AutoCloner

Multiple sequence alignment - TraesCS6A01G267100

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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	TraesCS6A01G267100	chr6A	100.000	2956	0	0	541	3496	492709545	492706590	0.000000e+00	5459.0
1	TraesCS6A01G267100	chr6A	100.000	364	0	0	1	364	492710085	492709722	0.000000e+00	673.0
2	TraesCS6A01G267100	chr6A	82.500	80	10	3	2768	2844	417623073	417623151	2.250000e-07	67.6
3	TraesCS6A01G267100	chr6D	94.694	2111	76	14	682	2780	351109556	351111642	0.000000e+00	3245.0
4	TraesCS6A01G267100	chr6D	95.341	601	19	9	2900	3496	351112130	351112725	0.000000e+00	946.0
5	TraesCS6A01G267100	chr6B	92.953	2086	91	24	682	2747	528624858	528622809	0.000000e+00	2987.0
6	TraesCS6A01G267100	chr6B	99.176	364	3	0	1	364	615233936	615234299	0.000000e+00	656.0
7	TraesCS6A01G267100	chr6B	97.253	364	10	0	1	364	126548493	126548130	4.960000e-173	617.0
8	TraesCS6A01G267100	chr6B	92.973	370	13	5	2901	3268	528622723	528622365	8.590000e-146	527.0
9	TraesCS6A01G267100	chr6B	97.835	231	3	2	3266	3496	528622262	528622034	7.030000e-107	398.0
10	TraesCS6A01G267100	chr6B	92.969	128	6	1	541	668	72116128	72116252	2.140000e-42	183.0
11	TraesCS6A01G267100	chr2B	99.451	364	2	0	1	364	617877423	617877060	0.000000e+00	662.0
12	TraesCS6A01G267100	chr2B	97.527	364	9	0	1	364	674723868	674723505	1.070000e-174	623.0
13	TraesCS6A01G267100	chr2B	95.349	129	0	1	541	669	617877033	617876911	2.130000e-47	200.0
14	TraesCS6A01G267100	chr2B	96.262	107	4	0	568	674	674723459	674723353	3.590000e-40	176.0
15	TraesCS6A01G267100	chr2B	91.228	57	5	0	2765	2821	493852652	493852708	1.040000e-10	78.7
16	TraesCS6A01G267100	chr7B	97.527	364	9	0	1	364	45432192	45432555	1.070000e-174	623.0
17	TraesCS6A01G267100	chr7B	97.527	364	9	0	1	364	591376149	591376512	1.070000e-174	623.0
18	TraesCS6A01G267100	chr7B	96.703	364	11	1	1	364	697642223	697641861	3.860000e-169	604.0
19	TraesCS6A01G267100	chr7B	98.058	103	2	0	567	669	45432602	45432704	2.770000e-41	180.0
20	TraesCS6A01G267100	chr7B	98.039	102	2	0	569	670	62664339	62664440	9.970000e-41	178.0
21	TraesCS6A01G267100	chr7B	97.087	103	3	0	570	672	697641812	697641710	1.290000e-39	174.0
22	TraesCS6A01G267100	chr1B	97.527	364	8	1	1	364	491701669	491701307	3.830000e-174	621.0
23	TraesCS6A01G267100	chr1B	99.029	103	1	0	567	669	491701260	491701158	5.960000e-43	185.0
24	TraesCS6A01G267100	chr2A	97.238	362	10	0	1	362	562725332	562725693	6.410000e-172	614.0
25	TraesCS6A01G267100	chr2A	96.330	109	4	0	570	678	562725742	562725850	2.770000e-41	180.0
