AutoCloner

Multiple sequence alignment - TraesCS7D01G314700

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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	TraesCS7D01G314700	chr7D	100.000	3215	0	0	1	3215	400855422	400858636	0.000000e+00	5938.0
1	TraesCS7D01G314700	chr7D	98.739	1031	11	2	2187	3215	101141707	101142737	0.000000e+00	1831.0
2	TraesCS7D01G314700	chr7D	98.738	1030	12	1	2187	3215	89273734	89272705	0.000000e+00	1829.0
3	TraesCS7D01G314700	chr7D	98.738	1030	12	1	2187	3215	224462475	224463504	0.000000e+00	1829.0
4	TraesCS7D01G314700	chr7D	83.133	913	89	25	132	1023	194211455	194212323	0.000000e+00	773.0
5	TraesCS7D01G314700	chr7D	85.563	568	50	12	3	542	194211186	194211749	1.670000e-157	566.0
6	TraesCS7D01G314700	chr3D	98.931	1029	11	0	2187	3215	297461381	297460353	0.000000e+00	1840.0
7	TraesCS7D01G314700	chr3D	98.834	1029	12	0	2187	3215	288119004	288117976	0.000000e+00	1834.0
8	TraesCS7D01G314700	chr3D	98.738	1030	12	1	2187	3215	429604962	429603933	0.000000e+00	1829.0
9	TraesCS7D01G314700	chr3D	83.443	912	85	32	132	1023	328548338	328547473	0.000000e+00	787.0
10	TraesCS7D01G314700	chr5D	98.738	1030	12	1	2187	3215	533563167	533562138	0.000000e+00	1829.0
11	TraesCS7D01G314700	chr5D	98.457	1037	14	2	2181	3215	59608420	59609456	0.000000e+00	1825.0
12	TraesCS7D01G314700	chr5D	84.096	918	86	25	132	1026	214867951	214867071	0.000000e+00	832.0
13	TraesCS7D01G314700	chr5D	84.629	566	52	18	5	541	214868218	214867659	6.110000e-147	531.0
14	TraesCS7D01G314700	chr5D	84.048	583	56	12	4	553	402189555	402190133	7.900000e-146	527.0
15	TraesCS7D01G314700	chr5D	84.144	473	37	19	569	1023	402190205	402190657	1.070000e-114	424.0
16	TraesCS7D01G314700	chr1D	98.738	1030	11	2	2187	3215	460321192	460320164	0.000000e+00	1829.0
17	TraesCS7D01G314700	chr7A	93.118	1148	57	4	1055	2186	458737925	458739066	0.000000e+00	1663.0
18	TraesCS7D01G314700	chr7A	85.355	915	85	30	132	1025	506483211	506482325	0.000000e+00	902.0
19	TraesCS7D01G314700	chr7A	88.861	404	41	4	140	542	506483315	506482915	8.010000e-136	494.0
20	TraesCS7D01G314700	chrUn	92.771	1079	61	7	1119	2186	86400352	86401424	0.000000e+00	1544.0
21	TraesCS7D01G314700	chr6D	92.664	1036	46	17	3	1025	357561404	357562422	0.000000e+00	1465.0
22	TraesCS7D01G314700	chr6D	86.545	929	78	23	132	1027	32618920	32618006	0.000000e+00	979.0
23	TraesCS7D01G314700	chr6D	83.368	481	71	9	132	608	83282326	83281851	1.370000e-118	436.0
24	TraesCS7D01G314700	chr6D	86.022	279	22	7	766	1027	269898560	269898282	1.890000e-72	283.0
25	TraesCS7D01G314700	chr6D	89.706	204	16	5	821	1023	324572693	324572494	4.120000e-64	255.0
26	TraesCS7D01G314700	chr6B	82.452	889	107	35	167	1028	133748804	133749670	0.000000e+00	732.0
