AutoCloner

Multiple sequence alignment - TraesCS4B01G078500

Loading Multiple Alignment...

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	TraesCS4B01G078500	chr4B	100.000	2276	0	0	1	2276	75653486	75651211	0.000000e+00	4204.0
1	TraesCS4B01G078500	chr4B	100.000	150	0	0	2127	2276	75678451	75678302	6.190000e-71	278.0
2	TraesCS4B01G078500	chrUn	100.000	643	0	0	259	901	249140032	249139390	0.000000e+00	1188.0
3	TraesCS4B01G078500	chrUn	100.000	150	0	0	2127	2276	249138791	249138642	6.190000e-71	278.0
4	TraesCS4B01G078500	chrUn	88.235	68	6	2	1546	1613	79226239	79226174	1.870000e-11	80.5
5	TraesCS4B01G078500	chr4A	87.123	862	69	23	706	1532	545124154	545125008	0.000000e+00	939.0
6	TraesCS4B01G078500	chr4A	82.368	1140	107	42	231	1311	545192220	545193324	0.000000e+00	905.0
7	TraesCS4B01G078500	chr4A	80.057	351	43	13	150	487	545121904	545122240	3.780000e-58	235.0
8	TraesCS4B01G078500	chr4D	83.865	1035	80	35	561	1542	51348713	51347713	0.000000e+00	905.0
9	TraesCS4B01G078500	chr4D	87.200	750	42	19	598	1310	51456328	51455596	0.000000e+00	804.0
10	TraesCS4B01G078500	chr4D	91.981	424	21	2	889	1311	51315335	51314924	1.170000e-162	582.0
11	TraesCS4B01G078500	chr4D	79.433	564	95	17	35	587	51316426	51315873	1.650000e-101	379.0
12	TraesCS4B01G078500	chr4D	93.607	219	12	2	1333	1551	51314870	51314654	2.180000e-85	326.0
13	TraesCS4B01G078500	chr4D	78.846	364	45	12	486	819	51315689	51315328	1.370000e-52	217.0
14	TraesCS4B01G078500	chr4D	83.815	173	19	7	1331	1499	51455547	51455380	3.030000e-34	156.0
15	TraesCS4B01G078500	chr4D	93.333	60	4	0	1492	1551	51349465	51349406	3.110000e-14	89.8
16	TraesCS4B01G078500	chr3B	91.311	610	39	8	1675	2276	699149836	699150439	0.000000e+00	821.0
17	TraesCS4B01G078500	chr3B	87.007	608	67	11	1674	2276	16283406	16284006	0.000000e+00	675.0
18	TraesCS4B01G078500	chr3B	88.276	145	13	3	1552	1694	699149668	699149810	1.080000e-38	171.0
19	TraesCS4B01G078500	chr1B	90.701	613	42	7	1675	2276	502062958	502063566	0.000000e+00	802.0
20	TraesCS4B01G078500	chr1B	82.211	579	67	17	1698	2244	609854268	609854842	1.230000e-127	466.0
21	TraesCS4B01G078500	chr6B	87.356	609	66	10	1674	2276	470832758	470833361	0.000000e+00	688.0
22	TraesCS4B01G078500	chr6B	84.380	621	67	15	1675	2273	718647651	718648263	1.170000e-162	582.0
23	TraesCS4B01G078500	chr6B	86.667	150	14	6	1547	1694	470832587	470832732	6.510000e-36	161.0
24	TraesCS4B01G078500	chr6D	85.089	617	67	15	1675	2272	356228233	356227623	6.950000e-170	606.0
25	TraesCS4B01G078500	chr7B	83.955	617	68	12	1674	2273	619073222	619073824	1.530000e-156	562.0
26	TraesCS4B01G078500	chr7B	80.775	619	81	24	1675	2276	329922696	329922099	1.240000e-122	449.0
