AutoCloner

Multiple sequence alignment - TraesCS4A01G168700

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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	TraesCS4A01G168700	chr4A	100.000	2321	0	0	1	2321	422763293	422760973	0.000000e+00	4287.0
1	TraesCS4A01G168700	chr4A	89.850	601	49	8	458	1051	306064649	306064054	0.000000e+00	761.0
2	TraesCS4A01G168700	chr4A	87.576	330	40	1	1002	1331	741807531	741807859	4.680000e-102	381.0
3	TraesCS4A01G168700	chr2B	95.009	2324	108	8	1	2318	502006441	502008762	0.000000e+00	3642.0
4	TraesCS4A01G168700	chr2B	94.000	100	6	0	2051	2150	782284313	782284214	3.990000e-33	152.0
5	TraesCS4A01G168700	chr2A	94.828	1682	81	6	1	1679	38124911	38123233	0.000000e+00	2619.0
6	TraesCS4A01G168700	chr2A	88.250	783	72	12	298	1063	545062398	545063177	0.000000e+00	918.0
7	TraesCS4A01G168700	chr2A	87.500	656	51	17	298	951	14862430	14861804	0.000000e+00	728.0
8	TraesCS4A01G168700	chr3B	93.660	1183	61	7	3	1183	52520301	52519131	0.000000e+00	1757.0
9	TraesCS4A01G168700	chr3B	93.443	976	51	8	1	973	510236829	510237794	0.000000e+00	1435.0
10	TraesCS4A01G168700	chr3B	90.588	170	12	1	2152	2321	761355553	761355388	3.000000e-54	222.0
11	TraesCS4A01G168700	chr3B	93.000	100	7	0	2051	2150	761355835	761355736	1.860000e-31	147.0
12	TraesCS4A01G168700	chr7B	90.437	1328	118	8	3	1324	725263211	725264535	0.000000e+00	1740.0
13	TraesCS4A01G168700	chr7B	89.308	159	7	2	1579	1737	743383474	743383622	8.460000e-45	191.0
14	TraesCS4A01G168700	chr7B	84.834	211	9	10	1858	2053	743383663	743383865	8.460000e-45	191.0
15	TraesCS4A01G168700	chr7B	90.909	77	4	1	1347	1420	743383297	743383373	1.470000e-17	100.0
16	TraesCS4A01G168700	chr7B	100.000	34	0	0	1789	1822	743383631	743383664	1.930000e-06	63.9
17	TraesCS4A01G168700	chr6B	95.125	923	43	2	1	921	432004029	432004951	0.000000e+00	1454.0
18	TraesCS4A01G168700	chr6B	90.000	600	49	6	298	889	391556393	391556989	0.000000e+00	765.0
19	TraesCS4A01G168700	chr6B	90.728	151	10	1	2168	2318	644284368	644284514	5.060000e-47	198.0
20	TraesCS4A01G168700	chr5D	88.715	576	40	8	749	1324	61857468	61858018	0.000000e+00	680.0
21	TraesCS4A01G168700	chr3D	92.781	471	28	3	726	1191	413349955	413349486	0.000000e+00	676.0
22	TraesCS4A01G168700	chr3D	89.096	376	37	4	881	1254	568344777	568344404	4.520000e-127	464.0
23	TraesCS4A01G168700	chr3D	94.333	300	15	2	1	300	505839963	505840260	2.100000e-125	459.0
24	TraesCS4A01G168700	chr3D	100.000	37	0	0	1250	1286	568319979	568319943	4.140000e-08	69.4
25	TraesCS4A01G168700	chr4B	83.210	673	76	20	664	1328	603002792	603003435	1.200000e-162	582.0
26	TraesCS4A01G168700	chr2D	80.134	745	108	28	1	737	598705596	598704884	9.510000e-144	520.0
27	TraesCS4A01G168700	chr2D	91.176	170	11	1	2152	2321	165690579	165690414	6.450000e-56	228.0
28	TraesCS4A01G168700	chr2D	95.000	100	5	0	2051	2150	165690861	165690762	8.590000e-35	158.0
29	TraesCS4A01G168700	chr6D	80.027	746	108	28	1	737	288780377	288781090	4.420000e-142	514.0
30	TraesCS4A01G168700	chr6A	82.309	537	71	15	1	530	99872554	99872035	5.880000e-121	444.0
