AutoCloner

Multiple sequence alignment - TraesCS6D01G047300

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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	TraesCS6D01G047300	chr6D	100.000	3062	0	0	1	3062	21915786	21912725	0.000000e+00	5655.0
1	TraesCS6D01G047300	chr6D	91.862	639	46	3	2351	2988	21613109	21613742	0.000000e+00	887.0
2	TraesCS6D01G047300	chr6D	93.212	604	23	5	1755	2346	21612431	21613028	0.000000e+00	872.0
3	TraesCS6D01G047300	chr6D	93.072	433	21	4	52	484	21611998	21612421	2.590000e-175	625.0
4	TraesCS6D01G047300	chr6D	79.503	483	72	18	1723	2193	21701223	21701690	4.930000e-83	318.0
5	TraesCS6D01G047300	chr6D	74.784	809	149	32	1552	2323	21052916	21053706	2.290000e-81	313.0
6	TraesCS6D01G047300	chr6D	86.585	82	2	2	2987	3060	21621518	21621598	7.040000e-12	82.4
7	TraesCS6D01G047300	chr6B	93.548	1984	111	7	1008	2988	36176117	36178086	0.000000e+00	2939.0
8	TraesCS6D01G047300	chr6B	91.024	1025	71	11	1	1019	36175008	36176017	0.000000e+00	1363.0
9	TraesCS6D01G047300	chr6B	77.444	1330	206	53	1028	2307	36039117	36040402	0.000000e+00	708.0
10	TraesCS6D01G047300	chr6B	78.394	1046	176	26	1017	2049	36137657	36138665	4.310000e-178	634.0
11	TraesCS6D01G047300	chr6B	86.667	75	2	1	2996	3062	36178523	36178597	3.270000e-10	76.8
12	TraesCS6D01G047300	chr6A	88.876	890	61	20	875	1736	21504981	21505860	0.000000e+00	1061.0
13	TraesCS6D01G047300	chr6A	85.965	684	77	13	167	844	21346668	21347338	0.000000e+00	713.0
14	TraesCS6D01G047300	chr6A	75.991	1362	229	50	1017	2323	21320984	21322302	5.610000e-172	614.0
15	TraesCS6D01G047300	chr6A	75.848	973	155	44	1405	2323	21315961	21316907	3.650000e-114	422.0
16	TraesCS6D01G047300	chr6A	75.848	973	155	44	1405	2323	21327602	21328548	3.650000e-114	422.0
17	TraesCS6D01G047300	chr6A	84.858	317	30	13	590	892	21449358	21449670	1.380000e-78	303.0
18	TraesCS6D01G047300	chr6A	86.250	80	2	2	2987	3058	21511759	21511837	9.100000e-11	78.7
19	TraesCS6D01G047300	chr4A	80.505	277	47	7	1092	1363	45149877	45149603	4.000000e-49	206.0
20	TraesCS6D01G047300	chr4B	78.125	352	55	16	1092	1438	517429771	517430105	1.440000e-48	204.0
21	TraesCS6D01G047300	chr2D	78.878	303	58	6	1060	1359	56193038	56193337	1.860000e-47	200.0
22	TraesCS6D01G047300	chr2D	79.182	269	50	6	1096	1363	628581699	628581436	6.740000e-42	182.0
23	TraesCS6D01G047300	chr2D	79.435	248	48	3	1098	1345	628663294	628663538	4.060000e-39	172.0
24	TraesCS6D01G047300	chr2D	97.872	47	1	0	1466	1512	628587450	628587404	7.040000e-12	82.4
25	TraesCS6D01G047300	chr2A	80.534	262	46	5	1100	1360	758583345	758583602	2.410000e-46	196.0
26	TraesCS6D01G047300	chr2A	97.872	47	1	0	1466	1512	758563504	758563550	7.040000e-12	82.4
27	TraesCS6D01G047300	chr2B	78.832	274	45	10	1099	1363	771823042	771822773	4.060000e-39	172.0
