AutoCloner

Multiple sequence alignment - TraesCS2D01G436900

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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	TraesCS2D01G436900	chr2D	100.000	2534	0	0	1	2534	547277373	547279906	0.000000e+00	4680
1	TraesCS2D01G436900	chr2D	91.690	1071	48	23	685	1727	547286210	547287267	0.000000e+00	1447
2	TraesCS2D01G436900	chr2D	92.703	836	30	12	904	1728	547427098	547427913	0.000000e+00	1177
3	TraesCS2D01G436900	chr2D	93.242	799	49	4	1738	2534	547287321	547288116	0.000000e+00	1171
4	TraesCS2D01G436900	chr2D	97.373	533	12	2	1	531	442496884	442496352	0.000000e+00	905
5	TraesCS2D01G436900	chr2D	81.926	1101	126	36	625	1693	547450456	547451515	0.000000e+00	863
6	TraesCS2D01G436900	chr2D	82.795	959	110	16	756	1693	547489048	547489972	0.000000e+00	806
7	TraesCS2D01G436900	chr2D	81.470	939	113	19	762	1670	547559282	547560189	0.000000e+00	713
8	TraesCS2D01G436900	chr2D	82.222	855	99	20	792	1616	547574425	547575256	0.000000e+00	688
9	TraesCS2D01G436900	chr2D	93.377	302	20	0	2233	2534	547428189	547428490	4.970000e-122	448
10	TraesCS2D01G436900	chr2D	83.471	484	45	10	1740	2215	547490058	547490514	3.900000e-113	418
11	TraesCS2D01G436900	chr2D	87.981	208	17	4	1736	1939	547427966	547428169	3.260000e-59	239
12	TraesCS2D01G436900	chr2A	90.164	1220	61	29	530	1722	690747053	690748240	0.000000e+00	1533
13	TraesCS2D01G436900	chr2A	80.740	919	116	19	771	1670	691392185	691391309	0.000000e+00	660
14	TraesCS2D01G436900	chr2A	92.019	426	32	2	2110	2534	690748432	690748856	4.670000e-167	597
15	TraesCS2D01G436900	chr2A	83.761	585	71	15	1942	2507	690807213	690807792	1.330000e-147	532
16	TraesCS2D01G436900	chr2A	93.750	128	8	0	1736	1863	690748299	690748426	2.570000e-45	193
17	TraesCS2D01G436900	chr2B	94.539	824	37	5	893	1714	653788317	653789134	0.000000e+00	1266
18	TraesCS2D01G436900	chr2B	90.989	799	62	6	1736	2534	653773214	653774002	0.000000e+00	1068
19	TraesCS2D01G436900	chr2B	91.982	661	43	3	1738	2388	653789208	653789868	0.000000e+00	918
20	TraesCS2D01G436900	chr2B	82.951	1003	107	30	695	1670	653808081	653809046	0.000000e+00	846
21	TraesCS2D01G436900	chr2B	81.854	1014	124	32	685	1676	653795997	653796972	0.000000e+00	798
22	TraesCS2D01G436900	chr2B	93.031	287	14	2	1434	1714	653772858	653773144	5.040000e-112	414
23	TraesCS2D01G436900	chr2B	87.857	280	17	4	530	808	653788015	653788278	1.890000e-81	313
24	TraesCS2D01G436900	chr6D	97.196	535	14	1	1	535	122707241	122707774	0.000000e+00	904
25	TraesCS2D01G436900	chr6D	97.180	532	14	1	1	531	14118337	14117806	0.000000e+00	898
26	TraesCS2D01G436900	chr5D	97.186	533	13	2	1	531	431218247	431217715	0.000000e+00	900
