AutoCloner

Multiple sequence alignment - TraesCS7B01G115600

Loading Multiple Alignment...

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	TraesCS7B01G115600	chr7B	100.000	3194	0	0	1	3194	134306000	134302807	0.000000e+00	5899.0
1	TraesCS7B01G115600	chr7D	93.103	1624	64	15	1606	3194	168811858	168810248	0.000000e+00	2335.0
2	TraesCS7B01G115600	chr7D	89.659	967	99	1	189	1155	169041815	169040850	0.000000e+00	1230.0
3	TraesCS7B01G115600	chr7D	92.800	125	9	0	1	125	168811983	168811859	7.040000e-42	182.0
4	TraesCS7B01G115600	chr7A	94.164	891	50	2	1	890	171282257	171281368	0.000000e+00	1356.0
5	TraesCS7B01G115600	chr7A	90.100	1000	77	12	1275	2263	171274459	171273471	0.000000e+00	1279.0
6	TraesCS7B01G115600	chr7A	87.907	860	47	21	2363	3194	171273609	171272779	0.000000e+00	959.0
7	TraesCS7B01G115600	chr7A	95.181	166	8	0	1068	1233	171281288	171281123	2.440000e-66	263.0
8	TraesCS7B01G115600	chr7A	95.714	70	3	0	919	988	171281368	171281299	2.600000e-21	113.0
9	TraesCS7B01G115600	chr1B	74.901	1267	224	46	1022	2253	517508027	517506820	2.860000e-135	492.0
10	TraesCS7B01G115600	chr1B	93.258	89	4	2	2364	2451	402041846	402041759	2.590000e-26	130.0
11	TraesCS7B01G115600	chr1B	85.000	120	11	4	2364	2481	517506943	517506829	7.240000e-22	115.0
12	TraesCS7B01G115600	chr1B	77.941	136	19	5	1011	1145	402047948	402047823	1.230000e-09	75.0
13	TraesCS7B01G115600	chr1B	82.927	82	7	5	2890	2965	351170398	351170478	2.060000e-07	67.6
14	TraesCS7B01G115600	chr1D	74.409	1270	232	50	1022	2253	385053035	385051821	2.900000e-125	459.0
15	TraesCS7B01G115600	chr1D	75.817	612	109	19	1011	1620	298606745	298606171	1.130000e-69	274.0
16	TraesCS7B01G115600	chr1D	93.258	89	4	2	2364	2451	298605794	298605707	2.590000e-26	130.0
17	TraesCS7B01G115600	chr1D	85.000	120	11	4	2364	2481	385051944	385051830	7.240000e-22	115.0
18	TraesCS7B01G115600	chr2A	93.478	46	3	0	1611	1656	47767385	47767430	5.720000e-08	69.4

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	TraesCS7B01G115600	chr7B	134302807	134306000	3193	True	5899.000000	5899	100.000000	1	3194	1	chr7B.!!$R1	3193
1	TraesCS7B01G115600	chr7D	168810248	168811983	1735	True	1258.500000	2335	92.951500	1	3194	2	chr7D.!!$R2	3193
2	TraesCS7B01G115600	chr7D	169040850	169041815	965	True	1230.000000	1230	89.659000	189	1155	1	chr7D.!!$R1	966
3	TraesCS7B01G115600	chr7A	171272779	171274459	1680	True	1119.000000	1279	89.003500	1275	3194	2	chr7A.!!$R1	1919
