AutoCloner

Multiple sequence alignment - TraesCS3B01G234700

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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	TraesCS3B01G234700	chr3B	100.000	5493	0	0	1	5493	367447820	367453312	0.000000e+00	10144.0
1	TraesCS3B01G234700	chr3B	88.337	463	43	5	4922	5383	331935658	331935206	3.740000e-151	545.0
2	TraesCS3B01G234700	chr3B	84.940	166	19	6	4758	4920	367454288	367454126	4.400000e-36	163.0
3	TraesCS3B01G234700	chr3D	94.141	2014	61	12	838	2810	274627927	274629924	0.000000e+00	3013.0
4	TraesCS3B01G234700	chr3D	93.992	2014	63	13	838	2810	274415893	274417889	0.000000e+00	2996.0
5	TraesCS3B01G234700	chr3D	96.965	1779	36	6	2807	4567	274417921	274419699	0.000000e+00	2970.0
6	TraesCS3B01G234700	chr3D	96.907	1778	38	7	2807	4567	274629956	274631733	0.000000e+00	2963.0
7	TraesCS3B01G234700	chr3D	89.806	206	6	4	4568	4761	274419662	274419864	3.290000e-62	250.0
8	TraesCS3B01G234700	chr3D	89.806	206	6	4	4568	4761	274631696	274631898	3.290000e-62	250.0
9	TraesCS3B01G234700	chr3A	92.805	1904	54	33	948	2810	365360595	365362456	0.000000e+00	2680.0
10	TraesCS3B01G234700	chr3A	96.741	583	15	2	3989	4567	365363937	365364519	0.000000e+00	968.0
11	TraesCS3B01G234700	chr3A	96.041	581	19	1	3410	3990	365363202	365363778	0.000000e+00	942.0
12	TraesCS3B01G234700	chr3A	94.884	606	15	2	2807	3411	365362488	365363078	0.000000e+00	933.0
13	TraesCS3B01G234700	chr3A	95.890	146	6	0	4616	4761	365364830	365364975	2.560000e-58	237.0
14	TraesCS3B01G234700	chrUn	97.398	1422	22	5	3161	4567	323138550	323137129	0.000000e+00	2407.0
15	TraesCS3B01G234700	chrUn	89.806	206	6	4	4568	4761	323137166	323136964	3.290000e-62	250.0
16	TraesCS3B01G234700	chr4A	96.638	803	24	2	1	801	5408431	5407630	0.000000e+00	1330.0
17	TraesCS3B01G234700	chr4A	86.147	462	52	6	4923	5383	116847284	116847734	6.400000e-134	488.0
18	TraesCS3B01G234700	chr6B	96.250	800	27	3	1	797	626212582	626213381	0.000000e+00	1308.0
19	TraesCS3B01G234700	chr6A	96.020	804	30	1	1	802	45759739	45758936	0.000000e+00	1306.0
20	TraesCS3B01G234700	chr7A	95.906	806	29	3	1	803	129870703	129869899	0.000000e+00	1303.0
21	TraesCS3B01G234700	chr5A	96.115	798	26	4	4	799	573654113	573653319	0.000000e+00	1297.0
22	TraesCS3B01G234700	chr5A	95.766	803	32	1	1	801	680883279	680884081	0.000000e+00	1293.0
23	TraesCS3B01G234700	chr5A	95.326	813	34	3	1	810	391987501	391988312	0.000000e+00	1288.0
24	TraesCS3B01G234700	chr2B	95.771	804	32	1	1	802	726124223	726125026	0.000000e+00	1295.0
25	TraesCS3B01G234700	chr1A	95.545	808	32	3	1	806	499618998	499618193	0.000000e+00	1290.0
