AutoCloner

Multiple sequence alignment - TraesCS4B01G314000

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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	TraesCS4B01G314000	chr4B	100.000	7584	0	0	1	7584	604054627	604047044	0.000000e+00	14006.0
1	TraesCS4B01G314000	chr4B	98.381	247	4	0	5344	5590	408980978	408980732	1.170000e-117	435.0
2	TraesCS4B01G314000	chr4B	97.638	254	5	1	5343	5596	408982387	408982135	1.170000e-117	435.0
3	TraesCS4B01G314000	chr4B	95.541	157	4	1	1652	1805	324329403	324329247	1.630000e-61	248.0
4	TraesCS4B01G314000	chr4B	87.864	206	13	5	1218	1416	324329628	324329428	1.650000e-56	231.0
5	TraesCS4B01G314000	chr4D	95.219	4915	166	36	120	5017	477897551	477892689	0.000000e+00	7710.0
6	TraesCS4B01G314000	chr4D	91.604	1060	51	10	5773	6797	477892196	477891140	0.000000e+00	1430.0
7	TraesCS4B01G314000	chr4D	88.533	375	17	11	6973	7334	477891019	477890658	1.510000e-116	431.0
8	TraesCS4B01G314000	chr4D	89.796	294	20	5	5050	5343	477892691	477892408	1.200000e-97	368.0
9	TraesCS4B01G314000	chr4D	93.519	216	14	0	5590	5805	477892412	477892197	9.490000e-84	322.0
10	TraesCS4B01G314000	chr4D	96.094	128	5	0	6754	6881	477891143	477891016	7.710000e-50	209.0
11	TraesCS4B01G314000	chr4A	93.234	3976	167	30	1402	5343	684589038	684585131	0.000000e+00	5758.0
12	TraesCS4B01G314000	chr4A	88.555	1398	98	29	1	1372	684590381	684589020	0.000000e+00	1639.0
13	TraesCS4B01G314000	chr4A	90.746	1167	70	19	5593	6726	684585132	684583971	0.000000e+00	1522.0
14	TraesCS4B01G314000	chr4A	92.424	330	11	4	7006	7334	684583944	684583628	6.930000e-125	459.0
15	TraesCS4B01G314000	chr4A	89.011	91	10	0	4924	5014	471931242	471931332	6.220000e-21	113.0
16	TraesCS4B01G314000	chr4A	88.889	90	9	1	4927	5015	85905017	85904928	8.050000e-20	110.0
17	TraesCS4B01G314000	chr1A	96.907	291	9	0	3526	3816	41753252	41752962	8.840000e-134	488.0
18	TraesCS4B01G314000	chr1A	87.500	112	12	2	6875	6986	340014999	340015108	2.220000e-25	128.0
19	TraesCS4B01G314000	chr5B	98.031	254	5	0	7331	7584	459570856	459571109	6.980000e-120	442.0
20	TraesCS4B01G314000	chr5B	87.069	116	11	4	6871	6984	693877786	693877673	2.220000e-25	128.0
21	TraesCS4B01G314000	chr7A	97.308	260	6	1	7325	7584	627156425	627156683	2.510000e-119	440.0
22	TraesCS4B01G314000	chr7A	96.552	261	8	1	7324	7584	620197325	620197066	1.510000e-116	431.0
23	TraesCS4B01G314000	chr6A	98.024	253	5	0	7332	7584	38758093	38757841	2.510000e-119	440.0
24	TraesCS4B01G314000	chr6A	97.638	254	6	0	7331	7584	371732392	371732645	3.250000e-118	436.0
25	TraesCS4B01G314000	chr6A	92.500	80	6	0	4935	5014	14351067	14350988	1.730000e-21	115.0
26	TraesCS4B01G314000	chr6A	100.000	44	0	0	1167	1210	52216302	52216259	1.750000e-11	82.4
27	TraesCS4B01G314000	chr2B	98.024	253	5	0	7332	7584	11723877	11723625	2.510000e-119	440.0
28	TraesCS4B01G314000	chr2B	82.934	334	33	14	1096	1416	125495848	125495526	5.790000e-71	279.0
29	TraesCS4B01G314000	chr2B	89.873	79	8	0	1640	1718	125495513	125495435	1.350000e-17	102.0