27	TraesCS7D01G314700	chr6B	80.863	904	114	29	138	1024	290231699	290232560	0.000000e+00	656.0
28	TraesCS7D01G314700	chr7B	83.753	794	83	25	250	1023	49420593	49419826	0.000000e+00	710.0
29	TraesCS7D01G314700	chr7B	81.579	912	99	31	132	1024	712067027	712066166	0.000000e+00	689.0
30	TraesCS7D01G314700	chr2A	81.858	904	108	25	142	1023	10369591	10368722	0.000000e+00	710.0
31	TraesCS7D01G314700	chr2A	81.522	552	83	18	132	672	10370049	10369506	1.370000e-118	436.0
32	TraesCS7D01G314700	chr1A	88.753	409	42	3	132	540	345295684	345296088	6.190000e-137	497.0
33	TraesCS7D01G314700	chr2B	87.893	413	45	4	132	542	741430539	741430948	6.240000e-132	481.0
34	TraesCS7D01G314700	chr2D	88.256	281	14	7	752	1022	279041427	279041156	5.180000e-83	318.0
35	TraesCS7D01G314700	chr3A	74.341	721	125	30	1119	1811	13192941	13193629	5.320000e-63	252.0
36	TraesCS7D01G314700	chr4D	78.899	109	14	8	2061	2165	454798498	454798395	7.440000e-07	65.8

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	TraesCS7D01G314700	chr7D	400855422	400858636	3214	False	5938.0	5938	100.0000	1	3215	1	chr7D.!!$F3	3214
1	TraesCS7D01G314700	chr7D	101141707	101142737	1030	False	1831.0	1831	98.7390	2187	3215	1	chr7D.!!$F1	1028
2	TraesCS7D01G314700	chr7D	89272705	89273734	1029	True	1829.0	1829	98.7380	2187	3215	1	chr7D.!!$R1	1028
3	TraesCS7D01G314700	chr7D	224462475	224463504	1029	False	1829.0	1829	98.7380	2187	3215	1	chr7D.!!$F2	1028
4	TraesCS7D01G314700	chr7D	194211186	194212323	1137	False	669.5	773	84.3480	3	1023	2	chr7D.!!$F4	1020
5	TraesCS7D01G314700	chr3D	297460353	297461381	1028	True	1840.0	1840	98.9310	2187	3215	1	chr3D.!!$R2	1028
6	TraesCS7D01G314700	chr3D	288117976	288119004	1028	True	1834.0	1834	98.8340	2187	3215	1	chr3D.!!$R1	1028
7	TraesCS7D01G314700	chr3D	429603933	429604962	1029	True	1829.0	1829	98.7380	2187	3215	1	chr3D.!!$R4	1028
8	TraesCS7D01G314700	chr3D	328547473	328548338	865	True	787.0	787	83.4430	132	1023	1	chr3D.!!$R3	891
9	TraesCS7D01G314700	chr5D	533562138	533563167	1029	True	1829.0	1829	98.7380	2187	3215	1	chr5D.!!$R1	1028
10	TraesCS7D01G314700	chr5D	59608420	59609456	1036	False	1825.0	1825	98.4570	2181	3215	1	chr5D.!!$F1	1034
11	TraesCS7D01G314700	chr5D	214867071	214868218	1147	True	681.5	832	84.3625	5	1026	2	chr5D.!!$R2	1021
12	TraesCS7D01G314700	chr5D	402189555	402190657	1102	False	475.5	527	84.0960	4	1023	2	chr5D.!!$F2	1019
13	TraesCS7D01G314700	chr1D	460320164	460321192	1028	True	1829.0	1829	98.7380	2187	3215	1	chr1D.!!$R1	1028
14	TraesCS7D01G314700	chr7A	458737925	458739066	1141	False	1663.0	1663	93.1180	1055	2186	1	chr7A.!!$F1	1131
15	TraesCS7D01G314700	chr7A	506482325	506483315	990	True	698.0	902	87.1080	132	1025	2	chr7A.!!$R1	893
