AutoCloner

Multiple sequence alignment - TraesCS4B01G205500

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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	TraesCS4B01G205500	chr4B	100.000	2267	0	0	1	2267	437837408	437835142	0.000000e+00	4187.0
1	TraesCS4B01G205500	chr4B	86.344	454	49	11	1826	2267	533730838	533730386	1.220000e-132	483.0
2	TraesCS4B01G205500	chr4B	84.459	444	41	7	1825	2267	527964641	527964225	1.620000e-111	412.0
3	TraesCS4B01G205500	chr4D	94.179	1735	65	17	1	1717	354051966	354050250	0.000000e+00	2612.0
4	TraesCS4B01G205500	chr4A	95.269	1374	60	2	62	1432	110875932	110877303	0.000000e+00	2172.0
5	TraesCS4B01G205500	chr4A	87.202	336	31	11	1825	2148	669862166	669862501	2.750000e-99	372.0
6	TraesCS4B01G205500	chr4A	88.779	303	20	8	1426	1719	110878324	110878621	2.140000e-95	359.0
7	TraesCS4B01G205500	chr4A	80.357	448	32	21	1827	2267	688107973	688108371	2.850000e-74	289.0
8	TraesCS4B01G205500	chr4A	83.333	294	18	10	1979	2267	12458538	12458805	2.250000e-60	243.0
9	TraesCS4B01G205500	chr4A	100.000	28	0	0	1722	1749	110879445	110879472	4.000000e-03	52.8
10	TraesCS4B01G205500	chr3B	85.811	444	35	8	1828	2267	762593292	762593711	1.600000e-121	446.0
11	TraesCS4B01G205500	chr3B	85.666	293	16	12	1979	2267	683837713	683837443	3.690000e-73	285.0
12	TraesCS4B01G205500	chr3B	91.617	167	10	3	2105	2267	760316505	760316339	6.300000e-56	228.0
13	TraesCS4B01G205500	chr7B	85.210	453	33	15	1825	2267	52507493	52507921	3.460000e-118	435.0
14	TraesCS4B01G205500	chr7B	85.111	450	34	16	1826	2267	578120550	578120126	1.610000e-116	429.0
15	TraesCS4B01G205500	chr7B	84.444	450	36	20	1825	2267	189712260	189711838	1.620000e-111	412.0
16	TraesCS4B01G205500	chr7B	80.132	453	36	21	1820	2267	6216125	6216528	2.850000e-74	289.0
17	TraesCS4B01G205500	chr7B	81.677	322	27	17	1949	2267	481888822	481889114	2.910000e-59	239.0
18	TraesCS4B01G205500	chr7B	89.286	168	13	5	2105	2267	131949672	131949505	2.950000e-49	206.0
19	TraesCS4B01G205500	chr7B	89.222	167	12	4	2105	2266	16148826	16148991	1.060000e-48	204.0
20	TraesCS4B01G205500	chr7B	79.688	256	41	10	1750	1995	717373160	717372906	8.320000e-40	174.0
21	TraesCS4B01G205500	chr2B	82.385	545	42	29	1749	2267	569249033	569249549	2.080000e-115	425.0
22	TraesCS4B01G205500	chr2B	84.773	440	34	16	1835	2262	14614687	14614269	5.830000e-111	411.0
23	TraesCS4B01G205500	chr2B	83.223	453	38	17	1822	2267	689744320	689744741	4.570000e-102	381.0
24	TraesCS4B01G205500	chr2B	85.348	273	13	11	1996	2266	723047188	723047435	8.030000e-65	257.0
