AutoCloner

Multiple sequence alignment - TraesCS6A01G258400

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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	TraesCS6A01G258400	chr6A	100.000	3175	0	0	932	4106	480644419	480647593	0.000000e+00	5864.0
1	TraesCS6A01G258400	chr6A	100.000	794	0	0	1	794	480643488	480644281	0.000000e+00	1467.0
2	TraesCS6A01G258400	chr6A	98.111	794	15	0	1	794	87960911	87961704	0.000000e+00	1384.0
3	TraesCS6A01G258400	chr6A	94.843	795	33	8	1	794	570896053	570896840	0.000000e+00	1234.0
4	TraesCS6A01G258400	chr6A	94.598	796	33	10	1	794	591846553	591847340	0.000000e+00	1223.0
5	TraesCS6A01G258400	chr6A	94.591	795	34	9	1	794	12687777	12686991	0.000000e+00	1221.0
6	TraesCS6A01G258400	chr6D	94.733	2753	118	10	932	3667	340463542	340466284	0.000000e+00	4255.0
7	TraesCS6A01G258400	chr6D	96.809	188	6	0	3919	4106	340467244	340467431	8.570000e-82	315.0
8	TraesCS6A01G258400	chr6D	91.000	200	15	2	3728	3926	340466981	340467178	2.430000e-67	267.0
9	TraesCS6A01G258400	chr6D	89.706	68	7	0	3667	3734	340466842	340466909	2.030000e-13	87.9
10	TraesCS6A01G258400	chr6B	95.283	2523	96	8	932	3431	480380040	480377518	0.000000e+00	3978.0
11	TraesCS6A01G258400	chr6B	94.843	795	32	9	1	794	21358881	21358095	0.000000e+00	1232.0
12	TraesCS6A01G258400	chr6B	97.340	188	5	0	3919	4106	480376470	480376283	1.840000e-83	320.0
13	TraesCS6A01G258400	chr6B	90.452	199	16	2	3728	3926	480376730	480376535	4.070000e-65	259.0
14	TraesCS6A01G258400	chr6B	84.112	214	25	5	3445	3654	480377261	480377053	9.000000e-47	198.0
15	TraesCS6A01G258400	chr7B	97.859	794	17	0	1	794	666520903	666520110	0.000000e+00	1373.0
16	TraesCS6A01G258400	chr7B	97.733	794	13	2	1	794	194133359	194134147	0.000000e+00	1362.0
17	TraesCS6A01G258400	chr4A	94.856	797	31	10	1	794	66552553	66551764	0.000000e+00	1236.0
18	TraesCS6A01G258400	chr7A	94.717	795	33	9	1	794	634136022	634136808	0.000000e+00	1227.0
19	TraesCS6A01G258400	chr7A	93.577	794	30	9	2	794	624753476	624752703	0.000000e+00	1164.0

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	TraesCS6A01G258400	chr6A	480643488	480647593	4105	False	3665.500	5864	100.00000	1	4106	2	chr6A.!!$F4	4105
1	TraesCS6A01G258400	chr6A	87960911	87961704	793	False	1384.000	1384	98.11100	1	794	1	chr6A.!!$F1	793
2	TraesCS6A01G258400	chr6A	570896053	570896840	787	False	1234.000	1234	94.84300	1	794	1	chr6A.!!$F2	793
3	TraesCS6A01G258400	chr6A	591846553	591847340	787	False	1223.000	1223	94.59800	1	794	1	chr6A.!!$F3	793
4	TraesCS6A01G258400	chr6A	12686991	12687777	786	True	1221.000	1221	94.59100	1	794	1	chr6A.!!$R1	793
