AutoCloner

Multiple sequence alignment - TraesCS6A01G131900

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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	TraesCS6A01G131900	chr6A	100.000	2987	0	0	1	2987	104115036	104112050	0.000000e+00	5517.0
1	TraesCS6A01G131900	chr6D	92.119	3020	158	43	6	2987	86603506	86600529	0.000000e+00	4185.0
2	TraesCS6A01G131900	chr6B	92.025	2069	72	26	8	2049	164035948	164033946	0.000000e+00	2820.0
3	TraesCS6A01G131900	chr6B	89.738	955	74	13	2038	2987	164033929	164032994	0.000000e+00	1199.0
4	TraesCS6A01G131900	chr6B	78.363	171	27	5	2166	2334	625843551	625843389	5.270000e-18	102.0
5	TraesCS6A01G131900	chr6B	76.608	171	26	13	2167	2333	584085124	584084964	6.860000e-12	82.4
6	TraesCS6A01G131900	chr7A	87.500	464	52	6	1266	1728	637864972	637864514	5.670000e-147	531.0
7	TraesCS6A01G131900	chr7A	80.488	246	37	8	1736	1971	637864398	637864154	8.510000e-41	178.0
8	TraesCS6A01G131900	chr7A	76.582	158	31	4	2166	2323	158665816	158665665	6.860000e-12	82.4
9	TraesCS6A01G131900	chr7A	88.000	50	6	0	2277	2326	189308006	189308055	3.220000e-05	60.2
10	TraesCS6A01G131900	chr7B	87.419	461	52	6	1266	1725	597082597	597082142	2.640000e-145	525.0
11	TraesCS6A01G131900	chr7B	80.498	241	37	7	1736	1966	597081997	597081757	3.060000e-40	176.0
12	TraesCS6A01G131900	chr7B	77.976	168	29	6	2166	2332	595050763	595050603	6.810000e-17	99.0
13	TraesCS6A01G131900	chr7D	86.551	461	56	6	1266	1725	552164993	552164538	1.240000e-138	503.0
14	TraesCS6A01G131900	chr7D	80.162	247	37	9	1736	1970	552164394	552164148	1.100000e-39	174.0
15	TraesCS6A01G131900	chr3D	79.412	170	27	5	2168	2336	427151762	427151600	2.430000e-21	113.0
16	TraesCS6A01G131900	chr3D	78.363	171	27	7	2166	2334	122694712	122694550	5.270000e-18	102.0
17	TraesCS6A01G131900	chr2B	78.235	170	29	3	2165	2333	787077483	787077645	5.270000e-18	102.0
18	TraesCS6A01G131900	chr3A	78.107	169	29	6	2167	2334	559603543	559603704	1.890000e-17	100.0
19	TraesCS6A01G131900	chr3A	75.439	171	32	8	2166	2334	43016445	43016283	1.150000e-09	75.0
20	TraesCS6A01G131900	chr3A	75.439	171	32	7	2166	2334	43639693	43639531	1.150000e-09	75.0
21	TraesCS6A01G131900	chr2A	77.914	163	23	9	2176	2334	754434006	754433853	4.100000e-14	89.8
22	TraesCS6A01G131900	chr5B	87.879	66	8	0	2163	2228	349138245	349138310	8.880000e-11	78.7
23	TraesCS6A01G131900	chr1D	85.915	71	8	2	2167	2236	89065636	89065705	1.150000e-09	75.0

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	TraesCS6A01G131900	chr6A	104112050	104115036	2986	True	5517.0	5517	100.0000	1	2987	1	chr6A.!!$R1	2986
