AutoCloner

Multiple sequence alignment - TraesCS4A01G295100

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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	TraesCS4A01G295100	chr4A	100.000	2354	0	0	1	2354	596003431	596001078	0.000000e+00	4348.0
1	TraesCS4A01G295100	chr4A	80.469	128	23	2	1010	1136	21631975	21632101	1.930000e-16	97.1
2	TraesCS4A01G295100	chr4D	90.227	2118	78	36	1	2044	7586267	7588329	0.000000e+00	2645.0
3	TraesCS4A01G295100	chr4D	93.814	194	12	0	2047	2240	7588406	7588599	2.290000e-75	292.0
4	TraesCS4A01G295100	chr4D	94.595	74	4	0	2252	2325	7588655	7588728	5.320000e-22	115.0
5	TraesCS4A01G295100	chr4B	90.122	1397	67	32	649	2008	13395107	13396469	0.000000e+00	1749.0
6	TraesCS4A01G295100	chr4B	91.133	609	23	8	1	578	13394381	13394989	0.000000e+00	797.0
7	TraesCS4A01G295100	chr4B	90.256	195	14	2	876	1066	291450800	291450993	1.400000e-62	250.0
8	TraesCS4A01G295100	chr4B	91.971	137	8	1	2098	2231	13396817	13396953	3.090000e-44	189.0
9	TraesCS4A01G295100	chr4B	80.315	127	25	0	1010	1136	556069781	556069655	1.930000e-16	97.1
10	TraesCS4A01G295100	chr4B	94.595	37	2	0	2047	2083	13396780	13396816	9.090000e-05	58.4
11	TraesCS4A01G295100	chr5B	90.256	195	14	2	876	1066	544816086	544816279	1.400000e-62	250.0
12	TraesCS4A01G295100	chr5B	87.923	207	16	5	876	1076	711785546	711785749	3.910000e-58	235.0
13	TraesCS4A01G295100	chr5B	78.689	183	33	4	1022	1198	568845543	568845725	1.480000e-22	117.0
14	TraesCS4A01G295100	chr3B	88.835	206	16	4	876	1076	727081905	727081702	1.810000e-61	246.0
15	TraesCS4A01G295100	chr7A	87.624	202	18	5	876	1073	649715410	649715608	6.540000e-56	228.0
16	TraesCS4A01G295100	chr1B	88.205	195	18	2	876	1066	588928655	588928848	6.540000e-56	228.0
17	TraesCS4A01G295100	chr3A	89.437	142	8	3	936	1076	612613609	612613744	3.110000e-39	172.0
18	TraesCS4A01G295100	chr5D	76.987	239	42	9	1027	1254	462746461	462746697	8.830000e-25	124.0
19	TraesCS4A01G295100	chr5D	79.444	180	27	7	1027	1198	462669800	462669977	4.110000e-23	119.0
20	TraesCS4A01G295100	chr5D	75.309	243	49	7	1022	1254	462895701	462895942	3.200000e-19	106.0
21	TraesCS4A01G295100	chrUn	76.151	239	48	6	1025	1254	199465921	199465683	1.480000e-22	117.0
22	TraesCS4A01G295100	chrUn	76.033	242	49	6	1022	1254	343570822	343571063	1.480000e-22	117.0
23	TraesCS4A01G295100	chrUn	76.033	242	49	6	1022	1254	343624734	343624975	1.480000e-22	117.0

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	TraesCS4A01G295100	chr4A	596001078	596003431	2353	True	4348.000000	4348	100.000000	1	2354	1	chr4A.!!$R1	2353
1	TraesCS4A01G295100	chr4D	7586267	7588728	2461	False	1017.333333	2645	92.878667	1	2325	3	chr4D.!!$F1	2324