4	TraesCS7B01G115600	chr7A	171281123	171282257	1134	True	577.333333	1356	95.019667	1	1233	3	chr7A.!!$R2	1232
5	TraesCS7B01G115600	chr1B	517506820	517508027	1207	True	303.500000	492	79.950500	1022	2481	2	chr1B.!!$R3	1459
6	TraesCS7B01G115600	chr1D	385051821	385053035	1214	True	287.000000	459	79.704500	1022	2481	2	chr1D.!!$R2	1459
7	TraesCS7B01G115600	chr1D	298605707	298606745	1038	True	202.000000	274	84.537500	1011	2451	2	chr1D.!!$R1	1440

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
550	551	0.737367	GCAGCACATCACGAGCTACA	60.737	55.0	0.00	0.0	39.83	2.74	F
1467	1468	0.109458	TGTACGCGCTGAAGTACAGG	60.109	55.0	18.23	0.0	45.49	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1682	1683	0.108756	GTCGAAGGAGTAGGTGTGGC	60.109	60.0	0.0	0.0	0.00	5.01	R
2682	2743	0.749818	TGCTAGAGAGACCTCGCCTG	60.750	60.0	0.0	0.0	44.08	4.85	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
105	106	2.058595	GCTCTTCTCCCGGCAGGTA	61.059	63.158	1.11	0.00	36.75	3.08
156	157	4.241555	AGGGTCATGATCGGCGGC	62.242	66.667	7.21	0.00	0.00	6.53
270	271	1.029947	TGTCCTGCATCGAGTCGCTA	61.030	55.000	7.92	0.00	0.00	4.26
505	506	2.360852	GGGGAGACGACGAGTGGA	60.361	66.667	0.00	0.00	0.00	4.02
538	539	4.724602	GCCGAGTCGAGCAGCACA	62.725	66.667	15.64	0.00	0.00	4.57
541	542	1.153958	CGAGTCGAGCAGCACATCA	60.154	57.895	6.73	0.00	0.00	3.07
544	545	1.444383	GTCGAGCAGCACATCACGA	60.444	57.895	0.00	0.00	0.00	4.35
550	551	0.737367	GCAGCACATCACGAGCTACA	60.737	55.000	0.00	0.00	39.83	2.74
650	651	0.999406	GCGCTCGAGAAAGCATACAA	59.001	50.000	18.75	0.00	42.62	2.41
728	729	2.202453	GTCGGAGAAGGTCGTCGC	60.202	66.667	0.00	0.00	39.69	5.19
744	745	4.241999	GCTGCTTATGGCGCGTGG	62.242	66.667	8.43	0.00	45.43	4.94
748	749	2.511373	CTTATGGCGCGTGGCTGA	60.511	61.111	23.71	8.44	42.94	4.26
750	751	1.835483	CTTATGGCGCGTGGCTGATC	61.835	60.000	23.71	0.00	42.94	2.92
813	814	4.263572	CTGGCCGGGTTGGTGTCA	62.264	66.667	2.57	0.00	41.21	3.58
816	817	2.112297	GCCGGGTTGGTGTCAGAA	59.888	61.111	2.18	0.00	41.21	3.02
838	839	1.270305	TGTTTGAAGGAGAGGACGCAG	60.270	52.381	0.00	0.00	0.00	5.18
907	908	1.153229	GCGGAGGTATGTGTTCCCC	60.153	63.158	0.00	0.00	0.00	4.81
908	909	1.143183	CGGAGGTATGTGTTCCCCG	59.857	63.158	0.00	0.00	33.76	5.73
915	916	0.912487	TATGTGTTCCCCGGCCTCTT	60.912	55.000	0.00	0.00	0.00	2.85
