AutoCloner

Multiple sequence alignment - TraesCS2A01G403600

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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	TraesCS2A01G403600	chr2A	100.000	2564	0	0	1	2564	659269856	659272419	0.000000e+00	4735.0
1	TraesCS2A01G403600	chr2D	95.619	1689	50	7	893	2564	515573838	515575519	0.000000e+00	2687.0
2	TraesCS2A01G403600	chr2B	94.609	1725	50	17	865	2564	607048554	607050260	0.000000e+00	2630.0
3	TraesCS2A01G403600	chr6B	95.520	759	25	6	102	853	705324776	705325532	0.000000e+00	1205.0
4	TraesCS2A01G403600	chr6B	95.833	96	4	0	1	96	705324618	705324713	3.420000e-34	156.0
5	TraesCS2A01G403600	chr7A	95.268	634	21	6	225	852	577682076	577681446	0.000000e+00	996.0
6	TraesCS2A01G403600	chr7A	93.750	96	6	0	1	96	577682242	577682147	7.390000e-31	145.0
7	TraesCS2A01G403600	chr5B	89.370	762	57	9	102	853	67954635	67955382	0.000000e+00	937.0
8	TraesCS2A01G403600	chr6D	95.694	418	13	2	108	520	126439795	126439378	0.000000e+00	667.0
9	TraesCS2A01G403600	chr6D	93.385	257	11	4	561	816	126439379	126439128	2.410000e-100	375.0
10	TraesCS2A01G403600	chr6D	95.050	101	4	1	1	100	126439959	126439859	9.500000e-35	158.0
11	TraesCS2A01G403600	chr4A	93.692	428	19	5	102	522	226038663	226039089	3.600000e-178	634.0
12	TraesCS2A01G403600	chr4A	92.878	337	21	3	518	852	226039361	226039696	1.070000e-133	486.0
13	TraesCS2A01G403600	chr1A	81.330	707	113	14	169	869	267848634	267847941	8.010000e-155	556.0
14	TraesCS2A01G403600	chr3D	87.692	455	48	7	232	683	44222834	44222385	8.130000e-145	523.0
15	TraesCS2A01G403600	chr3D	88.000	150	15	3	702	848	44222397	44222248	9.430000e-40	174.0
16	TraesCS2A01G403600	chr3D	77.049	183	22	11	112	291	612780754	612780919	1.260000e-13	87.9
17	TraesCS2A01G403600	chr3A	83.000	200	30	3	648	845	747521099	747520902	7.290000e-41	178.0

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	TraesCS2A01G403600	chr2A	659269856	659272419	2563	False	4735.0	4735	100.000000	1	2564	1	chr2A.!!$F1	2563
1	TraesCS2A01G403600	chr2D	515573838	515575519	1681	False	2687.0	2687	95.619000	893	2564	1	chr2D.!!$F1	1671
2	TraesCS2A01G403600	chr2B	607048554	607050260	1706	False	2630.0	2630	94.609000	865	2564	1	chr2B.!!$F1	1699
3	TraesCS2A01G403600	chr6B	705324618	705325532	914	False	680.5	1205	95.676500	1	853	2	chr6B.!!$F1	852
4	TraesCS2A01G403600	chr7A	577681446	577682242	796	True	570.5	996	94.509000	1	852	2	chr7A.!!$R1	851
5	TraesCS2A01G403600	chr5B	67954635	67955382	747	False	937.0	937	89.370000	102	853	1	chr5B.!!$F1	751
