AutoCloner

Multiple sequence alignment - TraesCS1B01G416300

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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	TraesCS1B01G416300	chr1B	100.000	1871	0	0	1	1871	641214405	641212535	0.000000e+00	3456.0
1	TraesCS1B01G416300	chr1B	93.683	839	30	7	831	1663	678907619	678908440	0.000000e+00	1234.0
2	TraesCS1B01G416300	chr1B	79.248	824	115	41	805	1600	678867610	678868405	7.700000e-145	523.0
3	TraesCS1B01G416300	chr1B	100.000	239	0	0	2193	2431	641212213	641211975	2.220000e-120	442.0
4	TraesCS1B01G416300	chr1B	95.556	225	10	0	610	834	678907050	678907274	6.390000e-96	361.0
5	TraesCS1B01G416300	chr1B	88.987	227	15	1	2193	2419	678908648	678908864	3.080000e-69	272.0
6	TraesCS1B01G416300	chr1B	93.939	165	9	1	1707	1871	678908437	678908600	5.190000e-62	248.0
7	TraesCS1B01G416300	chr1B	92.857	42	3	0	233	274	178090768	178090809	7.260000e-06	62.1
8	TraesCS1B01G416300	chr1D	93.214	1120	47	9	1	1115	487356491	487355396	0.000000e+00	1620.0
9	TraesCS1B01G416300	chr1D	92.647	476	18	4	1116	1588	487355262	487354801	0.000000e+00	669.0
10	TraesCS1B01G416300	chr1D	80.333	961	125	31	853	1788	487439760	487438839	0.000000e+00	669.0
11	TraesCS1B01G416300	chr1D	90.909	275	25	0	6	280	35936074	35935800	1.060000e-98	370.0
12	TraesCS1B01G416300	chr1D	93.839	211	7	2	2197	2401	487354100	487353890	1.810000e-81	313.0
13	TraesCS1B01G416300	chr1D	80.428	327	32	17	397	695	467900774	467901096	1.130000e-53	220.0
14	TraesCS1B01G416300	chr1A	83.301	521	63	17	914	1414	585391596	585391080	2.200000e-125	459.0
15	TraesCS1B01G416300	chr1A	84.133	271	32	6	847	1107	585452511	585452780	4.010000e-63	252.0
16	TraesCS1B01G416300	chr2B	82.263	327	23	21	400	695	793814642	793814320	1.440000e-62	250.0
17	TraesCS1B01G416300	chr6A	81.957	327	27	18	399	696	63094056	63094379	5.190000e-62	248.0
18	TraesCS1B01G416300	chr6A	83.607	122	14	5	241	357	18849769	18849649	2.560000e-20	110.0
19	TraesCS1B01G416300	chrUn	81.957	327	26	18	399	695	282890935	282890612	1.870000e-61	246.0
20	TraesCS1B01G416300	chrUn	81.957	327	26	18	399	695	295720606	295720929	1.870000e-61	246.0
21	TraesCS1B01G416300	chrUn	81.957	327	26	18	399	695	311088376	311088053	1.870000e-61	246.0
22	TraesCS1B01G416300	chrUn	73.991	446	74	27	894	1328	302757964	302757550	2.520000e-30	143.0
23	TraesCS1B01G416300	chr6B	80.793	328	28	17	397	695	34163954	34164275	8.750000e-55	224.0
24	TraesCS1B01G416300	chr6B	79.878	328	29	18	397	695	243238159	243238478	3.170000e-49	206.0
25	TraesCS1B01G416300	chr6B	79.747	316	29	17	397	683	477192214	477192523	1.910000e-46	196.0
26	TraesCS1B01G416300	chr7A	81.319	273	29	11	400	654	731885695	731885427	4.100000e-48	202.0
