AutoCloner

Multiple sequence alignment - TraesCS7D01G462100

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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	TraesCS7D01G462100	chr7D	100.000	1940	0	0	1	1940	577921104	577923043	0.000000e+00	3583.0
1	TraesCS7D01G462100	chr7D	100.000	308	0	0	2287	2594	577923390	577923697	1.040000e-158	569.0
2	TraesCS7D01G462100	chr7D	81.754	570	101	2	927	1493	577963504	577964073	8.400000e-130	473.0
3	TraesCS7D01G462100	chr7D	77.807	757	97	32	1	712	577962562	577963292	4.020000e-108	401.0
4	TraesCS7D01G462100	chr7D	78.873	568	105	9	932	1493	578465266	578465824	1.130000e-98	370.0
5	TraesCS7D01G462100	chr7D	88.953	172	16	3	121	290	578164349	578164179	2.620000e-50	209.0
6	TraesCS7D01G462100	chr7D	94.444	90	4	1	297	386	577885265	577885353	1.250000e-28	137.0
7	TraesCS7D01G462100	chr3D	94.536	1940	75	11	1	1940	55155633	55157541	0.000000e+00	2966.0
8	TraesCS7D01G462100	chr3D	90.964	166	15	0	2287	2452	55157569	55157734	9.340000e-55	224.0
9	TraesCS7D01G462100	chr3D	92.683	82	6	0	1859	1940	55157345	55157426	4.530000e-23	119.0
10	TraesCS7D01G462100	chr7A	91.786	1960	115	25	1	1940	670166560	670168493	0.000000e+00	2686.0
11	TraesCS7D01G462100	chr7A	81.261	571	93	8	932	1493	670342224	670341659	1.420000e-122	449.0
12	TraesCS7D01G462100	chr7A	78.345	568	108	9	932	1493	670536798	670537356	1.140000e-93	353.0
13	TraesCS7D01G462100	chr7A	77.236	492	55	29	345	783	670342841	670342354	4.320000e-58	235.0
14	TraesCS7D01G462100	chr7A	91.617	167	11	2	2287	2450	670168528	670168694	7.220000e-56	228.0
15	TraesCS7D01G462100	chr7B	93.669	1706	81	12	1	1698	641742918	641741232	0.000000e+00	2527.0
16	TraesCS7D01G462100	chr7B	92.861	1709	67	16	1	1698	641368088	641369752	0.000000e+00	2429.0
17	TraesCS7D01G462100	chr7B	81.754	570	98	4	927	1493	642076924	642076358	3.020000e-129	472.0
18	TraesCS7D01G462100	chr7B	92.887	239	16	1	1702	1940	641369791	641370028	1.910000e-91	346.0
19	TraesCS7D01G462100	chr7B	80.969	289	36	9	1	288	641459900	641460170	7.270000e-51	211.0
20	TraesCS7D01G462100	chr7B	76.596	376	52	19	345	693	642077476	642077110	9.540000e-40	174.0
21	TraesCS7D01G462100	chr7B	89.024	82	6	2	2464	2542	641370278	641370359	5.910000e-17	99.0
22	TraesCS7D01G462100	chr7B	94.444	54	3	0	2541	2594	641370386	641370439	1.650000e-12	84.2

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	TraesCS7D01G462100	chr7D	577921104	577923697	2593	False	2076.00	3583	100.000000	1	2594	2	chr7D.!!$F3	2593
1	TraesCS7D01G462100	chr7D	577962562	577964073	1511	False	437.00	473	79.780500	1	1493	2	chr7D.!!$F4	1492
2	TraesCS7D01G462100	chr7D	578465266	578465824	558	False	370.00	370	78.873000	932	1493	1	chr7D.!!$F2	561
