AutoCloner

Multiple sequence alignment - TraesCS1B01G176900

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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	TraesCS1B01G176900	chr1B	100.000	2482	0	0	626	3107	319966853	319969334	0.000000e+00	4584
1	TraesCS1B01G176900	chr1B	100.000	236	0	0	1	236	319966228	319966463	1.320000e-118	436
2	TraesCS1B01G176900	chr2A	97.140	1888	49	4	626	2508	532490532	532488645	0.000000e+00	3182
3	TraesCS1B01G176900	chr2A	97.225	1838	45	5	676	2508	774629383	774627547	0.000000e+00	3107
4	TraesCS1B01G176900	chr2A	85.481	613	59	3	2516	3107	665834442	665835045	2.050000e-171	612
5	TraesCS1B01G176900	chr2A	83.850	613	60	8	2516	3107	665833363	665833957	5.860000e-152	547
6	TraesCS1B01G176900	chr2A	94.068	236	12	1	1	236	532491195	532490962	1.060000e-94	357
7	TraesCS1B01G176900	chr2A	92.827	237	14	3	1	236	774630136	774629902	1.070000e-89	340
8	TraesCS1B01G176900	chr2A	91.983	237	14	4	1	236	694467453	694467685	8.310000e-86	327
9	TraesCS1B01G176900	chr5A	97.225	1874	48	3	639	2508	677170233	677168360	0.000000e+00	3169
10	TraesCS1B01G176900	chr5A	96.950	1836	52	3	674	2505	616881957	616883792	0.000000e+00	3077
11	TraesCS1B01G176900	chr5A	97.034	236	6	1	1	236	677170955	677170721	2.250000e-106	396
12	TraesCS1B01G176900	chr5A	91.983	237	13	5	1	236	496046668	496046437	8.310000e-86	327
13	TraesCS1B01G176900	chr1A	97.112	1870	49	4	645	2509	527964253	527966122	0.000000e+00	3149
14	TraesCS1B01G176900	chr1A	97.281	1839	45	4	674	2507	100297923	100299761	0.000000e+00	3114
15	TraesCS1B01G176900	chr1A	92.797	236	15	1	1	236	527963389	527963622	1.070000e-89	340
16	TraesCS1B01G176900	chr3A	96.958	1841	50	5	674	2508	552219007	552217167	0.000000e+00	3085
17	TraesCS1B01G176900	chr6A	96.846	1839	52	5	674	2507	510216699	510214862	0.000000e+00	3070
18	TraesCS1B01G176900	chr6A	96.471	1842	58	6	674	2509	84963757	84961917	0.000000e+00	3035
19	TraesCS1B01G176900	chr6A	84.590	610	55	9	2519	3107	102110967	102111558	1.250000e-158	569
20	TraesCS1B01G176900	chr6A	87.185	476	54	1	2630	3105	3276389	3276857	4.560000e-148	534
21	TraesCS1B01G176900	chr7B	85.774	478	59	3	2630	3107	382730631	382731099	5.980000e-137	497
22	TraesCS1B01G176900	chr7B	92.827	237	14	3	1	236	568389574	568389808	1.070000e-89	340
23	TraesCS1B01G176900	chr5B	86.885	427	47	2	2681	3107	693116782	693117199	1.300000e-128	470
24	TraesCS1B01G176900	chr3B	82.135	459	56	11	2661	3107	367489718	367489274	1.360000e-98	370
25	TraesCS1B01G176900	chr3B	91.983	237	15	4	1	236	50936611	50936378	2.310000e-86	329
26	TraesCS1B01G176900	chr7A	94.515	237	11	1	2	236	1973306	1973070	6.330000e-97	364
27	TraesCS1B01G176900	chr2D	82.418	182	24	6	2792	2972	604701962	604701788	5.370000e-33	152
28	TraesCS1B01G176900	chr5D	90.566	106	10	0	3002	3107	127879161	127879266	1.160000e-29	141
