AutoCloner

Multiple sequence alignment - TraesCS6D01G148400

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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	TraesCS6D01G148400	chr6D	100.000	3682	0	0	1	3682	121347466	121343785	0.000000e+00	6800.0
1	TraesCS6D01G148400	chr6D	90.998	1433	77	19	1279	2683	136389196	136390604	0.000000e+00	1884.0
2	TraesCS6D01G148400	chr6D	84.962	532	68	7	1743	2268	379338983	379338458	2.520000e-146	529.0
3	TraesCS6D01G148400	chr6D	99.291	282	2	0	3401	3682	299155636	299155917	9.120000e-141	510.0
4	TraesCS6D01G148400	chr6D	87.719	285	28	4	1304	1584	379339371	379339090	3.550000e-85	326.0
5	TraesCS6D01G148400	chr6D	86.667	240	17	4	998	1237	136388969	136389193	6.100000e-63	252.0
6	TraesCS6D01G148400	chr6D	90.576	191	16	2	2459	2648	379338320	379338131	6.100000e-63	252.0
7	TraesCS6D01G148400	chr6A	91.437	1343	55	28	1605	2894	162310263	162308928	0.000000e+00	1788.0
8	TraesCS6D01G148400	chr6A	84.375	1024	93	35	565	1584	162311280	162310320	0.000000e+00	942.0
9	TraesCS6D01G148400	chr6A	86.438	671	74	6	1678	2333	177697006	177697674	0.000000e+00	719.0
10	TraesCS6D01G148400	chr6A	88.476	538	32	9	2	534	162311985	162311473	1.120000e-174	623.0
11	TraesCS6D01G148400	chr6A	83.480	569	80	8	1707	2268	521648999	521649560	5.450000e-143	518.0
12	TraesCS6D01G148400	chr6A	97.945	292	5	1	3392	3682	472241146	472240855	4.240000e-139	505.0
13	TraesCS6D01G148400	chr6A	87.153	288	30	3	1301	1584	521648652	521648936	1.650000e-83	320.0
14	TraesCS6D01G148400	chr6A	92.473	186	13	1	2464	2648	521649705	521649890	7.840000e-67	265.0
15	TraesCS6D01G148400	chr6A	86.316	95	10	3	2885	2977	162308447	162308354	2.340000e-17	100.0
16	TraesCS6D01G148400	chr6A	97.222	36	1	0	994	1029	177689618	177689653	1.100000e-05	62.1
17	TraesCS6D01G148400	chr6B	94.199	1155	41	13	1615	2768	213467381	213468510	0.000000e+00	1738.0
18	TraesCS6D01G148400	chr6B	89.880	919	51	16	2	894	213465753	213466655	0.000000e+00	1144.0
19	TraesCS6D01G148400	chr6B	84.882	721	63	22	901	1598	213466626	213467323	0.000000e+00	686.0
20	TraesCS6D01G148400	chr6B	83.304	569	81	8	1707	2268	567611756	567612317	2.540000e-141	512.0
21	TraesCS6D01G148400	chr6B	85.764	288	34	4	1301	1584	567611409	567611693	7.730000e-77	298.0
22	TraesCS6D01G148400	chr6B	87.712	236	21	5	2420	2648	567612396	567612630	6.060000e-68	268.0
23	TraesCS6D01G148400	chr6B	89.091	110	3	1	2828	2937	213469907	213470007	1.070000e-25	128.0
24	TraesCS6D01G148400	chr6B	92.857	84	6	0	2591	2674	234658902	234658985	4.990000e-24	122.0
25	TraesCS6D01G148400	chr6B	94.030	67	4	0	1348	1414	695474265	695474331	6.510000e-18	102.0
26	TraesCS6D01G148400	chr3A	97.651	298	6	1	3386	3682	449904169	449904466	9.120000e-141	510.0
27	TraesCS6D01G148400	chr1D	99.291	282	2	0	3401	3682	233559886	233560167	9.120000e-141	510.0
28	TraesCS6D01G148400	chr7B	98.606	287	3	1	3396	3682	199553377	199553662	1.180000e-139	507.0
29	TraesCS6D01G148400	chr7B	97.619	294	5	2	3389	3682	558577300	558577591	1.530000e-138	503.0
30	TraesCS6D01G148400	chr4B	97.619	294	5	2	3389	3682	278447034	278447325	1.530000e-138	503.0
31	TraesCS6D01G148400	chr7A	96.990	299	6	3	3385	3682	247354646	247354350	1.970000e-137	499.0
32	TraesCS6D01G148400	chr3D	93.275	342	14	3	3059	3400	523901756	523902088	2.550000e-136	496.0
33	TraesCS6D01G148400	chr3D	92.690	342	17	2	3059	3400	66145469	66145802	1.540000e-133	486.0
34	TraesCS6D01G148400	chr3D	85.455	55	5	1	1387	1441	136564786	136564735	2.000000e-03	54.7
35	TraesCS6D01G148400	chr5D	93.023	344	14	4	3059	3400	272356409	272356074	9.190000e-136	494.0
36	TraesCS6D01G148400	chr5D	92.982	342	13	4	3059	3400	412713397	412713727	4.270000e-134	488.0
37	TraesCS6D01G148400	chr5D	93.827	324	13	5	3365	3682	350514642	350514320	7.150000e-132	481.0
38	TraesCS6D01G148400	chr5D	92.151	344	17	4	3059	3400	168014253	168013918	9.250000e-131	477.0
39	TraesCS6D01G148400	chr7D	93.003	343	14	4	3059	3399	75958691	75958357	3.300000e-135	492.0
40	TraesCS6D01G148400	chr7D	92.128	343	18	5	3059	3400	215099918	215099584	3.330000e-130	475.0
41	TraesCS6D01G148400	chr7D	77.778	180	32	7	2468	2646	170729871	170729699	1.810000e-18	104.0
42	TraesCS6D01G148400	chr2D	92.754	345	13	7	3059	3400	592373077	592373412	4.270000e-134	488.0
43	TraesCS6D01G148400	chr4D	92.690	342	17	3	3059	3400	385587063	385586730	1.540000e-133	486.0