5	TraesCS6A01G258400	chr6D	340463542	340467431	3889	False	1231.225	4255	93.06200	932	4106	4	chr6D.!!$F1	3174
6	TraesCS6A01G258400	chr6B	21358095	21358881	786	True	1232.000	1232	94.84300	1	794	1	chr6B.!!$R1	793
7	TraesCS6A01G258400	chr6B	480376283	480380040	3757	True	1188.750	3978	91.79675	932	4106	4	chr6B.!!$R2	3174
8	TraesCS6A01G258400	chr7B	666520110	666520903	793	True	1373.000	1373	97.85900	1	794	1	chr7B.!!$R1	793
9	TraesCS6A01G258400	chr7B	194133359	194134147	788	False	1362.000	1362	97.73300	1	794	1	chr7B.!!$F1	793
10	TraesCS6A01G258400	chr4A	66551764	66552553	789	True	1236.000	1236	94.85600	1	794	1	chr4A.!!$R1	793
11	TraesCS6A01G258400	chr7A	634136022	634136808	786	False	1227.000	1227	94.71700	1	794	1	chr7A.!!$F1	793
12	TraesCS6A01G258400	chr7A	624752703	624753476	773	True	1164.000	1164	93.57700	2	794	1	chr7A.!!$R1	792

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
404	408	1.527370	GTATGGCTCTGACCACCCC	59.473	63.158	1.87	0.0	44.17	4.95	F
1590	1608	0.743097	GATTGGCTTGCAGGGATGTC	59.257	55.000	0.00	0.0	0.00	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1757	1775	0.107017	AGCAACAAGAGTGTGCACCT	60.107	50.0	15.69	11.06	38.27	4.00	R
3548	3820	0.388907	GCACATGGGCACACACAATC	60.389	55.0	16.99	0.00	0.00	2.67	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
256	258	7.225734	GGTAGTTTTTGGCATGTTTAACACATT	59.774	33.333	0.00	0.00	44.40	2.71
282	285	6.093909	CAGCATGTTTAACATCTGGTGTGATA	59.906	38.462	17.53	0.00	41.14	2.15
297	300	4.202441	GTGTGATATGCCAGATTCACCTT	58.798	43.478	0.00	0.00	38.12	3.50
404	408	1.527370	GTATGGCTCTGACCACCCC	59.473	63.158	1.87	0.00	44.17	4.95
653	657	2.342279	CACGTTTGGCGAGGAGGA	59.658	61.111	0.00	0.00	44.77	3.71
752	757	3.814577	CCTCTTTTTCGCTCGAGGA	57.185	52.632	15.58	7.04	44.56	3.71
1290	1308	2.107953	GCCCTCATCTCGCTCCAC	59.892	66.667	0.00	0.00	0.00	4.02
1590	1608	0.743097	GATTGGCTTGCAGGGATGTC	59.257	55.000	0.00	0.00	0.00	3.06
1705	1723	4.021544	TCCTTCCCAACAATGTTACAATGC	60.022	41.667	0.00	0.00	0.00	3.56
1743	1761	1.372087	GCTCTTTGATGGGCCACTCG	61.372	60.000	9.28	0.00	0.00	4.18
1746	1764	2.196997	CTTTGATGGGCCACTCGGGA	62.197	60.000	9.28	0.00	40.01	5.14
1757	1775	1.001974	CCACTCGGGATTGTTCAGTCA	59.998	52.381	0.00	0.00	40.01	3.41
1765	1783	2.221169	GATTGTTCAGTCAGGTGCACA	58.779	47.619	20.43	0.00	0.00	4.57
1794	1812	3.702048	CGGTTGGGCCTCGAGGAA	61.702	66.667	35.69	17.74	37.39	3.36
2148	2166	0.467384	TCTCATGCCTAGCCAAGAGC	59.533	55.000	1.21	0.00	44.25	4.09
2235	2253	3.804036	TGATTTTGTCACGGTCTTGAGT	58.196	40.909	0.00	0.00	0.00	3.41
2291	2309	1.455217	AAGGGCAGATGCTCCATGC	60.455	57.895	0.00	0.00	44.25	4.06
2325	2343	5.888691	AATATGGTTTTGTGCACGATGTA	57.111	34.783	13.13	0.00	0.00	2.29