27	TraesCS1B01G416300	chr5B	86.034	179	12	7	408	576	23416437	23416262	1.920000e-41	180.0
28	TraesCS1B01G416300	chr4D	79.930	284	23	18	400	654	52781247	52780969	6.910000e-41	178.0
29	TraesCS1B01G416300	chr4A	81.373	204	23	12	397	589	544030832	544031031	4.190000e-33	152.0
30	TraesCS1B01G416300	chr7B	87.500	96	11	1	708	802	583083387	583083482	2.560000e-20	110.0
31	TraesCS1B01G416300	chr7D	85.294	102	14	1	702	802	539997378	539997479	1.190000e-18	104.0
32	TraesCS1B01G416300	chr2D	93.750	48	3	0	227	274	9255681	9255634	3.350000e-09	73.1

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	TraesCS1B01G416300	chr1B	641211975	641214405	2430	True	1949.000000	3456	100.000000	1	2431	2	chr1B.!!$R1	2430
1	TraesCS1B01G416300	chr1B	678907050	678908864	1814	False	528.750000	1234	93.041250	610	2419	4	chr1B.!!$F3	1809
2	TraesCS1B01G416300	chr1B	678867610	678868405	795	False	523.000000	523	79.248000	805	1600	1	chr1B.!!$F2	795
3	TraesCS1B01G416300	chr1D	487353890	487356491	2601	True	867.333333	1620	93.233333	1	2401	3	chr1D.!!$R3	2400
4	TraesCS1B01G416300	chr1D	487438839	487439760	921	True	669.000000	669	80.333000	853	1788	1	chr1D.!!$R2	935
5	TraesCS1B01G416300	chr1A	585391080	585391596	516	True	459.000000	459	83.301000	914	1414	1	chr1A.!!$R1	500

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
175	176	0.109412	GCAGCAACATCAGCCTTCAC	60.109	55.0	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1668	2210	0.035915	GCAAGAACTGACCCTCCCTC	60.036	60.0	0.0	0.0	0.0	4.3	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
19	20	2.917713	TTGGGTATGCCACAGGAAAT	57.082	45.000	1.04	0.00	36.17	2.17
49	50	1.521010	CGAGGAGCCACAGATGCAG	60.521	63.158	0.00	0.00	0.00	4.41
78	79	1.515521	CGTGGTCCTGTTTTCCTGCC	61.516	60.000	0.00	0.00	0.00	4.85
121	122	1.073199	CTCCCAGCCAAACTTCCGT	59.927	57.895	0.00	0.00	0.00	4.69
123	124	1.971695	CCCAGCCAAACTTCCGTCC	60.972	63.158	0.00	0.00	0.00	4.79
134	135	4.770362	TCCGTCCGATCCAGCCCA	62.770	66.667	0.00	0.00	0.00	5.36
175	176	0.109412	GCAGCAACATCAGCCTTCAC	60.109	55.000	0.00	0.00	0.00	3.18
232	233	3.849951	ATAGCACCACGGGAGCGG	61.850	66.667	6.68	0.00	43.81	5.52
318	323	3.876320	GAGAGTGCCTGAAGAAATGGATC	59.124	47.826	0.00	0.00	0.00	3.36
319	324	2.611292	GAGTGCCTGAAGAAATGGATCG	59.389	50.000	0.00	0.00	0.00	3.69
320	325	2.026822	AGTGCCTGAAGAAATGGATCGT	60.027	45.455	0.00	0.00	0.00	3.73
321	326	2.096496	GTGCCTGAAGAAATGGATCGTG	59.904	50.000	0.00	0.00	0.00	4.35
322	327	1.064654	GCCTGAAGAAATGGATCGTGC	59.935	52.381	0.00	0.00	0.00	5.34
323	328	1.672881	CCTGAAGAAATGGATCGTGCC	59.327	52.381	0.00	0.00	0.00	5.01
324	329	2.358957	CTGAAGAAATGGATCGTGCCA	58.641	47.619	1.72	1.72	43.23	4.92
325	330	2.083774	TGAAGAAATGGATCGTGCCAC	58.916	47.619	1.25	0.00	41.56	5.01
