Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 3 of 27
Found at i:265949 original size:24 final size:24
Alignment explanation
Indices: 265897--265972 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
265887 AATGTATAAA
* *
265897 TAATTTATTTTTATA-TA-AAATT
1 TAATATATTTTTATATTATATATT
265919 TAAAATATATTTTTATATTATATATT
1 T--AATATATTTTTATATTATATATT
*
265945 TAATAT-TTTATTATATAATCATATT
1 TAATATATTT-TTATATTAT-ATATT
265970 TAA
1 TAA
265973 AATTATTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.02
23 3 0.07
24 26 0.58
25 10 0.22
26 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATATATTTTTATATTATATATT
Found at i:266703 original size:28 final size:26
Alignment explanation
Indices: 266646--266704 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
266636 AGTGAGCATG
* *
266646 ATTTTATTGTTAATCAACTTACCAGT
1 ATTTTATTGCTAATCAACTTACCAAT
* *
266672 ATTTTATTGCTAGATGCCACTTGCCAAT
1 ATTTTATTGCTA-AT-CAACTTACCAAT
266700 ATTTT
1 ATTTT
266705 GTTATTTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.41
27 2 0.07
28 14 0.52
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (26 bp):
ATTTTATTGCTAATCAACTTACCAAT
Found at i:267266 original size:30 final size:29
Alignment explanation
Indices: 267230--267341 Score: 109
Period size: 29 Copynumber: 3.8 Consensus size: 29
267220 GCATTGATAA
*
267230 TTAATTTACATTCAAATAAATTATTAATTT
1 TTAATTTACATTCAAATAAA-TCTTAATTT
* * *
267260 TTAATTTATACGT-AAATAAATCTTAATTA
1 TTAATTTACA-TTCAAATAAATCTTAATTT
* *
267289 TTAATTTACGTTAAAATAAATCTTAATTT
1 TTAATTTACATTCAAATAAATCTTAATTT
* * * *
267318 ATAATATATACTCAAATAAATCTT
1 TTAATTTACATTCAAATAAATCTT
267342 GGACACGAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
28 1 0.02
29 48 0.73
30 16 0.24
31 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (29 bp):
TTAATTTACATTCAAATAAATCTTAATTT
Found at i:267337 original size:58 final size:59
Alignment explanation
Indices: 267229--267341 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 59
267219 AGCATTGATA
* * *
267229 ATTAATTTACATTCAAATAAATTATTAATTTTTAATTTATACGTAAATAAATCTTAATT
1 ATTAATTTACATTAAAATAAATTATTAATTTATAATATATACGTAAATAAATCTTAATT
* *
267288 ATTAATTTACGTTAAAATAAA-TCTTAATTTATAATATATAC-TCAAATAAATCTT
1 ATTAATTTACATTAAAATAAATTATTAATTTATAATATATACGT-AAATAAATCTT
267342 GGACACGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 1 0.02
58 28 0.58
59 19 0.40
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (59 bp):
ATTAATTTACATTAAAATAAATTATTAATTTATAATATATACGTAAATAAATCTTAATT
Found at i:268508 original size:21 final size:22
Alignment explanation
Indices: 268461--268509 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
268451 AAATCGTTCA
*
268461 AATTAAATTTTAAATATAATTT
1 AATTTAATTTTAAATATAATTT
* *
268483 -TTTTAATTTTAAAT-TGATTT
1 AATTTAATTTTAAATATAATTT
268503 AATTTAA
1 AATTTAA
268510 ATTATTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTAATTTTAAATATAATTT
Found at i:268563 original size:21 final size:21
Alignment explanation
Indices: 268539--268581 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
268529 AATATATTTT
*
268539 ATATTTAAAT-TTAATTATAAA
1 ATATATAAATATTAA-TATAAA
268560 ATATATAAATATTAATATAAA
1 ATATATAAATATTAATATAAA
268581 A
1 A
268582 ATAGTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATATAAATATTAATATAAA
Found at i:274068 original size:17 final size:16
Alignment explanation
Indices: 274035--274086 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
274025 TAATAATTAT
274035 AATTATAATTATAAAA
1 AATTATAATTATAAAA
*
274051 AATTAATAATTTTTAAAA
1 AATT-ATAA-TTATAAAA
* * *
274069 TATTTTATTTATAAAA
1 AATTATAATTATAAAA
274085 AA
1 AA
274087 ATTTATAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 12 0.43
17 6 0.21
18 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATAATTATAAAA
Found at i:279614 original size:22 final size:21
Alignment explanation
Indices: 279562--279625 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
279552 TAAAAATTTA
279562 AATATATTTTATATTAATATT
1 AATATATTTTATATTAATATT
*
279583 TATATAATTTTATAATTAA-ATT
1 AATAT-ATTTTAT-ATTAATATT
*
279605 AATACTATTTAAATATTAATA
1 AATA-TATTT-TATATTAATA
279626 AAAATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.11
22 22 0.63
23 9 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATATTTTATATTAATATT
Found at i:280056 original size:19 final size:18
Alignment explanation
Indices: 280028--280068 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
280018 ATTTTTAAAA
280028 AATTAATTATAAAATTTT
1 AATTAATTATAAAATTTT
*
280046 AATTAAATTATTAAATTTT
1 AATT-AATTATAAAATTTT
280065 AATT
1 AATT
280069 TCATTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTAATTATAAAATTTT
Found at i:286001 original size:31 final size:32
Alignment explanation
Indices: 285963--286055 Score: 106
Period size: 31 Copynumber: 3.0 Consensus size: 32
285953 CTTAATTGGA
*
285963 AAAAAAAAAAGAAAGAAA-GAGAAAAAG-AAAG
1 AAAAAAAAAAGAAAAAAATG-GAAAAAGAAAAG
**
285994 AAAAAAAAAAGAAAAAAATGGAAATGGAAAAG
1 AAAAAAAAAAGAAAAAAATGGAAAAAGAAAAG
286026 AAAAAGAAAAAG--AAAAATGG-AAAAGAAAAG
1 AAAAA-AAAAAGAAAAAAATGGAAAAAGAAAAG
286056 TGGACATACT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
30 8 0.15
31 30 0.56
32 10 0.19
33 6 0.11
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (32 bp):
AAAAAAAAAAGAAAAAAATGGAAAAAGAAAAG
Found at i:286030 original size:6 final size:6
Alignment explanation
Indices: 285961--286054 Score: 65
Period size: 6 Copynumber: 15.8 Consensus size: 6
285951 GGCTTAATTG
* *
285961 GAAAAA -AAAAA -AGAAA GAAAGA GAAAAA G--AAA GAAAAA -AAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
* *
286004 GAAAAA -AATGGAAA TGGAAAA GAAAAA GAAAAA GAAAAA TGGAAAA GAAAA
1 GAAAAA GAA---AAA -GAAAAA GAAAAA GAAAAA GAAAAA -GAAAAA GAAAA
286055 GTGGACATAC
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
4 4 0.06
5 16 0.23
6 38 0.54
7 8 0.11
8 3 0.04
10 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:286059 original size:13 final size:12
Alignment explanation
Indices: 286015--286059 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
286005 AAAAAAATGG
286015 AAATGGAAAAGA
1 AAATGGAAAAGA
* *
286027 AAAAGAAAAAGAA
1 AAATGGAAAAG-A
286040 AAATGGAAAAGA
1 AAATGGAAAAGA
286052 AAAGTGGA
1 AAA-TGGA
286060 CATACTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 13 0.48
13 14 0.52
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (12 bp):
AAATGGAAAAGA
Found at i:286887 original size:17 final size:17
Alignment explanation
Indices: 286865--286900 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
286855 TTTTTAAATT
286865 AAAAAAAAAAGAAAAGA
1 AAAAAAAAAAGAAAAGA
* *
286882 AAAAAAAAAGGGAAAGA
1 AAAAAAAAAAGAAAAGA
286899 AA
1 AA
286901 GATGCGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAGA
Found at i:287011 original size:16 final size:17
Alignment explanation
Indices: 286990--287021 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
286980 ATGTTATATT
286990 TATATTTA-ATAAATTA
1 TATATTTATATAAATTA
287006 TATATTTATATAAATT
1 TATATTTATATAAATT
287022 TTAATACGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTTATATAAATTA
Found at i:289653 original size:2 final size:2
Alignment explanation
Indices: 289646--289685 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
289636 TTCACTTGGA
289646 AT AT AT AT AT 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 AT AT AT AT AT
289686 GCTTTTAGTA
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):
AT
Found at i:290601 original size:22 final size:21
Alignment explanation
Indices: 290559--290603 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
290549 GGCAGGCTTC
*
290559 AAAAAATTATTAAAATTTTTT
1 AAAAAATTATTAAAATATTTT
**
290580 AAAAAATTTATTTTAATATTTT
1 AAAAAA-TTATTAAAATATTTT
290602 AA
1 AA
290604 TATCTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAAAATTATTAAAATATTTT
Found at i:290860 original size:12 final size:12
Alignment explanation
