AutoCloner

Multiple sequence alignment - TraesCS4B01G236200

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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	TraesCS4B01G236200	chr4B	100.000	3622	0	0	1	3622	494020328	494023949	0.000000e+00	6689
1	TraesCS4B01G236200	chr4B	90.583	223	20	1	1372	1594	13276372	13276151	9.840000e-76	294
2	TraesCS4B01G236200	chr4D	94.659	3651	128	23	1	3622	399776726	399780338	0.000000e+00	5600
3	TraesCS4B01G236200	chr4D	93.478	230	15	0	1892	2121	350265909	350266138	3.460000e-90	342
4	TraesCS4B01G236200	chr4D	91.057	246	22	0	2584	2829	350266135	350266380	2.080000e-87	333
5	TraesCS4B01G236200	chr4A	91.441	3365	171	42	1	3289	57812248	57815571	0.000000e+00	4510
6	TraesCS4B01G236200	chr4A	87.764	237	12	11	3394	3622	57815622	57815849	9.980000e-66	261
7	TraesCS4B01G236200	chr2A	88.881	1349	99	16	2145	3463	697070953	697069626	0.000000e+00	1613
8	TraesCS4B01G236200	chr2A	88.757	338	23	2	1372	1708	697071458	697071135	2.030000e-107	399
9	TraesCS4B01G236200	chr2A	92.683	164	5	1	1925	2081	697071114	697070951	2.810000e-56	230
10	TraesCS4B01G236200	chr5A	91.687	818	54	3	1907	2712	667025499	667024684	0.000000e+00	1122
11	TraesCS4B01G236200	chr5A	94.722	360	19	0	1584	1943	129233694	129233335	8.780000e-156	560
12	TraesCS4B01G236200	chr5A	94.083	338	19	1	1372	1708	667025832	667025495	2.490000e-141	512
13	TraesCS4B01G236200	chr5A	95.652	230	10	0	1892	2121	52485128	52485357	1.590000e-98	370
14	TraesCS4B01G236200	chr5A	92.889	225	16	0	2605	2829	52485366	52485590	9.700000e-86	327
15	TraesCS4B01G236200	chr7B	90.131	689	46	6	2032	2712	735911800	735912474	0.000000e+00	876
16	TraesCS4B01G236200	chr7B	93.750	288	17	1	1422	1708	735909814	735910101	7.180000e-117	431
17	TraesCS4B01G236200	chr7B	90.000	150	7	5	1907	2048	735910097	735910246	1.720000e-43	187
18	TraesCS4B01G236200	chr3D	96.676	361	12	0	1582	1942	470481483	470481843	5.170000e-168	601
19	TraesCS4B01G236200	chr3D	91.053	190	13	4	1372	1561	66334402	66334217	1.670000e-63	254
20	TraesCS4B01G236200	chr2D	96.122	361	14	0	1582	1942	287142733	287143093	1.120000e-164	590
21	TraesCS4B01G236200	chr1A	93.923	362	22	0	1582	1943	505305790	505306151	6.840000e-152	547
22	TraesCS4B01G236200	chr2B	88.789	223	24	1	1372	1594	152133766	152133987	4.610000e-69	272
23	TraesCS4B01G236200	chr7D	92.105	190	12	3	1372	1561	264483516	264483330	7.710000e-67	265

