AutoCloner

Multiple sequence alignment - TraesCS1D01G377800

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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	TraesCS1D01G377800	chr1D	100.000	2796	0	0	1	2796	454151199	454148404	0.000000e+00	5164.0
1	TraesCS1D01G377800	chr1D	92.857	70	4	1	580	648	490356559	490356628	1.770000e-17	100.0
2	TraesCS1D01G377800	chr1B	98.217	1795	27	5	1004	2796	624655875	624654084	0.000000e+00	3133.0
3	TraesCS1D01G377800	chr1B	95.138	905	22	7	1	884	624656920	624656017	0.000000e+00	1408.0
4	TraesCS1D01G377800	chr1B	88.636	572	54	7	4	568	45991205	45991772	0.000000e+00	686.0
5	TraesCS1D01G377800	chr1B	87.602	492	44	10	89	568	2039525	2039039	3.150000e-154	555.0
6	TraesCS1D01G377800	chr1B	94.366	71	4	0	954	1024	624655958	624655888	2.940000e-20	110.0
7	TraesCS1D01G377800	chr1B	100.000	34	0	0	901	934	624656033	624656000	2.330000e-06	63.9
8	TraesCS1D01G377800	chr1B	97.143	35	1	0	12	46	2039663	2039629	3.010000e-05	60.2
9	TraesCS1D01G377800	chr7A	88.850	574	53	8	4	570	339519008	339518439	0.000000e+00	695.0
10	TraesCS1D01G377800	chr7A	87.522	569	58	10	4	564	648046374	648045811	0.000000e+00	645.0
11	TraesCS1D01G377800	chr7A	87.244	439	45	6	143	572	635697012	635696576	9.000000e-135	490.0
12	TraesCS1D01G377800	chr2B	88.811	572	53	7	4	568	522215932	522215365	0.000000e+00	691.0
13	TraesCS1D01G377800	chr7B	88.259	494	46	5	85	568	12745147	12744656	5.190000e-162	580.0
14	TraesCS1D01G377800	chr5A	87.879	495	46	9	86	568	347535721	347536213	1.120000e-158	569.0
15	TraesCS1D01G377800	chr5A	81.214	346	39	15	1384	1722	536661850	536661524	3.570000e-64	255.0
16	TraesCS1D01G377800	chr2A	87.854	247	17	4	1	247	62632627	62632860	7.630000e-71	278.0
17	TraesCS1D01G377800	chr7D	91.667	120	9	1	86	205	70184407	70184289	6.200000e-37	165.0
18	TraesCS1D01G377800	chr6B	91.429	70	5	1	580	648	420747724	420747655	8.240000e-16	95.3
19	TraesCS1D01G377800	chr3B	91.429	70	5	1	580	648	526000488	526000419	8.240000e-16	95.3
20	TraesCS1D01G377800	chr3B	92.537	67	4	1	580	645	667859377	667859443	8.240000e-16	95.3
21	TraesCS1D01G377800	chr3B	97.143	35	1	0	12	46	586132135	586132101	3.010000e-05	60.2
22	TraesCS1D01G377800	chr4B	90.000	70	6	1	580	648	473906501	473906432	3.840000e-14	89.8

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	TraesCS1D01G377800	chr1D	454148404	454151199	2795	True	5164.000	5164	100.00000	1	2796	1	chr1D.!!$R1	2795
1	TraesCS1D01G377800	chr1B	624654084	624656920	2836	True	1178.725	3133	96.93025	1	2796	4	chr1B.!!$R2	2795
2	TraesCS1D01G377800	chr1B	45991205	45991772	567	False	686.000	686	88.63600	4	568	1	chr1B.!!$F1	564
