AutoCloner

Multiple sequence alignment - TraesCS7A01G084000

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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	TraesCS7A01G084000	chr7A	100.000	2994	0	0	1	2994	48714325	48717318	0.000000e+00	5529
1	TraesCS7A01G084000	chr7A	85.590	1499	166	32	847	2313	48583205	48584685	0.000000e+00	1526
2	TraesCS7A01G084000	chr7A	85.484	992	86	36	779	1742	48755486	48756447	0.000000e+00	981
3	TraesCS7A01G084000	chr7A	82.245	1087	132	32	1325	2385	48525972	48527023	0.000000e+00	881
4	TraesCS7A01G084000	chr7A	87.801	664	42	15	2352	2990	48584999	48585648	0.000000e+00	741
5	TraesCS7A01G084000	chr7A	88.651	608	64	4	1	603	48580680	48581287	0.000000e+00	736
6	TraesCS7A01G084000	chr7A	84.457	341	29	12	2278	2615	48527039	48527358	6.230000e-82	315
7	TraesCS7A01G084000	chr7A	90.769	130	9	1	602	731	48582702	48582828	1.430000e-38	171
8	TraesCS7A01G084000	chr7D	83.757	2284	230	68	779	2990	46671323	46669109	0.000000e+00	2032
9	TraesCS7A01G084000	chr7D	86.101	1108	100	27	1540	2615	46711926	46710841	0.000000e+00	1144
10	TraesCS7A01G084000	chr7D	82.544	1077	89	51	710	1743	46586950	46585930	0.000000e+00	856
11	TraesCS7A01G084000	chr7D	91.722	604	48	2	1	603	46672884	46672282	0.000000e+00	837
12	TraesCS7A01G084000	chr7D	91.892	74	6	0	658	731	46671406	46671333	1.470000e-18	104
13	TraesCS7A01G084000	chr4A	86.925	1522	129	38	709	2216	660624183	660625648	0.000000e+00	1644
14	TraesCS7A01G084000	chr4A	90.137	801	52	16	2209	2992	660628380	660629170	0.000000e+00	1016
15	TraesCS7A01G084000	chr4A	82.690	1011	85	44	780	1743	660653754	660654721	0.000000e+00	815
16	TraesCS7A01G084000	chr4A	80.797	1104	150	33	1325	2401	660452450	660453518	0.000000e+00	808
17	TraesCS7A01G084000	chr4A	89.292	607	59	5	1	603	660619549	660620153	0.000000e+00	756
18	TraesCS7A01G084000	chr4A	86.218	312	28	8	2286	2597	660453521	660453817	1.040000e-84	324
19	TraesCS7A01G084000	chr4A	75.796	471	79	21	141	603	660652675	660653118	3.910000e-49	206

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	TraesCS7A01G084000	chr7A	48714325	48717318	2993	False	5529.0	5529	100.000000	1	2994	1	chr7A.!!$F1	2993
1	TraesCS7A01G084000	chr7A	48755486	48756447	961	False	981.0	981	85.484000	779	1742	1	chr7A.!!$F2	963
2	TraesCS7A01G084000	chr7A	48580680	48585648	4968	False	793.5	1526	88.202750	1	2990	4	chr7A.!!$F4	2989
3	TraesCS7A01G084000	chr7A	48525972	48527358	1386	False	598.0	881	83.351000	1325	2615	2	chr7A.!!$F3	1290
4	TraesCS7A01G084000	chr7D	46710841	46711926	1085	True	1144.0	1144	86.101000	1540	2615	1	chr7D.!!$R2	1075
5	TraesCS7A01G084000	chr7D	46669109	46672884	3775	True	991.0	2032	89.123667	1	2990	3	chr7D.!!$R3	2989
