AutoCloner

Multiple sequence alignment - TraesCS2D01G462100

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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	TraesCS2D01G462100	chr2D	100.000	3671	0	0	1	3671	568194903	568191233	0.000000e+00	6780.0
1	TraesCS2D01G462100	chr2D	88.316	1669	159	17	841	2476	568130046	568128381	0.000000e+00	1969.0
2	TraesCS2D01G462100	chr2A	95.892	1704	47	1	815	2495	707737918	707736215	0.000000e+00	2737.0
3	TraesCS2D01G462100	chr2A	89.791	1675	134	13	841	2481	707634229	707632558	0.000000e+00	2111.0
4	TraesCS2D01G462100	chr2A	94.437	701	34	4	2783	3481	691607188	691606491	0.000000e+00	1074.0
5	TraesCS2D01G462100	chr2A	94.574	258	13	1	2526	2782	691607484	691607227	7.390000e-107	398.0
6	TraesCS2D01G462100	chr2A	88.727	275	18	5	556	817	728021080	728020806	1.270000e-84	324.0
7	TraesCS2D01G462100	chr2A	90.816	196	18	0	3476	3671	691572519	691572324	2.810000e-66	263.0
8	TraesCS2D01G462100	chr2B	93.977	1710	87	1	815	2508	680755102	680753393	0.000000e+00	2573.0
9	TraesCS2D01G462100	chr2B	89.701	1670	134	17	841	2476	680668397	680666732	0.000000e+00	2097.0
10	TraesCS2D01G462100	chr3D	99.731	744	2	0	2928	3671	605313689	605314432	0.000000e+00	1363.0
11	TraesCS2D01G462100	chr3D	78.716	296	49	6	3129	3411	559078970	559079264	6.260000e-43	185.0
12	TraesCS2D01G462100	chr3D	91.262	103	8	1	2507	2608	293810625	293810523	4.940000e-29	139.0
13	TraesCS2D01G462100	chr4A	92.601	892	54	7	2783	3671	727051173	727050291	0.000000e+00	1271.0
14	TraesCS2D01G462100	chr4A	96.029	277	10	1	2507	2782	727051490	727051214	2.010000e-122	449.0
15	TraesCS2D01G462100	chr4A	85.450	378	28	10	3	361	537187922	537187553	5.790000e-98	368.0
16	TraesCS2D01G462100	chr7A	93.932	791	39	4	2780	3567	10284845	10285629	0.000000e+00	1186.0
17	TraesCS2D01G462100	chr7A	95.307	277	12	1	2507	2782	10284531	10284807	4.350000e-119	438.0
18	TraesCS2D01G462100	chr7A	91.803	61	5	0	696	756	705665875	705665815	6.530000e-13	86.1
19	TraesCS2D01G462100	chr3B	92.487	772	50	5	2780	3549	636436393	636437158	0.000000e+00	1098.0
20	TraesCS2D01G462100	chr3B	89.531	277	18	7	2508	2782	636436089	636436356	1.260000e-89	340.0
21	TraesCS2D01G462100	chr3B	89.320	103	8	2	2507	2608	387434241	387434141	3.850000e-25	126.0
22	TraesCS2D01G462100	chr1D	92.031	778	50	8	2780	3550	256205134	256205906	0.000000e+00	1083.0
23	TraesCS2D01G462100	chr1D	90.288	278	17	5	2507	2782	256204828	256205097	4.510000e-94	355.0
24	TraesCS2D01G462100	chr1D	84.674	261	37	3	3285	3544	28229637	28229895	1.310000e-64	257.0
25	TraesCS2D01G462100	chr5D	88.330	874	44	28	1	822	419217288	419216421	0.000000e+00	996.0
