AutoCloner

Multiple sequence alignment - TraesCS5B01G122800

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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	TraesCS5B01G122800	chr5B	100.000	3492	0	0	1	3492	221162692	221159201	0.000000e+00	6449.0
1	TraesCS5B01G122800	chr3B	94.616	3473	161	18	38	3492	107250173	107253637	0.000000e+00	5354.0
2	TraesCS5B01G122800	chr3B	93.598	3452	194	22	57	3492	247151094	247154534	0.000000e+00	5125.0
3	TraesCS5B01G122800	chr7B	94.350	3469	170	19	38	3490	33969125	33972583	0.000000e+00	5297.0
4	TraesCS5B01G122800	chr1B	94.055	3448	183	17	57	3492	274298011	274301448	0.000000e+00	5212.0
5	TraesCS5B01G122800	chr1B	93.770	3451	186	21	57	3491	555898133	555894696	0.000000e+00	5155.0
6	TraesCS5B01G122800	chr1B	93.696	3458	185	23	57	3491	256486659	256483212	0.000000e+00	5147.0
7	TraesCS5B01G122800	chr4B	93.799	3451	188	17	57	3492	425954054	425950615	0.000000e+00	5164.0
8	TraesCS5B01G122800	chr4B	93.763	3431	192	16	57	3473	470135780	470139202	0.000000e+00	5131.0
9	TraesCS5B01G122800	chr4B	97.500	40	1	0	4	43	88314066	88314105	6.250000e-08	69.4
10	TraesCS5B01G122800	chr4B	100.000	37	0	0	3	39	163458805	163458841	6.250000e-08	69.4
11	TraesCS5B01G122800	chr6B	93.679	3433	190	21	57	3473	589452815	589456236	0.000000e+00	5112.0
12	TraesCS5B01G122800	chr1D	100.000	39	0	0	4	42	70373426	70373464	4.830000e-09	73.1
13	TraesCS5B01G122800	chr1D	97.500	40	1	0	4	43	138389156	138389195	6.250000e-08	69.4
14	TraesCS5B01G122800	chr1A	100.000	39	0	0	4	42	97073821	97073783	4.830000e-09	73.1
15	TraesCS5B01G122800	chr5A	97.500	40	1	0	3	42	100266733	100266694	6.250000e-08	69.4
16	TraesCS5B01G122800	chr3D	97.500	40	1	0	4	43	219735664	219735703	6.250000e-08	69.4
17	TraesCS5B01G122800	chr2D	97.500	40	1	0	4	43	198987647	198987608	6.250000e-08	69.4
18	TraesCS5B01G122800	chr3A	93.478	46	1	2	4	47	603119906	603119861	2.250000e-07	67.6

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	TraesCS5B01G122800	chr5B	221159201	221162692	3491	True	6449	6449	100.000	1	3492	1	chr5B.!!$R1	3491
1	TraesCS5B01G122800	chr3B	107250173	107253637	3464	False	5354	5354	94.616	38	3492	1	chr3B.!!$F1	3454
2	TraesCS5B01G122800	chr3B	247151094	247154534	3440	False	5125	5125	93.598	57	3492	1	chr3B.!!$F2	3435
3	TraesCS5B01G122800	chr7B	33969125	33972583	3458	False	5297	5297	94.350	38	3490	1	chr7B.!!$F1	3452
4	TraesCS5B01G122800	chr1B	274298011	274301448	3437	False	5212	5212	94.055	57	3492	1	chr1B.!!$F1	3435
5	TraesCS5B01G122800	chr1B	555894696	555898133	3437	True	5155	5155	93.770	57	3491	1	chr1B.!!$R2	3434
6	TraesCS5B01G122800	chr1B	256483212	256486659	3447	True	5147	5147	93.696	57	3491	1	chr1B.!!$R1	3434
7	TraesCS5B01G122800	chr4B	425950615	425954054	3439	True	5164	5164	93.799	57	3492	1	chr4B.!!$R1	3435
