AutoCloner

Multiple sequence alignment - TraesCS2D01G437400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS2D01G437400	chr2D	100.000	2558	0	0	1	2558	547558490	547561047	0.000000e+00	4724
1	TraesCS2D01G437400	chr2D	91.913	1657	93	18	911	2558	547574530	547576154	0.000000e+00	2279
2	TraesCS2D01G437400	chr2D	85.169	917	105	17	793	1700	547489054	547489948	0.000000e+00	911
3	TraesCS2D01G437400	chr2D	84.327	906	114	14	800	1700	547450609	547451491	0.000000e+00	861
4	TraesCS2D01G437400	chr2D	84.099	849	102	14	803	1640	547426983	547427809	0.000000e+00	789
5	TraesCS2D01G437400	chr2D	81.828	974	116	29	786	1724	547286282	547287229	0.000000e+00	761
6	TraesCS2D01G437400	chr2D	81.470	939	113	19	793	1700	547278134	547279042	0.000000e+00	713
7	TraesCS2D01G437400	chr2D	98.753	401	3	1	1	399	596567168	596567568	0.000000e+00	712
8	TraesCS2D01G437400	chr2D	86.798	356	46	1	2202	2556	547280383	547280738	1.840000e-106	396
9	TraesCS2D01G437400	chr2D	86.761	355	46	1	2202	2555	547452704	547453058	6.630000e-106	394
10	TraesCS2D01G437400	chr2D	86.286	350	47	1	2202	2550	547289047	547289396	1.860000e-101	379
11	TraesCS2D01G437400	chr2D	88.417	259	29	1	2297	2554	547491597	547491855	6.870000e-81	311
12	TraesCS2D01G437400	chr2D	79.830	352	59	7	423	765	387940137	387940485	1.970000e-61	246
13	TraesCS2D01G437400	chr2A	91.803	1769	108	10	804	2558	691392185	691390440	0.000000e+00	2429
14	TraesCS2D01G437400	chr2A	82.251	924	114	23	803	1700	690747284	690748183	0.000000e+00	752
15	TraesCS2D01G437400	chr2A	82.234	788	119	9	911	1697	690805346	690806113	0.000000e+00	660
16	TraesCS2D01G437400	chr2A	85.634	355	50	1	2202	2555	690808525	690808879	3.110000e-99	372
17	TraesCS2D01G437400	chr2A	92.105	152	9	3	797	945	690805064	690805215	7.170000e-51	211
18	TraesCS2D01G437400	chr2B	91.005	1423	89	13	908	2319	653808259	653809653	0.000000e+00	1882
19	TraesCS2D01G437400	chr2B	84.657	919	114	14	803	1718	653796087	653796981	0.000000e+00	891
20	TraesCS2D01G437400	chr2B	82.574	878	117	17	854	1724	653788261	653789109	0.000000e+00	741
21	TraesCS2D01G437400	chr2B	82.479	839	116	17	1746	2558	653800485	653801318	0.000000e+00	706
22	TraesCS2D01G437400	chr2B	87.339	545	64	3	2019	2558	653809682	653810226	1.010000e-173	619
23	TraesCS2D01G437400	chr2B	85.427	398	45	5	400	787	528970737	528970343	3.960000e-108	401
24	TraesCS2D01G437400	chr5D	99.000	400	2	1	1	398	551377470	551377071	0.000000e+00	715
25	TraesCS2D01G437400	chr5D	98.753	401	3	1	1	399	460112955	460112555	0.000000e+00	712
26	TraesCS2D01G437400	chr5D	85.217	230	27	6	565	791	141410445	141410220	1.980000e-56	230
27	TraesCS2D01G437400	chr1D	99.000	400	3	1	1	399	444431	444830	0.000000e+00	715
28	TraesCS2D01G437400	chr1D	98.753	401	4	1	1	400	457023435	457023035	0.000000e+00	712
29	TraesCS2D01G437400	chr1D	81.557	244	30	7	548	788	415664834	415664603	1.210000e-43	187
30	TraesCS2D01G437400	chr7D	98.997	399	2	1	1	397	605132241	605132639	0.000000e+00	713
31	TraesCS2D01G437400	chr6D	98.997	399	2	1	1	397	455684249	455683851	0.000000e+00	713
32	TraesCS2D01G437400	chr4D	99.000	400	1	1	1	397	314618778	314619177	0.000000e+00	713
33	TraesCS2D01G437400	chr3D	98.997	399	3	1	1	398	137083370	137082972	0.000000e+00	713
34	TraesCS2D01G437400	chr7A	79.045	377	67	6	423	788	97851495	97851120	5.470000e-62	248
35	TraesCS2D01G437400	chr5A	82.422	256	42	3	524	777	222626694	222626948	1.190000e-53	220
36	TraesCS2D01G437400	chr5A	79.725	291	41	9	1435	1720	602413163	602413440	7.220000e-46	195