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	TraesCS4B01G236200	chr4B	494020328	494023949	3621	False	6689.000000	6689	100.000000	1	3622	1	chr4B.!!$F1	3621
1	TraesCS4B01G236200	chr4D	399776726	399780338	3612	False	5600.000000	5600	94.659000	1	3622	1	chr4D.!!$F1	3621
2	TraesCS4B01G236200	chr4A	57812248	57815849	3601	False	2385.500000	4510	89.602500	1	3622	2	chr4A.!!$F1	3621
3	TraesCS4B01G236200	chr2A	697069626	697071458	1832	True	747.333333	1613	90.107000	1372	3463	3	chr2A.!!$R1	2091
4	TraesCS4B01G236200	chr5A	667024684	667025832	1148	True	817.000000	1122	92.885000	1372	2712	2	chr5A.!!$R2	1340
5	TraesCS4B01G236200	chr7B	735909814	735912474	2660	False	498.000000	876	91.293667	1422	2712	3	chr7B.!!$F1	1290

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
674	730	0.679640	CGCTCACTCCCACTCTCTCT	60.680	60.0	0.0	0.0	0.0	3.10	F
1499	1569	1.542187	GGTTCTCCAGGCGGTACACT	61.542	60.0	0.0	0.0	0.0	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2538	4196	0.615544	TTCCCCGGTCCAGATTACGT	60.616	55.0	0.0	0.0	0.00	3.57	R
3357	5067	0.806102	CGTTGCCAGGATACGGACAG	60.806	60.0	6.0	0.0	46.39	3.51	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
133	169	2.743928	CCGGTCAGCAGCCTCAAC	60.744	66.667	0.00	0.00	0.00	3.18
140	176	3.793144	GCAGCCTCAACTTCCGCG	61.793	66.667	0.00	0.00	0.00	6.46
223	259	4.574421	CCAAATGTTGAAAAGGGGAAACAC	59.426	41.667	0.00	0.00	35.51	3.32
282	318	9.010029	GGTAAAAATCACATCAAACCTAGAAGA	57.990	33.333	0.00	0.00	0.00	2.87
291	327	7.277539	CACATCAAACCTAGAAGAAGATCACTC	59.722	40.741	0.00	0.00	0.00	3.51
292	328	5.955488	TCAAACCTAGAAGAAGATCACTCG	58.045	41.667	0.00	0.00	0.00	4.18
294	330	5.570234	AACCTAGAAGAAGATCACTCGTC	57.430	43.478	0.00	0.00	0.00	4.20
310	349	3.689649	ACTCGTCAAAGGAAACCATATGC	59.310	43.478	0.00	0.00	0.00	3.14
421	460	2.100087	AGCGCCGAAGAAAAAGGAAAAA	59.900	40.909	2.29	0.00	0.00	1.94
423	462	3.121025	GCGCCGAAGAAAAAGGAAAAATG	60.121	43.478	0.00	0.00	0.00	2.32
445	486	4.631813	TGGAGCGAGAGAAAAGAAATTAGC	59.368	41.667	0.00	0.00	0.00	3.09
459	500	2.802787	ATTAGCAGTACCAGCGCTAG	57.197	50.000	10.99	5.02	39.29	3.42
565	615	1.538876	TCTGGTCCCAAGTCCCCAG	60.539	63.158	0.00	0.00	44.74	4.45
598	648	2.805313	ATCCCCTCTCACTCGCACCA	62.805	60.000	0.00	0.00	0.00	4.17
625	681	5.874261	CCAAGTAAAATTGCAAATCCGGATT	59.126	36.000	24.27	24.27	0.00	3.01
635	691	8.816640	ATTGCAAATCCGGATTATAATTTCAC	57.183	30.769	29.42	11.50	0.00	3.18
656	712	3.114558	GGATATTCCTGCTCGCTCG	57.885	57.895	0.00	0.00	32.53	5.03