27	TraesCS2D01G436900	chr5D	97.004	534	12	3	1	531	496932295	496931763	0.000000e+00	894
28	TraesCS2D01G436900	chrUn	97.186	533	12	3	1	531	19470945	19471476	0.000000e+00	898
29	TraesCS2D01G436900	chr7D	97.180	532	14	1	1	531	94786520	94787051	0.000000e+00	898
30	TraesCS2D01G436900	chr3D	97.180	532	13	2	1	531	49524855	49525385	0.000000e+00	898
31	TraesCS2D01G436900	chr1D	97.015	536	11	4	1	532	214544668	214545202	0.000000e+00	896
32	TraesCS2D01G436900	chr5A	89.423	312	27	2	1413	1718	602413162	602413473	3.060000e-104	388

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	TraesCS2D01G436900	chr2D	547277373	547279906	2533	False	4680.000000	4680	100.000000	1	2534	1	chr2D.!!$F1	2533
1	TraesCS2D01G436900	chr2D	547286210	547288116	1906	False	1309.000000	1447	92.466000	685	2534	2	chr2D.!!$F5	1849
2	TraesCS2D01G436900	chr2D	442496352	442496884	532	True	905.000000	905	97.373000	1	531	1	chr2D.!!$R1	530
3	TraesCS2D01G436900	chr2D	547450456	547451515	1059	False	863.000000	863	81.926000	625	1693	1	chr2D.!!$F2	1068
4	TraesCS2D01G436900	chr2D	547559282	547560189	907	False	713.000000	713	81.470000	762	1670	1	chr2D.!!$F3	908
5	TraesCS2D01G436900	chr2D	547574425	547575256	831	False	688.000000	688	82.222000	792	1616	1	chr2D.!!$F4	824
6	TraesCS2D01G436900	chr2D	547427098	547428490	1392	False	621.333333	1177	91.353667	904	2534	3	chr2D.!!$F6	1630
7	TraesCS2D01G436900	chr2D	547489048	547490514	1466	False	612.000000	806	83.133000	756	2215	2	chr2D.!!$F7	1459
8	TraesCS2D01G436900	chr2A	690747053	690748856	1803	False	774.333333	1533	91.977667	530	2534	3	chr2A.!!$F2	2004
9	TraesCS2D01G436900	chr2A	691391309	691392185	876	True	660.000000	660	80.740000	771	1670	1	chr2A.!!$R1	899
10	TraesCS2D01G436900	chr2A	690807213	690807792	579	False	532.000000	532	83.761000	1942	2507	1	chr2A.!!$F1	565
11	TraesCS2D01G436900	chr2B	653808081	653809046	965	False	846.000000	846	82.951000	695	1670	1	chr2B.!!$F2	975
12	TraesCS2D01G436900	chr2B	653788015	653789868	1853	False	832.333333	1266	91.459333	530	2388	3	chr2B.!!$F4	1858
13	TraesCS2D01G436900	chr2B	653795997	653796972	975	False	798.000000	798	81.854000	685	1676	1	chr2B.!!$F1	991
14	TraesCS2D01G436900	chr2B	653772858	653774002	1144	False	741.000000	1068	92.010000	1434	2534	2	chr2B.!!$F3	1100
15	TraesCS2D01G436900	chr6D	122707241	122707774	533	False	904.000000	904	97.196000	1	535	1	chr6D.!!$F1	534
16	TraesCS2D01G436900	chr6D	14117806	14118337	531	True	898.000000	898	97.180000	1	531	1	chr6D.!!$R1	530
17	TraesCS2D01G436900	chr5D	431217715	431218247	532	True	900.000000	900	97.186000	1	531	1	chr5D.!!$R1	530
18	TraesCS2D01G436900	chr5D	496931763	496932295	532	True	894.000000	894	97.004000	1	531	1	chr5D.!!$R2	530
