AutoCloner

Multiple sequence alignment - TraesCS3D01G126900

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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	TraesCS3D01G126900	chr3D	100.000	2801	0	0	1	2801	84694097	84691297	0.000000e+00	5173.0
1	TraesCS3D01G126900	chr3D	82.517	429	68	7	2364	2791	420058472	420058894	1.230000e-98	370.0
2	TraesCS3D01G126900	chr3D	76.433	628	101	28	1	590	84879908	84880526	2.110000e-76	296.0
3	TraesCS3D01G126900	chr3D	78.832	411	80	6	2364	2772	581192886	581193291	1.280000e-68	270.0
4	TraesCS3D01G126900	chr3D	100.000	30	0	0	267	296	23052863	23052834	3.900000e-04	56.5
5	TraesCS3D01G126900	chr3A	93.853	1334	47	11	596	1919	101332777	101331469	0.000000e+00	1977.0
6	TraesCS3D01G126900	chr3A	90.802	511	45	2	2291	2800	101317036	101316527	0.000000e+00	682.0
7	TraesCS3D01G126900	chr3A	90.196	255	12	7	2046	2287	101317380	101317126	1.250000e-83	320.0
8	TraesCS3D01G126900	chr3A	94.545	110	5	1	1915	2023	101325067	101324958	4.800000e-38	169.0
9	TraesCS3D01G126900	chr3A	96.429	56	2	0	2	57	101333906	101333851	2.970000e-15	93.5
10	TraesCS3D01G126900	chr3B	94.363	1153	31	15	750	1901	133373095	133371976	0.000000e+00	1738.0
11	TraesCS3D01G126900	chr3B	93.151	511	35	0	2290	2800	133367613	133367103	0.000000e+00	750.0
12	TraesCS3D01G126900	chr3B	85.064	549	50	8	1	545	133378431	133377911	5.310000e-147	531.0
13	TraesCS3D01G126900	chr3B	91.176	272	14	6	2026	2287	133367983	133367712	7.380000e-96	361.0
14	TraesCS3D01G126900	chr3B	91.538	130	10	1	1894	2023	133368285	133368157	7.970000e-41	178.0
15	TraesCS3D01G126900	chr5B	82.599	431	74	1	2365	2795	245011235	245011664	2.040000e-101	379.0
16	TraesCS3D01G126900	chr5B	93.333	60	3	1	1417	1476	15682595	15682653	1.380000e-13	87.9
17	TraesCS3D01G126900	chr5A	82.028	434	72	5	2364	2797	300909993	300909566	5.700000e-97	364.0
18	TraesCS3D01G126900	chr7A	95.775	142	6	0	1201	1342	3945874	3946015	2.170000e-56	230.0
19	TraesCS3D01G126900	chr7A	74.474	333	50	26	239	551	731010936	731010619	8.200000e-21	111.0
20	TraesCS3D01G126900	chr2A	92.174	115	9	0	1260	1374	734773853	734773967	2.230000e-36	163.0
21	TraesCS3D01G126900	chr2B	85.915	142	20	0	2658	2799	555388005	555388146	4.830000e-33	152.0
22	TraesCS3D01G126900	chr2B	83.761	117	19	0	2683	2799	555452482	555452598	8.200000e-21	111.0
23	TraesCS3D01G126900	chr2B	97.619	42	1	0	1421	1462	704751909	704751950	3.870000e-09	73.1
24	TraesCS3D01G126900	chr1B	97.619	84	2	0	1295	1378	125847820	125847737	8.090000e-31	145.0
25	TraesCS3D01G126900	chr7D	88.235	119	13	1	2590	2708	596468895	596468778	1.050000e-29	141.0
26	TraesCS3D01G126900	chr7D	82.540	126	16	6	267	386	119166934	119167059	3.820000e-19	106.0