30	TraesCS4B01G314000	chr6B	97.287	258	5	1	5336	5591	124083261	124083518	3.250000e-118	436.0
31	TraesCS4B01G314000	chr6B	98.008	251	4	1	5344	5593	346316905	346316655	1.170000e-117	435.0
32	TraesCS4B01G314000	chr6B	97.276	257	5	2	5340	5596	346318334	346318080	1.170000e-117	435.0
33	TraesCS4B01G314000	chr6B	97.628	253	5	1	5344	5596	124081339	124081590	4.200000e-117	433.0
34	TraesCS4B01G314000	chr3B	97.638	254	6	0	7331	7584	679723212	679723465	3.250000e-118	436.0
35	TraesCS4B01G314000	chr1B	98.387	248	4	0	5343	5590	641496443	641496196	3.250000e-118	436.0
36	TraesCS4B01G314000	chr1B	97.276	257	5	1	5336	5590	141119628	141119884	1.170000e-117	435.0
37	TraesCS4B01G314000	chr1B	96.154	260	9	1	5337	5596	141116914	141117172	2.530000e-114	424.0
38	TraesCS4B01G314000	chr1B	89.344	122	9	2	1688	1805	44977753	44977632	4.740000e-32	150.0
39	TraesCS4B01G314000	chr1B	90.476	105	8	1	6875	6977	341377973	341377869	3.690000e-28	137.0
40	TraesCS4B01G314000	chr1B	88.679	106	12	0	6876	6981	350726908	350726803	6.180000e-26	130.0
41	TraesCS4B01G314000	chr3A	96.863	255	8	0	7330	7584	673863753	673863499	1.960000e-115	427.0
42	TraesCS4B01G314000	chr1D	95.185	270	11	2	7317	7584	52666991	52666722	7.030000e-115	425.0
43	TraesCS4B01G314000	chr6D	85.671	328	28	10	1096	1416	19273326	19273011	2.040000e-85	327.0
44	TraesCS4B01G314000	chr6D	93.491	169	8	1	1640	1805	19272998	19272830	1.630000e-61	248.0
45	TraesCS4B01G314000	chr6D	92.683	82	5	1	4935	5015	131940434	131940515	4.810000e-22	117.0
46	TraesCS4B01G314000	chrUn	96.450	169	3	1	1640	1805	143930212	143930380	7.500000e-70	276.0
47	TraesCS4B01G314000	chr2D	93.491	169	8	1	1640	1805	362320107	362320275	1.630000e-61	248.0
48	TraesCS4B01G314000	chr2D	85.586	222	19	9	1092	1308	41850852	41851065	3.560000e-53	220.0
49	TraesCS4B01G314000	chr2D	81.463	205	19	10	1096	1298	392353530	392353717	4.740000e-32	150.0
50	TraesCS4B01G314000	chr2D	91.000	100	9	0	6875	6974	263505051	263505150	1.330000e-27	135.0
51	TraesCS4B01G314000	chr2D	87.500	112	12	2	6872	6982	98693495	98693605	2.220000e-25	128.0
52	TraesCS4B01G314000	chr7B	91.753	97	8	0	6878	6974	727421709	727421805	1.330000e-27	135.0
53	TraesCS4B01G314000	chr7B	91.579	95	8	0	6878	6972	665395533	665395439	1.720000e-26	132.0
54	TraesCS4B01G314000	chr7B	87.963	108	11	2	6875	6981	193955950	193955844	7.990000e-25	126.0
55	TraesCS4B01G314000	chr3D	92.683	82	4	2	4935	5015	108916341	108916261	4.810000e-22	117.0
56	TraesCS4B01G314000	chr3D	97.674	43	1	0	1168	1210	460727372	460727330	2.940000e-09	75.0
57	TraesCS4B01G314000	chr5A	87.037	108	6	6	4921	5021	521937811	521937917	1.730000e-21	115.0
58	TraesCS4B01G314000	chr5D	85.849	106	8	6	4921	5021	410399104	410399207	1.040000e-18	106.0
59	TraesCS4B01G314000	chr5D	95.745	47	2	0	1164	1210	238195671	238195717	8.160000e-10	76.8

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	TraesCS4B01G314000	chr4B	604047044	604054627	7583	True	14006.0	14006	100.000000	1	7584	1	chr4B.!!$R1	7583