26	TraesCS2D01G462100	chr5D	93.333	120	8	0	698	817	377300830	377300711	1.050000e-40	178.0
27	TraesCS2D01G462100	chrUn	98.872	532	6	0	2508	3039	467717545	467717014	0.000000e+00	950.0
28	TraesCS2D01G462100	chr6B	96.757	370	9	3	2781	3147	19324380	19324011	6.740000e-172	614.0
29	TraesCS2D01G462100	chr6B	90.253	277	16	6	551	816	578060379	578060655	5.830000e-93	351.0
30	TraesCS2D01G462100	chr6B	89.024	82	8	1	281	361	578060207	578060288	2.330000e-17	100.0
31	TraesCS2D01G462100	chr1A	88.278	273	19	5	556	815	568023500	568023228	7.650000e-82	315.0
32	TraesCS2D01G462100	chr6D	87.624	202	12	8	556	745	425085678	425085478	4.770000e-54	222.0
33	TraesCS2D01G462100	chr6D	93.701	127	7	1	684	810	425085476	425085351	4.840000e-44	189.0
34	TraesCS2D01G462100	chr6D	90.244	82	7	1	281	361	425085897	425085816	5.010000e-19	106.0
35	TraesCS2D01G462100	chr3A	77.778	297	50	8	3129	3411	695502924	695503218	6.300000e-38	169.0
36	TraesCS2D01G462100	chr3A	91.262	103	8	1	2507	2608	388095678	388095576	4.940000e-29	139.0
37	TraesCS2D01G462100	chr7B	88.793	116	12	1	711	825	705108095	705107980	1.370000e-29	141.0
38	TraesCS2D01G462100	chr7B	93.023	43	1	2	1243	1283	497027100	497027058	1.100000e-05	62.1
39	TraesCS2D01G462100	chr4B	90.909	66	4	2	611	675	581943805	581943869	1.820000e-13	87.9
40	TraesCS2D01G462100	chr7D	97.059	34	1	0	1243	1276	473096005	473095972	1.420000e-04	58.4
41	TraesCS2D01G462100	chr4D	100.000	31	0	0	2508	2538	426689858	426689828	1.420000e-04	58.4

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	TraesCS2D01G462100	chr2D	568191233	568194903	3670	True	6780	6780	100.0000	1	3671	1	chr2D.!!$R2	3670
1	TraesCS2D01G462100	chr2D	568128381	568130046	1665	True	1969	1969	88.3160	841	2476	1	chr2D.!!$R1	1635
2	TraesCS2D01G462100	chr2A	707736215	707737918	1703	True	2737	2737	95.8920	815	2495	1	chr2A.!!$R3	1680
3	TraesCS2D01G462100	chr2A	707632558	707634229	1671	True	2111	2111	89.7910	841	2481	1	chr2A.!!$R2	1640
4	TraesCS2D01G462100	chr2A	691606491	691607484	993	True	736	1074	94.5055	2526	3481	2	chr2A.!!$R5	955
5	TraesCS2D01G462100	chr2B	680753393	680755102	1709	True	2573	2573	93.9770	815	2508	1	chr2B.!!$R2	1693
6	TraesCS2D01G462100	chr2B	680666732	680668397	1665	True	2097	2097	89.7010	841	2476	1	chr2B.!!$R1	1635
7	TraesCS2D01G462100	chr3D	605313689	605314432	743	False	1363	1363	99.7310	2928	3671	1	chr3D.!!$F2	743
8	TraesCS2D01G462100	chr4A	727050291	727051490	1199	True	860	1271	94.3150	2507	3671	2	chr4A.!!$R2	1164
9	TraesCS2D01G462100	chr7A	10284531	10285629	1098	False	812	1186	94.6195	2507	3567	2	chr7A.!!$F1	1060
10	TraesCS2D01G462100	chr3B	636436089	636437158	1069	False	719	1098	91.0090	2508	3549	2	chr3B.!!$F1	1041
