AutoCloner

Multiple sequence alignment - TraesCS5B01G222300

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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	TraesCS5B01G222300	chr5B	100.000	3003	0	0	1	3003	396870702	396873704	0.000000e+00	5546
1	TraesCS5B01G222300	chr5B	95.139	3024	126	5	1	3003	396811536	396814559	0.000000e+00	4750
2	TraesCS5B01G222300	chr5B	94.673	901	48	0	1	901	396758002	396758902	0.000000e+00	1399
3	TraesCS5B01G222300	chr5B	92.529	937	66	4	1	936	181641890	181642823	0.000000e+00	1339
4	TraesCS5B01G222300	chr5B	92.201	936	71	2	1	935	303856840	303855906	0.000000e+00	1323
5	TraesCS5B01G222300	chr3B	92.291	934	69	3	1	933	611907717	611906786	0.000000e+00	1323
6	TraesCS5B01G222300	chr2D	92.366	930	70	1	6	935	544768758	544769686	0.000000e+00	1323
7	TraesCS5B01G222300	chr2D	84.487	419	39	17	2595	3002	493888892	493889295	1.010000e-104	390
8	TraesCS5B01G222300	chr1B	92.258	930	69	3	7	935	555187010	555186083	0.000000e+00	1315
9	TraesCS5B01G222300	chr7B	92.094	936	68	4	1	935	216947414	216946484	0.000000e+00	1314
10	TraesCS5B01G222300	chr2B	91.996	937	72	3	1	936	462283364	462284298	0.000000e+00	1312
11	TraesCS5B01G222300	chr5D	90.702	968	68	11	1160	2111	337714527	337715488	0.000000e+00	1269
12	TraesCS5B01G222300	chr5D	85.043	936	95	23	2094	3003	337754697	337755613	0.000000e+00	911
13	TraesCS5B01G222300	chr2A	87.037	324	26	10	2684	3002	639693173	639692861	4.760000e-93	351

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	TraesCS5B01G222300	chr5B	396870702	396873704	3002	False	5546	5546	100.000	1	3003	1	chr5B.!!$F4	3002
1	TraesCS5B01G222300	chr5B	396811536	396814559	3023	False	4750	4750	95.139	1	3003	1	chr5B.!!$F3	3002
2	TraesCS5B01G222300	chr5B	396758002	396758902	900	False	1399	1399	94.673	1	901	1	chr5B.!!$F2	900
3	TraesCS5B01G222300	chr5B	181641890	181642823	933	False	1339	1339	92.529	1	936	1	chr5B.!!$F1	935
4	TraesCS5B01G222300	chr5B	303855906	303856840	934	True	1323	1323	92.201	1	935	1	chr5B.!!$R1	934
5	TraesCS5B01G222300	chr3B	611906786	611907717	931	True	1323	1323	92.291	1	933	1	chr3B.!!$R1	932
6	TraesCS5B01G222300	chr2D	544768758	544769686	928	False	1323	1323	92.366	6	935	1	chr2D.!!$F2	929
7	TraesCS5B01G222300	chr1B	555186083	555187010	927	True	1315	1315	92.258	7	935	1	chr1B.!!$R1	928
8	TraesCS5B01G222300	chr7B	216946484	216947414	930	True	1314	1314	92.094	1	935	1	chr7B.!!$R1	934
9	TraesCS5B01G222300	chr2B	462283364	462284298	934	False	1312	1312	91.996	1	936	1	chr2B.!!$F1	935
10	TraesCS5B01G222300	chr5D	337714527	337715488	961	False	1269	1269	90.702	1160	2111	1	chr5D.!!$F1	951