916	917	2.359975	GTGTTCCCCGGCCTCTTG	60.360	66.667	0.00	0.00	0.00	3.02
917	918	3.646715	TGTTCCCCGGCCTCTTGG	61.647	66.667	0.00	0.00	0.00	3.61
956	957	1.037493	GGCGGTTTCTTTCTTGGGTT	58.963	50.000	0.00	0.00	0.00	4.11
989	990	3.624410	TCATGAATTTGCAGATCAGGTCG	59.376	43.478	0.00	0.00	0.00	4.79
995	996	1.332889	TGCAGATCAGGTCGCAGGAT	61.333	55.000	0.00	0.00	33.58	3.24
1004	1005	1.137872	AGGTCGCAGGATCTCAATGAC	59.862	52.381	0.00	0.00	0.00	3.06
1030	1031	6.907853	ATCATCAGATAATCAACTCGGAGA	57.092	37.500	12.86	0.00	31.14	3.71
1170	1171	2.224695	TGTTCTAGACGACTGGACCAGA	60.225	50.000	28.56	3.16	33.52	3.86
1195	1196	1.226974	ACCATCCGCAAGATCGACG	60.227	57.895	0.00	0.00	43.02	5.12
1233	1234	3.391382	CCCGACCTGGACCTGGAC	61.391	72.222	23.36	16.07	42.00	4.02
1234	1235	3.391382	CCGACCTGGACCTGGACC	61.391	72.222	23.36	8.34	42.00	4.46
1235	1236	2.283966	CGACCTGGACCTGGACCT	60.284	66.667	23.36	1.40	0.00	3.85
1236	1237	2.650116	CGACCTGGACCTGGACCTG	61.650	68.421	23.36	14.74	0.00	4.00
1238	1239	2.122729	CCTGGACCTGGACCTGGA	59.877	66.667	28.41	4.64	45.37	3.86
1266	1267	2.577593	GTCCGGCTAGTGTCACCC	59.422	66.667	0.00	0.00	0.00	4.61
1267	1268	3.066190	TCCGGCTAGTGTCACCCG	61.066	66.667	11.05	11.05	40.39	5.28
1273	1274	1.079819	CTAGTGTCACCCGCACCTG	60.080	63.158	0.00	0.00	37.56	4.00
1396	1397	4.779733	GCCCTCTCCTCCCGGACA	62.780	72.222	0.73	0.00	34.92	4.02
1398	1399	2.760385	CCTCTCCTCCCGGACACC	60.760	72.222	0.73	0.00	34.92	4.16
1467	1468	0.109458	TGTACGCGCTGAAGTACAGG	60.109	55.000	18.23	0.00	45.49	4.00
1478	1479	4.742417	CTGAAGTACAGGATCTGTGACAG	58.258	47.826	6.18	6.18	45.01	3.51
1512	1513	2.347490	GTGATGTCCACGGCCTGT	59.653	61.111	0.00	0.00	35.86	4.00
1525	1526	1.296715	GCCTGTGTCGAGGATTGGT	59.703	57.895	0.00	0.00	34.69	3.67
1661	1662	1.789464	CACTCTCTTCGTGTCTTGTGC	59.211	52.381	0.00	0.00	0.00	4.57
1672	1673	2.117779	TCTTGTGCAAACAGCCGCA	61.118	52.632	0.00	0.00	44.83	5.69
1674	1675	1.210545	CTTGTGCAAACAGCCGCAAG	61.211	55.000	0.00	0.00	43.53	4.01
1761	1765	2.368548	GTTGCCTTTCCAAAATCAGGGT	59.631	45.455	0.00	0.00	0.00	4.34
1800	1804	4.778143	GCATGGGTCGGCCTTCGT	62.778	66.667	5.77	0.00	40.32	3.85
2013	2047	7.289310	TCATGCTCTATATCACCATTTTTGGA	58.711	34.615	0.00	0.00	0.00	3.53
2042	2076	3.040206	GCCATGAGGGAGAGCTGCA	62.040	63.158	1.02	0.00	40.01	4.41
2043	2077	1.153208	CCATGAGGGAGAGCTGCAC	60.153	63.158	1.02	0.00	40.01	4.57
2044	2078	1.624479	CCATGAGGGAGAGCTGCACT	61.624	60.000	1.02	0.00	40.01	4.40
