AutoCloner

Multiple sequence alignment - TraesCS1B01G305100

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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	TraesCS1B01G305100	chr1B	100.000	3735	0	0	1	3735	527844367	527848101	0.000000e+00	6898
1	TraesCS1B01G305100	chr1A	94.998	3019	99	27	726	3732	491146600	491149578	0.000000e+00	4691
2	TraesCS1B01G305100	chr1A	89.512	963	67	15	1572	2528	386379004	386379938	0.000000e+00	1188
3	TraesCS1B01G305100	chr1A	84.459	740	91	17	1	730	514859029	514859754	0.000000e+00	708
4	TraesCS1B01G305100	chr1A	84.459	740	91	17	1	730	515115274	515115999	0.000000e+00	708
5	TraesCS1B01G305100	chr1A	89.855	483	40	5	3	480	465448699	465448221	2.470000e-171	612
6	TraesCS1B01G305100	chr1A	95.652	46	2	0	2529	2574	386379960	386380005	1.440000e-09	75
7	TraesCS1B01G305100	chr1D	95.597	1749	46	14	842	2577	394260124	394258394	0.000000e+00	2774
8	TraesCS1B01G305100	chr1D	95.383	1148	41	7	2591	3735	394258409	394257271	0.000000e+00	1816
9	TraesCS1B01G305100	chr2D	88.866	988	79	16	1549	2528	640612371	640611407	0.000000e+00	1186
10	TraesCS1B01G305100	chr2B	95.676	740	21	4	1	731	269539752	269539015	0.000000e+00	1179
11	TraesCS1B01G305100	chr5B	91.814	733	57	3	1	730	671746338	671745606	0.000000e+00	1018
12	TraesCS1B01G305100	chr6D	89.706	748	57	11	1	734	403034961	403034220	0.000000e+00	937
13	TraesCS1B01G305100	chr5D	89.799	745	56	12	1	731	294126154	294126892	0.000000e+00	937
14	TraesCS1B01G305100	chr7A	82.574	746	95	22	9	731	630032637	630031904	3.170000e-175	625
15	TraesCS1B01G305100	chr3B	85.484	558	58	14	1	542	564908811	564908261	9.060000e-156	560
16	TraesCS1B01G305100	chr7D	86.364	440	51	6	295	731	546750979	546750546	4.370000e-129	472

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	TraesCS1B01G305100	chr1B	527844367	527848101	3734	False	6898.0	6898	100.000	1	3735	1	chr1B.!!$F1	3734
1	TraesCS1B01G305100	chr1A	491146600	491149578	2978	False	4691.0	4691	94.998	726	3732	1	chr1A.!!$F1	3006
2	TraesCS1B01G305100	chr1A	514859029	514859754	725	False	708.0	708	84.459	1	730	1	chr1A.!!$F2	729
3	TraesCS1B01G305100	chr1A	515115274	515115999	725	False	708.0	708	84.459	1	730	1	chr1A.!!$F3	729
4	TraesCS1B01G305100	chr1A	386379004	386380005	1001	False	631.5	1188	92.582	1572	2574	2	chr1A.!!$F4	1002
5	TraesCS1B01G305100	chr1D	394257271	394260124	2853	True	2295.0	2774	95.490	842	3735	2	chr1D.!!$R1	2893
6	TraesCS1B01G305100	chr2D	640611407	640612371	964	True	1186.0	1186	88.866	1549	2528	1	chr2D.!!$R1	979
7	TraesCS1B01G305100	chr2B	269539015	269539752	737	True	1179.0	1179	95.676	1	731	1	chr2B.!!$R1	730
