AutoCloner

Multiple sequence alignment - TraesCS1A01G352900

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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	TraesCS1A01G352900	chr1A	100.000	3313	0	0	1	3313	536811791	536808479	0.000000e+00	6119.0
1	TraesCS1A01G352900	chr6D	95.345	3115	116	21	202	3313	27553984	27550896	0.000000e+00	4922.0
2	TraesCS1A01G352900	chr6D	85.108	2028	226	25	378	2339	27534836	27532819	0.000000e+00	2002.0
3	TraesCS1A01G352900	chr6D	86.546	996	99	28	2337	3313	27531249	27530270	0.000000e+00	1064.0
4	TraesCS1A01G352900	chr6D	81.164	1168	167	29	375	1503	27539149	27537996	0.000000e+00	889.0
5	TraesCS1A01G352900	chr6D	75.949	1185	183	54	2207	3313	27665302	27664142	1.760000e-142	516.0
6	TraesCS1A01G352900	chr6D	75.201	1121	228	33	436	1534	27708841	27707749	4.970000e-133	484.0
7	TraesCS1A01G352900	chr6D	95.025	201	8	2	1	200	27554229	27554030	6.900000e-82	315.0
8	TraesCS1A01G352900	chr6D	85.714	217	31	0	1317	1533	15175832	15175616	2.570000e-56	230.0
9	TraesCS1A01G352900	chr6D	74.359	273	65	5	1152	1420	28415233	28414962	9.720000e-21	111.0
10	TraesCS1A01G352900	chr6A	85.836	2810	307	50	282	3041	30455015	30457783	0.000000e+00	2900.0
11	TraesCS1A01G352900	chr6A	76.278	704	117	29	2171	2851	30441329	30442005	2.460000e-86	329.0
12	TraesCS1A01G352900	chr6A	87.407	270	27	6	3043	3311	30457875	30458138	1.490000e-78	303.0
13	TraesCS1A01G352900	chr6A	77.717	184	36	4	1238	1417	29472718	29472900	1.260000e-19	108.0
14	TraesCS1A01G352900	chr6A	87.805	82	10	0	1981	2062	45006959	45006878	2.720000e-16	97.1
15	TraesCS1A01G352900	chr6A	83.951	81	9	2	228	308	30454577	30454653	1.280000e-09	75.0
16	TraesCS1A01G352900	chr6B	86.269	1675	172	27	1009	2633	51310944	51309278	0.000000e+00	1766.0
17	TraesCS1A01G352900	chr6B	89.969	1306	128	3	199	1503	51353383	51352080	0.000000e+00	1683.0
18	TraesCS1A01G352900	chr6B	80.521	1191	196	24	368	1529	54148985	54150168	0.000000e+00	881.0
19	TraesCS1A01G352900	chr6B	76.720	1177	240	27	376	1534	51423462	51422302	2.810000e-175	625.0
20	TraesCS1A01G352900	chr6B	83.227	626	61	17	199	793	51311594	51310982	4.870000e-148	534.0
21	TraesCS1A01G352900	chr6B	84.270	534	57	13	2791	3313	51303211	51302694	2.300000e-136	496.0
22	TraesCS1A01G352900	chr6B	74.734	847	142	40	2207	3011	51422053	51421237	2.480000e-81	313.0
23	TraesCS1A01G352900	chr6B	76.432	454	85	17	379	824	52361271	52360832	3.330000e-55	226.0
24	TraesCS1A01G352900	chr6B	81.720	279	33	9	3045	3313	51411956	51411686	2.000000e-52	217.0
25	TraesCS1A01G352900	chr6B	76.010	421	88	10	380	794	51435771	51435358	4.330000e-49	206.0
26	TraesCS1A01G352900	chr6B	73.805	523	97	28	375	876	75510356	75509853	1.580000e-38	171.0
27	TraesCS1A01G352900	chr6B	77.852	298	46	11	1671	1953	51352084	51351792	2.040000e-37	167.0
28	TraesCS1A01G352900	chrUn	82.035	924	141	16	387	1293	137812373	137813288	0.000000e+00	763.0
