 CTTATTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 4 0.13
8 8 0.26
9 15 0.48
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:301504 original size:10 final size:10
Alignment explanation
Indices: 301489--301514 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
301479 CTTGGCCATG
301489 GGAAGGAAAA
1 GGAAGGAAAA
301499 GGAAGGAAAA
1 GGAAGGAAAA
301509 GGAAGG
1 GGAAGG
301515 CAGTATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (10 bp):
GGAAGGAAAA
Found at i:301702 original size:26 final size:26
Alignment explanation
Indices: 301673--301765 Score: 63
Period size: 26 Copynumber: 3.5 Consensus size: 26
301663 ATGAATATGA
301673 TATAATATAAATAAATTATTAAAATT
1 TATAATATAAATAAATTATTAAAATT
* *
301699 TAT-ATAATATATATTATATATTAAAATTTT
1 TATAAT-ATAAATA-AAT-TATTAAAA--TT
301729 TATAAATATAAAT--ATT-TT-AAA-T
1 TAT-AATATAAATAAATTATTAAAATT
301751 TATAATATAATATAA
1 TATAATATAA-ATAA
301766 TGTATAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
21 7 0.13
22 6 0.11
25 5 0.09
26 11 0.20
27 3 0.06
28 10 0.19
30 5 0.09
31 5 0.09
32 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TATAATATAAATAAATTATTAAAATT
Found at i:301704 original size:28 final size:26
Alignment explanation
Indices: 301672--301765 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 26
301662 TATGAATATG
301672 ATATAATATAAATAAATTATTAAAATTT
1 ATATAATATAAAT--ATTATTAAAATTT
*
301700 ATATAATATATATTATATATTAAAATTT
1 ATATAATATA-AATAT-TATTAAAATTT
*
301728 TTATAAATATAAATATT-TT-AAATTAT
1 ATAT-AATATAAATATTATTAAAATT-T
301754 AATATAATATAA
1 -ATATAATATAA
301766 TGTATAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
25 5 0.09
26 10 0.18
27 6 0.11
28 28 0.49
29 8 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATAATATAAATATTATTAAAATTT
Found at i:305619 original size:6 final size:6
Alignment explanation
Indices: 305599--305685 Score: 63
Period size: 6 Copynumber: 14.5 Consensus size: 6
305589 ATCATATTCA
* * * *
305599 ATAAAT TTAAAT ATAATT ATAAAAT ATAAAT AT-AAT ATAAAA ATAATT
1 ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT ATAAAT
* * *
305647 A-AAAG ATAAAA ATATAAT AT-AAT ATAAATT ATTAAT ATA
1 ATAAAT ATAAAT ATA-AAT ATAAAT ATAAA-T ATAAAT ATA
305686 TTAAAATTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
5 13 0.21
6 35 0.56
7 14 0.23
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (6 bp):
ATAAAT
Found at i:305635 original size:11 final size:11
Alignment explanation
Indices: 305621--305705 Score: 56
Period size: 11 Copynumber: 8.1 Consensus size: 11
305611 ATAATTATAA
305621 AATATAAATAT
1 AATATAAATAT
*
305632 AATATAAAAAT
1 AATATAAATAT
305643 AAT-TAAA-A-
1 AATATAAATAT
* *
305651 GATAAAAATAT
1 AATATAAATAT
305662 AATAT-AATAT
1 AATATAAATAT
*
305672 AAATTATTAATAT
1 -AA-TATAAATAT
*
305685 ATTA-AAAT-T
1 AATATAAATAT
*
305694 TATATAAATAT
1 AATATAAATAT
305705 A
1 A
305706 TAATATTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
8 2 0.04
9 7 0.12
10 17 0.30
11 21 0.38
12 4 0.07
13 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:305709 original size:45 final size:45
Alignment explanation
Indices: 305652--305758 Score: 112
Period size: 47 Copynumber: 2.3 Consensus size: 45
305642 TAATTAAAAG
* *
305652 ATAAAAATATAATA-T-AATATAAATTATTAATATATTAAAATTTA-T
1 ATAAATATATAATATTAAATAT-AATTATT-ATATA-TAAAATATATT
*
305697 ATAAATATATAATATTTTAAATATAATTATTTTATATAAAATATATT
1 ATAAATATATAATA--TTAAATATAATTATTATATATAAAATATATT
305744 ATAAATATATGAATA
1 ATAAATATAT-AATA
305759 ATTATATTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
45 13 0.25
46 8 0.15
47 15 0.28
48 12 0.23
49 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (45 bp):
ATAAATATATAATATTAAATATAATTATTATATATAAAATATATT
Found at i:305715 original size:20 final size:19
Alignment explanation
Indices: 305680--305741 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
305670 ATAAATTATT
*
305680 AATATATTAAAATTTATATA
1 AATATA-TAATATTTATATA
305700 AATATATAATA-TT-T-TA
1 AATATATAATATTTATATA
*
305716 AATATA-ATTATTTTATATA
1 AATATATAATA-TTTATATA
305735 AA-ATATA
1 AATATATA
305742 TTATAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