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS2D01G437400	chr2D	547558490	547561047	2557	False	4724.000000	4724	100.000000	1	2558	1	chr2D.!!$F3	2557
1	TraesCS2D01G437400	chr2D	547574530	547576154	1624	False	2279.000000	2279	91.913000	911	2558	1	chr2D.!!$F4	1647
2	TraesCS2D01G437400	chr2D	547426983	547427809	826	False	789.000000	789	84.099000	803	1640	1	chr2D.!!$F2	837
3	TraesCS2D01G437400	chr2D	547450609	547453058	2449	False	627.500000	861	85.544000	800	2555	2	chr2D.!!$F8	1755
4	TraesCS2D01G437400	chr2D	547489054	547491855	2801	False	611.000000	911	86.793000	793	2554	2	chr2D.!!$F9	1761
5	TraesCS2D01G437400	chr2D	547286282	547289396	3114	False	570.000000	761	84.057000	786	2550	2	chr2D.!!$F7	1764
6	TraesCS2D01G437400	chr2D	547278134	547280738	2604	False	554.500000	713	84.134000	793	2556	2	chr2D.!!$F6	1763
7	TraesCS2D01G437400	chr2A	691390440	691392185	1745	True	2429.000000	2429	91.803000	804	2558	1	chr2A.!!$R1	1754
8	TraesCS2D01G437400	chr2A	690747284	690748183	899	False	752.000000	752	82.251000	803	1700	1	chr2A.!!$F1	897
9	TraesCS2D01G437400	chr2A	690805064	690808879	3815	False	414.333333	660	86.657667	797	2555	3	chr2A.!!$F2	1758
10	TraesCS2D01G437400	chr2B	653808259	653810226	1967	False	1250.500000	1882	89.172000	908	2558	2	chr2B.!!$F3	1650
11	TraesCS2D01G437400	chr2B	653796087	653801318	5231	False	798.500000	891	83.568000	803	2558	2	chr2B.!!$F2	1755
12	TraesCS2D01G437400	chr2B	653788261	653789109	848	False	741.000000	741	82.574000	854	1724	1	chr2B.!!$F1	870

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
364	365	0.030638	CGGGATTAATGGCCTTTGCG	59.969	55.0	13.96	0.00	38.85	4.85	F
501	502	0.036388	ACGGGTTGCAATCGTCTCAT	60.036	50.0	20.07	3.16	30.89	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1497	1707	0.036164	ATCTGCAAACAGCCACGGTA	59.964	50.000	0.0	0.0	44.10	4.02	R
1611	1841	3.175976	AACGCCTTGTTTCGCACCG	62.176	57.895	0.0	0.0	37.59	4.94	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	9.889128	ATTCCTTTTGAATTCTTCTTGTTTGAA	57.111	25.926	7.05	0.00	40.92	2.69
34	35	9.717942	TTCCTTTTGAATTCTTCTTGTTTGAAA	57.282	25.926	7.05	0.00	0.00	2.69
35	36	9.889128	TCCTTTTGAATTCTTCTTGTTTGAAAT	57.111	25.926	7.05	0.00	0.00	2.17
45	46	9.761504	TTCTTCTTGTTTGAAATTTCATATGCA	57.238	25.926	21.10	13.98	37.00	3.96
46	47	9.932207	TCTTCTTGTTTGAAATTTCATATGCAT	57.068	25.926	21.10	3.79	37.00	3.96
47	48	9.967245	CTTCTTGTTTGAAATTTCATATGCATG	57.033	29.630	21.10	16.75	37.00	4.06
48	49	9.491675	TTCTTGTTTGAAATTTCATATGCATGT	57.508	25.926	21.10	0.00	37.00	3.21
63	64	9.555727	TCATATGCATGTATATAGTAGCGTAGA	57.444	33.333	14.95	3.89	33.57	2.59
76	77	8.843885	ATAGTAGCGTAGAATATGTGTACTGA	57.156	34.615	0.00	0.00	33.95	3.41
77	78	7.563888	AGTAGCGTAGAATATGTGTACTGAA	57.436	36.000	0.00	0.00	32.08	3.02
78	79	7.993101	AGTAGCGTAGAATATGTGTACTGAAA	58.007	34.615	0.00	0.00	32.08	2.69
79	80	7.914346	AGTAGCGTAGAATATGTGTACTGAAAC	59.086	37.037	0.00	0.00	32.08	2.78
80	81	6.864342	AGCGTAGAATATGTGTACTGAAACT	58.136	36.000	0.00	0.00	0.00	2.66
81	82	7.321153	AGCGTAGAATATGTGTACTGAAACTT	58.679	34.615	0.00	0.00	0.00	2.66
82	83	7.488471	AGCGTAGAATATGTGTACTGAAACTTC	59.512	37.037	0.00	0.00	0.00	3.01
83	84	7.274904	GCGTAGAATATGTGTACTGAAACTTCA	59.725	37.037	0.00	0.00	35.57	3.02
84	85	9.302345	CGTAGAATATGTGTACTGAAACTTCAT	57.698	33.333	0.00	0.00	36.46	2.57
87	88	9.725019	AGAATATGTGTACTGAAACTTCATCAA	57.275	29.630	0.00	0.00	36.46	2.57
153	154	9.594478	AACACTACAAATTAAAAAGAAACCAGG	57.406	29.630	0.00	0.00	0.00	4.45
154	155	8.755028	ACACTACAAATTAAAAAGAAACCAGGT	58.245	29.630	0.00	0.00	0.00	4.00
155	156	9.594478	CACTACAAATTAAAAAGAAACCAGGTT	57.406	29.630	0.00	0.00	0.00	3.50
159	160	9.607988	ACAAATTAAAAAGAAACCAGGTTTAGG	57.392	29.630	18.08	0.00	35.77	2.69
160	161	9.051679	CAAATTAAAAAGAAACCAGGTTTAGGG	57.948	33.333	18.08	0.00	35.77	3.53
161	162	6.734502	TTAAAAAGAAACCAGGTTTAGGGG	57.265	37.500	18.08	0.00	35.77	4.79
162	163	2.992847	AAGAAACCAGGTTTAGGGGG	57.007	50.000	18.08	0.00	35.77	5.40