3	TraesCS1D01G377800	chr1B	2039039	2039663	624	True	307.600	555	92.37250	12	568	2	chr1B.!!$R1	556
4	TraesCS1D01G377800	chr7A	339518439	339519008	569	True	695.000	695	88.85000	4	570	1	chr7A.!!$R1	566
5	TraesCS1D01G377800	chr7A	648045811	648046374	563	True	645.000	645	87.52200	4	564	1	chr7A.!!$R3	560
6	TraesCS1D01G377800	chr2B	522215365	522215932	567	True	691.000	691	88.81100	4	568	1	chr2B.!!$R1	564

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
935	1042	0.396811	CCACTCGTCCCCTGAAACTT	59.603	55.0	0.0	0.0	0.0	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2682	2848	1.139256	TGCTACACCAAACCGAAGTCA	59.861	47.619	0.0	0.0	0.0	3.41	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
166	239	3.435671	ACGATTTGCTAGTGTTGGTAAGC	59.564	43.478	0.00	0.00	35.51	3.09
306	391	9.787532	AATATGTTTTGTCTTATGTTTCGATGG	57.212	29.630	0.00	0.00	0.00	3.51
576	665	1.077716	GCCGCCACTGGTTAAGGAT	60.078	57.895	0.00	0.00	0.00	3.24
582	671	1.281867	CCACTGGTTAAGGATGAGGCA	59.718	52.381	0.00	0.00	0.00	4.75
587	676	2.760092	TGGTTAAGGATGAGGCAATTGC	59.240	45.455	22.47	22.47	41.14	3.56
610	699	4.202101	CGGGTGCCAAGCATTTGAATAATA	60.202	41.667	0.00	0.00	41.91	0.98
661	762	3.447586	TGTGCCGCTATCTCTTAGACTTT	59.552	43.478	0.00	0.00	0.00	2.66
756	863	1.960250	GCAGGAGATGAGCATCCGC	60.960	63.158	6.84	2.28	40.73	5.54
868	975	2.786539	ATTGGCGCTCGTTGCTCTCA	62.787	55.000	7.64	0.00	40.11	3.27
869	976	2.738521	GGCGCTCGTTGCTCTCAA	60.739	61.111	7.64	0.00	40.11	3.02
870	977	2.472049	GCGCTCGTTGCTCTCAAC	59.528	61.111	0.00	0.00	46.85	3.18
880	987	4.174411	GTTGCTCTCAACCAATAAACCC	57.826	45.455	0.00	0.00	45.15	4.11
881	988	2.802719	TGCTCTCAACCAATAAACCCC	58.197	47.619	0.00	0.00	0.00	4.95
882	989	2.378547	TGCTCTCAACCAATAAACCCCT	59.621	45.455	0.00	0.00	0.00	4.79
883	990	3.017442	GCTCTCAACCAATAAACCCCTC	58.983	50.000	0.00	0.00	0.00	4.30
884	991	3.561313	GCTCTCAACCAATAAACCCCTCA	60.561	47.826	0.00	0.00	0.00	3.86
885	992	4.662278	CTCTCAACCAATAAACCCCTCAA	58.338	43.478	0.00	0.00	0.00	3.02
886	993	5.068215	TCTCAACCAATAAACCCCTCAAA	57.932	39.130	0.00	0.00	0.00	2.69
887	994	5.459505	TCTCAACCAATAAACCCCTCAAAA	58.540	37.500	0.00	0.00	0.00	2.44
888	995	5.900123	TCTCAACCAATAAACCCCTCAAAAA	59.100	36.000	0.00	0.00	0.00	1.94
934	1041	0.471211	TCCACTCGTCCCCTGAAACT	60.471	55.000	0.00	0.00	0.00	2.66
935	1042	0.396811	CCACTCGTCCCCTGAAACTT	59.603	55.000	0.00	0.00	0.00	2.66
936	1043	1.202770	CCACTCGTCCCCTGAAACTTT	60.203	52.381	0.00	0.00	0.00	2.66
937	1044	2.572290	CACTCGTCCCCTGAAACTTTT	58.428	47.619	0.00	0.00	0.00	2.27
938	1045	2.949644	CACTCGTCCCCTGAAACTTTTT	59.050	45.455	0.00	0.00	0.00	1.94
978	1107	1.623811	TGGAACCCTTTCTCCTTCGAG	59.376	52.381	0.00	0.00	37.48	4.04
