AutoCloner

Multiple sequence alignment - TraesCS5D01G145200

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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	TraesCS5D01G145200	chr5D	100.000	2453	0	0	1	2453	231787218	231789670	0.000000e+00	4530.0
1	TraesCS5D01G145200	chr5D	98.295	704	11	1	1	703	319238872	319239575	0.000000e+00	1232.0
2	TraesCS5D01G145200	chr5D	97.727	704	15	1	1	703	52383995	52383292	0.000000e+00	1210.0
3	TraesCS5D01G145200	chr5B	91.549	1491	81	7	726	2187	273459646	273458172	0.000000e+00	2013.0
4	TraesCS5D01G145200	chr5B	90.698	215	19	1	2190	2404	273458199	273457986	3.990000e-73	285.0
5	TraesCS5D01G145200	chr5A	97.339	1090	27	1	704	1791	325184887	325183798	0.000000e+00	1851.0
6	TraesCS5D01G145200	chr5A	87.931	406	45	3	1782	2187	325180664	325180263	2.210000e-130	475.0
7	TraesCS5D01G145200	chr5A	90.698	215	16	2	2190	2404	325180290	325180080	1.440000e-72	283.0
8	TraesCS5D01G145200	chr2D	98.011	704	13	1	1	703	189367726	189367023	0.000000e+00	1221.0
9	TraesCS5D01G145200	chr2D	98.003	701	13	1	4	703	592645679	592644979	0.000000e+00	1216.0
10	TraesCS5D01G145200	chr2D	87.762	286	32	3	1903	2187	129957205	129957488	5.060000e-87	331.0
11	TraesCS5D01G145200	chr2D	86.713	286	33	5	1903	2187	43726531	43726250	1.830000e-81	313.0
12	TraesCS5D01G145200	chr2D	84.524	168	16	6	2247	2404	129957496	129957663	9.080000e-35	158.0
13	TraesCS5D01G145200	chr2D	97.727	88	2	0	1567	1654	34022967	34022880	4.220000e-33	152.0
14	TraesCS5D01G145200	chr2D	83.929	168	17	6	2247	2404	43726242	43726075	4.220000e-33	152.0
15	TraesCS5D01G145200	chr7D	97.869	704	14	1	1	703	400167696	400166993	0.000000e+00	1216.0
16	TraesCS5D01G145200	chr7D	97.305	705	17	2	1	703	111110384	111111088	0.000000e+00	1195.0
17	TraesCS5D01G145200	chr6D	97.724	703	15	1	1	702	85956905	85957607	0.000000e+00	1208.0
18	TraesCS5D01G145200	chr1D	97.582	703	15	2	3	703	416757399	416758101	0.000000e+00	1203.0
19	TraesCS5D01G145200	chrUn	97.163	705	17	3	1	703	22345040	22344337	0.000000e+00	1188.0
20	TraesCS5D01G145200	chr4A	82.584	534	58	24	1903	2404	705247104	705246574	2.900000e-119	438.0
21	TraesCS5D01G145200	chr3A	89.401	217	22	1	1906	2122	144533899	144533684	3.110000e-69	272.0
22	TraesCS5D01G145200	chr3A	84.746	177	19	5	2231	2403	144533572	144533400	1.170000e-38	171.0
23	TraesCS5D01G145200	chr2A	96.809	94	3	0	1903	1996	679266210	679266303	9.080000e-35	158.0
24	TraesCS5D01G145200	chr6B	94.595	37	2	0	2405	2441	216505565	216505529	9.470000e-05	58.4

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	TraesCS5D01G145200	chr5D	231787218	231789670	2452	False	4530.000000	4530	100.000000	1	2453	1	chr5D.!!$F1	2452
