AutoCloner

Multiple sequence alignment - TraesCS7A01G170000

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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	TraesCS7A01G170000	chr7A	100.000	3704	0	0	1	3704	126148504	126152207	0.000000e+00	6841
1	TraesCS7A01G170000	chr7A	94.083	507	22	2	3206	3704	8700340	8700846	0.000000e+00	763
2	TraesCS7A01G170000	chr3B	94.281	3270	117	27	1	3211	473235645	473238903	0.000000e+00	4939
3	TraesCS7A01G170000	chr3B	87.829	912	102	9	1	907	766341691	766342598	0.000000e+00	1061
4	TraesCS7A01G170000	chr3B	91.165	498	44	0	3206	3703	781391550	781392047	0.000000e+00	676
5	TraesCS7A01G170000	chr7B	93.417	3266	144	21	1	3206	51883760	51887014	0.000000e+00	4774
6	TraesCS7A01G170000	chr7B	84.488	1444	170	33	1	1393	73167724	73169164	0.000000e+00	1376
7	TraesCS7A01G170000	chr6B	93.323	3265	137	27	2	3208	48079457	48082698	0.000000e+00	4747
8	TraesCS7A01G170000	chr4B	92.969	3271	161	30	1	3212	321541993	321545253	0.000000e+00	4702
9	TraesCS7A01G170000	chr4B	92.763	2432	115	16	830	3206	587099150	587101575	0.000000e+00	3459
10	TraesCS7A01G170000	chr4B	94.836	794	38	3	1	793	587098356	587099147	0.000000e+00	1236
11	TraesCS7A01G170000	chr6A	95.010	2405	92	11	1	2386	182420402	182418007	0.000000e+00	3751
12	TraesCS7A01G170000	chr6A	93.912	1889	52	16	1354	3208	137393776	137391917	0.000000e+00	2793
13	TraesCS7A01G170000	chr6A	97.065	1363	37	3	1	1361	137493501	137492140	0.000000e+00	2292
14	TraesCS7A01G170000	chr6A	89.836	974	71	16	2254	3206	182418174	182417208	0.000000e+00	1225
15	TraesCS7A01G170000	chr2A	94.228	2408	92	13	1	2386	778648747	778651129	0.000000e+00	3633
16	TraesCS7A01G170000	chr2A	89.834	964	71	17	2269	3210	778650974	778651932	0.000000e+00	1212
17	TraesCS7A01G170000	chr6D	93.632	1382	49	10	1852	3208	16251411	16252778	0.000000e+00	2028
18	TraesCS7A01G170000	chr5A	82.177	2278	320	50	212	2426	514149474	514147220	0.000000e+00	1879
19	TraesCS7A01G170000	chr3A	97.929	821	14	2	2386	3206	644687580	644686763	0.000000e+00	1419
20	TraesCS7A01G170000	chr3A	95.238	861	38	3	1	860	153362640	153363498	0.000000e+00	1360
21	TraesCS7A01G170000	chr7D	83.875	1445	179	30	1	1393	83758720	83760162	0.000000e+00	1328
22	TraesCS7A01G170000	chr5B	86.643	569	70	6	362	929	489804794	489804231	3.140000e-175	625
23	TraesCS7A01G170000	chrUn	95.480	177	8	0	3206	3382	35763	35587	2.180000e-72	283
24	TraesCS7A01G170000	chr1A	97.279	147	4	0	3384	3530	2918284	2918430	2.210000e-62	250

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	TraesCS7A01G170000	chr7A	126148504	126152207	3703	False	6841.0	6841	100.0000	1	3704	1	chr7A.!!$F2	3703
1	TraesCS7A01G170000	chr7A	8700340	8700846	506	False	763.0	763	94.0830	3206	3704	1	chr7A.!!$F1	498