6	TraesCS7A01G084000	chr7D	46585930	46586950	1020	True	856.0	856	82.544000	710	1743	1	chr7D.!!$R1	1033
7	TraesCS7A01G084000	chr4A	660624183	660629170	4987	False	1330.0	1644	88.531000	709	2992	2	chr4A.!!$F3	2283
8	TraesCS7A01G084000	chr4A	660619549	660620153	604	False	756.0	756	89.292000	1	603	1	chr4A.!!$F1	602
9	TraesCS7A01G084000	chr4A	660452450	660453817	1367	False	566.0	808	83.507500	1325	2597	2	chr4A.!!$F2	1272
10	TraesCS7A01G084000	chr4A	660652675	660654721	2046	False	510.5	815	79.243000	141	1743	2	chr4A.!!$F4	1602

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
413	423	0.041047	CGTGGCATGTATCATTGGCG	60.041	55.0	0.00	0.0	41.0	5.69	F
988	2791	0.468214	TCTCAGATCGGATCGGGCTT	60.468	55.0	16.34	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1386	3245	0.471780	TGAAGCACTCCTCCAGGACA	60.472	55.0	0.0	0.0	39.78	4.02	R
2053	3988	0.943673	CGTGAGTTGTGACAATGCCA	59.056	50.0	0.0	0.0	0.00	4.92	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
24	27	1.881252	GCACGAGACAACCACACGT	60.881	57.895	0.00	0.00	37.68	4.49
65	68	1.361668	CGGTCCTGCATTGAGTTCCG	61.362	60.000	0.00	0.00	0.00	4.30
66	69	1.648467	GGTCCTGCATTGAGTTCCGC	61.648	60.000	0.00	0.00	0.00	5.54
70	73	2.099062	GCATTGAGTTCCGCTGCG	59.901	61.111	16.34	16.34	0.00	5.18
79	82	0.643820	GTTCCGCTGCGTACACATAC	59.356	55.000	21.59	4.27	0.00	2.39
117	120	1.454847	TGCAAGCCCAAGGAAACGT	60.455	52.632	0.00	0.00	0.00	3.99
156	159	1.149101	AGACAGGGCAAGGAAAGGAA	58.851	50.000	0.00	0.00	0.00	3.36
186	191	2.124403	CCAGGAGGAGCATGCACC	60.124	66.667	24.95	24.95	37.47	5.01
187	192	2.672908	CAGGAGGAGCATGCACCA	59.327	61.111	31.88	0.00	40.26	4.17
391	401	8.774586	CATAGCTAAAATTCTATAAGCCGTGTT	58.225	33.333	0.00	0.00	33.63	3.32
413	423	0.041047	CGTGGCATGTATCATTGGCG	60.041	55.000	0.00	0.00	41.00	5.69
443	453	9.979578	TTTTATTTGTTGTAGTACGAGGTCTTA	57.020	29.630	0.00	0.00	0.00	2.10
527	537	9.474313	TGGCATTTTCTTAGTAGGTTTTATCAT	57.526	29.630	0.00	0.00	0.00	2.45
576	586	7.601856	TGGATTGGTATTTCACATTTGTCTTC	58.398	34.615	0.00	0.00	0.00	2.87
580	590	8.642935	TTGGTATTTCACATTTGTCTTCCATA	57.357	30.769	0.00	0.00	0.00	2.74
644	2130	2.033448	TGGCGCGGAATGGAAACT	59.967	55.556	8.83	0.00	0.00	2.66
645	2131	1.022451	GTGGCGCGGAATGGAAACTA	61.022	55.000	8.83	0.00	0.00	2.24
646	2132	0.742990	TGGCGCGGAATGGAAACTAG	60.743	55.000	8.83	0.00	0.00	2.57
655	2141	6.422701	CGCGGAATGGAAACTAGTATTTATCA	59.577	38.462	0.00	0.00	0.00	2.15
656	2142	7.117812	CGCGGAATGGAAACTAGTATTTATCAT	59.882	37.037	0.00	0.00	0.00	2.45
684	2170	1.470051	ACCCATTAATTCACGGCCAC	58.530	50.000	2.24	0.00	0.00	5.01
695	2181	8.734218	TTAATTCACGGCCACTTAATAATACA	57.266	30.769	2.24	0.00	0.00	2.29
746	2232	5.913137	TTACCCATTTAATCACAGCCAAG	57.087	39.130	0.00	0.00	0.00	3.61
750	2236	5.777732	ACCCATTTAATCACAGCCAAGTAAA	59.222	36.000	0.00	0.00	0.00	2.01
