AutoCloner

Multiple sequence alignment - TraesCS2A01G087400

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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	TraesCS2A01G087400	chr2A	100.000	2606	0	0	1	2606	41102418	41105023	0.000000e+00	4813.0
1	TraesCS2A01G087400	chr2A	75.742	573	77	32	1015	1560	41170253	41170790	5.610000e-57	231.0
2	TraesCS2A01G087400	chr2A	78.025	314	45	19	1310	1608	41208491	41208795	2.670000e-40	176.0
3	TraesCS2A01G087400	chr2A	78.025	314	45	19	1310	1608	41218346	41218650	2.670000e-40	176.0
4	TraesCS2A01G087400	chr2D	96.652	1643	37	6	20	1655	36750162	36751793	0.000000e+00	2713.0
5	TraesCS2A01G087400	chr2D	93.009	801	47	3	1809	2606	36751986	36752780	0.000000e+00	1160.0
6	TraesCS2A01G087400	chr2D	77.674	533	67	27	1015	1530	36771124	36771621	7.100000e-71	278.0
7	TraesCS2A01G087400	chr2D	77.850	307	44	19	1317	1608	36783840	36784137	4.460000e-38	169.0
8	TraesCS2A01G087400	chr2D	95.082	61	2	1	1657	1717	36751839	36751898	7.680000e-16	95.3
9	TraesCS2A01G087400	chr2B	90.072	1672	117	29	1	1655	63093371	63095010	0.000000e+00	2122.0
10	TraesCS2A01G087400	chr2B	93.812	808	39	5	1802	2606	63100574	63101373	0.000000e+00	1205.0
11	TraesCS2A01G087400	chr2B	76.410	585	99	19	1048	1608	63260768	63261337	1.970000e-71	279.0
12	TraesCS2A01G087400	chr2B	77.256	532	72	25	1016	1530	63140650	63141149	1.540000e-67	267.0
13	TraesCS2A01G087400	chr2B	98.026	152	2	1	1662	1812	63095060	63095211	1.990000e-66	263.0
14	TraesCS2A01G087400	chr2B	74.554	617	97	38	1042	1607	63255255	63255862	5.650000e-52	215.0

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	TraesCS2A01G087400	chr2A	41102418	41105023	2605	False	4813.000000	4813	100.000000	1	2606	1	chr2A.!!$F1	2605
1	TraesCS2A01G087400	chr2A	41170253	41170790	537	False	231.000000	231	75.742000	1015	1560	1	chr2A.!!$F2	545
2	TraesCS2A01G087400	chr2D	36750162	36752780	2618	False	1322.766667	2713	94.914333	20	2606	3	chr2D.!!$F3	2586
3	TraesCS2A01G087400	chr2B	63100574	63101373	799	False	1205.000000	1205	93.812000	1802	2606	1	chr2B.!!$F1	804
4	TraesCS2A01G087400	chr2B	63093371	63095211	1840	False	1192.500000	2122	94.049000	1	1812	2	chr2B.!!$F5	1811
5	TraesCS2A01G087400	chr2B	63260768	63261337	569	False	279.000000	279	76.410000	1048	1608	1	chr2B.!!$F4	560
6	TraesCS2A01G087400	chr2B	63255255	63255862	607	False	215.000000	215	74.554000	1042	1607	1	chr2B.!!$F3	565

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
648	660	0.409484	ATGGTTGGAAGGTTGGGGAG	59.591	55.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2563	2742	0.537371	AAGCCCAGACAGGAAAACCG	60.537	55.0	0.0	0.0	41.22	4.44	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
135	136	3.472652	AGACGACAATTTGCTGTAACCA	58.527	40.909	0.00	0.00	0.00	3.67
206	207	1.160329	GCAAAGCTATGACCCGCGAT	61.160	55.000	8.23	0.00	0.00	4.58
317	318	4.209703	GGTCGTAGTTGTTCGTCAAAATCA	59.790	41.667	0.00	0.00	37.81	2.57
648	660	0.409484	ATGGTTGGAAGGTTGGGGAG	59.591	55.000	0.00	0.00	0.00	4.30
