AutoCloner

Multiple sequence alignment - TraesCS7D01G347800

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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	TraesCS7D01G347800	chr7D	100.000	2411	0	0	1	2411	447063142	447060732	0.000000e+00	4453.0
1	TraesCS7D01G347800	chr7D	91.364	799	61	2	28	826	631023164	631022374	0.000000e+00	1086.0
2	TraesCS7D01G347800	chr7D	81.437	167	24	4	1810	1976	509615423	509615264	1.950000e-26	130.0
3	TraesCS7D01G347800	chr7D	86.325	117	16	0	42	158	20479559	20479443	7.000000e-26	128.0
4	TraesCS7D01G347800	chr7B	93.870	1142	47	11	824	1954	464548989	464547860	0.000000e+00	1700.0
5	TraesCS7D01G347800	chr7B	89.824	796	75	3	30	825	34232610	34233399	0.000000e+00	1016.0
6	TraesCS7D01G347800	chr7B	88.731	843	78	8	1	827	186867782	186868623	0.000000e+00	1014.0
7	TraesCS7D01G347800	chr7B	96.603	471	12	1	1945	2411	464547757	464547287	0.000000e+00	778.0
8	TraesCS7D01G347800	chr2D	91.397	802	66	3	30	829	644242648	644243448	0.000000e+00	1096.0
9	TraesCS7D01G347800	chr2D	82.609	161	20	4	1810	1970	443243841	443243993	4.180000e-28	135.0
10	TraesCS7D01G347800	chr2B	91.080	796	69	2	30	825	734840226	734839433	0.000000e+00	1075.0
11	TraesCS7D01G347800	chr2B	90.238	799	76	2	30	827	461519108	461519905	0.000000e+00	1042.0
12	TraesCS7D01G347800	chr2B	97.222	36	1	0	1	36	461519063	461519098	7.200000e-06	62.1
13	TraesCS7D01G347800	chr3B	90.864	799	71	2	30	826	489693748	489694546	0.000000e+00	1070.0
14	TraesCS7D01G347800	chr3B	81.013	158	22	2	1810	1967	679632670	679632819	4.210000e-23	119.0
15	TraesCS7D01G347800	chr3D	90.921	793	58	8	37	827	23630299	23629519	0.000000e+00	1053.0
16	TraesCS7D01G347800	chr4B	90.488	799	68	7	30	827	81986368	81985577	0.000000e+00	1048.0
17	TraesCS7D01G347800	chr4B	81.410	156	14	9	1811	1965	454037974	454038115	1.960000e-21	113.0
18	TraesCS7D01G347800	chr4B	84.034	119	18	1	1809	1926	536122966	536122848	1.960000e-21	113.0
19	TraesCS7D01G347800	chr1A	90.100	798	78	1	30	827	23030593	23029797	0.000000e+00	1035.0
20	TraesCS7D01G347800	chr1A	97.368	38	1	0	1933	1970	394589796	394589833	5.560000e-07	65.8
21	TraesCS7D01G347800	chr7A	90.152	792	75	3	42	832	287486723	287485934	0.000000e+00	1027.0
22	TraesCS7D01G347800	chr7A	90.494	526	33	8	891	1413	498594499	498593988	0.000000e+00	678.0
23	TraesCS7D01G347800	chr7A	96.111	360	7	3	2059	2411	498593374	498593015	4.470000e-162	580.0
24	TraesCS7D01G347800	chr7A	88.117	446	29	13	1486	1910	498593979	498593537	2.140000e-140	508.0
25	TraesCS7D01G347800	chr7A	90.789	152	8	3	1953	2100	498593528	498593379	5.260000e-47	198.0
26	TraesCS7D01G347800	chr7A	92.308	78	5	1	832	908	498594592	498594515	2.530000e-20	110.0
27	TraesCS7D01G347800	chr5B	88.744	844	75	10	1	827	375801043	375801883	0.000000e+00	1014.0
28	TraesCS7D01G347800	chrUn	86.341	410	40	5	1	394	34095839	34096248	1.320000e-117	433.0
29	TraesCS7D01G347800	chrUn	86.341	410	40	5	1	394	234967946	234967537	1.320000e-117	433.0
30	TraesCS7D01G347800	chr4A	89.347	291	31	0	42	332	741029282	741029572	1.360000e-97	366.0
