AutoCloner

Multiple sequence alignment - TraesCS2A01G148500

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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	TraesCS2A01G148500	chr2A	100.000	2334	0	0	1	2334	95023200	95025533	0.000000e+00	4311.0
1	TraesCS2A01G148500	chr2A	92.045	792	55	4	443	1227	92976269	92975479	0.000000e+00	1107.0
2	TraesCS2A01G148500	chr2A	92.045	792	55	4	443	1227	388470557	388471347	0.000000e+00	1107.0
3	TraesCS2A01G148500	chr2A	91.919	792	56	4	443	1227	395716618	395715828	0.000000e+00	1101.0
4	TraesCS2A01G148500	chr2A	92.935	736	41	7	1222	1949	388471848	388472580	0.000000e+00	1061.0
5	TraesCS2A01G148500	chr2A	92.653	735	44	6	1222	1949	92974978	92974247	0.000000e+00	1050.0
6	TraesCS2A01G148500	chr2A	85.965	456	47	7	1	449	725592247	725591802	2.710000e-129	472.0
7	TraesCS2A01G148500	chr2A	85.965	456	47	7	1	449	725657328	725656883	2.710000e-129	472.0
8	TraesCS2A01G148500	chr2A	86.323	446	44	7	11	449	725538693	725538258	9.760000e-129	470.0
9	TraesCS2A01G148500	chr2A	89.385	179	16	1	271	449	395716844	395716669	3.020000e-54	222.0
10	TraesCS2A01G148500	chr2A	91.525	59	5	0	2273	2331	391111723	391111665	5.350000e-12	82.4
11	TraesCS2A01G148500	chr2D	95.180	1473	65	1	862	2334	616455587	616454121	0.000000e+00	2322.0
12	TraesCS2A01G148500	chr2D	94.655	449	21	3	1	449	616456438	616455993	0.000000e+00	693.0
13	TraesCS2A01G148500	chr6B	93.000	1200	84	0	862	2061	104121745	104122944	0.000000e+00	1751.0
14	TraesCS2A01G148500	chr6B	96.053	912	35	1	443	1353	420843372	420844283	0.000000e+00	1483.0
15	TraesCS2A01G148500	chr6B	92.172	792	54	4	443	1227	57587442	57588232	0.000000e+00	1112.0
16	TraesCS2A01G148500	chr6B	92.925	735	44	5	1222	1949	57588733	57589466	0.000000e+00	1062.0
17	TraesCS2A01G148500	chr6B	93.997	583	29	4	1754	2334	420844276	420844854	0.000000e+00	878.0
18	TraesCS2A01G148500	chr6B	93.289	447	24	5	1	446	420842877	420843318	0.000000e+00	654.0
19	TraesCS2A01G148500	chr6B	88.939	443	46	3	1	443	104120896	104121335	5.670000e-151	544.0
20	TraesCS2A01G148500	chr6B	92.746	193	12	2	2055	2245	104122902	104123094	6.350000e-71	278.0
21	TraesCS2A01G148500	chr6B	88.406	138	14	2	2195	2331	168775413	168775277	5.160000e-37	165.0
22	TraesCS2A01G148500	chr6B	91.597	119	10	0	2060	2178	168775585	168775467	5.160000e-37	165.0
23	TraesCS2A01G148500	chr1A	92.298	792	53	4	443	1227	458922952	458922162	0.000000e+00	1118.0
24	TraesCS2A01G148500	chr1A	93.061	735	43	5	1222	1949	458921661	458920928	0.000000e+00	1068.0
25	TraesCS2A01G148500	chrUn	91.919	792	56	4	443	1227	41816476	41817266	0.000000e+00	1101.0
26	TraesCS2A01G148500	chrUn	92.653	735	46	5	1222	1949	315701371	315702104	0.000000e+00	1051.0
27	TraesCS2A01G148500	chr5B	91.540	792	57	5	443	1227	480308415	480307627	0.000000e+00	1083.0
28	TraesCS2A01G148500	chr5B	85.746	456	48	5	1	449	237819201	237818756	1.260000e-127	466.0
29	TraesCS2A01G148500	chr5B	89.109	101	11	0	1961	2061	257027028	257026928	2.430000e-25	126.0