2358	2376	7.884354	TCCAATGCTCTAATAATCATGTATGCA	59.116	33.333	0.00	0.00	0.00	3.96
2370	2388	6.949352	ATCATGTATGCAAAGTTAGGAAGG	57.051	37.500	0.00	0.00	0.00	3.46
2394	2412	4.478206	TGATTCCGCTGAGAAGATCTTT	57.522	40.909	9.87	0.00	0.00	2.52
2395	2413	4.836825	TGATTCCGCTGAGAAGATCTTTT	58.163	39.130	9.87	3.31	0.00	2.27
2466	2484	0.687354	ATGGGATACACGGAGATGGC	59.313	55.000	0.00	0.00	39.74	4.40
2469	2487	0.687354	GGATACACGGAGATGGCCAT	59.313	55.000	20.96	20.96	0.00	4.40
2472	2490	0.104120	TACACGGAGATGGCCATTCG	59.896	55.000	21.84	24.02	0.00	3.34
2629	2647	1.396653	GGACCATGGAATTGAGCCTG	58.603	55.000	21.47	0.00	0.00	4.85
2658	2676	5.237344	GGATCATTATGCTTGTGTAGTGGAC	59.763	44.000	0.00	0.00	0.00	4.02
2683	2701	3.439857	TTGGAAGGTCTGGGAGATTTG	57.560	47.619	0.00	0.00	0.00	2.32
2685	2703	1.683319	GGAAGGTCTGGGAGATTTGCC	60.683	57.143	0.00	0.00	34.91	4.52
2730	2748	1.376037	GCCTGTTCCTCCCAACTCG	60.376	63.158	0.00	0.00	0.00	4.18
2835	2853	4.446371	CCTTGGAACCTGACAGTGATATC	58.554	47.826	0.00	0.00	0.00	1.63
2862	2880	7.430441	GGAGAGTCTCCTTGTCAAATATCTAC	58.570	42.308	28.96	0.00	46.41	2.59
2877	2895	3.506059	CTACGCATCGGCTGGGAGG	62.506	68.421	2.78	0.00	40.13	4.30
2912	2930	6.596888	TCTGCAAAGATTAGGACTGAAATGAG	59.403	38.462	0.00	0.00	0.00	2.90
3072	3090	0.250234	TGGCAGATGTAGCTGGTGAC	59.750	55.000	0.00	0.00	36.41	3.67
3152	3170	3.569194	TGCCAGAGTTACAAAGGTGAA	57.431	42.857	0.00	0.00	0.00	3.18
3194	3212	7.439655	AGACTGTGAACTTACTGACTTGAAATC	59.560	37.037	0.00	0.00	0.00	2.17
3235	3253	7.972832	TTTGTGTTCTGGGTGTAGTATAAAG	57.027	36.000	0.00	0.00	0.00	1.85
3294	3313	0.759346	AAGGAAACTGAGGACGCTGT	59.241	50.000	0.00	0.00	42.68	4.40
3356	3375	4.035675	GGTGTAGTCATCTAAATTGCCTGC	59.964	45.833	0.00	0.00	0.00	4.85
3414	3441	2.353357	TATGCCAGCAGAAATGGAGG	57.647	50.000	0.00	0.00	40.51	4.30
3415	3442	0.627451	ATGCCAGCAGAAATGGAGGA	59.373	50.000	0.00	0.00	40.51	3.71
3432	3461	5.135383	TGGAGGAAAATCTTGCTGATATGG	58.865	41.667	0.00	0.00	32.59	2.74
3491	3763	6.779860	AGGATTGGCAATACGAAATATAGGT	58.220	36.000	16.50	0.00	0.00	3.08
3505	3777	5.535753	AATATAGGTTGCCCAATTTCTGC	57.464	39.130	0.00	0.00	0.00	4.26
3525	3797	2.986479	GCAGGGTTCAAATTTTAGCACG	59.014	45.455	0.00	0.00	0.00	5.34
3548	3820	0.731417	GCTGCTGTATGCTGGTGAAG	59.269	55.000	0.00	0.00	43.37	3.02
3549	3821	1.676916	GCTGCTGTATGCTGGTGAAGA	60.677	52.381	0.00	0.00	43.37	2.87
3558	3834	1.948834	TGCTGGTGAAGATTGTGTGTG	59.051	47.619	0.00	0.00	0.00	3.82
3697	4675	4.749099	TGTTGCAAAAATTGGACTGCATAC	59.251	37.500	0.00	7.01	43.83	2.39
3728	4706	7.926018	GTGTTTTGAATAGTGACCCTTCATTTT	59.074	33.333	0.00	0.00	33.11	1.82
3816	4905	3.750130	GTCCTTAAGGTCCGGAAGAAAAC	59.250	47.826	21.04	3.77	36.34	2.43
