AutoCloner

Multiple sequence alignment - TraesCS1B01G165200

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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	TraesCS1B01G165200	chr1B	100.000	2276	0	0	1	2276	288444198	288441923	0.000000e+00	4204
1	TraesCS1B01G165200	chr2B	95.552	1304	57	1	2	1305	245813682	245812380	0.000000e+00	2085
2	TraesCS1B01G165200	chr3B	95.165	1303	61	2	1	1303	816086587	816087887	0.000000e+00	2056
3	TraesCS1B01G165200	chr5B	94.636	1305	69	1	1	1305	394007553	394008856	0.000000e+00	2021
4	TraesCS1B01G165200	chr5B	87.939	1310	154	4	1	1308	446409904	446411211	0.000000e+00	1541
5	TraesCS1B01G165200	chr7B	89.740	1306	132	2	1	1305	443324595	443325899	0.000000e+00	1668
6	TraesCS1B01G165200	chr7B	85.841	113	14	1	1306	1418	711220998	711220888	3.970000e-23	119
7	TraesCS1B01G165200	chr3D	88.145	1299	151	3	4	1302	284850695	284849400	0.000000e+00	1543
8	TraesCS1B01G165200	chr3D	83.104	1308	206	14	1	1301	44971320	44972619	0.000000e+00	1177
9	TraesCS1B01G165200	chr6A	88.095	1302	150	5	4	1304	604447812	604446515	0.000000e+00	1541
10	TraesCS1B01G165200	chr5A	87.414	1303	163	1	1	1303	635562658	635563959	0.000000e+00	1496
11	TraesCS1B01G165200	chr5A	86.902	397	39	9	1543	1935	607375191	607375578	1.250000e-117	433
12	TraesCS1B01G165200	chr5A	90.058	171	13	4	1370	1538	607374966	607375134	3.810000e-53	219
13	TraesCS1B01G165200	chr7D	93.173	498	30	4	1306	1799	629573134	629572637	0.000000e+00	728
14	TraesCS1B01G165200	chr5D	92.337	261	16	3	1677	1935	547837620	547837878	3.570000e-98	368
15	TraesCS1B01G165200	chr5D	83.333	336	43	3	1954	2276	547837942	547838277	4.750000e-77	298
16	TraesCS1B01G165200	chr2A	84.236	406	31	14	1539	1935	409182024	409181643	4.620000e-97	364
17	TraesCS1B01G165200	chr2A	81.481	351	52	10	1934	2276	409181600	409181255	2.230000e-70	276
18	TraesCS1B01G165200	chr6B	88.406	276	21	5	1643	1914	558596566	558596298	2.820000e-84	322
19	TraesCS1B01G165200	chr6B	89.202	213	20	3	1327	1538	558597414	558597204	1.730000e-66	263
20	TraesCS1B01G165200	chr1D	88.750	240	18	7	1306	1538	64205029	64204792	3.700000e-73	285
21	TraesCS1B01G165200	chr1D	76.338	355	55	22	1934	2276	64204309	64203972	1.810000e-36	163

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	TraesCS1B01G165200	chr1B	288441923	288444198	2275	True	4204.0	4204	100.0000	1	2276	1	chr1B.!!$R1	2275
