AutoCloner

Multiple sequence alignment - TraesCS7B01G014600

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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	TraesCS7B01G014600	chr7B	100.000	2550	0	0	1	2550	11743804	11746353	0.000000e+00	4710
1	TraesCS7B01G014600	chr7B	95.578	588	22	3	1	586	180286993	180287578	0.000000e+00	939
2	TraesCS7B01G014600	chr3D	93.690	1965	103	15	588	2547	546485995	546487943	0.000000e+00	2922
3	TraesCS7B01G014600	chr7D	93.256	1987	101	15	590	2550	90563634	90561655	0.000000e+00	2896
4	TraesCS7B01G014600	chr7D	95.556	585	22	3	4	586	90872575	90871993	0.000000e+00	933
5	TraesCS7B01G014600	chr1D	93.357	1972	103	19	588	2550	25464319	25466271	0.000000e+00	2891
6	TraesCS7B01G014600	chr1D	91.937	955	57	16	578	1522	435252064	435251120	0.000000e+00	1319
7	TraesCS7B01G014600	chr1D	95.578	588	23	2	1	586	388906600	388906014	0.000000e+00	939
8	TraesCS7B01G014600	chr2B	92.735	1982	118	21	588	2550	173503419	173501445	0.000000e+00	2839
9	TraesCS7B01G014600	chr2B	92.272	1967	116	16	588	2550	485690852	485692786	0.000000e+00	2758
10	TraesCS7B01G014600	chr2B	82.353	578	87	12	584	1151	57101377	57100805	2.950000e-134	488
11	TraesCS7B01G014600	chr5D	92.288	1984	112	29	588	2550	114516315	114518278	0.000000e+00	2778
12	TraesCS7B01G014600	chr5D	89.826	1268	106	15	588	1837	486728530	486727268	0.000000e+00	1605
13	TraesCS7B01G014600	chr5D	95.571	587	24	2	1	586	32222811	32223396	0.000000e+00	939
14	TraesCS7B01G014600	chr6D	92.378	1968	119	19	590	2550	12108135	12106192	0.000000e+00	2774
15	TraesCS7B01G014600	chr6D	90.532	1975	132	20	588	2550	312544302	312542371	0.000000e+00	2560
16	TraesCS7B01G014600	chr6D	95.719	584	22	2	5	586	269311765	269312347	0.000000e+00	937
17	TraesCS7B01G014600	chr6D	95.408	588	24	2	1	586	370320198	370319612	0.000000e+00	933
18	TraesCS7B01G014600	chr4B	92.085	1971	112	17	590	2550	251255863	251257799	0.000000e+00	2736
19	TraesCS7B01G014600	chr4B	96.599	588	17	2	1	586	454679644	454680230	0.000000e+00	972
20	TraesCS7B01G014600	chr4D	91.544	1975	98	24	588	2550	50776934	50778851	0.000000e+00	2658
21	TraesCS7B01G014600	chr4A	89.703	1748	119	29	584	2304	616373911	616375624	0.000000e+00	2174
22	TraesCS7B01G014600	chr6B	95.578	588	23	2	1	586	231240155	231240741	0.000000e+00	939
23	TraesCS7B01G014600	chr6B	95.578	588	22	3	1	586	580167728	580167143	0.000000e+00	939
24	TraesCS7B01G014600	chrUn	87.200	625	67	11	583	1200	110636347	110636965	0.000000e+00	699

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	TraesCS7B01G014600	chr7B	11743804	11746353	2549	False	4710	4710	100.000	1	2550	1	chr7B.!!$F1	2549
1	TraesCS7B01G014600	chr7B	180286993	180287578	585	False	939	939	95.578	1	586	1	chr7B.!!$F2	585
2	TraesCS7B01G014600	chr3D	546485995	546487943	1948	False	2922	2922	93.690	588	2547	1	chr3D.!!$F1	1959
3	TraesCS7B01G014600	chr7D	90561655	90563634	1979	True	2896	2896	93.256	590	2550	1	chr7D.!!$R1	1960