3819	4908	4.765339	CCTTAAGGTCCGGAAGAAAACAAT	59.235	41.667	13.83	0.00	0.00	2.71
3848	4937	8.879427	AACTTCCAAAATTATTGCTACCTAGT	57.121	30.769	0.00	0.00	0.00	2.57
3849	4938	9.969001	AACTTCCAAAATTATTGCTACCTAGTA	57.031	29.630	0.00	0.00	0.00	1.82
3914	5003	6.294731	GGAGAAACAAGCTGGATACACATTTT	60.295	38.462	0.00	0.00	46.17	1.82
3928	5092	8.784043	GGATACACATTTTTCTTCTTGTACAGT	58.216	33.333	0.00	0.00	0.00	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
76	77	9.416794	ACATGTGCAACGAAAAATTCATAAATA	57.583	25.926	0.00	0.00	42.39	1.40
117	119	7.133513	GCAAAATGAACAGAAAATTGATTGCA	58.866	30.769	0.00	0.00	38.42	4.08
256	258	4.216042	CACACCAGATGTTAAACATGCTGA	59.784	41.667	2.50	0.00	40.64	4.26
404	408	2.611292	CTGCTTCAAGATCTAAAGGGCG	59.389	50.000	15.79	3.87	0.00	6.13
455	459	3.173965	CCTTCTTCCTCCTCCTACACAA	58.826	50.000	0.00	0.00	0.00	3.33
551	555	3.564218	GCCATCTCTCGCCCCCAT	61.564	66.667	0.00	0.00	0.00	4.00
961	967	4.913784	TGGATTAACCACTTTGAGGTACC	58.086	43.478	2.73	2.73	44.64	3.34
1228	1246	3.000080	GCGTTTCGTCGAGCAGGTG	62.000	63.158	0.00	0.00	0.00	4.00
1273	1291	2.107953	GTGGAGCGAGATGAGGGC	59.892	66.667	0.00	0.00	0.00	5.19
1383	1401	2.660552	ACCGTGAACTCGTTGGCG	60.661	61.111	0.00	0.00	39.92	5.69
1590	1608	2.163818	TAACAGCAGTCCAGGAAACG	57.836	50.000	0.00	0.00	0.00	3.60
1705	1723	1.400846	GCATGCCTGAATGACACTCAG	59.599	52.381	6.36	6.94	40.08	3.35
1743	1761	1.168714	GCACCTGACTGAACAATCCC	58.831	55.000	0.00	0.00	0.00	3.85
1746	1764	1.949525	GTGTGCACCTGACTGAACAAT	59.050	47.619	15.69	0.00	0.00	2.71
1757	1775	0.107017	AGCAACAAGAGTGTGCACCT	60.107	50.000	15.69	11.06	38.27	4.00
1765	1783	0.535102	CCCAACCGAGCAACAAGAGT	60.535	55.000	0.00	0.00	0.00	3.24
1794	1812	4.003648	GAGAATTCACCACCGAAACATCT	58.996	43.478	8.44	0.00	0.00	2.90
2139	2157	3.887621	TTTACATAGTCGCTCTTGGCT	57.112	42.857	0.00	0.00	39.13	4.75
2148	2166	5.006746	GTCCAAGGCTTCATTTACATAGTCG	59.993	44.000	0.00	0.00	0.00	4.18
2220	2238	2.304092	ACTACACTCAAGACCGTGACA	58.696	47.619	0.00	0.00	35.23	3.58
2235	2253	0.983467	TGGAGCATGCCTGAACTACA	59.017	50.000	15.66	0.00	0.00	2.74
2271	2289	1.107538	CATGGAGCATCTGCCCTTGG	61.108	60.000	13.22	0.00	43.38	3.61
2291	2309	8.742188	GCACAAAACCATATTTTACGATGTATG	58.258	33.333	0.00	0.00	0.00	2.39
2298	2316	5.147865	TCGTGCACAAAACCATATTTTACG	58.852	37.500	18.64	0.00	0.00	3.18
2325	2343	7.845037	TGATTATTAGAGCATTGGAGATCGAT	58.155	34.615	0.00	0.00	0.00	3.59
2358	2376	4.640647	GCGGAATCAATCCTTCCTAACTTT	59.359	41.667	1.05	0.00	46.98	2.66
2370	2388	4.630111	AGATCTTCTCAGCGGAATCAATC	58.370	43.478	0.00	0.00	0.00	2.67
2394	2412	1.562008	TCCTTAACATCCATCCGCCAA	59.438	47.619	0.00	0.00	0.00	4.52
