AutoCloner

Multiple sequence alignment - TraesCS7D01G430200

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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	TraesCS7D01G430200	chr7D	100.000	2756	0	0	1	2756	549696524	549699279	0.000000e+00	5090
1	TraesCS7D01G430200	chr7D	84.960	1762	226	20	734	2467	549770437	549772187	0.000000e+00	1749
2	TraesCS7D01G430200	chr7D	84.295	1802	221	37	733	2511	549705318	549707080	0.000000e+00	1703
3	TraesCS7D01G430200	chr7D	82.994	1770	233	31	733	2467	549783183	549784919	0.000000e+00	1539
4	TraesCS7D01G430200	chr7A	96.193	2154	72	4	440	2585	635074418	635076569	0.000000e+00	3515
5	TraesCS7D01G430200	chr7A	81.792	2422	312	69	167	2530	635093450	635095800	0.000000e+00	1910
6	TraesCS7D01G430200	chr7A	84.544	1734	232	18	761	2467	635241133	635242857	0.000000e+00	1685
7	TraesCS7D01G430200	chr7A	83.968	1628	210	28	871	2467	635270704	635272311	0.000000e+00	1513
8	TraesCS7D01G430200	chr7A	83.402	1687	216	37	818	2467	635051461	635053120	0.000000e+00	1506
9	TraesCS7D01G430200	chr7A	90.878	296	17	6	57	352	635073995	635074280	3.330000e-104	388
10	TraesCS7D01G430200	chr7A	96.373	193	6	1	2564	2756	635078134	635078325	1.590000e-82	316
11	TraesCS7D01G430200	chr7A	82.667	150	20	4	2607	2756	635096268	635096411	8.010000e-26	128
12	TraesCS7D01G430200	chr7B	95.463	1080	40	3	841	1911	594035397	594036476	0.000000e+00	1714
13	TraesCS7D01G430200	chr7B	82.359	2052	257	51	732	2756	594048254	594050227	0.000000e+00	1687
14	TraesCS7D01G430200	chr7B	84.309	1759	241	18	734	2467	594063521	594065269	0.000000e+00	1687
15	TraesCS7D01G430200	chr7B	94.070	371	20	1	2386	2756	594043924	594044292	1.850000e-156	562
16	TraesCS7D01G430200	chr7B	90.732	410	29	3	440	841	594034904	594035312	3.120000e-149	538
17	TraesCS7D01G430200	chr7B	93.333	330	19	3	1	330	594029079	594029405	4.130000e-133	484
18	TraesCS7D01G430200	chr7B	90.909	154	14	0	199	352	594047650	594047803	1.000000e-49	207
19	TraesCS7D01G430200	chr7B	79.141	163	19	11	227	386	594110740	594110890	6.280000e-17	99

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	TraesCS7D01G430200	chr7D	549696524	549699279	2755	False	5090.000000	5090	100.000000	1	2756	1	chr7D.!!$F1	2755
1	TraesCS7D01G430200	chr7D	549770437	549772187	1750	False	1749.000000	1749	84.960000	734	2467	1	chr7D.!!$F3	1733
2	TraesCS7D01G430200	chr7D	549705318	549707080	1762	False	1703.000000	1703	84.295000	733	2511	1	chr7D.!!$F2	1778
3	TraesCS7D01G430200	chr7D	549783183	549784919	1736	False	1539.000000	1539	82.994000	733	2467	1	chr7D.!!$F4	1734
4	TraesCS7D01G430200	chr7A	635241133	635242857	1724	False	1685.000000	1685	84.544000	761	2467	1	chr7A.!!$F2	1706
5	TraesCS7D01G430200	chr7A	635270704	635272311	1607	False	1513.000000	1513	83.968000	871	2467	1	chr7A.!!$F3	1596