1	TraesCS1B01G165200	chr2B	245812380	245813682	1302	True	2085.0	2085	95.5520	2	1305	1	chr2B.!!$R1	1303
2	TraesCS1B01G165200	chr3B	816086587	816087887	1300	False	2056.0	2056	95.1650	1	1303	1	chr3B.!!$F1	1302
3	TraesCS1B01G165200	chr5B	394007553	394008856	1303	False	2021.0	2021	94.6360	1	1305	1	chr5B.!!$F1	1304
4	TraesCS1B01G165200	chr5B	446409904	446411211	1307	False	1541.0	1541	87.9390	1	1308	1	chr5B.!!$F2	1307
5	TraesCS1B01G165200	chr7B	443324595	443325899	1304	False	1668.0	1668	89.7400	1	1305	1	chr7B.!!$F1	1304
6	TraesCS1B01G165200	chr3D	284849400	284850695	1295	True	1543.0	1543	88.1450	4	1302	1	chr3D.!!$R1	1298
7	TraesCS1B01G165200	chr3D	44971320	44972619	1299	False	1177.0	1177	83.1040	1	1301	1	chr3D.!!$F1	1300
8	TraesCS1B01G165200	chr6A	604446515	604447812	1297	True	1541.0	1541	88.0950	4	1304	1	chr6A.!!$R1	1300
9	TraesCS1B01G165200	chr5A	635562658	635563959	1301	False	1496.0	1496	87.4140	1	1303	1	chr5A.!!$F1	1302
10	TraesCS1B01G165200	chr5A	607374966	607375578	612	False	326.0	433	88.4800	1370	1935	2	chr5A.!!$F2	565
11	TraesCS1B01G165200	chr5D	547837620	547838277	657	False	333.0	368	87.8350	1677	2276	2	chr5D.!!$F1	599
12	TraesCS1B01G165200	chr2A	409181255	409182024	769	True	320.0	364	82.8585	1539	2276	2	chr2A.!!$R1	737
13	TraesCS1B01G165200	chr6B	558596298	558597414	1116	True	292.5	322	88.8040	1327	1914	2	chr6B.!!$R1	587
14	TraesCS1B01G165200	chr1D	64203972	64205029	1057	True	224.0	285	82.5440	1306	2276	2	chr1D.!!$R1	970

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
696	700	0.689623	AAGAAGGCAGAGACCCAGTG	59.31	55.0	0.0	0.0	0.0	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1959	2567	0.324738	ACGAGGAGAGGATCAAGGCA	60.325	55.0	0.0	0.0	37.82	4.75	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
54	55	3.243907	ACCTCCGAGCACTAATATTCAGC	60.244	47.826	0.00	0.00	0.00	4.26
122	123	9.462606	CAGGAACTTATAAGGACAACCTTTATT	57.537	33.333	16.73	0.00	46.89	1.40
203	206	4.103103	GCTTGGGCCTTCGAACGC	62.103	66.667	4.53	10.25	0.00	4.84
277	280	1.265905	GCGTCTAGCTCTAGAGGAAGC	59.734	57.143	21.23	17.89	45.73	3.86
318	321	3.808728	ACGGATGATAAACAGATGTGGG	58.191	45.455	0.00	0.00	0.00	4.61
335	338	1.106285	GGGCAGCCTTATGGAAACTG	58.894	55.000	12.43	0.00	34.57	3.16
387	390	0.704664	GAGGGTGTTGAGGGGGATTT	59.295	55.000	0.00	0.00	0.00	2.17
490	493	6.375945	TCTCATGCATGCGTTAATACAATT	57.624	33.333	22.25	0.00	0.00	2.32
540	543	1.537202	GCTTGTGCTTGGTTCGATCTT	59.463	47.619	0.00	0.00	36.03	2.40
