AutoCloner

Multiple sequence alignment - TraesCS4A01G254800

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	TraesCS4A01G254800	chr4A	100.000	2527	0	0	1	2527	567035537	567038063	0.000000e+00	4667.0
1	TraesCS4A01G254800	chr4A	89.736	643	54	5	1875	2509	567471692	567471054	0.000000e+00	811.0
2	TraesCS4A01G254800	chr4A	83.942	137	19	1	77	213	567471894	567471761	7.340000e-26	128.0
3	TraesCS4A01G254800	chr5D	91.602	1536	71	13	257	1747	113748974	113747452	0.000000e+00	2069.0
4	TraesCS4A01G254800	chr5D	85.124	242	31	3	1060	1298	525465155	525465394	2.510000e-60	243.0
5	TraesCS4A01G254800	chr5D	100.000	36	0	0	1691	1726	499260693	499260658	1.620000e-07	67.6
6	TraesCS4A01G254800	chr5D	100.000	34	0	0	1693	1726	227774288	227774255	2.100000e-06	63.9
7	TraesCS4A01G254800	chr6D	89.732	1529	77	18	263	1730	429975209	429976718	0.000000e+00	1881.0
8	TraesCS4A01G254800	chr1A	89.037	1423	98	17	359	1739	427507028	427505622	0.000000e+00	1711.0
9	TraesCS4A01G254800	chr1B	88.624	1424	104	20	359	1742	368077859	368076454	0.000000e+00	1679.0
10	TraesCS4A01G254800	chr1B	82.584	356	42	9	1388	1726	551719562	551719210	1.900000e-76	296.0
11	TraesCS4A01G254800	chr4D	92.654	667	34	9	1866	2527	35171643	35172299	0.000000e+00	946.0
12	TraesCS4A01G254800	chr4D	91.406	640	43	6	1896	2527	35523036	35522401	0.000000e+00	867.0
13	TraesCS4A01G254800	chr4D	90.654	214	19	1	1	214	35523608	35523396	1.480000e-72	283.0
14	TraesCS4A01G254800	chr4D	95.000	40	2	0	220	259	88704750	88704789	2.100000e-06	63.9
15	TraesCS4A01G254800	chr4B	92.145	662	38	9	1875	2527	51124607	51125263	0.000000e+00	922.0
16	TraesCS4A01G254800	chr4B	88.722	665	57	6	1866	2527	51749751	51749102	0.000000e+00	797.0
17	TraesCS4A01G254800	chr4B	94.030	67	4	0	1	67	51753702	51753636	4.450000e-18	102.0
18	TraesCS4A01G254800	chr2B	82.992	976	110	33	377	1334	583670283	583671220	0.000000e+00	832.0
19	TraesCS4A01G254800	chr3D	83.103	941	111	31	377	1302	591724933	591724026	0.000000e+00	813.0
20	TraesCS4A01G254800	chr3D	100.000	34	0	0	1693	1726	27687226	27687193	2.100000e-06	63.9
21	TraesCS4A01G254800	chr7B	82.748	939	109	27	375	1298	60373633	60374533	0.000000e+00	787.0
22	TraesCS4A01G254800	chr3B	82.814	931	97	36	380	1293	727053726	727054610	0.000000e+00	774.0
23	TraesCS4A01G254800	chr3B	81.846	975	107	37	377	1335	792878286	792879206	0.000000e+00	756.0
24	TraesCS4A01G254800	chr7D	82.920	363	40	11	1386	1726	612285581	612285219	8.780000e-80	307.0
25	TraesCS4A01G254800	chr7D	82.143	364	43	10	1385	1726	228439659	228439296	2.460000e-75	292.0
26	TraesCS4A01G254800	chr7D	75.510	343	61	14	641	978	621608749	621608425	2.030000e-31	147.0
27	TraesCS4A01G254800	chr1D	82.825	361	39	14	1385	1724	400973381	400973023	4.090000e-78	302.0
28	TraesCS4A01G254800	chr1D	100.000	36	0	0	1691	1726	379466732	379466767	1.620000e-07	67.6
29	TraesCS4A01G254800	chr5A	86.347	271	27	5	1060	1321	651810618	651810887	1.140000e-73	287.0
30	TraesCS4A01G254800	chr7A	81.768	362	43	10	1386	1726	567386004	567385645	5.320000e-72	281.0