1026	1191	4.507916	CGGCGGAGGAGGAGGAGA	62.508	72.222	0.00	0.00	0.00	3.71
1028	1193	2.277404	GCGGAGGAGGAGGAGAGT	59.723	66.667	0.00	0.00	0.00	3.24
1029	1194	2.124693	GCGGAGGAGGAGGAGAGTG	61.125	68.421	0.00	0.00	0.00	3.51
1030	1195	1.610327	CGGAGGAGGAGGAGAGTGA	59.390	63.158	0.00	0.00	0.00	3.41
1587	1752	1.383664	CAGATGGAGGAGGAGGCCA	60.384	63.158	5.01	0.00	35.91	5.36
1623	1788	3.991051	CACGCACCCACCTCGACT	61.991	66.667	0.00	0.00	0.00	4.18
1700	1865	1.227089	CTCTGCCTTCATCGACCCG	60.227	63.158	0.00	0.00	0.00	5.28
1975	2141	3.563223	TGGATACCTGCTGGAGTAGTAC	58.437	50.000	17.64	0.00	37.04	2.73
1993	2159	2.440539	ACTTCTCTGTGGTACTTGCG	57.559	50.000	0.00	0.00	0.00	4.85
2110	2276	3.809832	GTGTCTGTGTGTGCTACAAGAAT	59.190	43.478	0.00	0.00	41.89	2.40
2114	2280	4.275689	TCTGTGTGTGCTACAAGAATTTGG	59.724	41.667	0.00	0.00	41.89	3.28
2156	2322	6.594744	TGATGATAGCACCATGACAATTACT	58.405	36.000	0.00	0.00	0.00	2.24
2235	2401	4.193090	TGGCTCAGAAACAAACGAGTTTA	58.807	39.130	0.50	0.00	41.48	2.01
2257	2423	0.830648	CAGGAGCACGAGGGGATTAA	59.169	55.000	0.00	0.00	0.00	1.40
2282	2448	5.530171	CCCTTCAATGATGTTGTAGATCCAG	59.470	44.000	0.00	0.00	0.00	3.86
2290	2456	0.750850	TTGTAGATCCAGTAGCGGCC	59.249	55.000	0.00	0.00	0.00	6.13
2533	2699	9.914834	AAAACCTTATATATAAGCCACAACTGA	57.085	29.630	22.25	0.00	38.69	3.41
2671	2837	4.080413	TGCATCTACCCTCATTGACATTGA	60.080	41.667	0.44	0.44	0.00	2.57
2682	2848	7.447545	CCCTCATTGACATTGATCTGTGAATAT	59.552	37.037	0.71	0.00	32.26	1.28
2784	2950	4.487948	GCAACAGACAATATGCAATGTGT	58.512	39.130	7.76	3.80	38.63	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
166	239	3.045601	ACCACTTGGACTCGATTCTTG	57.954	47.619	1.14	0.00	38.94	3.02
212	287	8.609176	GTTGTACTGAGTTGTGTATTCAAAGAA	58.391	33.333	0.00	0.00	0.00	2.52
213	288	7.766738	TGTTGTACTGAGTTGTGTATTCAAAGA	59.233	33.333	0.00	0.00	0.00	2.52
306	391	8.040716	ACACTATTTATGTTTGAACAGGCTAC	57.959	34.615	2.77	0.00	43.04	3.58
576	665	3.372730	GCACCCGCAATTGCCTCA	61.373	61.111	24.24	0.00	38.36	3.86
582	671	1.829523	AATGCTTGGCACCCGCAATT	61.830	50.000	9.00	3.18	43.04	2.32
587	676	0.247185	ATTCAAATGCTTGGCACCCG	59.753	50.000	0.00	0.00	43.04	5.28
610	699	5.135508	ACTAATTACTCTCGCGGCATTAT	57.864	39.130	6.13	0.00	0.00	1.28
756	863	2.358737	AAAACGGGAGAGCGCCAG	60.359	61.111	2.29	0.00	0.00	4.85
892	999	7.051623	GGAGTGGGTTTATTGGTTTTCTTTTT	58.948	34.615	0.00	0.00	0.00	1.94
893	1000	6.157123	TGGAGTGGGTTTATTGGTTTTCTTTT	59.843	34.615	0.00	0.00	0.00	2.27
894	1001	5.663556	TGGAGTGGGTTTATTGGTTTTCTTT	59.336	36.000	0.00	0.00	0.00	2.52
895	1002	5.069914	GTGGAGTGGGTTTATTGGTTTTCTT	59.930	40.000	0.00	0.00	0.00	2.52