6	TraesCS7D01G430200	chr7A	635051461	635053120	1659	False	1506.000000	1506	83.402000	818	2467	1	chr7A.!!$F1	1649
7	TraesCS7D01G430200	chr7A	635073995	635078325	4330	False	1406.333333	3515	94.481333	57	2756	3	chr7A.!!$F4	2699
8	TraesCS7D01G430200	chr7A	635093450	635096411	2961	False	1019.000000	1910	82.229500	167	2756	2	chr7A.!!$F5	2589
9	TraesCS7D01G430200	chr7B	594063521	594065269	1748	False	1687.000000	1687	84.309000	734	2467	1	chr7B.!!$F2	1733
10	TraesCS7D01G430200	chr7B	594034904	594036476	1572	False	1126.000000	1714	93.097500	440	1911	2	chr7B.!!$F4	1471
11	TraesCS7D01G430200	chr7B	594043924	594050227	6303	False	818.666667	1687	89.112667	199	2756	3	chr7B.!!$F5	2557

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
37	38	0.105039	GTCATCGCTAGTCCCTTGGG	59.895	60.0	0.0	0.0	0.0	4.12	F
210	3739	0.758685	CAGAAGATCCTCCTCGCCCT	60.759	60.0	0.0	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1694	5552	0.532573	CACGGCAGTCTCCATGTAGT	59.467	55.000	0.0	0.0	0.0	2.73	R
1964	5840	2.027469	TGACAACAGATCAGCAGCTCAT	60.027	45.455	0.0	0.0	0.0	2.90	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
21	22	4.002906	AGACGTATTTTGCTTGGAGTCA	57.997	40.909	0.00	0.00	0.00	3.41
23	24	4.631813	AGACGTATTTTGCTTGGAGTCATC	59.368	41.667	0.00	0.00	0.00	2.92
24	25	3.370978	ACGTATTTTGCTTGGAGTCATCG	59.629	43.478	0.00	0.00	0.00	3.84
26	27	1.896220	TTTTGCTTGGAGTCATCGCT	58.104	45.000	0.00	0.00	0.00	4.93
27	28	2.760634	TTTGCTTGGAGTCATCGCTA	57.239	45.000	0.00	0.00	0.00	4.26
28	29	2.299993	TTGCTTGGAGTCATCGCTAG	57.700	50.000	0.00	0.00	0.00	3.42
31	32	1.537135	GCTTGGAGTCATCGCTAGTCC	60.537	57.143	0.00	0.00	37.04	3.85
33	34	0.259065	TGGAGTCATCGCTAGTCCCT	59.741	55.000	0.00	0.00	35.86	4.20
35	36	1.067821	GGAGTCATCGCTAGTCCCTTG	59.932	57.143	0.00	0.00	31.27	3.61
37	38	0.105039	GTCATCGCTAGTCCCTTGGG	59.895	60.000	0.00	0.00	0.00	4.12
38	39	1.227674	CATCGCTAGTCCCTTGGGC	60.228	63.158	0.00	0.00	0.00	5.36
39	40	2.444256	ATCGCTAGTCCCTTGGGCC	61.444	63.158	0.00	0.00	0.00	5.80
40	41	4.176752	CGCTAGTCCCTTGGGCCC	62.177	72.222	17.59	17.59	0.00	5.80
41	42	3.810188	GCTAGTCCCTTGGGCCCC	61.810	72.222	22.27	1.37	0.00	5.80
42	43	3.480133	CTAGTCCCTTGGGCCCCG	61.480	72.222	22.27	10.65	0.00	5.73
120	121	2.125673	CAACGTACTCCGGCCCTG	60.126	66.667	0.00	0.00	42.24	4.45
157	158	3.140814	GCATTTCTGGCCGGGTCC	61.141	66.667	12.87	0.00	0.00	4.46
199	200	3.407657	CGCAGCAGCCAGAAGATC	58.592	61.111	0.00	0.00	37.52	2.75
202	203	0.814812	GCAGCAGCCAGAAGATCCTC	60.815	60.000	0.00	0.00	33.58	3.71
210	3739	0.758685	CAGAAGATCCTCCTCGCCCT	60.759	60.000	0.00	0.00	0.00	5.19
405	3965	7.941431	ACCAATTACTCCTACTCTATATCGG	57.059	40.000	0.00	0.00	0.00	4.18
406	3966	7.468496	ACCAATTACTCCTACTCTATATCGGT	58.532	38.462	0.00	0.00	0.00	4.69
411	3978	5.797051	ACTCCTACTCTATATCGGTCAGAC	58.203	45.833	0.00	0.00	0.00	3.51