15 3 0.09
16 8 0.23
17 3 0.09
18 6 0.17
19 9 0.26
20 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATATAATATTTATATA
Found at i:305722 original size:14 final size:14
Alignment explanation
Indices: 305703--305752 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
305693 TTATATAAAT
305703 ATATAATATTTTAA
1 ATATAATATTTTAA
*
305717 ATATAATTATTTTAT
1 ATATAA-TATTTTAA
*
305732 ATAAAATATATTATAA
1 ATATAATAT-TT-TAA
305748 ATATA
1 ATATA
305753 TGAATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 9 0.31
15 14 0.48
16 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATAATATTTTAA
Found at i:305986 original size:14 final size:15
Alignment explanation
Indices: 305961--306007 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
305951 TTATGATAAA
305961 TAAAATTATAAATAT
1 TAAAATTATAAATAT
*
305976 TAAAA-TATAAATTT
1 TAAAATTATAAATAT
**
305990 TAATTTTATTAAATAT
1 TAAAATTA-TAAATAT
306006 TA
1 TA
306008 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.42
15 7 0.27
16 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATTATAAATAT
Found at i:306844 original size:32 final size:32
Alignment explanation
Indices: 306808--306874 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
306798 ATGGTGGGGA
306808 AAGAAAATAAGAAAAAAGACCAGCTGTAGCCT
1 AAGAAAATAAGAAAAAAGACCAGCTGTAGCCT
306840 AAGAAAATAAGAAAAAAGACCAGCTGTAGCCT
1 AAGAAAATAAGAAAAAAGACCAGCTGTAGCCT
306872 AAG
1 AAG
306875 TTGTGTACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.54, C:0.15, G:0.19, T:0.12
Consensus pattern (32 bp):
AAGAAAATAAGAAAAAAGACCAGCTGTAGCCT
Found at i:307953 original size:45 final size:42
Alignment explanation
Indices: 307870--308007 Score: 126
Period size: 45 Copynumber: 3.2 Consensus size: 42
307860 AATAATTTTA
* *
307870 AATAT-AATTATATAATATAAA-ATAATATAAA-AAATAATAT
1 AATATAAATTAT-TTATATAAATATAATATAAATATATAATAT
* *
307910 AATATAAATTATTAATATATTAAATTTTATATAAATATATAATATTTT
1 AATATAAATTATT--TATA-TAAATATAATATAAATATATAATA---T
307958 AA-ATATAATTATTTATATAAATATAATATAAATATATAA-AT
1 AATATA-AATTATTTATATAAATATAATATAAATATATAATAT
307999 AAT-TAAATT
1 AATATAAATT
308008 TAAAAATAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
40 10 0.12
41 11 0.14
42 3 0.04
43 4 0.05
44 9 0.11
45 27 0.33
46 4 0.05
47 3 0.04
48 10 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (42 bp):
AATATAAATTATTTATATAAATATAATATAAATATATAATAT
Found at i:307965 original size:14 final size:16
Alignment explanation
Indices: 307868--307986 Score: 64
Period size: 18 Copynumber: 7.8 Consensus size: 16
307858 TCAATAATTT
307868 TAAATAT-A-ATTATA
1 TAAATATAATATTATA
* *
307882 T-AATATAAAATAATA
1 TAAATATAATATTATA
307897 TAAA-A-AATA--ATA
1 TAAATATAATATTATA
307909 T-AATATAA-ATTAT-
1 TAAATATAATATTATA
*
307922 TAATATATTAAATTTTATA
1 TAA-ATA-T-AATATTATA
307941 TAAATATATAATATT-T-
1 T-AA-ATATAATATTATA
307957 TAAATATAATTATTTATA
1 TAAATATAA-TA-TTATA
307975 TAAATATAATAT
1 TAAATATAATAT
307987 AAATATATAA
Statistics
Matches: 83, Mismatches: 4, Indels: 34
0.69 0.03 0.28
Matches are distributed among these distances:
11 2 0.02
12 6 0.07
13 8 0.10
14 14 0.17
15 14 0.17
16 7 0.08
17 6 0.07
18 18 0.22
19 2 0.02
20 6 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATATTATA
Found at i:308433 original size:12 final size:12
Alignment explanation
Indices: 308413--308442 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
308403 CACACATCTT
308413 TTTAAATTTTTA
1 TTTAAATTTTTA
*
308425 TTTATATTTTTA
1 TTTAAATTTTTA
308437 TTTAAA
1 TTTAAA
308443 ATAAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTAAATTTTTA
Found at i:308814 original size:6 final size:6
Alignment explanation
Indices: 308803--308831 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
308793 CAGGTCATGC
308803 ACAGGG ACAGGG ACAGGG ACAGGG ACAGG
1 ACAGGG ACAGGG ACAGGG ACAGGG ACAGG
308832 CCCTTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.48, T:0.00
Consensus pattern (6 bp):
ACAGGG
Found at i:309196 original size:14 final size:15
Alignment explanation
Indices: 309145--309201 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
309135 TTTTAAAAAA
*