896	1003	4.587262	GTGGAGTGGGTTTATTGGTTTTCT	59.413	41.667	0.00	0.00	0.00	2.52
897	1004	4.587262	AGTGGAGTGGGTTTATTGGTTTTC	59.413	41.667	0.00	0.00	0.00	2.29
898	1005	4.552674	AGTGGAGTGGGTTTATTGGTTTT	58.447	39.130	0.00	0.00	0.00	2.43
899	1006	4.149598	GAGTGGAGTGGGTTTATTGGTTT	58.850	43.478	0.00	0.00	0.00	3.27
935	1042	2.858787	AGGGTTGTGGGAAGGAAAAA	57.141	45.000	0.00	0.00	0.00	1.94
936	1043	2.673258	GAAGGGTTGTGGGAAGGAAAA	58.327	47.619	0.00	0.00	0.00	2.29
937	1044	1.133294	GGAAGGGTTGTGGGAAGGAAA	60.133	52.381	0.00	0.00	0.00	3.13
938	1045	0.481128	GGAAGGGTTGTGGGAAGGAA	59.519	55.000	0.00	0.00	0.00	3.36
939	1046	0.402861	AGGAAGGGTTGTGGGAAGGA	60.403	55.000	0.00	0.00	0.00	3.36
940	1047	0.251341	CAGGAAGGGTTGTGGGAAGG	60.251	60.000	0.00	0.00	0.00	3.46
942	1049	0.699577	TCCAGGAAGGGTTGTGGGAA	60.700	55.000	0.00	0.00	38.24	3.97
943	1050	0.699577	TTCCAGGAAGGGTTGTGGGA	60.700	55.000	0.00	0.00	38.24	4.37
944	1051	0.539669	GTTCCAGGAAGGGTTGTGGG	60.540	60.000	0.54	0.00	38.24	4.61
945	1052	0.539669	GGTTCCAGGAAGGGTTGTGG	60.540	60.000	0.54	0.00	38.24	4.17
947	1054	0.701310	AGGGTTCCAGGAAGGGTTGT	60.701	55.000	0.54	0.00	38.24	3.32
949	1056	1.147191	GAAAGGGTTCCAGGAAGGGTT	59.853	52.381	0.54	0.00	38.24	4.11
950	1057	0.778083	GAAAGGGTTCCAGGAAGGGT	59.222	55.000	0.54	0.00	38.24	4.34
951	1058	1.004862	GAGAAAGGGTTCCAGGAAGGG	59.995	57.143	0.54	0.00	38.24	3.95
952	1059	1.004862	GGAGAAAGGGTTCCAGGAAGG	59.995	57.143	0.54	0.00	33.92	3.46
978	1107	2.979649	GGTGAGGAACCCGAGGAC	59.020	66.667	0.00	0.00	44.02	3.85
1026	1191	1.751924	GAGCCTTAGGTCATCGTCACT	59.248	52.381	0.00	0.00	40.37	3.41
1028	1193	1.847328	TGAGCCTTAGGTCATCGTCA	58.153	50.000	0.00	0.00	45.34	4.35
1238	1403	4.509737	GTGGCGAGGTAGCGGGAC	62.510	72.222	0.00	0.00	38.18	4.46
1587	1752	1.522355	CTTCGTCCATGCTGCCGAT	60.522	57.895	0.00	0.00	0.00	4.18
1700	1865	2.666596	CTATGCCGGCCACCTCCTTC	62.667	65.000	26.77	0.00	0.00	3.46
1849	2015	6.433716	ACACATGACATGGTTTATCATTGACA	59.566	34.615	19.39	0.00	30.58	3.58
2043	2209	4.156477	TGGTGGAAAGGGGAACAAATTAG	58.844	43.478	0.00	0.00	0.00	1.73
2045	2211	2.972021	CTGGTGGAAAGGGGAACAAATT	59.028	45.455	0.00	0.00	0.00	1.82
2114	2280	5.245531	TCATCAGAACCAACAGGTCATTAC	58.754	41.667	0.00	0.00	33.53	1.89
2235	2401	2.522198	ATCCCCTCGTGCTCCTGAGT	62.522	60.000	0.00	0.00	0.00	3.41
2257	2423	5.044919	TGGATCTACAACATCATTGAAGGGT	60.045	40.000	0.00	0.00	0.00	4.34
2533	2699	5.477984	AGAAACTATGTGCATTGGTGAATGT	59.522	36.000	0.00	0.00	41.09	2.71
2671	2837	5.586243	CCAAACCGAAGTCATATTCACAGAT	59.414	40.000	0.00	0.00	0.00	2.90
2682	2848	1.139256	TGCTACACCAAACCGAAGTCA	59.861	47.619	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.