31	TraesCS7D01G347800	chr4A	84.000	125	20	0	1810	1934	715319457	715319333	1.170000e-23	121.0
32	TraesCS7D01G347800	chr4A	83.784	111	18	0	1816	1926	601184827	601184937	3.280000e-19	106.0
33	TraesCS7D01G347800	chr6B	82.019	317	40	9	1	301	27825738	27826053	1.110000e-63	254.0
34	TraesCS7D01G347800	chr6D	82.955	176	17	6	1807	1980	388119359	388119195	1.930000e-31	147.0
35	TraesCS7D01G347800	chr6A	85.106	141	14	1	1829	1969	517525539	517525406	1.160000e-28	137.0
36	TraesCS7D01G347800	chr1B	80.226	177	18	11	1805	1973	169532986	169533153	1.510000e-22	117.0
37	TraesCS7D01G347800	chr3A	80.247	162	20	5	1810	1969	651517255	651517406	7.050000e-21	111.0
38	TraesCS7D01G347800	chr1D	76.687	163	29	5	1810	1972	97556315	97556468	5.520000e-12	82.4

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	TraesCS7D01G347800	chr7D	447060732	447063142	2410	True	4453.00	4453	100.0000	1	2411	1	chr7D.!!$R2	2410
1	TraesCS7D01G347800	chr7D	631022374	631023164	790	True	1086.00	1086	91.3640	28	826	1	chr7D.!!$R4	798
2	TraesCS7D01G347800	chr7B	464547287	464548989	1702	True	1239.00	1700	95.2365	824	2411	2	chr7B.!!$R1	1587
3	TraesCS7D01G347800	chr7B	34232610	34233399	789	False	1016.00	1016	89.8240	30	825	1	chr7B.!!$F1	795
4	TraesCS7D01G347800	chr7B	186867782	186868623	841	False	1014.00	1014	88.7310	1	827	1	chr7B.!!$F2	826
5	TraesCS7D01G347800	chr2D	644242648	644243448	800	False	1096.00	1096	91.3970	30	829	1	chr2D.!!$F2	799
6	TraesCS7D01G347800	chr2B	734839433	734840226	793	True	1075.00	1075	91.0800	30	825	1	chr2B.!!$R1	795
7	TraesCS7D01G347800	chr2B	461519063	461519905	842	False	552.05	1042	93.7300	1	827	2	chr2B.!!$F1	826
8	TraesCS7D01G347800	chr3B	489693748	489694546	798	False	1070.00	1070	90.8640	30	826	1	chr3B.!!$F1	796
9	TraesCS7D01G347800	chr3D	23629519	23630299	780	True	1053.00	1053	90.9210	37	827	1	chr3D.!!$R1	790
10	TraesCS7D01G347800	chr4B	81985577	81986368	791	True	1048.00	1048	90.4880	30	827	1	chr4B.!!$R1	797
11	TraesCS7D01G347800	chr1A	23029797	23030593	796	True	1035.00	1035	90.1000	30	827	1	chr1A.!!$R1	797
12	TraesCS7D01G347800	chr7A	287485934	287486723	789	True	1027.00	1027	90.1520	42	832	1	chr7A.!!$R1	790
13	TraesCS7D01G347800	chr7A	498593015	498594592	1577	True	414.80	678	91.5638	832	2411	5	chr7A.!!$R2	1579
14	TraesCS7D01G347800	chr5B	375801043	375801883	840	False	1014.00	1014	88.7440	1	827	1	chr5B.!!$F1	826

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
515	545	0.391263	CCTTCTTGTAGGGTGTCGGC	60.391	60.0	0.0	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2054	2278	0.393808	TGCTAAAACCCGAGGGATGC	60.394	55.0	16.26	11.01	38.96	3.91	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
101	118	4.436998	GTGCTAGCGGTGTCGGCT	62.437	66.667	10.77	6.98	44.35	5.52
241	270	3.680786	CGGGCCTCTCACACGACA	61.681	66.667	0.84	0.00	0.00	4.35
243	272	2.574955	GGGCCTCTCACACGACAGT	61.575	63.158	0.84	0.00	0.00	3.55
291	320	2.594592	GGTGTTGCTGCTCCCGTT	60.595	61.111	0.00	0.00	0.00	4.44
405	434	2.203280	CGGTGGTTTGGCTGGTCA	60.203	61.111	0.00	0.00	0.00	4.02
