AutoCloner

Multiple sequence alignment - TraesCS4A01G182600

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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	TraesCS4A01G182600	chr4A	100.000	4527	0	0	1	4527	458859932	458855406	0.000000e+00	8360
1	TraesCS4A01G182600	chr4A	98.279	2150	35	2	1015	3162	584062947	584065096	0.000000e+00	3764
2	TraesCS4A01G182600	chr2A	98.613	1370	17	2	3160	4527	197934136	197935505	0.000000e+00	2423
3	TraesCS4A01G182600	chr2A	94.418	1039	24	12	8	1012	197931281	197932319	0.000000e+00	1567
4	TraesCS4A01G182600	chr6A	98.174	1369	22	2	3160	4527	575002075	575000709	0.000000e+00	2386
5	TraesCS4A01G182600	chr6A	98.101	1369	25	1	3160	4527	606002146	606000778	0.000000e+00	2383
6	TraesCS4A01G182600	chr6A	93.282	1042	29	7	8	1015	606004994	606003960	0.000000e+00	1498
7	TraesCS4A01G182600	chr6A	93.719	1003	31	3	45	1015	575004883	575003881	0.000000e+00	1474
8	TraesCS4A01G182600	chr6A	98.806	754	9	0	3160	3913	583750973	583751726	0.000000e+00	1343
9	TraesCS4A01G182600	chr6A	96.032	126	4	1	888	1012	583749031	583749156	2.140000e-48	204
10	TraesCS4A01G182600	chr7A	98.028	1369	25	2	3160	4527	17541604	17542971	0.000000e+00	2377
11	TraesCS4A01G182600	chr7A	97.736	1369	28	3	3160	4527	24236590	24235224	0.000000e+00	2353
12	TraesCS4A01G182600	chr7A	97.316	1006	26	1	8	1012	17539008	17540013	0.000000e+00	1707
13	TraesCS4A01G182600	chr5A	97.549	1387	30	4	3144	4527	630047359	630048744	0.000000e+00	2370
14	TraesCS4A01G182600	chr5A	96.154	1014	29	3	8	1012	630044547	630045559	0.000000e+00	1648
15	TraesCS4A01G182600	chr5A	90.568	827	37	11	9	810	568849134	568848324	0.000000e+00	1057
16	TraesCS4A01G182600	chr4D	91.311	1243	85	10	1459	2682	16361015	16359777	0.000000e+00	1676
17	TraesCS4A01G182600	chr4D	84.381	493	42	12	2678	3162	16359736	16359271	6.910000e-123	451
18	TraesCS4A01G182600	chr1A	97.436	975	24	1	3554	4527	547134652	547133678	0.000000e+00	1661
19	TraesCS4A01G182600	chr7D	96.821	975	30	1	3554	4527	561571328	561570354	0.000000e+00	1628
20	TraesCS4A01G182600	chr7D	96.410	975	33	2	3554	4527	44228018	44227045	0.000000e+00	1605
21	TraesCS4A01G182600	chr3D	89.746	1063	44	17	9	1012	482116073	482117129	0.000000e+00	1299
22	TraesCS4A01G182600	chr3D	97.229	397	6	2	3160	3556	482118946	482119337	0.000000e+00	667
23	TraesCS4A01G182600	chr5B	89.286	1064	54	12	8	1012	37898800	37899862	0.000000e+00	1279
24	TraesCS4A01G182600	chr5B	93.191	749	40	6	8	746	613241288	613242035	0.000000e+00	1090
25	TraesCS4A01G182600	chr5B	90.247	810	59	13	9	809	123003527	123002729	0.000000e+00	1040
26	TraesCS4A01G182600	chr5B	85.437	206	7	1	815	997	613242050	613242255	4.620000e-45	193
27	TraesCS4A01G182600	chr4B	91.079	908	66	11	1459	2358	28197887	28196987	0.000000e+00	1214
28	TraesCS4A01G182600	chr4B	96.977	397	12	0	3160	3556	359899789	359899393	0.000000e+00	667
29	TraesCS4A01G182600	chr4B	89.858	493	39	7	2678	3162	28196358	28195869	1.380000e-174	623