414	3981	6.408035	TCCTACTCTATATCGGTCAGACATC	58.592	44.000	2.17	0.00	0.00	3.06
431	3998	4.080863	AGACATCGGTAGAAAAGAAGCCAT	60.081	41.667	0.00	0.00	0.00	4.40
441	4008	7.993758	GGTAGAAAAGAAGCCATTATTAGTCCT	59.006	37.037	0.00	0.00	0.00	3.85
442	4009	7.872113	AGAAAAGAAGCCATTATTAGTCCTG	57.128	36.000	0.00	0.00	0.00	3.86
443	4010	6.319911	AGAAAAGAAGCCATTATTAGTCCTGC	59.680	38.462	0.00	0.00	0.00	4.85
451	4043	4.349342	CCATTATTAGTCCTGCCTCCTCTT	59.651	45.833	0.00	0.00	0.00	2.85
457	4049	0.914644	TCCTGCCTCCTCTTCCATTG	59.085	55.000	0.00	0.00	0.00	2.82
602	4207	3.754850	TGTTTGATGGCATCTCAACTGAG	59.245	43.478	28.09	0.00	43.36	3.35
757	4483	7.792374	TGATTTTCTGCTTATCATGTAGGAC	57.208	36.000	0.00	0.00	0.00	3.85
816	4542	1.803334	TGAGTTATGGTTCGTGCCAC	58.197	50.000	3.07	0.00	41.94	5.01
958	4778	4.082408	GCCAAGTTGAATTTAGGGGTACAC	60.082	45.833	3.87	0.00	0.00	2.90
959	4779	5.321927	CCAAGTTGAATTTAGGGGTACACT	58.678	41.667	3.87	0.00	0.00	3.55
1039	4878	4.095483	AGTCAATCGCCATGATGAAAAGAC	59.905	41.667	0.00	2.26	37.39	3.01
1445	5303	3.742433	ACCTCGAGTTCCATCATCATC	57.258	47.619	12.31	0.00	0.00	2.92
1446	5304	3.033909	ACCTCGAGTTCCATCATCATCA	58.966	45.455	12.31	0.00	0.00	3.07
1447	5305	3.069300	ACCTCGAGTTCCATCATCATCAG	59.931	47.826	12.31	0.00	0.00	2.90
1448	5306	3.058450	CTCGAGTTCCATCATCATCAGC	58.942	50.000	3.62	0.00	0.00	4.26
1449	5307	2.431782	TCGAGTTCCATCATCATCAGCA	59.568	45.455	0.00	0.00	0.00	4.41
1450	5308	3.118665	TCGAGTTCCATCATCATCAGCAA	60.119	43.478	0.00	0.00	0.00	3.91
1754	5612	2.485426	CAGTTACTCAGACGTTCCGGTA	59.515	50.000	0.00	0.00	0.00	4.02
1809	5667	2.480419	GTCGTTGTTGGAGATGGACAAG	59.520	50.000	0.00	0.00	34.29	3.16
1997	5873	0.602638	TGTTGTCACACTCCATCGGC	60.603	55.000	0.00	0.00	0.00	5.54
2230	6116	3.254166	GCCATGTATGCCTTTGGAGTATG	59.746	47.826	0.00	0.00	0.00	2.39
2419	6314	5.947663	TCCCCATTTACTTTCACTTCTCAA	58.052	37.500	0.00	0.00	0.00	3.02
2503	6401	1.585267	TTAGTGCAGCGTTGGCATGG	61.585	55.000	0.16	0.00	44.11	3.66
2540	6438	4.922206	TCTAGGAAAACAGTGCCATCAAT	58.078	39.130	0.00	0.00	0.00	2.57
2573	6471	5.645497	AGAGATGCAGTTGTAGTCATTTTCC	59.355	40.000	0.00	0.00	0.00	3.13
2579	6477	6.995686	TGCAGTTGTAGTCATTTTCCTTTAGA	59.004	34.615	0.00	0.00	0.00	2.10
2614	8506	0.471971	AGACGGTGGGGGAGATATGG	60.472	60.000	0.00	0.00	0.00	2.74
2650	8542	6.238648	AGAAGTTAATTGTGGGACTTGTAGG	58.761	40.000	0.00	0.00	32.85	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.002906	TGACTCCAAGCAAAATACGTCT	57.997	40.909	0.00	0.00	0.00	4.18
1	2	4.492570	CGATGACTCCAAGCAAAATACGTC	60.493	45.833	0.00	0.00	0.00	4.34
2	3	3.370978	CGATGACTCCAAGCAAAATACGT	59.629	43.478	0.00	0.00	0.00	3.57
4	5	3.375299	AGCGATGACTCCAAGCAAAATAC	59.625	43.478	0.00	0.00	34.08	1.89
5	6	3.609853	AGCGATGACTCCAAGCAAAATA	58.390	40.909	0.00	0.00	34.08	1.40