31	TraesCS4A01G254800	chr6A	89.831	59	3	2	675	732	554828334	554828390	3.490000e-09	73.1
32	TraesCS4A01G254800	chr2A	100.000	35	0	0	1692	1726	1891127	1891093	5.840000e-07	65.8
33	TraesCS4A01G254800	chr2A	97.143	35	1	0	1692	1726	11195334	11195300	2.710000e-05	60.2
34	TraesCS4A01G254800	chr6B	95.122	41	1	1	1822	1862	590670444	590670405	2.100000e-06	63.9

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	TraesCS4A01G254800	chr4A	567035537	567038063	2526	False	4667.0	4667	100.000	1	2527	1	chr4A.!!$F1	2526
1	TraesCS4A01G254800	chr4A	567471054	567471894	840	True	469.5	811	86.839	77	2509	2	chr4A.!!$R1	2432
2	TraesCS4A01G254800	chr5D	113747452	113748974	1522	True	2069.0	2069	91.602	257	1747	1	chr5D.!!$R1	1490
3	TraesCS4A01G254800	chr6D	429975209	429976718	1509	False	1881.0	1881	89.732	263	1730	1	chr6D.!!$F1	1467
4	TraesCS4A01G254800	chr1A	427505622	427507028	1406	True	1711.0	1711	89.037	359	1739	1	chr1A.!!$R1	1380
5	TraesCS4A01G254800	chr1B	368076454	368077859	1405	True	1679.0	1679	88.624	359	1742	1	chr1B.!!$R1	1383
6	TraesCS4A01G254800	chr4D	35171643	35172299	656	False	946.0	946	92.654	1866	2527	1	chr4D.!!$F1	661
7	TraesCS4A01G254800	chr4D	35522401	35523608	1207	True	575.0	867	91.030	1	2527	2	chr4D.!!$R1	2526
8	TraesCS4A01G254800	chr4B	51124607	51125263	656	False	922.0	922	92.145	1875	2527	1	chr4B.!!$F1	652
9	TraesCS4A01G254800	chr4B	51749102	51753702	4600	True	449.5	797	91.376	1	2527	2	chr4B.!!$R1	2526
10	TraesCS4A01G254800	chr2B	583670283	583671220	937	False	832.0	832	82.992	377	1334	1	chr2B.!!$F1	957
11	TraesCS4A01G254800	chr3D	591724026	591724933	907	True	813.0	813	83.103	377	1302	1	chr3D.!!$R2	925
12	TraesCS4A01G254800	chr7B	60373633	60374533	900	False	787.0	787	82.748	375	1298	1	chr7B.!!$F1	923
13	TraesCS4A01G254800	chr3B	727053726	727054610	884	False	774.0	774	82.814	380	1293	1	chr3B.!!$F1	913
14	TraesCS4A01G254800	chr3B	792878286	792879206	920	False	756.0	756	81.846	377	1335	1	chr3B.!!$F2	958

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
144	3719	0.826715	TCCTCTGTGGATGTAGCAGC	59.173	55.0	0.0	0.0	40.56	5.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1845	5647	0.25077	GTGGAACTCCCCCAACTGAC	60.251	60.0	0.0	0.0	35.12	3.51	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
50	3625	9.499479	AATTGATGAGGAATAGATACATGTGAC	57.501	33.333	9.11	2.14	0.00	3.67
69	3644	1.694150	ACAAGAGTGCTGCTAACAGGA	59.306	47.619	0.00	0.00	44.63	3.86
75	3650	0.835971	TGCTGCTAACAGGAGGGACA	60.836	55.000	0.00	0.00	44.63	4.02
85	3660	3.705051	ACAGGAGGGACACTTCGTATAA	58.295	45.455	0.00	0.00	0.00	0.98
144	3719	0.826715	TCCTCTGTGGATGTAGCAGC	59.173	55.000	0.00	0.00	40.56	5.25
147	3722	2.125147	TGTGGATGTAGCAGCGCC	60.125	61.111	2.29	0.00	0.00	6.53
149	3724	3.398310	TGGATGTAGCAGCGCCCA	61.398	61.111	2.29	0.00	0.00	5.36
381	4068	4.017037	TCACTTGACCTTATCCTCTCCTCT	60.017	45.833	0.00	0.00	0.00	3.69
689	4395	2.558795	TGCGGCTATGGCTTTGTTTTTA	59.441	40.909	0.00	0.00	38.73	1.52