2045	2079	0.462225	CATGAGGGAGAGCTGCACTG	60.462	60.000	3.82	0.00	0.00	3.66
2046	2080	2.125188	GAGGGAGAGCTGCACTGC	60.125	66.667	9.93	9.93	0.00	4.40
2204	2238	7.770801	TGGATCTGAATTAGTACGATTTGTG	57.229	36.000	0.00	0.00	0.00	3.33
2256	2290	1.484240	GTGGAACCTGCTGAGCTATCT	59.516	52.381	5.83	0.00	0.00	1.98
2472	2511	7.734924	AAAAATTCTTCTCTTGCCCATTTTC	57.265	32.000	0.00	0.00	0.00	2.29
2473	2512	6.423776	AAATTCTTCTCTTGCCCATTTTCA	57.576	33.333	0.00	0.00	0.00	2.69
2877	2956	1.470098	CGAGGCCACTCCATCTTTTTG	59.530	52.381	5.01	0.00	40.77	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
105	106	1.674057	CTTGGCGAGAACCACCTCT	59.326	57.895	0.00	0.00	40.19	3.69
183	184	4.504916	CTCTGCGTCCCTGAGCCG	62.505	72.222	0.00	0.00	33.56	5.52
246	247	4.794439	TCGATGCAGGACACGGCG	62.794	66.667	4.80	4.80	40.93	6.46
442	443	1.675720	AAGCTGGTGTTGTTGGCCAC	61.676	55.000	3.88	0.75	0.00	5.01
484	485	3.203412	CTCGTCGTCTCCCCCGAG	61.203	72.222	0.00	0.00	40.54	4.63
538	539	0.312416	GCCTCGATGTAGCTCGTGAT	59.688	55.000	0.00	0.00	39.62	3.06
541	542	0.382515	GAAGCCTCGATGTAGCTCGT	59.617	55.000	0.00	0.00	39.62	4.18
544	545	0.749649	CAGGAAGCCTCGATGTAGCT	59.250	55.000	0.00	0.00	38.88	3.32
550	551	3.854669	CGCCCAGGAAGCCTCGAT	61.855	66.667	0.00	0.00	0.00	3.59
728	729	4.241999	GCCACGCGCCATAAGCAG	62.242	66.667	5.73	0.00	44.04	4.24
748	749	1.377725	CAAGCTTGGGGTGCTCGAT	60.378	57.895	19.14	0.00	40.22	3.59
750	751	3.058160	CCAAGCTTGGGGTGCTCG	61.058	66.667	34.08	9.02	44.70	5.03
813	814	4.319177	CGTCCTCTCCTTCAAACAATTCT	58.681	43.478	0.00	0.00	0.00	2.40
816	817	2.224523	TGCGTCCTCTCCTTCAAACAAT	60.225	45.455	0.00	0.00	0.00	2.71
885	886	1.471676	GGAACACATACCTCCGCAGAG	60.472	57.143	0.00	0.00	40.09	3.35
892	893	1.153229	GCCGGGGAACACATACCTC	60.153	63.158	2.18	0.00	0.00	3.85
907	908	2.521958	ATCGAACACCCAAGAGGCCG	62.522	60.000	0.00	0.00	40.58	6.13
908	909	0.322546	AATCGAACACCCAAGAGGCC	60.323	55.000	0.00	0.00	40.58	5.19
915	916	1.811965	CTGATTGCAATCGAACACCCA	59.188	47.619	29.23	12.73	38.26	4.51
916	917	2.083774	TCTGATTGCAATCGAACACCC	58.916	47.619	29.23	8.92	38.26	4.61
917	918	2.096496	CCTCTGATTGCAATCGAACACC	59.904	50.000	29.23	9.61	38.26	4.16
956	957	8.347004	TCTGCAAATTCATGACCTATTTGTAA	57.653	30.769	22.97	15.14	39.97	2.41
989	990	3.461061	TGATTCGTCATTGAGATCCTGC	58.539	45.455	0.00	0.00	0.00	4.85
995	996	8.362639	TGATTATCTGATGATTCGTCATTGAGA	58.637	33.333	8.97	3.92	34.32	3.27
