AutoCloner

Multiple sequence alignment - TraesCS2B01G427200

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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	TraesCS2B01G427200	chr2B	100.000	4406	0	0	1	4406	614399951	614395546	0.000000e+00	8137.0
1	TraesCS2B01G427200	chr2B	99.532	1924	9	0	51	1974	614504859	614502936	0.000000e+00	3504.0
2	TraesCS2B01G427200	chr2B	99.466	1873	10	0	2534	4406	614502852	614500980	0.000000e+00	3404.0
3	TraesCS2B01G427200	chr2B	94.118	51	1	1	1	49	288025945	288025995	4.730000e-10	76.8
4	TraesCS2B01G427200	chr2A	94.203	3778	159	23	51	3778	666293990	666290223	0.000000e+00	5709.0
5	TraesCS2B01G427200	chr2A	83.791	364	37	8	3983	4326	666290230	666289869	4.250000e-85	326.0
6	TraesCS2B01G427200	chr2D	96.160	3177	104	10	492	3652	521410264	521413438	0.000000e+00	5175.0
7	TraesCS2B01G427200	chr2D	91.667	372	29	2	51	421	521409865	521410235	8.450000e-142	514.0
8	TraesCS2B01G427200	chr2D	86.179	369	24	3	3983	4329	521417865	521418228	1.500000e-99	374.0
9	TraesCS2B01G427200	chrUn	100.000	389	0	0	3936	4324	480197413	480197025	0.000000e+00	719.0
10	TraesCS2B01G427200	chrUn	95.833	48	2	0	1	48	55320203	55320156	1.310000e-10	78.7
11	TraesCS2B01G427200	chr6A	78.274	962	182	19	1132	2081	457020061	457019115	1.060000e-165	593.0
12	TraesCS2B01G427200	chr6B	78.112	964	181	20	1133	2081	504158258	504159206	6.350000e-163	584.0
13	TraesCS2B01G427200	chr6B	95.918	49	2	0	1	49	132510243	132510195	3.650000e-11	80.5
14	TraesCS2B01G427200	chr6D	77.859	962	186	19	1132	2081	319053016	319052070	4.940000e-159	571.0
15	TraesCS2B01G427200	chr1B	89.894	188	15	4	3801	3985	34204667	34204853	5.700000e-59	239.0
16	TraesCS2B01G427200	chr7D	94.366	71	4	0	3912	3982	84600499	84600569	4.660000e-20	110.0
17	TraesCS2B01G427200	chr7D	80.702	114	20	2	2676	2788	489114593	489114705	2.180000e-13	87.9
18	TraesCS2B01G427200	chr7B	80.702	114	20	2	2676	2788	517394238	517394350	2.180000e-13	87.9
19	TraesCS2B01G427200	chr7A	80.702	114	20	2	2676	2788	556299719	556299831	2.180000e-13	87.9
20	TraesCS2B01G427200	chr3B	97.917	48	1	0	1	48	273631866	273631819	2.820000e-12	84.2
21	TraesCS2B01G427200	chr4B	95.833	48	2	0	1	48	26727461	26727414	1.310000e-10	78.7
22	TraesCS2B01G427200	chr4A	95.833	48	2	0	1	48	695906224	695906271	1.310000e-10	78.7
23	TraesCS2B01G427200	chr4A	95.833	48	2	0	1	48	702876087	702876134	1.310000e-10	78.7
24	TraesCS2B01G427200	chr4A	95.833	48	2	0	1	48	732912493	732912446	1.310000e-10	78.7