11	TraesCS2D01G462100	chr1D	256204828	256205906	1078	False	719	1083	91.1595	2507	3550	2	chr1D.!!$F2	1043
12	TraesCS2D01G462100	chr5D	419216421	419217288	867	True	996	996	88.3300	1	822	1	chr5D.!!$R2	821
13	TraesCS2D01G462100	chrUn	467717014	467717545	531	True	950	950	98.8720	2508	3039	1	chrUn.!!$R1	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
913	966	0.037975	GTCCCTTTCGTCGCCTGTTA	60.038	55.0	0.00	0.0	0.0	2.41	F
954	1012	0.384309	ACACACACAGACGTCGACAT	59.616	50.0	17.16	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2405	2519	1.700955	GGAGCAGGTCCTTCGGTATA	58.299	55.0	11.76	0.0	42.99	1.47	R
2777	2893	6.385649	TTGACTCAAACATGTAGGGTTTTC	57.614	37.5	0.00	0.0	36.38	2.29	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
27	28	7.931275	AGCAAACTTTGTTCCTTAAGTTAGAG	58.069	34.615	0.97	0.00	42.17	2.43
58	60	2.037902	TCACCTTAATGACGCTGGAACA	59.962	45.455	0.00	0.00	0.00	3.18
76	78	3.981071	ACACAACTGAAGGCTATGCTA	57.019	42.857	0.00	0.00	0.00	3.49
88	90	6.095440	TGAAGGCTATGCTAAAATTCTTGGTC	59.905	38.462	0.00	0.00	0.00	4.02
98	100	7.389330	TGCTAAAATTCTTGGTCGATCTACAAA	59.611	33.333	0.00	0.00	0.00	2.83
99	101	7.692705	GCTAAAATTCTTGGTCGATCTACAAAC	59.307	37.037	0.00	0.00	0.00	2.93
154	156	9.632807	GTGTAGGCTTTTATATCATCTCAGTAG	57.367	37.037	0.00	0.00	0.00	2.57
178	181	2.445145	TCAAACAGACATCAAAGGGGGA	59.555	45.455	0.00	0.00	0.00	4.81
181	184	1.995542	ACAGACATCAAAGGGGGACAT	59.004	47.619	0.00	0.00	0.00	3.06
218	239	2.564771	CACCAGTAGTGTATGGCATGG	58.435	52.381	10.98	3.90	41.93	3.66
253	274	7.945109	ACATCAGTAGTCTATATTCCTGCAGTA	59.055	37.037	13.81	0.00	0.00	2.74
257	278	7.229707	CAGTAGTCTATATTCCTGCAGTAGTGT	59.770	40.741	13.81	0.00	0.00	3.55
275	296	3.531982	GTGTTGTTCACTGACGAAATCG	58.468	45.455	0.48	0.48	43.13	3.34
293	314	6.852345	CGAAATCGAACATATGCATCAAATCA	59.148	34.615	0.19	0.00	43.02	2.57
317	338	2.169352	ACTGCCTTGCTGATCTATTCGT	59.831	45.455	0.00	0.00	0.00	3.85
318	339	2.799412	CTGCCTTGCTGATCTATTCGTC	59.201	50.000	0.00	0.00	0.00	4.20
327	348	0.311165	ATCTATTCGTCGGCTCGGTG	59.689	55.000	0.00	0.00	0.00	4.94
350	371	0.102120	CTCCGTTCTAGCTGCAGAGG	59.898	60.000	20.43	6.28	0.00	3.69
355	376	1.134551	GTTCTAGCTGCAGAGGAAGGG	60.135	57.143	20.43	0.00	0.00	3.95
356	377	0.336392	TCTAGCTGCAGAGGAAGGGA	59.664	55.000	20.43	1.98	0.00	4.20
357	378	1.198713	CTAGCTGCAGAGGAAGGGAA	58.801	55.000	20.43	0.00	0.00	3.97
358	379	1.556911	CTAGCTGCAGAGGAAGGGAAA	59.443	52.381	20.43	0.00	0.00	3.13
373	394	3.022406	AGGGAAAGAAAGATGCATCAGC	58.978	45.455	27.81	15.90	42.57	4.26
506	527	2.178580	CAGAGTCTCAGAGAAAGGGCT	58.821	52.381	0.20	0.00	0.00	5.19