8	TraesCS5B01G122800	chr4B	470135780	470139202	3422	False	5131	5131	93.763	57	3473	1	chr4B.!!$F3	3416
9	TraesCS5B01G122800	chr6B	589452815	589456236	3421	False	5112	5112	93.679	57	3473	1	chr6B.!!$F1	3416

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	Hairpin	End Stability	Orientation
238	242	0.036294	TGTCCACACCACAACGAACA	60.036	50.000	0.00	0.00	3.18	F
395	404	0.604243	ACCCGTGCGCTGTATGAAAA	60.604	50.000	9.73	0.00	2.29	F
525	536	0.823356	TTGAGCAACAACTCCCAGGC	60.823	55.000	0.00	35.72	4.85	F
526	537	1.228245	GAGCAACAACTCCCAGGCA	60.228	57.895	0.00	0.00	4.75	F
527	538	1.518903	GAGCAACAACTCCCAGGCAC	61.519	60.000	0.00	0.00	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2124	2160	0.606401	CCGCTTGTCACCTCCAATGT	60.606	55.00	0.00	2.71	R
2300	2336	0.258774	AGTTTGTGGTCTGCCCTGTT	59.741	50.00	0.00	3.16	R
2383	2419	5.637810	GTCGATTGTCTTCCATGACTTGTAA	59.362	40.00	37.79	2.41	R
2418	2454	6.489603	TGCTCTTTTGAAATATCCCAACCTA	58.510	36.00	0.00	3.08	R
2532	2570	9.520204	CAAACTACAAATCTGAAACAACAAGAT	57.480	29.63	0.00	2.40	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
35	36	9.606631	AATCTATAAGAAATCAGTGTCAACCTC	57.393	33.333	0.00	0.00	0.00	3.85
36	37	8.367660	TCTATAAGAAATCAGTGTCAACCTCT	57.632	34.615	0.00	0.00	0.00	3.69
158	162	7.639113	TCTGACAAGTTCAACCACTAAAATT	57.361	32.000	0.00	0.00	32.21	1.82
238	242	0.036294	TGTCCACACCACAACGAACA	60.036	50.000	0.00	0.00	0.00	3.18
275	280	2.704198	TCAAACCCCCACCCCCAA	60.704	61.111	0.00	0.00	0.00	4.12
278	283	4.895675	AACCCCCACCCCCAACCT	62.896	66.667	0.00	0.00	0.00	3.50
281	286	2.622447	CCCCCACCCCCAACCTAAG	61.622	68.421	0.00	0.00	0.00	2.18
282	287	1.855451	CCCCACCCCCAACCTAAGT	60.855	63.158	0.00	0.00	0.00	2.24
283	288	1.440362	CCCCACCCCCAACCTAAGTT	61.440	60.000	0.00	0.00	36.33	2.66
285	290	1.927371	CCCACCCCCAACCTAAGTTAT	59.073	52.381	0.00	0.00	33.27	1.89
330	339	7.724305	ACAAACGACATCAGTACTAAAACAT	57.276	32.000	0.00	0.00	0.00	2.71
395	404	0.604243	ACCCGTGCGCTGTATGAAAA	60.604	50.000	9.73	0.00	0.00	2.29
422	431	8.500753	ACAATTCAGTTCACACAGTACTAAAA	57.499	30.769	0.00	0.00	0.00	1.52
455	466	9.677567	TGCACTAAAATGAGAATACAAAAACTC	57.322	29.630	0.00	0.00	0.00	3.01
525	536	0.823356	TTGAGCAACAACTCCCAGGC	60.823	55.000	0.00	0.00	35.72	4.85
526	537	1.228245	GAGCAACAACTCCCAGGCA	60.228	57.895	0.00	0.00	0.00	4.75
527	538	1.518903	GAGCAACAACTCCCAGGCAC	61.519	60.000	0.00	0.00	0.00	5.01
613	629	3.253188	CCACACGGAAAAACATCACAGAT	59.747	43.478	0.00	0.00	0.00	2.90
614	630	4.466828	CACACGGAAAAACATCACAGATC	58.533	43.478	0.00	0.00	0.00	2.75
719	735	4.214119	GCTTGACAAGACTAATCAGTGCAA	59.786	41.667	19.51	0.00	34.21	4.08
836	854	1.829533	ACGACCACTACACCCACGT	60.830	57.895	0.00	0.00	0.00	4.49
1800	1821	8.000780	AGAAAACTAAACTTGAATCAAGCAGT	57.999	30.769	21.69	18.05	44.43	4.40