6	TraesCS2A01G403600	chr6D	126439128	126439959	831	True	400.0	667	94.709667	1	816	3	chr6D.!!$R1	815
7	TraesCS2A01G403600	chr4A	226038663	226039696	1033	False	560.0	634	93.285000	102	852	2	chr4A.!!$F1	750
8	TraesCS2A01G403600	chr1A	267847941	267848634	693	True	556.0	556	81.330000	169	869	1	chr1A.!!$R1	700
9	TraesCS2A01G403600	chr3D	44222248	44222834	586	True	348.5	523	87.846000	232	848	2	chr3D.!!$R1	616

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
476	545	0.452784	GCGCCTCAATGTGAACGTTC	60.453	55.0	21.42	21.42	31.22	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1877	2248	0.329261	TCTGCCAATGCTAAGCACCT	59.671	50.0	0.0	0.0	43.04	4.0	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
66	67	1.883638	GCTTCAAGATGAGGTGTGGCA	60.884	52.381	0.00	0.00	0.00	4.92
96	97	0.666374	ACAGGTGGCGTTAGTTTTGC	59.334	50.000	0.00	0.00	0.00	3.68
97	98	0.665835	CAGGTGGCGTTAGTTTTGCA	59.334	50.000	0.00	0.00	0.00	4.08
98	99	1.269448	CAGGTGGCGTTAGTTTTGCAT	59.731	47.619	0.00	0.00	0.00	3.96
99	100	1.269448	AGGTGGCGTTAGTTTTGCATG	59.731	47.619	0.00	0.00	0.00	4.06
100	101	1.059942	GTGGCGTTAGTTTTGCATGC	58.940	50.000	11.82	11.82	0.00	4.06
105	163	3.168193	GCGTTAGTTTTGCATGCGTATT	58.832	40.909	14.09	0.02	0.00	1.89
106	164	3.237433	GCGTTAGTTTTGCATGCGTATTC	59.763	43.478	14.09	2.50	0.00	1.75
130	188	4.280174	GGAAATCTGCAGCACCATGATAAT	59.720	41.667	9.47	0.00	0.00	1.28
193	252	5.818678	TGTGGAAACTTCTAGCCTTCTAA	57.181	39.130	0.00	0.00	0.00	2.10
204	263	5.560724	TCTAGCCTTCTAAAACAAGCATGT	58.439	37.500	0.00	0.00	43.14	3.21
317	382	3.458487	GGAAATCTAGGGGGTGCTTCTTA	59.542	47.826	0.00	0.00	0.00	2.10
356	421	7.142306	CCATTGATATTGGCAGTTCTCTATG	57.858	40.000	0.00	0.00	0.00	2.23
419	486	6.016360	TGTTTGAGTACTTGCATTGCTATTGT	60.016	34.615	10.49	6.02	0.00	2.71
432	500	8.924691	TGCATTGCTATTGTTTTGACTTTATTC	58.075	29.630	10.49	0.00	0.00	1.75
476	545	0.452784	GCGCCTCAATGTGAACGTTC	60.453	55.000	21.42	21.42	31.22	3.95
509	578	2.240493	AACGTTCTGGAACCTGTGAG	57.760	50.000	0.00	0.00	38.03	3.51
654	1002	2.674852	ACTTGCACGCAACTCTATCATG	59.325	45.455	0.00	0.00	0.00	3.07
756	1105	9.837525	TCAAATCAAAAGAAAATTGTTTTGGTG	57.162	25.926	21.20	17.39	45.80	4.17
1525	1882	6.127730	GGGGAACTGATTTATGTTCGATTGTT	60.128	38.462	0.00	0.00	42.28	2.83
1681	2040	5.215160	GCTGTTATCCAACTTTTGAGTGTG	58.785	41.667	0.00	0.00	35.56	3.82
1706	2065	5.957842	TGTGGAAGTTGCTAAAATACCTG	57.042	39.130	0.00	0.00	0.00	4.00
1737	2096	5.771165	GGTTGGATCCTTAAAGTGTTGGTAA	59.229	40.000	14.23	0.00	0.00	2.85