3	TraesCS7D01G462100	chr3D	55155633	55157734	2101	False	1103.00	2966	92.727667	1	2452	3	chr3D.!!$F1	2451
4	TraesCS7D01G462100	chr7A	670166560	670168694	2134	False	1457.00	2686	91.701500	1	2450	2	chr7A.!!$F2	2449
5	TraesCS7D01G462100	chr7A	670536798	670537356	558	False	353.00	353	78.345000	932	1493	1	chr7A.!!$F1	561
6	TraesCS7D01G462100	chr7A	670341659	670342841	1182	True	342.00	449	79.248500	345	1493	2	chr7A.!!$R1	1148
7	TraesCS7D01G462100	chr7B	641741232	641742918	1686	True	2527.00	2527	93.669000	1	1698	1	chr7B.!!$R1	1697
8	TraesCS7D01G462100	chr7B	641368088	641370439	2351	False	739.55	2429	92.304000	1	2594	4	chr7B.!!$F2	2593
9	TraesCS7D01G462100	chr7B	642076358	642077476	1118	True	323.00	472	79.175000	345	1493	2	chr7B.!!$R2	1148

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
951	1107	0.957395	CTGCCGATTCACAGCCAACT	60.957	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2548	2806	0.250234	ATGATACCCCGCATCGATGG	59.75	55.0	26.0	15.7	0.0	3.51	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
24	25	4.558226	TCATGTTCACTGCTGGTATTCT	57.442	40.909	0.00	0.00	0.00	2.40
245	250	4.365111	TGTGGGGCATGCCTGGAC	62.365	66.667	34.70	26.24	36.10	4.02
400	409	1.953686	TGCTAAGTTTGTGGTGGCTTC	59.046	47.619	0.00	0.00	0.00	3.86
755	824	7.865385	AGATTGTCTTACTTTATGATCGAGCTC	59.135	37.037	2.73	2.73	0.00	4.09
758	827	7.142021	TGTCTTACTTTATGATCGAGCTCATC	58.858	38.462	15.40	15.31	37.13	2.92
761	838	8.363390	TCTTACTTTATGATCGAGCTCATCATT	58.637	33.333	29.80	20.73	40.69	2.57
765	842	9.499479	ACTTTATGATCGAGCTCATCATTATTT	57.501	29.630	29.80	17.94	40.69	1.40
772	849	9.327529	GATCGAGCTCATCATTATTTTTCATTC	57.672	33.333	15.40	0.00	0.00	2.67
938	1094	2.606213	TGATGTCACCCCTGCCGA	60.606	61.111	0.00	0.00	0.00	5.54
951	1107	0.957395	CTGCCGATTCACAGCCAACT	60.957	55.000	0.00	0.00	0.00	3.16
1258	1418	1.603931	CGATGAGGTCATGGATGGTCG	60.604	57.143	0.00	0.00	36.57	4.79
1322	1482	1.220206	CTGCTGTGGCTAGGACTGG	59.780	63.158	0.00	0.00	39.59	4.00
1374	1537	1.807573	CGAAGAGACGAAGCAGGGC	60.808	63.158	0.00	0.00	35.09	5.19
1476	1642	4.320456	CAGGTGGCAGGTGCGTCT	62.320	66.667	0.00	0.00	43.26	4.18
1500	1666	2.363276	TATGGTGGCCCGTCGACT	60.363	61.111	14.70	0.00	0.00	4.18
1604	1773	1.227674	GGCCCTGAAGCTATCACCG	60.228	63.158	0.00	0.00	33.47	4.94
1614	1783	1.342819	AGCTATCACCGGATTCAGAGC	59.657	52.381	9.46	9.11	33.49	4.09
1637	1806	2.151202	TCGTTTCAGCCTGGACATTTC	58.849	47.619	0.00	0.00	0.00	2.17
1687	1862	6.129168	GCTTTCATATGATCGTTATTCGTCGT	60.129	38.462	6.17	0.00	40.80	4.34
1690	1865	7.316687	TCATATGATCGTTATTCGTCGTTTC	57.683	36.000	0.00	0.00	40.80	2.78