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	TraesCS6D01G148400	chr6D	121343785	121347466	3681	True	6800.000000	6800	100.000000	1	3682	1	chr6D.!!$R1	3681
1	TraesCS6D01G148400	chr6D	136388969	136390604	1635	False	1068.000000	1884	88.832500	998	2683	2	chr6D.!!$F2	1685
2	TraesCS6D01G148400	chr6D	379338131	379339371	1240	True	369.000000	529	87.752333	1304	2648	3	chr6D.!!$R2	1344
3	TraesCS6D01G148400	chr6A	162308354	162311985	3631	True	863.250000	1788	87.651000	2	2977	4	chr6A.!!$R2	2975
4	TraesCS6D01G148400	chr6A	177697006	177697674	668	False	719.000000	719	86.438000	1678	2333	1	chr6A.!!$F2	655
5	TraesCS6D01G148400	chr6A	521648652	521649890	1238	False	367.666667	518	87.702000	1301	2648	3	chr6A.!!$F3	1347
6	TraesCS6D01G148400	chr6B	213465753	213470007	4254	False	924.000000	1738	89.513000	2	2937	4	chr6B.!!$F3	2935
7	TraesCS6D01G148400	chr6B	567611409	567612630	1221	False	359.333333	512	85.593333	1301	2648	3	chr6B.!!$F4	1347

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
391	412	0.039074	AGACGAGACTGCTGTTTCCG	60.039	55.0	8.41	9.4	0.0	4.30	F
981	1180	0.039617	CTCCTGATCTCCATCGCGTC	60.040	60.0	5.77	0.0	0.0	5.19	F
1601	1853	0.525668	GTACACGCCACATCTCTCGG	60.526	60.0	0.00	0.0	0.0	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1246	1454	0.461961	GATGACGAGGAGGAGTTGGG	59.538	60.0	0.0	0.0	0.0	4.12	R
2662	3021	0.950555	TCACTCAATGTCAGCACGCC	60.951	55.0	0.0	0.0	0.0	5.68	R
3002	5201	0.036875	GAACAGTCCACCTCCCCTTG	59.963	60.0	0.0	0.0	0.0	3.61	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
66	67	2.985896	TCTCAATCACGGTTGGGAATC	58.014	47.619	0.00	0.00	35.73	2.52
79	80	0.665298	GGGAATCGGAGAAATGCAGC	59.335	55.000	0.00	0.00	43.58	5.25
125	133	1.618837	CCTTCCTCTTTCTCGGTCACA	59.381	52.381	0.00	0.00	0.00	3.58
244	254	2.634982	TTGCATGAACGCAAGATTCC	57.365	45.000	0.00	0.00	46.61	3.01
252	262	2.573941	ACGCAAGATTCCTACGTACC	57.426	50.000	0.00	0.00	43.62	3.34
264	281	3.357919	CGTACCCGTGGTCTGTGA	58.642	61.111	0.00	0.00	37.09	3.58
280	297	2.668457	CTGTGATCGAGTGCACCTTTAC	59.332	50.000	14.63	6.43	34.19	2.01
305	322	8.816925	ACCATTAGGACAGTTTTTCTGGTTGAC	61.817	40.741	0.00	0.00	42.50	3.18
344	362	7.335422	GCATGTGCCTGTATATATAGAAAGCTT	59.665	37.037	8.00	0.00	34.31	3.74
391	412	0.039074	AGACGAGACTGCTGTTTCCG	60.039	55.000	8.41	9.40	0.00	4.30
396	417	1.070786	GACTGCTGTTTCCGGTCCA	59.929	57.895	0.00	0.00	33.48	4.02
412	433	2.630580	GGTCCAAACCATAACCAAGCAA	59.369	45.455	0.00	0.00	45.68	3.91
490	520	3.337694	TTTTTCCTTTCCGGATAGCGA	57.662	42.857	15.80	11.60	42.70	4.93
584	782	4.278170	TCGGTTTCAGAACATGCAGATTTT	59.722	37.500	0.00	0.00	37.51	1.82
612	810	3.068590	CCACCTGAATTTGACTTGCTTGT	59.931	43.478	0.00	0.00	0.00	3.16
621	819	0.233332	GACTTGCTTGTGACGTGCTC	59.767	55.000	0.00	0.00	0.00	4.26
633	831	1.446792	CGTGCTCCGTCAGAATGCT	60.447	57.895	0.00	0.00	34.76	3.79
635	833	1.536922	CGTGCTCCGTCAGAATGCTAT	60.537	52.381	0.00	0.00	34.76	2.97
688	887	0.962356	CGTGCCCAGGAGAATGCTTT	60.962	55.000	0.00	0.00	29.87	3.51
739	938	1.202336	GCAAATGCATGCAGTCTACCC	60.202	52.381	26.69	7.06	45.70	3.69
749	948	1.975407	AGTCTACCCGTGGTCCGTG	60.975	63.158	0.00	0.00	37.09	4.94
769	968	1.530323	GCCAAAGGAGAAACGGCTTA	58.470	50.000	0.00	0.00	39.73	3.09
770	969	1.199327	GCCAAAGGAGAAACGGCTTAC	59.801	52.381	0.00	0.00	39.73	2.34
771	970	2.779506	CCAAAGGAGAAACGGCTTACT	58.220	47.619	0.00	0.00	0.00	2.24
772	971	2.742589	CCAAAGGAGAAACGGCTTACTC	59.257	50.000	0.00	0.00	0.00	2.59