30	TraesCS2A01G148500	chr5B	97.143	35	1	0	2114	2148	61211295	61211261	2.500000e-05	60.2
31	TraesCS2A01G148500	chr3A	91.540	792	57	5	443	1227	35851586	35852374	0.000000e+00	1083.0
32	TraesCS2A01G148500	chr3A	91.938	707	47	7	1251	1949	35852875	35853579	0.000000e+00	981.0
33	TraesCS2A01G148500	chr3A	100.000	32	0	0	2147	2178	235369731	235369700	2.500000e-05	60.2
34	TraesCS2A01G148500	chr7B	91.915	705	49	5	1251	1949	520119296	520119998	0.000000e+00	979.0
35	TraesCS2A01G148500	chr7A	86.996	446	40	10	11	449	393337377	393336943	9.700000e-134	486.0
36	TraesCS2A01G148500	chr7A	84.978	446	48	8	11	449	401561879	401561446	3.560000e-118	435.0
37	TraesCS2A01G148500	chr7A	88.406	138	14	1	2060	2197	393332117	393331982	5.160000e-37	165.0
38	TraesCS2A01G148500	chr7A	88.406	138	14	1	2060	2197	401559335	401559200	5.160000e-37	165.0
39	TraesCS2A01G148500	chr1B	85.934	455	47	5	1	449	646746449	646746892	9.760000e-129	470.0
40	TraesCS2A01G148500	chr1B	93.103	145	6	3	2055	2197	646748940	646749082	2.350000e-50	209.0
41	TraesCS2A01G148500	chr1B	91.525	118	10	0	2060	2177	47213508	47213391	1.860000e-36	163.0

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	TraesCS2A01G148500	chr2A	95023200	95025533	2333	False	4311.000000	4311	100.000000	1	2334	1	chr2A.!!$F1	2333
1	TraesCS2A01G148500	chr2A	388470557	388472580	2023	False	1084.000000	1107	92.490000	443	1949	2	chr2A.!!$F2	1506
2	TraesCS2A01G148500	chr2A	92974247	92976269	2022	True	1078.500000	1107	92.349000	443	1949	2	chr2A.!!$R5	1506
3	TraesCS2A01G148500	chr2A	395715828	395716844	1016	True	661.500000	1101	90.652000	271	1227	2	chr2A.!!$R6	956
4	TraesCS2A01G148500	chr2D	616454121	616456438	2317	True	1507.500000	2322	94.917500	1	2334	2	chr2D.!!$R1	2333
5	TraesCS2A01G148500	chr6B	57587442	57589466	2024	False	1087.000000	1112	92.548500	443	1949	2	chr6B.!!$F1	1506
6	TraesCS2A01G148500	chr6B	420842877	420844854	1977	False	1005.000000	1483	94.446333	1	2334	3	chr6B.!!$F3	2333
7	TraesCS2A01G148500	chr6B	104120896	104123094	2198	False	857.666667	1751	91.561667	1	2245	3	chr6B.!!$F2	2244
8	TraesCS2A01G148500	chr1A	458920928	458922952	2024	True	1093.000000	1118	92.679500	443	1949	2	chr1A.!!$R1	1506
9	TraesCS2A01G148500	chrUn	41816476	41817266	790	False	1101.000000	1101	91.919000	443	1227	1	chrUn.!!$F1	784
10	TraesCS2A01G148500	chrUn	315701371	315702104	733	False	1051.000000	1051	92.653000	1222	1949	1	chrUn.!!$F2	727
11	TraesCS2A01G148500	chr5B	480307627	480308415	788	True	1083.000000	1083	91.540000	443	1227	1	chr5B.!!$R4	784
12	TraesCS2A01G148500	chr3A	35851586	35853579	1993	False	1032.000000	1083	91.739000	443	1949	2	chr3A.!!$F1	1506
13	TraesCS2A01G148500	chr7B	520119296	520119998	702	False	979.000000	979	91.915000	1251	1949	1	chr7B.!!$F1	698
14	TraesCS2A01G148500	chr7A	401559200	401561879	2679	True	300.000000	435	86.692000	11	2197	2	chr7A.!!$R3	2186