27	TraesCS4B01G078500	chr7B	92.089	316	12	7	1970	2274	714404743	714404430	1.250000e-117	433.0
28	TraesCS4B01G078500	chr7B	90.741	270	24	1	1674	1943	714405003	714404735	2.150000e-95	359.0
29	TraesCS4B01G078500	chr7B	96.154	52	2	0	1549	1600	475727043	475726992	4.030000e-13	86.1
30	TraesCS4B01G078500	chr7A	86.897	145	17	2	1552	1694	344654420	344654564	6.510000e-36	161.0
31	TraesCS4B01G078500	chr6A	88.000	75	7	2	1552	1625	261517055	261516982	1.120000e-13	87.9
32	TraesCS4B01G078500	chr6A	96.226	53	1	1	1552	1603	261511872	261511820	4.030000e-13	86.1
33	TraesCS4B01G078500	chr6A	94.545	55	2	1	1550	1603	261516993	261516939	1.450000e-12	84.2
34	TraesCS4B01G078500	chr6A	91.525	59	4	1	1552	1610	100234112	100234055	1.870000e-11	80.5

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	TraesCS4B01G078500	chr4B	75651211	75653486	2275	True	4204.0	4204	100.00000	1	2276	1	chr4B.!!$R1	2275
1	TraesCS4B01G078500	chrUn	249138642	249140032	1390	True	733.0	1188	100.00000	259	2276	2	chrUn.!!$R2	2017
2	TraesCS4B01G078500	chr4A	545192220	545193324	1104	False	905.0	905	82.36800	231	1311	1	chr4A.!!$F1	1080
3	TraesCS4B01G078500	chr4A	545121904	545125008	3104	False	587.0	939	83.59000	150	1532	2	chr4A.!!$F2	1382
4	TraesCS4B01G078500	chr4D	51347713	51349465	1752	True	497.4	905	88.59900	561	1551	2	chr4D.!!$R2	990
5	TraesCS4B01G078500	chr4D	51455380	51456328	948	True	480.0	804	85.50750	598	1499	2	chr4D.!!$R3	901
6	TraesCS4B01G078500	chr4D	51314654	51316426	1772	True	376.0	582	85.96675	35	1551	4	chr4D.!!$R1	1516
7	TraesCS4B01G078500	chr3B	16283406	16284006	600	False	675.0	675	87.00700	1674	2276	1	chr3B.!!$F1	602
8	TraesCS4B01G078500	chr3B	699149668	699150439	771	False	496.0	821	89.79350	1552	2276	2	chr3B.!!$F2	724
9	TraesCS4B01G078500	chr1B	502062958	502063566	608	False	802.0	802	90.70100	1675	2276	1	chr1B.!!$F1	601
10	TraesCS4B01G078500	chr1B	609854268	609854842	574	False	466.0	466	82.21100	1698	2244	1	chr1B.!!$F2	546
11	TraesCS4B01G078500	chr6B	718647651	718648263	612	False	582.0	582	84.38000	1675	2273	1	chr6B.!!$F1	598
12	TraesCS4B01G078500	chr6B	470832587	470833361	774	False	424.5	688	87.01150	1547	2276	2	chr6B.!!$F2	729
13	TraesCS4B01G078500	chr6D	356227623	356228233	610	True	606.0	606	85.08900	1675	2272	1	chr6D.!!$R1	597
14	TraesCS4B01G078500	chr7B	619073222	619073824	602	False	562.0	562	83.95500	1674	2273	1	chr7B.!!$F1	599
15	TraesCS4B01G078500	chr7B	329922099	329922696	597	True	449.0	449	80.77500	1675	2276	1	chr7B.!!$R1	601
16	TraesCS4B01G078500	chr7B	714404430	714405003	573	True	396.0	433	91.41500	1674	2274	2	chr7B.!!$R3	600

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