Showing 1 to 25 of 389 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	9.761504	TGCATATGAAATTTCAAACAAGAAGAA	57.238	25.926	23.91	1.93	41.13	2.52
20	21	9.932207	ATGCATATGAAATTTCAAACAAGAAGA	57.068	25.926	23.91	4.00	41.13	2.87
21	22	9.967245	CATGCATATGAAATTTCAAACAAGAAG	57.033	29.630	23.91	9.77	41.13	2.85
22	23	9.491675	ACATGCATATGAAATTTCAAACAAGAA	57.508	25.926	23.91	8.45	41.13	2.52
37	38	9.555727	TCTACGCTACTATATACATGCATATGA	57.444	33.333	6.97	0.00	37.73	2.15
50	51	9.933723	TCAGTACACATATTCTACGCTACTATA	57.066	33.333	0.00	0.00	0.00	1.31
51	52	8.843885	TCAGTACACATATTCTACGCTACTAT	57.156	34.615	0.00	0.00	0.00	2.12
52	53	8.667076	TTCAGTACACATATTCTACGCTACTA	57.333	34.615	0.00	0.00	0.00	1.82
53	54	7.563888	TTCAGTACACATATTCTACGCTACT	57.436	36.000	0.00	0.00	0.00	2.57
54	55	7.914346	AGTTTCAGTACACATATTCTACGCTAC	59.086	37.037	0.00	0.00	0.00	3.58
55	56	7.993101	AGTTTCAGTACACATATTCTACGCTA	58.007	34.615	0.00	0.00	0.00	4.26
56	57	6.864342	AGTTTCAGTACACATATTCTACGCT	58.136	36.000	0.00	0.00	0.00	5.07
57	58	7.274904	TGAAGTTTCAGTACACATATTCTACGC	59.725	37.037	0.00	0.00	32.50	4.42
58	59	8.683550	TGAAGTTTCAGTACACATATTCTACG	57.316	34.615	0.00	0.00	32.50	3.51
61	62	9.725019	TTGATGAAGTTTCAGTACACATATTCT	57.275	29.630	0.00	0.00	41.08	2.40
127	128	9.594478	CCTGGTTTCTTTTTAATTTGTAGTGTT	57.406	29.630	0.00	0.00	0.00	3.32
128	129	8.755028	ACCTGGTTTCTTTTTAATTTGTAGTGT	58.245	29.630	0.00	0.00	0.00	3.55
129	130	9.594478	AACCTGGTTTCTTTTTAATTTGTAGTG	57.406	29.630	6.18	0.00	0.00	2.74
133	134	9.607988	CCTAAACCTGGTTTCTTTTTAATTTGT	57.392	29.630	26.95	2.11	37.01	2.83
134	135	9.051679	CCCTAAACCTGGTTTCTTTTTAATTTG	57.948	33.333	26.95	2.02	37.01	2.32
135	136	8.215050	CCCCTAAACCTGGTTTCTTTTTAATTT	58.785	33.333	26.95	2.76	37.01	1.82
136	137	7.202149	CCCCCTAAACCTGGTTTCTTTTTAATT	60.202	37.037	26.95	3.28	37.01	1.40
137	138	6.271391	CCCCCTAAACCTGGTTTCTTTTTAAT	59.729	38.462	26.95	4.03	37.01	1.40
138	139	5.603395	CCCCCTAAACCTGGTTTCTTTTTAA	59.397	40.000	26.95	8.17	37.01	1.52
139	140	5.149239	CCCCCTAAACCTGGTTTCTTTTTA	58.851	41.667	26.95	8.87	37.01	1.52

Showing 1 to 25 of 429 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.