AutoCloner

Multiple sequence alignment - TraesCS7B01G283600

Loading Multiple Alignment...

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	TraesCS7B01G283600	chr7B	100.000	2531	0	0	1	2531	517900862	517903392	0.000000e+00	4674.0
1	TraesCS7B01G283600	chr7B	96.191	1654	49	4	892	2531	73167193	73168846	0.000000e+00	2693.0
2	TraesCS7B01G283600	chr7B	89.671	213	22	0	3	215	73166380	73166592	3.210000e-69	272.0
3	TraesCS7B01G283600	chr7B	91.129	124	11	0	310	433	427304863	427304740	4.330000e-38	169.0
4	TraesCS7B01G283600	chr7B	100.000	32	0	0	293	324	517901101	517901132	2.720000e-05	60.2
5	TraesCS7B01G283600	chr7B	100.000	32	0	0	240	271	517901154	517901185	2.720000e-05	60.2
6	TraesCS7B01G283600	chr7D	96.670	2072	49	4	475	2531	83757778	83759844	0.000000e+00	3426.0
7	TraesCS7B01G283600	chr7D	96.546	1245	34	3	475	1715	366438440	366437201	0.000000e+00	2052.0
8	TraesCS7B01G283600	chr7D	96.183	1048	35	2	475	1522	126714329	126715371	0.000000e+00	1709.0
9	TraesCS7B01G283600	chr7D	88.263	213	22	1	5	217	366438920	366438711	4.180000e-63	252.0
10	TraesCS7B01G283600	chr7D	88.710	124	14	0	310	433	412887680	412887557	4.360000e-33	152.0
11	TraesCS7B01G283600	chr2B	95.755	2073	70	5	475	2531	419937365	419939435	0.000000e+00	3325.0
12	TraesCS7B01G283600	chr2B	93.020	1662	92	9	892	2531	528810281	528808622	0.000000e+00	2405.0
13	TraesCS7B01G283600	chr6B	94.495	2071	82	11	475	2528	676682478	676684533	0.000000e+00	3164.0
14	TraesCS7B01G283600	chr6B	94.110	781	34	2	1760	2529	617031452	617032231	0.000000e+00	1177.0
15	TraesCS7B01G283600	chr6B	92.919	579	32	5	209	787	138632094	138632663	0.000000e+00	833.0
16	TraesCS7B01G283600	chr6B	92.414	580	32	8	209	787	138656828	138657396	0.000000e+00	817.0
17	TraesCS7B01G283600	chr6B	92.308	208	15	1	7	214	138631720	138631926	6.850000e-76	294.0
18	TraesCS7B01G283600	chr6B	87.736	212	25	1	3	214	676682064	676682274	1.940000e-61	246.0
19	TraesCS7B01G283600	chr6B	91.304	46	3	1	293	337	138632125	138632170	7.560000e-06	62.1
20	TraesCS7B01G283600	chr6B	91.304	46	3	1	293	337	138656859	138656904	7.560000e-06	62.1
21	TraesCS7B01G283600	chr3B	95.644	1653	59	3	892	2531	766341160	766342812	0.000000e+00	2641.0
22	TraesCS7B01G283600	chr3B	84.288	1553	192	29	996	2531	473235219	473236736	0.000000e+00	1469.0
23	TraesCS7B01G283600	chr3B	93.568	482	28	3	1	482	512368492	512368970	0.000000e+00	715.0
24	TraesCS7B01G283600	chr3B	89.202	213	23	0	3	215	766340361	766340573	1.490000e-67	267.0
25	TraesCS7B01G283600	chr3B	100.000	32	0	0	293	324	512368731	512368762	2.720000e-05	60.2
26	TraesCS7B01G283600	chr3B	100.000	30	0	0	240	269	512368783	512368812	3.520000e-04	56.5
27	TraesCS7B01G283600	chr4B	93.740	1262	63	4	1285	2531	43588041	43586781	0.000000e+00	1879.0
28	TraesCS7B01G283600	chr4B	93.661	1262	64	4	1285	2531	43574175	43572915	0.000000e+00	1873.0
29	TraesCS7B01G283600	chr2D	96.393	998	31	2	475	1472	238092672	238091680	0.000000e+00	1639.0