15	TraesCS2A01G148500	chr1B	646746449	646749082	2633	False	339.500000	470	89.518500	1	2197	2	chr1B.!!$F1	2196

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
366	379	0.254178	AAGGCAACAGCGAGATCCAT	59.746	50.0	0.0	0.0	41.41	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1553	2173	0.388649	GCTTTCTTCGCTGAGGACGA	60.389	55.0	0.0	0.0	37.86	4.2	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
178	187	1.076559	TCCTCCCATCGCCGAACTA	60.077	57.895	0.00	0.00	0.00	2.24
231	241	1.907807	GGGGCAGCAACACCATGAA	60.908	57.895	0.00	0.00	0.00	2.57
259	269	1.152943	AGGCGACGATCTCCTGCTA	60.153	57.895	0.00	0.00	28.88	3.49
355	368	4.659172	CGGGAGGCCAAGGCAACA	62.659	66.667	13.87	0.00	44.11	3.33
366	379	0.254178	AAGGCAACAGCGAGATCCAT	59.746	50.000	0.00	0.00	41.41	3.41
370	383	1.741732	GCAACAGCGAGATCCATGTCT	60.742	52.381	0.00	0.00	0.00	3.41
459	529	3.650139	GAAACTCTCCATGTGTACGTGT	58.350	45.455	0.00	0.00	0.00	4.49
506	576	3.568007	GGTTCTTCCAATGTGTGTGCTTA	59.432	43.478	0.00	0.00	35.97	3.09
561	631	1.846007	TGTGCCTGGTTCTTGTGTTT	58.154	45.000	0.00	0.00	0.00	2.83
723	811	8.177663	GTGATGCGTATAAATGGATAATTGAGG	58.822	37.037	0.00	0.00	0.00	3.86
809	897	9.904198	TGAGAATAATGGAATTTGAGATGTACA	57.096	29.630	0.00	0.00	37.87	2.90
850	939	7.577303	TCCATCTTGGAATTCTAAGCTACAAT	58.423	34.615	22.88	10.73	45.00	2.71
853	942	7.088589	TCTTGGAATTCTAAGCTACAATTGC	57.911	36.000	22.88	8.61	34.86	3.56
1007	1101	2.989571	GGATTCTTCAGGGGATGGGTAT	59.010	50.000	0.00	0.00	0.00	2.73
1145	1241	2.301346	CCTTGCAGGTTCAACTTCTGT	58.699	47.619	0.00	0.00	0.00	3.41
1201	1297	1.227556	GCTGTCAAGGTCCGTGTGT	60.228	57.895	4.63	0.00	0.00	3.72
1507	2126	1.686052	TGCCAACTGGGTGAACAAATC	59.314	47.619	0.00	0.00	39.65	2.17
1553	2173	4.394920	CACAATACCTTGCTAAACGATGGT	59.605	41.667	0.00	0.00	35.69	3.55
1600	2220	6.043243	TGTCTGTGACCCTCTAAAGAAGAAAT	59.957	38.462	0.00	0.00	32.46	2.17
1658	2278	5.997384	ACTTAATAGAAGTCGAACCCACT	57.003	39.130	0.00	0.00	0.00	4.00
1922	2551	1.751924	ACAGTCTAGCCGAACATCTCC	59.248	52.381	0.00	0.00	0.00	3.71
1939	2568	1.815003	CTCCCACAGATTTTGCCACTC	59.185	52.381	0.00	0.00	0.00	3.51
1975	2604	1.571919	CCGCATCCTTCTTTCTACCG	58.428	55.000	0.00	0.00	0.00	4.02
2099	2728	2.826287	CACCCCACGTGCACACAA	60.826	61.111	18.64	0.00	35.18	3.33
2114	2743	0.514255	CACAAGTCACTGCATCCACG	59.486	55.000	0.00	0.00	0.00	4.94
2200	2829	0.041238	TACTCCCTGCACCTGTAGCT	59.959	55.000	0.00	0.00	0.00	3.32
2221	2850	5.046448	AGCTTATTGCCATGAATTTGGTCAA	60.046	36.000	0.00	7.84	44.23	3.18
2239	2868	2.158667	TCAAAGTTGAGGAACTGGGTCC	60.159	50.000	0.00	0.00	41.87	4.46
2277	2906	2.912771	TGAAAAGCTCGTCAAGGACAA	58.087	42.857	0.00	0.00	32.09	3.18
2285	2914	3.717707	CTCGTCAAGGACAAAGTGAGAA	58.282	45.455	0.00	0.00	32.09	2.87
2287	2916	2.221981	CGTCAAGGACAAAGTGAGAAGC	59.778	50.000	0.00	0.00	32.09	3.86
2288	2917	2.550180	GTCAAGGACAAAGTGAGAAGCC	59.450	50.000	0.00	0.00	32.09	4.35
2291	2920	2.050144	AGGACAAAGTGAGAAGCCAGA	58.950	47.619	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	104	1.033746	CACGACGGGAGGGTAGCTAA	61.034	60.000	0.00	0.00	0.00	3.09