615	619	1.051812	GGATCAGGGATGTGGATCGT	58.948	55.000	0.00	0.00	38.61	3.73
695	699	0.980423	GAAGAAGGCAGAGACCCAGT	59.020	55.000	0.00	0.00	0.00	4.00
696	700	0.689623	AAGAAGGCAGAGACCCAGTG	59.310	55.000	0.00	0.00	0.00	3.66
784	788	1.378762	CCGGGACATGGTTGGAAGT	59.621	57.895	0.00	0.00	0.00	3.01
795	799	3.869473	TTGGAAGTCGCCGGAACCG	62.869	63.158	5.05	6.25	39.44	4.44
1212	1216	0.804989	CCGAATGTTGGCTTGAGGAC	59.195	55.000	0.00	0.00	0.00	3.85
1280	1284	7.210174	GGGAACTCTTTTGTTGAATAAAGCTT	58.790	34.615	0.00	0.00	32.67	3.74
1327	1332	5.652744	AATACATCCAGAAATTACGCGTC	57.347	39.130	18.63	0.00	0.00	5.19
1328	1333	2.967362	ACATCCAGAAATTACGCGTCA	58.033	42.857	18.63	4.77	0.00	4.35
1329	1334	2.930040	ACATCCAGAAATTACGCGTCAG	59.070	45.455	18.63	0.00	0.00	3.51
1332	1337	2.066262	CCAGAAATTACGCGTCAGTGT	58.934	47.619	18.63	0.00	44.29	3.55
1336	1341	3.367932	AGAAATTACGCGTCAGTGTGATG	59.632	43.478	18.63	0.00	41.79	3.07
1343	1348	1.605457	GCGTCAGTGTGATGAAGTCCA	60.605	52.381	0.17	0.00	35.46	4.02
1370	1375	2.819595	GCCATGCCATGTCGACGT	60.820	61.111	11.62	7.97	0.00	4.34
1380	1385	4.773117	GTCGACGTCGTCCTGCCC	62.773	72.222	34.40	12.90	40.80	5.36
1414	1419	8.868522	TCCAAGTTCTTGAATCTTGATATTGT	57.131	30.769	13.29	0.00	40.35	2.71
1425	1430	4.587306	TCTTGATATTGTCATTTTCGCGC	58.413	39.130	0.00	0.00	36.54	6.86
1444	1449	4.457496	CCCACATGGCGAGCTCGT	62.457	66.667	34.46	14.96	42.22	4.18
1483	1493	1.729470	CCGTCCTCCAGGAGATCACG	61.729	65.000	19.21	20.18	46.49	4.35
1509	1520	2.295909	TGCAACTGGGATAGTGCAAAAC	59.704	45.455	0.00	0.00	40.26	2.43
1511	1522	3.612479	GCAACTGGGATAGTGCAAAACTG	60.612	47.826	0.00	0.00	40.26	3.16
1551	1621	0.457853	TTGATAGTCGGCGTGTGCTC	60.458	55.000	6.85	0.00	42.25	4.26
1555	1625	4.681978	GTCGGCGTGTGCTCCCTT	62.682	66.667	6.85	0.00	42.25	3.95
1557	1627	2.509336	CGGCGTGTGCTCCCTTAG	60.509	66.667	0.00	0.00	42.25	2.18
1570	1640	0.695347	CCCTTAGGCCCTCATCCATC	59.305	60.000	0.00	0.00	0.00	3.51
1597	1667	3.637273	GTCCCCGTTGCCACTCCT	61.637	66.667	0.00	0.00	0.00	3.69
1601	1671	2.429930	CCGTTGCCACTCCTTCCA	59.570	61.111	0.00	0.00	0.00	3.53
1609	1679	0.036875	CCACTCCTTCCACCTCAACC	59.963	60.000	0.00	0.00	0.00	3.77
1620	1690	3.003173	CTCAACCCTCCAGCCGGA	61.003	66.667	5.05	0.00	39.79	5.14
1630	1701	3.390521	CAGCCGGACCCTGTGCTA	61.391	66.667	5.05	0.00	31.69	3.49
1692	2236	1.347707	TGGCTCGGTTCAGAACTTCAT	59.652	47.619	13.13	0.00	0.00	2.57