2	TraesCS7A01G170000	chr3B	473235645	473238903	3258	False	4939.0	4939	94.2810	1	3211	1	chr3B.!!$F1	3210
3	TraesCS7A01G170000	chr3B	766341691	766342598	907	False	1061.0	1061	87.8290	1	907	1	chr3B.!!$F2	906
4	TraesCS7A01G170000	chr7B	51883760	51887014	3254	False	4774.0	4774	93.4170	1	3206	1	chr7B.!!$F1	3205
5	TraesCS7A01G170000	chr7B	73167724	73169164	1440	False	1376.0	1376	84.4880	1	1393	1	chr7B.!!$F2	1392
6	TraesCS7A01G170000	chr6B	48079457	48082698	3241	False	4747.0	4747	93.3230	2	3208	1	chr6B.!!$F1	3206
7	TraesCS7A01G170000	chr4B	321541993	321545253	3260	False	4702.0	4702	92.9690	1	3212	1	chr4B.!!$F1	3211
8	TraesCS7A01G170000	chr4B	587098356	587101575	3219	False	2347.5	3459	93.7995	1	3206	2	chr4B.!!$F2	3205
9	TraesCS7A01G170000	chr6A	137391917	137393776	1859	True	2793.0	2793	93.9120	1354	3208	1	chr6A.!!$R1	1854
10	TraesCS7A01G170000	chr6A	182417208	182420402	3194	True	2488.0	3751	92.4230	1	3206	2	chr6A.!!$R3	3205
11	TraesCS7A01G170000	chr6A	137492140	137493501	1361	True	2292.0	2292	97.0650	1	1361	1	chr6A.!!$R2	1360
12	TraesCS7A01G170000	chr2A	778648747	778651932	3185	False	2422.5	3633	92.0310	1	3210	2	chr2A.!!$F1	3209
13	TraesCS7A01G170000	chr6D	16251411	16252778	1367	False	2028.0	2028	93.6320	1852	3208	1	chr6D.!!$F1	1356
14	TraesCS7A01G170000	chr5A	514147220	514149474	2254	True	1879.0	1879	82.1770	212	2426	1	chr5A.!!$R1	2214
15	TraesCS7A01G170000	chr3A	644686763	644687580	817	True	1419.0	1419	97.9290	2386	3206	1	chr3A.!!$R1	820
16	TraesCS7A01G170000	chr3A	153362640	153363498	858	False	1360.0	1360	95.2380	1	860	1	chr3A.!!$F1	859
17	TraesCS7A01G170000	chr7D	83758720	83760162	1442	False	1328.0	1328	83.8750	1	1393	1	chr7D.!!$F1	1392
18	TraesCS7A01G170000	chr5B	489804231	489804794	563	True	625.0	625	86.6430	362	929	1	chr5B.!!$R1	567

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
524	537	1.47851	CAGAATCCACCTCGTAGTGCT	59.521	52.381	2.59	0.0	36.38	4.40	F
1695	1815	1.15145	CTTTGGTGAGGCAGTGGGT	59.849	57.895	0.00	0.0	0.00	4.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1820	1940	1.216678	TCTTTGGCCTTGGTTCCTTCA	59.783	47.619	3.32	0.0	0.00	3.02	R
3394	3613	0.033090	GGTTTCGACGAACTGTCCCT	59.967	55.000	10.38	0.0	45.23	4.20	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
47	48	5.116084	TCCATTGCTACTTAAGAAGCCAT	57.884	39.130	10.09	0.00	37.97	4.40
117	118	9.522804	CAAGGTACATAGCTACTAAGAAAGAAG	57.477	37.037	0.00	0.00	33.01	2.85
177	187	5.401033	TGTTTGCACATTGTTGTTTATGC	57.599	34.783	0.00	0.00	32.34	3.14
524	537	1.478510	CAGAATCCACCTCGTAGTGCT	59.521	52.381	2.59	0.00	36.38	4.40
869	893	3.835478	ATAGACATAGGGCTGCTAGGA	57.165	47.619	0.00	0.00	0.00	2.94
1104	1190	2.409948	AAGCCTTGTATGAGCTGTCC	57.590	50.000	0.00	0.00	36.84	4.02