4	TraesCS7B01G014600	chr7D	90871993	90872575	582	True	933	933	95.556	4	586	1	chr7D.!!$R2	582
5	TraesCS7B01G014600	chr1D	25464319	25466271	1952	False	2891	2891	93.357	588	2550	1	chr1D.!!$F1	1962
6	TraesCS7B01G014600	chr1D	435251120	435252064	944	True	1319	1319	91.937	578	1522	1	chr1D.!!$R2	944
7	TraesCS7B01G014600	chr1D	388906014	388906600	586	True	939	939	95.578	1	586	1	chr1D.!!$R1	585
8	TraesCS7B01G014600	chr2B	173501445	173503419	1974	True	2839	2839	92.735	588	2550	1	chr2B.!!$R2	1962
9	TraesCS7B01G014600	chr2B	485690852	485692786	1934	False	2758	2758	92.272	588	2550	1	chr2B.!!$F1	1962
10	TraesCS7B01G014600	chr2B	57100805	57101377	572	True	488	488	82.353	584	1151	1	chr2B.!!$R1	567
11	TraesCS7B01G014600	chr5D	114516315	114518278	1963	False	2778	2778	92.288	588	2550	1	chr5D.!!$F2	1962
12	TraesCS7B01G014600	chr5D	486727268	486728530	1262	True	1605	1605	89.826	588	1837	1	chr5D.!!$R1	1249
13	TraesCS7B01G014600	chr5D	32222811	32223396	585	False	939	939	95.571	1	586	1	chr5D.!!$F1	585
14	TraesCS7B01G014600	chr6D	12106192	12108135	1943	True	2774	2774	92.378	590	2550	1	chr6D.!!$R1	1960
15	TraesCS7B01G014600	chr6D	312542371	312544302	1931	True	2560	2560	90.532	588	2550	1	chr6D.!!$R2	1962
16	TraesCS7B01G014600	chr6D	269311765	269312347	582	False	937	937	95.719	5	586	1	chr6D.!!$F1	581
17	TraesCS7B01G014600	chr6D	370319612	370320198	586	True	933	933	95.408	1	586	1	chr6D.!!$R3	585
18	TraesCS7B01G014600	chr4B	251255863	251257799	1936	False	2736	2736	92.085	590	2550	1	chr4B.!!$F1	1960
19	TraesCS7B01G014600	chr4B	454679644	454680230	586	False	972	972	96.599	1	586	1	chr4B.!!$F2	585
20	TraesCS7B01G014600	chr4D	50776934	50778851	1917	False	2658	2658	91.544	588	2550	1	chr4D.!!$F1	1962
21	TraesCS7B01G014600	chr4A	616373911	616375624	1713	False	2174	2174	89.703	584	2304	1	chr4A.!!$F1	1720
22	TraesCS7B01G014600	chr6B	231240155	231240741	586	False	939	939	95.578	1	586	1	chr6B.!!$F1	585
23	TraesCS7B01G014600	chr6B	580167143	580167728	585	True	939	939	95.578	1	586	1	chr6B.!!$R1	585
24	TraesCS7B01G014600	chrUn	110636347	110636965	618	False	699	699	87.200	583	1200	1	chrUn.!!$F1	617

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
869	887	1.519408	ATAAGCGGGTGACACACAAC	58.481	50.0	8.88	0.0	35.86	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2184	2399	2.497092	CGGTCATGCGTTCGAGTCG	61.497	63.158	6.09	6.09	0.0	4.18	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
30	31	5.471456	CCTAATGATATGCCTTTGTCCACTC	59.529	44.000	0.00	0.00	0.00	3.51
31	32	3.281727	TGATATGCCTTTGTCCACTCC	57.718	47.619	0.00	0.00	0.00	3.85
87	88	9.454859	TGAATTTTGTTGGTAGGAACAATTTTT	57.545	25.926	0.00	0.00	43.56	1.94
108	109	3.427161	GGTAACAACGCGTATAGAGGT	57.573	47.619	14.46	1.33	0.00	3.85
148	149	9.495572	GGTCATTTCCTAGTAATTCCTCTAATG	57.504	37.037	0.00	0.00	0.00	1.90
288	293	9.428097	GGAAAAATTGCTTAAGATTGATGAGTT	57.572	29.630	6.67	0.00	0.00	3.01