26	TraesCS6A01G267100	chr5A	90.769	130	11	1	541	670	389154716	389154588	4.640000e-39	172.0
27	TraesCS6A01G267100	chr3B	88.889	72	8	0	2768	2839	43181512	43181583	4.810000e-14	89.8
28	TraesCS6A01G267100	chr3B	90.000	60	6	0	2762	2821	128758835	128758776	1.040000e-10	78.7
29	TraesCS6A01G267100	chr3B	88.710	62	7	0	2760	2821	252934666	252934605	3.740000e-10	76.8
30	TraesCS6A01G267100	chr3B	82.759	87	9	6	2773	2856	72722966	72722883	4.840000e-09	73.1
31	TraesCS6A01G267100	chr7D	88.060	67	6	2	2756	2821	514348287	514348222	1.040000e-10	78.7
32	TraesCS6A01G267100	chr4D	86.301	73	8	1	2765	2837	424579604	424579674	1.040000e-10	78.7
33	TraesCS6A01G267100	chr4A	83.117	77	11	2	2747	2821	595811978	595812054	6.260000e-08	69.4
34	TraesCS6A01G267100	chr1D	92.500	40	2	1	2835	2873	442376636	442376675	4.870000e-04	56.5

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	TraesCS6A01G267100	chr6A	492706590	492710085	3495	True	3066.0	5459	100.0000	1	3496	2	chr6A.!!$R1	3495
1	TraesCS6A01G267100	chr6D	351109556	351112725	3169	False	2095.5	3245	95.0175	682	3496	2	chr6D.!!$F1	2814
2	TraesCS6A01G267100	chr6B	528622034	528624858	2824	True	1304.0	2987	94.5870	682	3496	3	chr6B.!!$R2	2814
3	TraesCS6A01G267100	chr2B	617876911	617877423	512	True	431.0	662	97.4000	1	669	2	chr2B.!!$R1	668
4	TraesCS6A01G267100	chr2B	674723353	674723868	515	True	399.5	623	96.8945	1	674	2	chr2B.!!$R2	673
5	TraesCS6A01G267100	chr7B	45432192	45432704	512	False	401.5	623	97.7925	1	669	2	chr7B.!!$F3	668
6	TraesCS6A01G267100	chr7B	697641710	697642223	513	True	389.0	604	96.8950	1	672	2	chr7B.!!$R1	671
7	TraesCS6A01G267100	chr1B	491701158	491701669	511	True	403.0	621	98.2780	1	669	2	chr1B.!!$R1	668
8	TraesCS6A01G267100	chr2A	562725332	562725850	518	False	397.0	614	96.7840	1	678	2	chr2A.!!$F1	677

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
561	562	0.398318	GAAGCTGGGGCCGATCTATT	59.602	55.0	0.00	0.0	39.73	1.73	F
1879	1896	0.542938	CCGATCCTGGAGATAGCCCA	60.543	60.0	1.52	0.0	34.42	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2060	2077	0.250295	TTCTCCCGTGGTTCTTGCTG	60.250	55.000	0.0	0.0	0.00	4.41	R
2963	3370	3.127533	GATGCACACAGCCGACCC	61.128	66.667	0.0	0.0	44.83	4.46	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
135	136	1.227350	CGAGCATCAATGGCGAGGA	60.227	57.895	0.00	0.00	36.08	3.71
560	561	0.472734	AGAAGCTGGGGCCGATCTAT	60.473	55.000	0.00	0.00	39.73	1.98
561	562	0.398318	GAAGCTGGGGCCGATCTATT	59.602	55.000	0.00	0.00	39.73	1.73
562	563	0.846693	AAGCTGGGGCCGATCTATTT	59.153	50.000	0.00	0.00	39.73	1.40
