AutoCloner

Multiple sequence alignment - TraesCS1A01G086400

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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	TraesCS1A01G086400	chr1A	100.000	2333	0	0	1	2333	73126489	73128821	0.000000e+00	4309.0
1	TraesCS1A01G086400	chr6A	94.241	1667	84	6	1	1662	428457234	428458893	0.000000e+00	2536.0
2	TraesCS1A01G086400	chr6A	88.614	1660	169	13	1	1656	91168646	91170289	0.000000e+00	2001.0
3	TraesCS1A01G086400	chr6A	92.896	1281	87	4	383	1662	439990214	439991491	0.000000e+00	1858.0
4	TraesCS1A01G086400	chr2D	91.521	1663	132	5	1	1661	617328360	617330015	0.000000e+00	2281.0
5	TraesCS1A01G086400	chr4A	89.790	1665	160	8	1	1661	11596866	11598524	0.000000e+00	2124.0
6	TraesCS1A01G086400	chr5A	87.545	1670	190	15	1	1661	464214205	464212545	0.000000e+00	1916.0
7	TraesCS1A01G086400	chr7A	87.590	1668	185	18	1	1658	706291609	706293264	0.000000e+00	1914.0
8	TraesCS1A01G086400	chr5B	86.724	1627	195	15	41	1661	534923575	534925186	0.000000e+00	1788.0
9	TraesCS1A01G086400	chr7B	83.945	1663	242	19	3	1657	107081984	107080339	0.000000e+00	1568.0
10	TraesCS1A01G086400	chr2B	83.675	1023	147	15	644	1661	82759238	82760245	0.000000e+00	946.0
11	TraesCS1A01G086400	chr1B	85.208	480	44	15	1840	2300	115546552	115547023	3.510000e-128	468.0
12	TraesCS1A01G086400	chr1B	88.770	187	11	6	1661	1839	115545647	115545831	1.090000e-53	220.0
13	TraesCS1A01G086400	chr1B	97.368	38	0	1	2296	2333	115579256	115579292	1.940000e-06	63.9
14	TraesCS1A01G086400	chr1D	82.387	511	30	23	1839	2333	73670710	73671176	7.820000e-105	390.0
15	TraesCS1A01G086400	chr1D	89.305	187	10	6	1661	1839	73669818	73670002	2.330000e-55	226.0
16	TraesCS1A01G086400	chr6D	85.139	323	31	4	1339	1661	285744183	285743878	4.840000e-82	315.0
17	TraesCS1A01G086400	chr6D	79.904	209	25	11	1453	1659	458334142	458333949	1.120000e-28	137.0
18	TraesCS1A01G086400	chr3B	89.542	153	16	0	1509	1661	13188134	13188286	6.580000e-46	195.0

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	TraesCS1A01G086400	chr1A	73126489	73128821	2332	False	4309	4309	100.000	1	2333	1	chr1A.!!$F1	2332
1	TraesCS1A01G086400	chr6A	428457234	428458893	1659	False	2536	2536	94.241	1	1662	1	chr6A.!!$F2	1661
2	TraesCS1A01G086400	chr6A	91168646	91170289	1643	False	2001	2001	88.614	1	1656	1	chr6A.!!$F1	1655
3	TraesCS1A01G086400	chr6A	439990214	439991491	1277	False	1858	1858	92.896	383	1662	1	chr6A.!!$F3	1279
4	TraesCS1A01G086400	chr2D	617328360	617330015	1655	False	2281	2281	91.521	1	1661	1	chr2D.!!$F1	1660
5	TraesCS1A01G086400	chr4A	11596866	11598524	1658	False	2124	2124	89.790	1	1661	1	chr4A.!!$F1	1660