29	TraesCS1A01G352900	chrUn	75.339	884	159	31	679	1533	137670338	137671191	1.450000e-98	370.0
30	TraesCS1A01G352900	chrUn	82.423	421	71	3	1716	2135	137820036	137820454	6.760000e-97	364.0
31	TraesCS1A01G352900	chrUn	77.019	483	91	16	398	867	112677078	112677553	3.280000e-65	259.0
32	TraesCS1A01G352900	chrUn	77.381	420	77	15	375	785	101886083	101886493	1.990000e-57	233.0
33	TraesCS1A01G352900	chrUn	71.593	954	214	50	379	1303	27965085	27964160	1.200000e-49	207.0
34	TraesCS1A01G352900	chr2A	84.416	77	11	1	1982	2058	761199698	761199623	1.280000e-09	75.0

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	TraesCS1A01G352900	chr1A	536808479	536811791	3312	True	6119.000000	6119	100.000000	1	3313	1	chr1A.!!$R1	3312
1	TraesCS1A01G352900	chr6D	27550896	27554229	3333	True	2618.500000	4922	95.185000	1	3313	2	chr6D.!!$R6	3312
2	TraesCS1A01G352900	chr6D	27530270	27539149	8879	True	1318.333333	2002	84.272667	375	3313	3	chr6D.!!$R5	2938
3	TraesCS1A01G352900	chr6D	27664142	27665302	1160	True	516.000000	516	75.949000	2207	3313	1	chr6D.!!$R2	1106
4	TraesCS1A01G352900	chr6D	27707749	27708841	1092	True	484.000000	484	75.201000	436	1534	1	chr6D.!!$R3	1098
5	TraesCS1A01G352900	chr6A	30454577	30458138	3561	False	1092.666667	2900	85.731333	228	3311	3	chr6A.!!$F3	3083
6	TraesCS1A01G352900	chr6A	30441329	30442005	676	False	329.000000	329	76.278000	2171	2851	1	chr6A.!!$F2	680
7	TraesCS1A01G352900	chr6B	51309278	51311594	2316	True	1150.000000	1766	84.748000	199	2633	2	chr6B.!!$R6	2434
8	TraesCS1A01G352900	chr6B	51351792	51353383	1591	True	925.000000	1683	83.910500	199	1953	2	chr6B.!!$R7	1754
9	TraesCS1A01G352900	chr6B	54148985	54150168	1183	False	881.000000	881	80.521000	368	1529	1	chr6B.!!$F1	1161
10	TraesCS1A01G352900	chr6B	51302694	51303211	517	True	496.000000	496	84.270000	2791	3313	1	chr6B.!!$R1	522
11	TraesCS1A01G352900	chr6B	51421237	51423462	2225	True	469.000000	625	75.727000	376	3011	2	chr6B.!!$R8	2635
12	TraesCS1A01G352900	chrUn	137812373	137813288	915	False	763.000000	763	82.035000	387	1293	1	chrUn.!!$F4	906
13	TraesCS1A01G352900	chrUn	137670338	137671191	853	False	370.000000	370	75.339000	679	1533	1	chrUn.!!$F3	854
14	TraesCS1A01G352900	chrUn	27964160	27965085	925	True	207.000000	207	71.593000	379	1303	1	chrUn.!!$R1	924

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
843	1354	0.458669	GTCGTGCTCCGGGAGATTTA	59.541	55.0	27.95	6.85	37.11	1.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2765	9319	2.226437	CCACAACAGCCAACATGTAGTC	59.774	50.0	0.0	0.0	0.0	2.59	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
20	21	1.560860	GCGCAGGTCTCACAGAACAC	61.561	60.000	0.30	0.00	33.37	3.32
64	65	6.717540	AGTAGCGTTAGATCTCTTCCATGTAT	59.282	38.462	0.00	0.00	0.00	2.29
93	94	0.672401	GCGACCGACCCAATCTTCAA	60.672	55.000	0.00	0.00	0.00	2.69
122	123	2.047179	GCCACTGACGTTCCCCTC	60.047	66.667	0.00	0.00	0.00	4.30