874	2962	0.666274	CGTGCACCGACACATGTAGT	60.666	55.0	12.15	0.0	40.73	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1696	3950	1.758592	CCTCAGGGTCGTGGGAAAA	59.241	57.895	0.0	0.0	0.0	2.29	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
45	46	2.158900	AGACGTATCAGCTGGGGATTTG	60.159	50.000	15.13	0.39	0.00	2.32
63	64	6.127842	GGGATTTGGCTCGTTTTGTATTAGAA	60.128	38.462	0.00	0.00	0.00	2.10
64	65	6.745907	GGATTTGGCTCGTTTTGTATTAGAAC	59.254	38.462	0.00	0.00	0.00	3.01
102	106	6.435904	TGGACCTTCAACAAAAATAGTATGGG	59.564	38.462	0.00	0.00	0.00	4.00
103	107	6.436218	GGACCTTCAACAAAAATAGTATGGGT	59.564	38.462	0.00	0.00	0.00	4.51
120	124	8.650143	AGTATGGGTGTTTTCTACAAAATCAT	57.350	30.769	0.00	0.00	38.80	2.45
122	126	6.007936	TGGGTGTTTTCTACAAAATCATCG	57.992	37.500	0.00	0.00	38.80	3.84
131	136	0.969917	CAAAATCATCGCCCCCACCA	60.970	55.000	0.00	0.00	0.00	4.17
139	144	3.580319	GCCCCCACCAACCTCAGT	61.580	66.667	0.00	0.00	0.00	3.41
244	261	2.034558	CACCCGCATCACAAGTTCTTTT	59.965	45.455	0.00	0.00	0.00	2.27
873	2961	1.955529	GCGTGCACCGACACATGTAG	61.956	60.000	12.15	0.00	40.73	2.74
874	2962	0.666274	CGTGCACCGACACATGTAGT	60.666	55.000	12.15	0.00	40.73	2.73
875	2963	1.401800	CGTGCACCGACACATGTAGTA	60.402	52.381	12.15	0.00	40.73	1.82
882	2973	2.098607	CCGACACATGTAGTACCACGAT	59.901	50.000	0.00	0.00	0.00	3.73
918	3030	4.274459	GCTATACAAACTCCCATCAGCTTG	59.726	45.833	0.00	0.00	0.00	4.01
957	3101	3.054875	TCAAGCTGAGCTACCATCACAAT	60.055	43.478	7.68	0.00	38.25	2.71
958	3102	3.641434	AGCTGAGCTACCATCACAATT	57.359	42.857	4.49	0.00	36.99	2.32
959	3103	3.539604	AGCTGAGCTACCATCACAATTC	58.460	45.455	4.49	0.00	36.99	2.17
960	3104	3.054875	AGCTGAGCTACCATCACAATTCA	60.055	43.478	4.49	0.00	36.99	2.57
961	3105	3.064545	GCTGAGCTACCATCACAATTCAC	59.935	47.826	0.00	0.00	0.00	3.18
962	3106	4.256110	CTGAGCTACCATCACAATTCACA	58.744	43.478	0.00	0.00	0.00	3.58
963	3107	4.650734	TGAGCTACCATCACAATTCACAA	58.349	39.130	0.00	0.00	0.00	3.33
964	3108	5.069318	TGAGCTACCATCACAATTCACAAA	58.931	37.500	0.00	0.00	0.00	2.83
1320	3512	3.381272	GCATCCAGCCAGTTAATTTGCTA	59.619	43.478	0.00	0.00	37.23	3.49
1322	3514	4.301072	TCCAGCCAGTTAATTTGCTACT	57.699	40.909	0.00	0.00	31.69	2.57
1323	3515	4.261801	TCCAGCCAGTTAATTTGCTACTC	58.738	43.478	0.00	0.00	31.69	2.59
1324	3516	3.378427	CCAGCCAGTTAATTTGCTACTCC	59.622	47.826	0.00	0.00	31.69	3.85
1327	3519	3.063588	GCCAGTTAATTTGCTACTCCGAC	59.936	47.826	0.00	0.00	0.00	4.79
1328	3520	4.250464	CCAGTTAATTTGCTACTCCGACA	58.750	43.478	0.00	0.00	0.00	4.35
1329	3521	4.693566	CCAGTTAATTTGCTACTCCGACAA	59.306	41.667	0.00	0.00	0.00	3.18
1410	3610	3.611766	GCATTTCGTTCCCTCTGTTTTCC	60.612	47.826	0.00	0.00	0.00	3.13
1414	3614	1.000506	CGTTCCCTCTGTTTTCCGAGA	59.999	52.381	0.00	0.00	33.87	4.04