666	722	3.443925	CTCGCTCGCTCACTCCCA	61.444	66.667	0.00	0.00	0.00	4.37
667	723	3.691744	CTCGCTCGCTCACTCCCAC	62.692	68.421	0.00	0.00	0.00	4.61
674	730	0.679640	CGCTCACTCCCACTCTCTCT	60.680	60.000	0.00	0.00	0.00	3.10
760	819	3.711782	CCCCTCCCCTCCCCTTCT	61.712	72.222	0.00	0.00	0.00	2.85
931	993	2.624838	CAAGAAAGAGGGAAAGCAAGCA	59.375	45.455	0.00	0.00	0.00	3.91
949	1011	3.321039	AGCAAGGAGGGTGATGATGATA	58.679	45.455	0.00	0.00	0.00	2.15
975	1037	1.823899	GTCGCCCCATGATTCACCC	60.824	63.158	0.00	0.00	0.00	4.61
1029	1091	3.740397	CCTCGCCGTCCGTGTACA	61.740	66.667	0.00	0.00	38.35	2.90
1499	1569	1.542187	GGTTCTCCAGGCGGTACACT	61.542	60.000	0.00	0.00	0.00	3.55
2214	3869	3.360956	ATACCCAACGCCGTCCGAC	62.361	63.158	0.00	0.00	41.02	4.79
2291	3946	4.408821	TGCAGGATGGTGCCCGAC	62.409	66.667	0.00	0.00	43.28	4.79
2538	4196	0.038166	GTTCCCATTGGTCAGCCTCA	59.962	55.000	1.20	0.00	35.27	3.86
2666	4332	3.154710	CATGGGAGTGGATGAATGGATG	58.845	50.000	0.00	0.00	0.00	3.51
2766	4440	6.986250	TGTACATGCAAATTGGTGTGAATTA	58.014	32.000	0.00	0.00	0.00	1.40
2977	4662	4.868734	GGTAGAATTGTACACAGTACTGCC	59.131	45.833	22.90	7.14	0.00	4.85
2991	4676	0.463654	ACTGCCGCTTCACAGTTCAA	60.464	50.000	0.00	0.00	44.59	2.69
3011	4696	2.327343	GCTCGAGTGCACATTGCCA	61.327	57.895	21.04	0.00	44.23	4.92
3055	4740	6.425735	TGAATTCTTCCTGCATCTTGGATTA	58.574	36.000	7.05	0.00	31.76	1.75
3079	4764	2.491693	TGATTCTCCGGTCAAATTTGGC	59.508	45.455	17.90	16.26	0.00	4.52
3173	4867	5.066593	GGAACAGTTGAAAGATCTGGTTCT	58.933	41.667	0.00	0.00	34.02	3.01
3178	4872	5.297776	CAGTTGAAAGATCTGGTTCTGTGTT	59.702	40.000	0.00	0.00	0.00	3.32
3215	4914	2.603021	TCTGCTCACCCTATCTCATCC	58.397	52.381	0.00	0.00	0.00	3.51
3216	4915	1.271934	CTGCTCACCCTATCTCATCCG	59.728	57.143	0.00	0.00	0.00	4.18
3218	4917	0.605589	CTCACCCTATCTCATCCGCC	59.394	60.000	0.00	0.00	0.00	6.13
3219	4918	0.188587	TCACCCTATCTCATCCGCCT	59.811	55.000	0.00	0.00	0.00	5.52
3257	4956	1.266718	TCGCAGTTGCATTTTCTGACC	59.733	47.619	4.84	0.00	42.21	4.02
3296	4997	6.735130	GGCAACCAATTGTTCCATATACTAC	58.265	40.000	4.43	0.00	38.17	2.73
3297	4998	6.546034	GGCAACCAATTGTTCCATATACTACT	59.454	38.462	4.43	0.00	38.17	2.57
3298	4999	7.717875	GGCAACCAATTGTTCCATATACTACTA	59.282	37.037	4.43	0.00	38.17	1.82
3299	5000	8.557029	GCAACCAATTGTTCCATATACTACTAC	58.443	37.037	4.43	0.00	38.17	2.73
3311	5019	8.582437	TCCATATACTACTACATTAACAGTGCC	58.418	37.037	0.00	0.00	0.00	5.01