31	TraesCS4A01G168700	chr6A	90.909	165	11	2	2152	2316	320935829	320935669	3.880000e-53	219.0
32	TraesCS4A01G168700	chr1B	88.650	326	34	1	1002	1324	687721323	687720998	6.010000e-106	394.0
33	TraesCS4A01G168700	chr1B	90.728	151	10	1	2168	2318	529988548	529988694	5.060000e-47	198.0
34	TraesCS4A01G168700	chr7D	91.765	170	10	1	2152	2321	262859585	262859420	1.390000e-57	233.0
35	TraesCS4A01G168700	chr7D	94.340	106	5	1	1608	1713	631818791	631818895	6.640000e-36	161.0
36	TraesCS4A01G168700	chr7D	85.207	169	12	5	1898	2053	631819326	631819494	6.640000e-36	161.0
37	TraesCS4A01G168700	chr7D	94.000	100	6	0	2051	2150	262859867	262859768	3.990000e-33	152.0
38	TraesCS4A01G168700	chr3A	91.176	170	10	2	2152	2321	549256786	549256622	2.320000e-55	226.0
39	TraesCS4A01G168700	chr3A	96.000	100	4	0	2051	2150	549257068	549256969	1.850000e-36	163.0
40	TraesCS4A01G168700	chr5B	90.000	170	13	1	2152	2321	15219805	15219640	1.400000e-52	217.0
41	TraesCS4A01G168700	chr7A	90.476	126	10	2	1574	1697	736552021	736551896	5.130000e-37	165.0
42	TraesCS4A01G168700	chr7A	81.579	152	18	5	1910	2051	736551490	736551339	1.460000e-22	117.0
43	TraesCS4A01G168700	chr7A	96.610	59	2	0	1350	1408	736552230	736552172	5.280000e-17	99.0
44	TraesCS4A01G168700	chr7A	82.432	74	11	2	1614	1686	736511265	736511337	1.930000e-06	63.9
45	TraesCS4A01G168700	chr5A	95.556	45	2	0	1347	1391	33888157	33888201	3.200000e-09	73.1
46	TraesCS4A01G168700	chr1D	95.238	42	2	0	1350	1391	156012355	156012314	1.490000e-07	67.6

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	TraesCS4A01G168700	chr4A	422760973	422763293	2320	True	4287	4287	100.000	1	2321	1	chr4A.!!$R2	2320
1	TraesCS4A01G168700	chr4A	306064054	306064649	595	True	761	761	89.850	458	1051	1	chr4A.!!$R1	593
2	TraesCS4A01G168700	chr2B	502006441	502008762	2321	False	3642	3642	95.009	1	2318	1	chr2B.!!$F1	2317
3	TraesCS4A01G168700	chr2A	38123233	38124911	1678	True	2619	2619	94.828	1	1679	1	chr2A.!!$R2	1678
4	TraesCS4A01G168700	chr2A	545062398	545063177	779	False	918	918	88.250	298	1063	1	chr2A.!!$F1	765
5	TraesCS4A01G168700	chr2A	14861804	14862430	626	True	728	728	87.500	298	951	1	chr2A.!!$R1	653
6	TraesCS4A01G168700	chr3B	52519131	52520301	1170	True	1757	1757	93.660	3	1183	1	chr3B.!!$R1	1180
7	TraesCS4A01G168700	chr3B	510236829	510237794	965	False	1435	1435	93.443	1	973	1	chr3B.!!$F1	972
8	TraesCS4A01G168700	chr7B	725263211	725264535	1324	False	1740	1740	90.437	3	1324	1	chr7B.!!$F1	1321
9	TraesCS4A01G168700	chr6B	432004029	432004951	922	False	1454	1454	95.125	1	921	1	chr6B.!!$F2	920
10	TraesCS4A01G168700	chr6B	391556393	391556989	596	False	765	765	90.000	298	889	1	chr6B.!!$F1	591
11	TraesCS4A01G168700	chr5D	61857468	61858018	550	False	680	680	88.715	749	1324	1	chr5D.!!$F1	575
12	TraesCS4A01G168700	chr4B	603002792	603003435	643	False	582	582	83.210	664	1328	1	chr4B.!!$F1	664
13	TraesCS4A01G168700	chr2D	598704884	598705596	712	True	520	520	80.134	1	737	1	chr2D.!!$R1	736
14	TraesCS4A01G168700	chr6D	288780377	288781090	713	False	514	514	80.027	1	737	1	chr6D.!!$F1	736