2	TraesCS4A01G295100	chr4B	13394381	13396953	2572	False	698.350000	1749	91.955250	1	2231	4	chr4B.!!$F2	2230

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
763	864	0.8951	GCCACCAACTGATGCCAGAA	60.895	55.0	0.0	0.0	43.02	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2245	2666	0.250727	GCTGTAAAGTCCCACCTGCA	60.251	55.0	0.0	0.0	0.0	4.41	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
114	119	2.366590	GGAATCCATTTGCCATCCTTCC	59.633	50.000	0.00	0.00	0.00	3.46
144	149	3.582780	GGTGTCAACCGACTAAAGGTAG	58.417	50.000	0.00	0.00	41.95	3.18
202	218	1.144057	GTGTATGCCCTCCACCTCG	59.856	63.158	0.00	0.00	0.00	4.63
368	385	3.820689	TGCGAACTCACAATTATGCAAC	58.179	40.909	0.00	0.00	0.00	4.17
443	460	8.100164	TGGACAGTATTGATTGACAAGAACATA	58.900	33.333	0.00	0.00	42.02	2.29
534	570	3.007920	CTCCCTCTGGCAGCTGGT	61.008	66.667	17.12	0.00	0.00	4.00
619	676	2.932261	ACCTGACAAAGAACCAACTCC	58.068	47.619	0.00	0.00	0.00	3.85
620	677	2.509964	ACCTGACAAAGAACCAACTCCT	59.490	45.455	0.00	0.00	0.00	3.69
621	678	3.053619	ACCTGACAAAGAACCAACTCCTT	60.054	43.478	0.00	0.00	0.00	3.36
624	681	5.592688	CCTGACAAAGAACCAACTCCTTTTA	59.407	40.000	0.00	0.00	0.00	1.52
763	864	0.895100	GCCACCAACTGATGCCAGAA	60.895	55.000	0.00	0.00	43.02	3.02
956	1076	2.908940	AAGGCCAGCACAGCACAC	60.909	61.111	5.01	0.00	0.00	3.82
966	1086	2.114670	ACAGCACACCACAGCACAC	61.115	57.895	0.00	0.00	0.00	3.82
970	1090	1.748500	CACACCACAGCACACCACA	60.749	57.895	0.00	0.00	0.00	4.17
1158	1281	1.301293	CAGGAAGAAGGCTCACCCC	59.699	63.158	0.00	0.00	36.11	4.95
1285	1408	1.227853	GGTGACTTGTCCAAGCCGT	60.228	57.895	6.94	0.00	41.99	5.68
1309	1438	1.623811	GCTCCTCCTCCAACAAGTACA	59.376	52.381	0.00	0.00	0.00	2.90
1390	1523	3.069586	CCATTCTATGGCTTGTAGACCGA	59.930	47.826	0.00	0.00	44.70	4.69
1393	1526	0.742505	TATGGCTTGTAGACCGACCG	59.257	55.000	0.00	0.00	0.00	4.79
1394	1527	2.508663	GGCTTGTAGACCGACCGC	60.509	66.667	0.00	0.00	0.00	5.68
1436	1569	5.673337	TGAATCTCCTGTTTCTTTTGTCG	57.327	39.130	0.00	0.00	0.00	4.35
1468	1601	8.404000	GGCATATATTCTTATGATGGCAAGAAG	58.596	37.037	5.00	0.00	42.38	2.85
1506	1639	8.514594	AGAAAGTCATAAATTGCTTCGAAATGA	58.485	29.630	0.00	0.61	0.00	2.57
1512	1645	5.773239	AAATTGCTTCGAAATGAATGCTG	57.227	34.783	0.00	0.00	35.63	4.41
1530	1667	2.686915	GCTGATAGTGCTTGGCTTTGAT	59.313	45.455	0.00	0.00	0.00	2.57
1536	1673	3.285484	AGTGCTTGGCTTTGATATGAGG	58.715	45.455	0.00	0.00	0.00	3.86
1544	1681	2.098117	GCTTTGATATGAGGCTGCGTTT	59.902	45.455	0.00	0.00	0.00	3.60
1545	1682	3.428045	GCTTTGATATGAGGCTGCGTTTT	60.428	43.478	0.00	0.00	0.00	2.43
1605	1742	9.857656	AGTTGCCAACATATACTACTACTACTA	57.142	33.333	10.69	0.00	0.00	1.82
1606	1743	9.890352	GTTGCCAACATATACTACTACTACTAC	57.110	37.037	1.91	0.00	0.00	2.73