16	TraesCS7D01G314700	chrUn	86400352	86401424	1072	False	1544.0	1544	92.7710	1119	2186	1	chrUn.!!$F1	1067
17	TraesCS7D01G314700	chr6D	357561404	357562422	1018	False	1465.0	1465	92.6640	3	1025	1	chr6D.!!$F1	1022
18	TraesCS7D01G314700	chr6D	32618006	32618920	914	True	979.0	979	86.5450	132	1027	1	chr6D.!!$R1	895
19	TraesCS7D01G314700	chr6B	133748804	133749670	866	False	732.0	732	82.4520	167	1028	1	chr6B.!!$F1	861
20	TraesCS7D01G314700	chr6B	290231699	290232560	861	False	656.0	656	80.8630	138	1024	1	chr6B.!!$F2	886
21	TraesCS7D01G314700	chr7B	49419826	49420593	767	True	710.0	710	83.7530	250	1023	1	chr7B.!!$R1	773
22	TraesCS7D01G314700	chr7B	712066166	712067027	861	True	689.0	689	81.5790	132	1024	1	chr7B.!!$R2	892
23	TraesCS7D01G314700	chr2A	10368722	10370049	1327	True	573.0	710	81.6900	132	1023	2	chr2A.!!$R1	891
24	TraesCS7D01G314700	chr3A	13192941	13193629	688	False	252.0	252	74.3410	1119	1811	1	chr3A.!!$F1	692

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
892	1470	2.276732	TTCTCAAAACCAGCTGGGAG	57.723	50.0	35.42	28.73	41.15	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2321	2954	0.468226	TTGATACTGCGGGGGATGTC	59.532	55.0	0.0	0.0	0.0	3.06	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
235	293	4.045636	ACAAATTTTGAAGCTGCGAACT	57.954	36.364	15.81	0.00	0.00	3.01
273	332	9.471742	GTGAACAAATTTTGTAACATGAACAAC	57.528	29.630	14.81	2.94	44.59	3.32
452	851	9.125906	CAAATCTGCAAACAAATTTTGAAAACA	57.874	25.926	15.81	7.57	0.00	2.83
876	1422	6.749036	TCAAGGAACCTTCTAGAAGTTTCT	57.251	37.500	30.35	23.30	39.08	2.52
892	1470	2.276732	TTCTCAAAACCAGCTGGGAG	57.723	50.000	35.42	28.73	41.15	4.30
1028	1607	3.797039	GCAAATAGCATTTTCCCCCTTC	58.203	45.455	0.00	0.00	44.79	3.46
1029	1608	3.737972	GCAAATAGCATTTTCCCCCTTCG	60.738	47.826	0.00	0.00	44.79	3.79
1030	1609	3.662759	AATAGCATTTTCCCCCTTCGA	57.337	42.857	0.00	0.00	0.00	3.71
1031	1610	3.884037	ATAGCATTTTCCCCCTTCGAT	57.116	42.857	0.00	0.00	0.00	3.59
1032	1611	2.058593	AGCATTTTCCCCCTTCGATC	57.941	50.000	0.00	0.00	0.00	3.69
1033	1612	1.566231	AGCATTTTCCCCCTTCGATCT	59.434	47.619	0.00	0.00	0.00	2.75
1034	1613	1.950216	GCATTTTCCCCCTTCGATCTC	59.050	52.381	0.00	0.00	0.00	2.75
1035	1614	2.213499	CATTTTCCCCCTTCGATCTCG	58.787	52.381	0.00	0.00	41.45	4.04
1036	1615	0.539986	TTTTCCCCCTTCGATCTCGG	59.460	55.000	0.00	0.00	40.29	4.63
1037	1616	0.616679	TTTCCCCCTTCGATCTCGGT	60.617	55.000	0.00	0.00	40.29	4.69
1038	1617	0.616679	TTCCCCCTTCGATCTCGGTT	60.617	55.000	0.00	0.00	40.29	4.44
1039	1618	0.259647	TCCCCCTTCGATCTCGGTTA	59.740	55.000	0.00	0.00	40.29	2.85
1040	1619	0.388294	CCCCCTTCGATCTCGGTTAC	59.612	60.000	0.00	0.00	40.29	2.50
1041	1620	1.400737	CCCCTTCGATCTCGGTTACT	58.599	55.000	0.00	0.00	40.29	2.24