1700	1910	2.296831	TCGTCGTTTCAAACAGGTCA	57.703	45.000	0.22	0.00	0.00	4.02
1730	1940	1.069358	TGCTGTTGTCATGGTGTCGTA	59.931	47.619	0.00	0.00	0.00	3.43
1736	1946	3.782889	TGTCATGGTGTCGTATGAGAG	57.217	47.619	0.00	0.00	34.25	3.20
1756	1966	8.948631	TGAGAGGTACTATGAATTTGTGATTC	57.051	34.615	0.00	0.00	41.55	2.52
1810	2020	0.744281	CAAAAGTTTGCCTCCGGTGT	59.256	50.000	0.00	0.00	0.00	4.16
1811	2021	1.950909	CAAAAGTTTGCCTCCGGTGTA	59.049	47.619	0.00	0.00	0.00	2.90
1812	2022	2.556622	CAAAAGTTTGCCTCCGGTGTAT	59.443	45.455	0.00	0.00	0.00	2.29
1813	2023	1.821216	AAGTTTGCCTCCGGTGTATG	58.179	50.000	0.00	0.00	0.00	2.39
1815	2025	1.377987	TTTGCCTCCGGTGTATGCC	60.378	57.895	0.00	0.00	0.00	4.40
1817	2027	1.847798	TTGCCTCCGGTGTATGCCTT	61.848	55.000	0.00	0.00	0.00	4.35
1818	2028	1.819632	GCCTCCGGTGTATGCCTTG	60.820	63.158	0.00	0.00	0.00	3.61
1832	2042	9.301153	GGTGTATGCCTTGTTTTTATTTCTATG	57.699	33.333	0.00	0.00	0.00	2.23
1896	2106	7.648142	TGTGATTTGAGACTAATTGGTCAAAC	58.352	34.615	22.20	13.62	40.67	2.93
2343	2558	2.591571	TCAGATCATGTTGAGCTCCG	57.408	50.000	12.15	0.00	39.11	4.63
2345	2560	1.137675	CAGATCATGTTGAGCTCCGGA	59.862	52.381	12.15	2.93	39.11	5.14
2349	2564	1.137675	TCATGTTGAGCTCCGGATGAG	59.862	52.381	12.15	0.00	44.47	2.90
2452	2670	4.579869	AGTAGTAACTGAATGCACAAGGG	58.420	43.478	0.00	0.00	33.57	3.95
2455	2673	1.620822	AACTGAATGCACAAGGGTCC	58.379	50.000	0.00	0.00	0.00	4.46
2457	2675	1.926511	CTGAATGCACAAGGGTCCGC	61.927	60.000	0.00	0.00	0.00	5.54
2458	2676	2.676471	AATGCACAAGGGTCCGCC	60.676	61.111	0.00	0.00	0.00	6.13
2468	2686	3.311110	GGTCCGCCCTGACACTGA	61.311	66.667	0.00	0.00	36.97	3.41
2475	2731	0.107312	GCCCTGACACTGATGATGCT	60.107	55.000	0.00	0.00	0.00	3.79
2487	2743	5.181811	CACTGATGATGCTGGTAGTCAAAAA	59.818	40.000	0.00	0.00	0.00	1.94
2488	2744	5.182001	ACTGATGATGCTGGTAGTCAAAAAC	59.818	40.000	0.00	0.00	0.00	2.43
2491	2747	1.600023	TGCTGGTAGTCAAAAACGGG	58.400	50.000	0.00	0.00	0.00	5.28
2558	2844	2.941333	GTGATGGCCATCGATGCG	59.059	61.111	34.70	13.83	40.63	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	6.488006	AGAAAAACCATATTCGCATCATAGCT	59.512	34.615	0.00	0.00	0.00	3.32
245	250	9.698309	ATCGATAGTGATAATGTGGTTTCTAAG	57.302	33.333	0.00	0.00	37.40	2.18
749	818	9.512435	AAAGAATGAAAAATAATGATGAGCTCG	57.488	29.630	9.64	0.00	0.00	5.03
938	1094	4.220602	GGAATGGTTAAGTTGGCTGTGAAT	59.779	41.667	0.00	0.00	0.00	2.57
1258	1418	3.435186	GCGCTTGTCCTCCTTGGC	61.435	66.667	0.00	0.00	35.26	4.52
1322	1482	7.781548	AAATCCAGCAAGAAATCATAAATGC	57.218	32.000	0.00	0.00	0.00	3.56
1374	1537	0.462759	CGGCCCTAGGAAGCAAGAAG	60.463	60.000	11.48	0.00	0.00	2.85
1476	1642	0.983905	ACGGGCCACCATACACCATA	60.984	55.000	4.39	0.00	36.13	2.74