30	TraesCS4A01G182600	chr7B	87.324	1065	59	14	8	1015	413038790	413037745	0.000000e+00	1149
31	TraesCS4A01G182600	chr7B	86.408	206	5	1	815	997	348042718	348042923	2.140000e-48	204
32	TraesCS4A01G182600	chr6B	91.810	757	44	12	8	749	272623780	272623027	0.000000e+00	1038
33	TraesCS4A01G182600	chr6B	93.651	189	6	1	815	997	272623017	272622829	1.240000e-70	278
34	TraesCS4A01G182600	chr2B	86.700	203	4	7	816	995	104865573	104865371	2.140000e-48	204
35	TraesCS4A01G182600	chr3B	86.275	204	5	5	816	996	755581395	755581598	2.760000e-47	200

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	TraesCS4A01G182600	chr4A	458855406	458859932	4526	True	8360.0	8360	100.0000	1	4527	1	chr4A.!!$R1	4526
1	TraesCS4A01G182600	chr4A	584062947	584065096	2149	False	3764.0	3764	98.2790	1015	3162	1	chr4A.!!$F1	2147
2	TraesCS4A01G182600	chr2A	197931281	197935505	4224	False	1995.0	2423	96.5155	8	4527	2	chr2A.!!$F1	4519
3	TraesCS4A01G182600	chr6A	606000778	606004994	4216	True	1940.5	2383	95.6915	8	4527	2	chr6A.!!$R2	4519
4	TraesCS4A01G182600	chr6A	575000709	575004883	4174	True	1930.0	2386	95.9465	45	4527	2	chr6A.!!$R1	4482
5	TraesCS4A01G182600	chr6A	583749031	583751726	2695	False	773.5	1343	97.4190	888	3913	2	chr6A.!!$F1	3025
6	TraesCS4A01G182600	chr7A	24235224	24236590	1366	True	2353.0	2353	97.7360	3160	4527	1	chr7A.!!$R1	1367
7	TraesCS4A01G182600	chr7A	17539008	17542971	3963	False	2042.0	2377	97.6720	8	4527	2	chr7A.!!$F1	4519
8	TraesCS4A01G182600	chr5A	630044547	630048744	4197	False	2009.0	2370	96.8515	8	4527	2	chr5A.!!$F1	4519
9	TraesCS4A01G182600	chr5A	568848324	568849134	810	True	1057.0	1057	90.5680	9	810	1	chr5A.!!$R1	801
10	TraesCS4A01G182600	chr4D	16359271	16361015	1744	True	1063.5	1676	87.8460	1459	3162	2	chr4D.!!$R1	1703
11	TraesCS4A01G182600	chr1A	547133678	547134652	974	True	1661.0	1661	97.4360	3554	4527	1	chr1A.!!$R1	973
12	TraesCS4A01G182600	chr7D	561570354	561571328	974	True	1628.0	1628	96.8210	3554	4527	1	chr7D.!!$R2	973
13	TraesCS4A01G182600	chr7D	44227045	44228018	973	True	1605.0	1605	96.4100	3554	4527	1	chr7D.!!$R1	973
14	TraesCS4A01G182600	chr3D	482116073	482119337	3264	False	983.0	1299	93.4875	9	3556	2	chr3D.!!$F1	3547
15	TraesCS4A01G182600	chr5B	37898800	37899862	1062	False	1279.0	1279	89.2860	8	1012	1	chr5B.!!$F1	1004
16	TraesCS4A01G182600	chr5B	123002729	123003527	798	True	1040.0	1040	90.2470	9	809	1	chr5B.!!$R1	800
17	TraesCS4A01G182600	chr5B	613241288	613242255	967	False	641.5	1090	89.3140	8	997	2	chr5B.!!$F2	989
18	TraesCS4A01G182600	chr4B	28195869	28197887	2018	True	918.5	1214	90.4685	1459	3162	2	chr4B.!!$R2	1703
19	TraesCS4A01G182600	chr7B	413037745	413038790	1045	True	1149.0	1149	87.3240	8	1015	1	chr7B.!!$R1	1007
20	TraesCS4A01G182600	chr6B	272622829	272623780	951	True	658.0	1038	92.7305	8	997	2	chr6B.!!$R1	989

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	End Stability	Orientation
656	663	4.180946	CCTCGTCGCTCTCACCCG	62.181	72.222	5.28	F
1285	1392	0.246635	AAATCAGCGAGCACCTACGT	59.753	50.000	3.57	F
