AutoCloner

Multiple sequence alignment - TraesCS1B01G018800

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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	TraesCS1B01G018800	chr1B	100.000	3096	0	0	1	3096	8916761	8919856	0.000000e+00	5718.0
1	TraesCS1B01G018800	chr1B	92.872	2918	139	33	216	3096	9262109	9259224	0.000000e+00	4172.0
2	TraesCS1B01G018800	chr1B	94.907	216	11	0	1	216	9262547	9262332	3.820000e-89	339.0
3	TraesCS1B01G018800	chr1B	76.546	469	87	16	901	1362	8915939	8915487	5.160000e-58	235.0
4	TraesCS1B01G018800	chr1D	90.641	1357	103	14	838	2174	6787756	6786404	0.000000e+00	1781.0
5	TraesCS1B01G018800	chr1D	78.652	534	40	33	1	468	6788692	6788167	1.400000e-73	287.0
6	TraesCS1B01G018800	chr1D	87.368	190	12	4	484	666	6788179	6787995	1.130000e-49	207.0
7	TraesCS1B01G018800	chr1D	97.561	41	1	0	2511	2551	34276718	34276758	1.540000e-08	71.3
8	TraesCS1B01G018800	chr1A	89.851	1340	109	17	838	2154	8292782	8291447	0.000000e+00	1696.0
9	TraesCS1B01G018800	chr1A	91.489	47	4	0	2166	2212	23427002	23426956	7.170000e-07	65.8
10	TraesCS1B01G018800	chr2A	79.580	524	79	19	848	1363	12287755	12288258	1.770000e-92	350.0
11	TraesCS1B01G018800	chr2D	79.238	525	79	20	848	1363	11774722	11775225	3.820000e-89	339.0
12	TraesCS1B01G018800	chr2B	79.087	526	76	22	848	1362	18178544	18178042	6.400000e-87	331.0
13	TraesCS1B01G018800	chr2B	91.489	47	3	1	2511	2556	625846493	625846539	2.580000e-06	63.9
14	TraesCS1B01G018800	chr2B	89.796	49	2	3	2162	2209	7900567	7900613	3.330000e-05	60.2
15	TraesCS1B01G018800	chr6A	90.566	53	4	1	2166	2217	579400160	579400108	5.540000e-08	69.4
16	TraesCS1B01G018800	chr6A	87.500	56	5	2	2511	2565	373223308	373223362	2.580000e-06	63.9
17	TraesCS1B01G018800	chr6D	95.122	41	2	0	2511	2551	265784571	265784531	7.170000e-07	65.8
18	TraesCS1B01G018800	chr6D	87.037	54	7	0	2511	2564	114596560	114596613	9.270000e-06	62.1
19	TraesCS1B01G018800	chr6B	93.182	44	3	0	2166	2209	127605805	127605848	7.170000e-07	65.8
20	TraesCS1B01G018800	chr6B	88.235	51	6	0	2159	2209	298288232	298288282	9.270000e-06	62.1
21	TraesCS1B01G018800	chr5A	90.196	51	3	1	2162	2212	688843144	688843096	7.170000e-07	65.8
22	TraesCS1B01G018800	chr7D	91.304	46	4	0	2172	2217	6767679	6767724	2.580000e-06	63.9
23	TraesCS1B01G018800	chr5B	91.489	47	3	1	2511	2556	122558745	122558699	2.580000e-06	63.9