326	331	1.401905	GAAGAAATGGATCGTGCCACC	59.598	52.381	1.25	0.00	41.56	4.61
327	332	0.394352	AGAAATGGATCGTGCCACCC	60.394	55.000	1.25	0.00	41.56	4.61
328	333	1.379843	AAATGGATCGTGCCACCCC	60.380	57.895	1.25	0.00	41.56	4.95
387	392	2.276201	CCGTGATAGCAAAACGATGGA	58.724	47.619	0.00	0.00	39.64	3.41
388	393	2.872245	CCGTGATAGCAAAACGATGGAT	59.128	45.455	0.00	0.00	39.64	3.41
410	415	4.731313	ACCAAGGTCCTTGAGAATTTCT	57.269	40.909	29.91	0.00	43.42	2.52
457	462	0.385029	TCAACAACGCATGCAGCTTT	59.615	45.000	19.57	1.98	42.61	3.51
481	486	8.812147	TTGTACAAACTACACTACAGATTCTG	57.188	34.615	12.17	12.17	37.52	3.02
632	637	8.044908	TCCTGTTTATAGGGTAATCACTTTGAC	58.955	37.037	0.00	0.00	38.42	3.18
633	638	8.047310	CCTGTTTATAGGGTAATCACTTTGACT	58.953	37.037	0.00	0.00	34.06	3.41
678	684	5.068198	ACATTTGGTACGTCTACGGTGATAT	59.932	40.000	7.50	0.00	44.95	1.63
696	702	6.265577	GTGATATAAAACTTCCGCAGCAATT	58.734	36.000	0.00	0.00	0.00	2.32
698	704	4.782019	ATAAAACTTCCGCAGCAATTCA	57.218	36.364	0.00	0.00	0.00	2.57
759	765	5.763204	TGTCATCAGGAAGTAGTTGTTTTCC	59.237	40.000	0.00	0.00	40.52	3.13
1076	1450	4.678743	GGCAACCCTTCCCGCCTT	62.679	66.667	0.00	0.00	41.50	4.35
1169	1688	1.812235	ATCTTGCGATGTTGAGCACA	58.188	45.000	0.00	0.00	43.69	4.57
1173	1692	1.521580	TGCGATGTTGAGCACAATGA	58.478	45.000	0.00	0.00	39.50	2.57
1265	1796	4.573900	TGGTTTTGTTTCATGTGTTTGCT	58.426	34.783	0.00	0.00	0.00	3.91
1309	1840	2.235898	AGAACTGCTTCCCAGATGACTC	59.764	50.000	0.00	0.00	44.64	3.36
1328	1859	2.942804	TCTCAGAAGAGATGCGAGGAT	58.057	47.619	0.00	0.00	45.73	3.24
1345	1876	5.936956	GCGAGGATGATCTTGGAAAAGATAT	59.063	40.000	1.09	0.00	39.47	1.63
1362	1893	7.944729	AAAGATATGTTAAGTGAATGCCAGT	57.055	32.000	0.00	0.00	0.00	4.00
1428	1959	2.102925	TGTTTTCGAAAGGACGGTACCT	59.897	45.455	10.98	0.00	42.69	3.08
1444	1975	6.469410	ACGGTACCTGAAAATGATAAACAGA	58.531	36.000	10.90	0.00	0.00	3.41
1485	2020	5.280164	GGGCAGATGATAGAACACATCCATA	60.280	44.000	0.00	0.00	42.38	2.74
1486	2021	6.413052	GGCAGATGATAGAACACATCCATAT	58.587	40.000	0.00	0.00	42.38	1.78
1487	2022	7.365028	GGGCAGATGATAGAACACATCCATATA	60.365	40.741	0.00	0.00	42.38	0.86
1488	2023	8.209584	GGCAGATGATAGAACACATCCATATAT	58.790	37.037	0.00	0.00	42.38	0.86
1659	2201	0.378962	TTTTGTGGCGCACTGTGTAC	59.621	50.000	10.83	1.74	35.11	2.90
1662	2204	0.606096	TGTGGCGCACTGTGTACTAT	59.394	50.000	10.83	0.00	35.11	2.12
1663	2205	1.819903	TGTGGCGCACTGTGTACTATA	59.180	47.619	10.83	0.00	35.11	1.31
1664	2206	2.429250	TGTGGCGCACTGTGTACTATAT	59.571	45.455	10.83	0.00	35.11	0.86
1665	2207	3.633065	TGTGGCGCACTGTGTACTATATA	59.367	43.478	10.83	0.00	35.11	0.86
1666	2208	4.279922	TGTGGCGCACTGTGTACTATATAT	59.720	41.667	10.83	0.00	35.11	0.86