6	TraesCS1A01G086400	chr5A	464212545	464214205	1660	True	1916	1916	87.545	1	1661	1	chr5A.!!$R1	1660
7	TraesCS1A01G086400	chr7A	706291609	706293264	1655	False	1914	1914	87.590	1	1658	1	chr7A.!!$F1	1657
8	TraesCS1A01G086400	chr5B	534923575	534925186	1611	False	1788	1788	86.724	41	1661	1	chr5B.!!$F1	1620
9	TraesCS1A01G086400	chr7B	107080339	107081984	1645	True	1568	1568	83.945	3	1657	1	chr7B.!!$R1	1654
10	TraesCS1A01G086400	chr2B	82759238	82760245	1007	False	946	946	83.675	644	1661	1	chr2B.!!$F1	1017
11	TraesCS1A01G086400	chr1B	115545647	115547023	1376	False	344	468	86.989	1661	2300	2	chr1B.!!$F2	639
12	TraesCS1A01G086400	chr1D	73669818	73671176	1358	False	308	390	85.846	1661	2333	2	chr1D.!!$F1	672

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
946	952	0.392706	TGTGAGACGGCACAACATCT	59.607	50.0	5.69	0.0	45.08	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2039	2812	0.31179	CATGTTGCTCGGTGTGCTTT	59.688	50.0	0.0	0.0	0.0	3.51	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
94	95	9.575868	CTGAATTCCTCCTTGTCTAGTATAGTA	57.424	37.037	2.27	0.00	40.38	1.82
187	188	1.607467	CTGGCAAAGTTGGGAGGGG	60.607	63.158	0.00	0.00	0.00	4.79
258	260	0.991355	AGGGTGGTCTGGGTGTGAAA	60.991	55.000	0.00	0.00	0.00	2.69
289	291	4.725790	AAACAAAATATCAGCCTCCTGC	57.274	40.909	0.00	0.00	39.00	4.85
524	526	1.419387	GAATGGACTGCCTCCTATGCT	59.581	52.381	0.00	0.00	40.26	3.79
529	531	2.170607	GGACTGCCTCCTATGCTTGTTA	59.829	50.000	0.00	0.00	35.89	2.41
615	618	2.325082	GGCTGGCGACATGTTTCGT	61.325	57.895	0.00	0.00	41.26	3.85
692	697	5.122239	TGTTGAATGCTATTTCTTCGACAGG	59.878	40.000	0.00	0.00	38.02	4.00
696	701	2.194271	GCTATTTCTTCGACAGGACCG	58.806	52.381	0.00	0.00	0.00	4.79
858	863	3.019564	GTGGCAGTTATTTCAGGATGCT	58.980	45.455	0.00	0.00	34.76	3.79
859	864	4.199310	GTGGCAGTTATTTCAGGATGCTA	58.801	43.478	0.00	0.00	34.76	3.49
946	952	0.392706	TGTGAGACGGCACAACATCT	59.607	50.000	5.69	0.00	45.08	2.90
1154	1164	4.036734	CAGAGCAACCTTTGAGTTTAAGCA	59.963	41.667	0.00	0.00	0.00	3.91
1271	1281	1.520342	GGTCGCAGATGCTGAGGAC	60.520	63.158	2.95	2.97	40.67	3.85
1312	1322	2.613739	GATCTGTGCCGCTGCGACTA	62.614	60.000	25.45	6.17	41.78	2.59
1352	1362	9.909644	GACTTAATAGACTGTGTCTTCAACTTA	57.090	33.333	5.52	0.00	40.28	2.24
1370	1383	1.570857	TACGTCTTCCTCCCCCGGTA	61.571	60.000	0.00	0.00	0.00	4.02
1405	1419	3.877508	GCTACTTTTGTGTTCACTCCTGT	59.122	43.478	4.59	2.24	0.00	4.00
1517	1534	1.152756	GCCCCACAACAGGTGTCTT	60.153	57.895	0.00	0.00	46.44	3.01
1529	1546	1.692519	AGGTGTCTTGTAGGCGAGTTT	59.307	47.619	0.00	0.00	0.00	2.66