Indices: 290843--290876 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
290833 TTTTATTCAT
*
290843 TTAATTTATTAG
1 TTAATTTATTAA
*
290855 TTAATTAATTAA
1 TTAATTTATTAA
290867 TTAATTTATT
1 TTAATTTATT
290877 TACATATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
TTAATTTATTAA
Found at i:294008 original size:18 final size:18
Alignment explanation
Indices: 293977--294015 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
293967 TTTTTTCTCC
* *
293977 CCTTTTCTCCTTTCTTTT
1 CCTTTCCTCCTTTCTTCT
*
293995 CCTTTCCTCTTTTCTTCT
1 CCTTTCCTCCTTTCTTCT
294013 CCT
1 CCT
294016 CTTGACCCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (18 bp):
CCTTTCCTCCTTTCTTCT
Found at i:294957 original size:21 final size:20
Alignment explanation
Indices: 294932--294972 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
294922 ATTTTTAAAA
294932 TATT-ATTTTATTTCTTAATTT
1 TATTAATTTT-TTTC-TAATTT
294953 TATTAATTTTTTTCTAATTT
1 TATTAATTTTTTTCTAATTT
294973 ATAAAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTAATTTTTTTCTAATTT
Found at i:295311 original size:18 final size:17
Alignment explanation
Indices: 295270--295314 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
295260 AAACTGAATT
295270 TGAAAAAATATAAAAAA
1 TGAAAAAATATAAAAAA
*
295287 TATAAAAAATAATAAAAAA
1 T-GAAAAAAT-ATAAAAAA
295306 TGAAAAAAT
1 TGAAAAAAT
295315 CAAGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 9 0.38
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
TGAAAAAATATAAAAAA
Found at i:295313 original size:9 final size:9
Alignment explanation
Indices: 295272--295306 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
295262 ACTGAATTTG
295272 AAAAAATAT
1 AAAAAATAT
295281 AAAAAATAT
1 AAAAAATAT
295290 AAAAAATAAT
1 AAAAAAT-AT
295300 AAAAAAT
1 AAAAAAT
295307 GAAAAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATAT
Found at i:295355 original size:13 final size:13
Alignment explanation
Indices: 295339--295385 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
295329 ATGTTAAATT
295339 TTTTTATTTGTTA
1 TTTTTATTTGTTA
295352 TTTTTATTTGTTCA
1 TTTTTATTTGTT-A
*
295366 CTTTTCT-TTTGTTT
1 -TTTT-TATTTGTTA
295380 TTTTTA
1 TTTTTA
295386 AAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
12 1 0.03
13 16 0.55
14 1 0.03
15 10 0.34
16 1 0.03
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTATTTGTTA
Found at i:296442 original size:11 final size:11
Alignment explanation
Indices: 296407--296460 Score: 74
Period size: 11 Copynumber: 4.9 Consensus size: 11
296397 TCATATTCAT
296407 TTTTTATATTA
1 TTTTTATATTA
296418 TGTTTTA-ATTA
1 T-TTTTATATTA
*
296429 TTTTTATATCA
1 TTTTTATATTA
*
296440 TTTTTTTATTA
1 TTTTTATATTA
296451 TTTTTATATT
1 TTTTTATATT
296461 TAAAGTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.14
11 27 0.73
12 5 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:296751 original size:22 final size:23
Alignment explanation
Indices: 296666--296751 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 23
296656 TCATCAAAAG
296666 TAAAT-ATTATTTAATATTTTAAA
1 TAAATAATTATTTAATA-TTTAAA
* * *
296689 TAAATAAATATCTAAT-TTAAAA
1 TAAATAATTATTTAATATTTAAA
*
296711 TAAATCAATGACTTTAATATTTAAA
1 TAAAT-AATTA-TTTAATATTTAAA
296736 TAAAT-ATTATTTAATA
1 TAAATAATTATTTAATA
296752 AAATTTATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
22 17 0.33
23 11 0.22
24 13 0.25
25 10 0.20
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (23 bp):
TAAATAATTATTTAATATTTAAA
Found at i:296875 original size:22 final size:22
Alignment explanation
Indices: 296850--296895 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
296840 TATCCAATTG
*
296850 AAATTAACATACAATTTTAAAT
1 AAATAAACATACAATTTTAAAT
* *
296872 AAATAAATATCCAATTTTAAAT
1 AAATAAACATACAATTTTAAAT
296894 AA
1 AA
296896 GTCAATGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAAACATACAATTTTAAAT
Found at i:297762 original size:34 final size:36
Alignment explanation
Indices: 297710--297776 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
297700 AAAATTATAC
297710 GAATATAAAATATATAAAATTATTAAAATATAATAT
1 GAATATAAAATATATAAAATTATTAAAATATAATAT
* * *
297746 GAATATATAAT-T-TAAAATTTTTATAATATAA
1 GAATATAAAATATATAAAATTATTAAAATATAA
297777 ATTATCAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 17 0.61
35 1 0.04
36 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (36 bp):
GAATATAAAATATATAAAATTATTAAAATATAATAT
Found at i:297787 original size:36 final size:37
Alignment explanation
Indices: 297692--297787 Score: 94
Period size: 36 Copynumber: 2.6 Consensus size: 37
297682 GAACTCATAA
297692 TTTTAAATA-AAATTATACGAATATAAAATATATAAAAT
1 TTTTAAATATAAATTAT-C-AATATAAAATATATAAAAT
* * *
297730 TATTAAA-ATATAA-TATGAATATATAAT-T-TAAAAT
1 TTTTAAATATA-AATTATCAATATAAAATATATAAAAT
297764 TTTTATAATATAAATTATCAATAT
1 TTTTA-AATATAAATTATCAATAT
297788 GTAAAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
34 10 0.21
35 5 0.10
36 20 0.42
37 1 0.02
38 10 0.21
39 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (37 bp):
TTTTAAATATAAATTATCAATATAAAATATATAAAAT
Found at i:308614 original size:19 final size:19
Alignment explanation
Indices: 308569--308616 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
308559 TAGTAAATAA
308569 AAATAATAAAAATATAAGAT
1 AAATAATAAAAATATAA-AT
*
308589 TAA-AATAAAAAT-TAAAT
1 AAATAATAAAAATATAAAT
308606 AAATTAATAAA
1 AAA-TAATAAA
308617 TTACTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 4 0.17
18 3 0.12
19 15 0.62
20 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATAATAAAAATATAAAT
Found at i:308624 original size:21 final size:20
Alignment explanation
Indices: 308592--308649 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
308582 ATAAGATTAA
308592 AATAAAA-A-TTAAATAAATT
1 AATAAAATACTTAAATAAA-T
*
308611 AATAAATTACTTAAATCAAAT
1 AATAAAATACTTAAAT-AAAT
* *
308632 ATTAAAATATTTAAATAA
1 AATAAAATACTTAAATAA
308650 GATTTACTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 3 0.09
21 20 0.62
22 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAAAATACTTAAATAAAT
Found at i:319738 original size:2 final size:2
Alignment explanation
Indices: 319733--319765 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
319723 TTCTTGGTGC
319733 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 A
319766 ATAAATTTAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:322482 original size:2 final size:2
Alignment explanation
Indices: 322475--322505 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
322465 AGTTTTTAGG
322475 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
322506 ATTGTATAAA
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:323287 original size:23 final size:23
Alignment explanation
Indices: 323261--323305 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
323251 TAAATAACTA
*
323261 ATTAGAGTTAAATTTTATTATAT
1 ATTAGAGTTAAATCTTATTATAT
323284 ATTAGAGTTAAATCTTATTATA
1 ATTAGAGTTAAATCTTATTATA
323306 ACGGAATCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (23 bp):
ATTAGAGTTAAATCTTATTATAT
Found at i:328789 original size:102 final size:102
Alignment explanation
Indices: 328639--328958 Score: 507
Period size: 102 Copynumber: 3.1 Consensus size: 102
328629 AAATAAATTT
** * * *
328639 ATTGTTGATTAAAT-AGTGATTTGGTAGTTTACCATTGTTGATTAAATGGATGATTTGTTGGTTT
1 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
* *
328703 TCCATTGTTGACTAAAAGGGAGATTTGGTAGCTTACC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
328740 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
* *
328805 GCTATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
328842 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
* * *
328907 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
66 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
328944 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
328959 GTGGTTTTTA
Statistics
Matches: 203, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