294	299	6.179756	TGCTTAAGATTGATGAGTTGGCTAA	58.820	36.000	6.67	0.00	0.00	3.09
323	328	8.258007	ACGTGGATAGAATTTCTCTTGATGTTA	58.742	33.333	1.27	0.00	35.41	2.41
586	591	7.873505	ACTGGAGATGAGTCAACTTTAGTTAAC	59.126	37.037	4.21	0.00	36.32	2.01
654	659	1.742761	CCCTCAGATGCGAATTGTGT	58.257	50.000	0.00	0.00	0.00	3.72
656	661	3.270027	CCCTCAGATGCGAATTGTGTTA	58.730	45.455	0.00	0.00	0.00	2.41
869	887	1.519408	ATAAGCGGGTGACACACAAC	58.481	50.000	8.88	0.00	35.86	3.32
871	889	3.645975	GCGGGTGACACACAACGG	61.646	66.667	8.88	0.00	37.02	4.44
872	890	3.645975	CGGGTGACACACAACGGC	61.646	66.667	8.88	0.00	37.02	5.68
873	891	3.645975	GGGTGACACACAACGGCG	61.646	66.667	4.80	4.80	37.02	6.46
874	892	3.645975	GGTGACACACAACGGCGG	61.646	66.667	13.24	0.00	35.86	6.13
875	893	2.893404	GTGACACACAACGGCGGT	60.893	61.111	13.24	0.00	34.08	5.68
876	894	2.892914	TGACACACAACGGCGGTG	60.893	61.111	25.44	25.44	41.95	4.94
877	895	2.586635	GACACACAACGGCGGTGA	60.587	61.111	34.02	0.00	39.53	4.02
878	896	2.877974	GACACACAACGGCGGTGAC	61.878	63.158	34.02	15.73	39.53	3.67
879	897	3.645975	CACACAACGGCGGTGACC	61.646	66.667	34.02	0.00	39.53	4.02
880	898	4.164087	ACACAACGGCGGTGACCA	62.164	61.111	34.02	0.00	39.53	4.02
957	1126	2.512515	CGGTGGGAAGCTAGCTGC	60.513	66.667	20.16	17.54	43.29	5.25
1166	1356	2.235155	TGTGCAGCGAGAATAGGGTAAA	59.765	45.455	0.00	0.00	0.00	2.01
1183	1373	2.785540	AAAAATCGGGGCAATTGCAT	57.214	40.000	30.32	13.52	44.36	3.96
1263	1453	3.318839	TGACATGCTTCTTTCTTTGGGTG	59.681	43.478	0.00	0.00	0.00	4.61
1270	1460	3.243359	TCTTTCTTTGGGTGGATGCTT	57.757	42.857	0.00	0.00	0.00	3.91
1284	1474	2.165998	GATGCTTTGGCCAAGACTCTT	58.834	47.619	19.48	7.27	37.74	2.85
1285	1475	2.949177	TGCTTTGGCCAAGACTCTTA	57.051	45.000	19.48	0.30	37.74	2.10
1510	1703	5.772004	TGGGCATTTGTAGGTATGGTAATT	58.228	37.500	0.00	0.00	0.00	1.40
1516	1709	7.012894	GCATTTGTAGGTATGGTAATTGCACTA	59.987	37.037	0.00	0.00	31.59	2.74
1618	1812	9.411189	ACCTAGTTTAAATGTTGGTCAAAGTTA	57.589	29.630	0.00	0.00	0.00	2.24
1837	2044	3.583228	TCTAATTAGGCCCATTCGAGGA	58.417	45.455	12.54	0.00	0.00	3.71
1868	2077	5.122554	TGCGTGTTTTTCTGTTTCTGTTCTA	59.877	36.000	0.00	0.00	0.00	2.10
1915	2124	5.596836	ATGCTGAAACTTTTTGTGGAAGA	57.403	34.783	0.00	0.00	0.00	2.87
2060	2272	1.999648	TGGAAAATGTGCCTCAGCTT	58.000	45.000	0.00	0.00	40.80	3.74
2184	2399	3.605013	AAAAATTGGTTCGGCAGGC	57.395	47.368	0.00	0.00	0.00	4.85
2230	2445	1.670083	GTGGCGTTTAGGGCTTCGT	60.670	57.895	0.00	0.00	0.00	3.85
2308	2525	4.495422	ACATAGTGAGACCGTGAATGTTC	58.505	43.478	0.00	0.00	0.00	3.18
2416	2648	3.826524	TGATTTTGGTTAGAGTGGCACA	58.173	40.909	21.41	0.00	0.00	4.57
2532	2771	4.141620	GGCATCTCACTCCCTCTGATTTTA	60.142	45.833	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
87	88	2.754552	ACCTCTATACGCGTTGTTACCA	59.245	45.455	20.78	0.00	0.00	3.25
288	293	5.353394	AATTCTATCCACGTTCTTAGCCA	57.647	39.130	0.00	0.00	0.00	4.75