1	TraesCS5D01G145200	chr5D	319238872	319239575	703	False	1232.000000	1232	98.295000	1	703	1	chr5D.!!$F2	702
2	TraesCS5D01G145200	chr5D	52383292	52383995	703	True	1210.000000	1210	97.727000	1	703	1	chr5D.!!$R1	702
3	TraesCS5D01G145200	chr5B	273457986	273459646	1660	True	1149.000000	2013	91.123500	726	2404	2	chr5B.!!$R1	1678
4	TraesCS5D01G145200	chr5A	325180080	325184887	4807	True	869.666667	1851	91.989333	704	2404	3	chr5A.!!$R1	1700
5	TraesCS5D01G145200	chr2D	189367023	189367726	703	True	1221.000000	1221	98.011000	1	703	1	chr2D.!!$R2	702
6	TraesCS5D01G145200	chr2D	592644979	592645679	700	True	1216.000000	1216	98.003000	4	703	1	chr2D.!!$R3	699
7	TraesCS5D01G145200	chr7D	400166993	400167696	703	True	1216.000000	1216	97.869000	1	703	1	chr7D.!!$R1	702
8	TraesCS5D01G145200	chr7D	111110384	111111088	704	False	1195.000000	1195	97.305000	1	703	1	chr7D.!!$F1	702
9	TraesCS5D01G145200	chr6D	85956905	85957607	702	False	1208.000000	1208	97.724000	1	702	1	chr6D.!!$F1	701
10	TraesCS5D01G145200	chr1D	416757399	416758101	702	False	1203.000000	1203	97.582000	3	703	1	chr1D.!!$F1	700
11	TraesCS5D01G145200	chrUn	22344337	22345040	703	True	1188.000000	1188	97.163000	1	703	1	chrUn.!!$R1	702
12	TraesCS5D01G145200	chr4A	705246574	705247104	530	True	438.000000	438	82.584000	1903	2404	1	chr4A.!!$R1	501

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
87	89	2.04783	GATTCTCGATACCCAACCCCT	58.952	52.381	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1891	5064	0.17914	AACAACACTGCAAACCAGCG	60.179	50.0	0.0	0.0	45.78	5.18	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
59	60	4.826274	ACTAAGCAGGCATCTGTTCTTA	57.174	40.909	0.00	0.00	42.78	2.10
87	89	2.047830	GATTCTCGATACCCAACCCCT	58.952	52.381	0.00	0.00	0.00	4.79
160	162	5.068855	TCTCTTAAGATCATCACTCTGCCAG	59.931	44.000	5.44	0.00	0.00	4.85
414	416	9.028284	GTAAGTAAAAGGTAAAGCCCCTAATTT	57.972	33.333	0.00	0.00	38.26	1.82
461	463	3.454082	CTCTTGTTCCTCCTTGGCTCTAT	59.546	47.826	0.00	0.00	35.26	1.98
706	709	7.899178	AACATATCGACTACAATGTTGTTGA	57.101	32.000	17.56	17.56	40.18	3.18
712	715	2.151202	CTACAATGTTGTTGAGCGGGT	58.849	47.619	3.45	0.00	42.35	5.28
741	744	4.639310	AGCTAGTTCTGCAAATTGAGGATG	59.361	41.667	0.00	0.00	0.00	3.51
749	752	2.159142	GCAAATTGAGGATGCAAGGGAG	60.159	50.000	0.00	0.00	39.81	4.30
827	830	2.357836	CCAGCTTCATGCCTGGGT	59.642	61.111	15.21	0.00	44.23	4.51
1629	1659	5.958321	TGGAGGAGATCAGTATCTGTGTAT	58.042	41.667	0.00	0.00	42.73	2.29
1794	1824	3.600388	CTCAAACGGATATATCTGGGCC	58.400	50.000	22.69	0.00	37.50	5.80
1804	4977	9.220906	ACGGATATATCTGGGCCTATTTTAATA	57.779	33.333	22.69	0.00	37.50	0.98