29	TraesCS1B01G176900	chr2B	88.679	106	12	0	3002	3107	1854189	1854084	2.510000e-26	130

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	TraesCS1B01G176900	chr1B	319966228	319969334	3106	False	2510.0	4584	100.0000	1	3107	2	chr1B.!!$F1	3106
1	TraesCS1B01G176900	chr2A	532488645	532491195	2550	True	1769.5	3182	95.6040	1	2508	2	chr2A.!!$R1	2507
2	TraesCS1B01G176900	chr2A	774627547	774630136	2589	True	1723.5	3107	95.0260	1	2508	2	chr2A.!!$R2	2507
3	TraesCS1B01G176900	chr2A	665833363	665835045	1682	False	579.5	612	84.6655	2516	3107	2	chr2A.!!$F2	591
4	TraesCS1B01G176900	chr5A	616881957	616883792	1835	False	3077.0	3077	96.9500	674	2505	1	chr5A.!!$F1	1831
5	TraesCS1B01G176900	chr5A	677168360	677170955	2595	True	1782.5	3169	97.1295	1	2508	2	chr5A.!!$R2	2507
6	TraesCS1B01G176900	chr1A	100297923	100299761	1838	False	3114.0	3114	97.2810	674	2507	1	chr1A.!!$F1	1833
7	TraesCS1B01G176900	chr1A	527963389	527966122	2733	False	1744.5	3149	94.9545	1	2509	2	chr1A.!!$F2	2508
8	TraesCS1B01G176900	chr3A	552217167	552219007	1840	True	3085.0	3085	96.9580	674	2508	1	chr3A.!!$R1	1834
9	TraesCS1B01G176900	chr6A	510214862	510216699	1837	True	3070.0	3070	96.8460	674	2507	1	chr6A.!!$R2	1833
10	TraesCS1B01G176900	chr6A	84961917	84963757	1840	True	3035.0	3035	96.4710	674	2509	1	chr6A.!!$R1	1835
11	TraesCS1B01G176900	chr6A	102110967	102111558	591	False	569.0	569	84.5900	2519	3107	1	chr6A.!!$F2	588

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
902	2449	1.645034	CTCCTCATCGACGTGCAATT	58.355	50.0	0.0	0.0	0.0	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2721	4294	0.183014	TCCAGGCCTAGTAGACCGAG	59.817	60.0	3.98	0.0	0.0	4.63	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
50	51	6.456501	ACGCAAAGACTAGAACATCTAAACT	58.543	36.000	0.00	0.00	0.00	2.66
63	64	5.799213	ACATCTAAACTCTCAAACCCTCAG	58.201	41.667	0.00	0.00	0.00	3.35
98	99	3.135712	GTCCAACCCTCAAACCCAATTTT	59.864	43.478	0.00	0.00	0.00	1.82
902	2449	1.645034	CTCCTCATCGACGTGCAATT	58.355	50.000	0.00	0.00	0.00	2.32
1341	2888	2.354805	GGCACCAAACGAGGAAGATACT	60.355	50.000	0.00	0.00	0.00	2.12
1612	3160	4.541250	TTAATTTCTGGGGATGCTCCAT	57.459	40.909	4.85	0.00	38.64	3.41
1947	3495	7.699878	AGTTAAACCTCCCTTGTTTCTATGAT	58.300	34.615	0.00	0.00	37.18	2.45
2053	3601	3.147595	CTCATGGTCGGCTCCGGA	61.148	66.667	2.93	2.93	40.25	5.14
2115	3663	3.057033	GCATTGGCCCATGATGTATCTTC	60.057	47.826	20.66	0.00	0.00	2.87
2346	3895	1.351350	GGGGTTGAGGCAAAGACTAGT	59.649	52.381	0.00	0.00	0.00	2.57
2347	3896	2.427506	GGGTTGAGGCAAAGACTAGTG	58.572	52.381	0.00	0.00	0.00	2.74
2369	3918	3.580895	GCCCTCAAATCCAACCCTTAAAA	59.419	43.478	0.00	0.00	0.00	1.52
2390	3942	3.975479	TTTAAGGGTTGGGTTTGAGGA	57.025	42.857	0.00	0.00	0.00	3.71