101 14 0.07
102 189 0.93
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (102 bp):
ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:328960 original size:34 final size:34
Alignment explanation
Indices: 328639--328960 Score: 359
Period size: 34 Copynumber: 9.5 Consensus size: 34
328629 AAATAAATTT
* *
328639 ATTGTTGATTAAATAGT-GATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGTAGATTTGGTAGCTTACC
* * * *
328672 ATTGTTGATTAAATGG-ATGATTTGTTGGTTTTCC
1 ATTGTTGATTAAATGGTA-GATTTGGTAGCTTACC
* * *
328706 ATTGTTGACTAAAAGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGTAGATTTGGTAGCTTACC
*
328740 ATTGTTGATTAAATGAG-AAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTAGATTTGGTAGCTTACC
* * * *
328774 ATTGTTGATTAAATGGGT-GATTTGGTGGTTTGCT
1 ATTGTTGATTAAAT-GGTAGATTTGGTAGCTTACC
* *
328808 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGTAGATTTGGTAGCTTACC
*
328842 ATTGTTGATTAAATGAG-AAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTAGATTTGGTAGCTTACC
* *
328876 ATTATTGATTAAATGGGT-GATTTGGTGGCTTACC
1 ATTGTTGATTAAAT-GGTAGATTTGGTAGCTTACC
* * *
328910 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGTAGATTTGGTAGCTTACC
328944 ATTGTTGATTAAATGGT
1 ATTGTTGATTAAATGGT
328961 GGTTTTTACC
Statistics
Matches: 243, Mismatches: 35, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
33 20 0.08
34 218 0.90
35 5 0.02
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGTAGATTTGGTAGCTTACC
Found at i:330985 original size:33 final size:33
Alignment explanation
Indices: 330948--331014 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
330938 TTCAACGATT
330948 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
330981 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
331014 T
1 T
331015 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:330986 original size:13 final size:13
Alignment explanation
Indices: 330968--330992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
330958 CATAAAATGT
330968 TGTATCGATACAA
1 TGTATCGATACAA
330981 TGTATCGATACA
1 TGTATCGATACA
330993 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:331073 original size:13 final size:13
Alignment explanation
Indices: 331055--331079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331045 ATTACTCAAA
331055 TGTATCGATACAT
1 TGTATCGATACAT
331068 TGTATCGATACA
1 TGTATCGATACA
331080 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:331181 original size:52 final size:52
Alignment explanation
Indices: 331088--331217 Score: 201
Period size: 52 Copynumber: 2.5 Consensus size: 52
331078 CACTGATCTT
* *
331088 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATT-AAA
331139 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
* *
331191 TGTATCGATACATGCAAGCAACTTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
331218 ATATTTCGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 19 0.26
52 51 0.70
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
Found at i:337184 original size:102 final size:101
Alignment explanation
Indices: 337009--337227 Score: 321
Period size: 102 Copynumber: 2.2 Consensus size: 101
336999 AAGTGGGAGA
** * * * * * *
337009 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTCGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGATCGCTTA
337074 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
337110 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGATGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGATCGCTT
* * *
337175 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
337212 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
337228 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 89 0.85
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGATCGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:337228 original size:34 final size:33
Alignment explanation
Indices: 337009--337229 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 33
336999 AAGTGGGAGA
*
337009 ATTGTTGATTAAATGGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
* * *
337042 ATTGTTGATTAAATGGGTGATTTGGTCGTTTGCC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* *
337076 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
**
337110 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGCTTACC
* * *
337144 ATTATTGATTAAATGCGTGATTTGATGGCTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGCTTACC
* * *
337178 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGT-GATTTGGTAGCTTACC
337212 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
337230 GTTTTTACCA
Statistics
Matches: 163, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
33 18 0.11
34 145 0.89
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
Found at i:338561 original size:15 final size:17
Alignment explanation
Indices: 338529--338563 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
338519 TTCTTATTGT
338529 TAAGATTTTATCTTAAA
1 TAAGATTTTATCTTAAA
338546 TAAGA-TTTAT-TTAAA
1 TAAGATTTTATCTTAAA
338561 TAA
1 TAA
338564 TATATCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 5 0.28
17 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (17 bp):
TAAGATTTTATCTTAAA
Found at i:339301 original size:50 final size:50
Alignment explanation
Indices: 339233--339465 Score: 308
Period size: 50 Copynumber: 4.6 Consensus size: 50
339223 AGTTGTTGTC
* * * * *
339233 ATTGTTGACTATTATTCACCAACCTTTGACAATAGAGAAAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGATCATA
* * * *
339283 ATTGTTGATGATTCTTCACCAATCTTTGACAATAGAGAGAGGT-AACTATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGATC-ATA
339333 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGT-AGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGA-TCATA
* * * *
339383 ATTGTTGACAATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGATCATA
339434 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
339466 ATGTGGTCAT
Statistics
Matches: 161, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.01
50 114 0.71
51 45 0.28
52 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGATCATA
Found at i:339410 original size:100 final size:101
Alignment explanation
Indices: 339233--339465 Score: 360
Period size: 100 Copynumber: 2.3 Consensus size: 101
339223 AGTTGTTGTC
* * * * **
339233 ATTGTTGACTATTATTCACCAACCTTTGACAATAGAGAAAGGTGGTCGTAATTGTTGATGATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAAGGTAGTCATAATTGTTGACAATTCT
* *
339298 TCACCAATCTTTGAC-AATAGAGAGAGGTAACTATT
66 TCACCAACCTTTGACAAATAGAGAGAGGTAACCATT
*
339333 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTAGTCATAATTGTTGACAATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAAGGTAGTCATAATTGTTGACAATTCT
* *
339398 TCACCAACCTTTGACAAATGGAGAGAGGTGACCATT
66 TCACCAACCTTTGACAAATAGAGAGAGGTAACCATT
339434 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
339466 ATGTGGTCAT
Statistics
Matches: 121, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 72 0.60
101 49 0.40
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (101 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAAGGTAGTCATAATTGTTGACAATTCT
TCACCAACCTTTGACAAATAGAGAGAGGTAACCATT
Found at i:344044 original size:101 final size:100
Alignment explanation
Indices: 343879--344061 Score: 285
Period size: 101 Copynumber: 1.8 Consensus size: 100
343869 AGTTGTTGCC
* * ** *
343879 ATTGTTGACTATCCTTCACCAACCTTTGATAATAGAGAGAGGTGGTCGTAATTGTTGACGATTCT
1 ATTGTTGACGATCCTTCACCAACCTTTGAAAATAGAGAGAGGTGACCATAATTGTTGACGATTCT
343944 TCACCAACCTTTGACAATAGAAAGAGGTGGCCATT
66 TCACCAACCTTTGACAATAGAAAGAGGTGGCCATT
* * *
343979 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGACCATTATTGTTGACGATTC
1 ATTGTTGACGATCCTTCACCAACCTTTGA-AAATAGAGAGAGGTGACCATAATTGTTGACGATTC
344044 TTCACCAACCTTTGACAA
65 TTCACCAACCTTTGACAA
344062 ATGTGGCCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 27 0.36
101 47 0.64
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (100 bp):
