AutoCloner

Multiple sequence alignment - TraesCS6A01G324900

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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	TraesCS6A01G324900	chr6A	100.000	2672	0	0	1	2672	558932591	558935262	0.000000e+00	4935.0
1	TraesCS6A01G324900	chr6A	90.090	1554	90	22	1173	2672	558920824	558922367	0.000000e+00	1958.0
2	TraesCS6A01G324900	chr6A	89.137	1344	101	11	18	1343	558919588	558920904	0.000000e+00	1631.0
3	TraesCS6A01G324900	chr6A	84.838	554	49	18	1746	2270	558950866	558951413	2.360000e-145	525.0
4	TraesCS6A01G324900	chr6A	85.124	121	16	2	1312	1431	558933635	558933754	3.610000e-24	122.0
5	TraesCS6A01G324900	chr6A	85.124	121	16	2	1045	1164	558933902	558934021	3.610000e-24	122.0
6	TraesCS6A01G324900	chr6A	90.805	87	6	2	1080	1165	558920998	558921083	6.040000e-22	115.0
7	TraesCS6A01G324900	chr6B	96.880	2660	54	9	18	2672	623444556	623447191	0.000000e+00	4425.0
8	TraesCS6A01G324900	chr6B	92.414	1450	84	11	383	1808	623368399	623369846	0.000000e+00	2045.0
9	TraesCS6A01G324900	chr6B	87.586	580	35	19	2119	2672	623388702	623389270	2.900000e-179	638.0
10	TraesCS6A01G324900	chr6B	89.209	278	13	11	1797	2065	623381735	623382004	5.510000e-87	331.0
11	TraesCS6A01G324900	chr6B	94.767	172	6	2	18	189	623367823	623367991	5.670000e-67	265.0
12	TraesCS6A01G324900	chr6B	93.452	168	11	0	188	355	623368096	623368263	1.590000e-62	250.0
13	TraesCS6A01G324900	chr6B	85.246	122	16	2	1045	1165	623445830	623445950	1.000000e-24	124.0
14	TraesCS6A01G324900	chr6B	85.124	121	16	2	1312	1431	623369082	623369201	3.610000e-24	122.0
15	TraesCS6A01G324900	chr6B	84.298	121	17	2	1312	1431	623445563	623445682	1.680000e-22	117.0
16	TraesCS6A01G324900	chr6B	88.235	68	4	4	35	101	623358132	623358196	7.930000e-11	78.7
17	TraesCS6A01G324900	chr6D	90.071	1551	93	24	1169	2672	413383745	413385281	0.000000e+00	1954.0
18	TraesCS6A01G324900	chr6D	89.576	1343	93	14	18	1343	413382472	413383784	0.000000e+00	1661.0
19	TraesCS6A01G324900	chr6D	84.138	870	70	23	1855	2672	413395887	413396740	0.000000e+00	780.0
20	TraesCS6A01G324900	chr6D	86.607	112	15	0	1312	1423	413383489	413383600	1.000000e-24	124.0
21	TraesCS6A01G324900	chr6D	84.615	117	16	2	1049	1164	413383892	413384007	6.040000e-22	115.0

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	TraesCS6A01G324900	chr6A	558932591	558935262	2671	False	1726.333333	4935	90.082667	1	2672	3	chr6A.!!$F3	2671
1	TraesCS6A01G324900	chr6A	558919588	558922367	2779	False	1234.666667	1958	90.010667	18	2672	3	chr6A.!!$F2	2654