3401	5117	6.961554	GCAAGTAGTACAGTATTGCAATTCAC	59.038	38.462	18.75	10.79	44.32	3.18
3457	5175	3.255642	TCAGCAAGGACAAATAAAGCCAC	59.744	43.478	0.00	0.00	0.00	5.01
3564	5296	4.319839	GCATCTGCATGATTGATCACAGAG	60.320	45.833	14.50	9.28	40.76	3.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	2.358125	CACGTGCGGTGGGATCAA	60.358	61.111	0.82	0.00	43.16	2.57
175	211	9.292846	GGTTTATTTTCAACTACGAAAACAGTT	57.707	29.630	1.25	0.00	45.09	3.16
177	213	8.844441	TGGTTTATTTTCAACTACGAAAACAG	57.156	30.769	1.25	0.00	45.09	3.16
223	259	2.684001	ATGAAATGCCCATGCTGTTG	57.316	45.000	0.00	0.00	38.71	3.33
282	318	4.065789	GGTTTCCTTTGACGAGTGATCTT	58.934	43.478	0.00	0.00	0.00	2.40
291	327	2.752354	TGGCATATGGTTTCCTTTGACG	59.248	45.455	4.56	0.00	0.00	4.35
292	328	3.119137	GGTGGCATATGGTTTCCTTTGAC	60.119	47.826	4.56	0.00	0.00	3.18
294	330	2.830923	TGGTGGCATATGGTTTCCTTTG	59.169	45.455	4.56	0.00	0.00	2.77
310	349	3.094572	AGAATCTTGCAGGAAATGGTGG	58.905	45.455	1.33	0.00	0.00	4.61
403	442	4.627058	TCCATTTTTCCTTTTTCTTCGGC	58.373	39.130	0.00	0.00	0.00	5.54
421	460	5.295540	GCTAATTTCTTTTCTCTCGCTCCAT	59.704	40.000	0.00	0.00	0.00	3.41
423	462	4.631813	TGCTAATTTCTTTTCTCTCGCTCC	59.368	41.667	0.00	0.00	0.00	4.70
445	486	5.289595	TCATTTATTCTAGCGCTGGTACTG	58.710	41.667	22.90	10.59	0.00	2.74
521	563	1.050988	AGCACACTCACTGACACCCT	61.051	55.000	0.00	0.00	0.00	4.34
565	615	1.153147	GGGATTGGACGAGGGAAGC	60.153	63.158	0.00	0.00	0.00	3.86
598	648	4.994217	CGGATTTGCAATTTTACTTGGGTT	59.006	37.500	0.00	0.00	0.00	4.11
656	712	1.102978	GAGAGAGAGTGGGAGTGAGC	58.897	60.000	0.00	0.00	0.00	4.26
666	722	0.040499	GGGAGGGTGTGAGAGAGAGT	59.960	60.000	0.00	0.00	0.00	3.24
667	723	0.334676	AGGGAGGGTGTGAGAGAGAG	59.665	60.000	0.00	0.00	0.00	3.20
674	730	1.645710	GAGAAGAAGGGAGGGTGTGA	58.354	55.000	0.00	0.00	0.00	3.58
750	809	3.157949	GCGAGGGAGAAGGGGAGG	61.158	72.222	0.00	0.00	0.00	4.30
755	814	2.311463	TCTGATAAGCGAGGGAGAAGG	58.689	52.381	0.00	0.00	0.00	3.46
757	816	3.823873	GAGATCTGATAAGCGAGGGAGAA	59.176	47.826	0.00	0.00	0.00	2.87
758	817	3.417101	GAGATCTGATAAGCGAGGGAGA	58.583	50.000	0.00	0.00	0.00	3.71
760	819	2.109128	AGGAGATCTGATAAGCGAGGGA	59.891	50.000	0.00	0.00	0.00	4.20
931	993	2.301296	CGCTATCATCATCACCCTCCTT	59.699	50.000	0.00	0.00	0.00	3.36
975	1037	2.280389	CAGGCGACGGGATGATGG	60.280	66.667	0.00	0.00	0.00	3.51
1000	1062	2.407428	GGCGAGGCCCTTTTAGCAC	61.407	63.158	0.00	0.00	44.06	4.40