1042	1621	1.337387	CCCCTTCGATCTCGGTTACTC	59.663	57.143	0.00	0.00	40.29	2.59
1043	1622	2.022195	CCCTTCGATCTCGGTTACTCA	58.978	52.381	0.00	0.00	40.29	3.41
1044	1623	2.426024	CCCTTCGATCTCGGTTACTCAA	59.574	50.000	0.00	0.00	40.29	3.02
1045	1624	3.119245	CCCTTCGATCTCGGTTACTCAAA	60.119	47.826	0.00	0.00	40.29	2.69
1046	1625	4.106197	CCTTCGATCTCGGTTACTCAAAG	58.894	47.826	0.00	0.00	40.29	2.77
1047	1626	4.142447	CCTTCGATCTCGGTTACTCAAAGA	60.142	45.833	0.00	0.00	40.29	2.52
1048	1627	5.381174	TTCGATCTCGGTTACTCAAAGAA	57.619	39.130	0.00	0.00	40.29	2.52
1049	1628	5.381174	TCGATCTCGGTTACTCAAAGAAA	57.619	39.130	0.00	0.00	40.29	2.52
1050	1629	5.775686	TCGATCTCGGTTACTCAAAGAAAA	58.224	37.500	0.00	0.00	40.29	2.29
1051	1630	6.218019	TCGATCTCGGTTACTCAAAGAAAAA	58.782	36.000	0.00	0.00	40.29	1.94
1074	1653	2.514458	ACCCTTGGATGTCCATCAAC	57.486	50.000	9.34	0.00	46.97	3.18
1160	1754	2.285220	CGCCTCGGTTATCATTGACAAG	59.715	50.000	0.00	0.00	0.00	3.16
1407	2012	2.100631	AGAATTCGAAGCGGCACCG	61.101	57.895	4.30	4.30	43.09	4.94
1433	2038	1.153289	GCCTGATCGTGTGCTCCAT	60.153	57.895	0.00	0.00	0.00	3.41
1524	2129	6.923508	TGAATATAAACCACTGTCTATCTGCG	59.076	38.462	0.00	0.00	0.00	5.18
1528	2133	0.452184	CCACTGTCTATCTGCGTCGT	59.548	55.000	0.00	0.00	0.00	4.34
1529	2134	1.539341	CACTGTCTATCTGCGTCGTG	58.461	55.000	0.00	0.00	0.00	4.35
1530	2135	0.179161	ACTGTCTATCTGCGTCGTGC	60.179	55.000	0.00	0.00	46.70	5.34
1531	2136	0.867753	CTGTCTATCTGCGTCGTGCC	60.868	60.000	0.00	0.00	45.60	5.01
1532	2137	1.939785	GTCTATCTGCGTCGTGCCG	60.940	63.158	0.00	0.00	45.60	5.69
1604	2221	2.184579	CCTTCGAAGAGGACCGCC	59.815	66.667	26.61	0.00	38.43	6.13
1747	2373	1.295423	CGAGGTGGGTTTGGTCGAT	59.705	57.895	0.00	0.00	32.32	3.59
1800	2426	3.691342	CGCGGACCCAGTCTTCCA	61.691	66.667	0.00	0.00	32.47	3.53
1829	2455	1.393603	GCTACCCAAGGCTGAATTCC	58.606	55.000	2.27	0.00	0.00	3.01
1915	2547	3.954258	TCATCCAGCTTGTCGAGATAGAA	59.046	43.478	0.00	0.00	0.00	2.10
2024	2656	4.927267	ATCTATGACTCGGAGATCCTCT	57.073	45.455	12.86	0.00	33.89	3.69
2035	2667	3.612004	CGGAGATCCTCTACCGCAATTAC	60.612	52.174	0.00	0.00	38.98	1.89
2100	2732	3.687212	CGGACATGTTACAGGCACAAATA	59.313	43.478	0.00	0.00	0.00	1.40
2131	2763	1.583495	GGCTTAAGGGGCACGTTGTC	61.583	60.000	3.66	0.00	0.00	3.18
2158	2790	5.877564	TGTTGATGGCTCGTTTGATTATGTA	59.122	36.000	0.00	0.00	0.00	2.29
2169	2801	4.481368	TTGATTATGTACCCGAGCTGTT	57.519	40.909	0.00	0.00	0.00	3.16
2176	2808	0.907704	TACCCGAGCTGTTGGATGGT	60.908	55.000	0.00	0.00	0.00	3.55
2321	2954	8.325421	AGTCGTATACCATAATGACTACTCTG	57.675	38.462	6.97	0.00	39.59	3.35
2396	3030	4.820894	ATCTTGAAACGGCTTAGTAGGT	57.179	40.909	0.00	0.00	0.00	3.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