563	564	0.846693	AGCTGGGGCCGATCTATTTT	59.153	50.000	0.00	0.00	39.73	1.82
564	565	1.215423	AGCTGGGGCCGATCTATTTTT	59.785	47.619	0.00	0.00	39.73	1.94
842	843	5.067674	CCAATATCACCAATCCGTCACATTT	59.932	40.000	0.00	0.00	0.00	2.32
1082	1083	1.002274	TGAGCTCCCCCTTCTCCTC	59.998	63.158	12.15	0.00	0.00	3.71
1110	1111	2.158519	TGTCTCCTATCTATCGTGCCCA	60.159	50.000	0.00	0.00	0.00	5.36
1114	1115	1.482593	CCTATCTATCGTGCCCATCCC	59.517	57.143	0.00	0.00	0.00	3.85
1177	1178	3.417101	AGAGATCTGCCTGTAGATACGG	58.583	50.000	0.00	0.00	37.53	4.02
1240	1250	7.172190	TCAGATTTGAGCTATTTCGATTGATCC	59.828	37.037	0.00	0.00	0.00	3.36
1279	1289	2.187946	GGATGGTGCGGTCTCCAG	59.812	66.667	0.00	0.00	39.02	3.86
1330	1340	7.557719	TCATCCTGTTCTTCAAATTAGGATTCC	59.442	37.037	0.00	0.00	41.72	3.01
1398	1415	7.317842	TCAAGATAGAGTTGAACCTACTACG	57.682	40.000	0.00	0.00	30.89	3.51
1399	1416	6.883217	TCAAGATAGAGTTGAACCTACTACGT	59.117	38.462	0.00	0.00	30.89	3.57
1400	1417	8.043113	TCAAGATAGAGTTGAACCTACTACGTA	58.957	37.037	0.00	0.00	30.89	3.57
1501	1518	4.234550	TGATGTGGGCAGTATAGGAGAAT	58.765	43.478	0.00	0.00	0.00	2.40
1541	1558	4.514545	TCGTAGCATAACATTCTTTGCG	57.485	40.909	0.00	0.00	40.00	4.85
1552	1569	2.448926	TTCTTTGCGGATTCGTCAGA	57.551	45.000	0.00	0.00	38.89	3.27
1553	1570	2.448926	TCTTTGCGGATTCGTCAGAA	57.551	45.000	0.00	0.00	41.13	3.02
1685	1702	8.023128	ACTCGGTTATTGTTCTTGATTGATTTG	58.977	33.333	0.00	0.00	0.00	2.32
1758	1775	7.340256	TCTAGTGAGTTAACAGTTTTGGGAAA	58.660	34.615	8.61	0.00	0.00	3.13
1879	1896	0.542938	CCGATCCTGGAGATAGCCCA	60.543	60.000	1.52	0.00	34.42	5.36
2055	2072	2.666508	GTGTTACGCATGTAGTCCACTG	59.333	50.000	13.57	0.00	0.00	3.66
2060	2077	0.449388	GCATGTAGTCCACTGCAAGC	59.551	55.000	8.86	8.86	43.49	4.01
2074	2091	1.283793	CAAGCAGCAAGAACCACGG	59.716	57.895	0.00	0.00	0.00	4.94
2141	2158	4.271696	TGTGTAGCAGAAATACAGCTGT	57.728	40.909	25.12	25.12	41.32	4.40
2230	2250	5.180117	CACCAGATAGTACAAGCATATTGGC	59.820	44.000	0.00	0.00	0.00	4.52
2250	2271	3.118223	GGCTCCTTACTGGCTTTACTCAT	60.118	47.826	0.00	0.00	35.26	2.90
2251	2272	4.518249	GCTCCTTACTGGCTTTACTCATT	58.482	43.478	0.00	0.00	35.26	2.57
2252	2273	4.333926	GCTCCTTACTGGCTTTACTCATTG	59.666	45.833	0.00	0.00	35.26	2.82
2253	2274	5.734720	CTCCTTACTGGCTTTACTCATTGA	58.265	41.667	0.00	0.00	35.26	2.57
2348	2369	0.530744	CGGTCGTGAAGGAAGGATCA	59.469	55.000	0.00	0.00	0.00	2.92
2476	2497	3.106407	GTGCGACGTGCCTGAGAC	61.106	66.667	0.00	0.00	45.60	3.36
2516	2537	1.101635	CCTGGATGCCGTCTCGACTA	61.102	60.000	0.00	0.00	0.00	2.59
2530	2551	6.073167	CCGTCTCGACTATATCTGTACATTGT	60.073	42.308	0.00	0.00	0.00	2.71