457	487	1.131315	GAGAAATCCTTGCTGGTTCGC	59.869	52.381	0.00	0.00	37.07	4.70
504	534	1.620822	GTGCCACCATTCCTTCTTGT	58.379	50.000	0.00	0.00	0.00	3.16
515	545	0.391263	CCTTCTTGTAGGGTGTCGGC	60.391	60.000	0.00	0.00	0.00	5.54
604	634	1.138069	TCGGCATCGCATTCCTTCTTA	59.862	47.619	0.00	0.00	36.13	2.10
607	637	3.181501	CGGCATCGCATTCCTTCTTAAAA	60.182	43.478	0.00	0.00	0.00	1.52
611	641	5.391950	GCATCGCATTCCTTCTTAAAAGTGA	60.392	40.000	0.00	0.00	0.00	3.41
633	663	2.607668	CTTGGTACGCGGCAGATCGA	62.608	60.000	12.47	0.00	0.00	3.59
643	673	3.082579	GCAGATCGAAGCCTCGGGT	62.083	63.158	4.63	0.00	45.49	5.28
661	691	1.683629	GGTTGTGGTGGTTTGTCTCCA	60.684	52.381	0.00	0.00	0.00	3.86
672	702	3.386237	GTCTCCAGAGGGCGCAGT	61.386	66.667	10.83	0.00	0.00	4.40
747	777	5.867903	TCTTTTTCTTTTGGGCTTGATGA	57.132	34.783	0.00	0.00	0.00	2.92
876	909	3.306225	GGGCATTTTCACTCAAGCATTCA	60.306	43.478	0.00	0.00	0.00	2.57
930	996	8.784043	GCATGACCTACCTAATTAACCAAATAG	58.216	37.037	0.00	0.00	0.00	1.73
974	1040	1.643880	GCATTTTACCATGCTGCACC	58.356	50.000	3.57	0.00	45.35	5.01
1021	1088	3.875023	TTCACCGGGGGCGTGAAA	61.875	61.111	2.42	0.00	44.94	2.69
1085	1155	2.791396	TTACTGGTGCTCGACGTCGC	62.791	60.000	32.19	19.90	39.60	5.19
1129	1205	2.124653	GAGGAGGAGAGCCGACGA	60.125	66.667	0.00	0.00	39.96	4.20
1352	1434	3.625897	CCCCTCCATATGCGCCGA	61.626	66.667	4.18	0.00	0.00	5.54
1368	1450	2.648102	GACGCCGACGACGATGAG	60.648	66.667	11.37	0.00	43.93	2.90
1398	1480	1.135373	CGTCAAGATGTAGGCTCGTGT	60.135	52.381	0.00	0.00	0.00	4.49
1427	1509	2.796651	GCATGTAGCAGCAGCACC	59.203	61.111	3.17	0.00	45.49	5.01
1428	1510	2.042259	GCATGTAGCAGCAGCACCA	61.042	57.895	3.17	0.00	45.49	4.17
1441	1523	2.665000	CACCAGCAGATCCGGTGT	59.335	61.111	0.00	0.00	44.27	4.16
1625	1730	0.238553	GCTCCACCTTCGTTGCTTTC	59.761	55.000	0.00	0.00	0.00	2.62
1633	1738	3.002791	CCTTCGTTGCTTTCTATCTGCA	58.997	45.455	0.00	0.00	34.69	4.41
1634	1739	3.436704	CCTTCGTTGCTTTCTATCTGCAA	59.563	43.478	0.00	0.00	43.25	4.08
1635	1740	4.436584	CCTTCGTTGCTTTCTATCTGCAAG	60.437	45.833	0.00	0.00	45.55	4.01
1762	1870	6.324522	GCAGCGAGCTAATAACTATATGTG	57.675	41.667	0.00	0.00	41.15	3.21
1884	1992	2.508526	ACAGGCTGAAATGAGTGAACC	58.491	47.619	23.66	0.00	0.00	3.62
1904	2012	3.372822	ACCAACACACTAAAACGTGTCAG	59.627	43.478	0.00	0.00	45.74	3.51
1914	2022	4.668576	AAAACGTGTCAGTATGCATCTG	57.331	40.909	0.19	10.96	34.76	2.90
1920	2028	4.208666	CGTGTCAGTATGCATCTGATTCAG	59.791	45.833	22.97	7.38	42.63	3.02
1926	2034	8.404000	GTCAGTATGCATCTGATTCAGAAAAAT	58.596	33.333	19.73	14.53	42.63	1.82
1927	2035	8.403236	TCAGTATGCATCTGATTCAGAAAAATG	58.597	33.333	19.73	14.09	39.18	2.32
1928	2036	7.648112	CAGTATGCATCTGATTCAGAAAAATGG	59.352	37.037	19.73	7.28	44.04	3.16
2056	2280	9.770097	TTCCATACAAAAACAAAATAAGATGCA	57.230	25.926	0.00	0.00	0.00	3.96
2140	2413	4.808414	TCTTCCCATCTACACACAAGAG	57.192	45.455	0.00	0.00	0.00	2.85
2174	2447	2.744202	GTTACCTCACAGCATGACCTTG	59.256	50.000	0.00	0.00	39.69	3.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