1416	3616	3.067833	GTTCCCTCTGTTTTCCGAGAAG	58.932	50.000	0.00	0.00	33.87	2.85
1481	3689	1.375908	GAGCTCACCGCCATGTCAA	60.376	57.895	9.40	0.00	40.39	3.18
1602	3810	3.004951	CATTCCCTGGCAGCCTCT	58.995	61.111	14.15	0.00	0.00	3.69
1603	3811	1.305623	CATTCCCTGGCAGCCTCTT	59.694	57.895	14.15	0.00	0.00	2.85
1616	3824	4.075682	GCAGCCTCTTAGAAAAGGAAAGT	58.924	43.478	0.00	0.00	34.35	2.66
1624	3832	7.256368	CCTCTTAGAAAAGGAAAGTACCTGTCT	60.256	40.741	0.00	0.00	40.49	3.41
1628	3836	1.954035	AGGAAAGTACCTGTCTCCCC	58.046	55.000	0.00	0.00	39.01	4.81
1629	3837	0.910338	GGAAAGTACCTGTCTCCCCC	59.090	60.000	0.00	0.00	0.00	5.40
1630	3838	1.652947	GAAAGTACCTGTCTCCCCCA	58.347	55.000	0.00	0.00	0.00	4.96
1631	3839	2.197465	GAAAGTACCTGTCTCCCCCAT	58.803	52.381	0.00	0.00	0.00	4.00
1633	3841	0.397254	AGTACCTGTCTCCCCCATCG	60.397	60.000	0.00	0.00	0.00	3.84
1634	3842	1.760875	TACCTGTCTCCCCCATCGC	60.761	63.158	0.00	0.00	0.00	4.58
1699	3953	4.678743	GCCCTCACCCCGGCTTTT	62.679	66.667	0.00	0.00	42.21	2.27
1797	4106	1.307647	GGCAGTTCCACCATCCCAT	59.692	57.895	0.00	0.00	34.01	4.00
1987	4348	9.167311	GTACAGAATTACTCTTGTTGATCCAAT	57.833	33.333	0.00	0.00	29.07	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.034812	CCCCAGCTGATACGTCTTCTAC	59.965	54.545	17.39	0.00	0.00	2.59
20	21	2.092049	TCCCCAGCTGATACGTCTTCTA	60.092	50.000	17.39	0.00	0.00	2.10
21	22	1.115467	CCCCAGCTGATACGTCTTCT	58.885	55.000	17.39	0.00	0.00	2.85
24	25	1.794714	AATCCCCAGCTGATACGTCT	58.205	50.000	17.39	0.00	0.00	4.18
26	27	1.134098	CCAAATCCCCAGCTGATACGT	60.134	52.381	17.39	0.00	0.00	3.57
27	28	1.597742	CCAAATCCCCAGCTGATACG	58.402	55.000	17.39	0.00	0.00	3.06
28	29	1.133668	AGCCAAATCCCCAGCTGATAC	60.134	52.381	17.39	0.00	33.41	2.24
29	30	1.143684	GAGCCAAATCCCCAGCTGATA	59.856	52.381	17.39	0.00	35.23	2.15
31	32	1.304282	GAGCCAAATCCCCAGCTGA	59.696	57.895	17.39	0.00	35.23	4.26
32	33	2.117156	CGAGCCAAATCCCCAGCTG	61.117	63.158	6.78	6.78	35.23	4.24
33	34	2.142292	AACGAGCCAAATCCCCAGCT	62.142	55.000	0.00	0.00	38.56	4.24
37	38	0.966179	ACAAAACGAGCCAAATCCCC	59.034	50.000	0.00	0.00	0.00	4.81
79	83	7.039993	ACACCCATACTATTTTTGTTGAAGGTC	60.040	37.037	0.00	0.00	0.00	3.85
84	88	8.919145	AGAAAACACCCATACTATTTTTGTTGA	58.081	29.630	0.00	0.00	0.00	3.18
102	106	4.857037	GGGCGATGATTTTGTAGAAAACAC	59.143	41.667	0.00	0.00	38.00	3.32
103	107	4.082463	GGGGCGATGATTTTGTAGAAAACA	60.082	41.667	0.00	2.05	33.86	2.83
122	126	3.146828	AACTGAGGTTGGTGGGGGC	62.147	63.158	0.00	0.00	33.96	5.80
131	136	1.070758	ACATGCGTCTCAACTGAGGTT	59.929	47.619	6.87	0.00	42.30	3.50
139	144	2.183478	AATGGTCACATGCGTCTCAA	57.817	45.000	0.00	0.00	37.40	3.02
205	210	1.159713	TGCGCTCTGGTCACAAACTG	61.160	55.000	9.73	0.00	0.00	3.16
244	261	5.798015	TTAGTTACACAACTCGCAAAACA	57.202	34.783	0.00	0.00	44.04	2.83