309145 TTAATATTTAATAAAT
1 TTAATATTT-ATAATT
309161 TT-ATAATTTA-AATT
1 TTAAT-ATTTATAATT
309175 TTAATATTTATAATT
1 TTAATATTTATAATT
*
309190 TT-TTATTTATAA
1 TTAATATTTATAA
309202 AATATAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
15 11 0.31
16 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATATTTATAATT
Found at i:309256 original size:22 final size:24
Alignment explanation
Indices: 309224--309282 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
309214 TTTTTATAAA
*
309224 AAATTTTATATTTTA-TATCAT-T
1 AAATTTAATATTTTATTATCATAT
*
309246 AAATTTAATA-TTAATTATCATAT
1 AAATTTAATATTTTATTATCATAT
309269 AAATTATAA-ATTTT
1 AAATT-TAATATTTT
309283 TAATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 7 0.23
24 5 0.17
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATTTAATATTTTATTATCATAT
Found at i:309326 original size:16 final size:16
Alignment explanation
Indices: 309292--309335 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
309282 TTAATTTTAT
309292 TAAATTATATTATT-A
1 TAAATTATATTATTAA
*
309307 -AAATTTTATTATTAA
1 TAAATTATATTATTAA
309322 TAAATTATATTATT
1 TAAATTATATTATT
309336 TACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.48
15 1 0.04
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTATATTATTAA
Found at i:309326 original size:30 final size:30
Alignment explanation
Indices: 309271--309335 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
309261 TATCATATAA
* *
309271 ATTA-TAAATTTTTAATTTTATTAAATTAT
1 ATTATTAAAATTTTAATTTTAATAAATTAT
309300 ATTATTAAAATTTT-ATTATTAATAAATTAT
1 ATTATTAAAATTTTAATT-TTAATAAATTAT
309330 ATTATT
1 ATTATT
309336 TACATTAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTATTAAAATTTTAATTTTAATAAATTAT
Found at i:309342 original size:14 final size:14
Alignment explanation
Indices: 309291--309342 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
309281 TTTAATTTTA
309291 TTAAATTATATTAT
1 TTAAATTATATTAT
* *
309305 TAAAATTTTATTAT
1 TTAAATTATATTAT
309319 TAATAAATTATATTAT
1 T--TAAATTATATTAT
*
309335 TTACATTA
1 TTAAATTA
309343 ACTTTCATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 19 0.61
16 12 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATTATATTAT
Found at i:309552 original size:24 final size:24
Alignment explanation
Indices: 309525--309610 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 24
309515 TATCAATAAG
309525 TAAATTTATTAAAAATAAAATATT
1 TAAATTTATTAAAAATAAAATATT
*
309549 TAAAAATATAATTTAATAAAATTAAAAT-TT
1 T--AAAT-TTA-TT-A-AAAA-TAAAATATT
309579 TATAATTTATATAAAAAT-AAATA-T
1 TA-AATTTAT-TAAAAATAAAATATT
309603 TAAATTTA
1 TAAATTTA
309611 ATAATTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 21
0.68 0.03 0.29
Matches are distributed among these distances:
23 6 0.12
24 8 0.16
25 1 0.02
26 8 0.16
27 4 0.08
28 6 0.12
29 4 0.08
30 7 0.14
31 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATTTATTAAAAATAAAATATT
Found at i:309568 original size:16 final size:16
Alignment explanation
Indices: 309526--309583 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
309516 ATCAATAAGT
*
309526 AAATTTATTAAAAATA
1 AAATTTAATAAAAATA
309542 AAATATT--TAAAAATA
1 AAAT-TTAATAAAAATA
* *
309557 TAATTTAATAAAATTA
1 AAATTTAATAAAAATA
*
309573 AAATTTTATAA
1 AAATTTAATAA
309584 TTTATATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 2 0.06
15 11 0.31
16 20 0.57
17 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTAATAAAAATA
Found at i:310949 original size:21 final size:22
Alignment explanation
Indices: 310925--310967 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
310915 TATTTATGTA
*
310925 TAATATATTT-ATAAAAAAAAT
1 TAATAAATTTAATAAAAAAAAT
*
310946 TAATAAATTTAATATAAAAAAT
1 TAATAAATTTAATAAAAAAAAT
310968 AATGAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATAAATTTAATAAAAAAAAT
Found at i:310970 original size:21 final size:20
Alignment explanation
Indices: 310924--310970 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
310914 TTATTTATGT
*
310924 ATAATATATTTATAAAAAAA
1 ATAATAAATTTATAAAAAAA
*
310944 ATTAATAAATTTAATATAAAAA
1 A-TAATAAATTT-ATAAAAAAA
310966 ATAAT
1 ATAAT