19	TraesCS2D01G436900	chrUn	19470945	19471476	531	False	898.000000	898	97.186000	1	531	1	chrUn.!!$F1	530
20	TraesCS2D01G436900	chr7D	94786520	94787051	531	False	898.000000	898	97.180000	1	531	1	chr7D.!!$F1	530
21	TraesCS2D01G436900	chr3D	49524855	49525385	530	False	898.000000	898	97.180000	1	531	1	chr3D.!!$F1	530
22	TraesCS2D01G436900	chr1D	214544668	214545202	534	False	896.000000	896	97.015000	1	532	1	chr1D.!!$F1	531

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
879	957	0.033366	ACTGACGCATACACAGCACA	59.967	50.0	0.0	0.0	35.38	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2189	2401	0.837272	ATGTCCATGGTAGAACGGGG	59.163	55.0	12.58	0.0	0.0	5.73	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
463	468	0.899019	GACAACACTCTCCCCTCTCC	59.101	60.000	0.00	0.00	0.00	3.71
602	609	6.930068	TTAAAGTTTAGAGGGTCTGCTAGT	57.070	37.500	0.00	0.00	0.00	2.57
629	636	3.593096	CCTTAGTTACCACTCCGAAACC	58.407	50.000	0.00	0.00	34.06	3.27
790	813	2.785562	ACATGCAAAACGGCTAACCTA	58.214	42.857	0.00	0.00	34.04	3.08
837	871	3.587797	TTACTCGGAGATGAACGCTTT	57.412	42.857	12.86	0.00	33.89	3.51
840	874	3.707793	ACTCGGAGATGAACGCTTTATC	58.292	45.455	12.86	0.00	33.89	1.75
851	885	6.920569	TGAACGCTTTATCTTAATTCTCCC	57.079	37.500	0.00	0.00	0.00	4.30
872	950	2.805671	CAAGTCCAAACTGACGCATACA	59.194	45.455	0.00	0.00	40.26	2.29
878	956	1.148310	AACTGACGCATACACAGCAC	58.852	50.000	0.00	0.00	35.38	4.40
879	957	0.033366	ACTGACGCATACACAGCACA	59.967	50.000	0.00	0.00	35.38	4.57
881	959	0.033366	TGACGCATACACAGCACACT	59.967	50.000	0.00	0.00	0.00	3.55
882	960	1.148310	GACGCATACACAGCACACTT	58.852	50.000	0.00	0.00	0.00	3.16
883	961	2.288518	TGACGCATACACAGCACACTTA	60.289	45.455	0.00	0.00	0.00	2.24
884	962	2.337583	ACGCATACACAGCACACTTAG	58.662	47.619	0.00	0.00	0.00	2.18
885	963	2.029380	ACGCATACACAGCACACTTAGA	60.029	45.455	0.00	0.00	0.00	2.10
886	964	3.190079	CGCATACACAGCACACTTAGAT	58.810	45.455	0.00	0.00	0.00	1.98
887	965	3.243877	CGCATACACAGCACACTTAGATC	59.756	47.826	0.00	0.00	0.00	2.75
888	966	3.557595	GCATACACAGCACACTTAGATCC	59.442	47.826	0.00	0.00	0.00	3.36
889	967	4.758688	CATACACAGCACACTTAGATCCA	58.241	43.478	0.00	0.00	0.00	3.41
950	1030	7.755822	CCTATATAAGCACGTCAATTCCTCTAC	59.244	40.741	0.00	0.00	0.00	2.59
1032	1118	0.901827	TCTGCCTCGCCATCTTGTTA	59.098	50.000	0.00	0.00	0.00	2.41
1043	1129	2.095059	CCATCTTGTTACTTGCACTGGC	60.095	50.000	0.00	0.00	41.68	4.85
1141	1227	2.743718	CGACCCAGTTCCTGCAGT	59.256	61.111	13.81	0.00	0.00	4.40
1654	1780	1.198637	GGACTACGTACGCTGTGACTT	59.801	52.381	16.72	0.00	0.00	3.01
1722	1863	9.720769	CACTTTATTTATCTGTAATCCCGGTAT	57.279	33.333	0.00	0.00	0.00	2.73
1728	1869	4.002906	TCTGTAATCCCGGTATTGCATC	57.997	45.455	10.81	0.00	32.16	3.91