1	TraesCS6A01G131900	chr6D	86600529	86603506	2977	True	4185.0	4185	92.1190	6	2987	1	chr6D.!!$R1	2981
2	TraesCS6A01G131900	chr6B	164032994	164035948	2954	True	2009.5	2820	90.8815	8	2987	2	chr6B.!!$R3	2979
3	TraesCS6A01G131900	chr7A	637864154	637864972	818	True	354.5	531	83.9940	1266	1971	2	chr7A.!!$R2	705
4	TraesCS6A01G131900	chr7B	597081757	597082597	840	True	350.5	525	83.9585	1266	1966	2	chr7B.!!$R2	700
5	TraesCS6A01G131900	chr7D	552164148	552164993	845	True	338.5	503	83.3565	1266	1970	2	chr7D.!!$R1	704

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
281	285	0.108585	AGAAAGCTGCCCGTCTTCAA	59.891	50.0	0.00	0.00	0.0	2.69	F
983	994	0.381089	TTGGTTTGGTTGGTTACGCG	59.619	50.0	3.53	3.53	0.0	6.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1969	2159	1.270068	GACTAGTTCGCCTTCTTCGC	58.730	55.0	0.0	0.0	0.0	4.70	R
2748	2974	0.041238	TCACAGGAGAACTCGGGGAT	59.959	55.0	0.0	0.0	0.0	3.85	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
56	57	1.292223	CTCGAAGGCAACGGAAGGA	59.708	57.895	3.84	0.00	46.39	3.36
150	154	0.329596	AATCCCAAGTGGCCAGTCTC	59.670	55.000	15.03	0.00	0.00	3.36
278	282	1.302832	CCAGAAAGCTGCCCGTCTT	60.303	57.895	0.00	0.00	40.91	3.01
279	283	1.301677	CCAGAAAGCTGCCCGTCTTC	61.302	60.000	0.00	0.00	40.91	2.87
280	284	0.603707	CAGAAAGCTGCCCGTCTTCA	60.604	55.000	0.00	0.00	34.95	3.02
281	285	0.108585	AGAAAGCTGCCCGTCTTCAA	59.891	50.000	0.00	0.00	0.00	2.69
289	293	3.334691	CTGCCCGTCTTCAATCAAAGTA	58.665	45.455	0.00	0.00	0.00	2.24
298	302	7.308589	CCGTCTTCAATCAAAGTACCAAAATCT	60.309	37.037	0.00	0.00	0.00	2.40
315	319	6.540995	CAAAATCTGGATCCATCTCCTGTAT	58.459	40.000	16.63	0.00	36.10	2.29
344	348	7.295322	TCAGGTAATTACTGATGATCCTCTG	57.705	40.000	15.05	9.49	39.87	3.35
452	459	4.796495	GTAGCCTGCCCGGGGTTG	62.796	72.222	25.28	7.68	38.18	3.77
477	484	1.016130	AGCTCAATCTGCGTTCCACG	61.016	55.000	0.00	0.00	45.88	4.94
495	502	1.000274	ACGCTGAAAGTTTTGGATGGC	60.000	47.619	0.00	0.00	35.30	4.40
571	578	1.029947	GTGCCCATCCAAACCTACCG	61.030	60.000	0.00	0.00	0.00	4.02
668	675	6.478588	CCAACTACTGATCAAACGCTTATTC	58.521	40.000	0.00	0.00	0.00	1.75
669	676	5.950965	ACTACTGATCAAACGCTTATTCG	57.049	39.130	0.00	0.00	0.00	3.34
715	722	7.352719	ACTTCGTCTTATTCTACTTTGCTTG	57.647	36.000	0.00	0.00	0.00	4.01
716	723	7.152645	ACTTCGTCTTATTCTACTTTGCTTGA	58.847	34.615	0.00	0.00	0.00	3.02
717	724	7.819900	ACTTCGTCTTATTCTACTTTGCTTGAT	59.180	33.333	0.00	0.00	0.00	2.57
718	725	8.547967	TTCGTCTTATTCTACTTTGCTTGATT	57.452	30.769	0.00	0.00	0.00	2.57
755	762	1.951895	GCTTGTCTGCCATCACATCCA	60.952	52.381	0.00	0.00	0.00	3.41