1	TraesCS4B01G314000	chr4B	408980732	408982387	1655	True	435.0	435	98.009500	5343	5596	2	chr4B.!!$R3	253
2	TraesCS4B01G314000	chr4D	477890658	477897551	6893	True	1745.0	7710	92.460833	120	7334	6	chr4D.!!$R1	7214
3	TraesCS4B01G314000	chr4A	684583628	684590381	6753	True	2344.5	5758	91.239750	1	7334	4	chr4A.!!$R2	7333
4	TraesCS4B01G314000	chr6B	346316655	346318334	1679	True	435.0	435	97.642000	5340	5596	2	chr6B.!!$R1	256
5	TraesCS4B01G314000	chr6B	124081339	124083518	2179	False	434.5	436	97.457500	5336	5596	2	chr6B.!!$F1	260
6	TraesCS4B01G314000	chr1B	141116914	141119884	2970	False	429.5	435	96.715000	5336	5596	2	chr1B.!!$F1	260

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
445	455	0.320374	TCTTGGCGATCGACCAAAGT	59.680	50.0	30.23	0.00	46.24	2.66	F
1826	1889	0.593618	TTTTGTGTGTGTGTGTGCGT	59.406	45.0	0.00	0.00	0.00	5.24	F
1828	1891	1.231296	TTGTGTGTGTGTGTGCGTGT	61.231	50.0	0.00	0.00	0.00	4.49	F
2695	2779	0.165944	GCACGAGTTTTCATGGTCGG	59.834	55.0	0.00	0.00	36.74	4.79	F
3085	3169	0.600782	CACCAGGGCAAATGCAACAC	60.601	55.0	7.80	0.00	44.36	3.32	F
4397	4483	0.466963	ATGCATCATCAGGTCTGCGA	59.533	50.0	0.00	0.00	37.44	5.10	F
5150	5240	0.167689	GAAGCAGCTGTAGCAAGTGC	59.832	55.0	16.64	7.48	45.16	4.40	F
5665	5755	0.804364	TGCGTGATAGCCTTTTGCAG	59.196	50.0	0.00	0.00	44.83	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2094	2157	0.106217	CCTGTCCTCTCTCTCCCTCC	60.106	65.000	0.00	4.30	R
2677	2761	0.796312	CCCGACCATGAAAACTCGTG	59.204	55.000	0.00	4.35	R
3115	3199	1.273324	ACACCAGGTAGAAGAGGAGGG	60.273	57.143	0.00	4.30	R
4080	4165	1.741028	TTTGGGGAGGACACATGAGA	58.259	50.000	0.00	3.27	R
4877	4967	0.322816	TCCTTCCACAAGCCAGATGC	60.323	55.000	41.71	3.91	R
5647	5737	1.086696	TCTGCAAAAGGCTATCACGC	58.913	50.000	45.15	5.34	R
6308	6436	1.152567	CCTGAGCCCCTCGATCTCT	60.153	63.158	32.35	3.10	R
7448	7664	0.034756	TGGAGTGTGTGATGTTCCGG	59.965	55.000	0.00	5.14	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	91	5.722263	TGCATGGATTTTCGTGATCATTTT	58.278	33.333	0.00	0.00	0.00	1.82
226	232	1.510480	GAGCAACCTGGTCAGCACAC	61.510	60.000	21.47	11.44	43.79	3.82
228	234	1.152984	CAACCTGGTCAGCACACCA	60.153	57.895	0.00	6.61	44.69	4.17
229	235	1.152963	AACCTGGTCAGCACACCAC	60.153	57.895	0.00	0.00	41.84	4.16
230	236	1.920734	AACCTGGTCAGCACACCACA	61.921	55.000	0.00	0.00	41.84	4.17
237	243	1.532868	GTCAGCACACCACAGAATCAC	59.467	52.381	0.00	0.00	0.00	3.06
259	265	5.468072	CACTGAGTATGGATTGCAGGATAAC	59.532	44.000	0.00	0.00	0.00	1.89
445	455	0.320374	TCTTGGCGATCGACCAAAGT	59.680	50.000	30.23	0.00	46.24	2.66
635	645	9.605275	GAATTATGCAGCTAATATAGTGGATGA	57.395	33.333	5.96	0.00	0.00	2.92
636	646	8.954950	ATTATGCAGCTAATATAGTGGATGAC	57.045	34.615	5.96	0.00	0.00	3.06
717	730	4.678309	CGAGGCTCTTACCGAGAAATCTTT	60.678	45.833	13.50	0.00	42.62	2.52
718	731	5.167303	AGGCTCTTACCGAGAAATCTTTT	57.833	39.130	0.00	0.00	42.62	2.27
719	732	5.179533	AGGCTCTTACCGAGAAATCTTTTC	58.820	41.667	0.00	0.00	42.62	2.29