1004	1005	6.152379	TCCGAGTTGATTATCTGATGATTCG	58.848	40.000	0.00	4.16	34.32	3.34
1030	1031	1.211456	CCTCCTCCCAAGATCTGCTT	58.789	55.000	0.00	0.00	37.29	3.91
1170	1171	1.377725	CTTGCGGATGGTGAAGCCT	60.378	57.895	0.00	0.00	38.35	4.58
1195	1196	3.188786	GCTGTCCATGGCGTCGAC	61.189	66.667	6.96	5.18	0.00	4.20
1248	1249	2.181021	GGTGACACTAGCCGGACG	59.819	66.667	5.05	0.00	0.00	4.79
1249	1250	2.577593	GGGTGACACTAGCCGGAC	59.422	66.667	5.05	0.00	0.00	4.79
1266	1267	0.390603	TCACGGGATAAACAGGTGCG	60.391	55.000	0.00	0.00	0.00	5.34
1267	1268	1.467342	GTTCACGGGATAAACAGGTGC	59.533	52.381	0.00	0.00	0.00	5.01
1467	1468	0.743701	CCTGCTGCCTGTCACAGATC	60.744	60.000	6.30	0.00	37.32	2.75
1525	1526	3.245479	GGGTTTGGGAAAGAGTTGGGATA	60.245	47.826	0.00	0.00	0.00	2.59
1532	1533	1.704641	GCTTGGGTTTGGGAAAGAGT	58.295	50.000	0.00	0.00	0.00	3.24
1575	1576	3.599285	GAATGGCGGTGGTGACGGA	62.599	63.158	0.00	0.00	0.00	4.69
1678	1679	4.468689	GGAGTAGGTGTGGCGGCC	62.469	72.222	13.32	13.32	0.00	6.13
1679	1680	2.854187	GAAGGAGTAGGTGTGGCGGC	62.854	65.000	0.00	0.00	0.00	6.53
1682	1683	0.108756	GTCGAAGGAGTAGGTGTGGC	60.109	60.000	0.00	0.00	0.00	5.01
1709	1713	1.591703	TGAGACGTCCACTCATGGC	59.408	57.895	13.01	0.00	46.80	4.40
1721	1725	2.202797	CCCAGTCGCCATGAGACG	60.203	66.667	13.17	6.14	42.97	4.18
1761	1765	1.154093	CAGCTCGCCGTCGAAGTAA	60.154	57.895	0.00	0.00	44.98	2.24
2013	2047	1.556911	CCCTCATGGCTGTACTTGAGT	59.443	52.381	0.00	0.00	39.61	3.41
2042	2076	4.579384	CGGGTGGTGGGTTGCAGT	62.579	66.667	0.00	0.00	0.00	4.40
2043	2077	4.579384	ACGGGTGGTGGGTTGCAG	62.579	66.667	0.00	0.00	0.00	4.41
2044	2078	4.572571	GACGGGTGGTGGGTTGCA	62.573	66.667	0.00	0.00	0.00	4.08
2102	2136	0.179040	AGAACGCCACGGGAGAAAAA	60.179	50.000	0.00	0.00	0.00	1.94
2256	2290	9.720769	ACAAGCTCTTTTGCTACTAATAGTAAA	57.279	29.630	1.48	0.00	43.24	2.01
2278	2312	4.177165	TGCTTCCATTGCAACATACAAG	57.823	40.909	0.00	1.23	37.51	3.16
2682	2743	0.749818	TGCTAGAGAGACCTCGCCTG	60.750	60.000	0.00	0.00	44.08	4.85
2741	2807	2.684001	TGCGGTATGGACCTTTACAG	57.316	50.000	0.00	0.00	44.46	2.74
2824	2902	2.420129	CCGGCCTATTTAAGTCACTGCT	60.420	50.000	0.00	0.00	0.00	4.24
2867	2945	7.841915	AAGGTAACAAACAACAAAAAGATGG	57.158	32.000	0.00	0.00	41.41	3.51
2877	2956	9.938670	AAAAGAAAACAAAAGGTAACAAACAAC	57.061	25.926	0.00	0.00	41.41	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.