27	TraesCS3D01G126900	chr6A	81.879	149	25	1	2611	2759	231886247	231886393	1.050000e-24	124.0
28	TraesCS3D01G126900	chr4D	93.617	47	3	0	267	313	15413427	15413473	1.390000e-08	71.3
29	TraesCS3D01G126900	chr1A	94.737	38	2	0	566	603	66329538	66329501	3.010000e-05	60.2
30	TraesCS3D01G126900	chr4A	88.000	50	3	2	280	327	547721619	547721667	3.900000e-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	TraesCS3D01G126900	chr3D	84691297	84694097	2800	True	5173.00	5173	100.000	1	2801	1	chr3D.!!$R2	2800
1	TraesCS3D01G126900	chr3D	84879908	84880526	618	False	296.00	296	76.433	1	590	1	chr3D.!!$F1	589
2	TraesCS3D01G126900	chr3A	101331469	101333906	2437	True	1035.25	1977	95.141	2	1919	2	chr3A.!!$R3	1917
3	TraesCS3D01G126900	chr3A	101316527	101317380	853	True	501.00	682	90.499	2046	2800	2	chr3A.!!$R2	754
4	TraesCS3D01G126900	chr3B	133367103	133373095	5992	True	756.75	1738	92.557	750	2800	4	chr3B.!!$R2	2050
5	TraesCS3D01G126900	chr3B	133377911	133378431	520	True	531.00	531	85.064	1	545	1	chr3B.!!$R1	544

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
641	1231	1.615107	CGCGAAAAGACAGACGGGAC	61.615	60.0	0.0	0.0	40.15	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2227	6708	0.107312	GCATCACCTCTGTGCCTCAT	60.107	55.0	0.0	0.0	42.46	2.9	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
208	219	8.498054	TTTCATTTGTATGCAAAGGTTTTTCA	57.502	26.923	18.22	0.00	46.30	2.69
394	581	8.844441	ACAATTTCAAATGCTTGTTTTGAATG	57.156	26.923	11.15	10.14	46.63	2.67
400	594	5.754543	AATGCTTGTTTTGAATGTTTGGG	57.245	34.783	0.00	0.00	0.00	4.12
534	794	3.461773	CCTCACGATCGCCTGGGT	61.462	66.667	16.60	0.00	0.00	4.51
558	818	4.344865	ATGTCGCCCTTGCCGGTT	62.345	61.111	1.90	0.00	0.00	4.44
559	819	2.961893	ATGTCGCCCTTGCCGGTTA	61.962	57.895	1.90	0.00	0.00	2.85
608	1197	1.906574	ACATATGGTCGCCCGGATAAT	59.093	47.619	0.73	0.00	0.00	1.28
634	1223	4.445545	GCGCCCGCGAAAAGACAG	62.446	66.667	14.24	0.00	42.83	3.51
641	1231	1.615107	CGCGAAAAGACAGACGGGAC	61.615	60.000	0.00	0.00	40.15	4.46
661	1254	6.907741	GGGACGTGATTAAGTATAGTAGGAC	58.092	44.000	0.00	0.00	0.00	3.85
797	1390	7.899178	TCTGTCTTGCGTTAATTTCTGATAA	57.101	32.000	0.00	0.00	0.00	1.75
906	1499	6.095160	ACCGTTATATATTCTCATCTCGTCCC	59.905	42.308	0.00	0.00	0.00	4.46
1003	1600	1.640428	AGCACGTACGTCAATCATGG	58.360	50.000	19.94	5.81	0.00	3.66
1005	1602	0.650512	CACGTACGTCAATCATGGCC	59.349	55.000	19.94	0.00	0.00	5.36
1053	1650	4.041917	GTGCGGGTGGTCGACGTA	62.042	66.667	9.92	0.00	0.00	3.57
1476	2073	4.681978	GCGTTCCTGCGGAGGTGT	62.682	66.667	23.44	0.00	40.76	4.16
1663	2260	0.471191	TCTATACGGACTCGGAGCCA	59.529	55.000	4.58	0.00	41.39	4.75
1664	2261	1.134007	TCTATACGGACTCGGAGCCAA	60.134	52.381	4.58	0.00	41.39	4.52