1545	1562	0.666374	GTTTCTGTGGTGGGTTTCCG	59.334	55.000	0.00	0.00	35.24	4.30
1575	1592	0.476771	TGAACTCGCTTCCCCCTTTT	59.523	50.000	0.00	0.00	0.00	2.27
1577	1594	0.476771	AACTCGCTTCCCCCTTTTCA	59.523	50.000	0.00	0.00	0.00	2.69
1582	1599	1.342074	GCTTCCCCCTTTTCAGCTTT	58.658	50.000	0.00	0.00	0.00	3.51
1603	1625	5.350504	TTCTTTCCAGCTCTATTCTGAGG	57.649	43.478	0.00	0.00	34.82	3.86
1712	1734	1.275010	TGTAGACAAATGCAGCCTCGA	59.725	47.619	0.00	0.00	0.00	4.04
1745	1767	1.974236	AGAGAGCAGCAGTTGTACCTT	59.026	47.619	0.00	0.00	0.00	3.50
1746	1768	3.165875	AGAGAGCAGCAGTTGTACCTTA	58.834	45.455	0.00	0.00	0.00	2.69
1747	1769	3.194542	AGAGAGCAGCAGTTGTACCTTAG	59.805	47.826	0.00	0.00	0.00	2.18
1768	1790	1.556911	GAGGAAAGGAGCCATCAGACA	59.443	52.381	0.00	0.00	0.00	3.41
1776	1798	4.458397	AGGAGCCATCAGACAACATATTG	58.542	43.478	0.00	0.00	41.98	1.90
1815	1841	4.605813	ACCATGGCCCCTACATAAATGATA	59.394	41.667	13.04	0.00	0.00	2.15
1890	2662	8.902540	AAACTGATGAAAATTCTTAAAACCCC	57.097	30.769	0.00	0.00	0.00	4.95
1894	2666	9.559732	CTGATGAAAATTCTTAAAACCCCTTTT	57.440	29.630	0.00	0.00	33.92	2.27
1910	2682	9.610104	AAACCCCTTTTAAGTTATAGGTTGATT	57.390	29.630	9.52	2.01	36.51	2.57
1912	2684	9.610104	ACCCCTTTTAAGTTATAGGTTGATTTT	57.390	29.630	9.52	0.00	0.00	1.82
1938	2711	2.045561	TTTGTCCTGTGCTTTCGGAA	57.954	45.000	0.00	0.00	0.00	4.30
2006	2779	2.072298	GCACGATGATCCTATTGAGCC	58.928	52.381	0.00	0.00	0.00	4.70
2009	2782	2.968574	ACGATGATCCTATTGAGCCTGT	59.031	45.455	0.00	0.00	0.00	4.00
2021	2794	6.431234	CCTATTGAGCCTGTTTCACTAAACTT	59.569	38.462	3.01	0.00	44.44	2.66
2024	2797	5.189928	TGAGCCTGTTTCACTAAACTTTGA	58.810	37.500	3.01	0.00	44.44	2.69
2039	2812	9.667107	ACTAAACTTTGAATTCGATGAATAGGA	57.333	29.630	14.01	0.00	31.46	2.94
2042	2815	9.846248	AAACTTTGAATTCGATGAATAGGAAAG	57.154	29.630	14.01	9.78	33.16	2.62
2043	2816	7.475840	ACTTTGAATTCGATGAATAGGAAAGC	58.524	34.615	14.01	0.00	31.80	3.51
2044	2817	7.121168	ACTTTGAATTCGATGAATAGGAAAGCA	59.879	33.333	14.01	0.00	31.80	3.91
2045	2818	6.363577	TGAATTCGATGAATAGGAAAGCAC	57.636	37.500	0.04	0.00	31.46	4.40
2046	2819	5.879777	TGAATTCGATGAATAGGAAAGCACA	59.120	36.000	0.04	0.00	31.46	4.57
2047	2820	5.741388	ATTCGATGAATAGGAAAGCACAC	57.259	39.130	0.00	0.00	29.72	3.82
2048	2821	3.531538	TCGATGAATAGGAAAGCACACC	58.468	45.455	0.00	0.00	0.00	4.16
2050	2823	3.531538	GATGAATAGGAAAGCACACCGA	58.468	45.455	0.00	0.00	0.00	4.69
2145	2933	8.270744	AGAGATCATAAGGAATGCAAAACTACT	58.729	33.333	0.00	0.00	35.38	2.57
2198	2987	7.596621	TCGTAGCACATTTTCATGCATTAAAAA	59.403	29.630	19.62	17.42	44.59	1.94
2222	3012	9.971922	AAATGATAAAGAATAACTATGGCTTGC	57.028	29.630	0.00	0.00	0.00	4.01