849	871	2.332654	GCGGCGGATGGTTTGAGTT	61.333	57.895	9.78	0.00	0.00	3.01
965	989	6.624204	GCCTCTCTTCTGTACTAGTTCTGTTC	60.624	46.154	0.00	0.00	0.00	3.18
1158	1186	2.507102	GAAGCTGCTCGCGTGCTA	60.507	61.111	30.29	17.30	45.59	3.49
1159	1187	1.880340	GAAGCTGCTCGCGTGCTAT	60.880	57.895	30.29	15.41	45.59	2.97
1210	1241	2.168313	TGTGCGGCTATGAAATCTCTCA	59.832	45.455	0.00	0.00	0.00	3.27
1381	1414	2.741486	TTTAGGGAGTGTGCCGGTGC	62.741	60.000	1.90	0.00	30.73	5.01
1535	1597	0.769247	GGTGGTGGGTAGGTGACTTT	59.231	55.000	0.00	0.00	43.67	2.66
1591	1654	4.082463	ACTTGTTATTTTGGTGGTATGCCG	60.082	41.667	0.00	0.00	37.67	5.69
1735	1798	9.326413	CTACACTTCGGTTTCCATCTATTTAAT	57.674	33.333	0.00	0.00	0.00	1.40
1825	1888	1.691127	TTTTTGTGTGTGTGTGTGCG	58.309	45.000	0.00	0.00	0.00	5.34
1826	1889	0.593618	TTTTGTGTGTGTGTGTGCGT	59.406	45.000	0.00	0.00	0.00	5.24
1828	1891	1.231296	TTGTGTGTGTGTGTGCGTGT	61.231	50.000	0.00	0.00	0.00	4.49

Showing 1 to 25 of 393 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	5.875359	CCCTAGTAATCACAAGGAAGTGTTC	59.125	44.000	0.00	0.00	40.37	3.18
54	55	5.461737	TCACGAAAATCCATGCAACTTTTTC	59.538	36.000	13.30	13.30	34.51	2.29
85	91	4.500603	TTGCCGGAAAATAGCGTAAAAA	57.499	36.364	5.05	0.00	0.00	1.94
90	96	3.250040	GTGATATTGCCGGAAAATAGCGT	59.750	43.478	5.05	0.00	30.30	5.07
102	108	4.808895	TCAAGTATGTGTCGTGATATTGCC	59.191	41.667	0.00	0.00	0.00	4.52
226	232	4.743057	TCCATACTCAGTGATTCTGTGG	57.257	45.455	0.00	0.00	43.97	4.17
228	234	5.121811	GCAATCCATACTCAGTGATTCTGT	58.878	41.667	0.00	0.00	43.97	3.41
229	235	5.121105	TGCAATCCATACTCAGTGATTCTG	58.879	41.667	0.00	0.00	44.85	3.02
230	236	5.363562	TGCAATCCATACTCAGTGATTCT	57.636	39.130	0.00	0.00	0.00	2.40
237	243	4.999950	GGTTATCCTGCAATCCATACTCAG	59.000	45.833	0.00	0.00	0.00	3.35
259	265	1.751927	GCAGGCATGGAGAGTTGGG	60.752	63.158	0.00	0.00	0.00	4.12
497	507	4.493547	CACTTCAGAGGTTCAGATCAGAC	58.506	47.826	0.00	0.00	0.00	3.51
545	555	1.519013	CTCCGCTTCAGAGCTCAGC	60.519	63.158	17.77	15.16	46.96	4.26
635	645	3.585862	ACATCTAATTGTTCGTCTGCGT	58.414	40.909	0.00	0.00	39.49	5.24
636	646	5.034797	TCTACATCTAATTGTTCGTCTGCG	58.965	41.667	0.00	0.00	39.92	5.18
717	730	4.011517	GCCTCCACGGAACCGGAA	62.012	66.667	9.46	1.81	44.69	4.30
834	850	1.197721	CTGACAACTCAAACCATCCGC	59.802	52.381	0.00	0.00	0.00	5.54
849	871	4.373116	GCTTCCGACGCCCTGACA	62.373	66.667	0.00	0.00	0.00	3.58
965	989	1.376812	GGAGTGGTGGCCTAAACCG	60.377	63.158	3.32	0.00	40.86	4.44
1132	1160	1.893786	GAGCAGCTTCGGAGAGGAA	59.106	57.895	0.00	0.00	38.43	3.36
1189	1220	2.168313	TGAGAGATTTCATAGCCGCACA	59.832	45.455	0.00	0.00	0.00	4.57
1382	1415	4.087892	CAGGAGACCAGCCACCGG	62.088	72.222	0.00	0.00	0.00	5.28
1384	1417	1.484444	AAGACAGGAGACCAGCCACC	61.484	60.000	0.00	0.00	0.00	4.61
1392	1425	3.433615	CCAAATTCGTGAAGACAGGAGAC	59.566	47.826	0.00	0.00	40.99	3.36
1393	1426	3.557054	CCCAAATTCGTGAAGACAGGAGA	60.557	47.826	0.00	0.00	40.99	3.71

Showing 1 to 25 of 371 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.