AutoCloner

Multiple sequence alignment - TraesCS2D01G234400

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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	TraesCS2D01G234400	chr2D	100.000	6002	0	0	1	6002	215827670	215833671	0.000000e+00	11084.0
1	TraesCS2D01G234400	chr2D	93.291	313	19	2	1	311	640638710	640639022	1.520000e-125	460.0
2	TraesCS2D01G234400	chr2D	84.058	69	9	2	767	834	644672778	644672711	1.400000e-06	65.8
3	TraesCS2D01G234400	chr2A	98.282	3143	41	4	818	3959	306145863	306148993	0.000000e+00	5493.0
4	TraesCS2D01G234400	chr2A	96.481	1165	17	12	4299	5449	306149298	306150452	0.000000e+00	1903.0
5	TraesCS2D01G234400	chr2A	96.334	491	17	1	5512	6002	306150455	306150944	0.000000e+00	806.0
6	TraesCS2D01G234400	chr2A	98.421	190	3	0	3956	4145	306149116	306149305	9.640000e-88	335.0
7	TraesCS2D01G234400	chr2A	100.000	35	0	0	4565	4599	306149627	306149661	1.400000e-06	65.8
8	TraesCS2D01G234400	chr2B	98.084	3132	53	2	828	3959	272670523	272673647	0.000000e+00	5445.0
9	TraesCS2D01G234400	chr2B	93.362	1145	30	4	4302	5413	272673771	272674902	0.000000e+00	1652.0
10	TraesCS2D01G234400	chr2B	98.134	268	5	0	5623	5890	272674903	272675170	9.110000e-128	468.0
11	TraesCS2D01G234400	chr2B	97.938	97	2	0	5906	6002	272681401	272681497	1.030000e-37	169.0
12	TraesCS2D01G234400	chr2B	85.294	68	6	3	767	831	711316663	711316729	3.880000e-07	67.6
13	TraesCS2D01G234400	chr2B	84.286	70	8	2	767	834	17586042	17585974	1.400000e-06	65.8
14	TraesCS2D01G234400	chr7B	87.662	462	44	9	313	768	490711850	490711396	5.330000e-145	525.0
15	TraesCS2D01G234400	chr7B	87.907	215	19	3	5411	5625	477049511	477049718	4.650000e-61	246.0
16	TraesCS2D01G234400	chr7B	94.000	50	1	2	783	832	604108731	604108684	2.320000e-09	75.0
17	TraesCS2D01G234400	chr7B	86.567	67	8	1	767	832	412341357	412341291	8.340000e-09	73.1
18	TraesCS2D01G234400	chr7B	93.617	47	2	1	784	829	89956342	89956388	1.080000e-07	69.4
19	TraesCS2D01G234400	chr7B	84.058	69	7	4	767	832	619662583	619662650	5.020000e-06	63.9
20	TraesCS2D01G234400	chr7A	87.179	468	45	12	313	772	174272061	174272521	8.920000e-143	518.0
21	TraesCS2D01G234400	chr7A	98.907	183	2	0	3958	4140	563515845	563515663	1.610000e-85	327.0
22	TraesCS2D01G234400	chr7A	98.039	153	3	0	4146	4298	428822173	428822325	3.570000e-67	267.0
23	TraesCS2D01G234400	chr7A	85.507	69	9	1	767	835	27258402	27258335	3.000000e-08	71.3
24	TraesCS2D01G234400	chr7A	84.848	66	9	1	767	832	58654336	58654400	1.400000e-06	65.8
25	TraesCS2D01G234400	chr5D	86.994	469	50	6	313	772	391292630	391293096	8.920000e-143	518.0
26	TraesCS2D01G234400	chr5D	86.200	471	51	11	313	775	102028679	102028215	1.160000e-136	497.0