2442	3994	5.519927	CCTTAAAAGTGTCAAAAAGTGGCAG	59.480	40.000	0.00	0.00	44.30	4.85
2459	4011	4.280929	GTGGCAGTTCTCAACCCTTAAAAT	59.719	41.667	0.00	0.00	0.00	1.82
2470	4022	4.801330	ACCCTTAAAATTGCTACAAGGC	57.199	40.909	0.00	0.00	35.46	4.35
2509	4061	6.961576	AGTTCTACTAGTAATGCTCTAAGCG	58.038	40.000	3.76	0.00	46.26	4.68
2510	4062	6.543100	AGTTCTACTAGTAATGCTCTAAGCGT	59.457	38.462	3.76	0.00	46.26	5.07
2582	4134	2.751479	CGCATTCTAGGTCCCTCTCTCT	60.751	54.545	0.00	0.00	0.00	3.10
2583	4135	2.890945	GCATTCTAGGTCCCTCTCTCTC	59.109	54.545	0.00	0.00	0.00	3.20
2587	4139	1.997256	TAGGTCCCTCTCTCTCCGCC	61.997	65.000	0.00	0.00	0.00	6.13
2645	4218	2.208132	TCGAGCAGAGGAAGAAGAGT	57.792	50.000	0.00	0.00	0.00	3.24
2646	4219	2.520069	TCGAGCAGAGGAAGAAGAGTT	58.480	47.619	0.00	0.00	0.00	3.01
2647	4220	2.230025	TCGAGCAGAGGAAGAAGAGTTG	59.770	50.000	0.00	0.00	0.00	3.16
2663	4236	1.454847	TTGTTCCGCACAAGGCCTT	60.455	52.632	13.78	13.78	40.71	4.35
2667	4240	3.365265	CCGCACAAGGCCTTGGTC	61.365	66.667	41.04	31.00	44.45	4.02
2671	4244	2.594592	ACAAGGCCTTGGTCGTGC	60.595	61.111	41.04	0.00	44.45	5.34
2708	4281	2.030562	CAAGGACGCCCGTGACTT	59.969	61.111	0.00	0.00	43.43	3.01
2710	4283	1.597027	AAGGACGCCCGTGACTTTG	60.597	57.895	0.00	0.00	37.58	2.77
2721	4294	1.228552	TGACTTTGGCCTTGGGAGC	60.229	57.895	3.32	0.00	0.00	4.70
2732	4305	1.409802	CCTTGGGAGCTCGGTCTACTA	60.410	57.143	7.83	0.00	0.00	1.82
2735	4308	1.174078	GGGAGCTCGGTCTACTAGGC	61.174	65.000	7.83	0.00	0.00	3.93
2785	4358	4.802051	CCCCCACGCCTCCACATG	62.802	72.222	0.00	0.00	0.00	3.21
2786	4359	4.802051	CCCCACGCCTCCACATGG	62.802	72.222	0.00	0.00	0.00	3.66
2787	4360	4.802051	CCCACGCCTCCACATGGG	62.802	72.222	0.00	0.00	45.79	4.00
2788	4361	4.802051	CCACGCCTCCACATGGGG	62.802	72.222	8.05	8.05	42.36	4.96
2789	4362	3.716195	CACGCCTCCACATGGGGA	61.716	66.667	17.84	17.84	38.16	4.81
2790	4363	2.933287	ACGCCTCCACATGGGGAA	60.933	61.111	19.55	1.77	38.16	3.97
2791	4364	2.124570	CGCCTCCACATGGGGAAG	60.125	66.667	19.55	13.87	38.16	3.46
2810	4383	2.115427	AGAGGAGGAAGAAGGCTTAGC	58.885	52.381	0.00	0.00	33.61	3.09
2821	4394	1.300233	GGCTTAGCGCGCTACATCT	60.300	57.895	38.48	17.21	40.44	2.90
2824	4397	0.030773	CTTAGCGCGCTACATCTCCA	59.969	55.000	38.48	21.76	0.00	3.86
2841	4414	1.839994	TCCATCAAGGCCTACTTCCTG	59.160	52.381	5.16	0.00	37.29	3.86
2843	4416	2.025887	CCATCAAGGCCTACTTCCTGTT	60.026	50.000	5.16	0.00	37.29	3.16
2871	4444	3.607209	GGTGAGTTAGAAGTTAGAACGCG	59.393	47.826	3.53	3.53	0.00	6.01
2898	4471	2.825532	GGTTGTATGCTGGGTGTTTGAT	59.174	45.455	0.00	0.00	0.00	2.57
2906	4479	4.406456	TGCTGGGTGTTTGATGATAGTTT	58.594	39.130	0.00	0.00	0.00	2.66
2913	4486	5.634859	GGTGTTTGATGATAGTTTTGCAAGG	59.365	40.000	0.00	0.00	0.00	3.61
2916	4489	7.437862	GTGTTTGATGATAGTTTTGCAAGGAAA	59.562	33.333	0.00	0.00	0.00	3.13