8	TraesCS1B01G305100	chr5B	671745606	671746338	732	True	1018.0	1018	91.814	1	730	1	chr5B.!!$R1	729
9	TraesCS1B01G305100	chr6D	403034220	403034961	741	True	937.0	937	89.706	1	734	1	chr6D.!!$R1	733
10	TraesCS1B01G305100	chr5D	294126154	294126892	738	False	937.0	937	89.799	1	731	1	chr5D.!!$F1	730
11	TraesCS1B01G305100	chr7A	630031904	630032637	733	True	625.0	625	82.574	9	731	1	chr7A.!!$R1	722
12	TraesCS1B01G305100	chr3B	564908261	564908811	550	True	560.0	560	85.484	1	542	1	chr3B.!!$R1	541

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
779	804	0.402121	GGCAGGGGAACTTCTTCAGT	59.598	55.0	0.0	0.0	37.3	3.41	F
1311	1348	0.390472	GCGGCTATGACTATGAGGGC	60.390	60.0	0.0	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1933	1986	0.105555	CTCTCCTCCTCCTGCTGGAT	60.106	60.000	13.33	0.00	42.29	3.41	R
3142	3228	1.069090	GATTCTATGGGCGCACCGA	59.931	57.895	7.46	2.32	44.64	4.69	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
109	121	0.472471	AGGCAATACCCATACCCGTG	59.528	55.000	0.00	0.00	40.58	4.94
220	237	6.795399	ACAACTTGTGAAGTAGATTTGTTGG	58.205	36.000	0.00	0.00	41.91	3.77
258	275	1.494721	TCTCCAGCCACCTTCAAAAGT	59.505	47.619	0.00	0.00	0.00	2.66
651	676	1.512230	GTGCGGGTACATGTACGGA	59.488	57.895	25.69	16.14	36.94	4.69
734	759	1.001641	GGGTGCCATGTTGAGCTCT	60.002	57.895	16.19	0.00	0.00	4.09
739	764	2.611292	GTGCCATGTTGAGCTCTACATC	59.389	50.000	32.19	24.28	39.59	3.06
752	777	4.582656	AGCTCTACATCTCTACACATGACC	59.417	45.833	0.00	0.00	0.00	4.02
755	780	1.202302	ACATCTCTACACATGACCGCG	60.202	52.381	0.00	0.00	0.00	6.46
771	796	4.016706	CGGTTCGGCAGGGGAACT	62.017	66.667	4.86	0.00	42.58	3.01
779	804	0.402121	GGCAGGGGAACTTCTTCAGT	59.598	55.000	0.00	0.00	37.30	3.41
781	806	2.587522	GCAGGGGAACTTCTTCAGTTT	58.412	47.619	0.00	0.00	46.53	2.66
790	815	5.359194	AACTTCTTCAGTTTCACTCTCCA	57.641	39.130	0.00	0.00	43.89	3.86
807	832	3.054582	TCTCCATGGAGTAGTACGAGTGT	60.055	47.826	35.34	0.00	42.49	3.55
812	837	3.748083	TGGAGTAGTACGAGTGTGACTT	58.252	45.455	0.00	0.00	0.00	3.01
822	847	2.597505	CGAGTGTGACTTGTTTCAAGCG	60.598	50.000	9.06	0.65	0.00	4.68
823	848	2.607635	GAGTGTGACTTGTTTCAAGCGA	59.392	45.455	9.06	0.00	0.00	4.93
838	863	4.686972	TCAAGCGAGATCCTATTGACAAG	58.313	43.478	0.00	0.00	0.00	3.16
839	864	4.160439	TCAAGCGAGATCCTATTGACAAGT	59.840	41.667	0.00	0.00	0.00	3.16
840	865	4.052159	AGCGAGATCCTATTGACAAGTG	57.948	45.455	0.00	0.00	0.00	3.16
1023	1060	2.686835	GCTGAGAGCTCCCCACCT	60.687	66.667	10.93	0.00	38.45	4.00
1024	1061	2.730524	GCTGAGAGCTCCCCACCTC	61.731	68.421	10.93	0.21	38.45	3.85
1025	1062	2.039624	TGAGAGCTCCCCACCTCC	59.960	66.667	10.93	0.00	0.00	4.30