1704	2248	7.278868	GGTTCAGAACTTCATATACTGGTCTTG	59.721	40.741	13.13	0.00	0.00	3.02
1749	2294	1.935933	AACGCCGACATCCATCTTAC	58.064	50.000	0.00	0.00	0.00	2.34
1790	2339	0.242017	GACCACATGGCTTGAAGCAC	59.758	55.000	19.89	8.98	44.75	4.40
1817	2366	3.198417	GGCATTCAATCTTGGGGAACAAT	59.802	43.478	0.00	0.00	38.65	2.71
1864	2426	3.050275	GGCAGCCACCACGTCTTC	61.050	66.667	6.55	0.00	0.00	2.87
1896	2459	7.331934	GCGAGTTGAATATTCAGATATTAGGCA	59.668	37.037	17.28	0.00	38.31	4.75
1927	2490	5.874810	CGACCACTATTCAGAGGAAATTTCA	59.125	40.000	19.49	0.00	36.14	2.69
1959	2567	2.311542	TGGGGTTGCAGGTATCAGATTT	59.688	45.455	0.00	0.00	0.00	2.17
1964	2572	3.370840	TGCAGGTATCAGATTTGCCTT	57.629	42.857	10.18	0.00	33.98	4.35
1977	2585	0.826715	TTGCCTTGATCCTCTCCTCG	59.173	55.000	0.00	0.00	0.00	4.63
1978	2586	0.324738	TGCCTTGATCCTCTCCTCGT	60.325	55.000	0.00	0.00	0.00	4.18
1985	2593	1.686052	GATCCTCTCCTCGTGCATCTT	59.314	52.381	0.00	0.00	0.00	2.40
1992	2600	2.658538	CTCGTGCATCTTGTCGAGG	58.341	57.895	12.82	0.00	43.67	4.63
2002	2610	4.757657	GCATCTTGTCGAGGAGAGATACTA	59.242	45.833	4.26	0.00	0.00	1.82
2005	2613	4.163649	TCTTGTCGAGGAGAGATACTACCA	59.836	45.833	0.00	0.00	0.00	3.25
2006	2614	4.708576	TGTCGAGGAGAGATACTACCAT	57.291	45.455	0.00	0.00	0.00	3.55
2010	2618	4.102681	TCGAGGAGAGATACTACCATGTCA	59.897	45.833	0.00	0.00	0.00	3.58
2041	2658	4.094294	CAGACCAACGAAAAAGAGACAACA	59.906	41.667	0.00	0.00	0.00	3.33
2046	2663	5.522460	CCAACGAAAAAGAGACAACAGTAGA	59.478	40.000	0.00	0.00	0.00	2.59
2075	2697	0.539051	GGCTACACACATCTCTGCCT	59.461	55.000	0.00	0.00	36.32	4.75
2120	2742	1.168407	GCGGATGCTGCATGTACCAT	61.168	55.000	21.53	0.00	38.39	3.55
2122	2744	1.541889	CGGATGCTGCATGTACCATCT	60.542	52.381	21.53	0.00	35.57	2.90
2126	2748	5.491070	GGATGCTGCATGTACCATCTATTA	58.509	41.667	21.53	0.00	35.57	0.98
2134	2756	5.583854	GCATGTACCATCTATTAGGAGCATG	59.416	44.000	0.33	0.33	40.19	4.06
2199	2821	1.585006	CGTCGTAGGGACACAAGCT	59.415	57.895	0.00	0.00	46.42	3.74
2206	2828	0.034059	AGGGACACAAGCTTCGACAG	59.966	55.000	0.00	0.00	0.00	3.51
2207	2829	0.951040	GGGACACAAGCTTCGACAGG	60.951	60.000	0.00	0.00	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	2.356069	TGTCAATCAGATCCGAGACTCG	59.644	50.000	18.08	18.08	40.07	4.18
122	123	1.125633	TAGCATCTGCATCTGGAGCA	58.874	50.000	4.79	0.00	45.16	4.26
203	206	5.700832	TGATTTAACAGTGTAGTTGCCTGAG	59.299	40.000	0.00	0.00	33.07	3.35