310971 GAATACATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 13 0.57
22 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATAAATTTATAAAAAAA
Found at i:310983 original size:24 final size:24
Alignment explanation
Indices: 310934--310985 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
310924 ATAATATATT
* *
310934 TATAAAAAAAATTAATAAATTTAA
1 TATAAAAAAAATGAATAAATTCAA
*
310958 TATAAAAAATAATGAATACA-TCAA
1 TATAAAAAA-AATGAATAAATTCAA
310982 TATA
1 TATA
310986 TAAATGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (24 bp):
TATAAAAAAAATGAATAAATTCAA
Found at i:311277 original size:16 final size:17
Alignment explanation
Indices: 311256--311306 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 17
311246 AAAAATAAAT
311256 AAATTAATTAATT-TAA
1 AAATTAATTAATTATAA
311272 AAATTAATTAAATATTATAA
1 AAATTAATT--A-ATTATAA
311292 AAATTAAATTAATTA
1 AAATT-AATTAATTA
311307 AATTAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.30
18 5 0.17
19 4 0.13
20 8 0.27
21 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAATTAATTATAA
Found at i:311280 original size:20 final size:20
Alignment explanation
Indices: 311252--311336 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
311242 AGTAAAAAAT
*
311252 AAATAAATTAATTAATTTAA
1 AAATTAATTAATTAATTTAA
*
311272 AAATTAATTAAAT-ATTATAA
1 AAATTAATTAATTAATT-TAA
*
311292 AAATTAAATTAATTAAATT-A
1 AAATT-AATTAATTAATTTAA
*
311312 AAATTAATAAATTTAATTTAA
1 AAATTAATTAA-TTAATTTAA
311333 AAAT
1 AAAT
311337 AAAAAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 8 0.15
20 31 0.57
21 13 0.24
22 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTAATTAATTAATTTAA
Found at i:311284 original size:9 final size:9
Alignment explanation
Indices: 311255--311312 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
311245 AAAAAATAAA
311255 TAAATTAAT
1 TAAATTAAT
*
311264 TAATTTAA-
1 TAAATTAAT
311272 -AAATTAAT
1 TAAATTAAT
311280 TAAA-T-AT
1 TAAATTAAT
*
311287 TATAA-AAAT
1 TA-AATTAAT
311296 TAAATTAAT
1 TAAATTAAT
311305 TAAATTAA
1 TAAATTAA
311313 AATTAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
7 10 0.25
8 5 0.12
9 25 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TAAATTAAT
Found at i:311327 original size:15 final size:15
Alignment explanation
Indices: 311256--311324 Score: 60
Period size: 14 Copynumber: 4.9 Consensus size: 15
311246 AAAAATAAAT
*
311256 AAATTAATTAATTTAA
1 AAATTAATTAAATT-A
311272 AAATTAATTAAA-TA
1 AAATTAATTAAATTA
**
311286 TTA-TAA--AAATT-
1 AAATTAATTAAATTA
311297 AAATTAATTAAATTA
1 AAATTAATTAAATTA
311312 AAATTAA-TAAATT
1 AAATTAATTAAATT
311325 TAATTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
11 4 0.09
12 4 0.09
13 3 0.07
14 13 0.30
15 8 0.19
16 11 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTAATTAAATTA
Found at i:311343 original size:20 final size:20
Alignment explanation
Indices: 311304--311343 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
311294 ATTAAATTAA
* *
311304 TTAAATTAAAATTAATAAAT
1 TTAAATTAAAAATAAAAAAT
*
311324 TTAATTTAAAAATAAAAAAT
1 TTAAATTAAAAATAAAAAAT
311344 ATATAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAATTAAAAATAAAAAAT
Found at i:311368 original size:14 final size:14
Alignment explanation
Indices: 311346--311396 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
311336 TAAAAAATAT
311346 ATAAATTTATTTAA
1 ATAAATTTATTTAA
*
311360 ATTAATTTATTTAA
1 ATAAATTTATTTAA
*
311374 ATAAATTTTATTACAA
1 ATAAA-TTTATT-TAA
311390 ATAAATT
1 ATAAATT
311397 AAATCCAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 17 0.53
15 8 0.25
16 7 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAAATTTATTTAA
Found at i:311656 original size:15 final size:15
Alignment explanation
Indices: 311612--311656 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
311602 AGTATAAAGT
311612 TTTTAAGATATTTTGA
1 TTTTAA-ATATTTTGA
*
311628 TTTTATATTATTTTGA
1 TTTTA-AATATTTTGA
311644 TTTTAAATATTTT
1 TTTTAAATATTTT
311657 TGAATGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 18 0.69
17 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (15 bp):
TTTTAAATATTTTGA