27	TraesCS2D01G234400	chr5D	93.291	313	19	2	1	311	550194552	550194240	1.520000e-125	460.0
28	TraesCS2D01G234400	chr5D	98.907	183	2	0	3958	4140	503225013	503224831	1.610000e-85	327.0
29	TraesCS2D01G234400	chr5D	98.052	154	3	0	4146	4299	257502136	257502289	9.920000e-68	268.0
30	TraesCS2D01G234400	chr5D	89.394	66	7	0	767	832	520081676	520081741	3.850000e-12	84.2
31	TraesCS2D01G234400	chr7D	86.780	469	47	11	313	772	635087480	635087942	5.370000e-140	508.0
32	TraesCS2D01G234400	chr7D	85.987	471	54	8	313	775	238938947	238938481	1.500000e-135	494.0
33	TraesCS2D01G234400	chr7D	94.249	313	16	2	1	311	164483839	164484151	1.510000e-130	477.0
34	TraesCS2D01G234400	chr7D	93.291	313	19	2	1	311	635086853	635087165	1.520000e-125	460.0
35	TraesCS2D01G234400	chr7D	98.734	158	1	1	4143	4299	617790748	617790591	4.580000e-71	279.0
36	TraesCS2D01G234400	chr7D	87.892	223	23	3	5411	5633	34482514	34482296	5.970000e-65	259.0
37	TraesCS2D01G234400	chr1A	86.667	465	50	9	313	768	494310154	494309693	6.940000e-139	505.0
38	TraesCS2D01G234400	chr1A	98.907	183	2	0	3958	4140	278527445	278527627	1.610000e-85	327.0
39	TraesCS2D01G234400	chr1A	89.252	214	20	3	5411	5624	559234356	559234146	1.280000e-66	265.0
40	TraesCS2D01G234400	chr1A	88.837	215	21	3	5412	5626	559234146	559234357	1.660000e-65	261.0
41	TraesCS2D01G234400	chr1A	95.092	163	6	2	4136	4298	99618355	99618515	7.720000e-64	255.0
42	TraesCS2D01G234400	chr6D	86.258	473	50	10	313	775	404320844	404320377	3.230000e-137	499.0
43	TraesCS2D01G234400	chr6D	93.930	313	17	2	1	311	404321471	404321159	7.040000e-129	472.0
44	TraesCS2D01G234400	chr6D	93.291	313	19	2	1	311	58106299	58106611	1.520000e-125	460.0
45	TraesCS2D01G234400	chr6D	98.907	183	2	0	3958	4140	168264464	168264282	1.610000e-85	327.0
46	TraesCS2D01G234400	chr6D	98.710	155	2	0	4144	4298	450831963	450832117	5.930000e-70	276.0
47	TraesCS2D01G234400	chr6D	84.475	219	29	3	5411	5627	8003502	8003717	1.690000e-50	211.0
48	TraesCS2D01G234400	chr6D	91.489	47	4	0	783	829	389334122	389334076	1.400000e-06	65.8
49	TraesCS2D01G234400	chr1D	85.835	473	56	9	313	775	476808527	476808998	5.400000e-135	492.0
50	TraesCS2D01G234400	chr1D	98.693	153	2	0	4146	4298	418199432	418199584	7.670000e-69	272.0
51	TraesCS2D01G234400	chr1D	85.333	225	24	5	5411	5626	455075278	455075502	2.180000e-54	224.0
52	TraesCS2D01G234400	chr1D	91.489	47	2	2	783	829	250749325	250749281	5.020000e-06	63.9
53	TraesCS2D01G234400	chr1D	88.235	51	3	3	782	831	465150942	465150894	2.340000e-04	58.4
54	TraesCS2D01G234400	chr3D	93.930	313	17	2	1	311	526969338	526969650	7.040000e-129	472.0