774	2267	7.628769	AAAAATTGAGTTGTTTGGATTGCTT	57.371	28.000	0.00	0.00	0.00	3.91
775	2268	8.729805	AAAAATTGAGTTGTTTGGATTGCTTA	57.270	26.923	0.00	0.00	0.00	3.09
776	2269	7.713764	AAATTGAGTTGTTTGGATTGCTTAC	57.286	32.000	0.00	0.00	0.00	2.34
777	2270	4.846779	TGAGTTGTTTGGATTGCTTACC	57.153	40.909	0.00	0.00	0.00	2.85
867	2660	4.666512	CTGCCTTATTTATAGCCCACCAT	58.333	43.478	0.00	0.00	0.00	3.55
897	2690	3.567579	ATGCCCACGGAACACCAGG	62.568	63.158	0.00	0.00	0.00	4.45
968	2771	1.133761	CCATCCTCTACACCGGAGAGA	60.134	57.143	17.94	11.32	42.69	3.10
988	2791	0.468214	TCTCAGATCGGATCGGGCTT	60.468	55.000	16.34	0.00	0.00	4.35
1091	2911	2.920912	GTCCTCCACCACCACCGA	60.921	66.667	0.00	0.00	0.00	4.69
1209	3056	2.032681	AACCAGCAGCGGAAGGAC	59.967	61.111	9.87	0.00	0.00	3.85
1410	3269	1.345741	CTGGAGGAGTGCTTCAAGACA	59.654	52.381	0.00	0.00	0.00	3.41
1473	3379	0.823769	ATCTATCCACCTCGCTCGCA	60.824	55.000	0.00	0.00	0.00	5.10
1543	3460	7.368059	ACCGAGGTTTCTTTATTGACAATTTC	58.632	34.615	5.89	0.00	0.00	2.17
1552	3469	7.950512	TCTTTATTGACAATTTCCAGAAGCAA	58.049	30.769	5.89	0.00	0.00	3.91
1562	3479	1.507141	CCAGAAGCAAAAGACGGCGT	61.507	55.000	14.65	14.65	34.54	5.68
1609	3526	1.152756	GCAGGTGGAGGTGTGGTTT	60.153	57.895	0.00	0.00	0.00	3.27
1726	3643	1.273606	CTCGAGAAGGAGGTTGCTGAA	59.726	52.381	6.58	0.00	0.00	3.02
1744	3661	4.394712	CTCCGGGCGCTCAAGGTT	62.395	66.667	8.62	0.00	0.00	3.50
1985	3917	2.342279	CGAAGGTGGTCAAGCCGA	59.658	61.111	0.00	0.00	41.21	5.54
2053	3988	3.698040	CCAGGCAAGCTAACAGAAATGAT	59.302	43.478	0.00	0.00	0.00	2.45
2072	4007	0.943673	TGGCATTGTCACAACTCACG	59.056	50.000	0.00	0.00	0.00	4.35
2085	4020	3.002348	ACAACTCACGAACTTAAGCAAGC	59.998	43.478	1.29	0.00	34.94	4.01
2104	4039	6.432472	AGCAAGCTTAGCAGAAAGTTTAATCT	59.568	34.615	18.74	0.00	29.97	2.40
2176	4113	1.000283	GGGCTGAATCGATCGATGAGT	60.000	52.381	29.99	15.67	34.70	3.41
2178	4115	2.728839	GGCTGAATCGATCGATGAGTTC	59.271	50.000	29.99	23.23	34.70	3.01
2273	6977	8.648693	ACTAGGAACTTACTAACATGTTGAGTT	58.351	33.333	21.42	21.23	41.75	3.01
2284	6988	9.032624	ACTAACATGTTGAGTTATAGTACACCT	57.967	33.333	21.42	0.00	31.64	4.00
2289	6993	9.302345	CATGTTGAGTTATAGTACACCTAACAG	57.698	37.037	12.09	0.00	0.00	3.16
2523	7645	4.620332	GCATTGCACTTGCCTATTTTACCA	60.620	41.667	9.22	0.00	41.18	3.25
2587	7717	5.634118	TGATCTCCTCATTTTGGTTGTTCT	58.366	37.500	0.00	0.00	0.00	3.01
2597	7727	7.786030	TCATTTTGGTTGTTCTGGTATTTCAA	58.214	30.769	0.00	0.00	0.00	2.69
2736	7885	2.812836	ATGGATTGCATGTGGAGACA	57.187	45.000	0.00	0.00	36.22	3.41
2743	7894	3.808466	TGCATGTGGAGACAGATAGAC	57.192	47.619	0.00	0.00	43.50	2.59
2780	7931	7.945033	TGTGAAATTTAGCATGAAAAAGGAC	57.055	32.000	0.00	0.00	0.00	3.85
2796	7947	9.581289	TGAAAAAGGACTTCTTTGTGGATATAA	57.419	29.630	0.00	0.00	44.30	0.98