24	TraesCS1B01G018800	chr3B	91.489	47	3	1	2511	2556	207755610	207755656	2.580000e-06	63.9
25	TraesCS1B01G018800	chr4A	85.965	57	7	1	2511	2566	148234956	148235012	3.330000e-05	60.2
26	TraesCS1B01G018800	chr3A	84.615	65	5	4	2173	2232	513027122	513027186	3.330000e-05	60.2

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	TraesCS1B01G018800	chr1B	8916761	8919856	3095	False	5718.000000	5718	100.000000	1	3096	1	chr1B.!!$F1	3095
1	TraesCS1B01G018800	chr1B	9259224	9262547	3323	True	2255.500000	4172	93.889500	1	3096	2	chr1B.!!$R2	3095
2	TraesCS1B01G018800	chr1D	6786404	6788692	2288	True	758.333333	1781	85.553667	1	2174	3	chr1D.!!$R1	2173
3	TraesCS1B01G018800	chr1A	8291447	8292782	1335	True	1696.000000	1696	89.851000	838	2154	1	chr1A.!!$R1	1316
4	TraesCS1B01G018800	chr2A	12287755	12288258	503	False	350.000000	350	79.580000	848	1363	1	chr2A.!!$F1	515
5	TraesCS1B01G018800	chr2D	11774722	11775225	503	False	339.000000	339	79.238000	848	1363	1	chr2D.!!$F1	515
6	TraesCS1B01G018800	chr2B	18178042	18178544	502	True	331.000000	331	79.087000	848	1362	1	chr2B.!!$R1	514

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
51	52	1.009335	GTTGGCGGTGAAAACGACC	60.009	57.895	0.0	0.0	38.97	4.79	F
1574	2025	0.250467	GCAGTTCCTCAAGGACAGCA	60.250	55.000	0.0	0.0	45.39	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1780	2231	0.042581	TGTGGAGGTAGAGGATGCCA	59.957	55.0	0.0	0.0	35.79	4.92	R
2566	3021	0.036388	TCCAGGCCGATGTCAGTTTC	60.036	55.0	0.0	0.0	0.00	2.78	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
51	52	1.009335	GTTGGCGGTGAAAACGACC	60.009	57.895	0.00	0.00	38.97	4.79
54	55	2.181521	GGCGGTGAAAACGACCACA	61.182	57.895	0.00	0.00	35.13	4.17
77	78	8.926710	CACAAGAGAAGAAACGAAGTGTATATT	58.073	33.333	0.00	0.00	45.00	1.28
85	86	7.327975	AGAAACGAAGTGTATATTCATGGTCA	58.672	34.615	0.00	0.00	45.00	4.02
108	112	4.471904	TGAAGCTTTCATCGGTCATACT	57.528	40.909	0.00	0.00	34.08	2.12
110	114	4.081697	TGAAGCTTTCATCGGTCATACTCA	60.082	41.667	0.00	0.00	34.08	3.41
141	170	1.606994	GCACAATGGAGGTGTCACGTA	60.607	52.381	0.00	0.00	38.51	3.57
515	804	4.695455	CCCTACTGTAGTCAACACAATTGG	59.305	45.833	10.83	1.35	33.45	3.16
625	920	4.813235	TGCTATGGCGGGGGCAAC	62.813	66.667	0.00	0.00	42.43	4.17
1215	1610	3.681835	GAGACGGTGCCGGTGTCT	61.682	66.667	16.90	16.90	45.18	3.41
1218	1613	2.599578	ACGGTGCCGGTGTCTAGT	60.600	61.111	15.44	0.00	44.69	2.57