2	TraesCS6A01G324900	chr6A	558950866	558951413	547	False	525.000000	525	84.838000	1746	2270	1	chr6A.!!$F1	524
3	TraesCS6A01G324900	chr6B	623444556	623447191	2635	False	1555.333333	4425	88.808000	18	2672	3	chr6B.!!$F5	2654
4	TraesCS6A01G324900	chr6B	623367823	623369846	2023	False	670.500000	2045	91.439250	18	1808	4	chr6B.!!$F4	1790
5	TraesCS6A01G324900	chr6B	623388702	623389270	568	False	638.000000	638	87.586000	2119	2672	1	chr6B.!!$F3	553
6	TraesCS6A01G324900	chr6D	413382472	413385281	2809	False	963.500000	1954	87.717250	18	2672	4	chr6D.!!$F2	2654
7	TraesCS6A01G324900	chr6D	413395887	413396740	853	False	780.000000	780	84.138000	1855	2672	1	chr6D.!!$F1	817

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
116	117	3.615592	GCAGTGTATTGTTCGTACTGGGA	60.616	47.826	0.0	0.0	39.21	4.37	F
1258	1746	2.439507	GGAGATAAGGGTGAGCAATCCA	59.560	50.000	0.0	0.0	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1555	2043	0.547471	TTCTCCCTGGATGTGGCAGA	60.547	55.0	0.0	0.0	0.00	4.26	R
2151	2696	2.095059	GTGTAATGTGCAGGAAGGCAAG	60.095	50.0	0.0	0.0	46.93	4.01	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
116	117	3.615592	GCAGTGTATTGTTCGTACTGGGA	60.616	47.826	0.00	0.00	39.21	4.37
682	933	7.927629	GGTTGTTGGATGCATATATGAAACAAT	59.072	33.333	17.10	1.56	38.22	2.71
877	1143	9.424319	CTGTACTACGATATTAATTTGCATCCT	57.576	33.333	0.00	0.00	0.00	3.24
889	1155	6.990341	AATTTGCATCCTAAAAATTGCTCC	57.010	33.333	0.00	0.00	33.42	4.70
890	1156	4.470334	TTGCATCCTAAAAATTGCTCCC	57.530	40.909	0.00	0.00	36.10	4.30
891	1157	3.711863	TGCATCCTAAAAATTGCTCCCT	58.288	40.909	0.00	0.00	36.10	4.20
892	1158	4.865905	TGCATCCTAAAAATTGCTCCCTA	58.134	39.130	0.00	0.00	36.10	3.53
893	1159	5.457686	TGCATCCTAAAAATTGCTCCCTAT	58.542	37.500	0.00	0.00	36.10	2.57
894	1160	6.609876	TGCATCCTAAAAATTGCTCCCTATA	58.390	36.000	0.00	0.00	36.10	1.31
895	1161	7.066142	TGCATCCTAAAAATTGCTCCCTATAA	58.934	34.615	0.00	0.00	36.10	0.98
896	1162	7.563188	TGCATCCTAAAAATTGCTCCCTATAAA	59.437	33.333	0.00	0.00	36.10	1.40
971	1237	6.531948	CGAAAGAGATTTAGTAAGAGTGTGGG	59.468	42.308	0.00	0.00	0.00	4.61
1258	1746	2.439507	GGAGATAAGGGTGAGCAATCCA	59.560	50.000	0.00	0.00	0.00	3.41
1268	1756	3.557054	GGTGAGCAATCCACTGACAAGTA	60.557	47.826	0.00	0.00	33.79	2.24
1555	2043	2.989824	CCCTTGCTGCTGCTGCTT	60.990	61.111	27.67	0.00	40.48	3.91
1560	2048	4.117661	GCTGCTGCTGCTTCTGCC	62.118	66.667	22.10	0.00	40.48	4.85
1561	2049	2.671963	CTGCTGCTGCTTCTGCCA	60.672	61.111	17.00	0.00	40.48	4.92
1699	2191	0.953727	GTGAACTGAGCAATGCACCA	59.046	50.000	8.35	4.00	0.00	4.17
1780	2276	6.347483	GGTCCGATGTTCACTTCTTTAACTTC	60.347	42.308	0.00	0.00	0.00	3.01