1607	1744	9.857656	TTGCCAACATATACTACTACTACTACT	57.142	33.333	0.00	0.00	0.00	2.57
1763	1903	8.853126	CCAAGAATCAAGGCAATCTATTTATCA	58.147	33.333	0.00	0.00	0.00	2.15
1864	2010	7.065803	GCTATAAAGTGACAGCATTTGGAACTA	59.934	37.037	0.00	0.00	34.13	2.24
1870	2016	3.935828	GACAGCATTTGGAACTACTCCTC	59.064	47.826	0.00	0.00	45.64	3.71
1894	2040	2.438800	TTCCCCTTTCCAACGTTCAA	57.561	45.000	0.00	0.00	0.00	2.69
1902	2048	6.033966	CCCTTTCCAACGTTCAAATTATAGC	58.966	40.000	0.00	0.00	0.00	2.97
1973	2119	9.270640	AGAAGTATTGTGATTTCTCATATGAGC	57.729	33.333	25.27	13.25	41.80	4.26
2044	2220	7.787028	GTCCTGAAGACAAGGATAGACTATTT	58.213	38.462	0.00	0.00	45.55	1.40
2045	2221	8.915036	GTCCTGAAGACAAGGATAGACTATTTA	58.085	37.037	0.00	0.00	45.55	1.40
2079	2497	4.041075	TGCTTAAGTGGAGTTGTGATGGTA	59.959	41.667	4.02	0.00	0.00	3.25
2201	2622	9.194271	GGATGGAACGTTATTTTACTCTATCTC	57.806	37.037	0.00	0.00	0.00	2.75
2203	2624	9.968870	ATGGAACGTTATTTTACTCTATCTCTC	57.031	33.333	0.00	0.00	0.00	3.20
2231	2652	1.440938	TTCCACGGTCAAAAGGCGTG	61.441	55.000	0.00	0.00	34.18	5.34
2240	2661	2.096248	TCAAAAGGCGTGGAACTGTTT	58.904	42.857	0.00	0.00	31.75	2.83
2241	2662	2.159310	TCAAAAGGCGTGGAACTGTTTG	60.159	45.455	0.00	0.00	31.75	2.93
2245	2666	2.858745	AGGCGTGGAACTGTTTGTAAT	58.141	42.857	0.00	0.00	31.75	1.89
2246	2667	2.552315	AGGCGTGGAACTGTTTGTAATG	59.448	45.455	0.00	0.00	31.75	1.90
2247	2668	2.315901	GCGTGGAACTGTTTGTAATGC	58.684	47.619	0.00	0.00	31.75	3.56
2249	2670	3.554524	CGTGGAACTGTTTGTAATGCAG	58.445	45.455	0.00	0.00	36.41	4.41
2250	2671	3.609175	CGTGGAACTGTTTGTAATGCAGG	60.609	47.826	0.00	0.00	34.79	4.85
2263	2728	2.496899	ATGCAGGTGGGACTTTACAG	57.503	50.000	0.00	0.00	0.00	2.74
2305	2770	4.558226	ATTGTTCAGTCATAGGCTCACA	57.442	40.909	0.00	0.00	0.00	3.58
2320	2785	4.161377	AGGCTCACAGTTCTATTTCCTCTC	59.839	45.833	0.00	0.00	0.00	3.20
2325	2790	7.041098	GCTCACAGTTCTATTTCCTCTCAAAAA	60.041	37.037	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	9.104965	AGATGAAATTGAATTGGTTATTGCATG	57.895	29.630	0.00	0.00	28.66	4.06
114	119	2.544267	GTCGGTTGACACCTCTTTTCAG	59.456	50.000	0.00	0.00	44.82	3.02
166	171	8.780249	GGCATACACGGTAGTATCAATTTTATT	58.220	33.333	0.00	0.00	32.56	1.40
202	218	3.629398	CAGCCACCTGTGATTAGGATTTC	59.371	47.826	0.00	0.00	40.42	2.17
368	385	4.709397	AGTTGGTTCCTGAGATACTCTGAG	59.291	45.833	2.45	2.45	32.36	3.35
443	460	4.000988	CCATAAACTCAAAGTGCCGTAGT	58.999	43.478	0.00	0.00	0.00	2.73
534	570	2.229792	GTTTCTGGTGACATGAGCCAA	58.770	47.619	0.00	0.00	41.51	4.52
624	681	9.847224	CCACCTAGTATACATATTTTTCAGGTT	57.153	33.333	5.50	0.00	30.40	3.50
645	702	3.256960	AATCCACCGGTGCCACCT	61.257	61.111	29.75	8.03	35.66	4.00