1317	1712	4.933064	GAGATCGCCGGCGTCCTG	62.933	72.222	44.16	20.39	40.74	3.86
1411	1806	5.215160	GCCATTAACACTTCAAACACTCTG	58.785	41.667	0.00	0.00	0.00	3.35
1413	1808	5.221028	CCATTAACACTTCAAACACTCTGCA	60.221	40.000	0.00	0.00	0.00	4.41
1414	1809	3.764885	AACACTTCAAACACTCTGCAC	57.235	42.857	0.00	0.00	0.00	4.57
1415	1810	2.991250	ACACTTCAAACACTCTGCACT	58.009	42.857	0.00	0.00	0.00	4.40
1416	1811	2.679837	ACACTTCAAACACTCTGCACTG	59.320	45.455	0.00	0.00	0.00	3.66
1419	1814	3.375299	ACTTCAAACACTCTGCACTGTTC	59.625	43.478	1.20	0.00	30.11	3.18
1433	1828	2.295349	CACTGTTCCATGCTCTGCTTTT	59.705	45.455	0.00	0.00	0.00	2.27
1434	1829	3.503363	CACTGTTCCATGCTCTGCTTTTA	59.497	43.478	0.00	0.00	0.00	1.52
1435	1830	4.022935	CACTGTTCCATGCTCTGCTTTTAA	60.023	41.667	0.00	0.00	0.00	1.52
1439	1834	3.754965	TCCATGCTCTGCTTTTAACTGT	58.245	40.909	0.00	0.00	0.00	3.55
1443	1838	5.412594	CCATGCTCTGCTTTTAACTGTTCTA	59.587	40.000	0.00	0.00	0.00	2.10
1452	1859	7.272978	TGCTTTTAACTGTTCTACTCTGTTCT	58.727	34.615	0.00	0.00	0.00	3.01
1484	1932	4.397730	TGCTTTAACTGCTCTGTTTTGTCA	59.602	37.500	0.00	0.00	0.00	3.58
1574	2025	0.250467	GCAGTTCCTCAAGGACAGCA	60.250	55.000	0.00	0.00	45.39	4.41
1591	2042	4.268939	ACCAACGACCGCGACGAA	62.269	61.111	26.02	0.00	41.64	3.85
1600	2051	1.028330	ACCGCGACGAAGAGTATGGA	61.028	55.000	8.23	0.00	0.00	3.41
1616	2067	2.973899	GAGGCAGCCTCGAGAACA	59.026	61.111	26.09	0.00	41.08	3.18
1629	2080	2.665185	GAACAGGTGCCGCTTCGT	60.665	61.111	0.00	0.00	0.00	3.85
1633	2084	4.626081	AGGTGCCGCTTCGTGCTT	62.626	61.111	0.00	0.00	40.11	3.91
1699	2150	4.516195	GTCCGCCTCTCGCCCTTC	62.516	72.222	0.00	0.00	36.73	3.46
1762	2213	1.304381	GCTCCTCATGGCCACCAAA	60.304	57.895	8.16	0.00	36.95	3.28
1769	2220	1.039068	CATGGCCACCAAACTCAACA	58.961	50.000	8.16	0.00	36.95	3.33
1770	2221	1.411977	CATGGCCACCAAACTCAACAA	59.588	47.619	8.16	0.00	36.95	2.83
1780	2231	1.974973	AACTCAACAACGTCCCCGGT	61.975	55.000	0.00	0.00	38.78	5.28
1861	2312	4.697756	CCGAAGAGGTTGCGGCCA	62.698	66.667	2.24	0.00	38.46	5.36
1930	2384	1.203701	AGGGAGGGGAATAAGGTGGTT	60.204	52.381	0.00	0.00	0.00	3.67
1986	2440	0.743345	CTTTTCCTAGCGAACCCGGG	60.743	60.000	22.25	22.25	36.06	5.73
2059	2513	1.664321	CCTTCTACACCTCCGACCCG	61.664	65.000	0.00	0.00	0.00	5.28
2160	2615	6.814644	TCCAGTACATATAGTTTCACCAAACG	59.185	38.462	0.00	0.00	45.81	3.60