1830	5003	2.159653	GCACATCAGTTTAAGCGTGAGG	60.160	50.000	0.00	2.04	0.00	3.86
1855	5028	5.495926	TTTTACGGTACCCTGGTATTTCA	57.504	39.130	6.25	0.00	32.82	2.69
1856	5029	5.495926	TTTACGGTACCCTGGTATTTCAA	57.504	39.130	6.25	0.00	32.82	2.69
1857	5030	5.697082	TTACGGTACCCTGGTATTTCAAT	57.303	39.130	6.25	0.00	32.82	2.57
1860	5033	3.875134	CGGTACCCTGGTATTTCAATGAC	59.125	47.826	6.25	0.00	32.82	3.06
1891	5064	1.798813	GTACCGATCAAATCCATCCGC	59.201	52.381	0.00	0.00	0.00	5.54
1892	5065	0.880278	ACCGATCAAATCCATCCGCG	60.880	55.000	0.00	0.00	0.00	6.46
1893	5066	1.205064	CGATCAAATCCATCCGCGC	59.795	57.895	0.00	0.00	0.00	6.86
2102	5279	6.140110	GCGAATAAAACATGTTGTAGTGTGT	58.860	36.000	13.25	0.00	0.00	3.72
2111	5288	5.526111	ACATGTTGTAGTGTGTAGTTTCCAC	59.474	40.000	0.00	0.00	0.00	4.02
2124	5302	4.345859	AGTTTCCACCAACGACAGATTA	57.654	40.909	0.00	0.00	0.00	1.75
2125	5303	4.906618	AGTTTCCACCAACGACAGATTAT	58.093	39.130	0.00	0.00	0.00	1.28
2149	5327	3.070878	TCTGGATTGCATAACTATCGCCA	59.929	43.478	0.00	0.00	32.00	5.69
2157	5335	5.308014	TGCATAACTATCGCCATCAGAAAT	58.692	37.500	0.00	0.00	0.00	2.17
2171	5349	9.410556	CGCCATCAGAAATATTTAATTTTAGGG	57.589	33.333	0.00	0.00	0.00	3.53
2172	5350	9.208022	GCCATCAGAAATATTTAATTTTAGGGC	57.792	33.333	0.00	3.55	0.00	5.19
2245	5474	1.218230	GGCATGTCGCTCGGAAGATC	61.218	60.000	0.00	0.00	41.91	2.75
2328	5557	7.277981	ACGAATTTCTTGCATAATCTACGTCTT	59.722	33.333	0.00	0.00	0.00	3.01
2347	5577	2.764128	ATCGGCTCCGTCCATGGT	60.764	61.111	12.58	0.00	40.74	3.55
2349	5579	2.593468	ATCGGCTCCGTCCATGGTTG	62.593	60.000	12.58	5.29	40.74	3.77
2408	5647	3.136123	CATGTGGCTGCCCCGAAG	61.136	66.667	17.53	0.00	35.87	3.79
2426	5665	3.748856	CGGAAAATTGCGCGGTTC	58.251	55.556	8.83	3.20	34.72	3.62
2427	5666	1.799916	CGGAAAATTGCGCGGTTCC	60.800	57.895	8.83	16.80	36.89	3.62
2428	5667	1.799916	GGAAAATTGCGCGGTTCCG	60.800	57.895	8.83	6.90	30.85	4.30
2429	5668	1.081708	GAAAATTGCGCGGTTCCGT	60.082	52.632	8.83	0.00	0.00	4.69
2430	5669	1.334288	GAAAATTGCGCGGTTCCGTG	61.334	55.000	18.66	18.66	42.05	4.94
2431	5670	1.787057	AAAATTGCGCGGTTCCGTGA	61.787	50.000	25.57	8.58	41.75	4.35
2432	5671	1.582610	AAATTGCGCGGTTCCGTGAT	61.583	50.000	25.57	10.40	41.75	3.06
2433	5672	2.252127	AATTGCGCGGTTCCGTGATG	62.252	55.000	25.57	9.17	41.75	3.07
2434	5673	4.673298	TGCGCGGTTCCGTGATGT	62.673	61.111	25.57	0.00	41.75	3.06
2435	5674	2.507547	GCGCGGTTCCGTGATGTA	60.508	61.111	25.57	0.00	41.75	2.29
2436	5675	2.795389	GCGCGGTTCCGTGATGTAC	61.795	63.158	25.57	6.34	41.75	2.90
2437	5676	2.162754	CGCGGTTCCGTGATGTACC	61.163	63.158	18.24	0.00	41.75	3.34
2438	5677	4.082192	CGGTTCCGTGATGTACCG	57.918	61.111	2.82	0.00	46.22	4.02
