AutoCloner

Multiple sequence alignment - TraesCS5D01G067100

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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	TraesCS5D01G067100	chr5D	100.000	4854	0	0	1	4854	62297288	62302141	0.000000e+00	8964.0
1	TraesCS5D01G067100	chr5D	90.194	3498	276	34	411	3881	62523207	62519750	0.000000e+00	4497.0
2	TraesCS5D01G067100	chr5D	91.727	278	21	2	3938	4214	62307818	62308094	7.620000e-103	385.0
3	TraesCS5D01G067100	chr5D	93.443	61	4	0	3877	3937	62519585	62519525	1.860000e-14	91.6
4	TraesCS5D01G067100	chr5A	95.800	3857	139	14	153	4003	52340891	52344730	0.000000e+00	6204.0
5	TraesCS5D01G067100	chr5A	90.596	3488	264	30	411	3881	52418123	52414683	0.000000e+00	4566.0
6	TraesCS5D01G067100	chr5A	90.899	868	68	8	3991	4854	52346236	52347096	0.000000e+00	1155.0
7	TraesCS5D01G067100	chr5A	90.764	314	22	3	3938	4246	52348925	52349236	3.500000e-111	412.0
8	TraesCS5D01G067100	chr5A	77.193	798	121	38	4077	4851	539863930	539864689	4.520000e-110	409.0
9	TraesCS5D01G067100	chr5A	96.753	154	5	0	1	154	52340544	52340697	1.730000e-64	257.0
10	TraesCS5D01G067100	chr5A	84.393	173	15	2	1	163	456475444	456475614	5.030000e-35	159.0
11	TraesCS5D01G067100	chr5B	94.929	3116	111	13	1744	4854	68188118	68185045	0.000000e+00	4835.0
12	TraesCS5D01G067100	chr5B	90.284	3345	263	34	591	3917	67959003	67962303	0.000000e+00	4320.0
13	TraesCS5D01G067100	chr5B	96.440	618	22	0	833	1450	68189087	68188470	0.000000e+00	1020.0
14	TraesCS5D01G067100	chr5B	95.302	298	12	1	1444	1741	68188441	68188146	5.690000e-129	472.0
15	TraesCS5D01G067100	chr5B	92.058	277	21	1	3938	4214	68176862	68176587	5.890000e-104	388.0
16	TraesCS5D01G067100	chr5B	92.251	271	13	5	442	710	68189545	68189281	1.280000e-100	377.0
17	TraesCS5D01G067100	chr5B	93.814	194	11	1	411	603	67958618	67958811	1.710000e-74	291.0
18	TraesCS5D01G067100	chr2A	79.812	1704	278	33	2268	3937	589791528	589793199	0.000000e+00	1181.0
19	TraesCS5D01G067100	chr2A	83.252	818	128	7	3038	3854	590639021	590639830	0.000000e+00	743.0
20	TraesCS5D01G067100	chr2A	85.629	501	66	4	2253	2752	589795689	589796184	5.570000e-144	521.0
21	TraesCS5D01G067100	chr2A	75.000	252	36	16	3938	4171	265155583	265155341	1.860000e-14	91.6
22	TraesCS5D01G067100	chr2B	79.898	1572	279	33	2268	3822	526379637	526381188	0.000000e+00	1118.0
23	TraesCS5D01G067100	chr2B	79.523	1636	265	33	2268	3865	525826375	525827978	0.000000e+00	1101.0
24	TraesCS5D01G067100	chr2D	79.635	1591	263	43	2268	3822	446603633	446605198	0.000000e+00	1086.0
25	TraesCS5D01G067100	chr2D	86.831	486	63	1	2268	2753	446318666	446319150	4.270000e-150	542.0
26	TraesCS5D01G067100	chr2D	82.328	232	39	2	1216	1446	446600214	446600444	2.960000e-47	200.0
27	TraesCS5D01G067100	chr3D	83.548	620	69	24	3988	4588	602778472	602777867	2.550000e-152	549.0
28	TraesCS5D01G067100	chr3D	84.397	141	17	2	4716	4854	602777481	602777344	3.050000e-27	134.0
29	TraesCS5D01G067100	chr3A	80.159	630	85	26	4231	4854	672682213	672681618	7.460000e-118	435.0
30	TraesCS5D01G067100	chr3A	83.486	436	65	5	4231	4665	652686662	652686233	2.720000e-107	399.0