180	181	5.306532	CAAGTTCTGGATCATGAAAGTGG	57.693	43.478	0.00	0.00	0.00	4.00
181	182	3.350833	AGTTCTGGATCATGAAAGTGGC	58.649	45.455	0.00	0.00	0.00	5.01
182	183	3.084039	GTTCTGGATCATGAAAGTGGCA	58.916	45.455	0.00	0.00	0.00	4.92
184	185	3.284617	TCTGGATCATGAAAGTGGCATG	58.715	45.455	0.00	0.00	43.39	4.06
200	201	3.243569	TGGCATGTTTTTAAGAACACGGG	60.244	43.478	13.26	7.86	41.86	5.28
202	203	4.364860	GCATGTTTTTAAGAACACGGGTT	58.635	39.130	13.26	0.56	41.86	4.11
277	711	6.559810	CACCAAATCAAATCCGCTTTACATA	58.440	36.000	0.00	0.00	0.00	2.29
486	957	2.357034	GTCTCCGCCGTCTGCAAA	60.357	61.111	0.00	0.00	41.33	3.68
489	960	1.135315	CTCCGCCGTCTGCAAATTG	59.865	57.895	0.00	0.00	41.33	2.32
564	1039	1.923909	CCGAAACCCTCCCCTCCTT	60.924	63.158	0.00	0.00	0.00	3.36
566	1041	1.489560	CGAAACCCTCCCCTCCTTGT	61.490	60.000	0.00	0.00	0.00	3.16
577	1052	1.153939	CTCCTTGTCTGCCTCGTCG	60.154	63.158	0.00	0.00	0.00	5.12
843	1354	0.458669	GTCGTGCTCCGGGAGATTTA	59.541	55.000	27.95	6.85	37.11	1.40
921	1438	1.336887	GCCTCTGTTTACTCGTCAGCA	60.337	52.381	0.00	0.00	0.00	4.41
925	1442	4.051922	CTCTGTTTACTCGTCAGCAACTT	58.948	43.478	0.00	0.00	0.00	2.66
927	1444	3.787785	TGTTTACTCGTCAGCAACTTGA	58.212	40.909	0.00	0.00	0.00	3.02
1026	1555	0.960364	CTGTGATGGTTGGGGGTTCG	60.960	60.000	0.00	0.00	0.00	3.95
1089	1627	5.885352	TGAATTTGATTTGGATAAGCGGAGA	59.115	36.000	0.00	0.00	0.00	3.71
1252	6093	1.331214	CAAGGGTGTTGCTTCATGGT	58.669	50.000	0.00	0.00	0.00	3.55
1254	6095	2.890311	CAAGGGTGTTGCTTCATGGTTA	59.110	45.455	0.00	0.00	0.00	2.85
1257	6098	2.488153	GGGTGTTGCTTCATGGTTACTC	59.512	50.000	0.00	0.00	0.00	2.59
1363	6204	6.432783	TGAGGTCAATAATGTGGTTTTACTGG	59.567	38.462	0.00	0.00	0.00	4.00
1373	6214	4.070009	GTGGTTTTACTGGGGACACTTAG	58.930	47.826	0.00	0.00	35.60	2.18
1656	6546	1.304254	AAAATTTTGTTGCGGGCCAC	58.696	45.000	4.39	0.00	0.00	5.01
1800	6711	6.484364	ACCAATTGAAATGTCAAAGAGGTT	57.516	33.333	7.12	0.00	46.66	3.50
1917	6828	5.390613	CAATAACGACCAGGTTTGATGTTC	58.609	41.667	0.00	0.00	0.00	3.18
1923	6834	4.610945	GACCAGGTTTGATGTTCACAAAG	58.389	43.478	0.00	0.00	37.80	2.77
2135	7050	3.259625	ACTTCTCCTTTCCTGTCTGCTAC	59.740	47.826	0.00	0.00	0.00	3.58
2168	7083	6.252599	TCTATTCCTAATGTTGCATCAGGT	57.747	37.500	3.50	0.00	0.00	4.00
2293	7236	2.329267	TGGTGGACCATATGGAGCTAG	58.671	52.381	28.77	0.47	42.01	3.42
2420	8957	4.959839	TCCCTTTCCTTTTACTTTTGCTGT	59.040	37.500	0.00	0.00	0.00	4.40
2505	9044	5.645067	TGTTTGTTGTTCCATCAATGCAAAA	59.355	32.000	0.00	0.00	30.78	2.44
2588	9140	4.612259	CGCTTGCCATTTCACATATAGCTC	60.612	45.833	0.00	0.00	0.00	4.09
2765	9319	4.822350	TCCAGTATAGTTCGTCTGATCCAG	59.178	45.833	0.00	0.00	0.00	3.86
3258	9953	4.800582	GCCAAAAAGACCCTGAGAAATTGG	60.801	45.833	0.00	0.00	38.21	3.16
3307	10002	5.417580	TCTTCCTACTGCTCTTCTCTCTTTC	59.582	44.000	0.00	0.00	0.00	2.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	3.378339	ACTTGTTCCTTTCACGACTACG	58.622	45.455	0.00	0.00	45.75	3.51