1862	1883	2.796593	GTGAAGCATTTGGTGAAGCAAC	59.203	45.455	0.00	0.00	0.00	4.17
1952	1974	5.823209	TTCTGAACTACATTCATGCATGG	57.177	39.130	25.97	12.93	46.37	3.66
2117	2153	6.206634	GGAGGAGAAATTGTACACATTTGTCA	59.793	38.462	24.67	3.56	37.15	3.58
2124	2160	8.994429	AAATTGTACACATTTGTCAGTTTCAA	57.006	26.923	12.33	0.00	37.15	2.69
2300	2336	4.186926	CGAAGGCATGAAGAAGAAGATGA	58.813	43.478	0.00	0.00	0.00	2.92
2532	2570	2.297880	TCGCGCTTATGCCTATCCTTAA	59.702	45.455	5.56	0.00	35.36	1.85
2589	2627	3.343617	TGTTGAACCAGCTACCTTATGC	58.656	45.455	0.00	0.00	0.00	3.14
2758	2796	3.338249	GCAGCACTAGTCATGGAGAAAA	58.662	45.455	0.00	0.00	0.00	2.29
2848	2893	2.327081	TCGACGCTCAGTACAACTTC	57.673	50.000	0.00	0.00	0.00	3.01
2872	2917	5.851703	CGACATGAACGGTAGTACTATCATG	59.148	44.000	27.51	27.51	45.89	3.07
2935	2984	2.341846	AAGTTTCAGCCGAGGACAAA	57.658	45.000	0.00	0.00	0.00	2.83
2957	3006	5.470845	ACATTCAGTACTAAAAGCATCGC	57.529	39.130	0.00	0.00	0.00	4.58
3004	3053	1.873591	AGTACTGCAACAGGAAAAGCG	59.126	47.619	0.00	0.00	35.51	4.68
3081	3131	3.430895	GGTACAGTTGAACACATGGTACG	59.569	47.826	0.00	0.00	33.65	3.67
3099	3149	9.650371	CATGGTACGTTCATTCTACAAAATATG	57.350	33.333	0.00	0.00	0.00	1.78
3131	3181	2.079925	GAAGCTTCAGTTCGCATTCCT	58.920	47.619	21.67	0.00	0.00	3.36
3145	3195	4.759693	TCGCATTCCTTAAAACAGTGACAT	59.240	37.500	0.00	0.00	0.00	3.06
3340	3391	3.317149	ACACAACAGAAGACGTACTAGCA	59.683	43.478	0.00	0.00	0.00	3.49
3405	3457	7.661437	AGCACAATTGAAATCTCAGTACAACTA	59.339	33.333	13.59	0.00	31.69	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	9.606631	GAGGTTGACACTGATTTCTTATAGATT	57.393	33.333	0.00	0.00	0.00	2.40
10	11	8.986991	AGAGGTTGACACTGATTTCTTATAGAT	58.013	33.333	0.00	0.00	0.00	1.98
11	12	8.367660	AGAGGTTGACACTGATTTCTTATAGA	57.632	34.615	0.00	0.00	0.00	1.98
12	13	7.433719	CGAGAGGTTGACACTGATTTCTTATAG	59.566	40.741	0.00	0.00	0.00	1.31
13	14	7.122204	TCGAGAGGTTGACACTGATTTCTTATA	59.878	37.037	0.00	0.00	0.00	0.98
14	15	6.071334	TCGAGAGGTTGACACTGATTTCTTAT	60.071	38.462	0.00	0.00	0.00	1.73
15	16	5.243060	TCGAGAGGTTGACACTGATTTCTTA	59.757	40.000	0.00	0.00	0.00	2.10
16	17	4.039245	TCGAGAGGTTGACACTGATTTCTT	59.961	41.667	0.00	0.00	0.00	2.52
17	18	3.574396	TCGAGAGGTTGACACTGATTTCT	59.426	43.478	0.00	0.00	0.00	2.52
18	19	3.914312	TCGAGAGGTTGACACTGATTTC	58.086	45.455	0.00	0.00	0.00	2.17
19	20	4.336889	TTCGAGAGGTTGACACTGATTT	57.663	40.909	0.00	0.00	0.00	2.17
20	21	4.543590	ATTCGAGAGGTTGACACTGATT	57.456	40.909	0.00	0.00	0.00	2.57
21	22	4.543590	AATTCGAGAGGTTGACACTGAT	57.456	40.909	0.00	0.00	0.00	2.90
22	23	5.462530	TTAATTCGAGAGGTTGACACTGA	57.537	39.130	0.00	0.00	0.00	3.41
23	24	6.539649	TTTTAATTCGAGAGGTTGACACTG	57.460	37.500	0.00	0.00	0.00	3.66
24	25	9.449719	AATATTTTAATTCGAGAGGTTGACACT	57.550	29.630	0.00	0.00	0.00	3.55
