AutoCloner

Multiple sequence alignment - TraesCS2D01G445400

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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	TraesCS2D01G445400	chr2D	100.000	3419	0	0	1	3419	556048494	556051912	0.000000e+00	6314.0
1	TraesCS2D01G445400	chr2D	84.591	318	41	5	4	314	614385922	614385606	3.310000e-80	309.0
2	TraesCS2D01G445400	chr2D	88.889	243	22	1	2684	2926	32609461	32609698	9.280000e-76	294.0
3	TraesCS2D01G445400	chr2D	78.113	265	38	4	4	266	174418837	174418591	2.130000e-32	150.0
4	TraesCS2D01G445400	chr2A	91.966	2502	118	37	863	3344	695469597	695472035	0.000000e+00	3430.0
5	TraesCS2D01G445400	chr2A	92.935	184	11	2	678	860	46345102	46345284	2.020000e-67	267.0
6	TraesCS2D01G445400	chr2A	91.209	182	14	2	678	858	24964445	24964625	2.640000e-61	246.0
7	TraesCS2D01G445400	chr2A	95.918	49	2	0	3371	3419	695472041	695472089	2.830000e-11	80.5
8	TraesCS2D01G445400	chr2B	91.063	2473	139	38	913	3344	663044915	663047346	0.000000e+00	3267.0
9	TraesCS2D01G445400	chr2B	91.161	1663	124	12	947	2589	54049020	54050679	0.000000e+00	2235.0
10	TraesCS2D01G445400	chr2B	92.055	1309	96	4	1288	2589	54034089	54035396	0.000000e+00	1834.0
11	TraesCS2D01G445400	chr2B	91.339	127	10	1	346	472	146781056	146781181	4.540000e-39	172.0
12	TraesCS2D01G445400	chr2B	91.489	47	0	1	3373	3419	663047354	663047396	1.020000e-05	62.1
13	TraesCS2D01G445400	chrUn	91.444	1087	83	8	947	2025	272459305	272458221	0.000000e+00	1483.0
14	TraesCS2D01G445400	chrUn	96.429	112	4	0	364	475	11239798	11239909	5.830000e-43	185.0
15	TraesCS2D01G445400	chrUn	92.742	124	6	3	354	477	32322720	32322840	3.510000e-40	176.0
16	TraesCS2D01G445400	chrUn	92.742	124	6	3	354	477	443254725	443254845	3.510000e-40	176.0
17	TraesCS2D01G445400	chr1A	82.880	368	54	5	4	363	247797047	247796681	4.260000e-84	322.0
18	TraesCS2D01G445400	chr1A	93.714	175	11	0	684	858	550840291	550840117	2.620000e-66	263.0
19	TraesCS2D01G445400	chr1A	92.818	181	13	0	678	858	562303551	562303731	2.620000e-66	263.0
20	TraesCS2D01G445400	chr1A	94.958	119	6	0	357	475	321876339	321876457	1.620000e-43	187.0
21	TraesCS2D01G445400	chr1D	84.424	321	40	7	2	314	408875624	408875306	1.190000e-79	307.0
22	TraesCS2D01G445400	chr1D	86.932	176	17	5	686	858	476406678	476406506	3.480000e-45	193.0
23	TraesCS2D01G445400	chr1D	96.429	112	4	0	364	475	440942567	440942678	5.830000e-43	185.0
24	TraesCS2D01G445400	chr7D	83.030	330	47	6	4	326	30248006	30247679	1.200000e-74	291.0
25	TraesCS2D01G445400	chr7D	92.262	168	12	1	685	852	37036457	37036623	1.590000e-58	237.0
26	TraesCS2D01G445400	chr5D	92.308	182	12	2	678	858	312120351	312120531	1.220000e-64	257.0
27	TraesCS2D01G445400	chr3D	92.486	173	13	0	684	856	516646843	516646671	7.330000e-62	248.0
28	TraesCS2D01G445400	chr3D	91.908	173	13	1	684	856	566102266	566102095	1.230000e-59	241.0
29	TraesCS2D01G445400	chr3D	90.152	132	11	2	364	494	263778272	263778142	1.630000e-38	171.0
30	TraesCS2D01G445400	chr4B	92.045	176	13	1	684	858	567416981	567417156	2.640000e-61	246.0
31	TraesCS2D01G445400	chr3B	79.940	334	50	13	4	326	93620468	93620795	2.650000e-56	230.0
32	TraesCS2D01G445400	chr3B	96.429	112	4	0	361	472	623661397	623661286	5.830000e-43	185.0
33	TraesCS2D01G445400	chr1B	81.852	270	43	4	4	267	40429582	40429851	4.440000e-54	222.0
34	TraesCS2D01G445400	chr1B	80.829	193	28	8	138	326	665125080	665124893	3.560000e-30	143.0
35	TraesCS2D01G445400	chr4A	84.141	227	32	4	139	363	690629718	690629494	2.070000e-52	217.0
36	TraesCS2D01G445400	chr6B	92.800	125	8	1	351	475	525565733	525565610	2.710000e-41	180.0