231	241	1.255667	ATCGTCGCCTGGGTGTTAGT	61.256	55.000	0.00	0.00	0.00	2.24
259	269	1.060163	AGCCCACACTAACCCACACT	61.060	55.000	0.00	0.00	0.00	3.55
311	321	1.006519	CTTCCTCCTCCTCTCTCCACA	59.993	57.143	0.00	0.00	0.00	4.17
355	368	0.965439	GGCTAGACATGGATCTCGCT	59.035	55.000	8.97	0.00	37.51	4.93
459	529	4.280425	TCAGATGCAGGCAAATACAACAAA	59.720	37.500	0.00	0.00	0.00	2.83
499	569	4.393834	TGCAGGTGTATTTCTTAAGCACA	58.606	39.130	10.92	4.44	0.00	4.57
561	631	4.956700	CAGGTAGTTCTATGTCCTGGAAGA	59.043	45.833	0.00	0.00	41.10	2.87
723	811	6.319658	ACATCTCATGAATAAATCACACCCAC	59.680	38.462	0.00	0.00	41.93	4.61
809	897	3.199508	AGATGGAGAGCAAACACATAGCT	59.800	43.478	0.00	0.00	42.17	3.32
850	939	5.129634	TCAAACCTATCAACACTTCAGCAA	58.870	37.500	0.00	0.00	0.00	3.91
853	942	6.867662	ACTTCAAACCTATCAACACTTCAG	57.132	37.500	0.00	0.00	0.00	3.02
914	1003	7.080353	TCTTGTAATTCGTCGAGTCAATCTA	57.920	36.000	0.00	0.00	0.00	1.98
945	1034	7.393234	CCTTTAACAGAACACCAAATCCAGATA	59.607	37.037	0.00	0.00	0.00	1.98
1007	1101	2.158827	TGAGCACTGTAACCAAGCAAGA	60.159	45.455	0.00	0.00	0.00	3.02
1145	1241	8.762645	ACAGAGTGATATCAGAAATTACCTCAA	58.237	33.333	5.42	0.00	0.00	3.02
1201	1297	3.674997	GAGCAAATCCAGGTTGTGTCTA	58.325	45.455	0.00	0.00	0.00	2.59
1428	2033	3.055385	TGACATACTTAACAGTCTGGGGC	60.055	47.826	4.53	0.00	32.53	5.80
1507	2126	7.279090	TGTGTACGGAACAATAACATAATCTGG	59.721	37.037	0.00	0.00	40.63	3.86
1553	2173	0.388649	GCTTTCTTCGCTGAGGACGA	60.389	55.000	0.00	0.00	37.86	4.20
1600	2220	6.644592	GCATTTGTTTCTTATGGCTTGTGTTA	59.355	34.615	0.00	0.00	0.00	2.41
1658	2278	4.155826	CGGTTATGCACTCCTCATTTTCAA	59.844	41.667	0.00	0.00	0.00	2.69
1852	2474	6.698766	GTGAATTTGAACATTCTATGGGATGC	59.301	38.462	0.00	0.00	34.66	3.91
1922	2551	2.165030	GGATGAGTGGCAAAATCTGTGG	59.835	50.000	0.00	0.00	0.00	4.17
1939	2568	1.202336	GCGGCCTTTTTCTCATGGATG	60.202	52.381	0.00	0.00	0.00	3.51
1953	2582	1.134371	GTAGAAAGAAGGATGCGGCCT	60.134	52.381	0.00	0.00	40.93	5.19
1957	2586	2.194271	GACGGTAGAAAGAAGGATGCG	58.806	52.381	0.00	0.00	0.00	4.73
1990	2619	2.296792	CATTGTGAACTGGACACCACA	58.703	47.619	0.00	0.00	37.70	4.17
2099	2728	2.743060	TGCGTGGATGCAGTGACT	59.257	55.556	0.00	0.00	40.62	3.41
2200	2829	6.767456	ACTTTGACCAAATTCATGGCAATAA	58.233	32.000	0.00	0.00	44.75	1.40
2221	2850	0.396811	CGGACCCAGTTCCTCAACTT	59.603	55.000	0.00	0.00	41.24	2.66
2239	2868	1.482182	TCATCTCCCTTGATGTGTCCG	59.518	52.381	0.00	0.00	43.03	4.79
2277	2906	6.229733	GCATCTATATTCTGGCTTCTCACTT	58.770	40.000	0.00	0.00	0.00	3.16
2285	2914	2.026449	GCCTGGCATCTATATTCTGGCT	60.026	50.000	15.17	0.00	38.73	4.75
2287	2916	2.625737	CGCCTGGCATCTATATTCTGG	58.374	52.381	20.29	0.00	0.00	3.86
2288	2917	2.625737	CCGCCTGGCATCTATATTCTG	58.374	52.381	20.29	0.00	0.00	3.02
2291	2920	1.279271	GTCCCGCCTGGCATCTATATT	59.721	52.381	20.29	0.00	0.00	1.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.