55	TraesCS2D01G234400	chr3D	93.291	313	19	2	1	311	572089450	572089762	1.520000e-125	460.0
56	TraesCS2D01G234400	chr3D	100.000	153	0	0	4146	4298	26165847	26165695	3.540000e-72	283.0
57	TraesCS2D01G234400	chr3D	86.667	60	6	2	775	833	414776347	414776405	1.400000e-06	65.8
58	TraesCS2D01G234400	chr3D	90.196	51	4	1	784	833	435313345	435313295	1.400000e-06	65.8
59	TraesCS2D01G234400	chr4D	93.291	313	19	2	1	311	70339373	70339685	1.520000e-125	460.0
60	TraesCS2D01G234400	chr4D	86.364	66	7	2	767	831	505533194	505533258	3.000000e-08	71.3
61	TraesCS2D01G234400	chr4D	97.143	35	1	0	798	832	39156319	39156285	6.500000e-05	60.2
62	TraesCS2D01G234400	chr4D	89.583	48	3	2	783	829	483455968	483456014	6.500000e-05	60.2
63	TraesCS2D01G234400	chr4D	92.683	41	2	1	794	833	337057245	337057285	2.340000e-04	58.4
64	TraesCS2D01G234400	chr4D	85.714	56	4	4	775	829	489954844	489954896	8.400000e-04	56.5
65	TraesCS2D01G234400	chr4D	94.286	35	2	0	798	832	488340371	488340337	3.000000e-03	54.7
66	TraesCS2D01G234400	chrUn	98.907	183	2	0	3958	4140	352978466	352978284	1.610000e-85	327.0
67	TraesCS2D01G234400	chrUn	100.000	30	0	0	805	834	455755287	455755258	8.400000e-04	56.5
68	TraesCS2D01G234400	chr3A	98.907	183	2	0	3958	4140	66010827	66011009	1.610000e-85	327.0
69	TraesCS2D01G234400	chr3A	98.907	183	2	0	3958	4140	495098507	495098325	1.610000e-85	327.0
70	TraesCS2D01G234400	chr3A	98.907	183	2	0	3958	4140	750740321	750740503	1.610000e-85	327.0
71	TraesCS2D01G234400	chr3A	98.039	153	2	1	4146	4298	593355867	593355716	1.280000e-66	265.0
72	TraesCS2D01G234400	chr5B	99.355	155	1	0	4145	4299	291786853	291787007	1.270000e-71	281.0
73	TraesCS2D01G234400	chr5B	88.235	51	4	2	782	831	491945359	491945408	6.500000e-05	60.2
74	TraesCS2D01G234400	chr5A	86.638	232	24	4	5404	5635	59700885	59701109	3.590000e-62	250.0
75	TraesCS2D01G234400	chr5A	86.977	215	21	5	5412	5626	466949264	466949471	1.010000e-57	235.0
76	TraesCS2D01G234400	chr5A	83.333	66	9	2	767	831	535564075	535564139	6.500000e-05	60.2
77	TraesCS2D01G234400	chr4A	90.741	108	5	4	4123	4227	238397458	238397563	8.110000e-29	139.0
78	TraesCS2D01G234400	chr4A	87.692	65	6	2	770	833	450856596	450856533	2.320000e-09	75.0
79	TraesCS2D01G234400	chr3B	85.135	74	6	4	767	838	720238784	720238714	3.000000e-08	71.3
80	TraesCS2D01G234400	chr6A	100.000	34	0	0	798	831	577761900	577761867	5.020000e-06	63.9
81	TraesCS2D01G234400	chr6A	91.111	45	2	2	789	832	574247629	574247586	6.500000e-05	60.2

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	TraesCS2D01G234400	chr2D	215827670	215833671	6001	False	11084.000000	11084	100.000000	1	6002	1	chr2D.!!$F1	6001
1	TraesCS2D01G234400	chr2A	306145863	306150944	5081	False	1720.560000	5493	97.903600	818	6002	5	chr2A.!!$F1	5184