1667	2209	4.857588	GTGGCGCACTGTGTACTATATATC	59.142	45.833	10.83	0.00	0.00	1.63
1668	2210	4.096311	GGCGCACTGTGTACTATATATCG	58.904	47.826	10.83	1.52	0.00	2.92
1669	2211	4.142752	GGCGCACTGTGTACTATATATCGA	60.143	45.833	10.83	0.00	0.00	3.59
1670	2212	5.022653	GCGCACTGTGTACTATATATCGAG	58.977	45.833	9.86	0.00	0.00	4.04
1671	2213	5.561070	CGCACTGTGTACTATATATCGAGG	58.439	45.833	9.86	0.00	0.00	4.63
1698	2240	4.332268	GGTCAGTTCTTGCATTGAGAGATC	59.668	45.833	0.00	0.00	0.00	2.75
1702	2244	6.315642	TCAGTTCTTGCATTGAGAGATCAATC	59.684	38.462	0.58	0.00	38.16	2.67
1799	2373	8.190784	GGTTTTGTGTAAGCTTCATTATAGCAT	58.809	33.333	0.00	0.00	41.11	3.79
1834	2408	3.913089	AGCGGACATTCCAAATCAAAAC	58.087	40.909	0.00	0.00	35.91	2.43
1860	2525	5.175859	TGGTTTTGATTAAGCTCTAGACCG	58.824	41.667	0.00	0.00	30.97	4.79
1861	2526	4.034163	GGTTTTGATTAAGCTCTAGACCGC	59.966	45.833	0.00	0.00	0.00	5.68
1864	2529	2.100916	TGATTAAGCTCTAGACCGCACC	59.899	50.000	6.73	0.00	0.00	5.01
1866	2531	1.041447	TAAGCTCTAGACCGCACCCC	61.041	60.000	6.73	0.00	0.00	4.95
1867	2532	2.760385	GCTCTAGACCGCACCCCT	60.760	66.667	0.00	0.00	0.00	4.79
1869	2534	1.736365	GCTCTAGACCGCACCCCTAC	61.736	65.000	0.00	0.00	0.00	3.18
2311	3040	0.818040	GCTGGTCCTGAACAAACCGT	60.818	55.000	0.00	0.00	35.76	4.83
2313	3042	2.874457	GCTGGTCCTGAACAAACCGTAT	60.874	50.000	0.00	0.00	35.76	3.06
2314	3043	2.742053	CTGGTCCTGAACAAACCGTATG	59.258	50.000	0.00	0.00	35.76	2.39
2339	3074	4.020617	CTCCACCTCGGCCAGCAA	62.021	66.667	2.24	0.00	33.14	3.91
2348	3083	1.600957	CTCGGCCAGCAAATCATACAG	59.399	52.381	2.24	0.00	0.00	2.74
2351	3086	1.753073	GGCCAGCAAATCATACAGCTT	59.247	47.619	0.00	0.00	34.61	3.74
2373	3108	3.392616	TCTCTTTCTTCTTCTGCACCCTT	59.607	43.478	0.00	0.00	0.00	3.95
2381	3116	2.037772	TCTTCTGCACCCTTCTCTTCAC	59.962	50.000	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	4.831155	TCCTCGTATGATCGGTTATTTCCT	59.169	41.667	0.00	0.00	0.00	3.36
19	20	1.884579	GGCTCCTCGTATGATCGGTTA	59.115	52.381	0.00	0.00	0.00	2.85
343	348	2.905880	CTATCCCCCGCGTCGTCT	60.906	66.667	4.92	0.00	0.00	4.18
387	392	6.394345	AGAAATTCTCAAGGACCTTGGTAT	57.606	37.500	29.76	18.61	41.33	2.73
388	393	5.843019	AGAAATTCTCAAGGACCTTGGTA	57.157	39.130	29.76	17.44	41.33	3.25
410	415	5.416639	TGTAGCAGTTAGGTCGTCTCATAAA	59.583	40.000	0.00	0.00	0.00	1.40
457	462	6.866770	GCAGAATCTGTAGTGTAGTTTGTACA	59.133	38.462	12.29	0.00	33.43	2.90
559	564	7.289782	AGGAGCTGACAGAAGATTACTAATGAT	59.710	37.037	6.65	0.00	0.00	2.45
583	588	8.378565	AGGAACAATATGTCATGGATAAGTAGG	58.621	37.037	0.00	0.00	0.00	3.18
656	662	5.779529	ATATCACCGTAGACGTACCAAAT	57.220	39.130	0.85	0.00	37.74	2.32
678	684	3.316588	TGTGAATTGCTGCGGAAGTTTTA	59.683	39.130	0.00	0.00	0.00	1.52
696	702	6.591448	CAGCTCTTATAGAAATGTGTGTGTGA	59.409	38.462	0.00	0.00	0.00	3.58