1730	1871	2.073816	GTAATCCCGGTATTGCATCGG	58.926	52.381	1.90	10.16	43.05	4.18
1732	1873	0.321671	ATCCCGGTATTGCATCGGAG	59.678	55.000	16.36	9.01	45.96	4.63
1733	1874	1.301716	CCCGGTATTGCATCGGAGG	60.302	63.158	16.36	5.68	45.96	4.30
1782	1971	2.595536	CACGTACGATTAGTTTCCCACG	59.404	50.000	24.41	0.00	0.00	4.94
1784	1973	2.848302	CGTACGATTAGTTTCCCACGAC	59.152	50.000	10.44	0.00	0.00	4.34
1863	2065	5.504665	CCACGATATCCTGATTTCTGTTTGC	60.505	44.000	3.54	0.00	0.00	3.68
1895	2100	4.864704	AACCAAACGGTTTGCATAGAAT	57.135	36.364	24.53	6.50	44.73	2.40
2051	2256	5.723672	AACTAACAACCTCGAGAGAATCA	57.276	39.130	15.71	0.00	41.32	2.57
2166	2378	2.346803	ACACTCGCAATAAAGACGCAT	58.653	42.857	0.00	0.00	0.00	4.73
2189	2401	7.060748	GCATGATGATGATCGAAATGAAATGAC	59.939	37.037	0.00	0.00	0.00	3.06
2210	2449	1.762957	CCCGTTCTACCATGGACATCT	59.237	52.381	21.47	0.00	0.00	2.90
2227	2466	4.848357	ACATCTGAACCATAACCCTTCTG	58.152	43.478	0.00	0.00	0.00	3.02
2235	2474	4.652822	ACCATAACCCTTCTGTTTCTCAC	58.347	43.478	0.00	0.00	0.00	3.51
2273	2513	8.840833	AGGAAACATAAACAAACAAAAAGTGT	57.159	26.923	0.00	0.00	44.64	3.55
2325	2565	1.070758	TCAGCAGAGGTGAAGGTGAAC	59.929	52.381	0.00	0.00	37.11	3.18
2361	2601	4.497006	GGCTGCATGAGACATAAACATCAC	60.497	45.833	0.50	0.00	0.00	3.06
2366	2606	5.163683	GCATGAGACATAAACATCACTTGCT	60.164	40.000	0.00	0.00	29.36	3.91
2370	2610	6.656270	TGAGACATAAACATCACTTGCTGATT	59.344	34.615	0.00	0.00	37.53	2.57
2373	2613	7.826252	AGACATAAACATCACTTGCTGATTACT	59.174	33.333	0.00	0.00	37.53	2.24
2407	2647	6.209192	AGTTCACATGTTCATAAAATGCAGGA	59.791	34.615	0.00	0.00	0.00	3.86
2436	2676	5.414765	TGAGTAGAGAATTCGAGCAGTACAA	59.585	40.000	0.00	0.00	0.00	2.41
2518	2758	7.886338	ACATTTGTCCCTAAGAAAACTCAATC	58.114	34.615	0.00	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
119	123	9.112725	CAATAGATCAATTGTTGTGTCTATGGA	57.887	33.333	5.13	0.00	38.44	3.41
463	468	4.072839	AGATCATGGTGATGCATAGCAAG	58.927	43.478	0.00	2.02	43.62	4.01
602	609	2.504175	GGAGTGGTAACTAAGGGCATCA	59.496	50.000	0.00	0.00	36.52	3.07
629	636	8.745837	GCCTGTTGAACATTTCATAAATATTCG	58.254	33.333	0.00	0.00	37.16	3.34
790	813	4.269183	TGGCATTCACACCGAGAATTAAT	58.731	39.130	0.00	0.00	33.64	1.40
837	871	7.829211	CAGTTTGGACTTGGGAGAATTAAGATA	59.171	37.037	0.00	0.00	32.54	1.98
840	874	6.003950	TCAGTTTGGACTTGGGAGAATTAAG	58.996	40.000	0.00	0.00	32.54	1.85
851	885	2.805671	TGTATGCGTCAGTTTGGACTTG	59.194	45.455	0.00	0.00	35.63	3.16
872	950	3.498397	CGTTTTGGATCTAAGTGTGCTGT	59.502	43.478	0.00	0.00	0.00	4.40
878	956	5.235186	CAGATAGGCGTTTTGGATCTAAGTG	59.765	44.000	0.00	0.00	0.00	3.16
879	957	5.360591	CAGATAGGCGTTTTGGATCTAAGT	58.639	41.667	0.00	0.00	0.00	2.24