Found at i:311713 original size:15 final size:15
Alignment explanation
Indices: 311669--311716 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
311659 AATGTGAAAT
311669 AATTAAATTAATATTTA
1 AATTAAA-TAA-ATTTA
*
311686 AATTAAATAAATTTG
1 AATTAAATAAATTTA
* *
311701 AATTAATTTAATTTA
1 AATTAAATAAATTTA
311716 A
1 A
311717 TATTTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATTAAATAAATTTA
Found at i:311758 original size:16 final size:15
Alignment explanation
Indices: 311718--311792 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 15
311708 TTAATTTAAT
311718 ATTTAAATTTATTTT-
1 ATTTAAA-TTATTTTA
**
311733 ATTTTGATTATTTATA
1 ATTTAAATTATTT-TA
311749 ATTTAAATTATTTTAA
1 ATTTAAATTATTTT-A
* *
311765 ATTTGAGTTATTTTTA
1 ATTTAAATTA-TTTTA
*
311781 TTTTAAATTATT
1 ATTTAAATTATT
311793 AATTTTTTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
14 6 0.13
15 9 0.19
16 28 0.60
17 4 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
ATTTAAATTATTTTA
Found at i:311786 original size:32 final size:30
Alignment explanation
Indices: 311718--311792 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 30
311708 TTAATTTAAT
*
311718 ATTTAAATTTATTTTATTTTGATTATTTATA
1 ATTTAAA-TTATTTTAATTTGATTATTTATA
*
311749 ATTTAAATTATTTTAAATTTGAGTTATTTTTA
1 ATTTAAATTATTTT-AATTTGA-TTATTTATA
*
311781 TTTTAAATTATT
1 ATTTAAATTATT
311793 AATTTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 7 0.18
31 13 0.33
32 19 0.49
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (30 bp):
ATTTAAATTATTTTAATTTGATTATTTATA
Found at i:315859 original size:19 final size:17
Alignment explanation
Indices: 315815--315859 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
315805 TAATTTTGTG
315815 ATTAAAAATATAAATAT
1 ATTAAAAATATAAATAT
* *
315832 AATATAAATATAAAAATAT
1 -AT-TAAAAATATAAATAT
315851 ATTAAAAAT
1 ATTAAAAAT
315860 TTATGTACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 4 0.17
19 13 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAAAATATAAATAT
Found at i:316428 original size:22 final size:22
Alignment explanation
Indices: 316397--316440 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
316387 TTTTGCTTTT
316397 AATATATAAA-AAATAAAATAAA
1 AATATATAAATAAAT-AAATAAA
*
316419 AATATTTAAATAAATAAATAAA
1 AATATATAAATAAATAAATAAA
316441 TAAATTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AATATATAAATAAATAAATAAA
Found at i:316788 original size:27 final size:28
Alignment explanation
Indices: 316750--316802 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
316740 ATCAATTTAA
316750 TTTTAAAATTAA-AAAATT-TAAATATT
1 TTTTAAAATTAATAAAATTATAAATATT
*
316776 TTTTAAGAATTAATCAAATTATAAATA
1 TTTTAA-AATTAATAAAATTATAAATA
316803 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 6 0.26
28 5 0.22
29 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTTAAAATTAATAAAATTATAAATATT
Found at i:316810 original size:14 final size:14
Alignment explanation
Indices: 316791--316833 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
316781 AGAATTAATC
316791 AAATTATAAATAAA-
1 AAATTA-AAATAAAT
*
316805 AAATTAAATTAAAT
1 AAATTAAAATAAAT
*
316819 AAATTAAAATTAAT
1 AAATTAAAATAAAT
316833 A
1 A
316834 GATTTGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAAAATAAAT
Found at i:317319 original size:2 final size:2
Alignment explanation
Indices: 317312--317346 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
317302 AGACCCGGAA
317312 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
317347 AGCTAACCTA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:320689 original size:20 final size:21
Alignment explanation
Indices: 320660--320705 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
320650 TAATATCATA
320660 TTTT-AATTTTATTATT-A-TT
1 TTTTAAATTTTATT-TTAACTT
320679 TTTTAAATTTTATTTTAACTT
1 TTTTAAATTTTATTTTAACTT
320700 TTTTAA
1 TTTTAA
320706 TAAAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 10 0.42
21 8 0.33
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTAAATTTTATTTTAACTT
Found at i:323423 original size:181 final size:174
Alignment explanation
Indices: 323127--323479 Score: 419