2973	4546	2.819595	CATTGTCGTGGGAGGCCG	60.820	66.667	0.00	0.00	0.00	6.13
2974	4547	4.778143	ATTGTCGTGGGAGGCCGC	62.778	66.667	0.00	0.00	0.00	6.53
3007	5668	3.064931	GACGAGGAATGAAAAACGACCT	58.935	45.455	0.00	0.00	0.00	3.85
3052	5713	0.739462	TTTACAGCATGGGAGCGACG	60.739	55.000	0.00	0.00	43.62	5.12
3088	5749	4.382254	CCACCTGGTCGCTAAACTACATTA	60.382	45.833	0.00	0.00	0.00	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	6.456501	AGTTTAGATGTTCTAGTCTTTGCGT	58.543	36.000	0.00	0.00	29.56	5.24
42	43	6.688073	TTCTGAGGGTTTGAGAGTTTAGAT	57.312	37.500	0.00	0.00	0.00	1.98
43	44	6.494666	TTTCTGAGGGTTTGAGAGTTTAGA	57.505	37.500	0.00	0.00	0.00	2.10
98	99	2.005370	ACCCTCACTTCTACGGTTCA	57.995	50.000	0.00	0.00	0.00	3.18
716	2263	5.673514	AGTGCCAACAATGAATCAAAAAGT	58.326	33.333	0.00	0.00	0.00	2.66
902	2449	0.941542	CCTCACGCGGTTTTCAAAGA	59.058	50.000	12.47	0.00	0.00	2.52
1455	3003	3.007074	TGGTAGCATCACGACTTTTACCA	59.993	43.478	0.00	0.00	37.37	3.25
1612	3160	5.534278	TGTCCATGATTTTGTAGTTGCAAGA	59.466	36.000	0.00	0.00	0.00	3.02
1887	3435	8.004801	TCCTCTAGGATCATGTTGTGTAGAATA	58.995	37.037	0.00	0.00	39.78	1.75
1922	3470	7.086685	TCATAGAAACAAGGGAGGTTTAACT	57.913	36.000	0.00	0.00	38.50	2.24
2053	3601	5.744300	GCCAGTGGTGCTCTATTAGATCATT	60.744	44.000	11.74	0.00	0.00	2.57
2346	3895	0.486879	AAGGGTTGGATTTGAGGGCA	59.513	50.000	0.00	0.00	0.00	5.36
2347	3896	2.525105	TAAGGGTTGGATTTGAGGGC	57.475	50.000	0.00	0.00	0.00	5.19
2369	3918	4.479156	TCCTCAAACCCAACCCTTAAAT	57.521	40.909	0.00	0.00	0.00	1.40
2390	3942	7.182060	TGAAAAATAGGGGCAAAGACTAGAAT	58.818	34.615	0.00	0.00	0.00	2.40
2442	3994	6.977213	TGTAGCAATTTTAAGGGTTGAGAAC	58.023	36.000	0.00	0.00	0.00	3.01
2459	4011	1.144913	ACCCTCAAAGCCTTGTAGCAA	59.855	47.619	0.00	0.00	33.94	3.91
2470	4022	6.361768	AGTAGAACTCCTAAACCCTCAAAG	57.638	41.667	0.00	0.00	0.00	2.77
2558	4110	1.112113	GAGGGACCTAGAATGCGACA	58.888	55.000	0.00	0.00	0.00	4.35
2565	4117	1.491332	CGGAGAGAGAGGGACCTAGAA	59.509	57.143	0.00	0.00	0.00	2.10
2569	4121	2.277404	GCGGAGAGAGAGGGACCT	59.723	66.667	0.00	0.00	0.00	3.85
2598	4150	4.244802	GCGACGGAGAGAGGAGCG	62.245	72.222	0.00	0.00	0.00	5.03
2601	4153	3.700831	GAGGGCGACGGAGAGAGGA	62.701	68.421	0.00	0.00	0.00	3.71
2645	4218	1.454847	AAGGCCTTGTGCGGAACAA	60.455	52.632	19.73	0.79	46.66	2.83
2646	4219	2.192861	CAAGGCCTTGTGCGGAACA	61.193	57.895	33.46	0.00	42.61	3.18
2647	4220	2.644992	CAAGGCCTTGTGCGGAAC	59.355	61.111	33.46	0.00	42.61	3.62
2652	4225	2.594592	ACGACCAAGGCCTTGTGC	60.595	61.111	37.09	27.86	38.85	4.57
2694	4267	3.047877	CCAAAGTCACGGGCGTCC	61.048	66.667	0.00	0.00	0.00	4.79
2703	4276	1.228552	GCTCCCAAGGCCAAAGTCA	60.229	57.895	5.01	0.00	0.00	3.41
2708	4281	4.033776	CCGAGCTCCCAAGGCCAA	62.034	66.667	8.47	0.00	0.00	4.52
2710	4283	4.475135	GACCGAGCTCCCAAGGCC	62.475	72.222	8.47	0.00	0.00	5.19