763	770	1.548081	CCATCACATCCAAACCTGCA	58.452	50.000	0.00	0.00	0.00	4.41
788	795	1.598130	GGCCAACAACTCTCACGCT	60.598	57.895	0.00	0.00	0.00	5.07
838	845	1.135094	TGAGCCATTCTCTCCATCCC	58.865	55.000	0.00	0.00	42.38	3.85
840	847	1.072159	GCCATTCTCTCCATCCCCG	59.928	63.158	0.00	0.00	0.00	5.73
841	848	1.700042	GCCATTCTCTCCATCCCCGT	61.700	60.000	0.00	0.00	0.00	5.28
843	850	0.394565	CATTCTCTCCATCCCCGTCC	59.605	60.000	0.00	0.00	0.00	4.79
845	852	1.886730	TTCTCTCCATCCCCGTCCCT	61.887	60.000	0.00	0.00	0.00	4.20
846	853	1.383248	CTCTCCATCCCCGTCCCTT	60.383	63.158	0.00	0.00	0.00	3.95
853	860	1.134491	CATCCCCGTCCCTTCTTGTAC	60.134	57.143	0.00	0.00	0.00	2.90
873	883	3.412386	ACTAACACCATTGCTCTTCACC	58.588	45.455	0.00	0.00	0.00	4.02
971	982	1.201647	CCTGCTCTGCTCATTGGTTTG	59.798	52.381	0.00	0.00	0.00	2.93
972	983	1.201647	CTGCTCTGCTCATTGGTTTGG	59.798	52.381	0.00	0.00	0.00	3.28
973	984	1.251251	GCTCTGCTCATTGGTTTGGT	58.749	50.000	0.00	0.00	0.00	3.67
974	985	1.615392	GCTCTGCTCATTGGTTTGGTT	59.385	47.619	0.00	0.00	0.00	3.67
975	986	2.608752	GCTCTGCTCATTGGTTTGGTTG	60.609	50.000	0.00	0.00	0.00	3.77
976	987	1.962807	TCTGCTCATTGGTTTGGTTGG	59.037	47.619	0.00	0.00	0.00	3.77
977	988	1.688197	CTGCTCATTGGTTTGGTTGGT	59.312	47.619	0.00	0.00	0.00	3.67
978	989	2.102925	CTGCTCATTGGTTTGGTTGGTT	59.897	45.455	0.00	0.00	0.00	3.67
979	990	3.300388	TGCTCATTGGTTTGGTTGGTTA	58.700	40.909	0.00	0.00	0.00	2.85
980	991	3.068873	TGCTCATTGGTTTGGTTGGTTAC	59.931	43.478	0.00	0.00	0.00	2.50
981	992	3.855524	GCTCATTGGTTTGGTTGGTTACG	60.856	47.826	0.00	0.00	0.00	3.18
982	993	2.034812	TCATTGGTTTGGTTGGTTACGC	59.965	45.455	0.00	0.00	0.00	4.42
983	994	0.381089	TTGGTTTGGTTGGTTACGCG	59.619	50.000	3.53	3.53	0.00	6.01
984	995	1.283487	GGTTTGGTTGGTTACGCGG	59.717	57.895	12.47	0.00	0.00	6.46
985	996	1.283487	GTTTGGTTGGTTACGCGGG	59.717	57.895	12.47	0.00	0.00	6.13
986	997	2.553727	TTTGGTTGGTTACGCGGGC	61.554	57.895	12.47	0.00	0.00	6.13
1494	1525	1.543358	GACGAGAACCCCTTCTACGTT	59.457	52.381	0.00	0.00	38.88	3.99
2041	2234	4.383118	CCTTGTACTTCGATCAGATGGGTT	60.383	45.833	0.00	0.00	0.00	4.11
2090	2311	0.312416	TGCACCGTTGTAAATGTGGC	59.688	50.000	0.00	0.00	33.64	5.01
2223	2447	6.539649	TTGAAAGGATCAAACTACAAGTCG	57.460	37.500	0.00	0.00	44.94	4.18
2224	2448	5.607477	TGAAAGGATCAAACTACAAGTCGT	58.393	37.500	0.00	0.00	34.30	4.34
2239	2463	6.925610	ACAAGTCGTGTATATACCGAACTA	57.074	37.500	20.68	1.47	39.29	2.24
2242	2466	4.151335	AGTCGTGTATATACCGAACTAGCG	59.849	45.833	20.68	9.42	33.22	4.26
2244	2468	4.386954	TCGTGTATATACCGAACTAGCGAG	59.613	45.833	18.24	0.00	0.00	5.03