ATTGTTGACGATCCTTCACCAACCTTTGAAAATAGAGAGAGGTGACCATAATTGTTGACGATTCT
TCACCAACCTTTGACAATAGAAAGAGGTGGCCATT
Found at i:344064 original size:51 final size:51
Alignment explanation
Indices: 343879--344063 Score: 275
Period size: 50 Copynumber: 3.7 Consensus size: 51
343869 AGTTGTTGCC
* * * * * *
343879 ATTGTTGACTATCCTTCACCAACCTTTGA-TAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
*
343929 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAAAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
* *
343979 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
344030 ATTGTTGACGATTCTTCACCAACCTTTGACAAAT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAAT
344064 GTGGCCATAA
Statistics
Matches: 124, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 73 0.59
51 51 0.41
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (51 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
Found at i:344653 original size:34 final size:33
Alignment explanation
Indices: 344591--344806 Score: 218
Period size: 34 Copynumber: 6.4 Consensus size: 33
344581 AAGTAGTTTC
* * * *
344591 TGTTAATTAAATAGTGATTTAGTAGTTTATCAT
1 TGTTGATTAAATGGAGATTTGGTAGTTTATCAT
* * * *
344624 TATTGATTAAATGGTTGATTTGGTGGTTTATTAT
1 TGTTGATTAAATGG-AGATTTGGTAGTTTATCAT
* * *
344658 TGTTGACTAAATAGGAGATTTAGTAGTTTACCAT
1 TGTTGATTAAAT-GGAGATTTGGTAGTTTATCAT
* *
344692 TGTTGATTAAATGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGAGATTTGGTAGTTTATCAT
* *
344725 TGTTGATTAAATGGGTGATTTGGTGGTTTA-CTAT
1 TGTTGATTAAAT-GGAGATTTGGTAGTTTATC-AT
* * *
344759 TGTTGACTAAATGGGAGATTTGGTAGGTTGTCAT
1 TGTTGATTAAAT-GGAGATTTGGTAGTTTATCAT
344793 TGTTGATTAAATGG
1 TGTTGATTAAATGG
344807 TGGTTTTTAC
Statistics
Matches: 153, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
33 45 0.29
34 105 0.69
35 3 0.02
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.44
Consensus pattern (33 bp):
TGTTGATTAAATGGAGATTTGGTAGTTTATCAT
Found at i:344684 original size:68 final size:65
Alignment explanation
Indices: 344591--344808 Score: 233
Period size: 67 Copynumber: 3.3 Consensus size: 65
344581 AAGTAGTTTC
* * *
344591 TGTTAATTAAATA-GTGATTTAGTAGTTTATCATTATTGATTAAATGGTTGATTTGGTGGTTTAT
1 TGTTGATTAAATAGGTGATTTAGTAGTTTA-CATTGTTGATTAAATGG-AGATTTGGTGG-TTAT
*
344655 TAT
63 CAT
* * * *
344658 TGTTGACTAAATAGGAGATTTAGTAGTTTACCATTGTTGATTAAATGGAGATTTGGTAGCTTACC
1 TGTTGATTAAATAGGTGATTTAGTAGTTTA-CATTGTTGATTAAATGGAGATTTGGT-GGTTATC
344723 AT
64 AT
* * * * *
344725 TGTTGATTAAATGGGTGATTTGGTGGTTTACTATTGTTGACTAAATGGGAGATTTGGTAGGTTGT
1 TGTTGATTAAATAGGTGATTTAGTAGTTTAC-ATTGTTGATTAAAT-GGAGATTTGGT-GGTTAT
344790 CAT
63 CAT
344793 TGTTGATTAAAT-GGTG
1 TGTTGATTAAATAGGTG
344809 GTTTTTACCA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
66 1 0.01
67 66 0.51
68 62 0.48
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.44
Consensus pattern (65 bp):
TGTTGATTAAATAGGTGATTTAGTAGTTTACATTGTTGATTAAATGGAGATTTGGTGGTTATCAT
Found at i:344776 original size:101 final size:101
Alignment explanation
Indices: 344591--344806 Score: 306
Period size: 101 Copynumber: 2.1 Consensus size: 101
344581 AAGTAGTTTC
* * * * * * *
344591 TGTTAATTAAATAGTGATTTAGTAGTTTATCATTATTGATTAAATGGTTGATTTGGTGGTTTATT
1 TGTTGATTAAATGGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACT
*
344656 ATTGTTGACTAAATAGGAGATTTAGTAGTTTACCAT
66 ATTGTTGACTAAATAGGAGATTTAGTAGGTTACCAT
* *
344692 TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTACT
1 TGTTGATTAAATGGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACT
* * **
344757 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGTCAT
66 ATTGTTGACTAAATAGGAGATTTAGTAGGTTACCAT
344793 TGTTGATTAAATGG
1 TGTTGATTAAATGG
344807 TGGTTTTTAC
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.44
Consensus pattern (101 bp):
TGTTGATTAAATGGAGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACT
ATTGTTGACTAAATAGGAGATTTAGTAGGTTACCAT
Found at i:345156 original size:19 final size:19
Alignment explanation
Indices: 345112--345161 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
345102 TTGGTTGTTG
345112 AGGTACTATTCACGTATAT
1 AGGTACTATTCACGTATAT
**
345131 AAATACTATTCACGTATAT
1 AGGTACTATTCACGTATAT
*
345150 GGGTACTATTCA
1 AGGTACTATTCA
345162 TGCATACGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (19 bp):
AGGTACTATTCACGTATAT
Found at i:349263 original size:34 final size:34
Alignment explanation
Indices: 349207--349391 Score: 237
Period size: 34 Copynumber: 5.5 Consensus size: 34
349197 AAGTGGGAGA
* *
349207 ATTGTTGATTAAA-CGGTGATTTGATAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGTTTACC
* * *
349240 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGTTTACC
* * *
349274 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGTTTACC
*
349308 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGTTTACC
* * * * *
349342 ATTGTTGACTAAATAGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGTTTACC
349376 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
349392 TGGTTTTTAC
Statistics
Matches: 128, Mismatches: 23, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 12 0.09
34 116 0.91
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGTTTACC
Found at i:349307 original size:68 final size:68
Alignment explanation
Indices: 349207--349391 Score: 273
Period size: 68 Copynumber: 2.7 Consensus size: 68
349197 AAGTGGGAGA
* * * * * *
349207 ATTGTTGATTAAA-CGGTGATTTGATAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
*
349271 GCC
66 ACC
*
349274 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
349339 ACC
66 ACC
* *
349342 ATTGTTGACTAAATAGGAGATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
349392 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 12 0.11
68 95 0.89
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.41
Consensus pattern (68 bp):
ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
ACC
Found at i:349355 original size:102 final size:101
Alignment explanation
Indices: 349207--349391 Score: 273
Period size: 102 Copynumber: 1.8 Consensus size: 101
349197 AAGTGGGAGA
* * *
349207 ATTGTTGATTAAACGGTGATTTGATAGTTTACCATTATTGATTAAATGGGTGATTTGGT-GGTTT
1 ATTGTTGATTAAACGGTGATTTGATAGTTTACCATTATTGACTAAATAGGAGATTTGGTAGG-TT
349271 GCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
65 GCCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* * * *
349308 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATAGGAGATTTGGTAGGTT
1 ATTGTTGATTAAA-CGGTGATTTGATAGTTTACCATTATTGACTAAATAGGAGATTTGGTAGGTT
*
349373 GCCATTGTTGATTAAATGG
65 GCCATTGTTGACTAAATGG
349392 TGGTTTTTAC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 13 0.18
102 59 0.80
103 2 0.03
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAACGGTGATTTGATAGTTTACCATTATTGACTAAATAGGAGATTTGGTAGGTTG
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:353007 original size:17 final size:17
Alignment explanation
Indices: 352987--353020 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
352977 AATTATGTCA
352987 TTATATTAATCATAAAT
1 TTATATTAATCATAAAT
* *
353004 TTATTTTAATTATAAAT
1 TTATATTAATCATAAAT
353021 CATTTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATTAATCATAAAT
Found at i:353833 original size:17 final size:18
Alignment explanation
Indices: 353788--353834 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
353778 TTTTAATAAA
353788 TTATTAAATTAATTAATTT
1 TTATTAAATT-ATTAATTT
* * *
353807 ATCTTTAATTATT-ATTT
1 TTATTAAATTATTAATTT
353824 TTATTAAATTA
1 TTATTAAATTA
353835 ATAAAATATT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
17 12 0.55
18 3 0.14
19 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTAAATTATTAATTT
Found at i:354465 original size:20 final size:21
Alignment explanation
Indices: 354424--354467 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
354414 ATAATTTAAA
*
354424 TAAATATTGATACAATTCTAG
1 TAAATATTGATACAATTATAG
*
354445 TAAATATTG-TATAATTATAG
1 TAAATATTGATACAATTATAG
