AutoCloner

Multiple sequence alignment - TraesCS2B01G105200

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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	TraesCS2B01G105200	chr2B	100.000	688	0	0	875	1562	65437321	65436634	0.000000e+00	1271.0
1	TraesCS2B01G105200	chr2B	100.000	641	0	0	1	641	65438195	65437555	0.000000e+00	1184.0
2	TraesCS2B01G105200	chr2B	91.420	641	55	0	1	641	548635932	548635292	0.000000e+00	880.0
3	TraesCS2B01G105200	chr2B	100.000	465	0	0	1812	2276	65436384	65435920	0.000000e+00	859.0
4	TraesCS2B01G105200	chr2B	90.967	631	57	0	1	631	442323980	442323350	0.000000e+00	850.0
5	TraesCS2B01G105200	chr2B	92.841	433	30	1	877	1308	442323140	442322708	5.340000e-176	627.0
6	TraesCS2B01G105200	chr2B	94.022	368	21	1	877	1243	548634404	548634037	7.100000e-155	556.0
7	TraesCS2B01G105200	chr2B	83.023	430	68	5	878	1305	91054290	91054716	3.550000e-103	385.0
8	TraesCS2B01G105200	chr3D	91.888	641	52	0	1	641	127221278	127220638	0.000000e+00	896.0
9	TraesCS2B01G105200	chr3D	94.639	429	22	1	875	1302	127220619	127220191	0.000000e+00	664.0
10	TraesCS2B01G105200	chr3D	77.354	393	51	24	1840	2204	560223614	560223996	4.960000e-47	198.0
11	TraesCS2B01G105200	chr1A	90.328	641	62	0	1	641	445913522	445914162	0.000000e+00	841.0
12	TraesCS2B01G105200	chr1A	91.972	436	32	3	875	1307	445914180	445914615	1.930000e-170	608.0
13	TraesCS2B01G105200	chr4A	89.704	641	65	1	1	641	285950113	285949474	0.000000e+00	817.0
14	TraesCS2B01G105200	chr4A	90.909	495	42	2	147	641	2782215	2781724	0.000000e+00	662.0
15	TraesCS2B01G105200	chr4A	93.968	431	25	1	875	1304	285949454	285949024	0.000000e+00	651.0
16	TraesCS2B01G105200	chr5A	84.602	591	90	1	1	591	69221232	69221821	9.060000e-164	586.0
17	TraesCS2B01G105200	chr5A	86.345	498	28	11	1812	2276	655049791	655049301	7.250000e-140	507.0
18	TraesCS2B01G105200	chr5A	84.430	456	36	6	1856	2276	689479955	689480410	1.260000e-112	416.0
19	TraesCS2B01G105200	chr5A	84.397	423	59	6	885	1304	69222068	69222486	2.100000e-110	409.0
20	TraesCS2B01G105200	chr5A	86.705	173	22	1	1383	1555	622983392	622983221	8.300000e-45	191.0
21	TraesCS2B01G105200	chrUn	85.740	554	77	2	1	553	335288693	335289245	3.260000e-163	584.0
22	TraesCS2B01G105200	chr1D	87.872	470	27	5	1830	2276	240139208	240139670	2.000000e-145	525.0
23	TraesCS2B01G105200	chr1D	89.516	248	20	5	1307	1553	240138875	240139117	2.200000e-80	309.0
24	TraesCS2B01G105200	chr1D	87.662	154	14	2	1307	1459	487143233	487143084	8.360000e-40	174.0