2439	5678	4.507879	GGTTCCGTGATGTACCGG	57.492	61.111	0.00	0.00	45.55	5.28
2440	5679	1.812507	GGTTCCGTGATGTACCGGC	60.813	63.158	0.00	0.00	43.87	6.13
2441	5680	2.162754	GTTCCGTGATGTACCGGCG	61.163	63.158	0.00	0.00	43.87	6.46
2442	5681	2.341875	TTCCGTGATGTACCGGCGA	61.342	57.895	9.30	0.00	43.87	5.54
2443	5682	2.546645	TTCCGTGATGTACCGGCGAC	62.547	60.000	9.30	0.00	43.87	5.19
2444	5683	2.488355	CGTGATGTACCGGCGACT	59.512	61.111	9.30	0.00	0.00	4.18
2445	5684	1.872234	CGTGATGTACCGGCGACTG	60.872	63.158	9.30	0.00	0.00	3.51
2446	5685	1.518572	GTGATGTACCGGCGACTGG	60.519	63.158	9.30	3.50	0.00	4.00
2447	5686	2.585247	GATGTACCGGCGACTGGC	60.585	66.667	9.30	0.00	42.51	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	4.030913	TGGGTATCGAGAATCTTGAGGTT	58.969	43.478	6.35	0.00	0.00	3.50
87	89	6.785337	TTATTTGTCGTCCTAAGGATCAGA	57.215	37.500	0.00	0.00	32.73	3.27
160	162	6.594159	TGGACTTCTATCGGTCAAGATTTTTC	59.406	38.462	0.00	0.00	34.49	2.29
414	416	6.350612	GGCTTATAGGCAATTGTTTGGTTGTA	60.351	38.462	9.27	0.00	40.97	2.41
461	463	1.953559	AGCGAGTTGTTCTGCTTTGA	58.046	45.000	0.00	0.00	33.81	2.69
703	706	3.563223	ACTAGCTAGATAACCCGCTCAA	58.437	45.455	27.45	0.00	34.14	3.02
704	707	3.225177	ACTAGCTAGATAACCCGCTCA	57.775	47.619	27.45	0.00	34.14	4.26
705	708	3.822167	AGAACTAGCTAGATAACCCGCTC	59.178	47.826	27.45	8.56	34.14	5.03
706	709	3.570550	CAGAACTAGCTAGATAACCCGCT	59.429	47.826	27.45	4.88	36.56	5.52
712	715	7.712639	CCTCAATTTGCAGAACTAGCTAGATAA	59.287	37.037	27.45	6.69	0.00	1.75
749	752	4.156556	TGTGTTTAGAGCTGGATGCAATTC	59.843	41.667	0.00	0.00	45.94	2.17
1629	1659	4.893524	TGGTACAAACTCTCAACTCTCAGA	59.106	41.667	0.00	0.00	31.92	3.27
1804	4977	4.094887	CACGCTTAAACTGATGTGCCTATT	59.905	41.667	0.00	0.00	0.00	1.73
1846	5019	5.249622	TCCCACACTAGTCATTGAAATACCA	59.750	40.000	0.00	0.00	0.00	3.25
1848	5021	6.407202	ACTCCCACACTAGTCATTGAAATAC	58.593	40.000	0.00	0.00	0.00	1.89
1849	5022	6.620877	ACTCCCACACTAGTCATTGAAATA	57.379	37.500	0.00	0.00	0.00	1.40
1850	5023	5.505181	ACTCCCACACTAGTCATTGAAAT	57.495	39.130	0.00	0.00	0.00	2.17
1852	5025	4.222145	GGTACTCCCACACTAGTCATTGAA	59.778	45.833	0.00	0.00	0.00	2.69
1853	5026	3.767673	GGTACTCCCACACTAGTCATTGA	59.232	47.826	0.00	0.00	0.00	2.57
1855	5028	2.758979	CGGTACTCCCACACTAGTCATT	59.241	50.000	0.00	0.00	0.00	2.57
1856	5029	2.025605	TCGGTACTCCCACACTAGTCAT	60.026	50.000	0.00	0.00	0.00	3.06
1857	5030	1.352017	TCGGTACTCCCACACTAGTCA	59.648	52.381	0.00	0.00	0.00	3.41
1860	5033	2.651455	TGATCGGTACTCCCACACTAG	58.349	52.381	0.00	0.00	0.00	2.57
1891	5064	0.179140	AACAACACTGCAAACCAGCG	60.179	50.000	0.00	0.00	45.78	5.18
1892	5065	2.008752	AAACAACACTGCAAACCAGC	57.991	45.000	0.00	0.00	45.78	4.85