354465 TAA
1 TAA
354468 CTTCTGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
TAAATATTGATACAATTATAG
Found at i:354497 original size:21 final size:21
Alignment explanation
Indices: 354454--354509 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
354444 GTAAATATTG
354454 TATAATTATAGTAACTTCTGA
1 TATAATTATAGTAACTTCTGA
*
354475 TA-AATTATTGTTAACATTC-GA
1 TATAATTATAG-TAAC-TTCTGA
*
354496 TATAATTTTAGTAA
1 TATAATTATAGTAA
354510 TATTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.24
21 13 0.45
22 9 0.31
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (21 bp):
TATAATTATAGTAACTTCTGA
Found at i:354519 original size:21 final size:20
Alignment explanation
Indices: 354495--354627 Score: 106
Period size: 21 Copynumber: 6.3 Consensus size: 20
354485 TTAACATTCG
354495 ATATAATTTT-AGTAATATTTA
1 ATATAATTTTGA-TAAT-TTTA
*
354516 ATATAATTTTAATAATTATTA
1 ATATAATTTTGATAATT-TTA
* * *
354537 TTATAATTGTGATAATTTTG
1 ATATAATTTTGATAATTTTA
*
354557 ATATAATTTTGATAATTTTTT
1 ATATAATTTTGATAA-TTTTA
*
354578 ATATAATTTTGTTAATCTTTA
1 ATATAATTTTGATAAT-TTTA
* * * *
354599 TTGTAATTTTTATAGGATTTTG
1 ATATAATTTTGATA--ATTTTA
354621 ATATAAT
1 ATATAAT
354628 ATAATATAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
20 17 0.19
21 62 0.69
22 9 0.10
23 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.56
Consensus pattern (20 bp):
ATATAATTTTGATAATTTTA
Found at i:354532 original size:9 final size:9
Alignment explanation
Indices: 354497--354575 Score: 50
Period size: 9 Copynumber: 7.9 Consensus size: 9
354487 AACATTCGAT
354497 ATAATTTTA
1 ATAATTTTA
*
354506 GTAATATTTAA
1 ATAAT-TTT-A
354517 TATAATTTTA
1 -ATAATTTTA
354527 ATAATTATTA
1 ATAATT-TTA
* *
354537 TTATAATTGTG
1 --ATAATTTTA
354548 ATAATTTTGA
1 ATAATTTT-A
*
354558 TATAATTTTG
1 -ATAATTTTA
354568 ATAATTTT
1 ATAATTTT
354576 TTATATAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
9 25 0.45
10 7 0.13
11 13 0.24
12 10 0.18
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.54
Consensus pattern (9 bp):
ATAATTTTA
Found at i:354560 original size:62 final size:63
Alignment explanation
Indices: 354494--354627 Score: 157
Period size: 62 Copynumber: 2.1 Consensus size: 63
354484 GTTAACATTC
354494 GATATAATTTT-AGTAATATTTAATATAATTTTAATAAT-TATTATTATAATTGTGATA-ATTTT
1 GATATAATTTTGA-TAATATTTAATATAATTTTAATAATCT-TTATTATAATTGTGATAGATTTT
* * ** * * *
354556 GATATAATTTTGATAATTTTTTATATAATTTTGTTAATCTTTATTGTAATTTTTATAGGATTTT
1 GATATAATTTTGATAATATTTAATATAATTTTAATAATCTTTATTATAATTGTGATA-GATTTT
354620 GATATAAT
1 GATATAAT
354628 ATAATATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
62 46 0.75
63 2 0.03
64 13 0.21
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (63 bp):
GATATAATTTTGATAATATTTAATATAATTTTAATAATCTTTATTATAATTGTGATAGATTTT
Found at i:354583 original size:41 final size:42
Alignment explanation
Indices: 354507--354608 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 42
354497 ATAATTTTAG
354507 TAATATTTAATATAATTTTAATAATTATTATTATAATTGTGA
1 TAATATTTAATATAATTTTAATAATTATTATTATAATTGTGA
* * * * *
354549 TAAT-TTTGATATAATTTTGATAATT-TTTTATATAATTTTGT
1 TAATATTTAATATAATTTTAATAATTATTAT-TATAATTGTGA
* * *
354590 TAATCTTTATTGTAATTTT
1 TAATATTTAATATAATTTT
354609 TATAGGATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
40 3 0.06
41 32 0.64
42 15 0.30
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (42 bp):
TAATATTTAATATAATTTTAATAATTATTATTATAATTGTGA
Found at i:354584 original size:32 final size:33
Alignment explanation
Indices: 354548--354644 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 33
354538 TATAATTGTG
354548 ATAATTTTGATATAATT-TTGATAATTTTTTAT
1 ATAATTTTGATATAATTATTGATAATTTTTTAT
* **
354580 ATAATTTTGTTAATCTTTATTG-TAA-TTTTTAT
1 ATAATTTTGAT-ATAATTATTGATAATTTTTTAT
** *
354612 AGGATTTTGATATAATATAAT-ATAATTTTTTAT
1 ATAATTTTGATATAAT-TATTGATAATTTTTTAT
354645 GATTTTGATA
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
31 3 0.06
32 31 0.61
33 14 0.27
34 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.58
Consensus pattern (33 bp):
ATAATTTTGATATAATTATTGATAATTTTTTAT
Found at i:354665 original size:19 final size:19
Alignment explanation
Indices: 354633--354744 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 19
354623 ATAATATAAT
* *
354633 ATAATTTTTTATGATTTTG
1 ATAACTTTTAATGATTTTG
* * *
354652 ATAACCTTTAATGATATTA
1 ATAACTTTTAATGATTTTG
* *
354671 ATAGCCTTTAAAGTGA-TTTG
1 ATA-ACTTTTAA-TGATTTTG
* *
354691 ATAGCTTTTACTATGATTTTA
1 ATAACTTTTA--ATGATTTTG
*
354712 ATAATCTTTTACATAATTTTG
1 ATAA-CTTTTA-ATGATTTTG
354733 ATAACTTTTAAT
1 ATAACTTTTAAT
354745 TTTAAAAATA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
19 24 0.34
20 19 0.27
21 21 0.30
22 6 0.09
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (19 bp):
ATAACTTTTAATGATTTTG
Found at i:354736 original size:21 final size:21
Alignment explanation
Indices: 354687--354742 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
354677 TTTAAAGTGA
* *
354687 TTTGATAGCTTTTACTATGAT
1 TTTGATAACTTTTACTATAAT
*
354708 TTTAATAATCTTTTAC-ATAAT
1 TTTGATAA-CTTTTACTATAAT
354729 TTTGATAACTTTTA
1 TTTGATAACTTTTA
354743 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.20
21 17 0.57
22 7 0.23
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTGATAACTTTTACTATAAT
Found at i:355056 original size:21 final size:20
Alignment explanation
Indices: 355008--355063 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
354998 TAATCTTGAT
355008 AATTTTGGATAATCTTTGATAA
1 AATTTTGG-TAA-CTTTGATAA
* *
355030 AATTTTGGTAACATTTTATAG
1 AATTTTGGTAAC-TTTGATAA
*
355051 AATTTTTGTAACT
1 AATTTTGGTAACT
355064 AATATTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 20 0.67
22 8 0.27
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (20 bp):
AATTTTGGTAACTTTGATAA
Found at i:355485 original size:20 final size:20
Alignment explanation
Indices: 355460--355502 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
355450 TAGATAGTAA
*
355460 TAAATAAAATTACAATTTTT
1 TAAATAAAATTACAATTTAT
* *
355480 TAAATATAATTATAATTTAT
1 TAAATAAAATTACAATTTAT
355500 TAA
1 TAA
355503 GTAATAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATAAAATTACAATTTAT
Found at i:355830 original size:21 final size:21
Alignment explanation
Indices: 355791--355830 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
355781 ATTTAAAATT
* **
355791 TTTTATATAATTTTGATAATA
1 TTTTAAATAATTTAAATAATA
355812 TTTTAAATAATTTAAATAA
1 TTTTAAATAATTTAAATAA
355831 GTTTTAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTTAAATAATTTAAATAATA
Found at i:357110 original size:11 final size:11
Alignment explanation
Indices: 357085--357130 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 11
357075 CTTGTAACAT
357085 TAATTTTAATA
1 TAATTTTAATA
*
357096 -AATTTTTATA
1 TAATTTTAATA
357106 TAATTTTAATA
1 TAATTTTAATA
*
357117 -AATTTTGATA
1 TAATTTTAATA
357127 TAAT
1 TAAT
357131 ATTATTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 18 0.60
11 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TAATTTTAATA
Found at i:357110 original size:21 final size:21
Alignment explanation
Indices: 357085--357130 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
357075 CTTGTAACAT
*
357085 TAATTTTAATAAATTTTTATA
1 TAATTTTAATAAATTTTGATA
357106 TAATTTTAATAAATTTTGATA
1 TAATTTTAATAAATTTTGATA
357127 TAAT
1 TAAT
357131 ATTATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TAATTTTAATAAATTTTGATA
Found at i:357401 original size:4 final size:4
Alignment explanation
Indices: 357392--357440 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
357382 TTTAATGTTT
* **
357392 TTAA TTAA TTAA TTAGA TAAA TTAA TGTTT TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTA-A TTAA TTAA T-TAA TTAA TTAA TTAA TTAA TTA
357441 GATAAATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 32 0.86
5 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:357414 original size:17 final size:17