25	TraesCS2B01G105200	chr1D	100.000	36	0	0	1383	1418	463503093	463503128	1.460000e-07	67.6
26	TraesCS2B01G105200	chr6B	83.565	432	66	5	878	1307	462172289	462172717	1.270000e-107	399.0
27	TraesCS2B01G105200	chr7D	83.607	427	64	6	883	1306	131449597	131450020	1.640000e-106	396.0
28	TraesCS2B01G105200	chr1B	82.983	476	44	7	1830	2274	572679126	572679595	1.640000e-106	396.0
29	TraesCS2B01G105200	chr7B	76.221	614	142	3	1	612	660722514	660721903	2.820000e-84	322.0
30	TraesCS2B01G105200	chr4B	87.379	206	21	1	1812	2012	289049335	289049130	4.890000e-57	231.0

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	TraesCS2B01G105200	chr2B	65435920	65438195	2275	True	1104.666667	1271	100.0000	1	2276	3	chr2B.!!$R1	2275
1	TraesCS2B01G105200	chr2B	442322708	442323980	1272	True	738.500000	850	91.9040	1	1308	2	chr2B.!!$R2	1307
2	TraesCS2B01G105200	chr2B	548634037	548635932	1895	True	718.000000	880	92.7210	1	1243	2	chr2B.!!$R3	1242
3	TraesCS2B01G105200	chr3D	127220191	127221278	1087	True	780.000000	896	93.2635	1	1302	2	chr3D.!!$R1	1301
4	TraesCS2B01G105200	chr1A	445913522	445914615	1093	False	724.500000	841	91.1500	1	1307	2	chr1A.!!$F1	1306
5	TraesCS2B01G105200	chr4A	285949024	285950113	1089	True	734.000000	817	91.8360	1	1304	2	chr4A.!!$R2	1303
6	TraesCS2B01G105200	chr5A	69221232	69222486	1254	False	497.500000	586	84.4995	1	1304	2	chr5A.!!$F2	1303
7	TraesCS2B01G105200	chrUn	335288693	335289245	552	False	584.000000	584	85.7400	1	553	1	chrUn.!!$F1	552
8	TraesCS2B01G105200	chr1D	240138875	240139670	795	False	417.000000	525	88.6940	1307	2276	2	chr1D.!!$F2	969
9	TraesCS2B01G105200	chr7B	660721903	660722514	611	True	322.000000	322	76.2210	1	612	1	chr7B.!!$R1	611

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
407	408	1.12053	TCGGATACTGAAAGGGCTCC	58.879	55.0	0.0	0.0	39.3	4.7	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2053	2937	0.1791	GCTTGGCTATCTCGTCTGCA	60.179	55.0	0.0	0.0	0.0	4.41	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
97	98	1.228184	ACCTCACAGACGGACGAGT	60.228	57.895	0.00	0.00	0.00	4.18
132	133	8.870075	AGAAACTATGGAAGCTCAAAGTATTT	57.130	30.769	0.00	0.00	40.26	1.40
159	160	2.018727	TACGTGTGTTCTGGTGGCGT	62.019	55.000	0.00	0.00	35.29	5.68
162	163	1.817520	TGTGTTCTGGTGGCGTGTG	60.818	57.895	0.00	0.00	0.00	3.82
201	202	1.639298	ATGAAAGCACTCTTCGGCGC	61.639	55.000	0.00	0.00	34.54	6.53
407	408	1.120530	TCGGATACTGAAAGGGCTCC	58.879	55.000	0.00	0.00	39.30	4.70
428	429	6.505048	TCCAATGATCTCAGTTATGTGGAT	57.495	37.500	0.00	0.00	0.00	3.41
440	441	5.180680	CAGTTATGTGGATGATATGGCACTG	59.819	44.000	0.00	0.00	0.00	3.66