30	TraesCS7B01G283600	chrUn	92.268	582	33	4	209	790	194986460	194985891	0.000000e+00	815.0
31	TraesCS7B01G283600	chrUn	88.043	92	8	3	805	894	194985822	194985732	3.440000e-19	106.0
32	TraesCS7B01G283600	chrUn	100.000	31	0	0	293	323	194986429	194986399	9.780000e-05	58.4
33	TraesCS7B01G283600	chr6D	91.748	206	14	3	13	217	446742356	446742559	1.480000e-72	283.0
34	TraesCS7B01G283600	chr7A	89.048	210	23	0	3	212	447284650	447284441	6.940000e-66	261.0
35	TraesCS7B01G283600	chr6A	88.038	209	25	0	9	217	360534825	360534617	5.410000e-62	248.0

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	TraesCS7B01G283600	chr7B	517900862	517903392	2530	False	1598.133333	4674	100.0000	1	2531	3	chr7B.!!$F2	2530
1	TraesCS7B01G283600	chr7B	73166380	73168846	2466	False	1482.500000	2693	92.9310	3	2531	2	chr7B.!!$F1	2528
2	TraesCS7B01G283600	chr7D	83757778	83759844	2066	False	3426.000000	3426	96.6700	475	2531	1	chr7D.!!$F1	2056
3	TraesCS7B01G283600	chr7D	126714329	126715371	1042	False	1709.000000	1709	96.1830	475	1522	1	chr7D.!!$F2	1047
4	TraesCS7B01G283600	chr7D	366437201	366438920	1719	True	1152.000000	2052	92.4045	5	1715	2	chr7D.!!$R2	1710
5	TraesCS7B01G283600	chr2B	419937365	419939435	2070	False	3325.000000	3325	95.7550	475	2531	1	chr2B.!!$F1	2056
6	TraesCS7B01G283600	chr2B	528808622	528810281	1659	True	2405.000000	2405	93.0200	892	2531	1	chr2B.!!$R1	1639
7	TraesCS7B01G283600	chr6B	676682064	676684533	2469	False	1705.000000	3164	91.1155	3	2528	2	chr6B.!!$F4	2525
8	TraesCS7B01G283600	chr6B	617031452	617032231	779	False	1177.000000	1177	94.1100	1760	2529	1	chr6B.!!$F1	769
9	TraesCS7B01G283600	chr6B	138656828	138657396	568	False	439.550000	817	91.8590	209	787	2	chr6B.!!$F3	578
10	TraesCS7B01G283600	chr6B	138631720	138632663	943	False	396.366667	833	92.1770	7	787	3	chr6B.!!$F2	780
11	TraesCS7B01G283600	chr3B	473235219	473236736	1517	False	1469.000000	1469	84.2880	996	2531	1	chr3B.!!$F1	1535
12	TraesCS7B01G283600	chr3B	766340361	766342812	2451	False	1454.000000	2641	92.4230	3	2531	2	chr3B.!!$F3	2528
13	TraesCS7B01G283600	chr4B	43586781	43588041	1260	True	1879.000000	1879	93.7400	1285	2531	1	chr4B.!!$R2	1246
14	TraesCS7B01G283600	chr4B	43572915	43574175	1260	True	1873.000000	1873	93.6610	1285	2531	1	chr4B.!!$R1	1246
15	TraesCS7B01G283600	chr2D	238091680	238092672	992	True	1639.000000	1639	96.3930	475	1472	1	chr2D.!!$R1	997
16	TraesCS7B01G283600	chrUn	194985732	194986460	728	True	326.466667	815	93.4370	209	894	3	chrUn.!!$R1	685

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
275	479	0.620030	CACCCATCACCATCACTCCA	59.380	55.000	0.0	0.0	0.0	3.86	F
277	481	1.492176	ACCCATCACCATCACTCCATC	59.508	52.381	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1188	1576	0.179137	TAGCGTCGCTCTCACCAATG	60.179	55.000	25.5	0.0	40.44	2.82	R
1770	2164	1.134491	CCCTAAGAACCCGACCATCAC	60.134	57.143	0.0	0.0	0.00	3.06	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