2021	2392	5.189145	TGGTCCCTTCTTCTGGTAGATAAAC	59.811	44.000	0.00	0.00	0.00	2.01
2029	2400	7.458409	TCTTCTGGTAGATAAACGTTACACT	57.542	36.000	0.00	3.79	0.00	3.55
2042	2413	9.762933	ATAAACGTTACACTTAGGACAAAACTA	57.237	29.630	0.00	0.00	0.00	2.24
2045	2416	7.267857	ACGTTACACTTAGGACAAAACTAACT	58.732	34.615	0.00	0.00	0.00	2.24
2065	2436	6.942532	AACTATGCTGTTGTTCTTTCTTCA	57.057	33.333	0.00	0.00	0.00	3.02
2114	2485	0.040067	CGTGTTCTCCTTTTGCTGGC	60.040	55.000	0.00	0.00	0.00	4.85
2133	2504	4.077108	TGGCCATGAGCTCATTTATCATC	58.923	43.478	26.70	12.00	43.05	2.92
2200	2571	5.925397	TGAAATGGTGTGTTTGTATTGATGC	59.075	36.000	0.00	0.00	0.00	3.91
2266	2638	7.907389	TGACAGGTGATTAACTCATCTTAGTT	58.093	34.615	0.00	0.00	43.03	2.24
2322	2698	7.895975	TCAGTTGTTCTCAATGTATCAGAAG	57.104	36.000	0.00	0.00	35.92	2.85
2328	2704	4.507710	TCTCAATGTATCAGAAGGTGCAC	58.492	43.478	8.80	8.80	0.00	4.57
2415	2791	7.163441	AGCAATTCCTTTATCTTGCATGTTTT	58.837	30.769	8.60	0.00	44.90	2.43
2434	2813	9.381027	CATGTTTTGTACTAGTAAACACATGTG	57.619	33.333	25.75	24.25	42.51	3.21
2435	2814	7.921787	TGTTTTGTACTAGTAAACACATGTGG	58.078	34.615	28.64	12.06	36.98	4.17
2436	2815	7.553402	TGTTTTGTACTAGTAAACACATGTGGT	59.447	33.333	28.64	21.46	36.98	4.16
2437	2816	9.044150	GTTTTGTACTAGTAAACACATGTGGTA	57.956	33.333	28.64	17.39	33.21	3.25
2438	2817	9.781633	TTTTGTACTAGTAAACACATGTGGTAT	57.218	29.630	28.64	16.43	34.19	2.73
2520	2899	6.142818	TGGTACATGCCAATTTATAACTGC	57.857	37.500	0.00	0.00	35.25	4.40
2534	2913	2.422276	AACTGCGTTTTCCATTCAGC	57.578	45.000	0.00	0.00	0.00	4.26
2538	2917	2.483877	CTGCGTTTTCCATTCAGCTGTA	59.516	45.455	14.67	4.08	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	3.558746	CCACACCTCATCTTGAAGCTCTT	60.559	47.826	0.00	0.00	0.00	2.85
66	67	1.839424	GCCACCTGTAATCTGCCTTT	58.161	50.000	0.00	0.00	0.00	3.11
96	97	2.287644	TGCAGATTTCCGAATACGCATG	59.712	45.455	0.00	0.00	38.29	4.06
97	98	2.545526	CTGCAGATTTCCGAATACGCAT	59.454	45.455	8.42	0.00	34.13	4.73
98	99	1.933181	CTGCAGATTTCCGAATACGCA	59.067	47.619	8.42	0.00	38.29	5.24
99	100	1.333258	GCTGCAGATTTCCGAATACGC	60.333	52.381	20.43	0.00	38.29	4.42
100	101	1.933181	TGCTGCAGATTTCCGAATACG	59.067	47.619	20.43	0.00	39.43	3.06
105	163	0.035152	ATGGTGCTGCAGATTTCCGA	60.035	50.000	20.43	5.01	0.00	4.55
106	164	0.099968	CATGGTGCTGCAGATTTCCG	59.900	55.000	20.43	0.00	0.00	4.30
317	382	7.886629	ATATCAATGGCAAATACTGAAGTGT	57.113	32.000	0.00	0.00	0.00	3.55