2547	2568	5.569355	ACATTGTTGTATCTTCCATCACCA	58.431	37.500	0.00	0.00	33.16	4.17
2761	2785	6.270927	ACTGCTGCTATGATCCTTCCTTATAA	59.729	38.462	0.00	0.00	0.00	0.98
2794	2818	9.495572	ACTGCCTCTGTAAATTAATATAAGAGC	57.504	33.333	9.98	7.62	0.00	4.09
2949	3356	9.474313	ACTAAAATGCCTTATGATGTTTAAGGA	57.526	29.630	12.50	0.56	45.76	3.36
2950	3357	9.956720	CTAAAATGCCTTATGATGTTTAAGGAG	57.043	33.333	12.50	0.00	45.76	3.69
2959	3366	3.459598	TGATGTTTAAGGAGGGGAGATGG	59.540	47.826	0.00	0.00	0.00	3.51
2963	3370	1.048724	TAAGGAGGGGAGATGGTGCG	61.049	60.000	0.00	0.00	0.00	5.34
2965	3372	3.866582	GAGGGGAGATGGTGCGGG	61.867	72.222	0.00	0.00	0.00	6.13
3028	3437	4.649218	TCCCTTCACAAAAGAAAAAGGAGG	59.351	41.667	1.10	0.00	39.05	4.30
3262	3671	3.398406	AGTGCATCATGTTCACGTTGTA	58.602	40.909	0.00	0.00	35.97	2.41
3301	3815	3.628646	ATTCCGCCCAGGTGTCAGC	62.629	63.158	0.00	0.00	41.99	4.26
3388	3903	3.325135	ACTCTCTCCCGAACTGAACATTT	59.675	43.478	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
135	136	2.502692	GAAGGTTGTAGCTCCGCCGT	62.503	60.000	0.00	0.00	0.00	5.68
842	843	5.121142	GCCTAAATCGCTAAAACTACACACA	59.879	40.000	0.00	0.00	0.00	3.72
890	891	2.288825	TGACTTGTCGGAGTGGCTTTAG	60.289	50.000	0.00	0.00	0.00	1.85
1062	1063	1.306568	GGAGAAGGGGGAGCTCACT	60.307	63.158	17.22	7.48	0.00	3.41
1082	1083	6.442952	CACGATAGATAGGAGACAAGAAAGG	58.557	44.000	0.00	0.00	41.38	3.11
1110	1111	5.971493	AGCAAGTAGGAATAGAGTAGGGAT	58.029	41.667	0.00	0.00	0.00	3.85
1114	1115	5.390387	AGGGAGCAAGTAGGAATAGAGTAG	58.610	45.833	0.00	0.00	0.00	2.57
1177	1178	6.957635	GCTAAAACAACGTAGCCTTTACATAC	59.042	38.462	0.00	0.00	37.37	2.39
1279	1289	2.184579	GGAGGAGCTACCGTGTGC	59.815	66.667	0.00	0.00	44.74	4.57
1297	1307	3.679389	TGAAGAACAGGATGAGGAAAGC	58.321	45.455	0.00	0.00	39.69	3.51
1330	1340	5.298026	GCTAAAGCAGAAATCCTCCCTAAAG	59.702	44.000	0.00	0.00	41.59	1.85
1486	1503	7.964666	ATTCCTACTATTCTCCTATACTGCC	57.035	40.000	0.00	0.00	0.00	4.85
1522	1539	4.875544	TCCGCAAAGAATGTTATGCTAC	57.124	40.909	0.00	0.00	36.67	3.58
1571	1588	6.547510	AGATCAAACTTTCCCCAATATAGCAC	59.452	38.462	0.00	0.00	0.00	4.40
1663	1680	9.921637	TTACCAAATCAATCAAGAACAATAACC	57.078	29.630	0.00	0.00	0.00	2.85
1685	1702	5.106277	GGTAACAACTGCTCTTGGATTTACC	60.106	44.000	0.00	0.00	39.54	2.85
1758	1775	9.661563	TCGTCAAATTAGTACTACCAATTTCAT	57.338	29.630	10.55	0.00	31.27	2.57
1781	1798	2.002586	CACCATCAGAGCGAAATTCGT	58.997	47.619	17.05	3.81	42.81	3.85
1782	1799	1.267732	GCACCATCAGAGCGAAATTCG	60.268	52.381	11.47	11.47	43.89	3.34
1879	1896	2.047274	CCGACCTCAATGCCGTGT	60.047	61.111	0.00	0.00	0.00	4.49