832	845	3.733727	GGCACGGACAAAACAAAATACTG	59.266	43.478	0.00	0.00	0.00	2.74
942	957	5.756833	TCGTCTCTTCCAAACCTAAACTTTC	59.243	40.000	0.00	0.00	0.00	2.62
946	961	4.818005	TCTTCCAAACCTAAACTTTCGTCC	59.182	41.667	0.00	0.00	0.00	4.79
960	975	3.482722	TTCGTCCAGTCGATTGTAGAC	57.517	47.619	7.19	7.13	39.57	2.59
963	978	3.620374	TCGTCCAGTCGATTGTAGACTAC	59.380	47.826	7.19	5.62	46.16	2.73
989	1004	2.300042	GTCGCGTGCGTTTTTATCAAA	58.700	42.857	14.47	0.00	40.74	2.69
990	1005	2.906161	GTCGCGTGCGTTTTTATCAAAT	59.094	40.909	14.47	0.00	40.74	2.32
991	1006	3.003408	GTCGCGTGCGTTTTTATCAAATC	60.003	43.478	14.47	0.00	40.74	2.17
993	1008	3.602062	CGCGTGCGTTTTTATCAAATCTT	59.398	39.130	6.00	0.00	34.35	2.40
994	1009	4.487004	CGCGTGCGTTTTTATCAAATCTTG	60.487	41.667	6.00	0.00	34.35	3.02
1339	1400	3.362797	ACGCCGAGCTCGAGTTCA	61.363	61.111	36.59	0.00	43.02	3.18
1379	1440	0.321298	ACGCTGATAAAGTGGCCGTT	60.321	50.000	0.00	0.00	40.99	4.44
1530	1591	1.663702	CAAGGTCACCGTCGTCCAC	60.664	63.158	0.00	0.00	0.00	4.02
1625	1710	2.146342	GATCATAGATGTGCCCCGTTG	58.854	52.381	0.00	0.00	0.00	4.10
1655	1741	0.611618	TGGCGCATTGTTGGGAGAAT	60.612	50.000	10.83	0.00	38.00	2.40
1656	1742	0.532115	GGCGCATTGTTGGGAGAATT	59.468	50.000	10.83	0.00	38.00	2.17
1660	1789	3.123453	GCGCATTGTTGGGAGAATTTTTC	59.877	43.478	0.30	0.00	38.00	2.29
1747	1923	1.766496	CTCGGTCTACCTCCTCTCTCT	59.234	57.143	0.00	0.00	0.00	3.10
1751	1927	1.144298	GTCTACCTCCTCTCTCTCCCC	59.856	61.905	0.00	0.00	0.00	4.81
2007	2186	2.033448	CCTTGGTGTGGCGCCTAA	59.967	61.111	29.70	13.28	34.70	2.69
2070	2249	6.479972	TTCTTCAACTTTCTAGACTGGTGA	57.520	37.500	7.57	7.57	0.00	4.02
2107	2286	2.672996	GTTGCGTGGGTGATGCCT	60.673	61.111	0.00	0.00	35.48	4.75
2141	2320	7.222031	TGTTTGTTCATCGATTATTAGACCTCG	59.778	37.037	0.00	0.00	0.00	4.63
2170	2349	3.789791	GCATCACATGGCTATTGTTGTCG	60.790	47.826	0.00	0.00	0.00	4.35
2270	2449	3.078837	GGGGCGTACAATCAAGAAAAGA	58.921	45.455	0.00	0.00	0.00	2.52
2443	2622	2.304761	ACGAGGTATCCAAAGCAAGGAA	59.695	45.455	0.00	0.00	38.93	3.36
2517	2696	1.074072	CCCATGACAACCCCAACGA	59.926	57.895	0.00	0.00	0.00	3.85
2519	2698	1.544724	CCATGACAACCCCAACGAAT	58.455	50.000	0.00	0.00	0.00	3.34
2565	2744	3.585856	CCAACGGAATGGGAACGG	58.414	61.111	0.00	0.00	36.79	4.44
2572	2751	1.884928	CGGAATGGGAACGGTTTTCCT	60.885	52.381	16.09	0.14	38.61	3.36
2596	2775	1.529713	GGCTTTCCCCAACGGACAA	60.530	57.895	0.00	0.00	41.83	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	0.325272	ACCCCCGCTTTCTCTTTCTC	59.675	55.000	0.00	0.00	0.00	2.87
15	16	0.771755	AACCCCCGCTTTCTCTTTCT	59.228	50.000	0.00	0.00	0.00	2.52
16	17	0.881796	CAACCCCCGCTTTCTCTTTC	59.118	55.000	0.00	0.00	0.00	2.62
17	18	0.185175	ACAACCCCCGCTTTCTCTTT	59.815	50.000	0.00	0.00	0.00	2.52
18	19	1.061546	TACAACCCCCGCTTTCTCTT	58.938	50.000	0.00	0.00	0.00	2.85
196	197	4.889856	CGATGCCATCGCGGGTCA	62.890	66.667	14.88	3.64	46.55	4.02
317	318	3.096092	TCAACAGTTGCAACTTTTCCCT	58.904	40.909	29.23	5.59	37.08	4.20