356	421	9.716531	AGGTAAAAGTAATACAAACAGAGTACC	57.283	33.333	0.00	0.00	0.00	3.34
385	451	4.702131	GCAAGTACTCAAACATGGAGGAAT	59.298	41.667	0.00	0.00	36.70	3.01
419	486	7.922278	GCATGCATCATAGGAATAAAGTCAAAA	59.078	33.333	14.21	0.00	0.00	2.44
476	545	6.851609	TCCAGAACGTTTATCAAATGATTGG	58.148	36.000	0.46	1.26	37.15	3.16
595	941	5.475564	GGTTAACTTTTAGATGGGCAGACAA	59.524	40.000	5.42	0.00	0.00	3.18
654	1002	2.004808	GCCGCCCCTTGTAAGCAATC	62.005	60.000	0.00	0.00	33.65	2.67
756	1105	3.782889	ACCACTCAAACAGTTTCAAGC	57.217	42.857	0.00	0.00	30.26	4.01
863	1215	9.696917	CCTAAATTTTGTGCTCTTGTATTTCTT	57.303	29.630	0.00	0.00	0.00	2.52
883	1235	9.674068	GAGAATCAGAGTTTCTTTACCCTAAAT	57.326	33.333	0.00	0.00	33.65	1.40
1210	1567	1.585521	GTCGATGGTGTAGTCGCCG	60.586	63.158	0.00	0.00	46.30	6.46
1637	1996	3.066621	GCAGCATCCGAAATTGTGGATTA	59.933	43.478	8.61	0.00	42.31	1.75
1656	2015	5.009010	ACACTCAAAAGTTGGATAACAGCAG	59.991	40.000	0.00	0.00	39.30	4.24
1681	2040	5.652452	AGGTATTTTAGCAACTTCCACATCC	59.348	40.000	0.00	0.00	0.00	3.51
1706	2065	3.732048	TTAAGGATCCAACCAACCCTC	57.268	47.619	15.82	0.00	0.00	4.30
1737	2096	6.012858	TCAGTGGATTTCTACATTACCCTGTT	60.013	38.462	0.00	0.00	0.00	3.16
1877	2248	0.329261	TCTGCCAATGCTAAGCACCT	59.671	50.000	0.00	0.00	43.04	4.00
2021	2392	7.704789	AGTTAGTTTTGTCCTAAGTGTAACG	57.295	36.000	0.00	0.00	45.86	3.18
2029	2400	7.717875	ACAACAGCATAGTTAGTTTTGTCCTAA	59.282	33.333	0.00	0.00	0.00	2.69
2042	2413	6.942532	TGAAGAAAGAACAACAGCATAGTT	57.057	33.333	0.00	0.00	0.00	2.24
2045	2416	7.509141	TCAATGAAGAAAGAACAACAGCATA	57.491	32.000	0.00	0.00	0.00	3.14
2065	2436	3.053320	GGGTCTTCCTTCTTCCCATCAAT	60.053	47.826	0.00	0.00	38.15	2.57
2181	2552	4.140536	TGAGCATCAATACAAACACACCA	58.859	39.130	0.00	0.00	45.97	4.17
2200	2571	4.393062	AGCTACATTCGGTTTGAACATGAG	59.607	41.667	0.00	0.00	40.00	2.90
2266	2638	0.953727	GTCCATCACAGCAGCAAACA	59.046	50.000	0.00	0.00	0.00	2.83
2322	2698	0.385390	CAGTTGTCCAAAGGTGCACC	59.615	55.000	29.22	29.22	0.00	5.01
2434	2813	6.642950	CCGAGAGTGAACATGAGATTTATACC	59.357	42.308	0.00	0.00	0.00	2.73
2435	2814	7.203910	ACCGAGAGTGAACATGAGATTTATAC	58.796	38.462	0.00	0.00	0.00	1.47
2436	2815	7.348080	ACCGAGAGTGAACATGAGATTTATA	57.652	36.000	0.00	0.00	0.00	0.98
2437	2816	6.227298	ACCGAGAGTGAACATGAGATTTAT	57.773	37.500	0.00	0.00	0.00	1.40
2438	2817	5.661056	ACCGAGAGTGAACATGAGATTTA	57.339	39.130	0.00	0.00	0.00	1.40
2520	2899	3.941483	AGGATACAGCTGAATGGAAAACG	59.059	43.478	23.35	0.00	41.41	3.60

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.