1026	1063	2.039624	GAGAGCTCCCCACCTCCA	59.960	66.667	10.93	0.00	0.00	3.86
1027	1064	2.284995	AGAGCTCCCCACCTCCAC	60.285	66.667	10.93	0.00	0.00	4.02
1028	1065	3.403558	GAGCTCCCCACCTCCACC	61.404	72.222	0.87	0.00	0.00	4.61
1129	1166	4.988598	CAACCACCTCGCCACGCT	62.989	66.667	0.00	0.00	0.00	5.07
1151	1188	1.493134	CTTTTATACGCGCCCCCGAC	61.493	60.000	5.73	0.00	36.29	4.79
1291	1328	1.389609	GGAGATCGTTACGGCCAGGA	61.390	60.000	2.24	0.00	0.00	3.86
1303	1340	3.543537	CCAGGAGCGGCTATGACT	58.456	61.111	14.42	3.70	0.00	3.41
1304	1341	2.733590	CCAGGAGCGGCTATGACTA	58.266	57.895	14.42	0.00	0.00	2.59
1305	1342	1.261480	CCAGGAGCGGCTATGACTAT	58.739	55.000	14.42	0.00	0.00	2.12
1311	1348	0.390472	GCGGCTATGACTATGAGGGC	60.390	60.000	0.00	0.00	0.00	5.19
1809	1859	2.974489	GACGTCCACGGAGAAGCGA	61.974	63.158	3.51	0.00	44.95	4.93
1863	1916	2.502080	GAGCACCACGACGACGAG	60.502	66.667	15.32	5.96	42.66	4.18
2325	2381	2.123632	AGGAAGGCCCTGAGCAGA	59.876	61.111	0.00	0.00	45.61	4.26
2568	2650	6.960468	TGCACATAGTACATTTCGTTTCAAA	58.040	32.000	0.00	0.00	0.00	2.69
2683	2769	2.636768	ATTTGCGCCTTACAAGCTTC	57.363	45.000	4.18	0.00	0.00	3.86
2710	2796	8.514594	TGCAGGATTTCACTAGTCAAATTTAAG	58.485	33.333	6.17	0.00	0.00	1.85
2740	2826	5.779241	AAAAGAACAGATCCCATCTACCA	57.221	39.130	0.00	0.00	37.58	3.25
2891	2977	1.136891	GGCAATTCCACAATGGGCTAC	59.863	52.381	0.00	0.00	38.32	3.58
2935	3021	1.529244	AAGCTCAGCCCACCACAAC	60.529	57.895	0.00	0.00	0.00	3.32
3007	3093	2.039951	CTCCGGGTTACCTCCCCA	59.960	66.667	0.00	0.00	44.32	4.96
3097	3183	0.835941	CCAAGGGGACTGATCTGAGG	59.164	60.000	6.60	0.00	42.68	3.86
3142	3228	2.017559	GCTTCTCGCCGGTGAGGTAT	62.018	60.000	37.63	0.00	43.70	2.73
3154	3240	3.161450	AGGTATCGGTGCGCCCAT	61.161	61.111	11.56	6.11	0.00	4.00
3169	3255	1.438469	CCCATAGAATCAGGAGGCCA	58.562	55.000	5.01	0.00	0.00	5.36
3304	3390	0.652592	CATCGCCGAAACTGATGTCC	59.347	55.000	0.00	0.00	35.81	4.02
3313	3399	4.201724	CCGAAACTGATGTCCGAAATCTTC	60.202	45.833	0.20	0.00	0.00	2.87
3355	3441	2.209838	ATATGCACGACGAGTTCAGG	57.790	50.000	0.00	0.00	27.74	3.86
3473	3559	3.485394	TCTGCCTCATTAACTGCAACAA	58.515	40.909	0.00	0.00	32.58	2.83
3491	3577	6.754209	TGCAACAAAAATGTTTCGATGTTAGT	59.246	30.769	0.00	0.00	30.48	2.24
3576	3662	5.928264	GGCAAGAAGAATAACAAAATGTGCT	59.072	36.000	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
109	121	2.223900	GGGTGTAGTAGTATGCGGGTTC	60.224	54.545	0.00	0.00	0.00	3.62
220	237	2.815647	CGCAAGGAAGGGAGACGC	60.816	66.667	0.00	0.00	0.00	5.19
258	275	3.570550	ACCGCAACACCTAAGCATTTTAA	59.429	39.130	0.00	0.00	0.00	1.52
734	759	2.032924	CGCGGTCATGTGTAGAGATGTA	59.967	50.000	0.00	0.00	0.00	2.29