2178	2633	8.508875	CACCAAACGTTTAAAATATGTACTCCT	58.491	33.333	14.20	0.00	0.00	3.69
2185	2640	6.913873	TTAAAATATGTACTCCTGCCGTTC	57.086	37.500	0.00	0.00	0.00	3.95
2196	2651	5.855045	ACTCCTGCCGTTCCTAAATATAAG	58.145	41.667	0.00	0.00	0.00	1.73
2334	2789	3.019564	CAAAAGGATTGGATCGGAGCTT	58.980	45.455	0.00	0.00	0.00	3.74
2392	2847	6.146601	ACGAATAGGAGGAAGTTTAGCTAC	57.853	41.667	0.00	0.00	0.00	3.58
2485	2940	4.843147	TCACTCTACAAACATTTTGTGCG	58.157	39.130	13.35	5.80	34.11	5.34
2491	2946	6.960468	TCTACAAACATTTTGTGCGTATTCA	58.040	32.000	13.35	0.00	34.11	2.57
2526	2981	2.094390	TGCATTCAATTGCTTCTGCTCC	60.094	45.455	16.66	0.00	43.18	4.70
2541	2996	1.626321	TGCTCCTCGTTGGGTTTGATA	59.374	47.619	0.00	0.00	36.20	2.15
2548	3003	5.246656	TCCTCGTTGGGTTTGATACTCTTAA	59.753	40.000	0.00	0.00	36.20	1.85
2584	3040	0.036010	AGAAACTGACATCGGCCTGG	60.036	55.000	0.00	0.00	0.00	4.45
2637	3093	2.662070	CGAAAGCCGGGAAGGGGTA	61.662	63.158	2.18	0.00	41.48	3.69
2648	3104	2.386779	GGAAGGGGTAGGAGAGTACAC	58.613	57.143	0.00	0.00	0.00	2.90
2716	3172	1.271054	ACTCCAGTCATGAAGGTGCAC	60.271	52.381	8.80	8.80	0.00	4.57
2766	3222	3.001634	CCGTAGCATGATGTTGTTAGCAG	59.998	47.826	0.00	0.00	0.00	4.24
2804	3260	4.808364	GTCAATGTGAGTAAGATGAGGAGC	59.192	45.833	0.00	0.00	0.00	4.70
2819	3275	2.567615	GAGGAGCAAGGTCTAGGTTCAA	59.432	50.000	0.00	0.00	0.00	2.69
2841	3297	1.755380	GAAGAGGCGCTTAGAACCCTA	59.245	52.381	7.64	0.00	36.83	3.53
2853	3309	1.565759	AGAACCCTAGCAATGATGGCA	59.434	47.619	0.00	0.00	0.00	4.92
2879	3335	5.221581	TGTGGTGAAGAGTAGGAGGTAAAAC	60.222	44.000	0.00	0.00	0.00	2.43
2882	3338	4.930405	GTGAAGAGTAGGAGGTAAAACAGC	59.070	45.833	0.00	0.00	0.00	4.40
2887	3343	4.104831	AGTAGGAGGTAAAACAGCAGGAT	58.895	43.478	0.00	0.00	0.00	3.24
2915	3371	4.472691	TGCAAGATTTTCAGTCGAGTTG	57.527	40.909	0.00	0.00	0.00	3.16
2981	3437	6.297080	TGGCATACAAACATTGGATTTCAT	57.703	33.333	0.00	0.00	29.73	2.57
2982	3438	7.415592	TGGCATACAAACATTGGATTTCATA	57.584	32.000	0.00	0.00	29.73	2.15
3006	3462	5.222337	AGGGTGGATGGAAACACTCTTATTT	60.222	40.000	0.00	0.00	45.73	1.40
3091	3547	3.371285	GTCGGAGTGACTTTAGAAATGCC	59.629	47.826	0.00	0.00	44.58	4.40
3092	3548	3.007506	TCGGAGTGACTTTAGAAATGCCA	59.992	43.478	0.00	0.00	0.00	4.92
3093	3549	3.941483	CGGAGTGACTTTAGAAATGCCAT	59.059	43.478	0.00	0.00	0.00	4.40
3095	3551	5.584649	CGGAGTGACTTTAGAAATGCCATAA	59.415	40.000	0.00	0.00	0.00	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	6.771188	ATACACTTCGTTTCTTCTCTTGTG	57.229	37.500	0.00	0.00	0.00	3.33