1774	2371	4.081142	ACCACGATGAGGAATATGTTGTGA	60.081	41.667	0.00	0.00	0.00	3.58
1788	2385	3.096092	TGTTGTGAAAAGGTTGCTTCCT	58.904	40.909	0.00	0.00	39.84	3.36
1824	2422	3.545703	GGAACAACATGATCCGGAGAAT	58.454	45.455	11.34	2.60	29.57	2.40
1825	2423	3.313526	GGAACAACATGATCCGGAGAATG	59.686	47.826	21.74	21.74	29.57	2.67
1828	2426	2.874701	CAACATGATCCGGAGAATGACC	59.125	50.000	27.40	6.19	0.00	4.02
1831	2429	0.031111	TGATCCGGAGAATGACCCCT	60.031	55.000	11.34	0.00	0.00	4.79
1832	2430	0.394565	GATCCGGAGAATGACCCCTG	59.605	60.000	11.34	0.00	0.00	4.45
1833	2431	0.031111	ATCCGGAGAATGACCCCTGA	60.031	55.000	11.34	0.00	0.00	3.86
1834	2432	0.252513	TCCGGAGAATGACCCCTGAA	60.253	55.000	0.00	0.00	0.00	3.02
1835	2433	0.107654	CCGGAGAATGACCCCTGAAC	60.108	60.000	0.00	0.00	0.00	3.18
1836	2434	0.613260	CGGAGAATGACCCCTGAACA	59.387	55.000	0.00	0.00	0.00	3.18
1837	2435	1.676014	CGGAGAATGACCCCTGAACAC	60.676	57.143	0.00	0.00	0.00	3.32
1838	2436	1.340114	GGAGAATGACCCCTGAACACC	60.340	57.143	0.00	0.00	0.00	4.16
1839	2437	1.630878	GAGAATGACCCCTGAACACCT	59.369	52.381	0.00	0.00	0.00	4.00
1951	6247	4.022329	CAGAAAAAGCTAATTGGGGAACGT	60.022	41.667	0.00	0.00	0.00	3.99
1969	6265	6.458342	GGGAACGTCAGATATTTTTGACATCC	60.458	42.308	14.62	14.62	42.94	3.51
1972	6268	5.943416	ACGTCAGATATTTTTGACATCCCAA	59.057	36.000	7.44	0.00	42.94	4.12
1974	6270	6.268566	GTCAGATATTTTTGACATCCCAAGC	58.731	40.000	2.55	0.00	42.47	4.01
1975	6271	5.360714	TCAGATATTTTTGACATCCCAAGCC	59.639	40.000	0.00	0.00	0.00	4.35
1985	6281	1.792757	ATCCCAAGCCAACTGCCTGA	61.793	55.000	0.00	0.00	42.71	3.86
1988	6284	2.281761	AAGCCAACTGCCTGACCG	60.282	61.111	0.00	0.00	42.71	4.79
2015	6311	1.933853	GATCGGAATCACGAACCTTGG	59.066	52.381	0.00	0.00	46.92	3.61
2019	6315	2.253414	GAATCACGAACCTTGGCGCC	62.253	60.000	22.73	22.73	0.00	6.53
2023	6319	4.745751	CGAACCTTGGCGCCCGTA	62.746	66.667	26.77	8.54	0.00	4.02
2024	6320	2.358984	GAACCTTGGCGCCCGTAA	60.359	61.111	26.77	11.15	0.00	3.18
2025	6321	2.359478	AACCTTGGCGCCCGTAAG	60.359	61.111	26.77	20.58	0.00	2.34
2028	6324	3.799755	CTTGGCGCCCGTAAGCAC	61.800	66.667	26.77	0.00	34.54	4.40
2041	6509	0.036164	TAAGCACGTTGACCTGCCAT	59.964	50.000	0.00	0.00	33.57	4.40
2123	6591	1.352083	CACTCCCTGGTCTTTCTCCA	58.648	55.000	0.00	0.00	0.00	3.86
2251	6732	2.749682	ACAGAGGTGATGCGGCAA	59.250	55.556	6.82	0.00	0.00	4.52
2264	6745	0.109179	GCGGCAACATCATTGCAGAA	60.109	50.000	14.59	0.00	46.58	3.02
2362	6939	7.222611	TGTCGTATCCATTGCATGAATATATCG	59.777	37.037	0.00	0.00	0.00	2.92
2388	6965	7.977853	GCTACAAAATTTCATCCATTCAGTGAT	59.022	33.333	0.00	0.00	0.00	3.06
2403	6980	3.932710	TCAGTGATAAAAGTCATGGCGAC	59.067	43.478	0.00	0.00	45.77	5.19