691	4397	3.366724	GCGGCTATGGCTTTGTTTTTAAC	59.633	43.478	0.00	0.00	38.73	2.01
736	4442	5.949735	TGATTTATCGGTTCCAGCTTTTTC	58.050	37.500	0.00	0.00	0.00	2.29
751	4457	3.294102	CTTTTTCTTTCGCCGGTTGTAC	58.706	45.455	1.90	0.00	0.00	2.90
781	4487	1.202758	TCCACGAGCACCAATCTTTGT	60.203	47.619	0.00	0.00	0.00	2.83
864	4570	2.827959	GATTTCGCCGGTCGCAACAC	62.828	60.000	12.56	4.38	37.30	3.32
878	4586	0.859232	CAACACTCCCACTTTCGACG	59.141	55.000	0.00	0.00	0.00	5.12
961	4669	4.044571	TGAAGGAAGGGGATCAATGAAGTT	59.955	41.667	0.00	0.00	0.00	2.66
1044	4755	1.621814	GGTACACCAGAGCTACAACCA	59.378	52.381	0.00	0.00	35.64	3.67
1186	4916	4.113815	CCATGCCTGCGAGGGGAA	62.114	66.667	4.65	0.00	35.37	3.97
1189	4919	1.689233	ATGCCTGCGAGGGGAACTA	60.689	57.895	4.65	0.00	35.37	2.24
1308	5074	3.913089	ACCGGCTAAAATTTTGCTTCAG	58.087	40.909	13.76	3.66	0.00	3.02
1430	5198	3.712881	GTGTTGCAGTCGACGCCC	61.713	66.667	23.01	16.20	32.25	6.13
1454	5222	1.004628	AGCTACCATGGATGCAACACA	59.995	47.619	26.36	0.00	0.00	3.72
1495	5263	3.364267	GCTACGGTTAACGACCTTTTTGG	60.364	47.826	0.00	0.00	46.92	3.28
1595	5363	2.764128	GGCTGAGGACCATCGGGA	60.764	66.667	0.00	0.00	38.05	5.14
1616	5385	1.539157	GCTGGTCTCTTTCCCCTTTG	58.461	55.000	0.00	0.00	0.00	2.77
1617	5386	1.539157	CTGGTCTCTTTCCCCTTTGC	58.461	55.000	0.00	0.00	0.00	3.68
1649	5439	1.202710	TCAGCGTTTTCTGTAAGGCCA	60.203	47.619	5.01	0.00	39.14	5.36
1682	5472	7.007697	CGGTTTATAAAAGCTATATCGTGTGC	58.992	38.462	0.00	0.00	0.00	4.57
1744	5537	2.222027	GCAGAGTTGCGCCCTATTTAT	58.778	47.619	4.18	0.00	41.13	1.40
1752	5545	3.806380	TGCGCCCTATTTATAAACGGAA	58.194	40.909	4.18	0.00	0.00	4.30
1759	5552	6.648310	GCCCTATTTATAAACGGAAGGAGTAC	59.352	42.308	14.11	0.00	0.00	2.73
1761	5554	7.871463	CCCTATTTATAAACGGAAGGAGTACAG	59.129	40.741	14.11	0.00	0.00	2.74
1762	5555	8.419442	CCTATTTATAAACGGAAGGAGTACAGT	58.581	37.037	0.00	0.00	0.00	3.55
1861	5663	5.632034	ATATAAGTCAGTTGGGGGAGTTC	57.368	43.478	0.00	0.00	0.00	3.01
1862	5664	0.771755	AAGTCAGTTGGGGGAGTTCC	59.228	55.000	0.00	0.00	0.00	3.62
1863	5665	0.401395	AGTCAGTTGGGGGAGTTCCA	60.401	55.000	0.00	0.00	37.91	3.53
1864	5666	0.250770	GTCAGTTGGGGGAGTTCCAC	60.251	60.000	0.00	0.00	40.15	4.02
2441	6339	0.249405	GGTTGTTGGACACGGTCGTA	60.249	55.000	0.00	0.00	32.65	3.43
2509	6410	2.810887	GCTCATCGCTGCACGTCA	60.811	61.111	0.00	0.00	44.19	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	3617	1.202734	AGCAGCACTCTTGTCACATGT	60.203	47.619	0.00	0.00	0.00	3.21
44	3619	3.070018	GTTAGCAGCACTCTTGTCACAT	58.930	45.455	0.00	0.00	0.00	3.21
50	3625	2.344950	CTCCTGTTAGCAGCACTCTTG	58.655	52.381	0.17	0.00	41.26	3.02
69	3644	4.222145	ACACACATTATACGAAGTGTCCCT	59.778	41.667	0.00	0.00	45.73	4.20
75	3650	6.494893	AATGCAACACACATTATACGAAGT	57.505	33.333	0.00	0.00	39.34	3.01
85	3660	5.296748	GGGTTTTTCTAATGCAACACACAT	58.703	37.500	0.00	0.00	0.00	3.21
144	3719	3.244976	GAAACATGAAATCAACTGGGCG	58.755	45.455	0.00	0.00	0.00	6.13
147	3722	5.362556	AGACGAAACATGAAATCAACTGG	57.637	39.130	0.00	0.00	0.00	4.00