2249	2473	3.644884	ATACCGAACTAGCGAGATTGG	57.355	47.619	8.59	8.59	35.53	3.16
2253	2477	2.860735	CCGAACTAGCGAGATTGGAAAG	59.139	50.000	4.55	0.00	31.79	2.62
2334	2558	4.584743	ACAAACAAGACCAAAGAATCCTCC	59.415	41.667	0.00	0.00	0.00	4.30
2449	2673	9.855021	AAGGCATAAATATGTTACAAGAAACAC	57.145	29.630	2.63	0.00	41.89	3.32
2508	2732	1.936547	CGCATAGCCAAAGAGGAAGAC	59.063	52.381	0.00	0.00	41.22	3.01
2525	2749	6.989659	AGGAAGACTCGTTGTGTTCTAATTA	58.010	36.000	15.83	0.00	45.10	1.40
2577	2801	7.476667	TGATCGTTACAATGTGTGTTCTTTTT	58.523	30.769	0.00	0.00	41.98	1.94
2589	2813	7.411274	TGTGTGTTCTTTTTATCCTAAACACG	58.589	34.615	10.48	0.00	45.77	4.49
2614	2838	7.115520	CGTAATGTGTATAGCTCAAGAGAATGG	59.884	40.741	0.32	0.00	0.00	3.16
2680	2906	6.426587	ACACCAGCAATTATCTAGGAATGTT	58.573	36.000	0.00	0.00	0.00	2.71
2835	3084	6.672266	TCTCTATTGAACAAGTCACTCCTT	57.328	37.500	0.00	0.00	35.39	3.36
2904	3153	4.657814	TGCTGAATTAAGGGGAGAAAGT	57.342	40.909	0.00	0.00	0.00	2.66
2911	3163	7.338710	TGAATTAAGGGGAGAAAGTACATCTG	58.661	38.462	5.98	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	1.653667	CACTGGCATGAAACACGCA	59.346	52.632	0.00	0.00	0.00	5.24
3	4	1.730547	GCACTGGCATGAAACACGC	60.731	57.895	0.00	0.00	40.72	5.34
4	5	0.311790	AAGCACTGGCATGAAACACG	59.688	50.000	0.00	0.00	44.61	4.49
56	57	0.824759	GAGGTGGCTGTCGGTCTATT	59.175	55.000	0.00	0.00	0.00	1.73
150	154	0.310854	GACAAGGGTGACGCAAAAGG	59.689	55.000	1.61	0.00	0.00	3.11
237	241	4.447054	GCCATCAGACTCAGATATCAAACG	59.553	45.833	5.32	0.00	0.00	3.60
315	319	7.345653	AGGATCATCAGTAATTACCTGAACAGA	59.654	37.037	12.05	13.11	0.00	3.41
344	348	1.745232	TGTGCCATTAACCCGATGAC	58.255	50.000	0.00	0.00	0.00	3.06
371	375	4.650131	TCCGTGTGGTATATGGAACACATA	59.350	41.667	13.63	0.00	44.53	2.29
477	484	1.669795	CCGCCATCCAAAACTTTCAGC	60.670	52.381	0.00	0.00	0.00	4.26
571	578	1.740025	CTTCGGAGTGGCTCAAATTCC	59.260	52.381	0.00	0.00	31.08	3.01
755	762	2.679996	GCCGGGGAATGCAGGTTT	60.680	61.111	2.18	0.00	0.00	3.27
763	770	1.304134	GAGTTGTTGGCCGGGGAAT	60.304	57.895	2.18	0.00	0.00	3.01
788	795	4.224594	AGAATGACATCTCAGCCTTTCAGA	59.775	41.667	0.00	0.00	0.00	3.27
838	845	3.582780	GTGTTAGTACAAGAAGGGACGG	58.417	50.000	0.00	0.00	35.69	4.79
840	847	4.612264	TGGTGTTAGTACAAGAAGGGAC	57.388	45.455	0.00	0.00	35.69	4.46
841	848	5.556915	CAATGGTGTTAGTACAAGAAGGGA	58.443	41.667	0.00	0.00	35.69	4.20
843	850	5.003804	AGCAATGGTGTTAGTACAAGAAGG	58.996	41.667	0.00	0.00	35.69	3.46
845	852	5.865085	AGAGCAATGGTGTTAGTACAAGAA	58.135	37.500	0.00	0.00	35.69	2.52
846	853	5.483685	AGAGCAATGGTGTTAGTACAAGA	57.516	39.130	0.00	0.00	35.69	3.02