1893	5066	5.095236	TTGGAAAACAACACTGCAAACCAG	61.095	41.667	0.00	0.00	39.82	4.00
2052	5229	6.846988	TCAAATTACCATACATCCTATGGCA	58.153	36.000	6.33	0.00	46.37	4.92
2102	5279	4.345859	AATCTGTCGTTGGTGGAAACTA	57.654	40.909	0.00	0.00	0.00	2.24
2124	5302	4.692625	GCGATAGTTATGCAATCCAGACAT	59.307	41.667	0.00	0.00	39.35	3.06
2125	5303	4.058124	GCGATAGTTATGCAATCCAGACA	58.942	43.478	0.00	0.00	39.35	3.41
2191	5369	9.693739	TGATCTGTAATTCAGCCCTAAAATTAA	57.306	29.630	0.00	0.00	43.32	1.40
2192	5370	9.866655	ATGATCTGTAATTCAGCCCTAAAATTA	57.133	29.630	0.00	0.00	43.32	1.40
2193	5371	8.773033	ATGATCTGTAATTCAGCCCTAAAATT	57.227	30.769	0.00	0.00	43.32	1.82
2194	5372	8.636213	CAATGATCTGTAATTCAGCCCTAAAAT	58.364	33.333	0.00	0.00	43.32	1.82
2195	5373	7.068593	CCAATGATCTGTAATTCAGCCCTAAAA	59.931	37.037	0.00	0.00	43.32	1.52
2196	5374	6.547141	CCAATGATCTGTAATTCAGCCCTAAA	59.453	38.462	0.00	0.00	43.32	1.85
2197	5375	6.064060	CCAATGATCTGTAATTCAGCCCTAA	58.936	40.000	0.00	0.00	43.32	2.69
2245	5474	6.524101	TTTAAGAAATTCTTTCCCATCCGG	57.476	37.500	13.89	0.00	40.54	5.14
2278	5507	3.265791	GCAGATCAACATCTTCCTCGTT	58.734	45.455	0.00	0.00	37.25	3.85
2328	5557	2.796193	CCATGGACGGAGCCGATGA	61.796	63.158	16.83	0.00	42.83	2.92
2404	5643	3.362838	GCGCAATTTTCCGCTTCG	58.637	55.556	0.30	0.00	46.14	3.79
2408	5647	2.430075	AACCGCGCAATTTTCCGC	60.430	55.556	8.75	5.16	46.17	5.54
2409	5648	1.799916	GGAACCGCGCAATTTTCCG	60.800	57.895	8.75	0.00	0.00	4.30
2410	5649	1.799916	CGGAACCGCGCAATTTTCC	60.800	57.895	8.75	11.90	35.16	3.13
2411	5650	1.081708	ACGGAACCGCGCAATTTTC	60.082	52.632	8.75	3.38	44.19	2.29
2412	5651	1.371145	CACGGAACCGCGCAATTTT	60.371	52.632	8.75	0.00	44.19	1.82
2413	5652	1.582610	ATCACGGAACCGCGCAATTT	61.583	50.000	8.75	0.00	44.19	1.82
2414	5653	2.038269	ATCACGGAACCGCGCAATT	61.038	52.632	8.75	0.00	44.19	2.32
2415	5654	2.435938	ATCACGGAACCGCGCAAT	60.436	55.556	8.75	0.00	44.19	3.56
2416	5655	2.766875	TACATCACGGAACCGCGCAA	62.767	55.000	8.75	0.00	44.19	4.85
2417	5656	3.284133	TACATCACGGAACCGCGCA	62.284	57.895	8.75	0.00	44.19	6.09
2418	5657	2.507547	TACATCACGGAACCGCGC	60.508	61.111	13.32	0.00	44.19	6.86
2419	5658	2.162754	GGTACATCACGGAACCGCG	61.163	63.158	13.32	0.00	44.19	6.46
2420	5659	3.790177	GGTACATCACGGAACCGC	58.210	61.111	13.32	0.00	44.19	5.68
2427	5666	1.872234	CAGTCGCCGGTACATCACG	60.872	63.158	1.90	0.00	0.00	4.35
2428	5667	1.518572	CCAGTCGCCGGTACATCAC	60.519	63.158	1.90	0.00	0.00	3.06
2429	5668	2.889617	CCAGTCGCCGGTACATCA	59.110	61.111	1.90	0.00	0.00	3.07
2430	5669	2.585247	GCCAGTCGCCGGTACATC	60.585	66.667	1.90	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.