26	TraesCS3B01G234700	chr4B	88.793	464	45	4	4922	5384	2014478	2014021	3.720000e-156	562.0
27	TraesCS3B01G234700	chr4B	88.553	463	46	4	4922	5383	2014666	2014210	6.220000e-154	555.0
28	TraesCS3B01G234700	chr4B	86.638	464	55	4	4921	5383	579705918	579706375	1.770000e-139	507.0
29	TraesCS3B01G234700	chr1B	87.473	471	46	8	4922	5385	485801547	485801083	1.050000e-146	531.0
30	TraesCS3B01G234700	chr1B	86.207	464	51	9	4922	5381	485801732	485801278	1.780000e-134	490.0
31	TraesCS3B01G234700	chr1B	91.824	159	10	2	4763	4920	606478000	606478156	9.260000e-53	219.0
32	TraesCS3B01G234700	chr1B	89.313	131	12	2	4771	4900	606479025	606478896	4.400000e-36	163.0
33	TraesCS3B01G234700	chr1B	89.000	100	6	2	5399	5493	606478196	606478295	9.670000e-23	119.0
34	TraesCS3B01G234700	chr1D	86.417	427	51	4	4922	5347	62799388	62799808	1.390000e-125	460.0
35	TraesCS3B01G234700	chr1D	79.851	134	13	7	4753	4884	467134990	467135111	9.800000e-13	86.1
36	TraesCS3B01G234700	chr7D	85.880	432	55	3	4953	5384	630506930	630506505	6.490000e-124	455.0
37	TraesCS3B01G234700	chr5B	84.663	163	21	4	4759	4920	556140240	556140399	5.700000e-35	159.0

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	TraesCS3B01G234700	chr3B	367447820	367453312	5492	False	10144.000000	10144	100.000000	1	5493	1	chr3B.!!$F1	5492
1	TraesCS3B01G234700	chr3D	274627927	274631898	3971	False	2075.333333	3013	93.618000	838	4761	3	chr3D.!!$F2	3923
2	TraesCS3B01G234700	chr3D	274415893	274419864	3971	False	2072.000000	2996	93.587667	838	4761	3	chr3D.!!$F1	3923
3	TraesCS3B01G234700	chr3A	365360595	365364975	4380	False	1152.000000	2680	95.272200	948	4761	5	chr3A.!!$F1	3813
4	TraesCS3B01G234700	chrUn	323136964	323138550	1586	True	1328.500000	2407	93.602000	3161	4761	2	chrUn.!!$R1	1600
5	TraesCS3B01G234700	chr4A	5407630	5408431	801	True	1330.000000	1330	96.638000	1	801	1	chr4A.!!$R1	800
6	TraesCS3B01G234700	chr6B	626212582	626213381	799	False	1308.000000	1308	96.250000	1	797	1	chr6B.!!$F1	796
7	TraesCS3B01G234700	chr6A	45758936	45759739	803	True	1306.000000	1306	96.020000	1	802	1	chr6A.!!$R1	801
8	TraesCS3B01G234700	chr7A	129869899	129870703	804	True	1303.000000	1303	95.906000	1	803	1	chr7A.!!$R1	802
9	TraesCS3B01G234700	chr5A	573653319	573654113	794	True	1297.000000	1297	96.115000	4	799	1	chr5A.!!$R1	795
10	TraesCS3B01G234700	chr5A	680883279	680884081	802	False	1293.000000	1293	95.766000	1	801	1	chr5A.!!$F2	800
11	TraesCS3B01G234700	chr5A	391987501	391988312	811	False	1288.000000	1288	95.326000	1	810	1	chr5A.!!$F1	809
12	TraesCS3B01G234700	chr2B	726124223	726125026	803	False	1295.000000	1295	95.771000	1	802	1	chr2B.!!$F1	801