1524	1690	2.832201	GGATGGCCCTGCTCTTGC	60.832	66.667	0.00	0.00	40.20	4.01
1604	1773	1.066143	TGAAACGAGGGCTCTGAATCC	60.066	52.381	0.00	0.00	0.00	3.01
1614	1783	1.376037	GTCCAGGCTGAAACGAGGG	60.376	63.158	17.94	0.00	0.00	4.30
1700	1910	3.951775	TGACAACAGCAACCAAACTTT	57.048	38.095	0.00	0.00	0.00	2.66
1730	1940	9.553064	GAATCACAAATTCATAGTACCTCTCAT	57.447	33.333	0.00	0.00	0.00	2.90
1736	1946	7.707035	AGTCTCGAATCACAAATTCATAGTACC	59.293	37.037	0.00	0.00	0.00	3.34
1756	1966	6.311935	TGGTAAAATTCGACCAATTAGTCTCG	59.688	38.462	8.59	0.00	42.81	4.04
1832	2042	5.511377	CCACACGCAAACATATCACAAATAC	59.489	40.000	0.00	0.00	0.00	1.89
1838	2048	1.895051	GCCACACGCAAACATATCAC	58.105	50.000	0.00	0.00	37.47	3.06
1896	2106	4.142116	ACTTTTGGGTTTGGAACGGTAAAG	60.142	41.667	0.00	0.00	33.03	1.85
2343	2558	3.399330	TCGGTTTCAGACAAACTCATCC	58.601	45.455	0.00	0.00	0.00	3.51
2345	2560	4.821805	ACATTCGGTTTCAGACAAACTCAT	59.178	37.500	0.00	0.00	0.00	2.90
2349	2564	3.042887	GCACATTCGGTTTCAGACAAAC	58.957	45.455	0.00	0.00	0.00	2.93
2452	2670	1.448540	CATCAGTGTCAGGGCGGAC	60.449	63.158	1.42	1.42	38.29	4.79
2455	2673	1.434622	GCATCATCAGTGTCAGGGCG	61.435	60.000	0.00	0.00	0.00	6.13
2457	2675	1.664873	CAGCATCATCAGTGTCAGGG	58.335	55.000	0.00	0.00	0.00	4.45
2458	2676	1.065636	ACCAGCATCATCAGTGTCAGG	60.066	52.381	0.00	0.00	0.00	3.86
2459	2677	2.398252	ACCAGCATCATCAGTGTCAG	57.602	50.000	0.00	0.00	0.00	3.51
2460	2678	2.833943	ACTACCAGCATCATCAGTGTCA	59.166	45.455	0.00	0.00	0.00	3.58
2462	2680	2.833943	TGACTACCAGCATCATCAGTGT	59.166	45.455	0.00	0.00	0.00	3.55
2463	2681	3.531934	TGACTACCAGCATCATCAGTG	57.468	47.619	0.00	0.00	0.00	3.66
2464	2682	4.558226	TTTGACTACCAGCATCATCAGT	57.442	40.909	0.00	0.00	0.00	3.41
2466	2684	4.154015	CGTTTTTGACTACCAGCATCATCA	59.846	41.667	0.00	0.00	0.00	3.07
2467	2685	4.437390	CCGTTTTTGACTACCAGCATCATC	60.437	45.833	0.00	0.00	0.00	2.92
2468	2686	3.440173	CCGTTTTTGACTACCAGCATCAT	59.560	43.478	0.00	0.00	0.00	2.45
2475	2731	1.970092	CCACCCGTTTTTGACTACCA	58.030	50.000	0.00	0.00	0.00	3.25
2542	2800	2.281002	CCGCATCGATGGCCATCA	60.281	61.111	38.08	27.17	37.69	3.07
2543	2801	3.052082	CCCGCATCGATGGCCATC	61.052	66.667	32.34	32.34	34.56	3.51
2544	2802	4.648626	CCCCGCATCGATGGCCAT	62.649	66.667	26.00	20.96	0.00	4.40
2547	2805	1.741770	GATACCCCGCATCGATGGC	60.742	63.158	26.00	16.78	0.00	4.40
2548	2806	0.250234	ATGATACCCCGCATCGATGG	59.750	55.000	26.00	15.70	0.00	3.51
2550	2808	3.450817	TGATAATGATACCCCGCATCGAT	59.549	43.478	0.00	0.00	0.00	3.59
2558	2844	4.572389	GTGATGCGATGATAATGATACCCC	59.428	45.833	0.00	0.00	0.00	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.