956	1076	2.516695	TGCTGTGGTGTGCTGTGG	60.517	61.111	0.00	0.00	0.00	4.17
966	1086	0.731417	GCTATTGCTCTGTGCTGTGG	59.269	55.000	3.20	0.00	43.37	4.17
970	1090	2.809665	GCTATGGCTATTGCTCTGTGCT	60.810	50.000	9.13	0.00	39.59	4.40
1191	1314	3.627577	TGGACTTGAACTTCTTGCAGAAC	59.372	43.478	0.00	0.00	29.89	3.01
1257	1380	4.003788	AAGTCACCGGACCGCCTG	62.004	66.667	9.46	5.89	45.48	4.85
1285	1408	2.683933	GTTGGAGGAGGAGCCCGA	60.684	66.667	0.00	0.00	37.37	5.14
1393	1526	1.090728	GCCTGAGAAAAGCACTAGGC	58.909	55.000	0.00	0.00	43.20	3.93
1394	1527	2.746362	CAAGCCTGAGAAAAGCACTAGG	59.254	50.000	0.00	0.00	0.00	3.02
1436	1569	9.143631	GCCATCATAAGAATATATGCCAAAAAC	57.856	33.333	0.00	0.00	34.05	2.43
1495	1628	5.203370	CACTATCAGCATTCATTTCGAAGC	58.797	41.667	0.00	0.00	36.95	3.86
1506	1639	2.431954	AGCCAAGCACTATCAGCATT	57.568	45.000	0.00	0.00	0.00	3.56
1512	1645	5.180868	CCTCATATCAAAGCCAAGCACTATC	59.819	44.000	0.00	0.00	0.00	2.08
1763	1903	6.285990	CAGCTTTAGGTAATACCGGTACATT	58.714	40.000	18.55	12.31	44.90	2.71
1842	1988	6.296026	AGTAGTTCCAAATGCTGTCACTTTA	58.704	36.000	0.00	0.00	0.00	1.85
1843	1989	5.133221	AGTAGTTCCAAATGCTGTCACTTT	58.867	37.500	0.00	0.00	0.00	2.66
1876	2022	2.438800	TTTGAACGTTGGAAAGGGGA	57.561	45.000	5.00	0.00	35.69	4.81
1888	2034	5.119279	AGCAGCTATCGCTATAATTTGAACG	59.881	40.000	0.00	0.00	46.99	3.95
1894	2040	4.021104	TGGTCAGCAGCTATCGCTATAATT	60.021	41.667	0.00	0.00	46.99	1.40
1902	2048	0.654683	GCTTTGGTCAGCAGCTATCG	59.345	55.000	0.00	0.00	39.83	2.92
1918	2064	5.416639	TCTTGATATCAAACTGCACATGCTT	59.583	36.000	18.47	0.00	37.39	3.91
1973	2119	3.254060	CTGTTCCTGATTAGACCACACG	58.746	50.000	0.00	0.00	0.00	4.49
2089	2507	6.588756	TGTTCGTAGAACTTGGTCATGAATAC	59.411	38.462	13.17	0.00	45.90	1.89
2201	2622	0.673644	ACCGTGGAATCTTTGGCGAG	60.674	55.000	0.00	0.00	0.00	5.03
2203	2624	0.953471	TGACCGTGGAATCTTTGGCG	60.953	55.000	0.00	0.00	0.00	5.69
2231	2652	3.305335	CCACCTGCATTACAAACAGTTCC	60.305	47.826	0.00	0.00	0.00	3.62
2240	2661	2.969821	AAAGTCCCACCTGCATTACA	57.030	45.000	0.00	0.00	0.00	2.41
2241	2662	3.681593	TGTAAAGTCCCACCTGCATTAC	58.318	45.455	0.00	0.00	0.00	1.89
2245	2666	0.250727	GCTGTAAAGTCCCACCTGCA	60.251	55.000	0.00	0.00	0.00	4.41
2246	2667	0.960861	GGCTGTAAAGTCCCACCTGC	60.961	60.000	0.00	0.00	0.00	4.85
2247	2668	0.693049	AGGCTGTAAAGTCCCACCTG	59.307	55.000	0.00	0.00	0.00	4.00
2249	2670	2.504175	TGATAGGCTGTAAAGTCCCACC	59.496	50.000	0.00	0.00	0.00	4.61
2250	2671	3.197983	ACTGATAGGCTGTAAAGTCCCAC	59.802	47.826	0.00	0.00	0.00	4.61
2263	2728	8.396272	ACAATATTGGTGATAAACTGATAGGC	57.604	34.615	19.37	0.00	0.00	3.93
2297	2762	4.100373	AGAGGAAATAGAACTGTGAGCCT	58.900	43.478	0.00	0.00	0.00	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.