2418	6995	1.522258	GGCGACGAAACAAGAAACGTA	59.478	47.619	0.00	0.00	39.04	3.57
2442	7019	6.170506	AGCCTAAAATCAACTTATGTGACGA	58.829	36.000	0.00	0.00	0.00	4.20
2466	7043	1.443872	CGTCTCGAGGTGTTTCCCG	60.444	63.158	13.56	0.00	36.75	5.14
2546	7123	0.108774	TTTGGGCATCACCACGTACA	59.891	50.000	0.00	0.00	41.03	2.90
2547	7124	0.604243	TTGGGCATCACCACGTACAC	60.604	55.000	0.00	0.00	41.03	2.90
2554	7131	2.172851	TCACCACGTACACCCATTTC	57.827	50.000	0.00	0.00	0.00	2.17
2584	7161	7.331193	AGACGATTTGTAGTGTTACTGGAAATC	59.669	37.037	12.68	12.68	35.73	2.17
2607	7184	5.830457	TCTTTGGTGTCACAATAAATGGTCA	59.170	36.000	5.12	0.00	0.00	4.02
2609	7186	4.724399	TGGTGTCACAATAAATGGTCAGT	58.276	39.130	5.12	0.00	0.00	3.41
2680	7257	5.300034	CAGTGCCTTATAATTTCTGCCATGA	59.700	40.000	0.00	0.00	0.00	3.07
2734	7311	5.711698	TCAGGGTTTAGGGTTCAAATTCTT	58.288	37.500	0.00	0.00	0.00	2.52
2736	7313	4.283467	AGGGTTTAGGGTTCAAATTCTTGC	59.717	41.667	0.00	0.00	32.14	4.01
2783	7361	5.355071	TCCGTACGTACTCATTGTAGTGAAT	59.645	40.000	22.55	0.00	0.00	2.57
2797	7375	8.820933	CATTGTAGTGAATTATGAGAACACGAT	58.179	33.333	0.00	0.00	36.71	3.73
2800	7378	8.032451	TGTAGTGAATTATGAGAACACGATCAA	58.968	33.333	0.00	0.00	36.71	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	105	6.614694	TGGCTATAAAAGTGTTCCTAGTGA	57.385	37.500	0.00	0.00	0.00	3.41
488	747	8.158132	ACAACCCCTTTTTCTGTTTTCTTTTTA	58.842	29.630	0.00	0.00	0.00	1.52
534	794	3.000819	AAGGGCGACATGGTCCGA	61.001	61.111	0.00	0.00	36.58	4.55
558	818	2.108168	AGCGAGATGTAGGGCAGTTTA	58.892	47.619	0.00	0.00	0.00	2.01
559	819	0.905357	AGCGAGATGTAGGGCAGTTT	59.095	50.000	0.00	0.00	0.00	2.66
599	1188	2.358737	GCGGCCTGATTATCCGGG	60.359	66.667	0.00	1.48	43.11	5.73
634	1223	5.429957	ACTATACTTAATCACGTCCCGTC	57.570	43.478	0.00	0.00	38.32	4.79
641	1231	7.068341	GTGTCGTCCTACTATACTTAATCACG	58.932	42.308	0.00	0.00	0.00	4.35
697	1290	8.508875	TCAACTTAATTTTTAACCACGAGATCC	58.491	33.333	0.00	0.00	0.00	3.36
965	1562	5.511571	GTGCTTAGTTTCTTGTTTCCTGAC	58.488	41.667	0.00	0.00	0.00	3.51
1003	1600	1.174712	CCGGATGATTCACCATGGGC	61.175	60.000	18.09	0.23	0.00	5.36
1005	1602	1.509644	CGCCGGATGATTCACCATGG	61.510	60.000	11.19	11.19	0.00	3.66
1053	1650	4.115199	GCCTCGTTCTGGGCCCAT	62.115	66.667	28.82	0.00	42.30	4.00
1476	2073	4.263435	ACAGTTGGGTGAAAAAGACGTTA	58.737	39.130	0.00	0.00	0.00	3.18
1485	2082	1.764134	AGGTCGTACAGTTGGGTGAAA	59.236	47.619	0.00	0.00	0.00	2.69
1489	2086	0.966920	CTCAGGTCGTACAGTTGGGT	59.033	55.000	0.00	0.00	0.00	4.51
1663	2260	0.326618	AGGAGGGGGTCATCATCGTT	60.327	55.000	0.00	0.00	0.00	3.85
1664	2261	0.760945	GAGGAGGGGGTCATCATCGT	60.761	60.000	0.00	0.00	35.93	3.73