272	275	2.202756	CCTGTAGCCGTCGCTTCC	60.203	66.667	0.00	0.00	45.55	3.46
277	280	1.805945	GAAGCACCTGTAGCCGTCG	60.806	63.158	0.00	0.00	0.00	5.12
318	321	3.507622	ACTTTCAGTTTCCATAAGGCTGC	59.492	43.478	0.00	0.00	33.74	5.25
335	338	2.488153	CCGAACCTTTGGGATCACTTTC	59.512	50.000	0.00	0.00	34.54	2.62
387	390	5.621555	GCTTGAGAGTACATTCGTCAGGTAA	60.622	44.000	0.00	0.00	0.00	2.85
534	537	2.841215	AGTCGAGGGAGTCTAAGATCG	58.159	52.381	0.00	0.00	0.00	3.69
540	543	2.775960	TGGATGTAGTCGAGGGAGTCTA	59.224	50.000	0.00	0.00	0.00	2.59
615	619	5.105269	CCACATGATGGTGATGATTTTTGGA	60.105	40.000	0.00	0.00	44.46	3.53
695	699	0.312102	CGTAGATCTCATCGCAGCCA	59.688	55.000	0.00	0.00	0.00	4.75
696	700	1.006314	GCGTAGATCTCATCGCAGCC	61.006	60.000	24.51	5.32	46.40	4.85
771	775	1.671054	CGGCGACTTCCAACCATGT	60.671	57.895	0.00	0.00	0.00	3.21
795	799	3.059597	CGCATGAAATCTTGATCGTACCC	60.060	47.826	0.00	0.00	0.00	3.69
972	976	1.209998	GCGATAGGCCTCGAAGTTTC	58.790	55.000	17.84	1.04	41.12	2.78
1280	1284	2.898729	TTTTTGCGGGCAAATCAGAA	57.101	40.000	18.43	8.04	44.14	3.02
1336	1341	2.923121	TGGCTGCTATGAATGGACTTC	58.077	47.619	0.00	0.00	0.00	3.01
1343	1348	2.304221	ATGGCATGGCTGCTATGAAT	57.696	45.000	27.24	16.91	46.58	2.57
1351	1356	2.816360	CGTCGACATGGCATGGCTG	61.816	63.158	29.40	22.07	35.65	4.85
1370	1375	4.697756	CTTTGGCGGGCAGGACGA	62.698	66.667	3.91	0.00	0.00	4.20
1380	1385	0.954452	AAGAACTTGGAGCTTTGGCG	59.046	50.000	0.00	0.00	44.37	5.69
1414	1419	3.059386	GTGGGGGCGCGAAAATGA	61.059	61.111	12.10	0.00	0.00	2.57
1474	1484	1.451927	TTGCATGCCCGTGATCTCC	60.452	57.895	16.68	0.00	0.00	3.71
1483	1493	0.106519	ACTATCCCAGTTGCATGCCC	60.107	55.000	16.68	5.73	31.59	5.36
1551	1621	0.695347	GATGGATGAGGGCCTAAGGG	59.305	60.000	5.73	0.00	0.00	3.95
1555	1625	2.217038	GGCGATGGATGAGGGCCTA	61.217	63.158	5.73	0.00	40.59	3.93
1557	1627	3.125376	AAGGCGATGGATGAGGGCC	62.125	63.158	0.00	0.00	44.07	5.80
1597	1667	1.779061	GCTGGAGGGTTGAGGTGGAA	61.779	60.000	0.00	0.00	0.00	3.53
1601	1671	3.322466	CGGCTGGAGGGTTGAGGT	61.322	66.667	0.00	0.00	0.00	3.85
1630	1701	2.044946	GGAGCACGGGGAGCAATT	60.045	61.111	0.00	0.00	0.00	2.32
1669	2213	2.048222	TTCTGAACCGAGCCAGCG	60.048	61.111	0.00	0.00	0.00	5.18
1670	2214	0.603975	AAGTTCTGAACCGAGCCAGC	60.604	55.000	16.48	0.00	0.00	4.85
1671	2215	1.270305	TGAAGTTCTGAACCGAGCCAG	60.270	52.381	16.48	0.00	0.00	4.85
1672	2216	0.756294	TGAAGTTCTGAACCGAGCCA	59.244	50.000	16.48	5.58	0.00	4.75