28	TraesCS6D01G047300	chr1B	91.304	69	5	1	1466	1534	471805631	471805564	3.250000e-15	93.5

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	TraesCS6D01G047300	chr6D	21912725	21915786	3061	True	5655.000000	5655	100.000000	1	3062	1	chr6D.!!$R1	3061
1	TraesCS6D01G047300	chr6D	21611998	21613742	1744	False	794.666667	887	92.715333	52	2988	3	chr6D.!!$F4	2936
2	TraesCS6D01G047300	chr6D	21052916	21053706	790	False	313.000000	313	74.784000	1552	2323	1	chr6D.!!$F1	771
3	TraesCS6D01G047300	chr6B	36175008	36178597	3589	False	1459.600000	2939	90.413000	1	3062	3	chr6B.!!$F3	3061
4	TraesCS6D01G047300	chr6B	36039117	36040402	1285	False	708.000000	708	77.444000	1028	2307	1	chr6B.!!$F1	1279
5	TraesCS6D01G047300	chr6B	36137657	36138665	1008	False	634.000000	634	78.394000	1017	2049	1	chr6B.!!$F2	1032
6	TraesCS6D01G047300	chr6A	21504981	21505860	879	False	1061.000000	1061	88.876000	875	1736	1	chr6A.!!$F6	861
7	TraesCS6D01G047300	chr6A	21346668	21347338	670	False	713.000000	713	85.965000	167	844	1	chr6A.!!$F4	677
8	TraesCS6D01G047300	chr6A	21320984	21322302	1318	False	614.000000	614	75.991000	1017	2323	1	chr6A.!!$F2	1306
9	TraesCS6D01G047300	chr6A	21315961	21316907	946	False	422.000000	422	75.848000	1405	2323	1	chr6A.!!$F1	918
10	TraesCS6D01G047300	chr6A	21327602	21328548	946	False	422.000000	422	75.848000	1405	2323	1	chr6A.!!$F3	918

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
320	321	0.034198	TCGCAACTGGGTCGATGAAA	59.966	50.0	0.0	0.0	0.0	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2092	2285	0.313672	TGGAATGTTTTGTCCAGCGC	59.686	50.0	0.0	0.0	39.04	5.92	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
32	33	6.239120	GCTATTATGGTGAATGCAATGAAGGT	60.239	38.462	0.00	0.00	0.00	3.50
58	59	2.363683	GAAGGAGGAGGAATGTGCAAG	58.636	52.381	0.00	0.00	0.00	4.01
94	95	8.548877	AGACATGTTAAGGTTAATGTCATACCT	58.451	33.333	14.92	1.89	43.98	3.08
124	125	2.850833	TCATGTGAAAGAGGAGGGGAT	58.149	47.619	0.00	0.00	0.00	3.85
128	129	2.027192	TGTGAAAGAGGAGGGGATTTCG	60.027	50.000	0.00	0.00	35.01	3.46
142	143	3.181510	GGGATTTCGTTGGAAGTGATTCG	60.182	47.826	0.00	0.00	32.80	3.34
187	188	4.166011	GAATGCCGCGACTGCCAC	62.166	66.667	8.23	0.00	38.08	5.01
218	219	1.649267	CGTGGAGATCTCGCGATCA	59.351	57.895	24.76	12.13	46.84	2.92
222	223	3.609409	CGTGGAGATCTCGCGATCAATTA	60.609	47.826	24.76	0.00	46.84	1.40
231	232	4.340097	TCTCGCGATCAATTAGGAAGGTTA	59.660	41.667	10.36	0.00	0.00	2.85
320	321	0.034198	TCGCAACTGGGTCGATGAAA	59.966	50.000	0.00	0.00	0.00	2.69
488	495	4.319177	CGTTTTCCTCATCTTCAACCTCT	58.681	43.478	0.00	0.00	0.00	3.69
511	518	3.634448	CAGACTCGACTACCATCCAATCT	59.366	47.826	0.00	0.00	0.00	2.40
540	547	0.034616	TGCAAAATGAAAAGGCCCCG	59.965	50.000	0.00	0.00	0.00	5.73
572	579	0.809385	TTAACTCTCGTCCTCGCCTG	59.191	55.000	0.00	0.00	36.96	4.85
607	614	3.812019	CGTCCTCGTCTCCGGTGG	61.812	72.222	0.00	0.00	33.95	4.61