1174	1260	4.263905	TGGTGATATTGGAGAAGCACCTTT	60.264	41.667	10.68	0.00	44.53	3.11
1189	1275	3.486383	CACCTTTCTGAAAAGTGCCCTA	58.514	45.455	16.39	0.00	40.30	3.53
1695	1815	1.151450	CTTTGGTGAGGCAGTGGGT	59.849	57.895	0.00	0.00	0.00	4.51
1765	1885	3.054802	GGACTTGATCTCAACAGGGACAT	60.055	47.826	0.00	0.00	0.00	3.06
1820	1940	4.479786	GAACTAGTTCCAAGAGGCAGAT	57.520	45.455	22.74	0.00	33.64	2.90
1863	1983	1.153628	GACGGGACCAAGTGATCCG	60.154	63.158	0.00	0.00	45.42	4.18
1893	2013	4.509230	GCGATGCTTCAAGATGTCAATAGA	59.491	41.667	0.08	0.00	0.00	1.98
2057	2178	1.153745	GCGAGATCGTTGAGGCTGT	60.154	57.895	3.94	0.00	42.22	4.40
2103	2224	6.589135	AGATCAGATGAACATGATGCTTACA	58.411	36.000	0.00	0.00	36.30	2.41
2178	2302	5.335976	CCTTTTGCTAAACTCCACAATCTCC	60.336	44.000	0.00	0.00	0.00	3.71
2648	2840	7.455641	TGGTTGTCTCTTGTTTGTTTCTTTA	57.544	32.000	0.00	0.00	0.00	1.85
3046	3262	3.277715	TGCATGTGAAAGTTGTCTGACA	58.722	40.909	6.36	6.36	0.00	3.58
3172	3391	2.669434	CGTGACCTGTTACCATTAACGG	59.331	50.000	0.00	0.00	42.29	4.44
3218	3437	2.640826	ACACCTCCTTAATGAAACGGGA	59.359	45.455	0.00	0.00	0.00	5.14
3239	3458	5.148502	GGATACTAGAGAATGGGACCTGAA	58.851	45.833	0.00	0.00	0.00	3.02
3254	3473	5.893824	GGGACCTGAATCTGATAAACCAAAT	59.106	40.000	0.00	0.00	0.00	2.32
3303	3522	0.846693	CCAAAATCCGGATCCCCTCT	59.153	55.000	19.43	0.00	0.00	3.69
3351	3570	2.610232	GCACTACGAGAAAAACGGGGTA	60.610	50.000	0.00	0.00	34.93	3.69
3356	3575	3.069289	ACGAGAAAAACGGGGTATTCAC	58.931	45.455	0.00	0.00	34.93	3.18
3369	3588	2.353803	GGTATTCACGGTGAAGAGTGCT	60.354	50.000	25.74	12.52	40.05	4.40
3379	3598	6.253727	CACGGTGAAGAGTGCTTATAAACTAG	59.746	42.308	0.74	0.00	33.61	2.57
3394	3613	3.678056	AACTAGCCGAACAACTCATGA	57.322	42.857	0.00	0.00	0.00	3.07
3404	3623	3.409026	ACAACTCATGAGGGACAGTTC	57.591	47.619	26.08	0.00	0.00	3.01
3424	3644	3.459145	TCGTCGAAACCATCAAACTCAA	58.541	40.909	0.00	0.00	0.00	3.02
3486	3713	2.001076	AGGCAAAGGTCCCTGAAAAG	57.999	50.000	0.00	0.00	0.00	2.27
3501	3728	5.336451	CCCTGAAAAGGTTAAAATCTTCGGG	60.336	44.000	8.52	8.52	38.52	5.14
3549	3776	5.064707	GGCGACAAAACATAATGCTCTAAGA	59.935	40.000	0.00	0.00	0.00	2.10
3563	3790	5.012239	TGCTCTAAGAAGAACCATTGCAAT	58.988	37.500	5.99	5.99	0.00	3.56
3573	3800	7.994911	AGAAGAACCATTGCAATAGATGACATA	59.005	33.333	12.53	0.00	0.00	2.29
3593	3820	7.226523	TGACATATGTGAAATCTACGGAAATGG	59.773	37.037	14.43	0.00	0.00	3.16
3632	3859	0.372679	GCTGTGATCACATGCACTCG	59.627	55.000	29.47	19.24	41.01	4.18
3690	3917	4.790765	GGAACTCCCAAAGAAGGAATTG	57.209	45.455	0.00	0.00	31.49	2.32
3696	3923	2.819608	CCCAAAGAAGGAATTGCTTCGA	59.180	45.455	27.51	0.00	34.99	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	2.091720	TGCAGTCCTCGGGTATAGGTTA	60.092	50.000	0.00	0.00	35.48	2.85