25	TraesCS4B01G205500	chr2B	82.192	292	20	11	1979	2267	759139438	759139176	2.930000e-54	222.0
26	TraesCS4B01G205500	chr2B	90.361	166	12	4	2105	2267	742643685	742643521	4.900000e-52	215.0
27	TraesCS4B01G205500	chr2B	94.937	79	4	0	1748	1826	643354872	643354950	8.500000e-25	124.0
28	TraesCS4B01G205500	chr2B	91.111	90	8	0	1735	1824	584468531	584468620	3.060000e-24	122.0
29	TraesCS4B01G205500	chr6B	84.944	445	35	10	1826	2267	234676719	234677134	2.690000e-114	422.0
30	TraesCS4B01G205500	chr2D	78.745	494	50	26	1799	2264	103169459	103169925	1.710000e-71	279.0
31	TraesCS4B01G205500	chr2D	79.039	458	44	28	1835	2267	497918232	497917802	1.330000e-67	267.0
32	TraesCS4B01G205500	chr2D	78.500	400	38	21	1885	2267	44472690	44472322	3.790000e-53	219.0
33	TraesCS4B01G205500	chr2D	89.881	168	11	5	2105	2267	639287197	639287363	6.340000e-51	211.0
34	TraesCS4B01G205500	chr2A	76.079	556	51	35	1736	2244	698123148	698123668	4.900000e-52	215.0
35	TraesCS4B01G205500	chr3A	80.247	324	31	19	1976	2267	7121965	7122287	1.760000e-51	213.0
36	TraesCS4B01G205500	chrUn	97.368	76	2	0	1749	1824	35731280	35731355	1.830000e-26	130.0
37	TraesCS4B01G205500	chrUn	97.368	76	2	0	1749	1824	242151031	242150956	1.830000e-26	130.0
38	TraesCS4B01G205500	chr5D	97.333	75	2	0	1750	1824	482542479	482542405	6.570000e-26	128.0
39	TraesCS4B01G205500	chr1B	96.104	77	3	0	1750	1826	183251229	183251305	2.360000e-25	126.0
40	TraesCS4B01G205500	chr5B	92.857	84	6	0	1741	1824	489848086	489848169	3.060000e-24	122.0

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	TraesCS4B01G205500	chr4B	437835142	437837408	2266	True	4187.000000	4187	100.000000	1	2267	1	chr4B.!!$R1	2266
1	TraesCS4B01G205500	chr4D	354050250	354051966	1716	True	2612.000000	2612	94.179000	1	1717	1	chr4D.!!$R1	1716
2	TraesCS4B01G205500	chr4A	110875932	110879472	3540	False	861.266667	2172	94.682667	62	1749	3	chr4A.!!$F4	1687
3	TraesCS4B01G205500	chr2B	569249033	569249549	516	False	425.000000	425	82.385000	1749	2267	1	chr2B.!!$F1	518
4	TraesCS4B01G205500	chr2A	698123148	698123668	520	False	215.000000	215	76.079000	1736	2244	1	chr2A.!!$F1	508

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
917	924	0.314302	ACTGACACGTAGCCACAGAC	59.686	55.0	0.0	0.0	33.53	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1848	3757	0.31636	GAAAAGCCGAAAACGCGTGA	60.316	50.0	14.98	0.0	0.0	4.35	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
44	45	7.148639	GGCGATTTATTATTTGCTATCGACAGA	60.149	37.037	0.00	0.00	41.75	3.41
45	46	7.895259	GCGATTTATTATTTGCTATCGACAGAG	59.105	37.037	0.00	0.00	37.62	3.35
46	47	8.916654	CGATTTATTATTTGCTATCGACAGAGT	58.083	33.333	0.00	0.00	37.62	3.24
