AutoCloner

Multiple sequence alignment - TraesCS2D01G188200

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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	TraesCS2D01G188200	chr2D	100.000	3560	0	0	1	3560	131452534	131456093	0.000000e+00	6575.0
1	TraesCS2D01G188200	chr2D	85.862	290	37	3	2276	2565	131463537	131463822	4.470000e-79	305.0
2	TraesCS2D01G188200	chr2D	91.038	212	13	3	1	206	387901189	387900978	7.520000e-72	281.0
3	TraesCS2D01G188200	chr2D	94.118	68	4	0	385	452	131452851	131452918	1.750000e-18	104.0
4	TraesCS2D01G188200	chr2D	94.118	68	4	0	318	385	131452918	131452985	1.750000e-18	104.0
5	TraesCS2D01G188200	chr2D	95.312	64	2	1	565	628	377261211	377261149	2.260000e-17	100.0
6	TraesCS2D01G188200	chr2D	95.312	64	2	1	565	628	578032376	578032438	2.260000e-17	100.0
7	TraesCS2D01G188200	chr2A	95.975	2733	85	14	848	3560	138162852	138165579	0.000000e+00	4414.0
8	TraesCS2D01G188200	chr2A	77.273	352	52	18	3017	3356	138165816	138166151	7.850000e-42	182.0
9	TraesCS2D01G188200	chr2A	93.548	62	3	1	565	626	2613499	2613439	1.360000e-14	91.6
10	TraesCS2D01G188200	chr2A	94.872	39	2	0	744	782	1597981	1597943	1.070000e-05	62.1
11	TraesCS2D01G188200	chr2A	94.872	39	2	0	744	782	1598828	1598790	1.070000e-05	62.1
12	TraesCS2D01G188200	chr2B	96.012	1956	66	3	927	2881	185797164	185799108	0.000000e+00	3169.0
13	TraesCS2D01G188200	chr2B	95.524	715	30	2	2846	3560	185799109	185799821	0.000000e+00	1142.0
14	TraesCS2D01G188200	chr2B	87.305	512	33	8	318	808	185795624	185796124	1.120000e-154	556.0
15	TraesCS2D01G188200	chr2B	92.157	255	16	3	202	455	185795377	185795628	1.220000e-94	357.0
16	TraesCS2D01G188200	chr2B	86.942	291	33	4	2276	2565	185804808	185805094	4.430000e-84	322.0
17	TraesCS2D01G188200	chr2B	96.403	139	4	1	318	455	185795557	185795695	9.940000e-56	228.0
18	TraesCS2D01G188200	chr2B	88.816	152	14	2	206	357	454852470	454852618	2.180000e-42	183.0
19	TraesCS2D01G188200	chr2B	94.068	118	6	1	801	917	185796285	185796402	1.020000e-40	178.0
20	TraesCS2D01G188200	chr2B	97.059	68	2	0	318	385	185795691	185795758	8.080000e-22	115.0
21	TraesCS2D01G188200	chr2B	92.405	79	4	2	848	926	185796478	185796554	1.040000e-20	111.0
22	TraesCS2D01G188200	chr1A	95.146	206	10	0	1	206	76488776	76488981	3.430000e-85	326.0
23	TraesCS2D01G188200	chr1A	89.806	206	21	0	1	206	302897599	302897804	7.580000e-67	265.0
24	TraesCS2D01G188200	chr7A	92.233	206	15	1	1	206	522500539	522500743	1.250000e-74	291.0
25	TraesCS2D01G188200	chr7A	87.324	71	7	1	740	808	317056820	317056750	2.950000e-11	80.5
26	TraesCS2D01G188200	chr3A	92.574	202	15	0	5	206	405987140	405987341	1.250000e-74	291.0
27	TraesCS2D01G188200	chr3A	90.141	213	14	1	1	206	594016881	594016669	1.630000e-68	270.0
28	TraesCS2D01G188200	chr1D	91.080	213	12	1	1	206	74398805	74399017	7.520000e-72	281.0
29	TraesCS2D01G188200	chr1D	95.000	60	3	0	749	808	468986299	468986240	1.050000e-15	95.3
30	TraesCS2D01G188200	chr3B	90.777	206	19	0	1	206	488539081	488538876	3.500000e-70	276.0
31	TraesCS2D01G188200	chr7D	88.182	220	12	1	1	206	401538878	401539097	2.120000e-62	250.0
32	TraesCS2D01G188200	chr7D	95.312	64	2	1	565	628	553413530	553413592	2.260000e-17	100.0
33	TraesCS2D01G188200	chr5B	95.385	65	3	0	744	808	28754641	28754577	1.750000e-18	104.0
34	TraesCS2D01G188200	chr5B	91.429	70	5	1	565	634	17599304	17599236	1.050000e-15	95.3
35	TraesCS2D01G188200	chr1B	92.537	67	5	0	2171	2237	30458459	30458393	2.930000e-16	97.1
36	TraesCS2D01G188200	chr3D	93.750	64	3	1	565	628	67055685	67055623	1.050000e-15	95.3
37	TraesCS2D01G188200	chr3D	92.000	50	1	3	742	788	216277990	216277941	2.290000e-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	TraesCS2D01G188200	chr2D	131452534	131456093	3559	False	2261	6575	96.078667	1	3560	3	chr2D.!!$F3	3559
1	TraesCS2D01G188200	chr2A	138162852	138166151	3299	False	2298	4414	86.624000	848	3560	2	chr2A.!!$F1	2712
2	TraesCS2D01G188200	chr2B	185795377	185799821	4444	False	732	3169	93.866625	202	3560	8	chr2B.!!$F3	3358