55	56	8.897872	TTTAGAGTTTTAGTAGGTGAACTTGG	57.102	34.615	0.00	0.00	32.85	3.61
128	129	7.264373	AGTGGTTGAACTTGTCAGATTTTAG	57.736	36.000	0.00	0.00	37.61	1.85
238	242	8.674607	GGTTTGAGATTATTTTACGACCAGATT	58.325	33.333	0.00	0.00	0.00	2.40
303	311	9.911138	TGTTTTAGTACTGATGTCGTTTGTATA	57.089	29.630	5.39	0.00	0.00	1.47
309	317	6.590292	CCTGATGTTTTAGTACTGATGTCGTT	59.410	38.462	5.39	0.00	0.00	3.85
330	339	0.252421	AGTGGCCTGACTGATCCTGA	60.252	55.000	3.32	0.00	0.00	3.86
395	404	9.772973	TTTAGTACTGTGTGAACTGAATTGTAT	57.227	29.630	5.39	0.00	0.00	2.29
422	431	9.448438	TGTATTCTCATTTTAGTGCACTTATGT	57.552	29.630	27.06	12.06	0.00	2.29
585	600	4.822350	TGATGTTTTTCCGTGTGGATGTTA	59.178	37.500	0.00	0.00	45.91	2.41
613	629	3.615592	GCACTGTTTAGGTGACGTATGGA	60.616	47.826	0.00	0.00	36.89	3.41
614	630	2.671396	GCACTGTTTAGGTGACGTATGG	59.329	50.000	0.00	0.00	36.89	2.74
855	873	2.278989	CGTCGACGGTGGTGTGTT	60.279	61.111	29.70	0.00	35.37	3.32
1091	1110	1.202440	TGAGCGTTTTGGTGTACTCGT	60.202	47.619	0.00	0.00	0.00	4.18
1255	1274	4.543590	TCTGTGGAGGTTCTTCTTCATC	57.456	45.455	0.00	0.00	0.00	2.92
1257	1276	4.277515	CATCTGTGGAGGTTCTTCTTCA	57.722	45.455	0.00	0.00	0.00	3.02
1408	1427	6.833933	AGTTCATCTAGTTGGGAAACAAGTTT	59.166	34.615	0.00	0.00	42.58	2.66
1800	1821	9.797642	ATTTTACCAGAGTCAATGATATATGCA	57.202	29.630	0.00	0.00	0.00	3.96
2117	2153	3.897239	TGTCACCTCCAATGTTGAAACT	58.103	40.909	0.00	0.00	0.00	2.66
2124	2160	0.606401	CCGCTTGTCACCTCCAATGT	60.606	55.000	0.00	0.00	0.00	2.71
2149	2185	5.047566	TGATTTCCAAACCAGACTTCTCA	57.952	39.130	0.00	0.00	0.00	3.27
2224	2260	3.677976	CGGCCAAGGAGTCGTAGTATTTT	60.678	47.826	2.24	0.00	0.00	1.82
2300	2336	0.258774	AGTTTGTGGTCTGCCCTGTT	59.741	50.000	0.00	0.00	0.00	3.16
2383	2419	5.637810	GTCGATTGTCTTCCATGACTTGTAA	59.362	40.000	0.00	0.00	37.79	2.41
2418	2454	6.489603	TGCTCTTTTGAAATATCCCAACCTA	58.510	36.000	0.00	0.00	0.00	3.08
2532	2570	9.520204	CAAACTACAAATCTGAAACAACAAGAT	57.480	29.630	0.00	0.00	0.00	2.40
2589	2627	4.133820	TGTTCAAACCCTGACACACATAG	58.866	43.478	0.00	0.00	32.21	2.23
2848	2893	5.413969	TGATAGTACTACCGTTCATGTCG	57.586	43.478	4.31	0.00	0.00	4.35
2935	2984	4.032900	CGCGATGCTTTTAGTACTGAATGT	59.967	41.667	0.00	0.00	0.00	2.71
2969	3018	9.332502	TGTTGCAGTACTTAGTGAATTTCTAAA	57.667	29.630	0.00	0.00	0.00	1.85
3004	3053	5.930569	AGGAAATACGTACTGGTGTTTCTTC	59.069	40.000	16.67	6.96	43.41	2.87
3099	3149	3.823304	ACTGAAGCTTCCTGTTCCATTTC	59.177	43.478	23.42	0.00	0.00	2.17
3103	3153	2.806745	CGAACTGAAGCTTCCTGTTCCA	60.807	50.000	32.87	15.39	36.85	3.53
3109	3159	2.079925	GAATGCGAACTGAAGCTTCCT	58.920	47.619	23.42	8.20	0.00	3.36
3296	3347	8.093927	TGTGTTTCTTGTGATTTTTCTCCTTTT	58.906	29.630	0.00	0.00	0.00	2.27
3405	3457	7.985184	TCATCATAGCACTTACCGAATAAACTT	59.015	33.333	0.00	0.00	0.00	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.