2924	8080	2.273370	TACTTTCTCGCTAGCAACCG	57.727	50.000	16.45	0.00	0.00	4.44
2928	8084	2.434185	CTCGCTAGCAACCGCCAA	60.434	61.111	16.45	0.00	39.83	4.52
2933	8089	0.179137	GCTAGCAACCGCCAATTTCC	60.179	55.000	10.63	0.00	39.83	3.13
2965	8121	3.953612	TGCATGTCACAAGTCTTCCTTTT	59.046	39.130	0.00	0.00	0.00	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	27	4.563993	CGAAGGGGTACAACAATCTTGGTA	60.564	45.833	0.00	0.00	0.00	3.25
70	73	6.489127	TGGCTAAATTGTGTGTATGTGTAC	57.511	37.500	0.00	0.00	0.00	2.90
79	82	3.983344	GCAGAACTTGGCTAAATTGTGTG	59.017	43.478	3.29	0.00	0.00	3.82
156	159	4.225573	CTCCTCCTGGATCTGAATCTTCT	58.774	47.826	0.00	0.00	42.29	2.85
363	369	9.419297	CACGGCTTATAGAATTTTAGCTATGTA	57.581	33.333	0.00	0.00	32.58	2.29
391	401	2.837498	CCAATGATACATGCCACGAGA	58.163	47.619	0.00	0.00	0.00	4.04
513	523	9.586435	GCTTTTAATGCAATGATAAAACCTACT	57.414	29.630	0.00	0.00	0.00	2.57
527	537	4.125703	CACTTTGGTGGCTTTTAATGCAA	58.874	39.130	5.25	0.00	39.59	4.08
655	2141	8.303876	GCCGTGAATTAATGGGTAAATAATGAT	58.696	33.333	3.04	0.00	0.00	2.45
656	2142	7.255660	GGCCGTGAATTAATGGGTAAATAATGA	60.256	37.037	3.04	0.00	0.00	2.57
672	2158	6.038936	GGTGTATTATTAAGTGGCCGTGAATT	59.961	38.462	0.00	0.00	0.00	2.17
695	2181	6.071984	TGGCGATAAATGGGTAAATAATGGT	58.928	36.000	0.00	0.00	0.00	3.55
750	2236	7.628769	AAGCAATCCAAACAACTCAATTTTT	57.371	28.000	0.00	0.00	0.00	1.94
753	2246	6.183360	TGGTAAGCAATCCAAACAACTCAATT	60.183	34.615	0.00	0.00	0.00	2.32
755	2248	4.646945	TGGTAAGCAATCCAAACAACTCAA	59.353	37.500	0.00	0.00	0.00	3.02
757	2250	4.518970	TCTGGTAAGCAATCCAAACAACTC	59.481	41.667	0.00	0.00	33.06	3.01
758	2251	4.469657	TCTGGTAAGCAATCCAAACAACT	58.530	39.130	0.00	0.00	33.06	3.16
760	2253	3.826157	CCTCTGGTAAGCAATCCAAACAA	59.174	43.478	0.00	0.00	33.06	2.83
763	2256	3.587061	TCTCCTCTGGTAAGCAATCCAAA	59.413	43.478	0.00	0.00	33.06	3.28
765	2258	2.768527	CTCTCCTCTGGTAAGCAATCCA	59.231	50.000	0.00	0.00	0.00	3.41
766	2259	2.103941	CCTCTCCTCTGGTAAGCAATCC	59.896	54.545	0.00	0.00	0.00	3.01
767	2260	3.034635	TCCTCTCCTCTGGTAAGCAATC	58.965	50.000	0.00	0.00	0.00	2.67
768	2261	3.037549	CTCCTCTCCTCTGGTAAGCAAT	58.962	50.000	0.00	0.00	0.00	3.56
769	2262	2.043115	TCTCCTCTCCTCTGGTAAGCAA	59.957	50.000	0.00	0.00	0.00	3.91
774	2267	2.445145	CTGGATCTCCTCTCCTCTGGTA	59.555	54.545	0.00	0.00	36.82	3.25
775	2268	1.217689	CTGGATCTCCTCTCCTCTGGT	59.782	57.143	0.00	0.00	36.82	4.00
776	2269	1.481055	CCTGGATCTCCTCTCCTCTGG	60.481	61.905	0.00	0.00	36.82	3.86
777	2270	1.999648	CCTGGATCTCCTCTCCTCTG	58.000	60.000	0.00	0.00	36.82	3.35
887	2680	0.257039	ATGATCTGGCCTGGTGTTCC	59.743	55.000	10.07	0.00	0.00	3.62
888	2681	1.065199	TGATGATCTGGCCTGGTGTTC	60.065	52.381	10.07	2.52	0.00	3.18