2721	4294	0.183014	TCCAGGCCTAGTAGACCGAG	59.817	60.000	3.98	0.00	0.00	4.63
2768	4341	4.802051	CATGTGGAGGCGTGGGGG	62.802	72.222	0.00	0.00	0.00	5.40
2773	4346	2.933287	TTCCCCATGTGGAGGCGT	60.933	61.111	0.00	0.00	35.37	5.68
2776	4349	0.621571	TCCTCTTCCCCATGTGGAGG	60.622	60.000	0.00	0.00	43.35	4.30
2780	4353	1.211457	CTTCCTCCTCTTCCCCATGTG	59.789	57.143	0.00	0.00	0.00	3.21
2783	4356	2.486716	CTTCTTCCTCCTCTTCCCCAT	58.513	52.381	0.00	0.00	0.00	4.00
2784	4357	1.555765	CCTTCTTCCTCCTCTTCCCCA	60.556	57.143	0.00	0.00	0.00	4.96
2785	4358	1.208706	CCTTCTTCCTCCTCTTCCCC	58.791	60.000	0.00	0.00	0.00	4.81
2786	4359	0.544223	GCCTTCTTCCTCCTCTTCCC	59.456	60.000	0.00	0.00	0.00	3.97
2787	4360	1.578897	AGCCTTCTTCCTCCTCTTCC	58.421	55.000	0.00	0.00	0.00	3.46
2788	4361	3.431626	GCTAAGCCTTCTTCCTCCTCTTC	60.432	52.174	0.00	0.00	33.85	2.87
2789	4362	2.503765	GCTAAGCCTTCTTCCTCCTCTT	59.496	50.000	0.00	0.00	33.85	2.85
2790	4363	2.115427	GCTAAGCCTTCTTCCTCCTCT	58.885	52.381	0.00	0.00	33.85	3.69
2791	4364	1.202475	CGCTAAGCCTTCTTCCTCCTC	60.202	57.143	0.00	0.00	33.85	3.71
2810	4383	1.135046	CTTGATGGAGATGTAGCGCG	58.865	55.000	0.00	0.00	0.00	6.86
2821	4394	1.839994	CAGGAAGTAGGCCTTGATGGA	59.160	52.381	12.58	0.00	38.35	3.41
2824	4397	2.912956	TGAACAGGAAGTAGGCCTTGAT	59.087	45.455	12.58	0.00	32.12	2.57
2841	4414	7.603651	TCTAACTTCTAACTCACCTGATGAAC	58.396	38.462	0.00	0.00	36.69	3.18
2843	4416	7.575155	CGTTCTAACTTCTAACTCACCTGATGA	60.575	40.741	0.00	0.00	35.45	2.92
2853	4426	4.457257	ACCTACGCGTTCTAACTTCTAACT	59.543	41.667	20.78	0.00	0.00	2.24
2854	4427	4.556523	CACCTACGCGTTCTAACTTCTAAC	59.443	45.833	20.78	0.00	0.00	2.34
2855	4428	4.379813	CCACCTACGCGTTCTAACTTCTAA	60.380	45.833	20.78	0.00	0.00	2.10
2856	4429	3.127548	CCACCTACGCGTTCTAACTTCTA	59.872	47.826	20.78	0.00	0.00	2.10
2857	4430	2.094854	CCACCTACGCGTTCTAACTTCT	60.095	50.000	20.78	0.00	0.00	2.85
2858	4431	2.257034	CCACCTACGCGTTCTAACTTC	58.743	52.381	20.78	0.00	0.00	3.01
2859	4432	1.615392	ACCACCTACGCGTTCTAACTT	59.385	47.619	20.78	0.00	0.00	2.66
2871	4444	1.280998	ACCCAGCATACAACCACCTAC	59.719	52.381	0.00	0.00	0.00	3.18
2913	4486	2.293399	CACAGTAGCCCACAAGGTTTTC	59.707	50.000	0.00	0.00	38.26	2.29
2916	4489	0.843984	ACACAGTAGCCCACAAGGTT	59.156	50.000	0.00	0.00	38.26	3.50
2973	4546	3.916392	CTCGTCACCAGACCACGGC	62.916	68.421	0.00	0.00	41.87	5.68
2974	4547	2.258591	CTCGTCACCAGACCACGG	59.741	66.667	0.00	0.00	41.87	4.94
2975	4548	1.802337	TTCCTCGTCACCAGACCACG	61.802	60.000	0.00	0.00	41.87	4.94
2979	4552	2.743636	TTCATTCCTCGTCACCAGAC	57.256	50.000	0.00	0.00	41.46	3.51
2981	4554	3.363970	CGTTTTTCATTCCTCGTCACCAG	60.364	47.826	0.00	0.00	0.00	4.00
2988	4561	4.219033	CAAAGGTCGTTTTTCATTCCTCG	58.781	43.478	0.00	0.00	0.00	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.