25	TraesCS2B01G427200	chr4A	95.833	48	2	0	1	48	734025307	734025260	1.310000e-10	78.7

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	TraesCS2B01G427200	chr2B	614395546	614399951	4405	True	8137.0	8137	100.0000	1	4406	1	chr2B.!!$R1	4405
1	TraesCS2B01G427200	chr2B	614500980	614504859	3879	True	3454.0	3504	99.4990	51	4406	2	chr2B.!!$R2	4355
2	TraesCS2B01G427200	chr2A	666289869	666293990	4121	True	3017.5	5709	88.9970	51	4326	2	chr2A.!!$R1	4275
3	TraesCS2B01G427200	chr2D	521409865	521413438	3573	False	2844.5	5175	93.9135	51	3652	2	chr2D.!!$F2	3601
4	TraesCS2B01G427200	chr6A	457019115	457020061	946	True	593.0	593	78.2740	1132	2081	1	chr6A.!!$R1	949
5	TraesCS2B01G427200	chr6B	504158258	504159206	948	False	584.0	584	78.1120	1133	2081	1	chr6B.!!$F1	948
6	TraesCS2B01G427200	chr6D	319052070	319053016	946	True	571.0	571	77.8590	1132	2081	1	chr6D.!!$R1	949

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
20	21	0.036010	ATTGTCTCCTGGTGAAGCGG	60.036	55.000	0.00	0.00	0.00	5.52	F
34	35	0.326264	AAGCGGGATCATATGCCTCC	59.674	55.000	13.15	13.15	38.84	4.30	F
45	46	0.384309	TATGCCTCCACGTCTAAGCG	59.616	55.000	0.00	0.00	37.94	4.68	F
366	372	1.376037	GACTGCCCGGAGTTGAAGG	60.376	63.158	0.73	0.00	0.00	3.46	F
561	594	2.625737	CGGCATCTTGACTGATTGTCT	58.374	47.619	0.00	0.00	45.54	3.41	F
2385	2438	3.488569	GGCCCGGTGATCATCCCA	61.489	66.667	0.00	0.00	0.00	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1974	2027	2.365635	AGGGCAGCGGTGTATCCT	60.366	61.111	17.07	16.72	0.00	3.24	R
2302	2355	1.079888	CGACCATTTTGGCCTTGGC	60.080	57.895	3.32	2.49	42.67	4.52	R
2385	2438	3.728373	GGGATGACGTGGGGCCTT	61.728	66.667	0.84	0.00	0.00	4.35	R
2419	2472	0.179018	AGCTTCTGCCCGACTTTGTT	60.179	50.000	0.00	0.00	40.80	2.83	R
2449	2502	1.074752	GCTTCTTTCTCGGACTGCAG	58.925	55.000	13.48	13.48	0.00	4.41	R
3517	3571	5.019470	AGATCGCATGTCAATATAGAGGGA	58.981	41.667	0.00	0.00	0.00	4.20	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
19	20	2.672961	TATTGTCTCCTGGTGAAGCG	57.327	50.000	0.00	0.00	0.00	4.68
20	21	0.036010	ATTGTCTCCTGGTGAAGCGG	60.036	55.000	0.00	0.00	0.00	5.52
21	22	2.111999	TTGTCTCCTGGTGAAGCGGG	62.112	60.000	0.00	0.66	0.00	6.13
22	23	2.119611	TCTCCTGGTGAAGCGGGA	59.880	61.111	9.62	9.62	0.00	5.14
23	24	1.306141	TCTCCTGGTGAAGCGGGAT	60.306	57.895	10.39	0.00	0.00	3.85
24	25	1.144936	CTCCTGGTGAAGCGGGATC	59.855	63.158	10.39	0.00	0.00	3.36
25	26	1.612146	TCCTGGTGAAGCGGGATCA	60.612	57.895	5.96	0.00	0.00	2.92