54	55	9.877178	ATGAATATACACTTCGTTTCTTCTCTT	57.123	29.630	0.00	0.00	0.00	2.85
515	804	4.260170	AGATGACTTTTGAGGACTGCATC	58.740	43.478	0.00	0.00	33.08	3.91
625	920	1.419922	GCAAGCCGTACGTGATGTG	59.580	57.895	15.21	5.97	0.00	3.21
1117	1497	2.045926	GATGACAGCGCCCTTGGT	60.046	61.111	2.29	0.00	0.00	3.67
1198	1593	2.267681	CTAGACACCGGCACCGTCTC	62.268	65.000	16.86	0.00	40.41	3.36
1199	1594	2.282674	TAGACACCGGCACCGTCT	60.283	61.111	17.34	17.34	42.49	4.18
1200	1595	1.308069	TACTAGACACCGGCACCGTC	61.308	60.000	0.00	3.26	37.81	4.79
1201	1596	1.303561	TACTAGACACCGGCACCGT	60.304	57.895	0.00	0.00	37.81	4.83
1203	1598	1.514553	GGTACTAGACACCGGCACC	59.485	63.158	0.00	0.00	0.00	5.01
1315	1710	1.893786	CCCTCCTGAAGTCGTCCAG	59.106	63.158	0.00	0.00	0.00	3.86
1317	1712	2.579738	GCCCTCCTGAAGTCGTCC	59.420	66.667	0.00	0.00	0.00	4.79
1385	1780	4.336993	AGTGTTTGAAGTGTTAATGGCGAA	59.663	37.500	0.00	0.00	0.00	4.70
1416	1811	4.022849	ACAGTTAAAAGCAGAGCATGGAAC	60.023	41.667	0.00	0.00	0.00	3.62
1419	1814	4.217118	AGAACAGTTAAAAGCAGAGCATGG	59.783	41.667	0.00	0.00	0.00	3.66
1433	1828	6.436261	CACGAAGAACAGAGTAGAACAGTTA	58.564	40.000	0.00	0.00	0.00	2.24
1434	1829	5.282510	CACGAAGAACAGAGTAGAACAGTT	58.717	41.667	0.00	0.00	0.00	3.16
1435	1830	4.793353	GCACGAAGAACAGAGTAGAACAGT	60.793	45.833	0.00	0.00	0.00	3.55
1439	1834	3.821600	AGAGCACGAAGAACAGAGTAGAA	59.178	43.478	0.00	0.00	0.00	2.10
1443	1838	1.604185	GCAGAGCACGAAGAACAGAGT	60.604	52.381	0.00	0.00	0.00	3.24
1452	1859	1.531149	GCAGTTAAAGCAGAGCACGAA	59.469	47.619	0.00	0.00	0.00	3.85
1574	2025	4.268939	TTCGTCGCGGTCGTTGGT	62.269	61.111	19.63	0.00	36.96	3.67
1591	2042	2.833244	GAGGCTGCCTCCATACTCT	58.167	57.895	33.62	4.02	44.36	3.24
1600	2051	2.654079	CCTGTTCTCGAGGCTGCCT	61.654	63.158	23.64	23.64	36.03	4.75
1699	2150	1.878522	GCAGTCCATGTAGTCCGCG	60.879	63.158	0.00	0.00	0.00	6.46
1702	2153	0.460284	CGTGGCAGTCCATGTAGTCC	60.460	60.000	0.00	0.00	45.62	3.85
1749	2200	1.327303	GTTGAGTTTGGTGGCCATGA	58.673	50.000	9.72	0.00	31.53	3.07
1780	2231	0.042581	TGTGGAGGTAGAGGATGCCA	59.957	55.000	0.00	0.00	35.79	4.92
1826	2277	3.004354	TACCACCCGCCGACCATT	61.004	61.111	0.00	0.00	0.00	3.16
1861	2312	3.534056	CCGAACGCCTCCCGGTAT	61.534	66.667	0.00	0.00	36.69	2.73
1930	2384	4.051167	TCGGCGTACCCCTCTCCA	62.051	66.667	6.85	0.00	0.00	3.86