1998	2015	5.630680	GCAATCATTCAAAAACGAGACACAT	59.369	36.000	0.00	0.00	0.00	3.21
2006	2023	6.420588	ACAAACATGCAATCATTCAAAAACG	58.579	32.000	0.00	0.00	0.00	3.60
2055	2072	1.370900	CGTGGTTCTTGCTGCTTGC	60.371	57.895	0.00	0.00	43.25	4.01
2060	2077	0.250295	TTCTCCCGTGGTTCTTGCTG	60.250	55.000	0.00	0.00	0.00	4.41
2074	2091	9.429359	CTTTGTGGTAGTGATATCATATTCTCC	57.571	37.037	9.02	6.96	0.00	3.71
2141	2158	0.320858	TAAAAGCCGGCATGTCGTCA	60.321	50.000	31.54	1.47	0.00	4.35
2180	2198	7.617723	GCTGGGAATATATAGAGAGAGGAAAGA	59.382	40.741	0.00	0.00	0.00	2.52
2190	2208	6.805016	ATCTGGTGCTGGGAATATATAGAG	57.195	41.667	0.00	0.00	0.00	2.43
2191	2209	7.422512	ACTATCTGGTGCTGGGAATATATAGA	58.577	38.462	0.00	0.00	0.00	1.98
2192	2210	7.667575	ACTATCTGGTGCTGGGAATATATAG	57.332	40.000	0.00	0.00	0.00	1.31
2230	2250	5.734720	TCAATGAGTAAAGCCAGTAAGGAG	58.265	41.667	0.00	0.00	41.22	3.69
2231	2251	5.755409	TCAATGAGTAAAGCCAGTAAGGA	57.245	39.130	0.00	0.00	41.22	3.36
2250	2271	4.646040	CCCATCCTAGCAACAATCAATCAA	59.354	41.667	0.00	0.00	0.00	2.57
2251	2272	4.079844	TCCCATCCTAGCAACAATCAATCA	60.080	41.667	0.00	0.00	0.00	2.57
2252	2273	4.464008	TCCCATCCTAGCAACAATCAATC	58.536	43.478	0.00	0.00	0.00	2.67
2253	2274	4.467769	CTCCCATCCTAGCAACAATCAAT	58.532	43.478	0.00	0.00	0.00	2.57
2327	2348	0.613853	ATCCTTCCTTCACGACCGGA	60.614	55.000	9.46	0.00	0.00	5.14
2348	2369	3.753434	CTGTCGGGCTCGAGCTGT	61.753	66.667	34.46	0.00	46.91	4.40
2530	2551	2.569853	ACGGTGGTGATGGAAGATACAA	59.430	45.455	0.00	0.00	0.00	2.41
2654	2677	4.443394	GCAAGTGCAGATTTCTTTTCACTG	59.557	41.667	0.00	0.00	41.59	3.66
2771	2795	8.535690	ACGCTCTTATATTAATTTACAGAGGC	57.464	34.615	16.85	12.16	0.00	4.70
2876	3214	6.342111	GGAGAACTAAAATACTCCCTCTGTG	58.658	44.000	0.00	0.00	41.89	3.66
2889	3227	5.950758	TTTTATGCAGCGGAGAACTAAAA	57.049	34.783	0.00	0.00	0.00	1.52
2947	3354	3.866582	CCGCACCATCTCCCCTCC	61.867	72.222	0.00	0.00	0.00	4.30
2949	3356	4.741239	ACCCGCACCATCTCCCCT	62.741	66.667	0.00	0.00	0.00	4.79
2950	3357	4.176752	GACCCGCACCATCTCCCC	62.177	72.222	0.00	0.00	0.00	4.81
2963	3370	3.127533	GATGCACACAGCCGACCC	61.128	66.667	0.00	0.00	44.83	4.46
2965	3372	4.152625	GCGATGCACACAGCCGAC	62.153	66.667	0.00	0.00	44.83	4.79
3166	3575	5.005094	CCTTTGGTGGCATGATTTGATTTT	58.995	37.500	0.00	0.00	0.00	1.82
3195	3604	6.417191	TTTCTGTTCTATTTGTCCGCATAC	57.583	37.500	0.00	0.00	0.00	2.39
3262	3671	6.547510	GGAATTTTGGAGGCTTACATGTATCT	59.452	38.462	6.36	5.10	0.00	1.98
3301	3815	7.305820	CGCTGATTCTTTTTGCTTTGCTATATG	60.306	37.037	0.00	0.00	0.00	1.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.