2227	3017	7.568199	AAAGAATAACTATGGCTTGCGTTAT	57.432	32.000	0.00	0.00	34.90	1.89
2272	3062	6.127423	ACCAACACTACTACATGGAGATGTAC	60.127	42.308	13.29	0.00	41.27	2.90
2273	3063	5.752892	ACACTACTACATGGAGATGTACG	57.247	43.478	13.29	1.93	41.27	3.67
2282	3072	5.520632	ACATGGAGATGTACGATTTCTACG	58.479	41.667	0.00	0.00	41.27	3.51
2303	3093	5.425630	ACGTGTTCTAATTTGGGGATCTAC	58.574	41.667	0.00	0.00	0.00	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
121	122	6.016610	CCAGTTTTTCGATGAAGGTTTTAGGA	60.017	38.462	0.00	0.00	0.00	2.94
187	188	5.022021	CGAACCAAGTGATATCTTTTTCGC	58.978	41.667	3.98	0.00	35.53	4.70
228	230	0.476771	GACCACCCTTGTCCTTGGAA	59.523	55.000	0.00	0.00	33.02	3.53
289	291	5.782893	TCAAGTTTCCACCACCATTTTAG	57.217	39.130	0.00	0.00	0.00	1.85
369	371	1.610363	TGCTTTTCACCGTGGCAATA	58.390	45.000	0.00	0.00	0.00	1.90
370	372	0.749649	TTGCTTTTCACCGTGGCAAT	59.250	45.000	8.35	0.00	37.87	3.56
524	526	4.605640	AACAGCTACGGGTACTTAACAA	57.394	40.909	0.00	0.00	0.00	2.83
529	531	2.564062	TGCTAAACAGCTACGGGTACTT	59.436	45.455	0.00	0.00	35.49	2.24
692	697	3.637273	AGCCAACCTGGTCCGGTC	61.637	66.667	14.70	0.00	40.46	4.79
858	863	9.952188	CGTTTCATAACATCTCTAGTCAGAATA	57.048	33.333	0.00	0.00	33.75	1.75
859	864	8.470805	ACGTTTCATAACATCTCTAGTCAGAAT	58.529	33.333	0.00	0.00	33.75	2.40
1154	1164	7.671398	ACACAATCTCAAATGGAGTTTTAGGAT	59.329	33.333	0.00	0.00	44.40	3.24
1167	1177	4.853924	AGCGGAAAACACAATCTCAAAT	57.146	36.364	0.00	0.00	0.00	2.32
1271	1281	1.542472	TCATCATGTTGCTTGTGCTGG	59.458	47.619	0.00	0.00	40.48	4.85
1312	1322	2.642139	TAAGTCGTCGCCGAATCTTT	57.358	45.000	0.00	0.00	46.26	2.52
1352	1362	2.922704	TACCGGGGGAGGAAGACGT	61.923	63.158	6.32	0.00	34.73	4.34
1370	1383	0.117340	AAGTAGCCCTGTCCTCCTGT	59.883	55.000	0.00	0.00	0.00	4.00
1405	1419	2.369633	ATCAGGCCACATCCTCGCA	61.370	57.895	5.01	0.00	33.25	5.10
1517	1534	1.045407	ACCACAGAAACTCGCCTACA	58.955	50.000	0.00	0.00	0.00	2.74
1529	1546	2.824880	CCCGGAAACCCACCACAGA	61.825	63.158	0.73	0.00	0.00	3.41
1545	1562	2.785258	GAGTTCAACGCATCGCCC	59.215	61.111	0.00	0.00	0.00	6.13
1582	1599	3.133721	GCCTCAGAATAGAGCTGGAAAGA	59.866	47.826	0.00	0.00	34.26	2.52
1695	1717	2.119801	AATCGAGGCTGCATTTGTCT	57.880	45.000	0.50	0.00	0.00	3.41
1745	1767	2.023015	TCTGATGGCTCCTTTCCTCCTA	60.023	50.000	0.00	0.00	0.00	2.94
1746	1768	1.211456	CTGATGGCTCCTTTCCTCCT	58.789	55.000	0.00	0.00	0.00	3.69
1747	1769	1.134250	GTCTGATGGCTCCTTTCCTCC	60.134	57.143	0.00	0.00	0.00	4.30
1768	1790	7.969690	TTGGTGGAATCATAACCAATATGTT	57.030	32.000	9.44	0.00	46.42	2.71
1776	1798	3.384467	CCATGGTTGGTGGAATCATAACC	59.616	47.826	2.57	0.00	40.39	2.85