122	123	7.174946	TGTTTGAGAACATAGCCCTTTTTCTAG	59.825	37.037	0.00	0.00	40.71	2.43
174	175	5.518487	CGTGTTCTTAAAAACATGCCACTTT	59.482	36.000	1.07	0.00	40.96	2.66
177	178	3.733727	CCGTGTTCTTAAAAACATGCCAC	59.266	43.478	8.15	0.00	42.33	5.01
178	179	3.243569	CCCGTGTTCTTAAAAACATGCCA	60.244	43.478	8.15	0.00	42.33	4.92
180	181	3.972403	ACCCGTGTTCTTAAAAACATGC	58.028	40.909	8.15	0.00	42.33	4.06
181	182	6.531948	TCAAAACCCGTGTTCTTAAAAACATG	59.468	34.615	6.86	6.86	42.98	3.21
182	183	6.631962	TCAAAACCCGTGTTCTTAAAAACAT	58.368	32.000	0.00	0.00	40.96	2.71
184	185	5.517411	CCTCAAAACCCGTGTTCTTAAAAAC	59.483	40.000	0.00	0.00	32.15	2.43
200	201	8.743099	CGACTTTTCAGATAAAAACCTCAAAAC	58.257	33.333	0.00	0.00	0.00	2.43
202	203	6.915843	GCGACTTTTCAGATAAAAACCTCAAA	59.084	34.615	0.00	0.00	0.00	2.69
277	711	1.270907	AGACTGAAGCCCACGAAGAT	58.729	50.000	0.00	0.00	0.00	2.40
564	1039	0.817654	AATCATCGACGAGGCAGACA	59.182	50.000	4.29	0.00	0.00	3.41
566	1041	2.672874	CAAAAATCATCGACGAGGCAGA	59.327	45.455	4.29	0.00	0.00	4.26
577	1052	2.094545	AGCGAACCTGGCAAAAATCATC	60.095	45.455	0.00	0.00	0.00	2.92
799	1304	1.501741	CCGCGTTGATCCAGGTTTG	59.498	57.895	4.92	0.00	0.00	2.93
921	1438	2.952310	GAGCTTGTCCCAAACTCAAGTT	59.048	45.455	0.00	0.00	40.14	2.66
925	1442	0.468226	ACGAGCTTGTCCCAAACTCA	59.532	50.000	0.00	0.00	0.00	3.41
927	1444	0.759346	AGACGAGCTTGTCCCAAACT	59.241	50.000	27.31	7.88	39.77	2.66
1026	1555	8.560355	AATTCCCATAAAGCAACCAATAAAAC	57.440	30.769	0.00	0.00	0.00	2.43
1089	1627	2.509548	TGGCATGGGTATCAAAGCTAGT	59.490	45.455	0.00	0.00	33.02	2.57
1252	6093	5.468746	CCAATTCAACAGTTCTTCCGAGTAA	59.531	40.000	0.00	0.00	0.00	2.24
1254	6095	3.815401	CCAATTCAACAGTTCTTCCGAGT	59.185	43.478	0.00	0.00	0.00	4.18
1257	6098	6.494893	TTATCCAATTCAACAGTTCTTCCG	57.505	37.500	0.00	0.00	0.00	4.30
1363	6204	2.501723	TGAAGATGCCTCTAAGTGTCCC	59.498	50.000	0.00	0.00	0.00	4.46
1373	6214	1.211457	ACTGGACCATGAAGATGCCTC	59.789	52.381	0.00	0.00	0.00	4.70
1639	6524	1.272212	CTAGTGGCCCGCAACAAAATT	59.728	47.619	0.00	0.00	0.00	1.82
1800	6711	4.156556	GCTTCAGAATGTACCAATTGAGCA	59.843	41.667	7.12	3.08	37.40	4.26
1923	6834	9.327628	AGGACTCTTCTAAAAGTGAAAAACTAC	57.672	33.333	0.00	0.00	38.56	2.73
2110	7025	5.273208	AGCAGACAGGAAAGGAGAAGTATA	58.727	41.667	0.00	0.00	0.00	1.47
2293	7236	7.482654	TCAGCTTACATATTGTGCAATACTC	57.517	36.000	6.76	0.00	36.24	2.59
2505	9044	7.182817	TGAGGTGCTGTTAGTTATCAACTAT	57.817	36.000	0.00	0.00	43.09	2.12
2588	9140	6.816136	AGTGTGAAATGGTTTCCCTAAAAAG	58.184	36.000	0.47	0.00	38.90	2.27
2765	9319	2.226437	CCACAACAGCCAACATGTAGTC	59.774	50.000	0.00	0.00	0.00	2.59
3131	9811	8.690203	TGTGAAACTTTCTTTCTTATCATGGA	57.310	30.769	3.22	0.00	38.04	3.41
3258	9953	4.765339	AGTTAATTTGTAGGGGCACACTTC	59.235	41.667	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.