613	620	1.812686	CTCGTCTCCGGTGGGTTGAA	61.813	60.000	0.00	0.00	33.95	2.69
621	628	0.321298	CGGTGGGTTGAATCGTCCTT	60.321	55.000	0.00	0.00	0.00	3.36
635	642	4.351054	CCTTGCTGGCGTCCCCTT	62.351	66.667	0.00	0.00	0.00	3.95
652	659	1.227943	TTGCCTCACTGCCACTCAC	60.228	57.895	0.00	0.00	0.00	3.51
677	684	0.179084	CGCCATGTCTCGGTATTGGT	60.179	55.000	0.00	0.00	0.00	3.67
725	732	8.076178	GGAATCGACATACCCAATTCTTATTTG	58.924	37.037	0.00	0.00	0.00	2.32
728	735	6.375736	TCGACATACCCAATTCTTATTTGCAA	59.624	34.615	0.00	0.00	0.00	4.08
749	756	6.538021	TGCAAACAACTGTTGAATAGCAAAAT	59.462	30.769	26.00	0.00	38.44	1.82
755	762	8.362639	ACAACTGTTGAATAGCAAAATCAGAAT	58.637	29.630	26.00	0.00	38.44	2.40
859	874	2.920724	TGTTCAGAAATGGACACCGA	57.079	45.000	0.00	0.00	0.00	4.69
893	908	2.673368	CCAGTCATCTAAAAGACACCGC	59.327	50.000	0.00	0.00	37.23	5.68
895	910	3.614616	CAGTCATCTAAAAGACACCGCTC	59.385	47.826	0.00	0.00	37.23	5.03
972	996	1.153349	GCAGAGCTAGGGTTTCCGG	60.153	63.158	0.00	0.00	38.33	5.14
1128	1282	3.518634	GAGCTCGTGGAAGAGATCTTT	57.481	47.619	0.00	0.00	46.67	2.52
1202	1356	1.915614	TTCTACCGTCTCGTCGCCAC	61.916	60.000	0.00	0.00	0.00	5.01
1268	1422	1.715862	CTCGGCTTCCTCGATCACGA	61.716	60.000	0.00	0.00	46.56	4.35
1278	1432	2.561733	TCGATCACGAGCGAGAATTT	57.438	45.000	2.84	0.00	44.77	1.82
1572	1738	0.394899	GATGGCAGACCTTCCTTGGG	60.395	60.000	0.00	0.00	34.70	4.12
1815	1987	4.840716	AATGGAGTTCTCTCTTGCTGAT	57.159	40.909	0.00	0.00	40.29	2.90
1919	2112	1.627834	TGTGCATCCAGGTCACACATA	59.372	47.619	6.98	0.00	36.39	2.29
1920	2113	2.239402	TGTGCATCCAGGTCACACATAT	59.761	45.455	6.98	0.00	36.39	1.78
1921	2114	3.454082	TGTGCATCCAGGTCACACATATA	59.546	43.478	6.98	0.00	36.39	0.86
2059	2252	0.381801	CTTGCTTCTGCGTTGTTGGT	59.618	50.000	0.00	0.00	43.34	3.67
2076	2269	0.181350	GGTGAGAATTCCCATCGCCT	59.819	55.000	15.18	0.00	39.90	5.52
2081	2274	1.072965	AGAATTCCCATCGCCTGATCC	59.927	52.381	0.65	0.00	30.49	3.36
2092	2285	2.772739	CCTGATCCAGGCACTTTCG	58.227	57.895	0.00	0.00	45.13	3.46
2214	2416	5.773575	TCATGCGGTAAACATTTTGCTTTA	58.226	33.333	0.00	0.00	0.00	1.85
2229	2431	8.787852	CATTTTGCTTTATCCTACCTATTCTCC	58.212	37.037	0.00	0.00	0.00	3.71
2307	2515	8.681806	TGATTAATTCTTGTTGACACTGTTTGA	58.318	29.630	0.00	0.00	0.00	2.69
2450	2736	4.744795	TTAAGGCCAAACAAAGCAAAGA	57.255	36.364	5.01	0.00	0.00	2.52
2463	2749	7.951530	ACAAAGCAAAGAATTTCCACATTAG	57.048	32.000	0.00	0.00	35.03	1.73
2496	2782	2.398588	AGAGGCCTCATGGAATCGTAA	58.601	47.619	33.90	0.00	34.57	3.18
2497	2783	2.771943	AGAGGCCTCATGGAATCGTAAA	59.228	45.455	33.90	0.00	34.57	2.01
2498	2784	3.199946	AGAGGCCTCATGGAATCGTAAAA	59.800	43.478	33.90	0.00	34.57	1.52
2499	2785	3.945285	GAGGCCTCATGGAATCGTAAAAA	59.055	43.478	28.43	0.00	34.57	1.94
2628	2915	4.631377	TCAAGTCAAGCGTTCCATATCTTG	59.369	41.667	0.00	0.00	37.76	3.02