739	764	0.108804	AACCGCGGTCATGTGTAGAG	60.109	55.000	34.29	0.00	0.00	2.43
755	780	1.674651	GAAGTTCCCCTGCCGAACC	60.675	63.158	0.00	0.00	40.43	3.62
779	804	4.398358	CGTACTACTCCATGGAGAGTGAAA	59.602	45.833	41.91	23.26	46.54	2.69
781	806	3.199289	TCGTACTACTCCATGGAGAGTGA	59.801	47.826	41.91	28.16	46.54	3.41
790	815	3.952931	AGTCACACTCGTACTACTCCAT	58.047	45.455	0.00	0.00	0.00	3.41
807	832	3.067106	GGATCTCGCTTGAAACAAGTCA	58.933	45.455	12.07	0.51	0.00	3.41
812	837	4.870426	GTCAATAGGATCTCGCTTGAAACA	59.130	41.667	0.00	0.00	0.00	2.83
822	847	6.484977	GGATTTCCACTTGTCAATAGGATCTC	59.515	42.308	6.89	6.93	35.64	2.75
823	848	6.360618	GGATTTCCACTTGTCAATAGGATCT	58.639	40.000	6.89	0.00	35.64	2.75
838	863	4.733405	GCGTGATTTATTTCGGATTTCCAC	59.267	41.667	0.00	0.00	35.14	4.02
839	864	4.638421	AGCGTGATTTATTTCGGATTTCCA	59.362	37.500	0.00	0.00	35.14	3.53
840	865	4.970003	CAGCGTGATTTATTTCGGATTTCC	59.030	41.667	0.00	0.00	0.00	3.13
1129	1166	1.820481	GGGGCGCGTATAAAAGGCA	60.820	57.895	8.43	0.00	38.96	4.75
1151	1188	1.233950	TGCATGCAACAGTGGTACGG	61.234	55.000	20.30	0.00	0.00	4.02
1193	1230	2.435586	CCGCTGCTGCTGCTACTT	60.436	61.111	25.43	0.00	40.48	2.24
1218	1255	3.053896	GGCTACGCAACCACCACC	61.054	66.667	0.00	0.00	0.00	4.61
1219	1256	3.419759	CGGCTACGCAACCACCAC	61.420	66.667	0.00	0.00	0.00	4.16
1220	1257	3.617735	TCGGCTACGCAACCACCA	61.618	61.111	0.00	0.00	40.69	4.17
1266	1303	0.104120	CCGTAACGATCTCCATGCCA	59.896	55.000	0.00	0.00	0.00	4.92
1291	1328	1.261480	CCCTCATAGTCATAGCCGCT	58.739	55.000	0.00	0.00	0.00	5.52
1299	1336	1.050988	GCTCCTGGCCCTCATAGTCA	61.051	60.000	0.00	0.00	34.27	3.41
1300	1337	1.050988	TGCTCCTGGCCCTCATAGTC	61.051	60.000	0.00	0.00	40.92	2.59
1301	1338	1.003442	TGCTCCTGGCCCTCATAGT	59.997	57.895	0.00	0.00	40.92	2.12
1302	1339	1.753470	CTGCTCCTGGCCCTCATAG	59.247	63.158	0.00	0.00	40.92	2.23
1303	1340	2.446848	GCTGCTCCTGGCCCTCATA	61.447	63.158	0.00	0.00	40.92	2.15
1304	1341	3.806667	GCTGCTCCTGGCCCTCAT	61.807	66.667	0.00	0.00	40.92	2.90
1311	1348	4.717313	TGCTGCTGCTGCTCCTGG	62.717	66.667	27.67	0.00	40.48	4.45
1593	1642	3.798511	TCGGTGGTGGTGTTGCCA	61.799	61.111	0.00	0.00	46.95	4.92
1809	1859	2.438434	CGCGGGGATTTCTTGGCT	60.438	61.111	0.00	0.00	0.00	4.75
1852	1902	2.479650	GTCCTCCTCGTCGTCGTG	59.520	66.667	1.33	0.00	38.33	4.35
1933	1986	0.105555	CTCTCCTCCTCCTGCTGGAT	60.106	60.000	13.33	0.00	42.29	3.41
2013	2066	2.750637	GACCTCGGAGGCGTCTCA	60.751	66.667	23.84	0.00	39.63	3.27
2590	2673	5.405331	ACAGTTCAGCGAAGACTTAAAAC	57.595	39.130	0.00	0.00	0.00	2.43
2594	2677	4.316205	TCAACAGTTCAGCGAAGACTTA	57.684	40.909	0.00	0.00	0.00	2.24