Showing 1 to 25 of 504 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.345653	TCCATTCTCAACTACCAAGTGATATCT	59.654	37.037	3.98	0.00	35.62	1.98
66	67	1.293924	CTACCAGCTGCATTTCTCCG	58.706	55.000	8.66	0.00	0.00	4.63
79	80	0.328258	CCCAGGTTCCCAACTACCAG	59.672	60.000	0.00	0.00	36.87	4.00
107	113	2.698797	AGTTGTGACCGAGAAAGAGGAA	59.301	45.455	0.00	0.00	0.00	3.36
125	133	7.898014	AGGATTGAAAGGAGTAAAAACAGTT	57.102	32.000	0.00	0.00	0.00	3.16
252	262	0.456824	CACTCGATCACAGACCACGG	60.457	60.000	0.00	0.00	0.00	4.94
258	275	0.969149	AAGGTGCACTCGATCACAGA	59.031	50.000	17.98	0.00	35.04	3.41
259	276	1.800805	AAAGGTGCACTCGATCACAG	58.199	50.000	17.98	0.00	35.04	3.66
260	277	2.611971	GGTAAAGGTGCACTCGATCACA	60.612	50.000	17.98	0.00	35.04	3.58
261	278	2.000447	GGTAAAGGTGCACTCGATCAC	59.000	52.381	17.98	7.46	0.00	3.06
262	279	1.621317	TGGTAAAGGTGCACTCGATCA	59.379	47.619	17.98	3.68	0.00	2.92
263	280	2.380084	TGGTAAAGGTGCACTCGATC	57.620	50.000	17.98	0.00	0.00	3.69
264	281	3.350219	AATGGTAAAGGTGCACTCGAT	57.650	42.857	17.98	3.58	0.00	3.59
280	297	5.534654	TCAACCAGAAAAACTGTCCTAATGG	59.465	40.000	0.00	0.00	44.40	3.16
305	322	4.682860	CAGGCACATGCTAAACTCTTTTTG	59.317	41.667	3.48	0.00	41.70	2.44
344	362	2.564771	ACGTTCGATCTACCACGGATA	58.435	47.619	9.59	0.00	36.95	2.59
391	412	2.243810	TGCTTGGTTATGGTTTGGACC	58.756	47.619	0.00	0.00	46.71	4.46
412	433	1.611977	GCTAGCTTTCCGTGGGTTTTT	59.388	47.619	7.70	0.00	0.00	1.94
490	520	4.002906	TCAAAACAGATCGTAAGCAGGT	57.997	40.909	0.00	0.00	37.18	4.00
584	782	1.686052	GTCAAATTCAGGTGGCCACAA	59.314	47.619	35.78	22.57	0.00	3.33
621	819	3.131396	GGTGGTTATAGCATTCTGACGG	58.869	50.000	0.00	0.00	0.00	4.79
633	831	7.829211	CCTTCTTTCTGAATTCTGGTGGTTATA	59.171	37.037	11.89	0.00	33.71	0.98
635	833	6.003950	CCTTCTTTCTGAATTCTGGTGGTTA	58.996	40.000	11.89	0.00	33.71	2.85
688	887	7.175797	TCCATAGTTTAAGACTCTCTCTGACA	58.824	38.462	0.00	0.00	39.86	3.58
749	948	1.179174	AAGCCGTTTCTCCTTTGGCC	61.179	55.000	0.00	0.00	46.92	5.36

Showing 1 to 25 of 481 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.