26	27	0.982852	TCCTGGTGAAGCGGGATCAT	60.983	55.000	5.96	0.00	0.00	2.45
27	28	0.758734	CCTGGTGAAGCGGGATCATA	59.241	55.000	0.82	0.00	0.00	2.15
28	29	1.349026	CCTGGTGAAGCGGGATCATAT	59.651	52.381	0.82	0.00	0.00	1.78
29	30	2.420642	CTGGTGAAGCGGGATCATATG	58.579	52.381	0.00	0.00	0.00	1.78
30	31	1.160137	GGTGAAGCGGGATCATATGC	58.840	55.000	0.00	0.00	0.00	3.14
31	32	1.160137	GTGAAGCGGGATCATATGCC	58.840	55.000	0.00	0.00	37.42	4.40
32	33	1.059098	TGAAGCGGGATCATATGCCT	58.941	50.000	0.00	0.00	38.84	4.75
33	34	1.002430	TGAAGCGGGATCATATGCCTC	59.998	52.381	0.00	0.00	38.84	4.70
34	35	0.326264	AAGCGGGATCATATGCCTCC	59.674	55.000	13.15	13.15	38.84	4.30
35	36	0.837691	AGCGGGATCATATGCCTCCA	60.838	55.000	19.72	0.00	38.84	3.86
36	37	0.674895	GCGGGATCATATGCCTCCAC	60.675	60.000	19.72	11.19	38.84	4.02
37	38	0.390340	CGGGATCATATGCCTCCACG	60.390	60.000	19.72	16.82	38.84	4.94
38	39	0.687354	GGGATCATATGCCTCCACGT	59.313	55.000	19.72	0.00	37.84	4.49
39	40	1.338200	GGGATCATATGCCTCCACGTC	60.338	57.143	19.72	5.10	37.84	4.34
40	41	1.620819	GGATCATATGCCTCCACGTCT	59.379	52.381	15.51	0.00	0.00	4.18
41	42	2.826128	GGATCATATGCCTCCACGTCTA	59.174	50.000	15.51	0.00	0.00	2.59
42	43	3.258372	GGATCATATGCCTCCACGTCTAA	59.742	47.826	15.51	0.00	0.00	2.10
43	44	4.489810	GATCATATGCCTCCACGTCTAAG	58.510	47.826	0.00	0.00	0.00	2.18
44	45	2.035961	TCATATGCCTCCACGTCTAAGC	59.964	50.000	0.00	0.00	0.00	3.09
45	46	0.384309	TATGCCTCCACGTCTAAGCG	59.616	55.000	0.00	0.00	37.94	4.68
46	47	2.202756	GCCTCCACGTCTAAGCGG	60.203	66.667	0.00	0.00	35.98	5.52
47	48	2.494918	CCTCCACGTCTAAGCGGG	59.505	66.667	0.00	0.00	35.98	6.13
48	49	2.050350	CCTCCACGTCTAAGCGGGA	61.050	63.158	0.00	0.00	37.48	5.14
49	50	1.392710	CCTCCACGTCTAAGCGGGAT	61.393	60.000	0.00	0.00	37.48	3.85
149	155	3.332919	CCGATCCTGGCATTATCAAGAG	58.667	50.000	9.16	0.00	0.00	2.85
248	254	2.290387	TGGTGCATGGTGTAAACCGTAT	60.290	45.455	0.00	0.00	33.41	3.06
363	369	2.525629	TGGACTGCCCGGAGTTGA	60.526	61.111	0.73	0.00	37.93	3.18
366	372	1.376037	GACTGCCCGGAGTTGAAGG	60.376	63.158	0.73	0.00	0.00	3.46
561	594	2.625737	CGGCATCTTGACTGATTGTCT	58.374	47.619	0.00	0.00	45.54	3.41
2385	2438	3.488569	GGCCCGGTGATCATCCCA	61.489	66.667	0.00	0.00	0.00	4.37
2449	2502	0.746204	GCAGAAGCTCAAGGCCTACC	60.746	60.000	5.16	0.00	43.05	3.18
3121	3174	2.962786	CGGTGACAAACGTCGGCA	60.963	61.111	0.00	0.00	36.09	5.69
3337	3390	0.036732	GATCCTCATATTGCCCGGCA	59.963	55.000	8.43	8.43	36.47	5.69