522	543	1.162800	GGCTAGGCAGAAATGGCGAG	61.163	60.000	12.16	7.42	39.40	5.03
540	572	3.864921	GCGAGAGATAGAGAGAGGAGGAC	60.865	56.522	0.00	0.00	0.00	3.85
548	580	0.622154	AGAGAGGAGGACGAGGAGGA	60.622	60.000	0.00	0.00	0.00	3.71
550	582	1.152839	GAGGAGGACGAGGAGGAGG	60.153	68.421	0.00	0.00	0.00	4.30
551	583	2.123640	GGAGGACGAGGAGGAGGG	60.124	72.222	0.00	0.00	0.00	4.30
553	585	2.617538	AGGACGAGGAGGAGGGGA	60.618	66.667	0.00	0.00	0.00	4.81
610	663	3.632700	CGCCGTCGGAACAGAAAA	58.367	55.556	17.49	0.00	0.00	2.29
666	719	1.801913	CTCGTCCGCCAGTTTCTCG	60.802	63.158	0.00	0.00	0.00	4.04
674	727	1.491505	GCCAGTTTCTCGCGGCTATC	61.492	60.000	6.13	0.00	41.50	2.08
675	728	1.209275	CCAGTTTCTCGCGGCTATCG	61.209	60.000	6.13	0.00	42.76	2.92
691	744	2.754946	ATCGGTAGCCAAGTTTTCGA	57.245	45.000	0.00	0.00	0.00	3.71
745	798	4.284178	CCATCACATCCTTCCTTCCAAAT	58.716	43.478	0.00	0.00	0.00	2.32
756	809	5.420104	CCTTCCTTCCAAATATATGGCATCC	59.580	44.000	1.65	0.00	40.46	3.51
760	813	5.336102	CTTCCAAATATATGGCATCCCCTT	58.664	41.667	1.65	0.00	40.46	3.95
786	839	0.544357	TGGCTATCCCTATCCCACCG	60.544	60.000	0.00	0.00	0.00	4.94
798	851	3.971894	CCACCGAGGGATAGCCTT	58.028	61.111	0.00	0.00	0.00	4.35
810	863	3.203716	GGATAGCCTTAGAACCAAACGG	58.796	50.000	0.00	0.00	0.00	4.44
913	966	0.037975	GTCCCTTTCGTCGCCTGTTA	60.038	55.000	0.00	0.00	0.00	2.41
954	1012	0.384309	ACACACACAGACGTCGACAT	59.616	50.000	17.16	0.00	0.00	3.06
964	1022	1.588932	CGTCGACATCATGGTCCGG	60.589	63.158	17.16	0.00	34.24	5.14
1085	1169	4.124351	CCGCCCGTTCTCGCTGTA	62.124	66.667	0.00	0.00	35.54	2.74
1384	1498	2.504244	CGACCTCACCGAGAACGC	60.504	66.667	0.00	0.00	38.29	4.84
1526	1640	1.002134	CCTGGACCTCGGCAACAAT	60.002	57.895	0.00	0.00	0.00	2.71
1669	1783	4.932200	CCAGATATTCGAGGCCTTTATGAC	59.068	45.833	6.77	0.00	0.00	3.06
2032	2146	2.429930	TGGGCTGTCCAAGAACCG	59.570	61.111	0.00	0.00	43.84	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	5.677178	GCGTCATTAAGGTGATCGATTTTTC	59.323	40.000	0.00	0.00	0.00	2.29
58	60	6.660949	AGAATTTTAGCATAGCCTTCAGTTGT	59.339	34.615	0.00	0.00	0.00	3.32
76	78	6.488683	TGGTTTGTAGATCGACCAAGAATTTT	59.511	34.615	3.33	0.00	39.11	1.82
88	90	9.169468	GCAATATTAACATTGGTTTGTAGATCG	57.831	33.333	8.48	0.00	38.45	3.69
98	100	5.068198	CAGCCTCTGCAATATTAACATTGGT	59.932	40.000	8.48	0.00	41.13	3.67
99	101	5.068198	ACAGCCTCTGCAATATTAACATTGG	59.932	40.000	8.48	0.00	41.13	3.16
154	156	4.399303	CCCCCTTTGATGTCTGTTTGATAC	59.601	45.833	0.00	0.00	0.00	2.24
178	181	1.069022	GCGTGTGTTTGATGCTGATGT	60.069	47.619	0.00	0.00	0.00	3.06
181	184	0.307453	GTGCGTGTGTTTGATGCTGA	59.693	50.000	0.00	0.00	0.00	4.26