2	TraesCS2D01G234400	chr2B	272670523	272675170	4647	False	2521.666667	5445	96.526667	828	5890	3	chr2B.!!$F3	5062
3	TraesCS2D01G234400	chr7D	635086853	635087942	1089	False	484.000000	508	90.035500	1	772	2	chr7D.!!$F2	771
4	TraesCS2D01G234400	chr6D	404320377	404321471	1094	True	485.500000	499	90.094000	1	775	2	chr6D.!!$R3	774

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
569	885	0.032416	ATCTAGCGGTAGTGGGTGGT	60.032	55.000	20.32	0.0	0.00	4.16	F
640	956	0.034896	AGGCGAATCTGGACGTTTGT	59.965	50.000	0.00	0.0	0.00	2.83	F
1500	1816	0.036952	ATGCCTTCCGTGTCACTGAG	60.037	55.000	0.65	0.0	0.00	3.35	F
1510	1826	2.143925	GTGTCACTGAGTTTGTAGCCC	58.856	52.381	0.00	0.0	0.00	5.19	F
2452	2768	4.696877	TGATTGATGAGCGTTCTGAATGTT	59.303	37.500	11.01	5.1	0.00	2.71	F
4180	4622	0.248949	GTAAGGCGACCTAAGGCGAG	60.249	60.000	4.41	0.0	39.33	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1500	1816	0.313987	GGTTGTGCTGGGCTACAAAC	59.686	55.000	0.0	0.0	38.40	2.93	R
1948	2264	1.412710	GAGTGGGTGATTATGCTCCGA	59.587	52.381	0.0	0.0	0.00	4.55	R
2605	2921	3.777106	TGCAGACAAGAACTCCATCTT	57.223	42.857	0.0	0.0	40.23	2.40	R
3596	3912	0.044855	ACCTACAATCTGCCCCCTCT	59.955	55.000	0.0	0.0	0.00	3.69	R
4223	4665	0.040425	CGCCTTACAAATATGCCCGC	60.040	55.000	0.0	0.0	0.00	6.13	R
5474	5963	0.038892	GCAGTCGGTCTCGTTGGTTA	60.039	55.000	0.0	0.0	37.69	2.85	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	1.152118	AGGTCCTGTGTGGCCACTA	60.152	57.895	34.75	22.67	42.34	2.74
23	24	2.221299	TCCTGTGTGGCCACTACCC	61.221	63.158	34.75	20.16	42.34	3.69
40	41	0.038166	CCCCAAGTACCACACTGCAT	59.962	55.000	0.00	0.00	37.63	3.96
62	63	1.209127	CCTTTGGCGCCTTTGTACG	59.791	57.895	29.70	8.61	0.00	3.67
115	116	2.618442	TCCAATGCATGCAGTCGATA	57.382	45.000	26.69	6.34	0.00	2.92
132	133	2.034685	CGATACTTCCAAGCATCCGAGA	59.965	50.000	0.00	0.00	0.00	4.04
140	141	3.019564	CCAAGCATCCGAGAAAATCCTT	58.980	45.455	0.00	0.00	0.00	3.36
152	153	4.572909	AGAAAATCCTTTTGCTGCATTCC	58.427	39.130	1.84	0.00	28.91	3.01
172	173	2.901975	TGCTAGGATCCGAGCAGTT	58.098	52.632	36.92	8.96	46.65	3.16
173	174	0.747255	TGCTAGGATCCGAGCAGTTC	59.253	55.000	36.92	15.57	46.65	3.01
174	175	1.036707	GCTAGGATCCGAGCAGTTCT	58.963	55.000	34.20	5.82	42.81	3.01
176	177	2.544903	GCTAGGATCCGAGCAGTTCTTC	60.545	54.545	34.20	8.71	42.81	2.87
177	178	1.561643	AGGATCCGAGCAGTTCTTCA	58.438	50.000	5.98	0.00	0.00	3.02
179	180	2.003301	GGATCCGAGCAGTTCTTCAAC	58.997	52.381	0.00	0.00	0.00	3.18
180	181	2.612972	GGATCCGAGCAGTTCTTCAACA	60.613	50.000	0.00	0.00	34.60	3.33
225	228	2.572333	AAACACTGCCACCACTGCCT	62.572	55.000	0.00	0.00	0.00	4.75