6	7	2.440409	AGCGATGACTCCAAGCAAAAT	58.560	42.857	0.00	0.00	34.08	1.82
9	10	1.550524	ACTAGCGATGACTCCAAGCAA	59.449	47.619	0.00	0.00	34.08	3.91
11	12	1.537135	GGACTAGCGATGACTCCAAGC	60.537	57.143	0.00	0.00	0.00	4.01
13	14	1.112113	GGGACTAGCGATGACTCCAA	58.888	55.000	0.00	0.00	0.00	3.53
14	15	0.259065	AGGGACTAGCGATGACTCCA	59.741	55.000	0.00	0.00	36.02	3.86
17	18	1.115467	CCAAGGGACTAGCGATGACT	58.885	55.000	0.00	0.00	38.49	3.41
18	19	0.105039	CCCAAGGGACTAGCGATGAC	59.895	60.000	0.00	0.00	38.49	3.06
20	21	1.227674	GCCCAAGGGACTAGCGATG	60.228	63.158	9.92	0.00	38.49	3.84
21	22	2.444256	GGCCCAAGGGACTAGCGAT	61.444	63.158	9.92	0.00	41.04	4.58
23	24	4.176752	GGGCCCAAGGGACTAGCG	62.177	72.222	19.95	0.00	44.51	4.26
24	25	3.810188	GGGGCCCAAGGGACTAGC	61.810	72.222	26.86	0.00	44.51	3.42
43	44	1.690219	ATTGGGAGACTGCCTAGCGG	61.690	60.000	14.77	0.00	41.29	5.52
44	45	0.531532	CATTGGGAGACTGCCTAGCG	60.532	60.000	14.77	0.00	0.00	4.26
45	46	0.543749	ACATTGGGAGACTGCCTAGC	59.456	55.000	14.77	0.00	0.00	3.42
46	47	3.452627	AGTTACATTGGGAGACTGCCTAG	59.547	47.826	14.77	6.48	0.00	3.02
48	49	2.026822	CAGTTACATTGGGAGACTGCCT	60.027	50.000	14.77	0.00	32.36	4.75
49	50	2.290323	ACAGTTACATTGGGAGACTGCC	60.290	50.000	5.96	5.96	40.95	4.85
50	51	3.059352	ACAGTTACATTGGGAGACTGC	57.941	47.619	0.00	0.00	40.95	4.40
51	52	4.935808	GGTTACAGTTACATTGGGAGACTG	59.064	45.833	0.00	0.00	42.48	3.51
52	53	4.595781	TGGTTACAGTTACATTGGGAGACT	59.404	41.667	0.00	0.00	0.00	3.24
54	55	4.564821	GCTGGTTACAGTTACATTGGGAGA	60.565	45.833	0.00	0.00	46.62	3.71
55	56	3.689649	GCTGGTTACAGTTACATTGGGAG	59.310	47.826	0.00	0.00	46.62	4.30
105	106	1.751927	CTACAGGGCCGGAGTACGT	60.752	63.158	11.67	0.00	42.24	3.57
136	137	2.409870	CCCGGCCAGAAATGCTGTC	61.410	63.158	2.24	0.00	43.33	3.51
140	141	3.140814	GGACCCGGCCAGAAATGC	61.141	66.667	2.24	0.00	0.00	3.56
157	158	2.776913	GGGAGAGGAGGCGACGAAG	61.777	68.421	0.00	0.00	0.00	3.79
190	191	1.745264	GGCGAGGAGGATCTTCTGG	59.255	63.158	4.68	0.00	39.36	3.86
191	192	0.758685	AGGGCGAGGAGGATCTTCTG	60.759	60.000	4.68	0.00	39.36	3.02
195	196	2.200092	GGAGGGCGAGGAGGATCT	59.800	66.667	0.00	0.00	33.73	2.75
202	203	2.755439	ATATGGGGAGGAGGGCGAGG	62.755	65.000	0.00	0.00	0.00	4.63
210	3739	0.832135	GCCGACAGATATGGGGAGGA	60.832	60.000	4.10	0.00	0.00	3.71
389	3949	5.795972	TGTCTGACCGATATAGAGTAGGAG	58.204	45.833	5.17	0.00	0.00	3.69
390	3950	5.820404	TGTCTGACCGATATAGAGTAGGA	57.180	43.478	5.17	0.00	0.00	2.94
391	3951	5.292345	CGATGTCTGACCGATATAGAGTAGG	59.708	48.000	5.17	0.00	0.00	3.18
392	3952	5.292345	CCGATGTCTGACCGATATAGAGTAG	59.708	48.000	5.17	0.00	0.00	2.57
393	3953	5.176592	CCGATGTCTGACCGATATAGAGTA	58.823	45.833	5.17	0.00	0.00	2.59
394	3954	4.004314	CCGATGTCTGACCGATATAGAGT	58.996	47.826	5.17	0.00	0.00	3.24
395	3955	4.004314	ACCGATGTCTGACCGATATAGAG	58.996	47.826	5.17	0.00	0.00	2.43