1879	2387	8.902806	AGTTTCAGACAAAACTCATTGATAACA	58.097	29.630	0.00	0.00	44.18	2.41
1910	2418	9.912634	CAAATTTGGCTCTAGAAATTAAACAGA	57.087	29.630	10.49	0.00	32.66	3.41
2151	2696	2.112815	GTGCTCCCCCGTGCATTAC	61.113	63.158	0.00	0.00	40.38	1.89
2203	2748	6.154192	TGCACATTCATTAGCTGGGATAAAAA	59.846	34.615	0.00	0.00	0.00	1.94
2303	2848	7.068348	ACTCTACACGTTCATACATCATAGGTT	59.932	37.037	0.00	0.00	0.00	3.50
2355	2934	0.675633	TGCAAAGCAAAAGAGGAGCC	59.324	50.000	0.00	0.00	34.76	4.70
2392	2971	3.510388	ACATCAGTGACACGTAGATGG	57.490	47.619	27.09	16.81	40.17	3.51
2487	3066	3.924686	CACTTGGCTTCAGATTCAAATGC	59.075	43.478	0.00	0.00	0.00	3.56
2547	3126	3.563808	TGTGGAAAATGAAGGAGTCAACG	59.436	43.478	0.00	0.00	40.50	4.10
2571	3150	6.538742	CGTACAAATATCTTGTTCCTGTGGAT	59.461	38.462	8.06	0.00	34.11	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.548451	TGCATCTGTCTTGTCTGAAGAT	57.452	40.909	0.00	0.00	0.00	2.40
1	2	4.548451	ATGCATCTGTCTTGTCTGAAGA	57.452	40.909	0.00	0.00	0.00	2.87
2	3	5.873712	ACTAATGCATCTGTCTTGTCTGAAG	59.126	40.000	0.00	0.00	0.00	3.02
3	4	5.798132	ACTAATGCATCTGTCTTGTCTGAA	58.202	37.500	0.00	0.00	0.00	3.02
4	5	5.411831	ACTAATGCATCTGTCTTGTCTGA	57.588	39.130	0.00	0.00	0.00	3.27
5	6	6.402983	GGAAACTAATGCATCTGTCTTGTCTG	60.403	42.308	0.00	0.00	0.00	3.51
6	7	5.645497	GGAAACTAATGCATCTGTCTTGTCT	59.355	40.000	0.00	0.00	0.00	3.41
7	8	5.412594	TGGAAACTAATGCATCTGTCTTGTC	59.587	40.000	0.00	0.00	0.00	3.18
8	9	5.316167	TGGAAACTAATGCATCTGTCTTGT	58.684	37.500	0.00	0.00	0.00	3.16
9	10	5.885230	TGGAAACTAATGCATCTGTCTTG	57.115	39.130	0.00	0.00	0.00	3.02
10	11	6.491403	AGTTTGGAAACTAATGCATCTGTCTT	59.509	34.615	0.00	0.28	46.75	3.01
11	12	6.006449	AGTTTGGAAACTAATGCATCTGTCT	58.994	36.000	0.00	0.00	46.75	3.41
12	13	6.088824	CAGTTTGGAAACTAATGCATCTGTC	58.911	40.000	0.00	0.00	46.89	3.51
13	14	5.565439	GCAGTTTGGAAACTAATGCATCTGT	60.565	40.000	0.00	0.00	46.89	3.41
14	15	4.860907	GCAGTTTGGAAACTAATGCATCTG	59.139	41.667	0.00	0.00	46.89	2.90
15	16	4.768968	AGCAGTTTGGAAACTAATGCATCT	59.231	37.500	0.00	0.00	46.89	2.90
16	17	5.064441	AGCAGTTTGGAAACTAATGCATC	57.936	39.130	0.00	0.00	46.89	3.91
65	66	2.949644	AGTAAATCATTAAGGCCGCACC	59.050	45.455	0.00	0.00	39.61	5.01
116	117	0.108207	GATAGCAGGCTGGCATGTCT	59.892	55.000	17.64	5.97	35.83	3.41
565	813	0.733150	CTGACGCTATGGTGAGTCGA	59.267	55.000	0.00	0.00	36.49	4.20
651	902	2.460757	ATGCATCCAACAACCAAAGC	57.539	45.000	0.00	0.00	0.00	3.51
682	933	1.153066	TTTCTTGCGGTGCTGGTGA	60.153	52.632	0.00	0.00	0.00	4.02
