AutoCloner

Multiple sequence alignment - TraesCS7B01G200800

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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	TraesCS7B01G200800	chr7B	100.000	2246	0	0	1	2246	365876209	365873964	0.000000e+00	4148.0
1	TraesCS7B01G200800	chr7B	94.382	178	10	0	2069	2246	69169223	69169400	7.900000e-70	274.0
2	TraesCS7B01G200800	chr4D	95.575	1695	72	3	1	1693	210026551	210024858	0.000000e+00	2712.0
3	TraesCS7B01G200800	chr4D	92.469	571	33	4	1686	2246	210024821	210024251	0.000000e+00	808.0
4	TraesCS7B01G200800	chr3A	93.754	1697	102	4	1	1693	575149678	575151374	0.000000e+00	2543.0
5	TraesCS7B01G200800	chr3A	95.552	1304	55	3	1	1302	433764537	433765839	0.000000e+00	2084.0
6	TraesCS7B01G200800	chr3A	91.264	538	37	4	1686	2213	575151411	575151948	0.000000e+00	725.0
7	TraesCS7B01G200800	chr5A	93.133	1529	91	8	1	1523	173529035	173527515	0.000000e+00	2230.0
8	TraesCS7B01G200800	chr5A	93.619	862	52	1	791	1652	683752375	683751517	0.000000e+00	1284.0
9	TraesCS7B01G200800	chr5A	92.067	895	67	2	791	1684	681747178	681748069	0.000000e+00	1256.0
10	TraesCS7B01G200800	chr5A	90.520	538	41	4	1686	2213	681748115	681748652	0.000000e+00	702.0
11	TraesCS7B01G200800	chr5A	90.149	538	43	4	1686	2213	683751443	683750906	0.000000e+00	691.0
12	TraesCS7B01G200800	chr5A	89.744	117	9	3	1843	1956	165685389	165685505	1.800000e-31	147.0
13	TraesCS7B01G200800	chr1B	94.672	1295	67	2	1	1293	40282523	40283817	0.000000e+00	2008.0
14	TraesCS7B01G200800	chr4B	93.974	1228	63	4	1	1226	239620486	239621704	0.000000e+00	1847.0
15	TraesCS7B01G200800	chr5B	96.182	812	29	2	1	810	415416737	415415926	0.000000e+00	1327.0
16	TraesCS7B01G200800	chr5B	91.987	312	17	3	1691	1994	415394934	415394623	4.430000e-117	431.0
17	TraesCS7B01G200800	chr5B	93.548	124	8	0	1523	1646	415415926	415415803	3.810000e-43	185.0
18	TraesCS7B01G200800	chr5B	91.429	105	7	2	1854	1956	37820942	37821046	2.330000e-30	143.0
19	TraesCS7B01G200800	chr5D	92.992	899	51	9	1	890	68971084	68971979	0.000000e+00	1301.0
20	TraesCS7B01G200800	chr5D	92.381	105	6	2	1854	1956	472758968	472759072	5.000000e-32	148.0
21	TraesCS7B01G200800	chr1A	92.522	896	53	10	1	890	558759029	558758142	0.000000e+00	1271.0
22	TraesCS7B01G200800	chr4A	92.049	893	60	8	1	890	292710036	292709152	0.000000e+00	1245.0
23	TraesCS7B01G200800	chr4A	89.091	55	0	1	1773	1821	52141022	52140968	1.860000e-06	63.9
24	TraesCS7B01G200800	chr7A	96.033	731	29	0	659	1389	617960339	617959609	0.000000e+00	1190.0
25	TraesCS7B01G200800	chr3B	94.586	314	17	0	1076	1389	782861145	782860832	9.320000e-134	486.0
26	TraesCS7B01G200800	chr6B	88.202	178	12	1	2069	2246	65426126	65426294	1.050000e-48	204.0
27	TraesCS7B01G200800	chr1D	91.429	105	7	2	1854	1956	475306658	475306762	2.330000e-30	143.0