1960	2414	3.202706	GCTAGGAAAAGCCGCCCG	61.203	66.667	0.00	0.00	43.43	6.13
1986	2440	1.443802	CTCAAACCTCTTCGGAAGGC	58.556	55.000	17.19	0.00	36.31	4.35
2160	2615	6.673154	ACGGCAGGAGTACATATTTTAAAC	57.327	37.500	0.00	0.00	0.00	2.01
2178	2633	5.881923	AGGTCTTATATTTAGGAACGGCA	57.118	39.130	0.00	0.00	0.00	5.69
2334	2789	9.760926	AGATATCATACATTAAGGAGACAGCTA	57.239	33.333	5.32	0.00	0.00	3.32
2370	2825	5.302313	AGGTAGCTAAACTTCCTCCTATTCG	59.698	44.000	0.00	0.00	42.18	3.34
2375	2830	4.844655	TCAAAGGTAGCTAAACTTCCTCCT	59.155	41.667	11.19	1.61	44.91	3.69
2392	2847	9.546428	AAGTTCAAAGTAATCCAAATTCAAAGG	57.454	29.630	0.00	0.00	0.00	3.11
2468	2923	6.634837	TGTGAATACGCACAAAATGTTTGTAG	59.365	34.615	6.07	6.52	45.08	2.74
2485	2940	6.194796	TGCAAGGAAAATAGCTGTGAATAC	57.805	37.500	0.00	0.00	0.00	1.89
2491	2946	5.726980	TTGAATGCAAGGAAAATAGCTGT	57.273	34.783	0.00	0.00	0.00	4.40
2526	2981	7.611213	AATTAAGAGTATCAAACCCAACGAG	57.389	36.000	0.00	0.00	37.82	4.18
2541	2996	9.944376	TCTATAGCACTGTTCAAAATTAAGAGT	57.056	29.630	0.00	0.00	31.17	3.24
2548	3003	8.507249	GTCAGTTTCTATAGCACTGTTCAAAAT	58.493	33.333	21.95	3.65	39.24	1.82
2566	3021	0.036388	TCCAGGCCGATGTCAGTTTC	60.036	55.000	0.00	0.00	0.00	2.78
2637	3093	6.235231	TCAAAACTTTCTGTGTACTCTCCT	57.765	37.500	0.00	0.00	0.00	3.69
2716	3172	0.806868	ATGCACGAATGGTCAAGCTG	59.193	50.000	0.00	0.00	0.00	4.24
2724	3180	2.609459	GGTCTAACAGATGCACGAATGG	59.391	50.000	0.00	0.00	0.00	3.16
2766	3222	1.231958	TTGACGAACATGAACCGGGC	61.232	55.000	6.32	0.00	0.00	6.13
2804	3260	4.238514	CTCTTCGTTGAACCTAGACCTTG	58.761	47.826	0.00	0.00	0.00	3.61
2819	3275	0.108756	GGTTCTAAGCGCCTCTTCGT	60.109	55.000	2.29	0.00	36.25	3.85
2841	3297	0.251474	ACCACACTGCCATCATTGCT	60.251	50.000	0.00	0.00	0.00	3.91
2853	3309	2.158295	ACCTCCTACTCTTCACCACACT	60.158	50.000	0.00	0.00	0.00	3.55
2879	3335	4.707030	TCTTGCAACAAATATCCTGCTG	57.293	40.909	0.00	0.00	35.78	4.41
2882	3338	7.816031	ACTGAAAATCTTGCAACAAATATCCTG	59.184	33.333	0.00	0.00	0.00	3.86
2887	3343	6.964908	TCGACTGAAAATCTTGCAACAAATA	58.035	32.000	0.00	0.00	0.00	1.40
2981	3437	2.915869	AGAGTGTTTCCATCCACCCTA	58.084	47.619	0.00	0.00	31.88	3.53
2982	3438	1.747444	AGAGTGTTTCCATCCACCCT	58.253	50.000	0.00	0.00	31.88	4.34
3057	3513	2.623416	TCACTCCGACTATACTGCCATG	59.377	50.000	0.00	0.00	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.