11	TraesCS5B01G222300	chr5D	337754697	337755613	916	False	911	911	85.043	2094	3003	1	chr5D.!!$F2	909

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
720	723	2.047061	GGTCATGTATGCCTGTCCCTA	58.953	52.381	0.00	0.0	0.0	3.53	F
1031	1035	1.219124	CGTACAGCTGAGTGGGCAT	59.781	57.895	23.35	0.0	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1725	1730	0.251742	TTGGTTCCCATTGCTCCTGG	60.252	55.0	0.0	0.0	31.53	4.45	R
2528	2583	0.324943	TAGCCAAGCCGAAGAAAGCT	59.675	50.0	0.0	0.0	42.40	3.74	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	7.848539	ACGTTTGCTTAATTTATGTTTTTGCAC	59.151	29.630	0.00	0.00	0.00	4.57
141	142	8.642020	GCTTAATTTATGTTTTTGCACAGAGAG	58.358	33.333	0.00	0.00	0.00	3.20
168	169	2.222217	CGCTAGTAGTTCCGCGTGC	61.222	63.158	4.92	0.00	40.64	5.34
194	195	2.665052	CGACGTTTAGCTTGTTACCTCC	59.335	50.000	0.00	0.00	0.00	4.30
245	246	6.132658	TCTTGTAGATAGTCAGGCTTCTCAT	58.867	40.000	0.00	0.00	0.00	2.90
406	408	2.536365	CATCTTGTGATGCCATGTTGC	58.464	47.619	0.00	0.00	42.83	4.17
685	688	3.944650	TGGGTTCATACATTGTTGATCGG	59.055	43.478	0.00	0.00	0.00	4.18
697	700	2.819019	TGTTGATCGGCACATTCATTGT	59.181	40.909	0.00	0.00	39.91	2.71
699	702	4.236935	GTTGATCGGCACATTCATTGTTT	58.763	39.130	0.00	0.00	36.00	2.83
720	723	2.047061	GGTCATGTATGCCTGTCCCTA	58.953	52.381	0.00	0.00	0.00	3.53
782	786	2.092646	TCCGGGTTCTTTGTCATATGGG	60.093	50.000	0.00	0.00	0.00	4.00
789	793	5.186198	GTTCTTTGTCATATGGGTGCTAGT	58.814	41.667	2.13	0.00	0.00	2.57
845	849	2.365901	CCCGGGCCAGGTAAGGTA	60.366	66.667	21.37	0.00	0.00	3.08
923	927	5.163405	GCTAGATTGGTGTGACTTAGGATCA	60.163	44.000	0.00	0.00	0.00	2.92
950	954	4.220821	TCCTGACACAAAGATAGACAGTCC	59.779	45.833	0.00	0.00	0.00	3.85
962	966	6.198639	AGATAGACAGTCCTCAACACCTAAT	58.801	40.000	0.00	0.00	0.00	1.73
963	967	4.543590	AGACAGTCCTCAACACCTAATG	57.456	45.455	0.00	0.00	0.00	1.90
981	985	6.815641	ACCTAATGCATATAAAGATCAGAGCG	59.184	38.462	0.00	0.00	0.00	5.03
1002	1006	5.006746	AGCGTAAAGATCGAAACAATCCATC	59.993	40.000	0.00	0.00	0.00	3.51
1031	1035	1.219124	CGTACAGCTGAGTGGGCAT	59.781	57.895	23.35	0.00	0.00	4.40
1040	1044	4.823442	CAGCTGAGTGGGCATATGATTTTA	59.177	41.667	8.42	0.00	0.00	1.52
1062	1066	2.967615	GATTCCTAGCACGCGCCC	60.968	66.667	5.73	0.00	39.83	6.13
1133	1137	5.422214	ACCTGATTATTTTCGACTGAGGT	57.578	39.130	0.00	0.00	0.00	3.85
1134	1138	5.805728	ACCTGATTATTTTCGACTGAGGTT	58.194	37.500	0.00	0.00	0.00	3.50
1206	1210	5.073428	TGCAACACATTAAAGACATACCCA	58.927	37.500	0.00	0.00	0.00	4.51
1332	1336	8.613060	AATTATATGCCTGTAGTGACATTCAG	57.387	34.615	0.00	0.00	34.24	3.02
1375	1379	6.794493	TGTCCTCCTTCCATCCATATTTCTAT	59.206	38.462	0.00	0.00	0.00	1.98