489	490	1.836166	CAGCTGGATCCCTTCTCTTCA	59.164	52.381	9.90	0.00	0.00	3.02
495	496	3.013219	GGATCCCTTCTCTTCAGTTTGC	58.987	50.000	0.00	0.00	0.00	3.68
612	613	3.338818	AAAATCAATACTGATGCGGCG	57.661	42.857	0.51	0.51	41.66	6.46
1324	2188	1.388547	AGCGAACAAAAACTCTGCCA	58.611	45.000	0.00	0.00	0.00	4.92
1340	2204	2.282110	CATTCCCACACCCGCACA	60.282	61.111	0.00	0.00	0.00	4.57
1355	2220	1.725066	CACAAGGAAACAACCGCGT	59.275	52.632	4.92	0.00	34.73	6.01
1356	2221	0.099791	CACAAGGAAACAACCGCGTT	59.900	50.000	4.92	0.00	34.73	4.84
1364	2229	1.223187	AACAACCGCGTTCTCGATTT	58.777	45.000	4.92	0.00	39.71	2.17
1378	2243	2.512515	ATTTCGCTCGCAGCTCCC	60.513	61.111	6.58	0.00	39.60	4.30
1379	2244	2.914777	GATTTCGCTCGCAGCTCCCT	62.915	60.000	6.58	0.00	39.60	4.20
1380	2245	1.676678	ATTTCGCTCGCAGCTCCCTA	61.677	55.000	6.58	0.00	39.60	3.53
1381	2246	1.884075	TTTCGCTCGCAGCTCCCTAA	61.884	55.000	6.58	0.00	39.60	2.69
1390	2255	4.189231	TCGCAGCTCCCTAACTAATTTTC	58.811	43.478	0.00	0.00	0.00	2.29
1418	2283	0.976641	TCCAACTGAATCGTGCCTCT	59.023	50.000	0.00	0.00	0.00	3.69
1420	2285	1.338105	CCAACTGAATCGTGCCTCTCA	60.338	52.381	0.00	0.00	0.00	3.27
1440	2305	2.102252	CAGATCCTTCTTTCTCTCCCCG	59.898	54.545	0.00	0.00	0.00	5.73
1441	2306	1.414550	GATCCTTCTTTCTCTCCCCGG	59.585	57.143	0.00	0.00	0.00	5.73
1444	2309	1.840635	CCTTCTTTCTCTCCCCGGATT	59.159	52.381	0.73	0.00	0.00	3.01
1452	2317	2.236395	TCTCTCCCCGGATTGAGAAAAC	59.764	50.000	0.73	0.00	37.19	2.43
1454	2319	1.282157	CTCCCCGGATTGAGAAAACCT	59.718	52.381	0.73	0.00	0.00	3.50
1459	2324	1.168714	GGATTGAGAAAACCTGCGCT	58.831	50.000	9.73	0.00	0.00	5.92
1499	2364	0.397941	CTTCTGTGCACTTCCCCTCA	59.602	55.000	19.41	0.00	0.00	3.86
1503	2368	0.770499	TGTGCACTTCCCCTCAATCA	59.230	50.000	19.41	0.00	0.00	2.57
1505	2370	1.541588	GTGCACTTCCCCTCAATCAAC	59.458	52.381	10.32	0.00	0.00	3.18
1850	2720	1.871408	GCATCCATCTACAGCGAGGTG	60.871	57.143	0.26	0.26	0.00	4.00
1886	2756	4.351054	CACACACTGCCCCTCCCC	62.351	72.222	0.00	0.00	0.00	4.81
1887	2757	4.599500	ACACACTGCCCCTCCCCT	62.599	66.667	0.00	0.00	0.00	4.79
1888	2758	3.260100	CACACTGCCCCTCCCCTT	61.260	66.667	0.00	0.00	0.00	3.95
1889	2759	2.936032	ACACTGCCCCTCCCCTTC	60.936	66.667	0.00	0.00	0.00	3.46
1890	2760	4.101448	CACTGCCCCTCCCCTTCG	62.101	72.222	0.00	0.00	0.00	3.79
1891	2761	4.658786	ACTGCCCCTCCCCTTCGT	62.659	66.667	0.00	0.00	0.00	3.85
1892	2762	3.787001	CTGCCCCTCCCCTTCGTC	61.787	72.222	0.00	0.00	0.00	4.20
1941	2811	4.057428	GACGAGCCGACCAGCACT	62.057	66.667	1.50	0.00	34.23	4.40