532	538	2.022195	TCCTTCATCGGTACTCCTTCG	58.978	52.381	0.00	0.00	0.00	3.79
648	660	3.067684	TCGGATTTGACTCCCTTTTCC	57.932	47.619	0.00	0.00	31.04	3.13
706	719	2.281208	CGGTCCAACTTTCGGCCA	60.281	61.111	2.24	0.00	0.00	5.36
832	845	0.038343	TACACTCCAAACGGCCGTAC	60.038	55.000	34.44	0.00	0.00	3.67
901	916	9.838975	GAAGAGACGATATATATATGCATGAGG	57.161	37.037	10.16	0.00	0.00	3.86
942	957	3.373130	TGTAGTCTACAATCGACTGGACG	59.627	47.826	10.37	0.00	41.52	4.79
960	975	1.129879	ACGCACGCGACGTATTGTAG	61.130	55.000	25.42	8.65	43.02	2.74
963	978	0.449831	AAAACGCACGCGACGTATTG	60.450	50.000	26.45	9.79	44.30	1.90
991	1006	9.049632	CACGTAGTAAGATGGCATCTTTCCAAG	62.050	44.444	38.87	28.11	43.55	3.61
993	1008	5.910958	CACGTAGTAAGATGGCATCTTTCCA	60.911	44.000	38.87	24.75	43.55	3.53
994	1009	4.508124	CACGTAGTAAGATGGCATCTTTCC	59.492	45.833	38.87	29.69	43.55	3.13
1301	1362	2.104111	TGGACGATGTTCTCCTTGTTGT	59.896	45.455	0.00	0.00	0.00	3.32
1302	1363	2.480419	GTGGACGATGTTCTCCTTGTTG	59.520	50.000	0.00	0.00	0.00	3.33
1303	1364	2.767505	GTGGACGATGTTCTCCTTGTT	58.232	47.619	0.00	0.00	0.00	2.83
1379	1440	2.875485	GTCTGCCGAGCGAGTGTA	59.125	61.111	0.00	0.00	0.00	2.90
1530	1591	1.654220	CCCTTTGACGGCACACTTG	59.346	57.895	0.00	0.00	0.00	3.16
1563	1642	1.526917	CCTAGCCAATGCCTTCCCG	60.527	63.158	0.00	0.00	38.69	5.14
1572	1651	4.662278	TGCAACTAAAGAACCTAGCCAAT	58.338	39.130	0.00	0.00	0.00	3.16
1751	1927	3.584052	CCGACTAGACCGCCCGAG	61.584	72.222	0.00	0.00	0.00	4.63
2007	2186	8.611757	GGCAAAACAAATGTAAAGAAGATGTTT	58.388	29.630	0.00	0.00	40.18	2.83
2070	2249	2.026262	ACGCAGGGTTGTAATCCTTCAT	60.026	45.455	0.00	0.00	0.00	2.57
2094	2273	2.509336	GTCGAGGCATCACCCACG	60.509	66.667	0.00	0.00	40.58	4.94
2107	2286	1.144969	GATGAACAAACAGCGGTCGA	58.855	50.000	0.00	0.00	0.00	4.20
2141	2320	5.297776	ACAATAGCCATGTGATGCTAGAAAC	59.702	40.000	7.36	0.00	42.85	2.78
2170	2349	3.491104	CCCTAGCCATACGAGACTTTGAC	60.491	52.174	0.00	0.00	0.00	3.18
2290	2469	9.995003	AATGTTTTTCTTGATAAATAGTGGCAA	57.005	25.926	0.00	0.00	0.00	4.52
2401	2580	5.649395	TCGTAACTACACTTATACACCTGCT	59.351	40.000	0.00	0.00	0.00	4.24
2402	2581	5.883661	TCGTAACTACACTTATACACCTGC	58.116	41.667	0.00	0.00	0.00	4.85
2403	2582	6.094603	ACCTCGTAACTACACTTATACACCTG	59.905	42.308	0.00	0.00	0.00	4.00
2404	2583	6.183347	ACCTCGTAACTACACTTATACACCT	58.817	40.000	0.00	0.00	0.00	4.00
2443	2622	4.387026	TTGTTGAGTTCATCCCATCCTT	57.613	40.909	0.00	0.00	0.00	3.36
2517	2696	3.245586	TGGGCCTATCTCAACCAACAATT	60.246	43.478	4.53	0.00	0.00	2.32
2519	2698	1.707989	TGGGCCTATCTCAACCAACAA	59.292	47.619	4.53	0.00	0.00	2.83
2525	2704	3.027419	GCCATGGGCCTATCTCAAC	57.973	57.895	15.13	0.00	44.06	3.18
2555	2734	2.158519	AGACAGGAAAACCGTTCCCATT	60.159	45.455	1.46	0.00	39.39	3.16
2563	2742	0.537371	AAGCCCAGACAGGAAAACCG	60.537	55.000	0.00	0.00	41.22	4.44
2565	2744	1.613925	GGAAAGCCCAGACAGGAAAAC	59.386	52.381	0.00	0.00	41.22	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.