Period size: 181 Copynumber: 2.0 Consensus size: 174
323117 TCTTTTAAAT
*
323127 TTTTTATATAATAATTTTTTTTGAAAAAATTAATTTTTAAAAAACTATTTATTTATTTTTAAATT
1 TTTTTATATAATAATTTTTTTTGAAAAAATTAATTTTTAAAAAACTATCTATTTATTTTTAAATT
* * * *
323192 ATTTTTAAGCAGATATTATTAATAAATTAAATCATGTAATATCTTTAAAAAATTTTAAAAATAAA
66 ATTTTTAAGCAGAAATTATTAAGAAATCAAATCATCTAATATCTTTAAAAAATTTTAAAAATAAA
** *
323257 TAT-AAAAA-TTTATTTTTAATAAGAGAATATTATTTAATTTAAG
131 TATAAAAAATTTTACGTTTAATAA-AAAATATTATTTAATTTAAG
*
323300 TTTTTATATAATAATTTTTTTTTGAAAACAATTAGTTTCTT-AAAAA-TGATCTATTTATTTTTT
1 TTTTTATATAATAA-TTTTTTTTGAAAA-AATTAATTT-TTAAAAAACT-ATCTATTTA-TTTTT
* * * * * *
323363 AAATTACCTATTTTTTAAGCATAAATTATTAAGGAATCAAATTATCTCAT-TTTATTAAAAATTT
61 AAA-T---TA-TTTTTAAGCAGAAATTATTAAGAAATCAAATCATCTAATATCT-TTAAAAAATT
*
323427 TTAAAAATAAATATAAAAAATTTTACGTTTATTAAAAAATATTATTTAATTTA
120 TTAAAAATAAATATAAAAAATTTTACGTTTAATAAAAAATATTATTTAATTTA
323480 TTAATAATAT
Statistics
Matches: 151, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
173 14 0.09
174 14 0.09
175 21 0.14
176 10 0.07
177 1 0.01
180 4 0.03
181 54 0.36
182 22 0.15
183 11 0.07
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (174 bp):
TTTTTATATAATAATTTTTTTTGAAAAAATTAATTTTTAAAAAACTATCTATTTATTTTTAAATT
ATTTTTAAGCAGAAATTATTAAGAAATCAAATCATCTAATATCTTTAAAAAATTTTAAAAATAAA
TATAAAAAATTTTACGTTTAATAAAAAATATTATTTAATTTAAG
Found at i:323734 original size:20 final size:21
Alignment explanation
Indices: 323709--323747 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
323699 ATAAAATAAA
323709 ATTTAAAAA-TTTTAATTATT
1 ATTTAAAAATTTTTAATTATT
323729 ATTTAAAAATTTTTAATTA
1 ATTTAAAAATTTTTAATTA
323748 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAAAAATTTTTAATTATT
Found at i:328612 original size:13 final size:14
Alignment explanation
Indices: 328586--328650 Score: 52
Period size: 14 Copynumber: 5.1 Consensus size: 14
328576 CAAAAAAAAT
328586 TATAAATATTTAAA
1 TATAAATATTTAAA
328600 TATAAAT-TTT--A
1 TATAAATATTTAAA
328611 -A-AAATA-TTAAA
1 TATAAATATTTAAA
*
328622 TATTAATATTTAAA
1 TATAAATATTTAAA
* * *
328636 AATAATTATATAAA
1 TATAAATATTTAAA
328650 T
1 T
328651 CAATTAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
9 6 0.15
10 1 0.03
11 2 0.05
12 1 0.03
13 7 0.18
14 22 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAATATTTAAA
Found at i:328623 original size:22 final size:24
Alignment explanation
Indices: 328589--328639 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
328579 AAAAAATTAT
328589 AAATATTTAAATATAAAT-TTTAA
1 AAATATTTAAATATAAATATTTAA
*
328612 AAATA-TTAAATATTAATATTTAA
1 AAATATTTAAATATAAATATTTAA
328635 AAATA
1 AAATA
328640 ATTATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATATTTAAATATAAATATTTAA
Found at i:328646 original size:22 final size:21
Alignment explanation
Indices: 328589--328650 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
328579 AAAAAATTAT
328589 AAATATTTAAATATAAATTTTAA
1 AAATA-TT-AATATAAATTTTAA
*
328612 AAATATTAAATATTAATATTTAA
1 AAATATT-AATATAAAT-TTTAA
328635 AAATAATT-ATATAAAT
1 AAAT-ATTAATATAAAT
328651 CAATTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 18 0.51
23 14 0.40
24 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATTAATATAAATTTTAA
Found at i:328848 original size:20 final size:18
Alignment explanation
Indices: 328823--328869 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
328813 TAAACATAAT
328823 ATAATTATATAATATAAATA
1 ATAATTA-A-AATATAAATA
328843 ATAATTAAAATATAAA-A
1 ATAATTAAAATATAAATA
328860 A-AA-TAAAATA
1 ATAATTAAAATA
328870 CAATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 2 0.07
18 8 0.30
19 1 0.04
20 7 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATTAAAATATAAATA
Found at i:328883 original size:20 final size:20
Alignment explanation
Indices: 328829--328929 Score: 85
Period size: 20 Copynumber: 4.8 Consensus size: 20
328819 TAATATAATT
328829 ATATAATATAAATAATAATTAAA
1 ATAT-ATATAAATAA-AA-TAAA
* * *
328852 ATATAAAAAAATAAAATACA
1 ATATATATAAATAAAATAAA
* *
328872 ATATATATAAATATATTAAA
1 ATATATATAAATAAAATAAA
* *
328892 ATTTATATAAATAAAATATTA
1 ATATATATAAATAAAATA-AA
*
328913 ATATATCATATATAAAA