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	TraesCS2D01G445400	chr2D	556048494	556051912	3418	False	6314.00	6314	100.000	1	3419	1	chr2D.!!$F2	3418
1	TraesCS2D01G445400	chr2A	695469597	695472089	2492	False	1755.25	3430	93.942	863	3419	2	chr2A.!!$F3	2556
2	TraesCS2D01G445400	chr2B	54049020	54050679	1659	False	2235.00	2235	91.161	947	2589	1	chr2B.!!$F2	1642
3	TraesCS2D01G445400	chr2B	54034089	54035396	1307	False	1834.00	1834	92.055	1288	2589	1	chr2B.!!$F1	1301
4	TraesCS2D01G445400	chr2B	663044915	663047396	2481	False	1664.55	3267	91.276	913	3419	2	chr2B.!!$F4	2506
5	TraesCS2D01G445400	chrUn	272458221	272459305	1084	True	1483.00	1483	91.444	947	2025	1	chrUn.!!$R1	1078

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
300	301	0.034337	TCGGTTACAGTGGTTGCCTC	59.966	55.0	0.0	0.0	0.0	4.70	F
302	303	0.034337	GGTTACAGTGGTTGCCTCGA	59.966	55.0	0.0	0.0	0.0	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2011	2025	0.394762	GCAGCATCAACATCCCCTGA	60.395	55.000	0.0	0.0	0.0	3.86	R
2421	2443	5.086727	GCAACATACGAAGCTTAAAGAACC	58.913	41.667	0.0	0.0	0.0	3.62	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
17	18	4.321966	TGTTGATGGCGGCGTCCA	62.322	61.111	26.41	21.73	40.97	4.02
18	19	3.053291	GTTGATGGCGGCGTCCAA	61.053	61.111	26.41	17.61	39.96	3.53
19	20	2.281831	TTGATGGCGGCGTCCAAA	60.282	55.556	26.41	13.54	39.96	3.28
20	21	2.331893	TTGATGGCGGCGTCCAAAG	61.332	57.895	26.41	0.00	39.96	2.77
21	22	2.746277	GATGGCGGCGTCCAAAGT	60.746	61.111	22.91	10.14	39.96	2.66
22	23	2.282180	ATGGCGGCGTCCAAAGTT	60.282	55.556	22.91	7.56	39.96	2.66
23	24	2.253414	GATGGCGGCGTCCAAAGTTC	62.253	60.000	22.91	14.04	39.96	3.01
24	25	3.733960	GGCGGCGTCCAAAGTTCC	61.734	66.667	9.37	0.00	0.00	3.62
25	26	4.084888	GCGGCGTCCAAAGTTCCG	62.085	66.667	9.37	0.00	42.68	4.30
26	27	2.356553	CGGCGTCCAAAGTTCCGA	60.357	61.111	0.00	0.00	42.43	4.55
27	28	1.740296	CGGCGTCCAAAGTTCCGAT	60.740	57.895	0.00	0.00	42.43	4.18
28	29	1.794222	GGCGTCCAAAGTTCCGATG	59.206	57.895	0.00	0.00	0.00	3.84
29	30	0.672401	GGCGTCCAAAGTTCCGATGA	60.672	55.000	0.00	0.00	0.00	2.92
30	31	0.442699	GCGTCCAAAGTTCCGATGAC	59.557	55.000	0.00	0.00	0.00	3.06
31	32	0.713883	CGTCCAAAGTTCCGATGACG	59.286	55.000	0.00	0.00	39.43	4.35
32	33	1.667756	CGTCCAAAGTTCCGATGACGA	60.668	52.381	3.98	0.00	42.66	4.20
33	34	2.409975	GTCCAAAGTTCCGATGACGAA	58.590	47.619	0.00	0.00	42.66	3.85
34	35	2.157085	GTCCAAAGTTCCGATGACGAAC	59.843	50.000	0.00	0.00	42.66	3.95
35	36	2.139917	CCAAAGTTCCGATGACGAACA	58.860	47.619	3.76	0.00	42.66	3.18
36	37	2.546368	CCAAAGTTCCGATGACGAACAA	59.454	45.455	3.76	0.00	42.66	2.83
37	38	3.541711	CAAAGTTCCGATGACGAACAAC	58.458	45.455	3.76	0.00	42.66	3.32
38	39	1.792006	AGTTCCGATGACGAACAACC	58.208	50.000	3.76	0.00	42.66	3.77
39	40	1.343465	AGTTCCGATGACGAACAACCT	59.657	47.619	3.76	0.00	42.66	3.50
40	41	1.725164	GTTCCGATGACGAACAACCTC	59.275	52.381	0.00	0.00	42.66	3.85
41	42	0.245539	TCCGATGACGAACAACCTCC	59.754	55.000	0.00	0.00	42.66	4.30