2395	2413	1.134220	GTCCTTAACATCCATCCGCCA	60.134	52.381	0.00	0.00	0.00	5.69
2466	2484	5.007724	GTGGAAATACTTTAGAGCCGAATGG	59.992	44.000	0.00	0.00	38.77	3.16
2469	2487	4.020039	TGGTGGAAATACTTTAGAGCCGAA	60.020	41.667	0.00	0.00	0.00	4.30
2472	2490	3.628032	GCTGGTGGAAATACTTTAGAGCC	59.372	47.826	0.00	0.00	0.00	4.70
2658	2676	0.771127	TCCCAGACCTTCCAAACAGG	59.229	55.000	0.00	0.00	37.45	4.00
2683	2701	1.601430	GATGAATTCTTCTGCCTCGGC	59.399	52.381	12.81	0.00	42.35	5.54
2685	2703	2.871022	CCTGATGAATTCTTCTGCCTCG	59.129	50.000	18.92	5.70	0.00	4.63
2763	2781	4.679662	CAAGATCAACATTCCCATGAAGC	58.320	43.478	0.00	0.00	33.05	3.86
2877	2895	5.123027	CCTAATCTTTGCAGAGTCTTTCCAC	59.877	44.000	3.90	0.00	30.36	4.02
2912	2930	2.299297	TCCTTTCTCAAACCGACTCTCC	59.701	50.000	0.00	0.00	0.00	3.71
3072	3090	1.082679	CCAGACTCAGCTGATGCACG	61.083	60.000	18.63	7.67	42.74	5.34
3194	3212	8.950210	AGAACACAAATTAATAGATCTGGTGTG	58.050	33.333	5.18	10.63	37.08	3.82
3356	3375	5.514204	CGTGAGGACTATTACCTTTACAACG	59.486	44.000	0.00	0.00	37.93	4.10
3414	3441	7.565323	AGAACTCCATATCAGCAAGATTTTC	57.435	36.000	0.00	0.00	38.19	2.29
3415	3442	7.951347	AAGAACTCCATATCAGCAAGATTTT	57.049	32.000	0.00	0.00	38.19	1.82
3432	3461	7.442364	TCAGCAACCATATTAGCATAAGAACTC	59.558	37.037	0.00	0.00	0.00	3.01
3491	3763	0.471591	ACCCTGCAGAAATTGGGCAA	60.472	50.000	17.39	0.00	43.25	4.52
3495	3767	3.749665	TTTGAACCCTGCAGAAATTGG	57.250	42.857	17.39	10.04	0.00	3.16
3505	3777	4.237349	ACGTGCTAAAATTTGAACCCTG	57.763	40.909	0.00	0.00	0.00	4.45
3533	3805	4.005650	ACACAATCTTCACCAGCATACAG	58.994	43.478	0.00	0.00	0.00	2.74
3548	3820	0.388907	GCACATGGGCACACACAATC	60.389	55.000	16.99	0.00	0.00	2.67
3549	3821	0.828762	AGCACATGGGCACACACAAT	60.829	50.000	24.51	0.00	35.83	2.71
3558	3834	5.407407	AGTATACTACATAGCACATGGGC	57.593	43.478	13.49	13.49	0.00	5.36
3697	4675	4.082245	GGGTCACTATTCAAAACACATGGG	60.082	45.833	0.00	0.00	0.00	4.00
3796	4885	3.746940	TGTTTTCTTCCGGACCTTAAGG	58.253	45.455	20.42	20.42	42.17	2.69
3819	4908	9.528489	AGGTAGCAATAATTTTGGAAGTTCTTA	57.472	29.630	2.25	0.00	0.00	2.10
3835	4924	5.647230	TGCAGGGTATACTAGGTAGCAATA	58.353	41.667	2.25	0.00	0.00	1.90
3843	4932	4.649674	TCTTGTCTTGCAGGGTATACTAGG	59.350	45.833	2.25	0.00	0.00	3.02
3848	4937	6.553953	TGTATTCTTGTCTTGCAGGGTATA	57.446	37.500	0.00	0.00	0.00	1.47
3849	4938	5.435686	TGTATTCTTGTCTTGCAGGGTAT	57.564	39.130	0.00	0.00	0.00	2.73
3894	4983	6.655078	AGAAAAATGTGTATCCAGCTTGTT	57.345	33.333	0.00	0.00	0.00	2.83
3977	5141	0.179100	TCCTGATGCGCAAGTAGAGC	60.179	55.000	17.11	0.00	44.03	4.09
3986	5150	0.872021	CCGTAGTTCTCCTGATGCGC	60.872	60.000	0.00	0.00	0.00	6.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.