1750	2347	4.034394	CACAACATATTCCTCATCGTGGTG	59.966	45.833	0.00	0.00	0.00	4.17
1774	2371	5.539955	ACATAATCACAGGAAGCAACCTTTT	59.460	36.000	0.00	0.00	38.32	2.27
1788	2385	5.306394	TGTTGTTCCGGTTACATAATCACA	58.694	37.500	11.86	10.10	0.00	3.58
1824	2422	1.518367	AAAGAGGTGTTCAGGGGTCA	58.482	50.000	0.00	0.00	0.00	4.02
1825	2423	2.658807	AAAAGAGGTGTTCAGGGGTC	57.341	50.000	0.00	0.00	0.00	4.46
1927	6223	4.217550	CGTTCCCCAATTAGCTTTTTCTGA	59.782	41.667	0.00	0.00	0.00	3.27
1928	6224	4.022329	ACGTTCCCCAATTAGCTTTTTCTG	60.022	41.667	0.00	0.00	0.00	3.02
1929	6225	4.149598	ACGTTCCCCAATTAGCTTTTTCT	58.850	39.130	0.00	0.00	0.00	2.52
1951	6247	5.360714	GGCTTGGGATGTCAAAAATATCTGA	59.639	40.000	0.00	0.00	0.00	3.27
2015	6311	4.439472	CAACGTGCTTACGGGCGC	62.439	66.667	0.00	0.00	39.09	6.53
2019	6315	2.150424	CAGGTCAACGTGCTTACGG	58.850	57.895	4.79	0.00	37.45	4.02
2026	6322	1.868997	GACATGGCAGGTCAACGTG	59.131	57.895	25.77	3.05	35.36	4.49
2027	6323	1.667830	CGACATGGCAGGTCAACGT	60.668	57.895	28.94	0.00	34.97	3.99
2028	6324	2.390599	CCGACATGGCAGGTCAACG	61.391	63.158	28.94	17.32	34.97	4.10
2041	6509	2.590291	ATGTGCGTGTTGCCGACA	60.590	55.556	0.00	0.00	45.60	4.35
2227	6708	0.107312	GCATCACCTCTGTGCCTCAT	60.107	55.000	0.00	0.00	42.46	2.90
2251	6732	3.005554	CCGTCTTCTTCTGCAATGATGT	58.994	45.455	0.00	0.00	0.00	3.06
2264	6745	2.579201	CACCGATGGCCGTCTTCT	59.421	61.111	22.53	1.83	36.31	2.85
2287	6768	3.313012	TTCACTATTCCACACCGTCTG	57.687	47.619	0.00	0.00	0.00	3.51
2288	6769	4.020573	TCAATTCACTATTCCACACCGTCT	60.021	41.667	0.00	0.00	0.00	4.18
2362	6939	7.315142	TCACTGAATGGATGAAATTTTGTAGC	58.685	34.615	0.00	0.00	0.00	3.58
2378	6955	5.065090	TCGCCATGACTTTTATCACTGAATG	59.935	40.000	0.00	0.00	0.00	2.67
2388	6965	3.132160	TGTTTCGTCGCCATGACTTTTA	58.868	40.909	0.00	0.00	45.87	1.52
2403	6980	4.977741	TTAGGCTACGTTTCTTGTTTCG	57.022	40.909	0.00	0.00	0.00	3.46
2418	6995	6.170506	TCGTCACATAAGTTGATTTTAGGCT	58.829	36.000	0.00	0.00	0.00	4.58
2442	7019	3.604629	CACCTCGAGACGGTGGAT	58.395	61.111	15.71	0.00	46.38	3.41
2452	7029	1.301401	CTTGCGGGAAACACCTCGA	60.301	57.895	0.00	0.00	38.98	4.04
2466	7043	4.715523	TACGGTGCTGCCCCTTGC	62.716	66.667	0.00	0.00	41.77	4.01
2546	7123	3.244911	ACAAATCGTCTCAGGAAATGGGT	60.245	43.478	0.00	0.00	0.00	4.51
2547	7124	3.347216	ACAAATCGTCTCAGGAAATGGG	58.653	45.455	0.00	0.00	0.00	4.00
2554	7131	5.573282	CAGTAACACTACAAATCGTCTCAGG	59.427	44.000	0.00	0.00	0.00	3.86
2584	7161	6.083098	TGACCATTTATTGTGACACCAAAG	57.917	37.500	2.45	0.00	0.00	2.77
2734	7311	8.568676	AAAAATGATCAATGGATTTCAATGCA	57.431	26.923	0.00	0.00	41.06	3.96
2736	7313	8.332464	CGGAAAAATGATCAATGGATTTCAATG	58.668	33.333	0.00	0.00	32.67	2.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.