13	TraesCS3B01G234700	chr1A	499618193	499618998	805	True	1290.000000	1290	95.545000	1	806	1	chr1A.!!$R1	805
14	TraesCS3B01G234700	chr4B	2014021	2014666	645	True	558.500000	562	88.673000	4922	5384	2	chr4B.!!$R1	462
15	TraesCS3B01G234700	chr1B	485801083	485801732	649	True	510.500000	531	86.840000	4922	5385	2	chr1B.!!$R2	463

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
726	733	0.179001	GTAGGTGTGTGGGCTGGTTT	60.179	55.000	0.00	0.00	0.00	3.27	F
1037	1044	0.247736	TTCTCCTCTCAAGCCTTCGC	59.752	55.000	0.00	0.00	0.00	4.70	F
2060	2106	1.671328	CTGATGGCATCAAGCTGTCAG	59.329	52.381	28.50	13.12	43.08	3.51	F
2191	2237	1.985473	ATTGCTGGCACTGTTTCTGA	58.015	45.000	0.00	0.00	0.00	3.27	F
2848	2937	3.002791	TGTTGGAAGCTTAAGCATCTCG	58.997	45.455	28.39	0.00	45.16	4.04	F
3146	3238	3.055094	AGTGCAAGTTATGTTCGAGGGAT	60.055	43.478	0.00	0.00	0.00	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1548	1591	1.340991	ACACAACACAGGAACAAGCCT	60.341	47.619	39.37	4.58	R
2714	2767	1.702182	TTTGGTGAAGCTCATTGCCA	58.298	45.000	44.23	4.92	R
3473	3691	1.070309	GTCAAGCTCGCACTGAACAAG	60.070	52.381	0.00	3.16	R
3842	4060	2.614057	CGATTTGGGTGGAGCATAGAAC	59.386	50.000	0.00	3.01	R
4426	4819	0.479815	ATCCACCGAATCATGGGCAT	59.520	50.000	36.56	4.40	R
4882	5547	0.101579	AACGAAAACCACCCAAAGCG	59.898	50.000	0.00	4.68	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	54	1.673033	CCACGTAAGCTGCTAGTTGCT	60.673	52.381	0.90	5.92	42.08	3.91
150	155	1.117994	TGCCATGTGTTTTTGCAGGA	58.882	45.000	0.00	0.00	0.00	3.86
152	157	2.070783	GCCATGTGTTTTTGCAGGATG	58.929	47.619	0.00	0.00	40.87	3.51
269	274	1.720805	CACGTACATGGCAACTGCTA	58.279	50.000	1.06	0.00	41.70	3.49
383	389	4.891992	AGTGTTAGTATGTGGCAACTCT	57.108	40.909	0.00	0.00	37.61	3.24
620	626	4.769063	CATACGGGCGTGTGGGCA	62.769	66.667	0.00	0.00	44.56	5.36
694	701	4.568072	AGATGTGTGTGGGCATTAGTTA	57.432	40.909	0.00	0.00	0.00	2.24
726	733	0.179001	GTAGGTGTGTGGGCTGGTTT	60.179	55.000	0.00	0.00	0.00	3.27
745	752	1.184970	TCTGTCCATGCCACACGAGA	61.185	55.000	0.00	0.00	0.00	4.04
802	809	2.758423	GCAGTTATCGGGACCCAAAAAT	59.242	45.455	12.15	0.64	0.00	1.82
806	813	6.327154	CAGTTATCGGGACCCAAAAATAAAC	58.673	40.000	12.15	4.75	0.00	2.01
810	817	3.158676	CGGGACCCAAAAATAAACCAGA	58.841	45.455	12.15	0.00	0.00	3.86
811	818	3.574826	CGGGACCCAAAAATAAACCAGAA	59.425	43.478	12.15	0.00	0.00	3.02
812	819	4.559906	CGGGACCCAAAAATAAACCAGAAC	60.560	45.833	12.15	0.00	0.00	3.01
813	820	4.552355	GGACCCAAAAATAAACCAGAACG	58.448	43.478	0.00	0.00	0.00	3.95
814	821	4.278919	GGACCCAAAAATAAACCAGAACGA	59.721	41.667	0.00	0.00	0.00	3.85