149	3724	9.599866	TCATATAGACGAAACATGAAATCAACT	57.400	29.630	0.00	0.06	0.00	3.16
254	3919	8.400186	CCGATTGGAAACGTTTACCTTATAAAT	58.600	33.333	20.37	11.73	37.49	1.40
255	3920	7.626028	GCCGATTGGAAACGTTTACCTTATAAA	60.626	37.037	20.37	7.30	37.49	1.40
259	3924	3.436359	GCCGATTGGAAACGTTTACCTTA	59.564	43.478	20.37	6.54	37.49	2.69
362	4048	4.264850	TGGAAGAGGAGAGGATAAGGTCAA	60.265	45.833	0.00	0.00	0.00	3.18
381	4068	6.014499	AGAGATAGGAAAGAAAACGAGTGGAA	60.014	38.462	0.00	0.00	0.00	3.53
595	4285	3.869934	TCACAGGGGAGGGGTGGT	61.870	66.667	0.00	0.00	33.45	4.16
596	4286	3.011517	CTCACAGGGGAGGGGTGG	61.012	72.222	0.00	0.00	33.45	4.61
597	4287	3.721706	GCTCACAGGGGAGGGGTG	61.722	72.222	0.02	0.00	35.41	4.61
598	4288	3.507143	AAGCTCACAGGGGAGGGGT	62.507	63.158	0.02	0.00	35.41	4.95
689	4395	4.736126	AAGTTGCAACTGGCTAAAAGTT	57.264	36.364	31.73	9.99	45.15	2.66
691	4397	5.580297	TCAAAAAGTTGCAACTGGCTAAAAG	59.420	36.000	31.73	15.94	45.15	2.27
736	4442	4.364817	TGGTACAACCGGCGAAAG	57.635	55.556	9.30	0.00	42.58	2.62
751	4457	2.415893	GGTGCTCGTGGATGAAAATTGG	60.416	50.000	0.00	0.00	0.00	3.16
864	4570	0.458025	GCTACCGTCGAAAGTGGGAG	60.458	60.000	0.00	2.84	40.24	4.30
878	4586	7.158099	ACCTATGAATCAAAAAGTTGCTACC	57.842	36.000	0.00	0.00	34.50	3.18
983	4694	2.483877	CGCATGGTTGAAGCTTCTGTAA	59.516	45.455	26.09	10.57	0.00	2.41
984	4695	2.076100	CGCATGGTTGAAGCTTCTGTA	58.924	47.619	26.09	11.13	0.00	2.74
1430	5198	1.302033	GCATCCATGGTAGCTCCGG	60.302	63.158	19.41	0.00	39.52	5.14
1454	5222	0.322008	CGGCCTTTTCTCTTGCCTCT	60.322	55.000	0.00	0.00	41.80	3.69
1595	5363	1.128188	AAGGGGAAAGAGACCAGCGT	61.128	55.000	0.00	0.00	0.00	5.07
1731	5524	3.472283	TCCGTTTATAAATAGGGCGCA	57.528	42.857	10.83	0.00	0.00	6.09
1744	5537	6.888632	AGATAGAACTGTACTCCTTCCGTTTA	59.111	38.462	0.00	0.00	0.00	2.01
1752	5545	6.486056	TGTGAAGAGATAGAACTGTACTCCT	58.514	40.000	0.00	0.00	0.00	3.69
1761	5554	9.813080	GTGTGTAAAATTGTGAAGAGATAGAAC	57.187	33.333	0.00	0.00	0.00	3.01
1762	5555	9.778741	AGTGTGTAAAATTGTGAAGAGATAGAA	57.221	29.630	0.00	0.00	0.00	2.10
1826	5628	8.331022	CAACTGACTTATATTTCGGAACAGATG	58.669	37.037	0.00	0.00	0.00	2.90
1827	5629	7.495934	CCAACTGACTTATATTTCGGAACAGAT	59.504	37.037	0.00	0.00	0.00	2.90
1834	5636	4.134563	CCCCCAACTGACTTATATTTCGG	58.865	47.826	0.00	0.00	0.00	4.30
1845	5647	0.250770	GTGGAACTCCCCCAACTGAC	60.251	60.000	0.00	0.00	35.12	3.51
1862	5664	1.555075	AGTGCACCCTACCATGTAGTG	59.445	52.381	14.63	0.00	0.00	2.74
1863	5665	1.952621	AGTGCACCCTACCATGTAGT	58.047	50.000	14.63	0.00	0.00	2.73
1864	5666	2.764010	TGTAGTGCACCCTACCATGTAG	59.236	50.000	14.63	0.00	37.16	2.74
1959	5839	3.866582	GGTGATCCCGGCCAGGAG	61.867	72.222	14.46	5.03	45.00	3.69
2099	5979	1.883021	CATTTGGAGCGGTTGGACC	59.117	57.895	0.00	0.00	34.05	4.46
2222	6111	2.098831	GTTCCTTGCCGCCTACGTC	61.099	63.158	0.00	0.00	37.70	4.34
2234	6123	2.424302	CACCACGACCCGTTCCTT	59.576	61.111	0.00	0.00	38.32	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.