1029	1091	1.821061	CTTCCACCGCTCACTGGAGT	61.821	60.000	0.00	0.00	43.37	3.85
1279	1349	3.958147	ATGAAGACGGCCGGCACAG	62.958	63.158	36.60	20.98	0.00	3.66
1280	1350	3.950794	GATGAAGACGGCCGGCACA	62.951	63.158	36.60	31.42	0.00	4.57
2214	3869	1.153489	CGGACACCCTCATCAGCAG	60.153	63.158	0.00	0.00	0.00	4.24
2491	4149	3.744238	TCGACTCAAATCACAACCAGA	57.256	42.857	0.00	0.00	0.00	3.86
2492	4150	3.996363	TCATCGACTCAAATCACAACCAG	59.004	43.478	0.00	0.00	0.00	4.00
2493	4151	4.001618	TCATCGACTCAAATCACAACCA	57.998	40.909	0.00	0.00	0.00	3.67
2538	4196	0.615544	TTCCCCGGTCCAGATTACGT	60.616	55.000	0.00	0.00	0.00	3.57
2991	4676	1.871772	GCAATGTGCACTCGAGCTT	59.128	52.632	19.41	0.00	44.26	3.74
3079	4764	4.625742	AGCTATACGCAAAGTGTACACTTG	59.374	41.667	35.46	28.28	44.90	3.16
3095	4782	6.651975	ATCCAGTAGTGGTACAAGCTATAC	57.348	41.667	16.36	0.00	44.16	1.47
3173	4867	0.888619	TTCCGGCACAACAAAACACA	59.111	45.000	0.00	0.00	0.00	3.72
3178	4872	2.801342	GCAGAAATTCCGGCACAACAAA	60.801	45.455	0.00	0.00	0.00	2.83
3215	4914	2.545526	GTGGAACATGATACATGAGGCG	59.454	50.000	16.86	0.00	44.52	5.52
3216	4915	3.812053	GAGTGGAACATGATACATGAGGC	59.188	47.826	16.86	6.69	44.52	4.70
3218	4917	3.492383	GCGAGTGGAACATGATACATGAG	59.508	47.826	16.86	0.00	44.52	2.90
3219	4918	3.118811	TGCGAGTGGAACATGATACATGA	60.119	43.478	16.86	0.00	44.52	3.07
3257	4956	4.269183	TGGTTGCCCAATACACTGAATAG	58.731	43.478	0.00	0.00	37.98	1.73
3296	4997	6.312918	ACGTCAATTAGGCACTGTTAATGTAG	59.687	38.462	0.00	0.00	41.52	2.74
3297	4998	6.167685	ACGTCAATTAGGCACTGTTAATGTA	58.832	36.000	0.00	0.00	41.52	2.29
3298	4999	5.001232	ACGTCAATTAGGCACTGTTAATGT	58.999	37.500	0.00	0.00	41.52	2.71
3299	5000	5.545658	ACGTCAATTAGGCACTGTTAATG	57.454	39.130	0.00	0.00	41.52	1.90
3304	5012	4.737855	ATCTACGTCAATTAGGCACTGT	57.262	40.909	0.00	0.00	41.52	3.55
3357	5067	0.806102	CGTTGCCAGGATACGGACAG	60.806	60.000	6.00	0.00	46.39	3.51
3384	5100	6.539826	CCTCTGATGTGAATTGCAATACTGTA	59.460	38.462	13.39	0.00	0.00	2.74
3385	5101	5.356190	CCTCTGATGTGAATTGCAATACTGT	59.644	40.000	13.39	0.00	0.00	3.55
3386	5102	5.220989	CCCTCTGATGTGAATTGCAATACTG	60.221	44.000	13.39	5.14	0.00	2.74
3401	5117	1.381872	AGGACCGGACCCTCTGATG	60.382	63.158	19.83	0.00	0.00	3.07
3457	5175	2.507102	CCTAGTGTGCGACGCAGG	60.507	66.667	25.21	16.77	40.08	4.85
3564	5296	0.808755	CTGCACGATGTAAAACCCCC	59.191	55.000	0.00	0.00	0.00	5.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.