1712	1985	0.545309	CAAGGTGGTGAGAGGAGGGA	60.545	60.000	4.20	F
1840	2128	1.686052	GGGTTCCACATGCTGTTTTCA	59.314	47.619	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1619	1892	3.016971	CAGGGCCATCCACCTCCA	61.017	66.667	6.18	38.24	3.86	R
2928	3234	1.299089	GTGCAACGAACTTGGTGGC	60.299	57.895	0.00	34.85	5.01	R
3196	4495	5.913137	TGAAAAGAGAACTCAAGCCAAAA	57.087	34.783	4.64	0.00	2.44	R
3753	5053	1.002134	CGGACTTGGACTGGGCAAT	60.002	57.895	0.00	0.00	3.56	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
80	81	5.239087	GGCAACATTGTTTGTCATTCCAATT	59.761	36.000	0.00	0.00	37.68	2.32
86	87	5.021033	TGTTTGTCATTCCAATTTGCACT	57.979	34.783	0.00	0.00	0.00	4.40
256	257	9.241317	GTGAATTATAAAATTGATGTGCTCCAG	57.759	33.333	0.00	0.00	35.41	3.86
656	663	4.180946	CCTCGTCGCTCTCACCCG	62.181	72.222	0.00	0.00	0.00	5.28
1008	1114	2.592861	GGCGCCATCATGGACCTC	60.593	66.667	24.80	0.00	40.96	3.85
1012	1119	1.689243	CGCCATCATGGACCTCCTCA	61.689	60.000	8.30	0.00	40.96	3.86
1015	1122	2.052468	CCATCATGGACCTCCTCATCA	58.948	52.381	0.00	0.00	40.96	3.07
1016	1123	2.440627	CCATCATGGACCTCCTCATCAA	59.559	50.000	0.00	0.00	40.96	2.57
1017	1124	3.496337	CCATCATGGACCTCCTCATCAAG	60.496	52.174	0.00	0.00	40.96	3.02
1028	1135	2.514592	CATCAAGCATCCGCCCGT	60.515	61.111	0.00	0.00	39.83	5.28
1126	1233	2.833582	GACGGCCGAGGAGATCCA	60.834	66.667	35.90	0.00	38.89	3.41
1197	1304	0.842467	CCCCTCCACCCTCTCACTTT	60.842	60.000	0.00	0.00	0.00	2.66
1231	1338	3.966930	GAGGCGTCTCCCCTGACCT	62.967	68.421	5.50	0.00	34.01	3.85
1256	1363	1.263356	CTTGTCCCCGTGTTCTCCTA	58.737	55.000	0.00	0.00	0.00	2.94
1267	1374	1.079621	TTCTCCTACCCTCCCGCAA	59.920	57.895	0.00	0.00	0.00	4.85
1282	1389	2.767536	GCAAATCAGCGAGCACCTA	58.232	52.632	0.00	0.00	0.00	3.08
1285	1392	0.246635	AAATCAGCGAGCACCTACGT	59.753	50.000	0.00	0.00	0.00	3.57
1293	1400	3.315949	GCACCTACGTGACCCCCA	61.316	66.667	0.00	0.00	43.14	4.96
1398	1624	2.887568	CGCCTCTCGCTTCGCATT	60.888	61.111	0.00	0.00	34.21	3.56
1417	1643	2.011122	TTCCTTCTCGTCCCTGTCTT	57.989	50.000	0.00	0.00	0.00	3.01
1424	1650	2.432874	TCTCGTCCCTGTCTTTGTTTCA	59.567	45.455	0.00	0.00	0.00	2.69
1712	1985	0.545309	CAAGGTGGTGAGAGGAGGGA	60.545	60.000	0.00	0.00	0.00	4.20
1781	2057	2.197465	GAGGGTGAGTAAGGGGAATGT	58.803	52.381	0.00	0.00	0.00	2.71
1840	2128	1.686052	GGGTTCCACATGCTGTTTTCA	59.314	47.619	0.00	0.00	0.00	2.69
2293	2598	8.571461	TCATCAACTTAGCAATTCTCTCAATT	57.429	30.769	0.00	0.00	0.00	2.32
2512	2817	6.620877	TTCCTCAGATAGGTGTTGTGTTAT	57.379	37.500	0.00	0.00	46.62	1.89
2735	3040	4.158579	GCCTGCTTACAGCTTTTCCTTAAT	59.841	41.667	0.00	0.00	42.97	1.40
2802	3108	8.776470	CAACATTTTTCTTGATTGCTTTACCAT	58.224	29.630	0.00	0.00	0.00	3.55
2871	3177	8.315391	TGTCATTTTGTGTTTGTTGAAAATCA	57.685	26.923	0.00	0.00	0.00	2.57
2928	3234	2.741553	GCACCCCCAGTTTTCAACTTTG	60.742	50.000	0.00	0.00	40.46	2.77
3169	4468	2.771372	TCATGTCACTATTGGCCAGCTA	59.229	45.455	5.11	0.75	0.00	3.32
3196	4495	8.082242	GGTGCTTTTCTAGTTCAACATAACATT	58.918	33.333	0.00	0.00	0.00	2.71