889	2682	0.994247	TGATGATCTGGCCTGGTGTT	59.006	50.000	10.07	0.00	0.00	3.32
890	2683	0.254178	GTGATGATCTGGCCTGGTGT	59.746	55.000	10.07	0.00	0.00	4.16
891	2684	0.253894	TGTGATGATCTGGCCTGGTG	59.746	55.000	10.07	0.00	0.00	4.17
897	2690	1.945394	GTGGTGATGTGATGATCTGGC	59.055	52.381	0.00	0.00	0.00	4.85
968	2771	0.251564	AGCCCGATCCGATCTGAGAT	60.252	55.000	6.81	0.00	0.00	2.75
988	2791	1.005748	GCATCATCGATCTCCGGCA	60.006	57.895	0.00	0.00	39.14	5.69
1019	2839	2.361357	CGAGGTCCAGGTCGAGGT	60.361	66.667	0.00	0.00	38.50	3.85
1112	2932	3.699894	AGTGCTGCGAGTGGGAGG	61.700	66.667	0.00	0.00	34.11	4.30
1113	2933	2.433838	CAGTGCTGCGAGTGGGAG	60.434	66.667	0.00	0.00	37.12	4.30
1164	3005	2.986979	TGCAGCCCGTACGACTCA	60.987	61.111	18.76	10.67	0.00	3.41
1321	3171	2.278013	GTCATCGTCCTCGTCGCC	60.278	66.667	0.00	0.00	38.33	5.54
1386	3245	0.471780	TGAAGCACTCCTCCAGGACA	60.472	55.000	0.00	0.00	39.78	4.02
1410	3269	2.591715	GGGTTGAGCGTGCTGTGT	60.592	61.111	0.00	0.00	0.00	3.72
1473	3379	3.711704	AGGAATCCATGGACGAACACTAT	59.288	43.478	18.99	0.00	0.00	2.12
1543	3460	1.207593	CGCCGTCTTTTGCTTCTGG	59.792	57.895	0.00	0.00	0.00	3.86
1552	3469	2.589442	TTCGCCAACGCCGTCTTT	60.589	55.556	0.00	0.00	39.84	2.52
1609	3526	4.717629	CGAGCACGGCGGTTCTGA	62.718	66.667	13.24	0.00	35.72	3.27
1621	3538	1.004560	CTTCAGCTTGGTCCGAGCA	60.005	57.895	29.42	10.22	42.91	4.26
1723	3640	3.589654	CTTGAGCGCCCGGAGTTCA	62.590	63.158	0.73	7.76	0.00	3.18
1888	3805	1.379710	TTGTTCGGGGGATGGCATG	60.380	57.895	3.81	0.00	0.00	4.06
1985	3917	5.361285	ACAGAGATAGCTCGTTTTATCTGGT	59.639	40.000	1.62	0.00	45.98	4.00
1993	3925	2.732597	GCGTCACAGAGATAGCTCGTTT	60.733	50.000	1.62	0.00	45.98	3.60
2034	3966	3.736126	GCCATCATTTCTGTTAGCTTGCC	60.736	47.826	0.00	0.00	0.00	4.52
2053	3988	0.943673	CGTGAGTTGTGACAATGCCA	59.056	50.000	0.00	0.00	0.00	4.92
2072	4007	5.613358	TTCTGCTAAGCTTGCTTAAGTTC	57.387	39.130	9.86	6.60	0.00	3.01
2192	4137	6.682113	GCTTTTCACATGCATACATTCATCCT	60.682	38.462	0.00	0.00	32.87	3.24
2289	6993	9.569167	GGTAGCAAATTAGAAAATTACTCAACC	57.431	33.333	0.00	0.00	34.12	3.77
2523	7645	8.472007	TGTTACTTGGACATGGAAAATTAACT	57.528	30.769	0.00	0.00	0.00	2.24
2551	7677	6.046290	TGAGGAGATCATGCACCTAATATG	57.954	41.667	0.00	0.00	31.12	1.78
2566	7696	4.768968	CCAGAACAACCAAAATGAGGAGAT	59.231	41.667	0.00	0.00	0.00	2.75
2597	7727	9.090103	TCCGAATATCACATAGAAAATAGAGGT	57.910	33.333	0.00	0.00	0.00	3.85
2770	7921	9.581289	TTATATCCACAAAGAAGTCCTTTTTCA	57.419	29.630	0.00	0.00	42.13	2.69
2924	8080	1.402107	ATGGGGATGCGGAAATTGGC	61.402	55.000	0.00	0.00	0.00	4.52
2928	8084	3.860681	GCATGGGGATGCGGAAAT	58.139	55.556	0.00	0.00	37.84	2.17
2965	8121	3.401033	TCTTGCAGATCGACCAAAAGA	57.599	42.857	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.