1673	2217	2.100605	ATGAAGTTCTGAACCGAGCC	57.899	50.000	16.48	3.25	0.00	4.70
1674	2218	5.460419	CAGTATATGAAGTTCTGAACCGAGC	59.540	44.000	16.48	5.03	0.00	5.03
1675	2219	5.980116	CCAGTATATGAAGTTCTGAACCGAG	59.020	44.000	16.48	0.00	0.00	4.63
1692	2236	2.831526	TCAGCAGCACAAGACCAGTATA	59.168	45.455	0.00	0.00	0.00	1.47
1704	2248	2.033801	ACACAGTGAATTTCAGCAGCAC	59.966	45.455	7.81	0.00	0.00	4.40
1790	2339	2.093869	CCCCAAGATTGAATGCCAGTTG	60.094	50.000	0.00	0.00	0.00	3.16
1838	2390	2.599597	GTGGCTGCCAGATCCCAT	59.400	61.111	24.10	0.00	32.34	4.00
1864	2426	6.653273	TCTGAATATTCAACTCGCTCAAAG	57.347	37.500	18.47	3.54	36.64	2.77
1896	2459	1.226603	GAATAGTGGTCGCGCTCGT	60.227	57.895	5.56	0.00	36.96	4.18
1927	2490	1.302949	CAACCCCATCATGGTCGGT	59.697	57.895	2.07	0.22	34.15	4.69
1959	2567	0.324738	ACGAGGAGAGGATCAAGGCA	60.325	55.000	0.00	0.00	37.82	4.75
1964	2572	1.035923	GATGCACGAGGAGAGGATCA	58.964	55.000	0.00	0.00	37.97	2.92
1977	2585	1.474478	TCTCTCCTCGACAAGATGCAC	59.526	52.381	0.00	0.00	0.00	4.57
1978	2586	1.839424	TCTCTCCTCGACAAGATGCA	58.161	50.000	0.00	0.00	0.00	3.96
1985	2593	4.141459	ACATGGTAGTATCTCTCCTCGACA	60.141	45.833	0.00	0.00	0.00	4.35
1992	2600	6.458232	ACAACTGACATGGTAGTATCTCTC	57.542	41.667	0.00	0.00	0.00	3.20
2002	2610	3.582647	TGGTCTGATACAACTGACATGGT	59.417	43.478	0.00	0.00	39.38	3.55
2005	2613	4.021456	TCGTTGGTCTGATACAACTGACAT	60.021	41.667	19.12	0.00	43.52	3.06
2006	2614	3.319689	TCGTTGGTCTGATACAACTGACA	59.680	43.478	19.12	5.12	43.52	3.58
2010	2618	6.053005	TCTTTTTCGTTGGTCTGATACAACT	58.947	36.000	19.12	0.00	43.52	3.16
2064	2681	2.038659	GGAAGCTCTAGGCAGAGATGT	58.961	52.381	15.26	3.59	46.78	3.06
2075	2697	1.628846	GGACAAGGTTGGGAAGCTCTA	59.371	52.381	0.00	0.00	38.49	2.43
2120	2742	5.304614	GGACCTACAACATGCTCCTAATAGA	59.695	44.000	0.00	0.00	0.00	1.98
2122	2744	4.966168	TGGACCTACAACATGCTCCTAATA	59.034	41.667	0.00	0.00	0.00	0.98
2126	2748	1.656587	TGGACCTACAACATGCTCCT	58.343	50.000	0.00	0.00	0.00	3.69
2134	2756	2.945668	GCCTGATCAATGGACCTACAAC	59.054	50.000	5.19	0.00	0.00	3.32
2172	2794	4.446413	CCTACGACGGGTGGTGCC	62.446	72.222	0.00	0.00	0.00	5.01
2180	2802	1.445582	GCTTGTGTCCCTACGACGG	60.446	63.158	0.00	0.00	45.23	4.79
2199	2821	4.393155	AGCCGCATGCCTGTCGAA	62.393	61.111	13.15	0.00	42.71	3.71
2235	2861	1.153289	GGCCACGATGATGCTGTCT	60.153	57.895	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.