3517	3571	0.686789	TGTATGTGTGGCTGCAGTCT	59.313	50.000	20.86	0.33	0.00	3.24
3876	3932	6.717084	CCCCTCAATTAATCTTCACTAATCCC	59.283	42.308	0.00	0.00	0.00	3.85
3934	3990	6.813152	CACCAATTAAATGTTCCCATCTCAAC	59.187	38.462	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.207089	CCGCTTCACCAGGAGACAATA	59.793	52.381	0.00	0.00	0.00	1.90
1	2	0.036010	CCGCTTCACCAGGAGACAAT	60.036	55.000	0.00	0.00	0.00	2.71
2	3	1.371183	CCGCTTCACCAGGAGACAA	59.629	57.895	0.00	0.00	0.00	3.18
3	4	2.583441	CCCGCTTCACCAGGAGACA	61.583	63.158	0.00	0.00	0.00	3.41
4	5	1.617947	ATCCCGCTTCACCAGGAGAC	61.618	60.000	0.00	0.00	0.00	3.36
5	6	1.306141	ATCCCGCTTCACCAGGAGA	60.306	57.895	0.00	0.00	0.00	3.71
6	7	1.144936	GATCCCGCTTCACCAGGAG	59.855	63.158	0.00	0.00	0.00	3.69
7	8	0.982852	ATGATCCCGCTTCACCAGGA	60.983	55.000	0.00	0.00	0.00	3.86
8	9	0.758734	TATGATCCCGCTTCACCAGG	59.241	55.000	0.00	0.00	0.00	4.45
9	10	2.420642	CATATGATCCCGCTTCACCAG	58.579	52.381	0.00	0.00	0.00	4.00
10	11	1.543208	GCATATGATCCCGCTTCACCA	60.543	52.381	6.97	0.00	0.00	4.17
11	12	1.160137	GCATATGATCCCGCTTCACC	58.840	55.000	6.97	0.00	0.00	4.02
12	13	1.160137	GGCATATGATCCCGCTTCAC	58.840	55.000	6.97	0.00	0.00	3.18
13	14	1.002430	GAGGCATATGATCCCGCTTCA	59.998	52.381	6.97	0.00	31.39	3.02
14	15	1.677217	GGAGGCATATGATCCCGCTTC	60.677	57.143	6.97	0.00	0.00	3.86
15	16	0.326264	GGAGGCATATGATCCCGCTT	59.674	55.000	6.97	0.00	0.00	4.68
16	17	0.837691	TGGAGGCATATGATCCCGCT	60.838	55.000	19.34	0.00	31.73	5.52
17	18	0.674895	GTGGAGGCATATGATCCCGC	60.675	60.000	19.34	12.74	31.73	6.13
18	19	0.390340	CGTGGAGGCATATGATCCCG	60.390	60.000	19.34	17.67	31.73	5.14
19	20	0.687354	ACGTGGAGGCATATGATCCC	59.313	55.000	19.34	11.20	31.73	3.85
20	21	1.620819	AGACGTGGAGGCATATGATCC	59.379	52.381	16.66	16.66	0.00	3.36
21	22	4.489810	CTTAGACGTGGAGGCATATGATC	58.510	47.826	6.97	3.32	0.00	2.92
22	23	3.306364	GCTTAGACGTGGAGGCATATGAT	60.306	47.826	6.97	0.00	0.00	2.45
23	24	2.035961	GCTTAGACGTGGAGGCATATGA	59.964	50.000	6.97	0.00	0.00	2.15
24	25	2.408050	GCTTAGACGTGGAGGCATATG	58.592	52.381	0.00	0.00	0.00	1.78
25	26	1.000163	CGCTTAGACGTGGAGGCATAT	60.000	52.381	0.00	0.00	0.00	1.78
26	27	0.384309	CGCTTAGACGTGGAGGCATA	59.616	55.000	0.00	0.00	0.00	3.14
27	28	1.141881	CGCTTAGACGTGGAGGCAT	59.858	57.895	0.00	0.00	0.00	4.40
28	29	2.571757	CGCTTAGACGTGGAGGCA	59.428	61.111	0.00	0.00	0.00	4.75
29	30	2.202756	CCGCTTAGACGTGGAGGC	60.203	66.667	0.00	0.00	36.68	4.70
30	31	1.392710	ATCCCGCTTAGACGTGGAGG	61.393	60.000	0.00	0.00	36.36	4.30