294	299	6.936279	TCAAGAGAAATTCTATCCACGTTCT	58.064	36.000	0.00	0.00	34.14	3.01
499	504	7.770801	TTTAATAGGAGTCACATCAATCACG	57.229	36.000	0.00	0.00	0.00	4.35
533	538	8.746530	CCCATCTTTATCAAGATTCATATTGGG	58.253	37.037	7.50	7.50	46.07	4.12
586	591	4.800023	AGGGGAAAAGGATAATTAACCCG	58.200	43.478	8.09	0.00	40.52	5.28
654	659	4.340617	CATGGACTAGGGGCAAAACTTAA	58.659	43.478	0.00	0.00	0.00	1.85
656	661	2.807676	CATGGACTAGGGGCAAAACTT	58.192	47.619	0.00	0.00	0.00	2.66
872	890	4.429212	TCATCGCCGTGGTCACCG	62.429	66.667	0.00	0.00	0.00	4.94
873	891	2.813908	GTCATCGCCGTGGTCACC	60.814	66.667	0.00	0.00	0.00	4.02
874	892	2.813908	GGTCATCGCCGTGGTCAC	60.814	66.667	0.00	0.00	0.00	3.67
875	893	3.307108	TGGTCATCGCCGTGGTCA	61.307	61.111	0.00	0.00	0.00	4.02
876	894	2.813908	GTGGTCATCGCCGTGGTC	60.814	66.667	0.00	0.00	0.00	4.02
877	895	4.735132	CGTGGTCATCGCCGTGGT	62.735	66.667	0.00	0.00	0.00	4.16
886	904	1.938657	CTCTCTGTCGCCGTGGTCAT	61.939	60.000	0.00	0.00	0.00	3.06
1091	1262	0.466963	AGAAACCCTCCGAACAACGT	59.533	50.000	0.00	0.00	40.78	3.99
1166	1356	1.193323	TGATGCAATTGCCCCGATTT	58.807	45.000	26.94	3.74	41.18	2.17
1183	1373	1.553248	AGATCCCGACCACGAAAATGA	59.447	47.619	0.00	0.00	42.66	2.57
1263	1453	0.813821	GAGTCTTGGCCAAAGCATCC	59.186	55.000	20.91	3.18	42.56	3.51
1270	1460	5.569355	TCATTCATTAAGAGTCTTGGCCAA	58.431	37.500	19.25	19.25	0.00	4.52
1284	1474	5.706833	TGCTCTTCTTGCAGTTCATTCATTA	59.293	36.000	0.00	0.00	35.31	1.90
1285	1475	4.521639	TGCTCTTCTTGCAGTTCATTCATT	59.478	37.500	0.00	0.00	35.31	2.57
1411	1601	4.748892	TCTTCTTCAACATCCTAAGCTCG	58.251	43.478	0.00	0.00	0.00	5.03
1466	1659	5.641636	CCCAAAAGTATTTGCAAATGGGTAC	59.358	40.000	30.43	21.21	43.11	3.34
1510	1703	7.711846	ACATTTTCAACATTACAACTAGTGCA	58.288	30.769	0.00	0.00	0.00	4.57
1633	1833	7.410120	AAATGTTGGTCACTTCTTCTTCTTT	57.590	32.000	0.00	0.00	0.00	2.52
1634	1834	8.519799	TTAAATGTTGGTCACTTCTTCTTCTT	57.480	30.769	0.00	0.00	0.00	2.52
1635	1835	8.519799	TTTAAATGTTGGTCACTTCTTCTTCT	57.480	30.769	0.00	0.00	0.00	2.85
1705	1909	5.250235	CAGAGAGCTGCATTTCATTGATT	57.750	39.130	1.02	0.00	34.95	2.57
1799	2006	2.761786	AGATGCAGTTGGCCCATTAT	57.238	45.000	0.00	0.00	43.89	1.28
1837	2044	4.900635	ACAGAAAAACACGCAAGAGAAT	57.099	36.364	0.00	0.00	43.62	2.40
1915	2124	8.980596	TGTTTGGCTCTGGAATAATTCAATTAT	58.019	29.630	0.00	0.00	37.05	1.28
2028	2240	5.931146	GCACATTTTCCATGACATTTTGGTA	59.069	36.000	0.00	0.00	34.48	3.25
2060	2272	3.071892	CACCAGGTGTAAACCTCTACCAA	59.928	47.826	11.99	0.00	38.22	3.67
2141	2354	5.304101	TGTGCATTCTACACCCTTCATTTTT	59.696	36.000	0.00	0.00	37.22	1.94
2176	2391	4.415332	GTTCGAGTCGCCTGCCGA	62.415	66.667	7.92	0.00	45.15	5.54
2184	2399	2.497092	CGGTCATGCGTTCGAGTCG	61.497	63.158	6.09	6.09	0.00	4.18
2230	2445	3.197766	CCATCTGTCCTAGCAGTTACCAA	59.802	47.826	0.00	0.00	37.70	3.67
2416	2648	2.916934	TGCCACTCTAACCCTAAACCAT	59.083	45.455	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.