177	187	3.589988	ACGCTCCAAGACAATTCTACAG	58.410	45.455	0.00	0.00	0.00	2.74
426	439	2.556189	TCGCATTTGTGTAACCAGCATT	59.444	40.909	0.00	0.00	34.36	3.56
524	537	3.792401	CCGCATGTTGTAATACTCCTCA	58.208	45.455	0.00	0.00	0.00	3.86
1174	1260	3.476552	CACAACTAGGGCACTTTTCAGA	58.523	45.455	0.00	0.00	0.00	3.27
1189	1275	4.265073	GGAATTGCAGAGATACCACAACT	58.735	43.478	0.00	0.00	0.00	3.16
1331	1420	6.941857	TCTACCTTACAATGTGCTTCATACA	58.058	36.000	0.00	0.00	35.48	2.29
1695	1815	8.811017	TCCATAGCAATTTCATTTTCCAAGTTA	58.189	29.630	0.00	0.00	0.00	2.24
1765	1885	3.715495	GAGTATCGACAGACCGTCTAGA	58.285	50.000	0.00	2.13	42.98	2.43
1820	1940	1.216678	TCTTTGGCCTTGGTTCCTTCA	59.783	47.619	3.32	0.00	0.00	3.02
1893	2013	2.642427	TGTGTCACATTGTTCAGCTGT	58.358	42.857	14.67	0.00	0.00	4.40
2057	2178	7.104043	TCTAGAGCTTTAGCAAATACGGTTA	57.896	36.000	6.41	0.00	45.16	2.85
2103	2224	3.265479	CCCTCCTCAGATTTTCTGGAAGT	59.735	47.826	4.78	0.00	44.39	3.01
2178	2302	6.498304	TCAAAGCTGAAAGAGTTTAGCAAAG	58.502	36.000	6.08	0.00	38.59	2.77
2830	3023	6.555315	ACTCAGACTTCAACAACAATTCAAC	58.445	36.000	0.00	0.00	0.00	3.18
2832	3025	6.757897	AACTCAGACTTCAACAACAATTCA	57.242	33.333	0.00	0.00	0.00	2.57
3046	3262	5.126067	GGTGTGGCACTGTAATCTGAATAT	58.874	41.667	19.83	0.00	34.40	1.28
3218	3437	6.496565	CAGATTCAGGTCCCATTCTCTAGTAT	59.503	42.308	0.00	0.00	0.00	2.12
3254	3473	4.321899	CCTCGGCATCAAAGGAATGAAAAA	60.322	41.667	0.00	0.00	32.06	1.94
3303	3522	2.236146	AGCCGTGTCTTCATATTCCACA	59.764	45.455	0.00	0.00	0.00	4.17
3351	3570	2.550830	AAGCACTCTTCACCGTGAAT	57.449	45.000	14.29	0.00	35.59	2.57
3356	3575	5.232414	GCTAGTTTATAAGCACTCTTCACCG	59.768	44.000	1.97	0.00	38.63	4.94
3369	3588	7.324935	TCATGAGTTGTTCGGCTAGTTTATAA	58.675	34.615	0.00	0.00	0.00	0.98
3379	3598	0.036388	TCCCTCATGAGTTGTTCGGC	60.036	55.000	21.11	0.00	0.00	5.54
3394	3613	0.033090	GGTTTCGACGAACTGTCCCT	59.967	55.000	10.38	0.00	45.23	4.20
3404	3623	3.363970	CCTTGAGTTTGATGGTTTCGACG	60.364	47.826	0.00	0.00	0.00	5.12
3424	3644	2.997897	GTCACCCACCTCGCTCCT	60.998	66.667	0.00	0.00	0.00	3.69
3486	3713	1.131693	CGCCACCCGAAGATTTTAACC	59.868	52.381	0.00	0.00	40.02	2.85
3549	3776	8.573885	CATATGTCATCTATTGCAATGGTTCTT	58.426	33.333	22.27	10.88	0.00	2.52
3563	3790	8.404107	TCCGTAGATTTCACATATGTCATCTA	57.596	34.615	17.54	17.54	31.84	1.98
3573	3800	5.590259	CCTTCCATTTCCGTAGATTTCACAT	59.410	40.000	0.00	0.00	0.00	3.21
3584	3811	1.212935	CATCCTCCCTTCCATTTCCGT	59.787	52.381	0.00	0.00	0.00	4.69
3593	3820	2.807108	GCGTGGTATTCATCCTCCCTTC	60.807	54.545	0.00	0.00	0.00	3.46
3632	3859	7.766278	TCATCTCATTTCTAACAGCCTTACTTC	59.234	37.037	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.