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	TraesCS7B01G200800	chr7B	365873964	365876209	2245	True	4148.0	4148	100.0000	1	2246	1	chr7B.!!$R1	2245
1	TraesCS7B01G200800	chr4D	210024251	210026551	2300	True	1760.0	2712	94.0220	1	2246	2	chr4D.!!$R1	2245
2	TraesCS7B01G200800	chr3A	433764537	433765839	1302	False	2084.0	2084	95.5520	1	1302	1	chr3A.!!$F1	1301
3	TraesCS7B01G200800	chr3A	575149678	575151948	2270	False	1634.0	2543	92.5090	1	2213	2	chr3A.!!$F2	2212
4	TraesCS7B01G200800	chr5A	173527515	173529035	1520	True	2230.0	2230	93.1330	1	1523	1	chr5A.!!$R1	1522
5	TraesCS7B01G200800	chr5A	683750906	683752375	1469	True	987.5	1284	91.8840	791	2213	2	chr5A.!!$R2	1422
6	TraesCS7B01G200800	chr5A	681747178	681748652	1474	False	979.0	1256	91.2935	791	2213	2	chr5A.!!$F2	1422
7	TraesCS7B01G200800	chr1B	40282523	40283817	1294	False	2008.0	2008	94.6720	1	1293	1	chr1B.!!$F1	1292
8	TraesCS7B01G200800	chr4B	239620486	239621704	1218	False	1847.0	1847	93.9740	1	1226	1	chr4B.!!$F1	1225
9	TraesCS7B01G200800	chr5B	415415803	415416737	934	True	756.0	1327	94.8650	1	1646	2	chr5B.!!$R2	1645
10	TraesCS7B01G200800	chr5D	68971084	68971979	895	False	1301.0	1301	92.9920	1	890	1	chr5D.!!$F1	889
11	TraesCS7B01G200800	chr1A	558758142	558759029	887	True	1271.0	1271	92.5220	1	890	1	chr1A.!!$R1	889
12	TraesCS7B01G200800	chr4A	292709152	292710036	884	True	1245.0	1245	92.0490	1	890	1	chr4A.!!$R2	889
13	TraesCS7B01G200800	chr7A	617959609	617960339	730	True	1190.0	1190	96.0330	659	1389	1	chr7A.!!$R1	730

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
566	578	4.006319	CTGAAGAAGGAAACCCAGATCAC	58.994	47.826	0.0	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2031	2104	0.029035	GCTTCGAGCTCAATGCCATG	59.971	55.0	15.4	0.0	44.23	3.66	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
149	151	6.757010	AGCAAGTAAATACTACTCCAATCACG	59.243	38.462	0.00	0.00	34.99	4.35
261	264	8.030106	AGAACCAGAATTTAAACGTTTGAACAA	58.970	29.630	23.46	6.83	0.00	2.83
355	365	8.080417	TCAACGAAGTATACATACTAATCAGGC	58.920	37.037	5.50	0.00	45.00	4.85
525	536	7.160049	AGAAAGCAGTACCCTAAAGAAAGTAC	58.840	38.462	0.00	0.00	36.23	2.73
566	578	4.006319	CTGAAGAAGGAAACCCAGATCAC	58.994	47.826	0.00	0.00	0.00	3.06
663	676	8.352942	AGGAAAACAACAGTTTAAATCAGCTAG	58.647	33.333	0.00	0.00	34.53	3.42
1004	1020	0.704076	AAAGCCCTAACAGCCATGGA	59.296	50.000	18.40	0.00	0.00	3.41
1023	1039	4.442706	TGGAATCGAATAGAAGAGTTGGC	58.557	43.478	0.00	0.00	0.00	4.52
1026	1042	3.146618	TCGAATAGAAGAGTTGGCGTC	57.853	47.619	0.00	0.00	0.00	5.19
1045	1061	3.246699	CGTCCAAAGAAAAAGCGACTACA	59.753	43.478	0.00	0.00	0.00	2.74
1049	1065	5.763204	TCCAAAGAAAAAGCGACTACATCTT	59.237	36.000	0.00	0.00	0.00	2.40