1377	1381	6.155221	TCCTCCTTCCATCCATATTTCTATCG	59.845	42.308	0.00	0.00	0.00	2.92
1675	1680	5.730296	TTTTCACTTTTGGACCAACTTGA	57.270	34.783	6.36	6.94	0.00	3.02
1681	1686	5.519927	CACTTTTGGACCAACTTGAAACATC	59.480	40.000	6.36	0.00	0.00	3.06
1762	1767	4.839121	ACCAATAATAACGAGCAAGTCCA	58.161	39.130	0.00	0.00	0.00	4.02
1821	1829	1.405526	GCGACCTCAAGTTATGCAGGA	60.406	52.381	0.00	0.00	33.26	3.86
1877	1891	3.530535	TGCAACGAAATGCTGCTATCTA	58.469	40.909	0.00	0.00	46.54	1.98
1921	1935	3.366883	CCTCTCACTTGTGTGCTAGACTC	60.367	52.174	0.00	0.00	43.49	3.36
1931	1945	2.820197	TGTGCTAGACTCGATTCAGTGT	59.180	45.455	5.50	0.00	0.00	3.55
1957	1971	5.865552	GCAGTTGTGATAATTGCAAGTGATT	59.134	36.000	10.14	0.00	42.78	2.57
2231	2249	2.426842	AGACATAGCAAAAGAGCCCC	57.573	50.000	0.00	0.00	34.23	5.80
2234	2252	1.031571	CATAGCAAAAGAGCCCCGCA	61.032	55.000	0.00	0.00	34.23	5.69
2360	2397	4.219288	GCACATCCCTTCAGATTTTTCTGT	59.781	41.667	3.15	0.00	38.75	3.41
2391	2428	7.281100	CACCCTTTCTTTTAGGACACTGATATC	59.719	40.741	0.00	0.00	34.56	1.63
2427	2482	4.199310	CCATCATTTCGTTGGGTATGAGT	58.801	43.478	0.00	0.00	31.64	3.41
2528	2583	1.146041	AGTGCGACCAGTTTGCTCA	59.854	52.632	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.672342	CAGCAAGCCAGCTTTGACTT	59.328	50.000	1.19	0.00	43.70	3.01
135	136	3.006940	ACTAGCGAGACTGAACTCTCTG	58.993	50.000	0.00	0.00	35.43	3.35
141	142	3.485546	CGGAACTACTAGCGAGACTGAAC	60.486	52.174	0.00	0.00	0.00	3.18
168	169	3.854286	AACAAGCTAAACGTCGAAGTG	57.146	42.857	4.34	0.00	0.00	3.16
194	195	0.872021	GAGGGCACAAGATCGTAGCG	60.872	60.000	0.00	0.00	0.00	4.26
245	246	6.126409	ACAGACAACTACAAATGAAAAGGGA	58.874	36.000	0.00	0.00	0.00	4.20
685	688	4.309099	ACATGACCAAACAATGAATGTGC	58.691	39.130	0.00	0.00	42.99	4.57
697	700	2.620367	GGGACAGGCATACATGACCAAA	60.620	50.000	0.00	0.00	36.08	3.28
699	702	0.546122	GGGACAGGCATACATGACCA	59.454	55.000	0.00	0.00	36.08	4.02
720	723	1.408266	CCCAAGGTGGCGCTAACTTAT	60.408	52.381	24.41	0.00	35.79	1.73
761	765	2.092646	CCCATATGACAAAGAACCCGGA	60.093	50.000	0.73	0.00	0.00	5.14
789	793	3.004419	GGCTCACGTATATGACTGTGCTA	59.996	47.826	0.00	0.00	34.56	3.49
845	849	1.480954	CACGGTATTCCTACAGGTGCT	59.519	52.381	0.00	0.00	36.34	4.40
854	858	1.515954	CCTCACGCACGGTATTCCT	59.484	57.895	0.00	0.00	0.00	3.36
923	927	3.515901	GTCTATCTTTGTGTCAGGACCCT	59.484	47.826	0.00	0.00	0.00	4.34
938	942	4.054359	AGGTGTTGAGGACTGTCTATCT	57.946	45.455	7.85	0.00	0.00	1.98
950	954	9.276590	TGATCTTTATATGCATTAGGTGTTGAG	57.723	33.333	3.54	0.00	0.00	3.02
962	966	7.433680	TCTTTACGCTCTGATCTTTATATGCA	58.566	34.615	0.00	0.00	0.00	3.96