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
21	22	0.028505	CAAATGCATCTTCGAGGGCG	59.971	55.0	0.00	0.00	39.35	6.13	F
146	147	0.031585	ACGCGCACTAGTTTCACTGA	59.968	50.0	5.73	0.00	0.00	3.41	F
504	639	0.037447	TGTGGCGTTCAATGGATCCA	59.963	50.0	18.88	18.88	0.00	3.41	F
749	905	0.680921	ATCAGTTTCCGTGGCCATGG	60.681	55.0	34.89	34.89	38.85	3.66	F
1986	3066	0.975556	TGTATGGGCTCTTGGCGAGA	60.976	55.0	3.99	3.99	42.62	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1731	2811	0.317854	CGATCTCTTCGTATGCCGCA	60.318	55.000	0.00	0.00	43.01	5.69	R
1986	3066	2.284699	CCTTCCCTCACCCTCCGT	60.285	66.667	0.00	0.00	0.00	4.69	R
2250	3330	4.316823	TCCAGTGTCCTCCCCGCT	62.317	66.667	0.00	0.00	0.00	5.52	R
2524	3604	3.384146	GCTTCTGACTCCTGAGATGATGA	59.616	47.826	0.22	0.00	0.00	2.92	R
3234	4352	2.795175	TGTCAGACTTCGAAGGTGTC	57.205	50.000	27.86	20.56	0.00	3.67	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
20	21	1.098050	ACAAATGCATCTTCGAGGGC	58.902	50.000	0.00	0.00	0.00	5.19
21	22	0.028505	CAAATGCATCTTCGAGGGCG	59.971	55.000	0.00	0.00	39.35	6.13
22	23	1.718757	AAATGCATCTTCGAGGGCGC	61.719	55.000	0.00	0.00	37.46	6.53
23	24	4.838152	TGCATCTTCGAGGGCGCC	62.838	66.667	21.18	21.18	37.46	6.53
24	25	4.537433	GCATCTTCGAGGGCGCCT	62.537	66.667	28.56	12.77	37.46	5.52
25	26	3.129300	CATCTTCGAGGGCGCCTA	58.871	61.111	28.56	6.83	37.46	3.93
26	27	1.006805	CATCTTCGAGGGCGCCTAG	60.007	63.158	28.56	17.71	37.46	3.02
36	37	4.858680	GCGCCTAGCCCCTGGTTC	62.859	72.222	0.00	0.00	40.81	3.62
37	38	3.399181	CGCCTAGCCCCTGGTTCA	61.399	66.667	0.00	0.00	0.00	3.18
38	39	2.592308	GCCTAGCCCCTGGTTCAG	59.408	66.667	0.00	0.00	0.00	3.02
46	47	2.352805	CCTGGTTCAGGTCCTGGC	59.647	66.667	19.11	11.75	45.82	4.85
47	48	2.352805	CTGGTTCAGGTCCTGGCC	59.647	66.667	19.11	19.70	31.51	5.36
48	49	2.121963	TGGTTCAGGTCCTGGCCT	60.122	61.111	24.35	4.13	39.99	5.19
49	50	2.190488	CTGGTTCAGGTCCTGGCCTC	62.190	65.000	24.35	12.49	36.58	4.70
50	51	2.266055	GTTCAGGTCCTGGCCTCG	59.734	66.667	19.11	0.00	36.58	4.63
51	52	2.119611	TTCAGGTCCTGGCCTCGA	59.880	61.111	19.11	0.00	36.58	4.04
52	53	1.306141	TTCAGGTCCTGGCCTCGAT	60.306	57.895	19.11	0.00	36.58	3.59
53	54	1.617018	TTCAGGTCCTGGCCTCGATG	61.617	60.000	19.11	0.00	36.58	3.84
54	55	2.060383	CAGGTCCTGGCCTCGATGA	61.060	63.158	11.46	0.00	36.58	2.92
55	56	1.074926	AGGTCCTGGCCTCGATGAT	60.075	57.895	3.32	0.00	32.39	2.45
56	57	1.118356	AGGTCCTGGCCTCGATGATC	61.118	60.000	3.32	0.00	32.39	2.92
57	58	1.402896	GGTCCTGGCCTCGATGATCA	61.403	60.000	3.32	0.00	0.00	2.92
58	59	0.465705	GTCCTGGCCTCGATGATCAA	59.534	55.000	3.32	0.00	0.00	2.57
59	60	1.134401	GTCCTGGCCTCGATGATCAAA	60.134	52.381	3.32	0.00	0.00	2.69
60	61	1.139654	TCCTGGCCTCGATGATCAAAG	59.860	52.381	3.32	0.00	0.00	2.77