881	959	4.127171	GCAGATAGGCGTTTTGGATCTAA	58.873	43.478	0.00	0.00	0.00	2.10
882	960	3.133901	TGCAGATAGGCGTTTTGGATCTA	59.866	43.478	0.00	0.00	36.28	1.98
883	961	2.092968	TGCAGATAGGCGTTTTGGATCT	60.093	45.455	0.00	0.00	36.28	2.75
884	962	2.288666	TGCAGATAGGCGTTTTGGATC	58.711	47.619	0.00	0.00	36.28	3.36
885	963	2.418368	TGCAGATAGGCGTTTTGGAT	57.582	45.000	0.00	0.00	36.28	3.41
886	964	2.083774	CTTGCAGATAGGCGTTTTGGA	58.916	47.619	0.00	0.00	36.28	3.53
887	965	1.812571	ACTTGCAGATAGGCGTTTTGG	59.187	47.619	0.00	0.00	36.28	3.28
888	966	3.559238	AACTTGCAGATAGGCGTTTTG	57.441	42.857	0.00	0.00	36.28	2.44
889	967	4.082949	GGTTAACTTGCAGATAGGCGTTTT	60.083	41.667	5.42	0.00	36.28	2.43
950	1030	4.037208	AGCTCAGTTGATTTGGTGAAGTTG	59.963	41.667	0.00	0.00	0.00	3.16
1067	1153	0.035056	GTTGCTAGTGCTGGGGATGT	60.035	55.000	0.00	0.00	40.48	3.06
1594	1706	1.033574	AAAAATCGCCGGACCAAACA	58.966	45.000	5.05	0.00	0.00	2.83
1654	1780	5.883673	ACCAAACAAAGTAACAGACAGCTTA	59.116	36.000	0.00	0.00	0.00	3.09
1722	1863	0.884259	CACACACACCTCCGATGCAA	60.884	55.000	0.00	0.00	0.00	4.08
1728	1869	0.959553	ACTAGTCACACACACCTCCG	59.040	55.000	0.00	0.00	0.00	4.63
1730	1871	3.489785	CGAAAACTAGTCACACACACCTC	59.510	47.826	0.00	0.00	0.00	3.85
1732	1873	3.244579	GTCGAAAACTAGTCACACACACC	59.755	47.826	0.00	0.00	0.00	4.16
1733	1874	4.110482	AGTCGAAAACTAGTCACACACAC	58.890	43.478	0.00	0.00	36.07	3.82
1782	1971	2.872858	AGAAAGGCGTTCAGAGTTTGTC	59.127	45.455	15.39	0.00	38.86	3.18
1784	1973	2.224314	GGAGAAAGGCGTTCAGAGTTTG	59.776	50.000	15.39	0.00	38.86	2.93
1932	2137	5.597594	TGATGCCATGGCTATTCAAATACAA	59.402	36.000	35.53	12.58	42.51	2.41
1939	2144	3.581265	TCTTGATGCCATGGCTATTCA	57.419	42.857	35.53	29.15	42.51	2.57
2051	2256	9.689501	TTATATTTGGTTTTCCCTCGTCTTAAT	57.310	29.630	0.00	0.00	39.73	1.40
2166	2378	6.016860	GGGTCATTTCATTTCGATCATCATCA	60.017	38.462	0.00	0.00	0.00	3.07
2189	2401	0.837272	ATGTCCATGGTAGAACGGGG	59.163	55.000	12.58	0.00	0.00	5.73
2235	2474	6.925610	TTATGTTTCCTCTCATGATTTCCG	57.074	37.500	0.00	0.00	0.00	4.30
2273	2513	5.781210	TTTGTTATTGGTGCATGAACTGA	57.219	34.783	3.21	0.00	0.00	3.41
2325	2565	1.102809	TGCAGCCTTGTGGAGTGTTG	61.103	55.000	0.00	0.00	34.57	3.33
2361	2601	2.430465	ACACCTGCAGTAATCAGCAAG	58.570	47.619	13.81	0.00	40.73	4.01
2366	2606	4.566004	GTGAACTACACCTGCAGTAATCA	58.434	43.478	13.81	4.43	43.05	2.57
2407	2647	7.721402	ACTGCTCGAATTCTCTACTCATATTT	58.279	34.615	3.52	0.00	0.00	1.40
2419	2659	7.324178	AGTAATCTTTGTACTGCTCGAATTCT	58.676	34.615	3.52	0.00	30.52	2.40
2482	2722	7.669722	TCTTAGGGACAAATGTAGCAGATTTTT	59.330	33.333	0.00	0.00	0.00	1.94
2498	2738	6.003950	CCTTGATTGAGTTTTCTTAGGGACA	58.996	40.000	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.