212	270	4.869861	AGTTCGCAGCTTCAAAATTTGTTT	59.130	33.333	5.56	0.00	0.00	2.83
246	305	8.190888	TGTTCATGTTACAAAATTTGTTCACC	57.809	30.769	16.99	3.70	42.22	4.02
427	492	9.344309	CTGTTTTCAAAATTTGTTTGCAGATTT	57.656	25.926	5.56	0.00	39.95	2.17
452	851	5.163426	TGGTCACAATTCAAAAATGCTCACT	60.163	36.000	0.00	0.00	0.00	3.41
876	1422	1.228552	GGCTCCCAGCTGGTTTTGA	60.229	57.895	30.63	19.16	41.99	2.69
1028	1607	6.462073	TTTTTCTTTGAGTAACCGAGATCG	57.538	37.500	0.00	0.00	39.44	3.69
1048	1627	3.922375	TGGACATCCAAGGGTTCTTTTT	58.078	40.909	0.00	0.00	44.35	1.94
1049	1628	3.611025	TGGACATCCAAGGGTTCTTTT	57.389	42.857	0.00	0.00	44.35	2.27
1065	1644	1.534175	CGTAGCTCTCGGTTGATGGAC	60.534	57.143	0.00	0.00	0.00	4.02
1160	1754	3.379445	TCGTCGAAGTGGGCCTCC	61.379	66.667	4.53	0.00	0.00	4.30
1407	2012	1.953138	CACGATCAGGCGATCCAGC	60.953	63.158	11.75	0.00	44.55	4.85
1528	2133	2.894257	ATCTTCACTGGGCACGGCA	61.894	57.895	0.00	0.00	0.00	5.69
1529	2134	2.045926	ATCTTCACTGGGCACGGC	60.046	61.111	0.00	0.00	0.00	5.68
1530	2135	1.746615	CCATCTTCACTGGGCACGG	60.747	63.158	0.00	0.00	0.00	4.94
1531	2136	1.746615	CCCATCTTCACTGGGCACG	60.747	63.158	0.00	0.00	46.62	5.34
1532	2137	4.326255	CCCATCTTCACTGGGCAC	57.674	61.111	0.00	0.00	46.62	5.01
1554	2171	2.897350	GGAAAGCGGCGATGAGGG	60.897	66.667	12.98	0.00	0.00	4.30
1579	2196	0.103208	CCTCTTCGAAGGCGCTACAT	59.897	55.000	24.37	0.00	37.46	2.29
1604	2221	1.066114	GTCTTGGACGAGAAGACGCG	61.066	60.000	3.53	3.53	39.87	6.01
1800	2426	2.748465	GCCTTGGGTAGCGGTATGAAAT	60.748	50.000	0.00	0.00	0.00	2.17
1829	2455	4.018490	TCCCAATTGTCATTGTCATGGAG	58.982	43.478	4.43	0.00	38.58	3.86
2024	2656	1.519013	GACGGGCGTAATTGCGGTA	60.519	57.895	17.69	0.00	35.06	4.02
2035	2667	3.659089	AATGAGTTCCGGACGGGCG	62.659	63.158	1.83	0.00	34.94	6.13
2100	2732	3.117131	CCCCTTAAGCCAATAGTCCCAAT	60.117	47.826	0.00	0.00	0.00	3.16
2131	2763	1.731709	TCAAACGAGCCATCAACATCG	59.268	47.619	0.00	0.00	40.86	3.84
2158	2790	2.224159	ACCATCCAACAGCTCGGGT	61.224	57.895	0.00	0.00	0.00	5.28
2169	2801	3.014538	ATCCGGCACCACCATCCA	61.015	61.111	0.00	0.00	39.03	3.41
2176	2808	1.675310	CAGCTTTCATCCGGCACCA	60.675	57.895	0.00	0.00	0.00	4.17
2214	2847	2.098614	TGTATGCCGCACCAAATCATT	58.901	42.857	0.00	0.00	0.00	2.57
2321	2954	0.468226	TTGATACTGCGGGGGATGTC	59.532	55.000	0.00	0.00	0.00	3.06
2396	3030	3.820467	CTGACATTTTCACCAAGGCACTA	59.180	43.478	0.00	0.00	38.49	2.74
2427	3061	2.846206	TGCTTCATGTTCCCTCTATGGT	59.154	45.455	0.00	0.00	0.00	3.55
2430	3064	2.173569	GGGTGCTTCATGTTCCCTCTAT	59.826	50.000	0.00	0.00	35.63	1.98
2514	3148	2.217750	CAATCCAGTTCAACACCGACA	58.782	47.619	0.00	0.00	0.00	4.35
3120	3754	1.601914	CCTTTTTCTTTCCCAACGCCG	60.602	52.381	0.00	0.00	0.00	6.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.