448	453	0.942721	AGCTAAGGGTAGGCCTAGGT	59.057	55.000	14.38	4.53	34.45	3.08
633	638	1.516386	CGTACGGGTGCTACTGCTG	60.516	63.158	7.57	0.00	40.48	4.41
650	655	1.081892	CTGACCACTTTGAGATGGCG	58.918	55.000	0.00	0.00	39.84	5.69
684	691	1.006922	GCTGTTGTGCCTTCCTTGC	60.007	57.895	0.00	0.00	0.00	4.01
698	705	2.032620	TCCTTGCCTCTCTCGATTACC	58.967	52.381	0.00	0.00	0.00	2.85
717	724	3.893763	GCGCTCAGCTCTCGCCTA	61.894	66.667	0.00	0.00	42.71	3.93
805	812	3.895232	TGCACTATTCTGGACTCTTCC	57.105	47.619	0.00	0.00	43.19	3.46
823	830	0.530744	CCCTCCACGTTTCAGATCGA	59.469	55.000	0.00	0.00	0.00	3.59
836	843	1.753649	CAGATCGAGCCCTTCTTCTCA	59.246	52.381	0.00	0.00	0.00	3.27
917	924	0.314302	ACTGACACGTAGCCACAGAC	59.686	55.000	0.00	0.00	33.53	3.51
994	1008	1.303888	ACAGCCCAGCACCATCAAG	60.304	57.895	0.00	0.00	0.00	3.02
1146	1163	1.926511	GCAAGGACGAGCATGGGTTG	61.927	60.000	0.00	0.00	0.00	3.77
1194	1211	3.637273	GACGCCACTGGGAAGGGT	61.637	66.667	0.00	0.00	35.59	4.34
1344	1361	9.170584	CATAAACTGTGATGTACTCGTAGTATG	57.829	37.037	0.00	0.00	32.65	2.39
1345	1362	6.754702	AACTGTGATGTACTCGTAGTATGT	57.245	37.500	0.00	0.00	32.65	2.29
1346	1363	7.854557	AACTGTGATGTACTCGTAGTATGTA	57.145	36.000	0.00	0.00	32.65	2.29
1347	1364	7.479897	ACTGTGATGTACTCGTAGTATGTAG	57.520	40.000	0.00	0.00	32.65	2.74
1348	1365	7.270779	ACTGTGATGTACTCGTAGTATGTAGA	58.729	38.462	0.00	0.00	32.65	2.59
1461	2519	3.941704	AAGTCATCTTCCCCATCTTCC	57.058	47.619	0.00	0.00	0.00	3.46
1545	2603	2.491693	ACCATCATCGCCAAAACGAAAT	59.508	40.909	0.00	0.00	46.59	2.17
1546	2604	3.692101	ACCATCATCGCCAAAACGAAATA	59.308	39.130	0.00	0.00	46.59	1.40
1553	2611	3.872771	TCGCCAAAACGAAATATCCTACC	59.127	43.478	0.00	0.00	39.54	3.18
1554	2612	3.002965	CGCCAAAACGAAATATCCTACCC	59.997	47.826	0.00	0.00	34.06	3.69
1555	2613	3.949113	GCCAAAACGAAATATCCTACCCA	59.051	43.478	0.00	0.00	0.00	4.51
1559	2617	4.417426	AACGAAATATCCTACCCACCAG	57.583	45.455	0.00	0.00	0.00	4.00
1675	2737	0.391927	CATCCCGTTAAACCTCGCCA	60.392	55.000	0.00	0.00	0.00	5.69
1678	2740	0.604511	CCCGTTAAACCTCGCCAGTT	60.605	55.000	0.00	0.00	0.00	3.16
1710	2772	2.125673	GCCGAGCGCTTAACCTCA	60.126	61.111	13.26	0.00	0.00	3.86
1719	2781	1.808133	CGCTTAACCTCATGGGCTCTC	60.808	57.143	0.00	0.00	39.10	3.20
1720	2782	1.488393	GCTTAACCTCATGGGCTCTCT	59.512	52.381	0.00	0.00	39.10	3.10
1806	3689	1.358725	GCAACGATCAGCGCCACTTA	61.359	55.000	2.29	0.00	46.04	2.24
1808	3691	0.246635	AACGATCAGCGCCACTTAGT	59.753	50.000	2.29	0.00	46.04	2.24
1819	3702	1.080995	CCACTTAGTGCGCTCTCAGC	61.081	60.000	16.36	0.00	38.02	4.26