18	19	3.770040	TCACATCAGTCGCCGGGG	61.770	66.667	13.31	13.31	0.00	5.73
40	41	3.838271	CCTCGCTAGCCGCCTCAA	61.838	66.667	9.66	0.00	36.73	3.02
45	46	2.125512	CTAGCCGCCTCAAACGCT	60.126	61.111	0.00	0.00	0.00	5.07
83	84	4.143333	GCCGCCTACGAGGAGCAA	62.143	66.667	5.24	0.00	43.93	3.91
91	92	1.476845	TACGAGGAGCAACAAGGCCA	61.477	55.000	5.01	0.00	0.00	5.36
142	143	2.314852	TCCTCCATCAACCTCCTACTGA	59.685	50.000	0.00	0.00	0.00	3.41
171	172	6.383147	TCTCAAGGTTAGGGTTACTAATCCAG	59.617	42.308	0.78	0.00	42.63	3.86
235	439	8.894768	ATCTTTTATAGGTTGATGTCTAGCAC	57.105	34.615	0.00	0.00	0.00	4.40
271	475	1.098050	GCTTCACCCATCACCATCAC	58.902	55.000	0.00	0.00	0.00	3.06
273	477	2.636830	CTTCACCCATCACCATCACTC	58.363	52.381	0.00	0.00	0.00	3.51
274	478	0.911769	TCACCCATCACCATCACTCC	59.088	55.000	0.00	0.00	0.00	3.85
275	479	0.620030	CACCCATCACCATCACTCCA	59.380	55.000	0.00	0.00	0.00	3.86
277	481	1.492176	ACCCATCACCATCACTCCATC	59.508	52.381	0.00	0.00	0.00	3.51
279	483	2.486727	CCCATCACCATCACTCCATCAG	60.487	54.545	0.00	0.00	0.00	2.90
280	484	2.436911	CCATCACCATCACTCCATCAGA	59.563	50.000	0.00	0.00	0.00	3.27
282	486	3.105959	TCACCATCACTCCATCAGAGA	57.894	47.619	0.00	0.00	46.50	3.10
283	487	3.029570	TCACCATCACTCCATCAGAGAG	58.970	50.000	0.00	0.00	46.50	3.20
284	488	1.761784	ACCATCACTCCATCAGAGAGC	59.238	52.381	0.00	0.00	46.50	4.09
285	489	2.040939	CCATCACTCCATCAGAGAGCT	58.959	52.381	0.00	0.00	46.50	4.09
326	531	2.165030	GCTTCACCCATCACCATCAAAG	59.835	50.000	0.00	0.00	0.00	2.77
335	540	4.281688	CCATCACCATCAAAGAGTTGGTTT	59.718	41.667	0.00	0.00	45.87	3.27
380	585	3.653344	TCTATCATGTATTGAGTGCGCC	58.347	45.455	4.18	0.00	37.89	6.53
511	800	7.119846	GGATGACTAATGGAGTATAATTGGTGC	59.880	40.741	0.00	0.00	39.06	5.01
522	811	6.116126	AGTATAATTGGTGCTCTGTCCTTTC	58.884	40.000	0.00	0.00	0.00	2.62
548	837	9.552114	CTATTTTTGTGATGTGTTCTTGATCTC	57.448	33.333	0.00	0.00	0.00	2.75
588	877	5.835280	AGGCAAATAGATGAATTAGGTTGGG	59.165	40.000	0.00	0.00	0.00	4.12
596	885	3.605634	TGAATTAGGTTGGGTGATCACG	58.394	45.455	19.33	0.00	0.00	4.35
674	963	7.664082	TCTTCTTTAGCTTTCTGATGTGAAG	57.336	36.000	0.00	0.00	0.00	3.02
1027	1415	2.347731	GTCTTCCTTTAAGTGCGAGGG	58.652	52.381	0.00	0.00	36.51	4.30
1139	1527	5.665916	AGGAGAAAATGTTGGCAAATAGG	57.334	39.130	0.00	0.00	0.00	2.57
1188	1576	3.067040	GGGGAGAGAACTTGTATCGACTC	59.933	52.174	0.00	0.00	0.00	3.36
1212	1600	1.226688	TGAGAGCGACGCTATGTGC	60.227	57.895	23.39	9.67	39.88	4.57
1226	1614	4.568359	CGCTATGTGCATAAGTCAACTTCT	59.432	41.667	0.00	0.00	43.06	2.85
1393	1781	6.099845	AGGAAAATTCTTCTATCGAAGCCCTA	59.900	38.462	2.13	0.00	45.01	3.53
1488	1876	3.641906	CTGAACCTATACCCGAGGATTGT	59.358	47.826	0.00	0.00	37.53	2.71
1681	2075	4.442706	TGAAAGGAAGGTATCGATCAAGC	58.557	43.478	0.00	0.00	0.00	4.01
1770	2164	1.515521	GGTTGGGAAGGTTCTGCACG	61.516	60.000	0.00	0.00	0.00	5.34
2272	2680	5.667626	AGGGCATGTATAATAGACATAGGGG	59.332	44.000	0.00	0.00	35.75	4.79