Alignment explanation
Indices: 357394--357449 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
357384 TAATGTTTTT
357394 AATTAATTAATTAGATA
1 AATTAATTAATTAGATA
** *
357411 AATTAATGTTTTTA-ATT
1 AATTAAT-TAATTAGATA
357428 AATTAATTAATTAGATA
1 AATTAATTAATTAGATA
357445 AATTA
1 AATTA
357450 GGGTCATAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 4 0.13
17 23 0.74
18 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
AATTAATTAATTAGATA
Found at i:357417 original size:30 final size:31
Alignment explanation
Indices: 357377--357436 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
357367 GTAAATATCC
357377 ATAAATTTAATGTTTTTAATTAATTAATTAG
1 ATAAATTTAATGTTTTTAATTAATTAATTAG
357408 ATAAA-TTAATGTTTTTAATTAATTAATTA
1 ATAAATTTAATGTTTTTAATTAATTAATTA
357437 ATTAGATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (31 bp):
ATAAATTTAATGTTTTTAATTAATTAATTAG
Found at i:361039 original size:2 final size:2
Alignment explanation
Indices: 361032--361072 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
361022 GCAAATCATT
* *
361032 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG 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
361073 CAATCAAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:361545 original size:20 final size:22
Alignment explanation
Indices: 361509--361550 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
361499 TTTATTAAAT
361509 TAATTATTTTATCTATAATTAA
1 TAATTATTTTATCTATAATTAA
*
361531 TAATT-TTTTAT-TATATTTAA
1 TAATTATTTTATCTATAATTAA
361551 GTATTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATTATTTTATCTATAATTAA
Found at i:375082 original size:13 final size:13
Alignment explanation
Indices: 375064--375102 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
375054 CAGCATTCTC
375064 TGTATCGATACAT
1 TGTATCGATACAT
*
375077 TGTATCGATACAC
1 TGTATCGATACAT
375090 TGTATCGATACAT
1 TGTATCGATACAT
375103 GGCAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:377588 original size:13 final size:13
Alignment explanation
Indices: 377570--377594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
377560 ATAATGCACA
377570 GTATCGATACATT
1 GTATCGATACATT
377583 GTATCGATACAT
1 GTATCGATACAT
377595 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:377683 original size:32 final size:33
Alignment explanation
Indices: 377642--377709 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
377632 CCTTAACTGT
*
377642 TTGTATCGATACAT-A-CAAGATATATCGATACA
1 TTGTATCGATACATGACCAA-ATATATAGATACA
*
377674 TTGTATCGATACATGACCAAATGTATAGATACA
1 TTGTATCGATACATGACCAAATATATAGATACA
377707 TTG
1 TTG
377710 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 15 0.47
34 3 0.09
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATATATAGATACA
Found at i:384671 original size:28 final size:28
Alignment explanation
Indices: 384639--384696 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
384629 TTTAGGCAGA
* *
384639 GTAATGAAGGAAAATGTGAAAACTTTAG
1 GTAATGAAGAAAAATGTGAAAACTTCAG
384667 GTAATGAAGAAAAATGTGAAAACTTCAG
1 GTAATGAAGAAAAATGTGAAAACTTCAG
384695 GT
1 GT
384697 TGTTGATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (28 bp):
GTAATGAAGAAAAATGTGAAAACTTCAG
Found at i:385839 original size:15 final size:16
Alignment explanation
Indices: 385819--385848 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
385809 CTTTTTTAAA
385819 AATAA-TATAAAAAAT
1 AATAATTATAAAAAAT
385834 AATAATTATAAAAAA
1 AATAATTATAAAAAA
385849 ATATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAATTATAAAAAAT
Found at i:385855 original size:12 final size:13
Alignment explanation
Indices: 385815--385855 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
385805 TTCTCTTTTT
385815 TAAAAATAATATA
1 TAAAAATAATATA
385828 -AAAAATAATAATTA
1 TAAAAATAAT-A-TA
385842 TAAAAA-AATATA
1 TAAAAATAATATA
385854 TA
1 TA
385856 TCATAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 13 0.52
13 2 0.08
14 5 0.20
15 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAAAAATAATATA
Found at i:385861 original size:17 final size:17
Alignment explanation
Indices: 385819--385863 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
385809 CTTTTTTAAA
385819 AATAAT-AT-AAAAAAT
1 AATAATCATAAAAAAAT
*
385834 AATAATTATAAAAAAAT
1 AATAATCATAAAAAAAT
385851 -ATATATCATAAAA
1 AATA-ATCATAAAA
385864 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.23
16 5 0.19
17 15 0.58
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATCATAAAAAAAT
Found at i:385871 original size:26 final size:28
Alignment explanation
Indices: 385811--385871 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 28
385801 ATTTTTCTCT
385811 TTTTTAAAAATAATATAAAAAATAATAA
1 TTTTTAAAAATAATATAAAAAATAATAA
* * **
385839 -TTATAAAAA-AATATATATCATAA-AA
1 TTTTTAAAAATAATATAAAAAATAATAA
385864 TTTTTAAA
1 TTTTTAAA
385872 TTTTATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
25 2 0.07
26 17 0.63
27 8 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTTTAAAAATAATATAAAAAATAATAA
Found at i:385938 original size:22 final size:22
Alignment explanation
Indices: 385876--385939 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
385866 TTTAAATTTT
* *
385876 ATAAATATAATATATTTTAAAT
1 ATAAATAAAATATATTTTAAAA
** *
385898 ATATCTAAAA-ATTAATTTAAAA
1 ATAAATAAAATA-TATTTTAAAA
385920 ATAAATAAAATATATTTTAA
1 ATAAATAAAATATATTTTAA
385940 CTTTTAAGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATAAAATATATTTTAAAA
Found at i:386047 original size:5 final size:5
Alignment explanation
Indices: 386033--386070 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
386023 GGAGGGAAGG
386033 TTTT- TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
386071 TACGGCCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:387980 original size:11 final size:11
Alignment explanation
Indices: 387964--387999 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
387954 TTTATTTTAC
387964 ATATTTATGTT
1 ATATTTATGTT
*
387975 ATATTTATATT
1 ATATTTATGTT
*
387986 ATTTTTATGTT
1 ATATTTATGTT
387997 ATA
1 ATA
388000 ACTATATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (11 bp):
ATATTTATGTT
Found at i:388026 original size:28 final size:28
Alignment explanation
Indices: 387974--388027 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
387964 ATATTTATGT
* *
387974 TATATTTATATTATTTTTATGTTATAAC
1 TATATTTAAATTATTTATATGTTATAAC
388002 TATATTTAAATTATTATATAT-TTATA
1 TATATTTAAATTATT-TATATGTTATA
388028 TAACTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
TATATTTAAATTATTTATATGTTATAAC
Found at i:388791 original size:24 final size:21
Alignment explanation
Indices: 388763--388827 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 21
388753 ATATTAATTA
*
388763 ATTATATTATATAAATTTTGATAT
1 ATTATATTAT-T-AA-TTTAATAT
388787 ATTATA-TATTAATTTAATAT
1 ATTATATTATTAATTTAATAT
**
388807 -TTATATTATTTTTTTAATAT
1 ATTATATTATTAATTTAATAT
388827 A
1 A
388828 ATAGTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.14
20 19 0.53
21 2 0.06
22 1 0.03
23 3 0.08
24 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTATATTATTAATTTAATAT
Found at i:388811 original size:17 final size:17
Alignment explanation
Indices: 388752--388814 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 17
388742 TTTATTTTAA
388752 TATATTAA-TTAATTATAT
1 TATATTAATTTAA-TAT-T
*
388770 TATATAAATTTTGATATATT
1 TATATTAA-TTT-A-ATATT
388790 ATATATTAATTTAATATT
1 -TATATTAATTTAATATT
388808 TATATTA
1 TATATTA
388815 TTTTTTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
17 7 0.18
18 12 0.32
19 1 0.03
20 6 0.16
21 11 0.29
22 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATATTAATTTAATATT
Found at i:389265 original size:20 final size:21
Alignment explanation
Indices: 389240--389283 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
389230 TCACATATTT
* *
389240 TATTTTTT-AATTATTTTTTA
1 TATTTTTTAAATTAATTTTAA
389260 TATTTTTTAAATTAATTTTAA
1 TATTTTTTAAATTAATTTTAA
389281 TAT