397	3957	5.176592	TCTACCGATGTCTGACCGATATAG	58.823	45.833	5.17	2.80	0.00	1.31
400	3960	3.480505	TCTACCGATGTCTGACCGATA	57.519	47.619	5.17	0.00	0.00	2.92
401	3961	2.343484	TCTACCGATGTCTGACCGAT	57.657	50.000	5.17	0.00	0.00	4.18
403	3963	2.933495	TTTCTACCGATGTCTGACCG	57.067	50.000	5.17	2.44	0.00	4.79
404	3964	4.451629	TCTTTTCTACCGATGTCTGACC	57.548	45.455	5.17	0.00	0.00	4.02
405	3965	4.327627	GCTTCTTTTCTACCGATGTCTGAC	59.672	45.833	0.00	0.00	0.00	3.51
406	3966	4.495422	GCTTCTTTTCTACCGATGTCTGA	58.505	43.478	0.00	0.00	0.00	3.27
411	3978	6.867662	ATAATGGCTTCTTTTCTACCGATG	57.132	37.500	0.00	0.00	0.00	3.84
414	3981	7.041984	GGACTAATAATGGCTTCTTTTCTACCG	60.042	40.741	0.00	0.00	0.00	4.02
431	3998	3.967987	GGAAGAGGAGGCAGGACTAATAA	59.032	47.826	0.00	0.00	0.00	1.40
441	4008	1.210204	AGGCAATGGAAGAGGAGGCA	61.210	55.000	0.00	0.00	0.00	4.75
442	4009	0.750911	CAGGCAATGGAAGAGGAGGC	60.751	60.000	0.00	0.00	0.00	4.70
443	4010	0.914644	TCAGGCAATGGAAGAGGAGG	59.085	55.000	0.00	0.00	0.00	4.30
457	4049	1.270274	TGTGTTGTGATTGCATCAGGC	59.730	47.619	0.00	0.00	40.53	4.85
602	4207	3.197766	TCACATCATAGTTCTGGTGACCC	59.802	47.826	0.00	0.00	31.49	4.46
757	4483	4.155280	AGAATTTTACAATTGTCGTCCCGG	59.845	41.667	15.85	0.00	32.35	5.73
777	4503	5.827797	ACTCAAAAGTGTGAATTGGCTAGAA	59.172	36.000	0.00	0.00	33.32	2.10
816	4542	2.825861	AAAGTGCAGCCAAAATCCAG	57.174	45.000	0.00	0.00	0.00	3.86
906	4723	5.334105	GCATAACAGTATTTGGCATAGGTCG	60.334	44.000	0.00	0.00	0.00	4.79
958	4778	7.804843	AAAGATGGAGATGATTGAGCTTAAG	57.195	36.000	0.00	0.00	0.00	1.85
959	4779	8.585471	AAAAAGATGGAGATGATTGAGCTTAA	57.415	30.769	0.00	0.00	0.00	1.85
1014	4853	1.957668	TCATCATGGCGATTGACTGG	58.042	50.000	0.00	0.00	29.21	4.00
1239	5079	2.544267	GACAACGAACCTGACTCCTTTG	59.456	50.000	0.00	0.00	0.00	2.77
1648	5506	0.661020	CGGTGGTTGACTTGTGAACC	59.339	55.000	13.80	13.80	41.85	3.62
1694	5552	0.532573	CACGGCAGTCTCCATGTAGT	59.467	55.000	0.00	0.00	0.00	2.73
1754	5612	4.479993	GGCCAGGACTGCGCATCT	62.480	66.667	12.24	6.37	0.00	2.90
1964	5840	2.027469	TGACAACAGATCAGCAGCTCAT	60.027	45.455	0.00	0.00	0.00	2.90
1997	5873	2.213499	GCAACAGATAATCAGGACCCG	58.787	52.381	0.00	0.00	0.00	5.28
2230	6116	3.019564	ACCTTGTGCTCATAAAGGATGC	58.980	45.455	16.40	0.00	42.65	3.91
2313	6207	0.988832	AAAAGGCACCCGATGGTAGA	59.011	50.000	0.00	0.00	45.57	2.59
2419	6314	5.412594	CAGTGCCATTCACACTACTTAACAT	59.587	40.000	0.00	0.00	46.44	2.71
2503	6401	4.342862	TCCTAGAAACCATGCTAGATGC	57.657	45.455	6.66	0.00	36.97	3.91
2540	6438	9.534565	GACTACAACTGCATCTCTCATATTTTA	57.465	33.333	0.00	0.00	0.00	1.52
2579	6477	7.038516	CCCCACCGTCTTATAAAAGTATATCCT	60.039	40.741	0.00	0.00	34.13	3.24
2650	8542	6.263617	TCCAAACTAACCATTCCAACAACTAC	59.736	38.462	0.00	0.00	0.00	2.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.