1942	2812	2.675423	ACGAGCCGACCAGCACTA	60.675	61.111	1.50	0.00	34.23	2.74
1988	2858	0.838987	ACGCCCTCTTTCCTGGGTTA	60.839	55.000	0.00	0.00	45.06	2.85
2013	2897	3.089874	CCCGGATCTTGGGCTGGA	61.090	66.667	0.73	0.00	40.47	3.86
2038	2922	4.943093	GGGTTTGAATTTGGGATTTGATGG	59.057	41.667	0.00	0.00	0.00	3.51
2048	2932	3.278574	GGGATTTGATGGTCGTCATTCA	58.721	45.455	0.00	0.00	35.97	2.57
2053	2937	6.183360	GGATTTGATGGTCGTCATTCAATCTT	60.183	38.462	12.19	3.06	36.20	2.40
2056	2940	2.777094	TGGTCGTCATTCAATCTTGCA	58.223	42.857	0.00	0.00	0.00	4.08
2071	2955	2.159184	TCTTGCAGACGAGATAGCCAAG	60.159	50.000	0.00	0.00	30.88	3.61
2144	3036	2.509336	CCGCTCAAGATCGGCGTT	60.509	61.111	6.85	0.00	46.23	4.84
2153	3045	2.746277	ATCGGCGTTGTGCTTCCC	60.746	61.111	6.85	0.00	45.43	3.97
2187	3079	1.002069	AGGGGGACAATTGATCAGCA	58.998	50.000	13.59	0.00	0.00	4.41
2214	3106	2.531206	GTAAGTGCGACTGATCTCCAC	58.469	52.381	0.00	0.00	0.00	4.02
2215	3107	0.247736	AAGTGCGACTGATCTCCACC	59.752	55.000	0.00	0.00	0.00	4.61
2219	3111	0.459237	GCGACTGATCTCCACCTGTG	60.459	60.000	0.00	0.00	0.00	3.66
2261	3154	6.957920	TGAGACCAACTGAAATTGAAATCA	57.042	33.333	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	3.029570	GGTAACCGTCCCTTCATCTAGT	58.970	50.000	0.00	0.00	0.00	2.57
97	98	6.156949	AGCTTCCATAGTTTCTTCCACATCTA	59.843	38.462	0.00	0.00	0.00	1.98
132	133	1.001048	CAGAACACACGTACCTTCGGA	60.001	52.381	0.00	0.00	34.94	4.55
159	160	1.002403	TAGGATTCCCCTCGGCACA	59.998	57.895	0.00	0.00	43.31	4.57
162	163	1.759459	CTGGTAGGATTCCCCTCGGC	61.759	65.000	0.00	0.00	43.31	5.54
164	165	1.620819	CATCTGGTAGGATTCCCCTCG	59.379	57.143	0.00	0.00	43.31	4.63
201	202	7.534085	TCTGCTTATAACTTTAATGTGACGG	57.466	36.000	0.00	0.00	0.00	4.79
399	400	2.203584	ACTGAGATCATTGGAGCCCTT	58.796	47.619	0.00	0.00	0.00	3.95
407	408	7.981102	ATCATCCACATAACTGAGATCATTG	57.019	36.000	0.00	0.00	0.00	2.82
428	429	5.164620	TCTGTTTCTTCAGTGCCATATCA	57.835	39.130	0.00	0.00	36.85	2.15
440	441	4.398247	GTCATGCGTGATTCTGTTTCTTC	58.602	43.478	12.67	0.00	36.60	2.87
489	490	0.392193	CCTCTCTGATGCGGCAAACT	60.392	55.000	6.82	0.00	0.00	2.66
495	496	1.440893	CAGGTCCTCTCTGATGCGG	59.559	63.158	0.00	0.00	34.36	5.69
577	578	9.088987	AGTATTGATTTTAACCACACCAAGATT	57.911	29.630	0.00	0.00	0.00	2.40
612	613	7.389053	CCCACTTTATCTGAGTCCATATTTAGC	59.611	40.741	0.00	0.00	0.00	3.09
998	1862	2.158475	TCCAGGCAGTCTGTTTCCATTT	60.158	45.455	0.24	0.00	41.83	2.32
1005	1869	1.701847	ACAATCTCCAGGCAGTCTGTT	59.298	47.619	0.24	0.00	41.83	3.16
1173	2037	2.359107	ACCATCAGTGTGCAGGCG	60.359	61.111	0.00	0.00	0.00	5.52