1 TAT
389284 AAATATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTTTAAATTAATTTTAA
Found at i:402033 original size:18 final size:18
Alignment explanation
Indices: 402010--402044 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
402000 TTCTTCATCT
*
402010 TCTTCTTCATCGTCGTCG
1 TCTTCTTCATCGCCGTCG
402028 TCTTCTTCATCGCCGTC
1 TCTTCTTCATCGCCGTC
402045 ATCGTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.37, G:0.14, T:0.43
Consensus pattern (18 bp):
TCTTCTTCATCGCCGTCG
Found at i:402887 original size:11 final size:11
Alignment explanation
Indices: 402860--402909 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
402850 AAATTTAGCC
*
402860 AATAAATTTAT
1 AATAAAATTAT
*
402871 AA-AAAATTAA
1 AATAAAATTAT
402881 AATAAAATTAT
1 AATAAAATTAT
*
402892 AAT-AATTATAT
1 AATAAAAT-TAT
402903 AATAAAA
1 AATAAAA
402910 AAACTTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 11 0.35
11 18 0.58
12 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAAAATTAT
Found at i:403932 original size:24 final size:20
Alignment explanation
Indices: 403905--403958 Score: 54
Period size: 24 Copynumber: 2.5 Consensus size: 20
403895 TTAATATAAA
403905 AATAATTTTAAAATATATAATTAT
1 AATAATTTT-AAATAT-T--TTAT
*
403929 AATAATAATTAAATATTTTAT
1 AATAAT-TTTAAATATTTTAT
403950 AATAATTTT
1 AATAATTTT
403959 TTTATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.07
21 10 0.37
23 1 0.04
24 12 0.44
25 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTTAAATATTTTAT
Found at i:404066 original size:22 final size:21
Alignment explanation
Indices: 404036--404078 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
404026 TTTTTATATC
* *
404036 TTAATATATTATAATATAAAT
1 TTAATATATAATAAGATAAAT
404057 TTAATGATATAATAAGATAAAT
1 TTAAT-ATATAATAAGATAAAT
404079 GTATTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
TTAATATATAATAAGATAAAT
Found at i:404297 original size:20 final size:20
Alignment explanation
Indices: 404272--404323 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
404262 ATAACACGAA
404272 AAATAATATAAATAGGACAT
1 AAATAATATAAATAGGACAT
*
404292 AAATAATATAAATAGGATAT
1 AAATAATATAAATAGGACAT
*
404312 GAATAAT-TAAAT
1 AAATAATATAAAT
404324 TTATCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATAATATAAATAGGACAT
Found at i:404667 original size:18 final size:19
Alignment explanation
Indices: 404644--404682 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
404634 TCTTAAATTT
*
404644 AATATAATACAAA-ATATA
1 AATATAACACAAATATATA
*
404662 AATATAACATAAATATATA
1 AATATAACACAAATATATA
404681 AA
1 AA
404683 AAAATTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATAACACAAATATATA
Found at i:406271 original size:32 final size:31
Alignment explanation
Indices: 406216--406280 Score: 78
Period size: 33 Copynumber: 2.1 Consensus size: 31
406206 AGTAAAAAAT
406216 AATTTAAAAATAAAAAATAATTATAAATTTTAA
1 AATTTAAAAATAAAAAATAATTAT--ATTTTAA
* **
406249 AATTTAAAATTATTAAAT-ATTATATTTTAA
1 AATTTAAAAATAAAAAATAATTATATTTTAA
406279 AA
1 AA
406281 ATAATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 9 0.31
32 5 0.17
33 15 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AATTTAAAAATAAAAAATAATTATATTTTAA
Found at i:411656 original size:20 final size:20
Alignment explanation
Indices: 411633--411671 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
411623 CTATTTTTAT
*
411633 TATTTTTTTAATATTAAAAA
1 TATTTTTTTAACATTAAAAA
411653 TATTTTTTTAACATTAAAA
1 TATTTTTTTAACATTAAAA
411672 TTCAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTTTTTAACATTAAAAA
Found at i:417961 original size:15 final size:16
Alignment explanation
Indices: 417941--417970 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
417931 GTTGTCACTG
417941 ATTTTAATA-AAAATA
1 ATTTTAATATAAAATA
417956 ATTTTAATATAAAAT
1 ATTTTAATATAAAAT
417971 TAAAAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTTAATATAAAATA
Found at i:420004 original size:8 final size:8
Alignment explanation
Indices: 419991--420017 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
419981 GGACATTTAC
419991 AATCATTT
1 AATCATTT
419999 AATCATTT
1 AATCATTT
420007 AATCATTT
1 AATCATTT
420015 AAT
1 AAT
420018 AAATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (8 bp):
AATCATTT
Found at i:421212 original size:28 final size:28
Alignment explanation
Indices: 421181--421276 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
421171 TGAAATAATT
*
421181 AAAATAATTAAAATATTATGTAATATTA
1 AAAATAATTAAAATATTATATAATATTA
* * *
421209 AAAATAA-TATAAATATAATATAAAAATA
1 AAAATAATTA-AAATATTATATAATATTA
* *
421237 TAAATATATTAAAAT-TTATATAATATGA
1 AAAATA-ATTAAAATATTATATAATATTA
*
421265 ATAAATTATTAA
1 A-AAATAATTAA
421277 TATTTAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.04
28 40 0.75
29 9 0.17
30 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATAATTAAAATATTATATAATATTA
Found at i:421259 original size:20 final size:20
Alignment explanation
Indices: 421203--421308 Score: 61
Period size: 19 Copynumber: 5.6 Consensus size: 20
421193 ATATTATGTA
* *
421203 ATATTAAAAATAATATAAAT
1 ATATTAAAATTTATATAAAT
421223 ATAATATAAAA---ATATAAAT
1 AT-AT-TAAAATTTATATAAAT
421242 ATATTAAAATTTATAT-AAT
1 ATATTAAAATTTATATAAAT
*
421261 ATGAAT-AAA-TTAT-T-AAT
1 AT-ATTAAAATTTATATAAAT
*
421278 AT-TTAAAATTTTTTATAAAT
1 ATATTAAAA-TTTATATAAAT
*
421298 AT-TTAATATTT
1 ATATTAAAATTT
421309 TAAATCTAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 23
0.72 0.04 0.23
Matches are distributed among these distances:
15 1 0.01
16 3 0.04
17 11 0.15
18 9 0.13
19 22 0.31
20 18 0.25
21 2 0.03
22 5 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (20 bp):
ATATTAAAATTTATATAAAT
Found at i:421261 original size:19 final size:19
Alignment explanation
Indices: 421183--421288 Score: 59
Period size: 17 Copynumber: 5.8 Consensus size: 19
421173 AAATAATTAA
*
421183 AATA-ATTAAAATATTATGT
1 AATATATTAAAAT-TTATAT
* *
421202 -A-ATATTAAAAATAATAT
1 AATATATTAAAATTTATAT
*
421219 AAATATAATATAAAA-ATATA-
1 -AATAT-AT-TAAAATTTATAT
421239 AATATATTAAAATTTATAT
1 AATATATTAAAATTTATAT
*
421258 AATATGAAT-AAA-TTAT-T
1 AATAT-ATTAAAATTTATAT
421275 AATAT-TTAAAATTT
1 AATATATTAAAATTT
421289 TTTATAAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
15 1 0.01
16 3 0.04
17 18 0.26
18 18 0.26
19 14 0.21
20 4 0.06
21 5 0.07
22 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AATATATTAAAATTTATAT
Found at i:421295 original size:36 final size:33
Alignment explanation
Indices: 421221--421288 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 33
421211 AATAATATAA
421221 ATATAATATAAAAATATAAATATATTAAAATTT
1 ATATAATATAAAAATATAAATATATTAAAATTT
*
421254 ATATAATATGAATAAATTATTAATAT-TTAAAATTT
1 ATATAATAT-AA-AAA-TATAAATATATTAAAATTT
421289 TTTATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 9 0.29
34 2 0.06
35 12 0.39
36 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
ATATAATATAAAAATATAAATATATTAAAATTT
Found at i:421309 original size:20 final size:20
Alignment explanation
Indices: 421270--421309 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
421260 TATGAATAAA
*
421270 TTATTAATATTTAAAATTTT
1 TTATAAATATTTAAAATTTT
*
421290 TTATAAATATTTAATATTTT
1 TTATAAATATTTAAAATTTT
421310 AAATCTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATAAATATTTAAAATTTT
Found at i:421585 original size:21 final size:21
Alignment explanation
Indices: 421536--421579 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
421526 TTAATATAAA
421536 AAAT-TAATTATAAAAAAATAT
1 AAATATAA-TATAAAAAAATAT
*
421557 AAATATAATATAAATAAATAT
1 AAATATAATATAAAAAAATAT
421578 AA
1 AA
421580 TAATAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATATAATATAAAAAAATAT
Found at i:423869 original size:20 final size:20
Alignment explanation
Indices: 423840--423878 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
423830 CTATCTTTAT
423840 TATTTCTTTAATATTAAAAA
1 TATTTCTTTAATATTAAAAA
*
423860 TATTTTTTTAATATTAAAA