1863	2635	9.541143	GGGTTTTAAGAATTTTCATCAGTTTCA	57.459	29.630	0.00	0.00	0.00	2.69
1883	2655	9.610104	ATCAACCTATAACTTAAAAGGGGTTTT	57.390	29.630	0.00	0.00	34.17	2.43
1922	2695	3.798202	AGATATTCCGAAAGCACAGGAC	58.202	45.455	0.00	0.00	33.16	3.85
1925	2698	7.308782	AGTAAAAGATATTCCGAAAGCACAG	57.691	36.000	0.00	0.00	0.00	3.66
1938	2711	8.634444	ACTCGACATGCTTCTAGTAAAAGATAT	58.366	33.333	0.00	0.00	0.00	1.63
1976	2749	2.549754	GGATCATCGTGCCTACAATTGG	59.450	50.000	10.83	0.00	0.00	3.16
1977	2750	3.470709	AGGATCATCGTGCCTACAATTG	58.529	45.455	3.24	3.24	0.00	2.32
1978	2751	3.845781	AGGATCATCGTGCCTACAATT	57.154	42.857	0.00	0.00	0.00	2.32
1979	2752	5.012046	TCAATAGGATCATCGTGCCTACAAT	59.988	40.000	0.00	0.00	37.13	2.71
1991	2764	5.104193	AGTGAAACAGGCTCAATAGGATCAT	60.104	40.000	0.00	0.00	41.43	2.45
2006	2779	8.895845	CATCGAATTCAAAGTTTAGTGAAACAG	58.104	33.333	6.22	0.00	46.30	3.16
2021	2794	6.374053	TGTGCTTTCCTATTCATCGAATTCAA	59.626	34.615	6.22	0.00	33.95	2.69
2024	2797	5.066505	GGTGTGCTTTCCTATTCATCGAATT	59.933	40.000	0.00	0.00	33.95	2.17
2039	2812	0.311790	CATGTTGCTCGGTGTGCTTT	59.688	50.000	0.00	0.00	0.00	3.51
2042	2815	1.230635	ACTCATGTTGCTCGGTGTGC	61.231	55.000	0.00	0.00	0.00	4.57
2043	2816	1.069703	CAACTCATGTTGCTCGGTGTG	60.070	52.381	0.00	0.00	45.57	3.82
2044	2817	1.229428	CAACTCATGTTGCTCGGTGT	58.771	50.000	0.00	0.00	45.57	4.16
2167	2955	5.123027	TGCATGAAAATGTGCTACGATTGTA	59.877	36.000	0.00	0.00	41.78	2.41
2168	2956	4.082841	TGCATGAAAATGTGCTACGATTGT	60.083	37.500	0.00	0.00	41.78	2.71
2169	2957	4.413969	TGCATGAAAATGTGCTACGATTG	58.586	39.130	0.00	0.00	41.78	2.67
2173	2961	6.867799	TTTAATGCATGAAAATGTGCTACG	57.132	33.333	6.76	0.00	41.78	3.51
2198	2987	7.445402	ACGCAAGCCATAGTTATTCTTTATCAT	59.555	33.333	0.00	0.00	45.62	2.45
2213	3002	3.885901	TGGCAAATATAACGCAAGCCATA	59.114	39.130	0.00	0.00	44.89	2.74
2214	3003	2.692557	TGGCAAATATAACGCAAGCCAT	59.307	40.909	0.00	0.00	44.89	4.40
2215	3004	2.861462	GGCAAATATAACGCAAGCCA	57.139	45.000	0.00	0.00	45.62	4.75
2219	3008	2.542618	CCGCATGGCAAATATAACGCAA	60.543	45.455	0.00	0.00	0.00	4.85
2222	3012	1.606668	ACCCGCATGGCAAATATAACG	59.393	47.619	0.00	0.00	37.83	3.18
2227	3017	1.515020	GCAACCCGCATGGCAAATA	59.485	52.632	0.00	0.00	41.79	1.40
2272	3062	6.456449	CCCCAAATTAGAACACGTAGAAATCG	60.456	42.308	0.00	0.00	0.00	3.34
2273	3063	6.596497	TCCCCAAATTAGAACACGTAGAAATC	59.404	38.462	0.00	0.00	0.00	2.17
2282	3072	4.814771	CGGTAGATCCCCAAATTAGAACAC	59.185	45.833	0.00	0.00	0.00	3.32
2303	3093	4.307432	AGTGATTACGAGAATAATGGCGG	58.693	43.478	0.00	0.00	0.00	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.