2733	3020	2.512515	GAGCCATCGCCACCACTC	60.513	66.667	0.00	0.00	34.57	3.51
2773	3060	6.985188	TGATATGAGTAAAGTTGAAGTGGC	57.015	37.500	0.00	0.00	0.00	5.01
2791	3078	5.656480	AGTGGCGAAATTTGTTACTTTTGT	58.344	33.333	0.00	0.00	0.00	2.83
2793	3080	6.035542	AGTGGCGAAATTTGTTACTTTTGTTG	59.964	34.615	0.00	0.00	0.00	3.33
2867	3154	6.189859	TGATTCAAAATGAACTAGGGCATCT	58.810	36.000	0.00	0.00	39.45	2.90
2882	3169	6.018433	AGGGCATCTATATTTGTTTGGACT	57.982	37.500	0.00	0.00	0.00	3.85
2900	3187	5.187687	TGGACTGTTTAAACTTTCGACCTT	58.812	37.500	18.72	0.00	0.00	3.50
2910	3197	4.701651	ACTTTCGACCTTCCTTTACCTT	57.298	40.909	0.00	0.00	0.00	3.50
2918	3205	6.042437	TCGACCTTCCTTTACCTTAGTCTTTT	59.958	38.462	0.00	0.00	0.00	2.27
2920	3207	7.874528	CGACCTTCCTTTACCTTAGTCTTTTAA	59.125	37.037	0.00	0.00	0.00	1.52
2988	3275	5.997746	ACAGAGCACACACATAGTTTATTGT	59.002	36.000	0.00	0.00	0.00	2.71
2990	3277	6.369890	CAGAGCACACACATAGTTTATTGTCT	59.630	38.462	0.00	0.00	0.00	3.41
2991	3278	6.936900	AGAGCACACACATAGTTTATTGTCTT	59.063	34.615	0.00	0.00	0.00	3.01
2992	3279	8.094548	AGAGCACACACATAGTTTATTGTCTTA	58.905	33.333	0.00	0.00	0.00	2.10
2993	3280	8.792830	AGCACACACATAGTTTATTGTCTTAT	57.207	30.769	0.00	0.00	0.00	1.73
2994	3281	9.231297	AGCACACACATAGTTTATTGTCTTATT	57.769	29.630	0.00	0.00	0.00	1.40
2995	3282	9.277565	GCACACACATAGTTTATTGTCTTATTG	57.722	33.333	0.00	0.00	0.00	1.90
3047	3771	4.460263	ACTCTTATGAACCTTGCAACACA	58.540	39.130	0.00	0.00	0.00	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	5.518848	TGCATTCACCATAATAGCCAAAG	57.481	39.130	0.00	0.00	0.00	2.77
9	10	7.490840	CAACCTTCATTGCATTCACCATAATA	58.509	34.615	0.00	0.00	0.00	0.98
14	15	3.663995	CAACCTTCATTGCATTCACCA	57.336	42.857	0.00	0.00	0.00	4.17
32	33	1.283029	CATTCCTCCTCCTTCCTGCAA	59.717	52.381	0.00	0.00	0.00	4.08
36	37	0.915364	GCACATTCCTCCTCCTTCCT	59.085	55.000	0.00	0.00	0.00	3.36
58	59	3.462021	CTTAACATGTCTAGGGCTCAGC	58.538	50.000	0.00	0.00	0.00	4.26
94	95	7.252612	TCCTCTTTCACATGATTACACCTTA	57.747	36.000	0.00	0.00	0.00	2.69
124	125	2.147958	CCCGAATCACTTCCAACGAAA	58.852	47.619	0.00	0.00	0.00	3.46
128	129	1.133025	CATGCCCGAATCACTTCCAAC	59.867	52.381	0.00	0.00	0.00	3.77
187	188	0.096976	CTCCACGCAAACCGCATAAG	59.903	55.000	0.00	0.00	42.60	1.73
222	223	6.406370	GGCAATGCTTAAATTTAACCTTCCT	58.594	36.000	4.82	0.00	0.00	3.36
231	232	5.643379	TCTCTTCGGCAATGCTTAAATTT	57.357	34.783	4.82	0.00	0.00	1.82
287	288	7.312899	ACCCAGTTGCGATTTTCTAATAAAAG	58.687	34.615	0.00	0.00	0.00	2.27
302	303	0.165944	GTTTCATCGACCCAGTTGCG	59.834	55.000	0.00	0.00	0.00	4.85
320	321	1.898863	ACATGGAAGATAGCCAGGGT	58.101	50.000	0.00	0.00	41.27	4.34
488	495	2.801077	TGGATGGTAGTCGAGTCTGA	57.199	50.000	0.00	0.00	0.00	3.27
511	518	0.602060	TCATTTTGCATTGCCGCTCA	59.398	45.000	6.12	0.00	0.00	4.26
540	547	4.082354	ACGAGAGTTAACAGGTACATGGTC	60.082	45.833	12.79	0.00	46.40	4.02