2596	2679	2.890808	TCAACAGTTCAGCGAAGACT	57.109	45.000	0.00	0.00	0.00	3.24
2601	2684	3.006940	ACTTGTTTCAACAGTTCAGCGA	58.993	40.909	0.00	0.00	40.50	4.93
2683	2769	6.506500	AATTTGACTAGTGAAATCCTGCAG	57.493	37.500	18.80	6.78	0.00	4.41
2722	2808	5.745227	TCTTTTGGTAGATGGGATCTGTTC	58.255	41.667	0.00	0.00	40.51	3.18
2725	2811	4.572389	CGTTCTTTTGGTAGATGGGATCTG	59.428	45.833	0.00	0.00	40.51	2.90
2726	2812	4.469945	TCGTTCTTTTGGTAGATGGGATCT	59.530	41.667	0.00	0.00	43.33	2.75
2727	2813	4.766375	TCGTTCTTTTGGTAGATGGGATC	58.234	43.478	0.00	0.00	0.00	3.36
2728	2814	4.837093	TCGTTCTTTTGGTAGATGGGAT	57.163	40.909	0.00	0.00	0.00	3.85
2729	2815	4.627284	TTCGTTCTTTTGGTAGATGGGA	57.373	40.909	0.00	0.00	0.00	4.37
2730	2816	5.001232	TCTTTCGTTCTTTTGGTAGATGGG	58.999	41.667	0.00	0.00	0.00	4.00
2731	2817	6.554334	TTCTTTCGTTCTTTTGGTAGATGG	57.446	37.500	0.00	0.00	0.00	3.51
2733	2819	8.936864	CACTATTCTTTCGTTCTTTTGGTAGAT	58.063	33.333	0.00	0.00	0.00	1.98
2734	2820	7.929785	ACACTATTCTTTCGTTCTTTTGGTAGA	59.070	33.333	0.00	0.00	0.00	2.59
2736	2822	7.711772	TCACACTATTCTTTCGTTCTTTTGGTA	59.288	33.333	0.00	0.00	0.00	3.25
2737	2823	6.540914	TCACACTATTCTTTCGTTCTTTTGGT	59.459	34.615	0.00	0.00	0.00	3.67
2738	2824	6.954944	TCACACTATTCTTTCGTTCTTTTGG	58.045	36.000	0.00	0.00	0.00	3.28
2739	2825	6.575201	GCTCACACTATTCTTTCGTTCTTTTG	59.425	38.462	0.00	0.00	0.00	2.44
2740	2826	6.260050	TGCTCACACTATTCTTTCGTTCTTTT	59.740	34.615	0.00	0.00	0.00	2.27
2891	2977	8.148351	TGAAATCCTAACGGTATAGAGAAATGG	58.852	37.037	0.00	0.00	0.00	3.16
2935	3021	1.887707	GACCCCAAGGAATAGCGCG	60.888	63.158	0.00	0.00	36.73	6.86
3127	3213	2.331805	CGATACCTCACCGGCGAG	59.668	66.667	12.75	12.75	35.61	5.03
3142	3228	1.069090	GATTCTATGGGCGCACCGA	59.931	57.895	7.46	2.32	44.64	4.69
3154	3240	2.111384	GACACTGGCCTCCTGATTCTA	58.889	52.381	3.32	0.00	0.00	2.10
3169	3255	1.336887	CGTCCGTTCTCCAATGACACT	60.337	52.381	0.00	0.00	0.00	3.55
3313	3399	3.000080	GACCGAAGACAACGCTGCG	62.000	63.158	21.91	21.91	36.68	5.18
3355	3441	5.622346	ATCCTCCTGTGATCCTAAGAAAC	57.378	43.478	0.00	0.00	0.00	2.78
3519	3605	4.083908	CGTGCTACTAGCCTACTAAGTAGC	60.084	50.000	21.11	21.11	45.02	3.58
3521	3607	5.163364	ACTCGTGCTACTAGCCTACTAAGTA	60.163	44.000	5.58	0.00	41.51	2.24
3522	3608	4.128643	CTCGTGCTACTAGCCTACTAAGT	58.871	47.826	5.58	0.00	41.51	2.24
3523	3609	4.128643	ACTCGTGCTACTAGCCTACTAAG	58.871	47.826	5.58	2.20	41.51	2.18
3524	3610	4.125703	GACTCGTGCTACTAGCCTACTAA	58.874	47.826	5.58	0.00	41.51	2.24
3576	3662	2.865079	TGCACGGTAAGAATTCCCAAA	58.135	42.857	0.65	0.00	0.00	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.