Showing 1 to 25 of 162 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.474077	GCCCTCGAAGATGCATTTGTT	59.526	47.619	0.00	0.00	34.83	2.83
1	2	1.098050	GCCCTCGAAGATGCATTTGT	58.902	50.000	0.00	0.00	34.83	2.83
2	3	0.028505	CGCCCTCGAAGATGCATTTG	59.971	55.000	0.00	0.00	38.10	2.32
3	4	1.718757	GCGCCCTCGAAGATGCATTT	61.719	55.000	0.00	0.00	38.10	2.32
5	6	2.590007	GCGCCCTCGAAGATGCAT	60.590	61.111	0.00	0.00	38.10	3.96
7	8	3.151958	TAGGCGCCCTCGAAGATGC	62.152	63.158	26.15	0.00	38.10	3.91
8	9	1.006805	CTAGGCGCCCTCGAAGATG	60.007	63.158	26.15	0.00	38.10	2.90
9	10	2.862223	GCTAGGCGCCCTCGAAGAT	61.862	63.158	26.15	3.86	38.10	2.40
10	11	3.528370	GCTAGGCGCCCTCGAAGA	61.528	66.667	26.15	0.00	38.10	2.87
19	20	4.858680	GAACCAGGGGCTAGGCGC	62.859	72.222	23.85	23.85	40.84	6.53
20	21	3.391665	CTGAACCAGGGGCTAGGCG	62.392	68.421	10.58	0.00	0.00	5.52
21	22	2.592308	CTGAACCAGGGGCTAGGC	59.408	66.667	8.00	8.00	0.00	3.93
30	31	2.190488	GAGGCCAGGACCTGAACCAG	62.190	65.000	26.45	11.91	41.32	4.00
31	32	2.121963	AGGCCAGGACCTGAACCA	60.122	61.111	26.45	0.00	39.13	3.67
32	33	2.671682	GAGGCCAGGACCTGAACC	59.328	66.667	23.77	21.84	41.32	3.62
33	34	1.617947	ATCGAGGCCAGGACCTGAAC	61.618	60.000	23.77	14.47	41.32	3.18
34	35	1.306141	ATCGAGGCCAGGACCTGAA	60.306	57.895	23.77	1.43	41.32	3.02
35	36	2.060383	CATCGAGGCCAGGACCTGA	61.060	63.158	23.77	1.47	41.32	3.86
36	37	1.406065	ATCATCGAGGCCAGGACCTG	61.406	60.000	15.15	15.15	41.32	4.00
37	38	1.074926	ATCATCGAGGCCAGGACCT	60.075	57.895	5.01	2.25	45.04	3.85
38	39	1.369321	GATCATCGAGGCCAGGACC	59.631	63.158	5.01	0.00	0.00	4.46
39	40	0.465705	TTGATCATCGAGGCCAGGAC	59.534	55.000	5.01	0.00	0.00	3.85
40	41	1.139654	CTTTGATCATCGAGGCCAGGA	59.860	52.381	5.01	0.74	0.00	3.86
41	42	1.139654	TCTTTGATCATCGAGGCCAGG	59.860	52.381	5.01	0.00	0.00	4.45
42	43	2.481854	CTCTTTGATCATCGAGGCCAG	58.518	52.381	5.01	0.00	0.00	4.85

Showing 1 to 25 of 191 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.