873	2961	0.947244	ATCGGGTCGTATCGTGGTAC	59.053	55.000	0.00	0.00	0.00	3.34
874	2962	1.229428	GATCGGGTCGTATCGTGGTA	58.771	55.000	0.00	0.00	0.00	3.25
875	2963	1.779025	CGATCGGGTCGTATCGTGGT	61.779	60.000	7.38	0.00	45.19	4.16
901	3013	2.233271	ACACAAGCTGATGGGAGTTTG	58.767	47.619	0.00	0.00	39.39	2.93
918	3030	3.120649	GCTTGATCAGGTACGTCAAACAC	60.121	47.826	6.70	0.00	32.08	3.32
962	3106	3.186119	CGTGACCTGCAAAATGTGTTTT	58.814	40.909	0.00	0.00	38.03	2.43
963	3107	2.808244	CGTGACCTGCAAAATGTGTTT	58.192	42.857	0.00	0.00	0.00	2.83
964	3108	1.535860	GCGTGACCTGCAAAATGTGTT	60.536	47.619	0.00	0.00	0.00	3.32
1327	3519	2.593436	AAAGCCCGTCCACCGTTG	60.593	61.111	0.00	0.00	33.66	4.10
1328	3520	2.593436	CAAAGCCCGTCCACCGTT	60.593	61.111	0.00	0.00	33.66	4.44
1329	3521	4.636435	CCAAAGCCCGTCCACCGT	62.636	66.667	0.00	0.00	33.66	4.83
1466	3669	1.227999	AACGTTGACATGGCGGTGAG	61.228	55.000	0.00	0.00	0.00	3.51
1470	3673	2.126888	GCAACGTTGACATGGCGG	60.127	61.111	31.62	2.06	0.00	6.13
1542	3750	5.316167	TCCCTAGACGCGTCCTTTATTATA	58.684	41.667	34.08	16.72	0.00	0.98
1544	3752	3.554934	TCCCTAGACGCGTCCTTTATTA	58.445	45.455	34.08	18.13	0.00	0.98
1545	3753	2.361438	CTCCCTAGACGCGTCCTTTATT	59.639	50.000	34.08	17.97	0.00	1.40
1550	3758	2.829458	GCTCCCTAGACGCGTCCT	60.829	66.667	34.08	23.01	0.00	3.85
1586	3794	0.842635	CTAAGAGGCTGCCAGGGAAT	59.157	55.000	22.65	0.00	0.00	3.01
1602	3810	6.239800	GGGAGACAGGTACTTTCCTTTTCTAA	60.240	42.308	0.00	0.00	35.41	2.10
1603	3811	5.247792	GGGAGACAGGTACTTTCCTTTTCTA	59.752	44.000	0.00	0.00	35.41	2.10
1616	3824	1.760875	GCGATGGGGGAGACAGGTA	60.761	63.158	0.00	0.00	0.00	3.08
1657	3865	2.354403	CGGGGGACTAGGTTTTGTAGTG	60.354	54.545	0.00	0.00	30.60	2.74
1661	3869	1.377612	GCGGGGGACTAGGTTTTGT	59.622	57.895	0.00	0.00	0.00	2.83
1662	3870	1.378119	GGCGGGGGACTAGGTTTTG	60.378	63.158	0.00	0.00	0.00	2.44
1693	3947	1.971695	CAGGGTCGTGGGAAAAGCC	60.972	63.158	0.00	0.00	0.00	4.35
1696	3950	1.758592	CCTCAGGGTCGTGGGAAAA	59.241	57.895	0.00	0.00	0.00	2.29
1697	3951	2.890766	GCCTCAGGGTCGTGGGAAA	61.891	63.158	0.00	0.00	34.45	3.13
1698	3952	3.319198	GCCTCAGGGTCGTGGGAA	61.319	66.667	0.00	0.00	34.45	3.97
1797	4106	5.191722	ACAGGGCTATGAAGGTTTTCAGATA	59.808	40.000	0.00	0.00	45.89	1.98
1931	4257	4.316025	AGCATAAGGGCAAAAGTAAGGA	57.684	40.909	0.00	0.00	35.83	3.36
1987	4348	4.081406	AGATGCAGCAAACCAAAGACATA	58.919	39.130	4.07	0.00	0.00	2.29
2056	4430	4.101114	GGGGTGGATTTGATTTTAGGGTT	58.899	43.478	0.00	0.00	0.00	4.11
2057	4431	3.567886	GGGGGTGGATTTGATTTTAGGGT	60.568	47.826	0.00	0.00	0.00	4.34
2085	4489	3.987547	TGAGCAGAGAAACAACAGAGAG	58.012	45.455	0.00	0.00	0.00	3.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.