Showing 1 to 25 of 605 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	3.834013	TTGGACGCCGCCATCAACA	62.834	57.895	1.26	37.86	3.33
1	2	2.527547	CTTTGGACGCCGCCATCAAC	62.528	60.000	1.26	37.86	3.18
2	3	2.281831	TTTGGACGCCGCCATCAA	60.282	55.556	1.26	37.86	2.57
4	5	2.253414	GAACTTTGGACGCCGCCATC	62.253	60.000	1.26	37.86	3.51
5	6	2.282180	AACTTTGGACGCCGCCAT	60.282	55.556	1.26	37.86	4.40
6	7	2.975799	GAACTTTGGACGCCGCCA	60.976	61.111	0.00	35.78	5.69
7	8	3.733960	GGAACTTTGGACGCCGCC	61.734	66.667	0.00	0.00	6.13
8	9	4.084888	CGGAACTTTGGACGCCGC	62.085	66.667	0.00	35.17	6.53
9	10	1.740296	ATCGGAACTTTGGACGCCG	60.740	57.895	0.00	43.11	6.46
10	11	0.672401	TCATCGGAACTTTGGACGCC	60.672	55.000	0.00	0.00	5.68
11	12	0.442699	GTCATCGGAACTTTGGACGC	59.557	55.000	0.00	0.00	5.19
12	13	0.713883	CGTCATCGGAACTTTGGACG	59.286	55.000	0.00	0.00	4.79
13	14	2.074547	TCGTCATCGGAACTTTGGAC	57.925	50.000	0.00	37.69	4.02
14	15	2.224090	TGTTCGTCATCGGAACTTTGGA	60.224	45.455	6.28	37.69	3.53
15	16	2.139917	TGTTCGTCATCGGAACTTTGG	58.860	47.619	6.28	37.69	3.28
16	17	3.541711	GTTGTTCGTCATCGGAACTTTG	58.458	45.455	6.28	37.69	2.77
17	18	2.546789	GGTTGTTCGTCATCGGAACTTT	59.453	45.455	6.28	37.69	2.66
18	19	2.140717	GGTTGTTCGTCATCGGAACTT	58.859	47.619	6.28	37.69	2.66
19	20	1.343465	AGGTTGTTCGTCATCGGAACT	59.657	47.619	6.28	37.69	3.01
20	21	1.725164	GAGGTTGTTCGTCATCGGAAC	59.275	52.381	0.00	37.69	3.62
21	22	1.337447	GGAGGTTGTTCGTCATCGGAA	60.337	52.381	0.00	37.69	4.30
22	23	0.245539	GGAGGTTGTTCGTCATCGGA	59.754	55.000	0.00	37.69	4.55
23	24	0.037697	TGGAGGTTGTTCGTCATCGG	60.038	55.000	0.00	37.69	4.18
24	25	1.067846	TCTGGAGGTTGTTCGTCATCG	60.068	52.381	0.00	38.55	3.84
25	26	2.338500	GTCTGGAGGTTGTTCGTCATC	58.662	52.381	0.00	33.18	2.92

Showing 1 to 25 of 675 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.