815	822	5.221283	GGACCCAAAAATAAACCAGAACGAA	60.221	40.000	0.00	0.00	0.00	3.85
816	823	5.838529	ACCCAAAAATAAACCAGAACGAAG	58.161	37.500	0.00	0.00	0.00	3.79
817	824	5.221362	ACCCAAAAATAAACCAGAACGAAGG	60.221	40.000	0.00	0.00	0.00	3.46
818	825	5.221362	CCCAAAAATAAACCAGAACGAAGGT	60.221	40.000	0.00	0.00	40.61	3.50
819	826	5.689961	CCAAAAATAAACCAGAACGAAGGTG	59.310	40.000	0.00	0.00	38.37	4.00
820	827	6.270064	CAAAAATAAACCAGAACGAAGGTGT	58.730	36.000	0.00	0.00	38.37	4.16
821	828	7.419204	CAAAAATAAACCAGAACGAAGGTGTA	58.581	34.615	0.00	0.00	38.37	2.90
822	829	6.549912	AAATAAACCAGAACGAAGGTGTAC	57.450	37.500	0.00	0.00	38.37	2.90
823	830	2.144482	AACCAGAACGAAGGTGTACG	57.856	50.000	0.00	0.00	38.37	3.67

Showing 1 to 25 of 344 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
19	20	1.310933	TTACGTGGGAGAGGAGACGC	61.311	60.000	0.00	35.21	5.19
51	54	1.066152	TGTGCGCTGCAAAAACACATA	59.934	42.857	9.73	41.47	2.29
620	626	2.006888	CGTGTGGGCGAAGTTGATAAT	58.993	47.619	0.00	0.00	1.28
694	701	1.243902	CACCTACGTGTGGGCAAAAT	58.756	50.000	12.88	35.10	1.82
726	733	1.184970	TCTCGTGTGGCATGGACAGA	61.185	55.000	0.00	0.00	3.41
745	752	1.610038	TCGGATAGTTGTGTCACACGT	59.390	47.619	4.80	37.14	4.49
802	809	3.068024	ACGTACACCTTCGTTCTGGTTTA	59.932	43.478	0.00	36.93	2.01
806	813	2.415090	CCTACGTACACCTTCGTTCTGG	60.415	54.545	0.00	40.70	3.86
810	817	5.643379	TTTATCCTACGTACACCTTCGTT	57.357	39.130	0.00	40.70	3.85
811	818	5.643379	TTTTATCCTACGTACACCTTCGT	57.357	39.130	0.00	42.82	3.85
831	838	2.647846	AGGAATGCCCCTGGATTTTT	57.352	45.000	0.00	34.68	1.94
891	898	3.897239	TGCGGATGGGAAGAATATGTTT	58.103	40.909	0.00	0.00	2.83
927	934	7.039011	GGGGAGGAATATGTGTTTCTTTTCTTT	60.039	37.037	0.00	0.00	2.52
928	935	6.437477	GGGGAGGAATATGTGTTTCTTTTCTT	59.563	38.462	0.00	0.00	2.52
929	936	5.952347	GGGGAGGAATATGTGTTTCTTTTCT	59.048	40.000	0.00	0.00	2.52
930	937	5.127194	GGGGGAGGAATATGTGTTTCTTTTC	59.873	44.000	0.00	0.00	2.29
931	938	5.023452	GGGGGAGGAATATGTGTTTCTTTT	58.977	41.667	0.00	0.00	2.27
932	939	4.610333	GGGGGAGGAATATGTGTTTCTTT	58.390	43.478	0.00	0.00	2.52
970	977	0.385598	GTTCGCTTTGCCTTCGTTCC	60.386	55.000	0.00	0.00	3.62
973	980	1.092921	TGTGTTCGCTTTGCCTTCGT	61.093	50.000	0.00	0.00	3.85
1007	1014	0.104409	AGAGGAGAAGTGGGTGGGTT	60.104	55.000	0.00	0.00	4.11
1008	1015	0.545548	GAGAGGAGAAGTGGGTGGGT	60.546	60.000	0.00	0.00	4.51
1009	1016	0.545309	TGAGAGGAGAAGTGGGTGGG	60.545	60.000	0.00	0.00	4.61
1010	1017	1.277557	CTTGAGAGGAGAAGTGGGTGG	59.722	57.143	0.00	0.00	4.61
1011	1018	1.338579	GCTTGAGAGGAGAAGTGGGTG	60.339	57.143	0.00	0.00	4.61

Showing 1 to 25 of 325 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.