1 ATATAT-ATAAATAAAA
328930 AATATTTTAA
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
20 33 0.53
21 8 0.13
22 17 0.27
23 4 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATATATAAATAAAATAAA
Found at i:328890 original size:40 final size:43
Alignment explanation
Indices: 328829--328927 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 43
328819 TAATATAATT
328829 ATATAATATAAATAATAATTAAAATATAAAAAAATAAAATA-CA
1 ATAT-ATATAAATAATAATTAAAATATAAAAAAATAAAATATCA
* * * *
328872 ATATATATAAAT-AT-ATTAAAATTTATATAAATAAAATATTA
1 ATATATATAAATAATAATTAAAATATAAAAAAATAAAATATCA
*
328913 ATATATCATATATAA
1 ATATAT-ATAAATAA
328928 AAAATATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
40 21 0.44
41 9 0.19
42 13 0.27
43 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (43 bp):
ATATATATAAATAATAATTAAAATATAAAAAAATAAAATATCA
Found at i:328958 original size:31 final size:33
Alignment explanation
Indices: 328905--328966 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
328895 TATATAAATA
*
328905 AAATATTAATATATCATATATAAAAAATATTTT
1 AAATATTAATATATAATATATAAAAAATATTTT
328938 AAATA-TAAT-TATAATATATAAAAAATATT
1 AAATATTAATATATAATATATAAAAAATATT
328967 AATACAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 19 0.68
32 4 0.14
33 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (33 bp):
AAATATTAATATATAATATATAAAAAATATTTT
Found at i:329620 original size:2 final size:2
Alignment explanation
Indices: 329613--329649 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
329603 GGTTTACTTT
329613 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 T
329650 GCAAGTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:330940 original size:14 final size:14
Alignment explanation
Indices: 330921--330973 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
330911 ATTTAAATGA
*
330921 ATAAAACATAAAAT
1 ATAAAAAATAAAAT
330935 ATAAAAAATAAAAT
1 ATAAAAAATAAAAT
330949 A-AAATAAATATAAATT
1 ATAAA-AAATA-AAA-T
330965 ATATAAAAA
1 ATA-AAAAA
330974 AATGATGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 3 0.09
14 19 0.58
15 3 0.09
16 2 0.06
17 4 0.12
18 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAAAAAATAAAAT
Found at i:330970 original size:20 final size:22
Alignment explanation
Indices: 330947--330994 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
330937 AAAAAATAAA
*
330947 ATAAAATAAAT-AT-AAATTAT
1 ATAAAATAAATGATGAAAGTAT
330967 ATAAAA-AAATGATGAAAGTAT
1 ATAAAATAAATGATGAAAGTAT
330988 ATAAAAT
1 ATAAAAT
330995 TATATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 8 0.33
21 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
ATAAAATAAATGATGAAAGTAT
Found at i:331364 original size:16 final size:15
Alignment explanation
Indices: 331329--331366 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
331319 TTTAAAATAA
331329 TATTTA-AAATATTT
1 TATTTATAAATATTT
*
331343 TTTTTATAAATATTT
1 TATTTATAAATATTT
331358 TAATTTATA
1 T-ATTTATA
331367 TTTTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 9 0.45
16 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATAAATATTT
Found at i:331549 original size:2 final size:2
Alignment explanation
Indices: 331542--331569 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
331532 GCAAAAATAC
331542 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
331570 GACAAGGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:336059 original size:13 final size:11
Alignment explanation
Indices: 336003--336051 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
335993 TACACAATAT
336003 TAATATAATAAA
1 TAATATAA-AAA
336015 TAAT-TAAAACA
1 TAATATAAAA-A
336026 TAA-A-AAAAA
1 TAATATAAAAA
336035 TAATATAAAAA
1 TAATATAAAAA
336046 TAATAT
1 TAATAT
336052 GTAAAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.12
10 7 0.21
11 18 0.55
12 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATATAAAAA
Found at i:336300 original size:36 final size:36
Alignment explanation
Indices: 336251--336326 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
336241 TTTTTCTTTA
* *
336251 TTTGGGTAGTTTCCCAAAAATAAAAATAGAGTTGCC