31	TraesCS5D01G067100	chr3A	80.000	545	84	18	4122	4650	652638627	652638092	3.550000e-101	379.0
32	TraesCS5D01G067100	chr3A	80.994	463	64	17	4152	4607	652347401	652346956	3.600000e-91	346.0
33	TraesCS5D01G067100	chr3A	82.908	392	60	5	4234	4624	652398455	652398070	3.600000e-91	346.0
34	TraesCS5D01G067100	chr3A	84.615	169	18	2	1	163	20203917	20203751	1.400000e-35	161.0
35	TraesCS5D01G067100	chr6B	80.175	570	79	22	4290	4854	29913563	29913023	3.520000e-106	396.0
36	TraesCS5D01G067100	chr6B	82.569	436	71	4	4234	4667	240244153	240243721	3.550000e-101	379.0
37	TraesCS5D01G067100	chr7A	87.037	162	11	4	12	163	672030819	672030980	1.800000e-39	174.0
38	TraesCS5D01G067100	chr6A	85.799	169	16	2	1	163	77506949	77506783	6.460000e-39	172.0
39	TraesCS5D01G067100	chr7D	85.380	171	15	1	1	161	580547807	580547977	8.360000e-38	169.0

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	TraesCS5D01G067100	chr5D	62297288	62302141	4853	False	8964.0	8964	100.0000	1	4854	1	chr5D.!!$F1	4853
1	TraesCS5D01G067100	chr5D	62519525	62523207	3682	True	2294.3	4497	91.8185	411	3937	2	chr5D.!!$R1	3526
2	TraesCS5D01G067100	chr5A	52414683	52418123	3440	True	4566.0	4566	90.5960	411	3881	1	chr5A.!!$R1	3470
3	TraesCS5D01G067100	chr5A	52340544	52349236	8692	False	2007.0	6204	93.5540	1	4854	4	chr5A.!!$F3	4853
4	TraesCS5D01G067100	chr5A	539863930	539864689	759	False	409.0	409	77.1930	4077	4851	1	chr5A.!!$F2	774
5	TraesCS5D01G067100	chr5B	67958618	67962303	3685	False	2305.5	4320	92.0490	411	3917	2	chr5B.!!$F1	3506
6	TraesCS5D01G067100	chr5B	68185045	68189545	4500	True	1676.0	4835	94.7305	442	4854	4	chr5B.!!$R2	4412
7	TraesCS5D01G067100	chr2A	589791528	589796184	4656	False	851.0	1181	82.7205	2253	3937	2	chr2A.!!$F2	1684
8	TraesCS5D01G067100	chr2A	590639021	590639830	809	False	743.0	743	83.2520	3038	3854	1	chr2A.!!$F1	816
9	TraesCS5D01G067100	chr2B	526379637	526381188	1551	False	1118.0	1118	79.8980	2268	3822	1	chr2B.!!$F2	1554
10	TraesCS5D01G067100	chr2B	525826375	525827978	1603	False	1101.0	1101	79.5230	2268	3865	1	chr2B.!!$F1	1597
11	TraesCS5D01G067100	chr2D	446600214	446605198	4984	False	643.0	1086	80.9815	1216	3822	2	chr2D.!!$F2	2606
12	TraesCS5D01G067100	chr3D	602777344	602778472	1128	True	341.5	549	83.9725	3988	4854	2	chr3D.!!$R1	866
13	TraesCS5D01G067100	chr3A	672681618	672682213	595	True	435.0	435	80.1590	4231	4854	1	chr3A.!!$R6	623
14	TraesCS5D01G067100	chr3A	652638092	652638627	535	True	379.0	379	80.0000	4122	4650	1	chr3A.!!$R4	528
15	TraesCS5D01G067100	chr6B	29913023	29913563	540	True	396.0	396	80.1750	4290	4854	1	chr6B.!!$R1	564

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
293	490	0.036732	AGGCATCTTGTTCGGCTTCA	59.963	50.000	0.00	0.00	30.19	3.02	F
1212	1759	1.581602	CACTTTTGTGCGTTGTTTCCG	59.418	47.619	0.00	0.00	44.07	4.30	F
2063	5116	0.373716	CCGCGGTATGCTGAAACTTC	59.626	55.000	19.50	0.00	43.27	3.01	F
2940	6279	1.067776	AGACTCGGTGAATCGAACCAC	60.068	52.381	10.88	10.88	38.77	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1325	1872	1.472480	GGCGCCAAAGAAATTAGCAGA	59.528	47.619	24.80	0.00	0.00	4.26	R