291	320	1.593787	CGGAGAGAAGAGCCAAGCA	59.406	57.895	0.00	0.00	0.00	3.91
420	449	4.278513	CCCGCACTCCAACCCCAA	62.279	66.667	0.00	0.00	0.00	4.12
504	534	3.142838	GCTACCGCCGACACCCTA	61.143	66.667	0.00	0.00	0.00	3.53
515	545	1.473434	GGAAGTGAAGGATGGCTACCG	60.473	57.143	0.00	0.00	0.00	4.02
589	619	6.678900	GCATCACTTTTAAGAAGGAATGCGAT	60.679	38.462	15.08	0.00	31.18	4.58
604	634	1.196808	CGCGTACCAAGCATCACTTTT	59.803	47.619	0.00	0.00	36.04	2.27
607	637	1.447838	CCGCGTACCAAGCATCACT	60.448	57.895	4.92	0.00	34.19	3.41
611	641	2.593468	ATCTGCCGCGTACCAAGCAT	62.593	55.000	4.92	0.00	34.16	3.79
633	663	2.113139	CACCACAACCCGAGGCTT	59.887	61.111	0.00	0.00	0.00	4.35
643	673	1.562008	TCTGGAGACAAACCACCACAA	59.438	47.619	0.00	0.00	42.06	3.33
672	702	4.635769	GTGGATGAATCGCCACCA	57.364	55.556	12.34	0.00	46.91	4.17
680	710	2.802816	GCTCGATAAAGCGTGGATGAAT	59.197	45.455	0.00	0.00	31.56	2.57
695	725	2.034879	CCAACAACGGCAGCTCGAT	61.035	57.895	9.87	0.00	0.00	3.59
856	888	5.636121	TGAATGAATGCTTGAGTGAAAATGC	59.364	36.000	0.00	0.00	0.00	3.56
869	902	4.951715	TCTAGCAACCAATGAATGAATGCT	59.048	37.500	0.00	0.00	46.06	3.79
876	909	4.872691	CGTCTTCTCTAGCAACCAATGAAT	59.127	41.667	0.00	0.00	0.00	2.57
930	996	2.380084	TAAGACGTGACAGGATTGGC	57.620	50.000	0.00	0.00	0.00	4.52
1020	1087	6.434340	ACAAGAAGAAGAGAACTGGTTTGTTT	59.566	34.615	0.00	0.00	0.00	2.83
1021	1088	5.946377	ACAAGAAGAAGAGAACTGGTTTGTT	59.054	36.000	0.00	0.00	0.00	2.83
1352	1434	3.097137	CTCTCATCGTCGTCGGCGT	62.097	63.158	19.81	3.73	39.49	5.68
1365	1447	2.477972	CTTGACGCAGGTCGCTCTCA	62.478	60.000	0.00	0.00	46.49	3.27
1366	1448	1.803519	CTTGACGCAGGTCGCTCTC	60.804	63.158	0.00	0.00	46.49	3.20
1367	1449	1.599606	ATCTTGACGCAGGTCGCTCT	61.600	55.000	0.00	0.00	46.49	4.09
1368	1450	1.153745	ATCTTGACGCAGGTCGCTC	60.154	57.895	0.00	0.00	46.49	5.03
1398	1480	2.094442	TGCTACATGCTACGTTGCAGTA	60.094	45.455	27.30	24.14	46.71	2.74
1427	1509	2.401766	GGCAACACCGGATCTGCTG	61.402	63.158	9.46	0.00	35.13	4.41
1428	1510	2.045926	GGCAACACCGGATCTGCT	60.046	61.111	9.46	0.00	35.13	4.24
1441	1523	2.303175	AGTGTAAAGAAAAGGCGGCAA	58.697	42.857	13.08	0.00	0.00	4.52
1625	1730	8.986847	CCATAGTTAACTGATTCTTGCAGATAG	58.013	37.037	18.56	0.00	36.86	2.08
1650	1757	5.404366	GCAATTGCATCATCAACATGATACC	59.596	40.000	25.36	0.00	46.44	2.73
1722	1830	2.012673	CTGCTGGTAATCTGAGGTTGC	58.987	52.381	0.00	0.00	0.00	4.17
1758	1866	5.584253	ATCGTCTAAAGTCTGTAGCACAT	57.416	39.130	0.00	0.00	0.00	3.21
1761	1869	5.638596	TGAATCGTCTAAAGTCTGTAGCA	57.361	39.130	0.00	0.00	0.00	3.49
1762	1870	5.288952	GGTTGAATCGTCTAAAGTCTGTAGC	59.711	44.000	0.00	0.00	0.00	3.58
1868	1976	3.066621	TGTGTTGGTTCACTCATTTCAGC	59.933	43.478	0.00	0.00	38.90	4.26
1904	2012	7.486647	ACCATTTTTCTGAATCAGATGCATAC	58.513	34.615	14.31	0.00	40.39	2.39
1941	2049	8.160106	ACTCCCTCCATTCACAAATATAAGATC	58.840	37.037	0.00	0.00	0.00	2.75
2054	2278	0.393808	TGCTAAAACCCGAGGGATGC	60.394	55.000	16.26	11.01	38.96	3.91
2056	2280	1.064685	CCTTGCTAAAACCCGAGGGAT	60.065	52.381	16.26	0.00	38.96	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.