877	1143	8.830915	TGACCATTTATAGGGAGCAATTTTTA	57.169	30.769	0.00	0.00	0.00	1.52
880	1146	5.835280	CCTGACCATTTATAGGGAGCAATTT	59.165	40.000	0.00	0.00	0.00	1.82
883	1149	4.044308	TCCTGACCATTTATAGGGAGCAA	58.956	43.478	0.00	0.00	0.00	3.91
885	1151	3.904339	TCTCCTGACCATTTATAGGGAGC	59.096	47.826	0.00	0.00	38.81	4.70
887	1153	6.150332	TCAATCTCCTGACCATTTATAGGGA	58.850	40.000	0.00	0.00	0.00	4.20
888	1154	6.439636	TCAATCTCCTGACCATTTATAGGG	57.560	41.667	0.00	0.00	0.00	3.53
889	1155	7.605691	GTGATCAATCTCCTGACCATTTATAGG	59.394	40.741	0.00	0.00	0.00	2.57
890	1156	7.330454	CGTGATCAATCTCCTGACCATTTATAG	59.670	40.741	0.00	0.00	0.00	1.31
891	1157	7.154656	CGTGATCAATCTCCTGACCATTTATA	58.845	38.462	0.00	0.00	0.00	0.98
892	1158	5.994054	CGTGATCAATCTCCTGACCATTTAT	59.006	40.000	0.00	0.00	0.00	1.40
893	1159	5.359756	CGTGATCAATCTCCTGACCATTTA	58.640	41.667	0.00	0.00	0.00	1.40
894	1160	4.194640	CGTGATCAATCTCCTGACCATTT	58.805	43.478	0.00	0.00	0.00	2.32
895	1161	3.432749	CCGTGATCAATCTCCTGACCATT	60.433	47.826	0.00	0.00	0.00	3.16
896	1162	2.103771	CCGTGATCAATCTCCTGACCAT	59.896	50.000	0.00	0.00	0.00	3.55
971	1237	6.755206	TCACTCTGTACTCTCTAGATCTAGC	58.245	44.000	22.81	9.80	33.32	3.42
1258	1746	3.553922	GCAGAGAGCTTGTACTTGTCAGT	60.554	47.826	0.00	0.00	41.15	3.41
1268	1756	2.566279	TCATCTTCTGCAGAGAGCTTGT	59.434	45.455	17.43	0.00	45.94	3.16
1555	2043	0.547471	TTCTCCCTGGATGTGGCAGA	60.547	55.000	0.00	0.00	0.00	4.26
1560	2048	1.871418	TCTCCTTCTCCCTGGATGTG	58.129	55.000	0.00	0.00	0.00	3.21
1561	2049	2.192263	GTTCTCCTTCTCCCTGGATGT	58.808	52.381	0.00	0.00	0.00	3.06
1729	2221	4.435425	ACACAAGTTGTTTCACGTAGCTA	58.565	39.130	5.57	0.00	33.09	3.32
1735	2227	3.372822	ACCAGTACACAAGTTGTTTCACG	59.627	43.478	5.57	0.00	39.91	4.35
1780	2276	3.893200	TGTATATGGGGTAGACTTGGTCG	59.107	47.826	0.00	0.00	37.67	4.79
1910	2418	6.223120	GTTTGGTCATGTTTTCTTTGGCTAT	58.777	36.000	0.00	0.00	0.00	2.97
1911	2419	5.452636	GGTTTGGTCATGTTTTCTTTGGCTA	60.453	40.000	0.00	0.00	0.00	3.93
2151	2696	2.095059	GTGTAATGTGCAGGAAGGCAAG	60.095	50.000	0.00	0.00	46.93	4.01
2203	2748	6.471233	TGCTCTTCTACTGCATATGTACTT	57.529	37.500	4.29	0.00	0.00	2.24
2240	2785	7.430502	GTGATCTGCTACTGATTAAATTTGTGC	59.569	37.037	0.00	0.00	0.00	4.57
2355	2934	6.583427	CACTGATGTTATGAATTGGTTGTGTG	59.417	38.462	0.00	0.00	0.00	3.82
2392	2971	5.829829	CCTAGTAAGGTTACTGATTCCGAC	58.170	45.833	11.88	0.00	43.44	4.79
2487	3066	3.806380	AGCTATGAGATCTTGTGCAAGG	58.194	45.455	11.47	0.00	38.88	3.61
2547	3126	7.865706	ATCCACAGGAACAAGATATTTGTAC	57.134	36.000	4.43	0.00	34.34	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.