1826	3709	2.042259	TGCGCTCTCAGCCATTTGG	61.042	57.895	9.73	0.00	38.18	3.28
1827	3710	1.746615	GCGCTCTCAGCCATTTGGA	60.747	57.895	0.00	0.00	38.18	3.53
1828	3711	1.099879	GCGCTCTCAGCCATTTGGAT	61.100	55.000	0.00	0.00	38.18	3.41
1829	3712	1.386533	CGCTCTCAGCCATTTGGATT	58.613	50.000	0.00	0.00	38.18	3.01
1830	3713	1.747355	CGCTCTCAGCCATTTGGATTT	59.253	47.619	0.00	0.00	38.18	2.17
1832	3715	3.378112	CGCTCTCAGCCATTTGGATTTTA	59.622	43.478	0.00	0.00	38.18	1.52
1833	3716	4.676546	GCTCTCAGCCATTTGGATTTTAC	58.323	43.478	0.00	0.00	34.48	2.01
1867	3776	0.316360	TCACGCGTTTTCGGCTTTTC	60.316	50.000	10.22	0.00	44.29	2.29
1918	3829	0.956633	GGTTTTTCACCGGTCTTCCC	59.043	55.000	2.59	0.00	35.12	3.97
1927	3838	1.703513	ACCGGTCTTCCCTAGCTTTTT	59.296	47.619	0.00	0.00	0.00	1.94
1999	3922	3.921119	TTCGCTAGAGTCACGGTTTTA	57.079	42.857	0.00	0.00	0.00	1.52
2035	3958	0.944311	GGTTGTGCTTTCGCGAGAGA	60.944	55.000	28.81	12.02	43.69	3.10
2112	4036	0.668535	GAGAGGCACGGTTTTGCTTT	59.331	50.000	0.00	0.00	42.56	3.51
2124	4048	3.043713	TGCTTTCGCAGAGGCACG	61.044	61.111	0.00	0.00	42.25	5.34
2125	4049	3.793144	GCTTTCGCAGAGGCACGG	61.793	66.667	0.00	0.00	41.24	4.94
2126	4050	2.357517	CTTTCGCAGAGGCACGGT	60.358	61.111	0.00	0.00	41.24	4.83
2127	4051	1.961277	CTTTCGCAGAGGCACGGTT	60.961	57.895	0.00	0.00	41.24	4.44
2128	4052	1.507141	CTTTCGCAGAGGCACGGTTT	61.507	55.000	0.00	0.00	41.24	3.27
2129	4053	1.098712	TTTCGCAGAGGCACGGTTTT	61.099	50.000	0.00	0.00	41.24	2.43
2130	4054	1.781025	TTCGCAGAGGCACGGTTTTG	61.781	55.000	0.00	0.00	41.24	2.44
2131	4055	2.050077	GCAGAGGCACGGTTTTGC	60.050	61.111	0.00	0.00	42.18	3.68
2132	4056	2.555547	GCAGAGGCACGGTTTTGCT	61.556	57.895	0.00	0.00	42.56	3.91
2133	4057	2.032981	CAGAGGCACGGTTTTGCTT	58.967	52.632	0.00	0.00	42.56	3.91
2134	4058	0.040067	CAGAGGCACGGTTTTGCTTC	60.040	55.000	0.28	0.28	46.31	3.86
2135	4059	1.172812	AGAGGCACGGTTTTGCTTCC	61.173	55.000	4.54	0.00	46.96	3.46
2170	4094	1.442184	GCTTTCGCGAGAGTCACGA	60.442	57.895	25.34	6.50	43.69	4.35
2180	4104	3.628280	GAGTCACGACCGTGCCTCC	62.628	68.421	19.08	7.50	43.00	4.30
2182	4106	3.371063	TCACGACCGTGCCTCCTC	61.371	66.667	16.76	0.00	45.04	3.71
2188	4112	1.289800	GACCGTGCCTCCTCGAAAAC	61.290	60.000	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	6.425417	TGTCGATAGCAAATAATAAATCGCCA	59.575	34.615	0.00	0.00	36.92	5.69
44	45	8.294954	ACTGTAATGACTAGTAATGCTGTACT	57.705	34.615	0.00	5.41	37.98	2.73
45	46	9.666626	CTACTGTAATGACTAGTAATGCTGTAC	57.333	37.037	0.00	0.00	0.00	2.90
46	47	9.623000	TCTACTGTAATGACTAGTAATGCTGTA	57.377	33.333	0.00	5.26	0.00	2.74