1 TATTTCTTTAATATTAAAA
423879 TTCAATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTCTTTAATATTAAAAA
Found at i:431506 original size:38 final size:36
Alignment explanation
Indices: 431431--431498 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
431421 TGTGTTAGTA
431431 TTTATATTATTTTTTTCATATTTAAAATATTATATT
1 TTTATATTATTTTTTTCATATTTAAAATATTATATT
431467 TTTATA-TATTTTTTT-ATATATTAATAAT-TTAT
1 TTTATATTATTTTTTTCATAT-TTAA-AATATTAT
431499 TTTATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 4 0.13
35 17 0.57
36 9 0.30
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (36 bp):
TTTATATTATTTTTTTCATATTTAAAATATTATATT
Found at i:431714 original size:22 final size:20
Alignment explanation
Indices: 431673--431714 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
431663 TATTTATATT
*
431673 ATTTTTTATATTATGTTTTA
1 ATTTTTTATATTATCTTTTA
431693 ATTTTTTATATCTATCTATTTA
1 ATTTTTTATAT-TATCT-TTTA
431715 TCTATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTTATATTATCTTTTA
Found at i:432007 original size:14 final size:14
Alignment explanation
Indices: 431971--432019 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
431961 TATTTCATGT
* *
431971 ATATATTATTTT-T
1 ATATTTTATTTTAA
*
431984 ATATTATATTTTAA
1 ATATTTTATTTTAA
431998 ATATTTTATTTTAA
1 ATATTTTATTTTAA
*
432012 AAATTTTA
1 ATATTTTA
432020 AAAATTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATATTTTATTTTAA
Found at i:433586 original size:21 final size:22
Alignment explanation
Indices: 433556--433604 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
433546 ATATATTATA
*
433556 TTTATGTTTTTTAT-ATAAAAT
1 TTTATATTTTTTATAATAAAAT
**
433577 TTTATA-TTTTTATAATAATTT
1 TTTATATTTTTTATAATAAAAT
433598 TTTATAT
1 TTTATAT
433605 ATTAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATATTTTTTATAATAAAAT
Found at i:433610 original size:18 final size:17
Alignment explanation
Indices: 433589--433641 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
433579 TATATTTTTA
433589 TAATAATTTTTTATATAT
1 TAATAATTTTTTATAT-T
433607 TAATAATTTATTT-TATT
1 TAATAATTT-TTTATATT
*
433624 TCATATAAATTTTTATAT
1 T-A-ATAATTTTTTATAT
433642 GTATGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.07
18 16 0.53
19 12 0.40
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATAATTTTTTATATT
Found at i:433661 original size:57 final size:55
Alignment explanation
Indices: 433545--433661 Score: 123
Period size: 58 Copynumber: 2.1 Consensus size: 55
433535 AGAAAAAAAT
* * *
433545 TATATATTATATTTATGTTTTTTATATAAAATTTTATATTTTTATAATAATTTTT
1 TATATATTATATTTATGTTTTTTATATAAAATTTTATATGTATATAATAATTTTG
* *
433600 TATATATTAATAATTTAT-TTTATTTCATATAAATTTTTATATGTATGT-AT-ATTTATG
1 TATATATT-AT-ATTTATGTTT-TTT-ATATAAAATTTTATATGTATATAATAATTT-TG
433657 TATAT
1 TATAT
433662 GCATATTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
55 8 0.15
56 9 0.17
57 17 0.33
58 18 0.35
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (55 bp):
TATATATTATATTTATGTTTTTTATATAAAATTTTATATGTATATAATAATTTTG
Found at i:433938 original size:15 final size:16
Alignment explanation
Indices: 433902--433941 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
433892 TTTAATATTT
*
433902 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
433919 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
433934 ATAAAATT
1 ATAAAATT
433942 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:433944 original size:16 final size:17
Alignment explanation
Indices: 433902--433944 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
433892 TTTAATATTT
*
433902 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
433919 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
433934 ATAAAATTTAT
1 ATAAAATTTAT
433945 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:435039 original size:28 final size:27
Alignment explanation
Indices: 434999--435064 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 27
434989 TATATTTAAG
**
434999 TAATTAATTTTTATGTTAAATTATAAAA
1 TAATTAAAATTTATGTTAAATT-TAAAA
* * *
435027 TAATTAAAATTTATTTTTAATTTTAAA
1 TAATTAAAATTTATGTTAAATTTAAAA
435054 T-A-TAAAATTTA
1 TAATTAAAATTTA
435065 AATATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 9 0.27
26 1 0.03
27 5 0.15
28 18 0.55
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TAATTAAAATTTATGTTAAATTTAAAA
Found at i:435139 original size:21 final size:22
Alignment explanation
Indices: 435098--435149 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
435088 AAGTTATTTT
* *
435098 ATAATT-AAATTTTTATTAATA
1 ATAATTAAAATTTATATAAATA
435119 ATAATTAAAATTTATA-AAATA
1 ATAATTAAAATTTATATAAATA
*
435140 A-AAATAAAAT
1 ATAATTAAAAT
435150 ACTCCACCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.30
21 11 0.41
22 8 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATTAAAATTTATATAAATA
Found at i:435534 original size:18 final size:18
Alignment explanation
Indices: 435478--435519 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
435468 GAGATTTAGT
435478 ATAATACTTATGAAATCA
1 ATAATACTTATGAAATCA
435496 ATAATACTTATGAAATCA
1 ATAATACTTATGAAATCA
435514 ATAATA
1 ATAATA
435520 TTGATGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (18 bp):
ATAATACTTATGAAATCA
Found at i:436104 original size:38 final size:38
Alignment explanation
Indices: 436053--436129 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
436043 GATCCCAGAG
436053 TAAGTTTCCAGGAAGTCAAGAAATTGCTGTAAAGAGGC
1 TAAGTTTCCAGGAAGTCAAGAAATTGCTGTAAAGAGGC
436091 TAAGTTTCCAGGAAGTCAAGAAATTGCTGTAAAGAGGC
1 TAAGTTTCCAGGAAGTCAAGAAATTGCTGTAAAGAGGC
436129 T
1 T
436130 CCCCAGTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (38 bp):
TAAGTTTCCAGGAAGTCAAGAAATTGCTGTAAAGAGGC
Found at i:436999 original size:29 final size:29
Alignment explanation
Indices: 436918--437000 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
436908 AAATTTAATA
*
436918 AATAAATAAATAAAATAATTATCTAATCATTT
1 AATAAATAAATAAAACAA-T-T-TAATCATTT
* ** *
436950 AATAGATATTTACAATC-ATTTAATCATTT
1 AATAAATAAATA-AAACAATTTAATCATTT
436979 AATAAATAAATAAAACAATTTA
1 AATAAATAAATAAAACAATTTA
437001 TCTAAAAGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
28 3 0.08
29 23 0.57
30 1 0.03
31 1 0.03
32 10 0.25
33 2 0.05
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (29 bp):
AATAAATAAATAAAACAATTTAATCATTT
Found at i:437444 original size:125 final size:127
Alignment explanation
Indices: 437315--437549 Score: 307
Period size: 125 Copynumber: 1.9 Consensus size: 127
437305 TCAATGATGG
* ** *
437315 AAAGTTTAGATTAATAAGGACTTT-AAGATAAGTAAGAAAATAATAAATAAATTTTAGTTAATAT
1 AAAGTTTAAATTAATAAGGA-TTTCAAGATAAGTAAGAAAATAATAAATAAAGATTAGGTAATA-
*
437379 TTTAA-TA-AAAAAATCA-TTAATAAAAACTTAGATTAAAAATTAATTAATAAGAAAAAATATA
64 TTTAATTATAAAAAATCATTTAATAAAAAATTAGATTAAAAATTAATTAATAAGAAAAAATATA
* * *
437440 AAAGTTTAAATTAATTAGGATTTCAAGGTTAGTAAGAAAATAATAAATAAAGATTAGGTAATATT
1 AAAGTTTAAATTAATAAGGATTTCAAGATAAGTAAGAAAATAATAAATAAAGATTAGGTAATATT
* **
437505 TAATTTATTAAAAATTCATTTAATAAAAAATTATTTTAAAAATTA
66 TAA-TTA-TAAAAAATCATTTAATAAAAAATTAGATTAAAAATTA
437550 GATAAAACTA
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
124 8 0.09
125 52 0.56
126 2 0.02
128 8 0.09
129 23 0.25
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (127 bp):
AAAGTTTAAATTAATAAGGATTTCAAGATAAGTAAGAAAATAATAAATAAAGATTAGGTAATATT
TAATTATAAAAAATCATTTAATAAAAAATTAGATTAAAAATTAATTAATAAGAAAAAATATA
Found at i:448900 original size:22 final size:24
Alignment explanation
Indices: 448863--448928 Score: 88
Period size: 22 Copynumber: 3.0 Consensus size: 24
448853 GATCTTATTT
*
448863 ATATT-ATTATATAAATAATA-AA
1 ATATTAATTATAAAAATAATATAA
448885 AT-TTAATTATAAAAAT-ATATAA
1 ATATTAATTATAAAAATAATATAA
448907 ATATTAATT-TAAAAATAATATA
1 ATATTAATTATAAAAATAATATA
448929 TTTTAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 5 0.13
22 23 0.59
23 11 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTAATTATAAAAATAATATAA
Done.