15	TraesCS4A01G168700	chr6A	99872035	99872554	519	True	444	444	82.309	1	530	1	chr6A.!!$R1	529

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
874	911	2.039879	CCAACTAGCCCTAACACAACCT	59.96	50.0	0.0	0.0	0.0	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2286	2350	0.26023	TTGCTTGGAACAGAACCCCA	59.74	50.0	0.0	0.0	42.39	4.96	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
100	102	5.659079	AGGTGGATCAAAACTTTTTACACCA	59.341	36.000	17.38	9.39	39.55	4.17
412	422	2.091541	CCATGGGCATAACTGTTCGTT	58.908	47.619	2.85	0.00	39.64	3.85
874	911	2.039879	CCAACTAGCCCTAACACAACCT	59.960	50.000	0.00	0.00	0.00	3.50
999	1061	0.815734	CAACGACCCTCACCGTAGAT	59.184	55.000	0.00	0.00	38.13	1.98
1000	1062	2.019249	CAACGACCCTCACCGTAGATA	58.981	52.381	0.00	0.00	38.13	1.98
1080	1142	2.273619	GCCTCCTGGATCCTATTCCAT	58.726	52.381	14.23	0.00	44.66	3.41
1134	1196	0.539051	CCGACATGCTCTTCCTCCTT	59.461	55.000	0.00	0.00	0.00	3.36
1211	1273	3.790437	CATCCCCGACCTGCAGCT	61.790	66.667	8.66	0.00	0.00	4.24
1240	1302	3.815396	AGCTCGACGCGCTCATCA	61.815	61.111	6.50	0.00	45.59	3.07
1379	1441	4.155733	TTCCGCGCCGTCATGGAT	62.156	61.111	0.00	0.00	42.00	3.41
1444	1506	6.387465	TCCTACTTGAAGTAGTGAATGTTCG	58.613	40.000	25.70	11.03	45.12	3.95
1445	1507	6.208007	TCCTACTTGAAGTAGTGAATGTTCGA	59.792	38.462	25.70	12.81	45.12	3.71
1580	1643	5.768980	TTGATTCAGAGACTCCAATCCTT	57.231	39.130	16.73	0.00	0.00	3.36
1583	1646	4.982241	TTCAGAGACTCCAATCCTTTGT	57.018	40.909	0.00	0.00	0.00	2.83
1595	1658	3.902881	ATCCTTTGTTTGTGGTTGCAA	57.097	38.095	0.00	0.00	0.00	4.08
1700	1763	1.779221	AGTATGCTCTGCTCTGCTCT	58.221	50.000	0.00	0.00	0.00	4.09
1701	1764	1.409790	AGTATGCTCTGCTCTGCTCTG	59.590	52.381	0.00	0.00	0.00	3.35
1713	1776	2.499289	CTCTGCTCTGCTTTTCTCCCTA	59.501	50.000	0.00	0.00	0.00	3.53
1742	1805	0.244450	CTGAAATGCAATGCGGGTGT	59.756	50.000	0.00	0.00	0.00	4.16
1748	1811	2.751436	CAATGCGGGTGTCCCTGG	60.751	66.667	3.25	0.00	42.67	4.45
1765	1828	7.819900	GTGTCCCTGGCTTTTATCTGTATATAG	59.180	40.741	0.00	0.00	0.00	1.31
1934	1998	8.217131	TGTTCCAAGTTTGATGATGATATCTG	57.783	34.615	3.98	0.00	0.00	2.90
1961	2025	5.469760	CCCCTTTTTGTTTTGTTCATCATCC	59.530	40.000	0.00	0.00	0.00	3.51
2022	2086	1.154016	CACCACCGAGTCTGCTACG	60.154	63.158	0.00	0.00	0.00	3.51
2071	2135	1.137404	CTTTGATTCCTTGCGGCGG	59.863	57.895	9.78	0.00	0.00	6.13
2098	2162	2.330041	CGCCGTTGGTGTTGTTCC	59.670	61.111	0.00	0.00	0.00	3.62
2120	2184	2.046023	CTGCCCGTGCCAGATTCA	60.046	61.111	0.00	0.00	36.33	2.57
2130	2194	3.202548	CCAGATTCATGGCCTTGCT	57.797	52.632	13.75	2.79	32.48	3.91
2139	2203	4.888326	TCATGGCCTTGCTTGTTTAATT	57.112	36.364	13.75	0.00	0.00	1.40
2150	2214	4.345257	TGCTTGTTTAATTGGGTGCCTTAA	59.655	37.500	0.00	0.00	0.00	1.85
2215	2279	5.232463	TCCGTTAATGTACACAAGGAGTTC	58.768	41.667	0.00	0.00	0.00	3.01
2225	2289	5.924475	ACACAAGGAGTTCGTTTAATCTG	57.076	39.130	0.00	0.00	0.00	2.90
2286	2350	5.014228	AGGTTGTTACATAAGGAAGGAGCTT	59.986	40.000	0.00	0.00	0.00	3.74
2294	2358	0.476611	AGGAAGGAGCTTGGGGTTCT	60.477	55.000	0.00	0.00	0.00	3.01
2306	2370	0.673985	GGGGTTCTGTTCCAAGCAAC	59.326	55.000	0.00	0.00	0.00	4.17