1312	2176	2.365293	GTGTGGGAATGGCAGAGTTTTT	59.635	45.455	0.00	0.00	0.00	1.94
1324	2188	1.603455	CTTGTGCGGGTGTGGGAAT	60.603	57.895	0.00	0.00	0.00	3.01
1340	2204	0.942252	GAGAACGCGGTTGTTTCCTT	59.058	50.000	12.47	0.00	30.75	3.36
1355	2220	1.413767	GCTGCGAGCGAAATCGAGAA	61.414	55.000	7.06	0.00	45.56	2.87
1356	2221	1.874019	GCTGCGAGCGAAATCGAGA	60.874	57.895	7.06	0.00	45.56	4.04
1378	2243	4.024302	GGAATCGGCCCGAAAATTAGTTAG	60.024	45.833	11.19	0.00	39.99	2.34
1379	2244	3.878699	GGAATCGGCCCGAAAATTAGTTA	59.121	43.478	11.19	0.00	39.99	2.24
1380	2245	2.686405	GGAATCGGCCCGAAAATTAGTT	59.314	45.455	11.19	0.00	39.99	2.24
1381	2246	2.294979	GGAATCGGCCCGAAAATTAGT	58.705	47.619	11.19	0.00	39.99	2.24
1390	2255	0.748005	ATTCAGTTGGAATCGGCCCG	60.748	55.000	0.00	0.00	42.62	6.13
1411	2276	3.197549	AGAAAGAAGGATCTGAGAGGCAC	59.802	47.826	0.00	0.00	35.59	5.01
1418	2283	3.379452	GGGGAGAGAAAGAAGGATCTGA	58.621	50.000	0.00	0.00	35.59	3.27
1420	2285	2.393646	CGGGGAGAGAAAGAAGGATCT	58.606	52.381	0.00	0.00	37.57	2.75
1440	2305	1.135575	CAGCGCAGGTTTTCTCAATCC	60.136	52.381	11.47	0.00	33.74	3.01
1441	2306	1.730446	GCAGCGCAGGTTTTCTCAATC	60.730	52.381	11.47	0.00	33.74	2.67
1444	2309	2.260869	GGCAGCGCAGGTTTTCTCA	61.261	57.895	11.47	0.00	33.74	3.27
1473	2338	0.689623	AAGTGCACAGAAGGAGGAGG	59.310	55.000	21.04	0.00	0.00	4.30
1499	2364	1.595357	GTCGACTCGGGGGTTGATT	59.405	57.895	8.70	0.00	32.93	2.57
1503	2368	4.312152	AGGGTCGACTCGGGGGTT	62.312	66.667	16.46	0.00	0.00	4.11
1822	2687	2.818169	TAGATGGATGCACCCGGGC	61.818	63.158	24.08	8.36	38.00	6.13
1874	2744	4.658786	ACGAAGGGGAGGGGCAGT	62.659	66.667	0.00	0.00	0.00	4.40
1890	2760	3.519930	GAGCGGAGGACGGAGGAC	61.520	72.222	0.00	0.00	44.51	3.85
1891	2761	4.816984	GGAGCGGAGGACGGAGGA	62.817	72.222	0.00	0.00	44.51	3.71
2013	2897	5.839517	TCAAATCCCAAATTCAAACCCAT	57.160	34.783	0.00	0.00	0.00	4.00
2053	2937	0.179100	GCTTGGCTATCTCGTCTGCA	60.179	55.000	0.00	0.00	0.00	4.41
2056	2940	1.479709	ACAGCTTGGCTATCTCGTCT	58.520	50.000	0.00	0.00	36.40	4.18
2153	3045	4.722700	CCTGGAACCTGGCCACCG	62.723	72.222	0.00	0.00	0.00	4.94
2162	3054	0.407918	TCAATTGTCCCCCTGGAACC	59.592	55.000	5.13	0.00	44.07	3.62
2187	3079	3.678056	TCAGTCGCACTTACCAAAGAT	57.322	42.857	0.00	0.00	36.50	2.40
2214	3106	0.584396	TTGCTAAACGAACGCACAGG	59.416	50.000	0.00	0.00	32.71	4.00
2215	3107	2.594529	ATTGCTAAACGAACGCACAG	57.405	45.000	0.00	0.00	32.71	3.66
2219	3111	4.090930	TCTCAACTATTGCTAAACGAACGC	59.909	41.667	0.00	0.00	0.00	4.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.