31	32	0.030908	GATCCCGCTTAGACGTGGAG	59.969	60.000	0.00	0.00	36.36	3.86
32	33	0.681887	TGATCCCGCTTAGACGTGGA	60.682	55.000	0.00	0.00	36.68	4.02
33	34	0.389391	ATGATCCCGCTTAGACGTGG	59.611	55.000	0.00	0.00	0.00	4.94
34	35	3.577649	ATATGATCCCGCTTAGACGTG	57.422	47.619	0.00	0.00	0.00	4.49
35	36	3.128938	GCTATATGATCCCGCTTAGACGT	59.871	47.826	0.00	0.00	0.00	4.34
36	37	3.696898	GCTATATGATCCCGCTTAGACG	58.303	50.000	0.00	0.00	0.00	4.18
37	38	3.128938	ACGCTATATGATCCCGCTTAGAC	59.871	47.826	0.00	0.00	0.00	2.59
38	39	3.353557	ACGCTATATGATCCCGCTTAGA	58.646	45.455	0.00	0.00	0.00	2.10
39	40	3.784701	ACGCTATATGATCCCGCTTAG	57.215	47.619	0.00	0.00	0.00	2.18
40	41	4.460034	TGTTACGCTATATGATCCCGCTTA	59.540	41.667	0.00	0.00	0.00	3.09
41	42	3.257375	TGTTACGCTATATGATCCCGCTT	59.743	43.478	0.00	0.00	0.00	4.68
42	43	2.823747	TGTTACGCTATATGATCCCGCT	59.176	45.455	0.00	0.00	0.00	5.52
43	44	3.179830	CTGTTACGCTATATGATCCCGC	58.820	50.000	0.00	0.00	0.00	6.13
44	45	4.166523	CACTGTTACGCTATATGATCCCG	58.833	47.826	0.00	0.00	0.00	5.14
45	46	5.135508	ACACTGTTACGCTATATGATCCC	57.864	43.478	0.00	0.00	0.00	3.85
46	47	8.583810	TTTTACACTGTTACGCTATATGATCC	57.416	34.615	0.00	0.00	0.00	3.36
48	49	9.758651	TCATTTTACACTGTTACGCTATATGAT	57.241	29.630	0.00	0.00	0.00	2.45
49	50	9.027129	GTCATTTTACACTGTTACGCTATATGA	57.973	33.333	0.00	0.00	0.00	2.15
248	254	2.183679	GGTGGCCCAAAAATATCCACA	58.816	47.619	0.00	0.00	46.62	4.17
363	369	1.602377	GCGACTGTTACAAAGTGCCTT	59.398	47.619	0.00	0.00	0.00	4.35
366	372	0.941542	TGGCGACTGTTACAAAGTGC	59.058	50.000	0.00	0.00	0.00	4.40
561	594	6.946340	TCAGACAGCTTGATTTCAGGTATTA	58.054	36.000	0.00	0.00	0.00	0.98
1974	2027	2.365635	AGGGCAGCGGTGTATCCT	60.366	61.111	17.07	16.72	0.00	3.24
2302	2355	1.079888	CGACCATTTTGGCCTTGGC	60.080	57.895	3.32	2.49	42.67	4.52
2385	2438	3.728373	GGGATGACGTGGGGCCTT	61.728	66.667	0.84	0.00	0.00	4.35
2398	2451	2.047274	CACTTGCACCGTCGGGAT	60.047	61.111	17.28	0.00	36.97	3.85
2419	2472	0.179018	AGCTTCTGCCCGACTTTGTT	60.179	50.000	0.00	0.00	40.80	2.83
2449	2502	1.074752	GCTTCTTTCTCGGACTGCAG	58.925	55.000	13.48	13.48	0.00	4.41
3121	3174	2.511600	GTACGCCGAGCTTGCCAT	60.512	61.111	0.00	0.00	0.00	4.40
3133	3186	0.454600	TCAACCTCCATCTCGTACGC	59.545	55.000	11.24	0.00	0.00	4.42
3517	3571	5.019470	AGATCGCATGTCAATATAGAGGGA	58.981	41.667	0.00	0.00	0.00	4.20
3934	3990	6.737254	ATTCTACGGAATTGTTGTTACAGG	57.263	37.500	0.00	0.00	38.89	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.