3753	5053	4.030913	ACTCTTTTCCCCTGATATCGTCA	58.969	43.478	0.00	0.00	35.05	4.35
3838	5138	2.632987	AGGCACTGGTACGAAAGTTT	57.367	45.000	0.00	0.00	42.11	2.66
4112	5419	1.065491	TGCCCAAACGATGCTCATAGT	60.065	47.619	0.00	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	9.816354	CTAAGGAAGTTTTCATTTTCTTTGGAA	57.184	29.630	0.00	0.00	35.11	3.53
86	87	9.585369	TTAAATGATCCCATATTATGCACAAGA	57.415	29.630	0.00	0.00	31.59	3.02
102	103	6.371809	TGGCATAGTTCGTTTAAATGATCC	57.628	37.500	10.85	5.43	0.00	3.36
474	478	4.996788	AGATTTTGAATCATGTCTGCCC	57.003	40.909	3.76	0.00	0.00	5.36
810	862	1.202166	CGGTGGGTTTCGTTTCGTTTT	60.202	47.619	0.00	0.00	0.00	2.43
997	1103	2.106166	GCTTGATGAGGAGGTCCATGAT	59.894	50.000	0.00	0.00	38.89	2.45
1008	1114	1.895707	GGGCGGATGCTTGATGAGG	60.896	63.158	0.00	0.00	42.25	3.86
1012	1119	2.203070	GACGGGCGGATGCTTGAT	60.203	61.111	0.00	0.00	42.25	2.57
1028	1135	3.037715	GAGGGAGGGAGGATGGGA	58.962	66.667	0.00	0.00	0.00	4.37
1104	1211	0.684805	ATCTCCTCGGCCGTCTTCTT	60.685	55.000	27.15	4.71	0.00	2.52
1197	1304	4.770362	TCGATGGCCACGGAGGGA	62.770	66.667	21.98	6.52	38.09	4.20
1231	1338	0.681564	AACACGGGGACAAGCAAACA	60.682	50.000	0.00	0.00	0.00	2.83
1256	1363	2.044946	GCTGATTTGCGGGAGGGT	60.045	61.111	0.00	0.00	0.00	4.34
1267	1374	0.458543	CACGTAGGTGCTCGCTGATT	60.459	55.000	2.09	0.00	37.35	2.57
1278	1385	1.916777	CCTTGGGGGTCACGTAGGT	60.917	63.158	0.00	0.00	0.00	3.08
1396	1622	2.541466	AGACAGGGACGAGAAGGAAAT	58.459	47.619	0.00	0.00	0.00	2.17
1398	1624	2.011122	AAGACAGGGACGAGAAGGAA	57.989	50.000	0.00	0.00	0.00	3.36
1417	1643	4.992688	AGAAAAATCACGCACTGAAACAA	58.007	34.783	0.00	0.00	30.60	2.83
1424	1650	1.534729	GGGGAGAAAAATCACGCACT	58.465	50.000	0.00	0.00	0.00	4.40
1619	1892	3.016971	CAGGGCCATCCACCTCCA	61.017	66.667	6.18	0.00	38.24	3.86
1781	2057	4.517285	GCACACTATCTCCTCCAAAATCA	58.483	43.478	0.00	0.00	0.00	2.57
2293	2598	5.042463	TGATGTTGGAAGACCACAAACTA	57.958	39.130	0.00	0.00	46.80	2.24
2512	2817	4.912317	TTAGTTATAACTGCACCACCCA	57.088	40.909	25.27	1.93	40.07	4.51
2693	2998	7.335627	AGCAGGCAATGTTATTGTAAGTACTA	58.664	34.615	0.00	0.00	0.00	1.82
2735	3040	8.610896	GGAAAACAATGAACAAATTTCACATGA	58.389	29.630	0.00	0.00	0.00	3.07
2802	3108	5.610398	TGAAATTGAAGCTGTAGAGTGTGA	58.390	37.500	0.00	0.00	0.00	3.58
2928	3234	1.299089	GTGCAACGAACTTGGTGGC	60.299	57.895	0.00	0.00	34.85	5.01
3002	3894	9.107177	CAAGTGATCTAGAAGTTTATTCAGCAT	57.893	33.333	0.00	0.00	0.00	3.79
3169	4468	6.770785	TGTTATGTTGAACTAGAAAAGCACCT	59.229	34.615	0.00	0.00	0.00	4.00
3196	4495	5.913137	TGAAAAGAGAACTCAAGCCAAAA	57.087	34.783	4.64	0.00	0.00	2.44
3753	5053	1.002134	CGGACTTGGACTGGGCAAT	60.002	57.895	0.00	0.00	0.00	3.56
3838	5138	5.068198	GGTATACTATGTTCGTGTCAAGGGA	59.932	44.000	2.25	0.00	0.00	4.20
4112	5419	1.961793	AACGCAGGCTAACAGAAACA	58.038	45.000	0.00	0.00	0.00	2.83
4164	5472	2.438021	AGAAGTAGAACCACTGTGCCAA	59.562	45.455	1.29	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.