1062	1078	2.400467	ACATCTTAGGGGCCGTAGAT	57.600	50.000	6.02	6.92	0.00	1.98
1155	1171	2.178890	CCTTGAGCTGCCGCATCTC	61.179	63.158	15.82	15.82	39.10	2.75
1219	1235	2.367894	CAGCATGAAGAGGATGAGGCTA	59.632	50.000	0.00	0.00	39.69	3.93
1319	1335	7.181125	AGTCAGTATATTCCCTCCCAATCATAC	59.819	40.741	0.00	0.00	0.00	2.39
1359	1377	2.905676	GATGCCACCTCCCTCCCTCT	62.906	65.000	0.00	0.00	0.00	3.69
1422	1440	2.762327	GTGAACCTACCGAACCATAGGA	59.238	50.000	4.33	0.00	40.53	2.94
1432	1450	4.006989	CCGAACCATAGGAACATCAACAA	58.993	43.478	0.00	0.00	0.00	2.83
1493	1511	8.748582	CGAATAAATACTACTAACGTGAATGCA	58.251	33.333	0.00	0.00	0.00	3.96
1619	1637	2.157834	ATCAAACGAGTAACGCCACA	57.842	45.000	0.00	0.00	46.94	4.17
1748	1813	4.335647	AGAACCCCCACGCTGCAG	62.336	66.667	10.11	10.11	0.00	4.41
1762	1827	0.097674	CTGCAGCCAGTATTGTTCGC	59.902	55.000	0.00	0.00	34.31	4.70
1824	1895	5.742453	GTGATGCTTATGATTGCAGAACAAG	59.258	40.000	0.00	0.00	42.87	3.16
1929	2002	0.490017	TGTAGTGGAGAAGGGGTCCA	59.510	55.000	0.00	0.00	42.06	4.02
1933	2006	1.216990	GTGGAGAAGGGGTCCATGAT	58.783	55.000	0.00	0.00	45.91	2.45
1943	2016	0.396060	GGTCCATGATGAGAGCTCCC	59.604	60.000	10.93	0.00	0.00	4.30
1987	2060	1.398692	GAGGGAACAAAGTGGTTGCA	58.601	50.000	0.00	0.00	41.31	4.08
1995	2068	3.027412	ACAAAGTGGTTGCATAACACCA	58.973	40.909	3.79	3.79	41.31	4.17
2030	2103	0.769873	CATGGCCCTTAGCAGATCCT	59.230	55.000	0.00	0.00	46.50	3.24
2031	2104	1.063183	ATGGCCCTTAGCAGATCCTC	58.937	55.000	0.00	0.00	46.50	3.71
2032	2105	0.326522	TGGCCCTTAGCAGATCCTCA	60.327	55.000	0.00	0.00	46.50	3.86
2033	2106	1.063183	GGCCCTTAGCAGATCCTCAT	58.937	55.000	0.00	0.00	46.50	2.90
2034	2107	1.271271	GGCCCTTAGCAGATCCTCATG	60.271	57.143	0.00	0.00	46.50	3.07
2036	2109	1.271271	CCCTTAGCAGATCCTCATGGC	60.271	57.143	0.00	0.00	0.00	4.40
2037	2110	1.419012	CCTTAGCAGATCCTCATGGCA	59.581	52.381	0.00	0.00	0.00	4.92
2038	2111	2.040012	CCTTAGCAGATCCTCATGGCAT	59.960	50.000	0.00	0.00	0.00	4.40
2039	2112	3.498121	CCTTAGCAGATCCTCATGGCATT	60.498	47.826	0.00	0.00	0.00	3.56
2058	2132	3.612371	GAGCTCGAAGCCGTGTCGT	62.612	63.158	0.00	0.00	43.77	4.34
2193	2267	7.400052	AGAAAACTACATTAGGCCAAATGGAAT	59.600	33.333	5.01	0.00	40.48	3.01
2224	2298	2.203788	ACCTTGGCGTGGAGGAGA	60.204	61.111	7.03	0.00	36.84	3.71
2229	2303	0.039180	TTGGCGTGGAGGAGAGTCTA	59.961	55.000	0.00	0.00	0.00	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
149	151	7.225931	TCGCATTTATAGGATTGTAAACCTGAC	59.774	37.037	3.92	0.00	37.68	3.51
355	365	9.884465	GTATTTGGCTTCTATGTGCTAATTAAG	57.116	33.333	0.00	0.00	30.27	1.85
525	536	7.202526	TCTTCAGAAGTAAAATGTTTGCTTGG	58.797	34.615	10.09	2.43	0.00	3.61
566	578	2.040544	GCGGTCATGGTGAAGGTGG	61.041	63.158	0.00	0.00	0.00	4.61