853	860	2.749621	GGGTGAAGAGCAATGGTGTTAG	59.250	50.000	0.00	0.00	0.00	2.34
873	883	2.125552	TGTGATCTTGCGCTCCGG	60.126	61.111	9.73	0.00	0.00	5.14
880	890	3.181497	ACCATTTATGCGTGTGATCTTGC	60.181	43.478	0.00	0.00	0.00	4.01
905	916	0.954452	CTTGTGCCCCTGTGTTTCTC	59.046	55.000	0.00	0.00	0.00	2.87
906	917	0.550914	TCTTGTGCCCCTGTGTTTCT	59.449	50.000	0.00	0.00	0.00	2.52
976	987	4.878682	CTACCCGGCCCGCGTAAC	62.879	72.222	4.92	0.00	0.00	2.50
983	994	3.469978	ATCTCTCCCTACCCGGCCC	62.470	68.421	0.00	0.00	0.00	5.80
984	995	2.201771	ATCTCTCCCTACCCGGCC	59.798	66.667	0.00	0.00	0.00	6.13
985	996	0.759436	TTCATCTCTCCCTACCCGGC	60.759	60.000	0.00	0.00	0.00	6.13
986	997	1.333177	CTTCATCTCTCCCTACCCGG	58.667	60.000	0.00	0.00	0.00	5.73
987	998	1.333177	CCTTCATCTCTCCCTACCCG	58.667	60.000	0.00	0.00	0.00	5.28
988	999	1.052617	GCCTTCATCTCTCCCTACCC	58.947	60.000	0.00	0.00	0.00	3.69
1755	1924	4.514577	ACCGCCGCCGAGAAGATG	62.515	66.667	0.00	0.00	36.29	2.90
1969	2159	1.270068	GACTAGTTCGCCTTCTTCGC	58.730	55.000	0.00	0.00	0.00	4.70
2041	2234	1.535028	CAAAGCGCACACAATAGACCA	59.465	47.619	11.47	0.00	0.00	4.02
2137	2359	3.898741	TGCCGGAAACCCTCTTAAAAATT	59.101	39.130	5.05	0.00	0.00	1.82
2147	2369	1.937191	AAAATGATGCCGGAAACCCT	58.063	45.000	5.05	0.00	0.00	4.34
2171	2395	6.624352	ATGAGACATGTATTACCATGCAAC	57.376	37.500	0.00	0.00	44.88	4.17
2172	2396	7.643569	AAATGAGACATGTATTACCATGCAA	57.356	32.000	0.00	0.00	44.88	4.08
2212	2436	6.925610	TCGGTATATACACGACTTGTAGTT	57.074	37.500	14.70	0.00	44.14	2.24
2223	2447	5.852738	TCTCGCTAGTTCGGTATATACAC	57.147	43.478	14.70	4.67	0.00	2.90
2224	2448	6.128090	CCAATCTCGCTAGTTCGGTATATACA	60.128	42.308	14.70	0.00	0.00	2.29
2266	2490	9.124807	GTATTTCTTTATGCAAAACTAGCGTTT	57.875	29.630	0.00	0.00	44.87	3.60
2334	2558	3.673338	TCATTCTAAACTTGCTCGTGACG	59.327	43.478	0.00	0.00	0.00	4.35
2449	2673	2.930040	CGGTAGCACCAAGTTATGTGAG	59.070	50.000	8.48	0.00	38.47	3.51
2488	2712	1.936547	GTCTTCCTCTTTGGCTATGCG	59.063	52.381	0.00	0.00	35.26	4.73
2589	2813	8.144478	TCCATTCTCTTGAGCTATACACATTAC	58.856	37.037	0.00	0.00	0.00	1.89
2598	2822	5.069781	GTGGTACTCCATTCTCTTGAGCTAT	59.930	44.000	0.00	0.00	46.20	2.97
2703	2929	3.250762	TCAATTTCACATAGCCTATGCGC	59.749	43.478	11.65	0.00	44.33	6.09
2748	2974	0.041238	TCACAGGAGAACTCGGGGAT	59.959	55.000	0.00	0.00	0.00	3.85
2749	2975	0.041238	ATCACAGGAGAACTCGGGGA	59.959	55.000	0.00	0.00	0.00	4.81
2904	3153	5.912149	ATCCTATCTTTTGGCCAGATGTA	57.088	39.130	14.62	0.00	32.94	2.29
2952	3205	5.363580	ACATGTGTGGAGAAACTTTGGAAAT	59.636	36.000	0.00	0.00	0.00	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.