47	48	8.407064	GTCTACTGTAATGACTAGTAATGCTGT	58.593	37.037	0.00	4.38	0.00	4.40
48	49	8.406297	TGTCTACTGTAATGACTAGTAATGCTG	58.594	37.037	0.00	0.00	0.00	4.41
133	138	0.175073	GTCGGCTACGTCAGGGATTT	59.825	55.000	0.00	0.00	41.85	2.17
135	140	2.125961	GGTCGGCTACGTCAGGGAT	61.126	63.158	0.00	0.00	41.85	3.85
435	440	0.551396	ATTTGCACCTAGGCCTACCC	59.449	55.000	8.91	0.00	36.11	3.69
448	453	2.250921	AATCCCCATCACCATTTGCA	57.749	45.000	0.00	0.00	0.00	4.08
508	513	4.493747	GCCTTCTACGCCGACGCT	62.494	66.667	0.00	0.00	45.53	5.07
531	536	1.728426	GTCGACGACGTGGTCAAGG	60.728	63.158	26.93	13.31	40.69	3.61
556	561	1.386961	CTAAGCTCGCGTACATCGTC	58.613	55.000	5.77	0.00	42.13	4.20
633	638	1.796796	GCGCCATCTCAAAGTGGTC	59.203	57.895	0.00	0.00	37.81	4.02
650	655	2.050077	GCTCAAGGCAAACACCGC	60.050	61.111	0.00	0.00	41.35	5.68
717	724	2.971307	CCGCATTAAAAGGCAAACCAT	58.029	42.857	0.00	0.00	39.06	3.55
805	812	1.914634	CTCGATCTGAAACGTGGAGG	58.085	55.000	0.00	0.00	0.00	4.30
823	830	1.346068	GTGTCACTGAGAAGAAGGGCT	59.654	52.381	0.00	0.00	0.00	5.19
836	843	2.027605	CAGTCCACGCGTGTCACT	59.972	61.111	34.81	30.42	0.00	3.41
917	924	3.259902	GGCTTCTTAAACTAGGACGTGG	58.740	50.000	0.00	0.00	0.00	4.94
1146	1163	1.880340	CTCGAGCATCTTCACCGGC	60.880	63.158	0.00	0.00	0.00	6.13
1522	2580	0.247655	CGTTTTGGCGATGATGGTCG	60.248	55.000	0.00	0.00	44.14	4.79
1545	2603	1.046472	CGGCACTGGTGGGTAGGATA	61.046	60.000	2.84	0.00	0.00	2.59
1546	2604	2.367202	CGGCACTGGTGGGTAGGAT	61.367	63.158	2.84	0.00	0.00	3.24
1710	2772	7.380423	AAGTAACATATTACAGAGAGCCCAT	57.620	36.000	0.00	0.00	42.83	4.00
1806	3689	1.002868	AAATGGCTGAGAGCGCACT	60.003	52.632	11.47	9.28	43.62	4.40
1808	3691	2.042259	CCAAATGGCTGAGAGCGCA	61.042	57.895	11.47	0.00	43.62	6.09
1848	3757	0.316360	GAAAAGCCGAAAACGCGTGA	60.316	50.000	14.98	0.00	0.00	4.35
1981	3892	5.526010	AAAATAAAACCGTGACTCTAGCG	57.474	39.130	0.00	0.00	0.00	4.26
1982	3893	5.548250	CGAAAATAAAACCGTGACTCTAGC	58.452	41.667	0.00	0.00	0.00	3.42
1983	3894	5.548250	GCGAAAATAAAACCGTGACTCTAG	58.452	41.667	0.00	0.00	0.00	2.43
2112	4036	2.110213	AAAACCGTGCCTCTGCGA	59.890	55.556	0.00	0.00	41.78	5.10
2117	4041	1.285950	GGAAGCAAAACCGTGCCTC	59.714	57.895	0.00	0.00	46.14	4.70
2118	4042	2.551912	CGGAAGCAAAACCGTGCCT	61.552	57.895	0.00	0.00	46.14	4.75
2119	4043	2.050442	CGGAAGCAAAACCGTGCC	60.050	61.111	0.00	0.00	46.14	5.01
2135	4059	3.716006	CACAACCGTGCCTCTGCG	61.716	66.667	0.00	0.00	41.78	5.18
2170	4094	1.301479	GTTTTCGAGGAGGCACGGT	60.301	57.895	0.00	0.00	0.00	4.83
2221	4150	0.465460	AAGCAAAACCGTGCCTCTCA	60.465	50.000	0.00	0.00	46.14	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.