698	704	6.701340	TCAGCTCTTATAGAAATGTGTGTGT	58.299	36.000	0.00	0.00	0.00	3.72
1265	1796	1.418264	TGGACCTCGAAACATCCAACA	59.582	47.619	4.58	0.00	38.30	3.33
1309	1840	2.622470	TCATCCTCGCATCTCTTCTGAG	59.378	50.000	0.00	0.00	41.51	3.35
1328	1859	9.958180	TCACTTAACATATCTTTTCCAAGATCA	57.042	29.630	0.68	0.00	45.26	2.92
1345	1876	2.107378	TCCCACTGGCATTCACTTAACA	59.893	45.455	0.00	0.00	0.00	2.41
1362	1893	1.783071	TGTAGTACGCCATGATCCCA	58.217	50.000	0.00	0.00	0.00	4.37
1444	1975	4.012374	CTGCCCATCATCAACTAAACACT	58.988	43.478	0.00	0.00	0.00	3.55
1495	2030	9.809096	GTGGATCGAACAGACAATCATATATAT	57.191	33.333	0.00	0.00	0.00	0.86
1496	2031	8.251026	GGTGGATCGAACAGACAATCATATATA	58.749	37.037	0.00	0.00	0.00	0.86
1659	2201	5.118729	ACTGACCCTCCCTCGATATATAG	57.881	47.826	0.00	0.00	0.00	1.31
1662	2204	3.398292	AGAACTGACCCTCCCTCGATATA	59.602	47.826	0.00	0.00	0.00	0.86
1663	2205	2.178106	AGAACTGACCCTCCCTCGATAT	59.822	50.000	0.00	0.00	0.00	1.63
1664	2206	1.569548	AGAACTGACCCTCCCTCGATA	59.430	52.381	0.00	0.00	0.00	2.92
1665	2207	0.336737	AGAACTGACCCTCCCTCGAT	59.663	55.000	0.00	0.00	0.00	3.59
1666	2208	0.114560	AAGAACTGACCCTCCCTCGA	59.885	55.000	0.00	0.00	0.00	4.04
1667	2209	0.247736	CAAGAACTGACCCTCCCTCG	59.752	60.000	0.00	0.00	0.00	4.63
1668	2210	0.035915	GCAAGAACTGACCCTCCCTC	60.036	60.000	0.00	0.00	0.00	4.30
1669	2211	0.768221	TGCAAGAACTGACCCTCCCT	60.768	55.000	0.00	0.00	0.00	4.20
1670	2212	0.329596	ATGCAAGAACTGACCCTCCC	59.670	55.000	0.00	0.00	0.00	4.30
1671	2213	1.815003	CAATGCAAGAACTGACCCTCC	59.185	52.381	0.00	0.00	0.00	4.30
1698	2240	6.764308	AACAATGTGAAGATAGGTGGATTG	57.236	37.500	0.00	0.00	0.00	2.67
1702	2244	6.573664	TGAAAACAATGTGAAGATAGGTGG	57.426	37.500	0.00	0.00	0.00	4.61
1799	2373	0.245266	TCCGCTTGCGACTTGATACA	59.755	50.000	16.99	0.00	0.00	2.29
1834	2408	6.094186	GGTCTAGAGCTTAATCAAAACCAAGG	59.906	42.308	14.73	0.00	0.00	3.61
1845	2510	1.413077	GGGTGCGGTCTAGAGCTTAAT	59.587	52.381	19.17	0.00	0.00	1.40
1851	2516	0.395311	TGTAGGGGTGCGGTCTAGAG	60.395	60.000	0.00	0.00	0.00	2.43
2311	3040	2.026636	CCGAGGTGGAGGAAAAACCATA	60.027	50.000	0.00	0.00	42.00	2.74
2313	3042	0.109723	CCGAGGTGGAGGAAAAACCA	59.890	55.000	0.00	0.00	42.00	3.67
2314	3043	1.241990	GCCGAGGTGGAGGAAAAACC	61.242	60.000	0.00	0.00	42.00	3.27
2339	3074	8.320617	AGAAGAAGAAAGAGAAGCTGTATGATT	58.679	33.333	0.00	0.00	0.00	2.57
2348	3083	3.188254	GGTGCAGAAGAAGAAAGAGAAGC	59.812	47.826	0.00	0.00	0.00	3.86
2351	3086	2.975489	AGGGTGCAGAAGAAGAAAGAGA	59.025	45.455	0.00	0.00	0.00	3.10
2373	3108	1.248486	CACACGAGGAGGTGAAGAGA	58.752	55.000	0.00	0.00	40.38	3.10
2381	3116	3.775654	GAGGGCCACACGAGGAGG	61.776	72.222	6.18	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.