870	884	7.990314	TGCACAATGAGCTTACCTTTGTATATA	59.010	33.333	4.08	0.00	32.78	0.86
1004	1020	4.113354	GACGCCAACTCTTCTATTCGATT	58.887	43.478	0.00	0.00	0.00	3.34
1023	1039	3.246699	TGTAGTCGCTTTTTCTTTGGACG	59.753	43.478	0.00	0.00	0.00	4.79
1026	1042	5.613358	AGATGTAGTCGCTTTTTCTTTGG	57.387	39.130	0.00	0.00	0.00	3.28
1045	1061	1.645710	CCATCTACGGCCCCTAAGAT	58.354	55.000	0.00	0.00	0.00	2.40
1068	1084	1.678970	GGCAACACCAGGGTCATCC	60.679	63.158	0.00	0.00	38.86	3.51
1155	1171	1.301165	GTTTGCTGCCTTGCCTTGG	60.301	57.895	0.00	0.00	0.00	3.61
1219	1235	0.034059	CTTCTTGTCCACGGCAGAGT	59.966	55.000	0.00	0.00	0.00	3.24
1226	1242	5.292101	CCTAGCTAAAATCTTCTTGTCCACG	59.708	44.000	0.00	0.00	0.00	4.94
1319	1335	6.072286	GCATCCCAAATCATACTTGTCTATGG	60.072	42.308	0.00	0.00	0.00	2.74
1359	1377	9.555727	GTAACACCCAAGCAATTATTATAGAGA	57.444	33.333	0.00	0.00	0.00	3.10
1422	1440	8.352942	GGACTCAAGTTAAATCTTGTTGATGTT	58.647	33.333	5.90	0.00	43.44	2.71
1530	1548	2.142761	TGGGCAGTGACTGAGCTGT	61.143	57.895	18.18	0.00	35.33	4.40
1571	1589	1.204146	GGGGAGTAATCTGAGGCACA	58.796	55.000	0.00	0.00	0.00	4.57
1619	1637	0.779997	AACTGGGCAGGTCCTTTCAT	59.220	50.000	0.00	0.00	34.39	2.57
1689	1709	0.460284	CTCCTCATGGTTCCGTTCGG	60.460	60.000	4.74	4.74	34.23	4.30
1748	1813	2.076863	AGTTCAGCGAACAATACTGGC	58.923	47.619	18.86	0.00	44.11	4.85
1787	1852	6.552725	TCATAAGCATCACTCTGGTCTTAGAT	59.447	38.462	0.00	0.00	0.00	1.98
1929	2002	0.473501	GGGAGGGGAGCTCTCATCAT	60.474	60.000	28.08	5.07	33.18	2.45
1933	2006	3.347590	TCGGGAGGGGAGCTCTCA	61.348	66.667	17.22	0.00	33.18	3.27
1943	2016	2.047844	CTGTGTGCTGTCGGGAGG	60.048	66.667	0.00	0.00	0.00	4.30
1987	2060	0.107654	GCGAGGAGCCTTGGTGTTAT	60.108	55.000	5.93	0.00	40.81	1.89
2021	2094	1.493446	TCAATGCCATGAGGATCTGCT	59.507	47.619	0.00	0.00	36.89	4.24
2030	2103	1.660167	CTTCGAGCTCAATGCCATGA	58.340	50.000	15.40	0.00	44.23	3.07
2031	2104	0.029035	GCTTCGAGCTCAATGCCATG	59.971	55.000	15.40	0.00	44.23	3.66
2032	2105	1.099879	GGCTTCGAGCTCAATGCCAT	61.100	55.000	23.05	0.00	41.99	4.40
2033	2106	1.746615	GGCTTCGAGCTCAATGCCA	60.747	57.895	23.05	0.00	41.99	4.92
2034	2107	2.817423	CGGCTTCGAGCTCAATGCC	61.817	63.158	19.20	19.20	41.99	4.40
2036	2109	1.016130	ACACGGCTTCGAGCTCAATG	61.016	55.000	15.40	0.00	41.99	2.82
2037	2110	0.737715	GACACGGCTTCGAGCTCAAT	60.738	55.000	15.40	0.00	41.99	2.57
2038	2111	1.372997	GACACGGCTTCGAGCTCAA	60.373	57.895	15.40	6.48	41.99	3.02
2039	2112	2.258591	GACACGGCTTCGAGCTCA	59.741	61.111	15.40	0.00	41.99	4.26
2214	2288	2.171027	AGGTAGTAGACTCTCCTCCACG	59.829	54.545	1.86	0.00	0.00	4.94
2217	2291	4.457466	CTTCAGGTAGTAGACTCTCCTCC	58.543	52.174	4.10	0.00	31.36	4.30
2224	2298	2.684334	CGCCTCCTTCAGGTAGTAGACT	60.684	54.545	0.00	0.00	45.61	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.