1 TTTGGGCACTTTCCCAAAAATAAAAATAGAGTTGCC
*
336287 TTTGGGCACTTTCCCAAAAATAACAATAGAGTTGCC
1 TTTGGGCACTTTCCCAAAAATAAAAATAGAGTTGCC
336323 TTTG
1 TTTG
336327 ATGAAATGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (36 bp):
TTTGGGCACTTTCCCAAAAATAAAAATAGAGTTGCC
Found at i:337076 original size:15 final size:15
Alignment explanation
Indices: 337055--337100 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
337045 TCATTGGTTC
337055 CGAGCTTGGAATCA-
1 CGAGCTTGGAATCAT
*
337069 CTGAGCTTGGAGTCAT
1 C-GAGCTTGGAATCAT
337085 CGAGCTTGGAATCAT
1 CGAGCTTGGAATCAT
337100 C
1 C
337101 ATGCTCAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (15 bp):
CGAGCTTGGAATCAT
Found at i:340405 original size:3 final size:3
Alignment explanation
Indices: 340397--340480 Score: 73
Period size: 3 Copynumber: 26.7 Consensus size: 3
340387 CTTAATTATA
* *
340397 AAT AAT AAT AAT AAAT AAT AGT AAC AAT AAAT AAAT AAAT AAT AAT -AT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT -AAT -AAT AAT AAT AAT
*
340445 AA- AAT AAT AGT AAT AAT AAT AAAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AA
340481 AAAGTTAGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.06
3 45 0.65
4 20 0.29
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:340416 original size:16 final size:16
Alignment explanation
Indices: 340397--340480 Score: 86
Period size: 16 Copynumber: 5.3 Consensus size: 16
340387 CTTAATTATA
340397 AATAATAATAATAAAT
1 AATAATAATAATAAAT
* *
340413 AATAGTAACAATAAAT
1 AATAATAATAATAAAT
340429 -A-AATAAATAATAATAT
1 AATAAT-AATAATAA-AT
*
340445 AA-AATAATAGT-AAT
1 AATAATAATAATAAAT
340459 AATAATAAATAATAAAT
1 AATAAT-AATAATAAAT
340476 AATAA
1 AATAA
340481 AAAGTTAGGG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.11
15 12 0.21
16 26 0.46
17 12 0.21
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAAAT
Found at i:340440 original size:37 final size:37
Alignment explanation
Indices: 340394--340480 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
340384 ATTCTTAATT
340394 ATAAATAATAATAAT-AAATAATAGTAACAATAAATAA
1 ATAAATAATAATAATAAAATAATAGTAACAAT-AATAA
*
340431 ATAAATAATAAT-ATAAAATAATAGTAATAATAATAA
1 ATAAATAATAATAATAAAATAATAGTAACAATAATAA
340467 AT-AATAAATAATAA
1 ATAAAT-AATAATAA
340481 AAAGTTAGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
35 3 0.07
36 15 0.33
37 28 0.61
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (37 bp):
ATAAATAATAATAATAAAATAATAGTAACAATAATAA
Found at i:340946 original size:20 final size:20
Alignment explanation
Indices: 340921--340962 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
340911 CTCATTAAAA
340921 TATATTTTTAT-ATTAATATT
1 TATATTTTTATAATTAA-ATT
340941 TATATTTTTATAATTAAATT
1 TATATTTTTATAATTAAATT
340961 TA
1 TA
340963 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTTTTATAATTAAATT
Found at i:341608 original size:21 final size:22
Alignment explanation
Indices: 341582--341626 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
341572 TTTTAATGTT
*
341582 TAAAAAATC-ACAAAAGAAAAA
1 TAAAAAATCTAAAAAAGAAAAA
*
341603 TAAAAAATCTAAAAAATAAAAA
1 TAAAAAATCTAAAAAAGAAAAA
341625 TA
1 TA
341627 TATAAGTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (22 bp):
TAAAAAATCTAAAAAAGAAAAA
Found at i:341892 original size:26 final size:27
Alignment explanation
Indices: 341831--341894 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
341821 TAAAATTTAA
341831 ATTTAATTCTATTAATATTTTATAAATT
1 ATTTAATT-TATTAATATTTTATAAATT
*
341859 -TTTAAATTT-TTAATTTTTTA-ATAATT
1 ATTT-AATTTATTAATATTTTATA-AATT
341885 ATTTAATTTA
1 ATTTAATTTA
341895 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
25 1 0.03
26 19 0.61
27 7 0.23
28 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTAATTTATTAATATTTTATAAATT
Found at i:342471 original size:22 final size:23
Alignment explanation
Indices: 342431--342474 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
342421 TTATTATATT
* *
342431 AATATTTTTATTATTTAAATAAA
1 AATATTTTTAATATATAAATAAA
342454 AATATTTTTAATA-ATAAATAA
1 AATATTTTTAATATATAAATAA
342475 TAATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTTTTAATATATAAATAAA
Done.