208	229	3.016031	TGTGTGTTCATCCATGCCATAC	58.984	45.455	0.00	0.00	0.00	2.39
218	239	9.973450	AATATAGACTACTGATGTGTGTTCATC	57.027	33.333	0.00	0.00	42.95	2.92
253	274	3.245284	CGATTTCGTCAGTGAACAACACT	59.755	43.478	0.00	0.00	46.21	3.55
257	278	3.866327	TGTTCGATTTCGTCAGTGAACAA	59.134	39.130	0.00	0.00	41.70	2.83
275	296	6.436261	CAGTCCTGATTTGATGCATATGTTC	58.564	40.000	0.00	2.95	0.00	3.18
327	348	1.227118	GCAGCTAGAACGGAGGAGC	60.227	63.158	0.00	0.00	35.07	4.70
350	371	4.439837	GCTGATGCATCTTTCTTTCCCTTC	60.440	45.833	26.32	0.00	39.41	3.46
355	376	3.734293	GCCAGCTGATGCATCTTTCTTTC	60.734	47.826	26.32	10.60	42.74	2.62
356	377	2.165845	GCCAGCTGATGCATCTTTCTTT	59.834	45.455	26.32	4.81	42.74	2.52
357	378	1.749634	GCCAGCTGATGCATCTTTCTT	59.250	47.619	26.32	6.15	42.74	2.52
358	379	1.390565	GCCAGCTGATGCATCTTTCT	58.609	50.000	26.32	16.84	42.74	2.52
373	394	4.821589	GGAGAACGGAGGCGCCAG	62.822	72.222	31.54	21.56	35.94	4.85
423	444	1.156645	GGCTGCTATGGAAGTGAGCG	61.157	60.000	0.00	0.00	39.14	5.03
506	527	1.485124	TCTCTCGCCATTTCTGCCTA	58.515	50.000	0.00	0.00	0.00	3.93
522	543	3.306780	CCTCGTCCTCCTCTCTCTATCTC	60.307	56.522	0.00	0.00	0.00	2.75
593	646	1.935925	TTTTTCTGTTCCGACGGCG	59.064	52.632	9.66	1.94	37.24	6.46
639	692	4.509737	GCGGACGAGGGTAGCCAC	62.510	72.222	14.62	5.96	0.00	5.01
645	698	3.236003	GAAACTGGCGGACGAGGGT	62.236	63.158	0.00	0.00	0.00	4.34
674	727	1.396996	CCATCGAAAACTTGGCTACCG	59.603	52.381	0.00	0.00	0.00	4.02
675	728	2.706890	TCCATCGAAAACTTGGCTACC	58.293	47.619	0.00	0.00	0.00	3.18
691	744	4.906618	ACCCGATTTAGCGAATATTCCAT	58.093	39.130	9.87	1.46	0.00	3.41
745	798	6.493166	CCAGATTTTAAGGGGATGCCATATA	58.507	40.000	5.30	0.00	0.00	0.86
756	809	4.731313	AGGGATAGCCAGATTTTAAGGG	57.269	45.455	0.00	0.00	35.15	3.95
760	813	5.250774	GTGGGATAGGGATAGCCAGATTTTA	59.749	44.000	0.00	0.00	35.15	1.52
786	839	4.452825	GTTTGGTTCTAAGGCTATCCCTC	58.547	47.826	0.00	0.00	45.62	4.30
798	851	2.872842	GCTTAGGTGCCGTTTGGTTCTA	60.873	50.000	0.00	0.00	37.67	2.10
810	863	3.813596	CCGACATGGCTTAGGTGC	58.186	61.111	0.00	0.00	0.00	5.01
848	901	5.481824	GGGAAGTTTGATTCAAAGGGAGAAT	59.518	40.000	12.02	0.00	38.35	2.40
954	1012	0.687920	TAAGCAACACCGGACCATGA	59.312	50.000	9.46	0.00	0.00	3.07
1643	1757	0.972883	AGGCCTCGAATATCTGGAGC	59.027	55.000	0.00	0.00	0.00	4.70
2032	2146	4.593864	GGATCGAGCCGGTCAGCC	62.594	72.222	2.80	0.00	38.92	4.85
2126	2240	4.221703	AGGTTGACAAGATTCGTCAGAGAT	59.778	41.667	0.00	0.00	43.85	2.75
2405	2519	1.700955	GGAGCAGGTCCTTCGGTATA	58.299	55.000	11.76	0.00	42.99	1.47
2777	2893	6.385649	TTGACTCAAACATGTAGGGTTTTC	57.614	37.500	0.00	0.00	36.38	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.