284	287	1.227234	CATGCGCCCATAGTCGTCA	60.227	57.895	4.18	0.00	0.00	4.35
329	645	1.500108	CTCCATGAGATGCTCTTCGC	58.500	55.000	0.00	0.00	39.77	4.70
338	654	4.070552	GCTCTTCGCCCTGGACGT	62.071	66.667	1.51	0.00	0.00	4.34
365	681	2.668120	GCTTCCTCCTCCAGCAGCT	61.668	63.158	0.00	0.00	33.45	4.24
366	682	1.989620	CTTCCTCCTCCAGCAGCTT	59.010	57.895	0.00	0.00	0.00	3.74
367	683	0.107752	CTTCCTCCTCCAGCAGCTTC	60.108	60.000	0.00	0.00	0.00	3.86
368	684	1.892819	TTCCTCCTCCAGCAGCTTCG	61.893	60.000	0.00	0.00	0.00	3.79
369	685	2.654079	CCTCCTCCAGCAGCTTCGT	61.654	63.158	0.00	0.00	0.00	3.85
370	686	1.447489	CTCCTCCAGCAGCTTCGTG	60.447	63.158	0.00	0.00	0.00	4.35

Showing 1 to 25 of 320 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.349542	TGCAGTGTGGTACTTGGGGT	61.350	55.000	0.00	0.00	37.60	4.95
23	24	1.453155	GGATGCAGTGTGGTACTTGG	58.547	55.000	0.00	0.00	37.60	3.61
62	63	1.005450	TCCATTTGCTTGGTAGGGGAC	59.995	52.381	1.68	0.00	38.01	4.46
115	116	2.859165	TTTCTCGGATGCTTGGAAGT	57.141	45.000	0.00	0.00	0.00	3.01
152	153	1.007964	CTGCTCGGATCCTAGCACG	60.008	63.158	31.38	23.42	43.56	5.34
172	173	1.003003	TGCGATCACCCATGTTGAAGA	59.997	47.619	0.00	0.00	0.00	2.87
173	174	1.452110	TGCGATCACCCATGTTGAAG	58.548	50.000	0.00	0.00	0.00	3.02
174	175	1.811965	CTTGCGATCACCCATGTTGAA	59.188	47.619	0.00	0.00	0.00	2.69
176	177	1.167851	ACTTGCGATCACCCATGTTG	58.832	50.000	0.00	0.00	0.00	3.33
177	178	2.779755	TACTTGCGATCACCCATGTT	57.220	45.000	0.00	0.00	0.00	2.71
179	180	3.614159	CAATACTTGCGATCACCCATG	57.386	47.619	0.00	0.00	0.00	3.66
225	228	5.182487	TGAGTGTTTCTACAAGTTCTGCAA	58.818	37.500	0.00	0.00	35.69	4.08
284	287	0.250513	GAGCTCCCGGTGATTCACTT	59.749	55.000	16.02	0.00	34.40	3.16
329	645	4.873129	CGATGCCGACGTCCAGGG	62.873	72.222	10.58	6.80	38.22	4.45
338	654	3.849951	GGAGGAAGCCGATGCCGA	61.850	66.667	0.00	0.00	38.69	5.54
374	690	2.622546	GACTCAGACAACGAGGAGTC	57.377	55.000	5.06	5.06	46.39	3.36
375	691	1.249407	GGACTCAGACAACGAGGAGT	58.751	55.000	0.00	0.00	42.90	3.85
376	692	1.068194	GTGGACTCAGACAACGAGGAG	60.068	57.143	0.00	0.00	34.66	3.69
377	693	0.959553	GTGGACTCAGACAACGAGGA	59.040	55.000	0.00	0.00	34.66	3.71
378	694	0.038159	GGTGGACTCAGACAACGAGG	60.038	60.000	0.00	0.00	34.66	4.63
379	695	3.498676	GGTGGACTCAGACAACGAG	57.501	57.895	0.00	0.00	36.53	4.18
381	697	4.245054	CGGTGGACTCAGACAACG	57.755	61.111	0.00	0.00	41.70	4.10
382	698	1.668151	GGCGGTGGACTCAGACAAC	60.668	63.158	0.00	0.00	0.00	3.32
383	699	2.741092	GGCGGTGGACTCAGACAA	59.259	61.111	0.00	0.00	0.00	3.18
384	700	3.680786	CGGCGGTGGACTCAGACA	61.681	66.667	0.00	0.00	0.00	3.41

Showing 1 to 25 of 326 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.