582	589	3.164011	GACGAGGACGACGCAACG	61.164	66.667	0.00	0.00	42.66	4.10
607	614	0.804989	CCAGCAAGGACGATTCAACC	59.195	55.000	0.00	0.00	41.22	3.77
613	620	2.125512	GACGCCAGCAAGGACGAT	60.126	61.111	15.03	4.19	41.22	3.73
662	669	3.388024	ACATAGCACCAATACCGAGACAT	59.612	43.478	0.00	0.00	0.00	3.06
725	732	5.964887	TTTGCTATTCAACAGTTGTTTGC	57.035	34.783	13.14	13.63	35.83	3.68
728	735	7.715657	TCTGATTTTGCTATTCAACAGTTGTT	58.284	30.769	13.14	5.14	39.12	2.83
810	825	3.686241	CCAGTGACACATGTGAATGTAGG	59.314	47.826	31.94	19.89	32.74	3.18
811	826	4.318332	ACCAGTGACACATGTGAATGTAG	58.682	43.478	31.94	17.20	32.74	2.74
812	827	4.350368	ACCAGTGACACATGTGAATGTA	57.650	40.909	31.94	10.04	32.74	2.29
859	874	2.885135	TGACTGGGCATGTGAAGAAT	57.115	45.000	0.00	0.00	0.00	2.40
893	908	4.457257	GGAAAGTGTCCATTTCTGAAGGAG	59.543	45.833	0.00	0.00	46.97	3.69
895	910	4.773323	GGAAAGTGTCCATTTCTGAAGG	57.227	45.455	0.00	0.00	46.97	3.46
972	996	1.737201	GGAGAACGAGGAGCTAGCC	59.263	63.158	12.13	2.59	0.00	3.93
1398	1552	2.158959	GTTGCGGACGTCCTCGATG	61.159	63.158	30.92	16.74	40.62	3.84
1815	1987	1.076727	TCTCGCTTCAGGTGGGAGA	59.923	57.895	6.44	6.44	46.43	3.71
1840	2012	2.526304	ATATCCACATCACGTTCCGG	57.474	50.000	0.00	0.00	0.00	5.14
1921	2114	9.929180	TCGCTTAATTAGATAACTGATGCTATT	57.071	29.630	0.00	0.00	0.00	1.73
1969	2162	3.753294	TGTCTTCTCCAACTTCCACTC	57.247	47.619	0.00	0.00	0.00	3.51
2059	2252	1.203237	TCAGGCGATGGGAATTCTCA	58.797	50.000	11.20	11.20	0.00	3.27
2076	2269	1.741401	CGCGAAAGTGCCTGGATCA	60.741	57.895	0.00	0.00	33.37	2.92
2092	2285	0.313672	TGGAATGTTTTGTCCAGCGC	59.686	50.000	0.00	0.00	39.04	5.92
2214	2416	4.423960	TGGAGGAAGGAGAATAGGTAGGAT	59.576	45.833	0.00	0.00	0.00	3.24
2229	2431	7.269514	AGGTGTGTGAAACCTATGGAGGAAG	62.270	48.000	0.00	0.00	46.44	3.46
2358	2642	5.376854	GCTTGATTAGCCTTGAAACAAGA	57.623	39.130	12.25	0.00	44.48	3.02
2450	2736	8.814038	AGAATGCTACTTCTAATGTGGAAATT	57.186	30.769	0.00	0.00	33.73	1.82
2463	2749	3.639094	TGAGGCCTCTAGAATGCTACTTC	59.361	47.826	32.28	2.27	0.00	3.01
2773	3060	8.812329	TCCATTCAACAAAAGTAACAAATTTCG	58.188	29.630	0.00	0.00	0.00	3.46
2835	3122	8.514594	CCTAGTTCATTTTGAATCAAACAGCTA	58.485	33.333	8.06	6.45	38.79	3.32
2848	3135	9.903682	CAAATATAGATGCCCTAGTTCATTTTG	57.096	33.333	0.00	0.00	0.00	2.44
2882	3169	6.762702	AAAGGAAGGTCGAAAGTTTAAACA	57.237	33.333	20.06	0.00	0.00	2.83
2894	3181	5.402997	AAGACTAAGGTAAAGGAAGGTCG	57.597	43.478	0.00	0.00	0.00	4.79
2900	3187	8.255905	CCTCGATTAAAAGACTAAGGTAAAGGA	58.744	37.037	0.00	0.00	0.00	3.36
2910	3197	5.730550	ACATGTGCCTCGATTAAAAGACTA	58.269	37.500	0.00	0.00	0.00	2.59
2918	3205	5.912892	TGAATTAGACATGTGCCTCGATTA	58.087	37.500	1.15	0.00	0.00	1.75
2920	3207	4.406648	TGAATTAGACATGTGCCTCGAT	57.593	40.909	1.15	0.00	0.00	3.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.