963	967	7.875316	TCTTTACGCTCTGATCTTTATATGC	57.125	36.000	0.00	0.00	0.00	3.14
981	985	6.255887	ACGAGATGGATTGTTTCGATCTTTAC	59.744	38.462	0.00	0.00	46.37	2.01
1002	1006	1.443872	GCTGTACGGTCCACACGAG	60.444	63.158	3.10	0.00	34.93	4.18
1012	1016	2.125512	GCCCACTCAGCTGTACGG	60.126	66.667	14.67	11.89	0.00	4.02
1031	1035	8.300286	CGTGCTAGGAATCTCTCTAAAATCATA	58.700	37.037	0.00	0.00	0.00	2.15
1040	1044	0.665835	CGCGTGCTAGGAATCTCTCT	59.334	55.000	0.00	0.00	0.00	3.10
1119	1123	8.801882	TTTGGAATATAACCTCAGTCGAAAAT	57.198	30.769	0.00	0.00	0.00	1.82
1157	1161	2.107366	TCCAATCCGTGCATGAGACTA	58.893	47.619	7.72	0.00	0.00	2.59
1332	1336	9.091220	AGGAGGACACTTTATATATGAAGGTAC	57.909	37.037	18.48	14.12	0.00	3.34
1375	1379	4.370917	GTTCTTTGTGTTGTACTACCCGA	58.629	43.478	4.98	0.00	0.00	5.14
1377	1381	3.495753	CGGTTCTTTGTGTTGTACTACCC	59.504	47.826	4.98	0.00	0.00	3.69
1446	1450	7.239438	AGAAGGACGATAATAAGGGTGATAGA	58.761	38.462	0.00	0.00	0.00	1.98
1725	1730	0.251742	TTGGTTCCCATTGCTCCTGG	60.252	55.000	0.00	0.00	31.53	4.45
1745	1750	6.459670	TGTAGATGGACTTGCTCGTTATTA	57.540	37.500	0.00	0.00	0.00	0.98
1750	1755	3.430929	GGATTGTAGATGGACTTGCTCGT	60.431	47.826	0.00	0.00	0.00	4.18
1762	1767	5.374921	CCATCAGCTTCAAGGATTGTAGAT	58.625	41.667	0.93	0.00	45.03	1.98
1821	1829	1.274167	CTTGCAGGAACAATGGCATGT	59.726	47.619	0.00	0.00	35.98	3.21
1886	1900	2.022129	GAGAGGTCGTTGCGTGGTG	61.022	63.158	0.00	0.00	0.00	4.17
1921	1935	1.069703	CACAACTGCCACACTGAATCG	60.070	52.381	0.00	0.00	0.00	3.34
1931	1945	3.573538	ACTTGCAATTATCACAACTGCCA	59.426	39.130	0.00	0.00	31.92	4.92
1957	1971	5.065235	CCAATCCATCATGTACATGCAGTA	58.935	41.667	27.71	13.40	38.65	2.74
2043	2061	5.279106	CCCTCAATTGCTGAAAGTCAAATCA	60.279	40.000	0.00	0.00	34.59	2.57
2231	2249	6.578020	ATGTGATATTTTTCTTGCAATGCG	57.422	33.333	0.00	0.00	0.00	4.73
2234	2252	9.656040	TGCTAAATGTGATATTTTTCTTGCAAT	57.344	25.926	0.00	0.00	0.00	3.56
2336	2356	4.219070	CAGAAAAATCTGAAGGGATGTGCA	59.781	41.667	0.00	0.00	39.99	4.57
2360	2397	4.079253	GTCCTAAAAGAAAGGGTGCATGA	58.921	43.478	0.00	0.00	34.66	3.07
2391	2428	4.096003	ATGGGGGACGTTCGGCAG	62.096	66.667	0.00	0.00	0.00	4.85
2427	2482	2.445845	ATTCGGGCGGAGGGATCA	60.446	61.111	0.00	0.00	0.00	2.92
2456	2511	3.669686	CGGAGGGATCGCTCGTAT	58.330	61.111	27.65	0.96	0.00	3.06
2491	2546	0.543410	TGTTGGTTCGGGCTAGGAGA	60.543	55.000	0.00	0.00	0.00	3.71
2528	2583	0.324943	TAGCCAAGCCGAAGAAAGCT	59.675	50.000	0.00	0.00	42.40	3.74
2654	2711	9.905713	GCCATATATTCTATGGGTGATTTTCTA	57.094	33.333	12.04	0.00	43.52	2.10
2780	2838	8.999431	AGTTTTCACAGTATAATCGTGATTTGT	58.001	29.630	0.00	0.00	39.29	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.