2277	2685	7.624549	CATGTATAATAGACATAGGGGTGCTT	58.375	38.462	0.00	0.00	35.75	3.91
2370	2780	9.698309	TTGTTTCCTTTCAATTATATTTGCGAA	57.302	25.926	3.01	0.00	0.00	4.70
2471	2882	1.204146	ATGGACCGTGTGGATAGCTT	58.796	50.000	0.00	0.00	39.21	3.74
2479	2890	0.894835	TGTGGATAGCTTGAGCACGA	59.105	50.000	5.70	0.00	45.16	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	4.908877	GCGGCTAGCGAGGTCGTC	62.909	72.222	9.00	0.00	42.22	4.20
29	30	2.238847	ATCAGCGTTTGAGGCGGCTA	62.239	55.000	13.24	0.00	39.68	3.93
39	40	0.321653	GTCCACCCTCATCAGCGTTT	60.322	55.000	0.00	0.00	0.00	3.60
40	41	1.296715	GTCCACCCTCATCAGCGTT	59.703	57.895	0.00	0.00	0.00	4.84
45	46	1.667595	TCAATGGTCCACCCTCATCA	58.332	50.000	0.00	0.00	34.29	3.07
91	92	0.689623	GATCCGGAGATGGGCAGATT	59.310	55.000	11.34	0.00	30.90	2.40
142	143	8.625467	ATTAGTAACCCTAACCTTGAGATCTT	57.375	34.615	0.00	0.00	38.45	2.40
235	439	4.452455	GTGAAGCTACGGGATGGAAATATG	59.548	45.833	0.00	0.00	0.00	1.78
299	504	0.462047	GTGATGGGTGAAGCTACGGG	60.462	60.000	0.00	0.00	0.00	5.28
326	531	3.211045	TGGCTACACAGAAAACCAACTC	58.789	45.455	0.00	0.00	0.00	3.01
335	540	3.517296	TGGGAAATTGGCTACACAGAA	57.483	42.857	0.00	0.00	0.00	3.02
380	585	0.391263	GTGGGCTTCCGGTTCTAGTG	60.391	60.000	0.00	0.00	0.00	2.74
451	740	4.788201	GCAAATCGGCGCATATAGACAAAA	60.788	41.667	10.83	0.00	0.00	2.44
454	743	1.798223	GCAAATCGGCGCATATAGACA	59.202	47.619	10.83	0.00	0.00	3.41
494	783	5.455326	GGACAGAGCACCAATTATACTCCAT	60.455	44.000	0.00	0.00	0.00	3.41
511	800	8.019669	CACATCACAAAAATAGAAAGGACAGAG	58.980	37.037	0.00	0.00	0.00	3.35
522	811	9.552114	GAGATCAAGAACACATCACAAAAATAG	57.448	33.333	0.00	0.00	0.00	1.73
588	877	3.437049	CCTTCCTTCCTTTTCGTGATCAC	59.563	47.826	16.21	16.21	0.00	3.06
596	885	4.207955	ACAAGACACCTTCCTTCCTTTTC	58.792	43.478	0.00	0.00	0.00	2.29
674	963	5.234466	AGTTCCAAGTATCAGGATATGCC	57.766	43.478	0.00	0.00	33.10	4.40
740	1033	5.675538	AGGAACAGTCAACCAATATCTAGC	58.324	41.667	0.00	0.00	0.00	3.42
950	1338	8.990163	TTTAAGGTTGGTATGACTTTCTTTCT	57.010	30.769	0.00	0.00	0.00	2.52
1027	1415	5.859205	AATATTGCATTTCTCCTTCCACC	57.141	39.130	0.00	0.00	0.00	4.61
1188	1576	0.179137	TAGCGTCGCTCTCACCAATG	60.179	55.000	25.50	0.00	40.44	2.82
1393	1781	6.567891	GCGTTGAAGTTTCTACTAATTGGCTT	60.568	38.462	5.25	0.00	33.17	4.35
1488	1876	8.014070	TGAAATACTTCCACTTATCATCGGTA	57.986	34.615	0.00	0.00	0.00	4.02
1681	2075	8.908786	ACACATTTGTATCTATATCACCCAAG	57.091	34.615	0.00	0.00	32.60	3.61
1770	2164	1.134491	CCCTAAGAACCCGACCATCAC	60.134	57.143	0.00	0.00	0.00	3.06
1846	2240	1.442769	CGTTTGTGTAGCCAGCATCT	58.557	50.000	0.00	0.00	0.00	2.90
2277	2685	1.488812	ACTTATACCTCAATGCGCCCA	59.511	47.619	4.18	0.00	0.00	5.36
2368	2778	4.554973	GCAAACGAGATGCAATTGTAGTTC	59.445	41.667	7.40	3.91	43.29	3.01
2370	2780	4.083581	GCAAACGAGATGCAATTGTAGT	57.916	40.909	7.40	0.00	43.29	2.73
2479	2890	1.048601	TTCTTGCCTCTTCCACGAGT	58.951	50.000	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.