2308	2372	1.963515	GGGTTCTGTTCCAAGCAACAT	59.036	47.619	0.00	0.00	35.70	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
284	289	1.833630	TGTCTAGGGTGCATCTTGGAG	59.166	52.381	0.00	0.00	0.00	3.86
405	415	3.276091	CACCCGCAGCAACGAACA	61.276	61.111	0.00	0.00	34.06	3.18
412	422	0.392461	GTAAGATTCCACCCGCAGCA	60.392	55.000	0.00	0.00	0.00	4.41
517	538	6.904463	ACCGGGTCAAATTTAAACTACAAT	57.096	33.333	6.32	0.00	0.00	2.71
590	613	4.096231	CCAACTTGTATGCATTTCCGATCA	59.904	41.667	3.54	0.00	0.00	2.92
754	783	1.511613	GGGGGAGATGTCCTGATTGA	58.488	55.000	9.08	0.00	43.36	2.57
874	911	2.276116	GGAGAGGACGAGTGGTGCA	61.276	63.158	0.00	0.00	39.86	4.57
981	1043	2.425143	TATCTACGGTGAGGGTCGTT	57.575	50.000	0.00	0.00	40.31	3.85
999	1061	2.744318	CGGCGCCACAACACCATA	60.744	61.111	28.98	0.00	0.00	2.74
1000	1062	4.634703	TCGGCGCCACAACACCAT	62.635	61.111	28.98	0.00	0.00	3.55
1444	1506	1.190643	CAGAGAACAGAGGAGGGGTC	58.809	60.000	0.00	0.00	0.00	4.46
1445	1507	0.489567	ACAGAGAACAGAGGAGGGGT	59.510	55.000	0.00	0.00	0.00	4.95
1580	1643	0.459237	CGCCTTGCAACCACAAACAA	60.459	50.000	0.00	0.00	0.00	2.83
1583	1646	1.435515	GTCGCCTTGCAACCACAAA	59.564	52.632	0.00	0.00	0.00	2.83
1651	1714	1.078214	CCTCCTTTGCCGATGAGCA	60.078	57.895	0.00	0.00	42.17	4.26
1700	1763	3.456380	AAGCCAATAGGGAGAAAAGCA	57.544	42.857	0.00	0.00	40.01	3.91
1701	1764	3.677148	GCAAAGCCAATAGGGAGAAAAGC	60.677	47.826	0.00	0.00	40.01	3.51
1713	1776	2.843401	TGCATTTCAGCAAAGCCAAT	57.157	40.000	0.00	0.00	42.46	3.16
1742	1805	6.730977	AGCTATATACAGATAAAAGCCAGGGA	59.269	38.462	0.00	0.00	33.85	4.20
1748	1811	7.099764	TGGAGCAGCTATATACAGATAAAAGC	58.900	38.462	0.00	0.00	33.68	3.51
1765	1828	2.952245	CAGCACTGTTGGAGCAGC	59.048	61.111	0.00	0.00	39.96	5.25
1934	1998	3.867857	TGAACAAAACAAAAAGGGGAGC	58.132	40.909	0.00	0.00	0.00	4.70
1961	2025	1.078759	CCGCTTCAGCTAACGACCTG	61.079	60.000	0.00	0.00	39.32	4.00
1980	2044	3.270877	AGACCGTGATTCCAGCATTTAC	58.729	45.455	0.00	0.00	0.00	2.01
1981	2045	3.531538	GAGACCGTGATTCCAGCATTTA	58.468	45.455	0.00	0.00	0.00	1.40
1985	2049	1.215382	CGAGACCGTGATTCCAGCA	59.785	57.895	0.00	0.00	0.00	4.41
2022	2086	5.763204	TCTTAACCAGTCTGTCATTGAAACC	59.237	40.000	0.00	0.00	0.00	3.27
2085	2149	0.464916	AGACCCGGAACAACACCAAC	60.465	55.000	0.73	0.00	0.00	3.77
2120	2184	3.307621	CCCAATTAAACAAGCAAGGCCAT	60.308	43.478	5.01	0.00	0.00	4.40
2127	2191	2.324541	AGGCACCCAATTAAACAAGCA	58.675	42.857	0.00	0.00	0.00	3.91
2130	2194	6.426646	ACATTAAGGCACCCAATTAAACAA	57.573	33.333	0.00	0.00	0.00	2.83
2139	2203	4.616553	TCTAGACTACATTAAGGCACCCA	58.383	43.478	0.00	0.00	0.00	4.51
2150	2214	8.414629	TCATGTGCTGATTATCTAGACTACAT	57.585	34.615	0.00	0.00	0.00	2.29
2215	2279	9.840427	AGATTTGTACAATTTCCAGATTAAACG	57.160	29.630	9.56	0.00	0.00	3.60
2225	2289	6.019318	GCATGATGCAGATTTGTACAATTTCC	60.019	38.462	13.36	0.00	44.26	3.13
2286	2350	0.260230	TTGCTTGGAACAGAACCCCA	59.740	50.000	0.00	0.00	42.39	4.96
2294	2358	1.411977	CAACCCATGTTGCTTGGAACA	59.588	47.619	9.91	9.91	44.86	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.