3190	6552	1.218875	CTTGCTGCACCGTGAACGTA	61.219	55.000	0.00	0.00	37.74	3.57	R
3736	7099	1.016130	CGAGCAATCCGACAACAGCT	61.016	55.000	0.00	0.00	34.61	4.24	R
4304	11653	2.609737	GGATTTTACCGGCGATCGAGAT	60.610	50.000	21.57	0.42	42.43	2.75	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
140	141	5.542635	ACACTGTCCAATAGACCTAACAAGA	59.457	40.000	0.00	0.00	45.68	3.02
156	352	5.422214	AACAAGATTAGGTACTCAGGGTG	57.578	43.478	0.00	0.00	41.75	4.61
166	362	1.072266	ACTCAGGGTGGTTAATGCCA	58.928	50.000	0.00	0.00	35.93	4.92
169	365	2.689983	CTCAGGGTGGTTAATGCCAATC	59.310	50.000	0.00	0.00	40.68	2.67
177	374	4.099266	GTGGTTAATGCCAATCTATTGCCA	59.901	41.667	0.00	0.00	40.68	4.92
232	429	1.267121	GCGGGGAGCCAGAATAGATA	58.733	55.000	0.00	0.00	40.81	1.98
242	439	1.805945	GAATAGATAGGCGCCGGCG	60.806	63.158	43.13	43.13	41.24	6.46
265	462	0.391263	GGACCACCTCGTCATCCAAC	60.391	60.000	0.00	0.00	34.24	3.77
293	490	0.036732	AGGCATCTTGTTCGGCTTCA	59.963	50.000	0.00	0.00	30.19	3.02
340	537	2.737039	CGCAGAGACTAAGGCCTTCTTC	60.737	54.545	24.49	19.06	36.93	2.87
394	591	2.939103	GACATACAAATCAAGCTCGGCT	59.061	45.455	0.00	0.00	42.56	5.52
478	675	6.531503	TTTGTTTGTCATTGTAGGTTTGGA	57.468	33.333	0.00	0.00	0.00	3.53
587	786	2.771089	TGAATCAGTCAAGGTGCACTC	58.229	47.619	17.98	7.02	31.51	3.51
732	1144	6.879458	GTGGATTTTTAGTCACATGTACCTCT	59.121	38.462	0.00	0.00	0.00	3.69
741	1153	6.465084	AGTCACATGTACCTCTTTTTCTACC	58.535	40.000	0.00	0.00	0.00	3.18
775	1187	1.769733	TCCGTTTTGTACCGTCGAAG	58.230	50.000	0.00	0.00	0.00	3.79
831	1368	9.757859	GCAATGTAATTCAAATAAATGTTGGTG	57.242	29.630	0.00	0.00	31.22	4.17
914	1460	5.103000	GTCCTCCGAATATGAATATCCACG	58.897	45.833	0.00	0.00	0.00	4.94
937	1483	9.204570	CACGTTCTATTTATACCCCTCTTATTG	57.795	37.037	0.00	0.00	0.00	1.90
997	1543	2.628178	TCAGAAGGACGAAGAAGAAGCA	59.372	45.455	0.00	0.00	0.00	3.91
1013	1559	2.998279	GCACCATGGCACTTGGAGC	61.998	63.158	13.04	13.24	42.27	4.70
1212	1759	1.581602	CACTTTTGTGCGTTGTTTCCG	59.418	47.619	0.00	0.00	44.07	4.30
1222	1769	2.350007	GCGTTGTTTCCGATTTGCAGTA	60.350	45.455	0.00	0.00	0.00	2.74
1325	1872	0.968901	TTCGGGCTCGGTGACTACAT	60.969	55.000	5.94	0.00	36.95	2.29
1731	4758	6.957920	TTCTTCATTTCAATGTGGTCTCAA	57.042	33.333	0.00	0.00	37.65	3.02
1866	4918	5.660629	TCGTTAACAAAATCAGCGAGAAA	57.339	34.783	6.39	0.00	0.00	2.52
1920	4972	1.066002	CAACCATTTAGCCTGGCATCG	59.934	52.381	22.65	0.73	37.27	3.84
1921	4973	0.546122	ACCATTTAGCCTGGCATCGA	59.454	50.000	22.65	3.91	37.27	3.59
1922	4974	1.143684	ACCATTTAGCCTGGCATCGAT	59.856	47.619	22.65	6.25	37.27	3.59
1923	4975	1.808945	CCATTTAGCCTGGCATCGATC	59.191	52.381	22.65	0.00	0.00	3.69
2045	5097	4.551729	TGCGCCTTTAGCATACCC	57.448	55.556	4.18	0.00	44.04	3.69
2063	5116	0.373716	CCGCGGTATGCTGAAACTTC	59.626	55.000	19.50	0.00	43.27	3.01
2165	5257	7.825331	TGACAATGAAACCCACTTATTAACA	57.175	32.000	0.00	0.00	0.00	2.41
2266	5359	5.989168	AGCATAATTGATCAACCATGCATTG	59.011	36.000	34.83	18.22	40.48	2.82
2894	6229	1.278238	GACAGGTTACAATCGCTCGG	58.722	55.000	0.00	0.00	0.00	4.63
2940	6279	1.067776	AGACTCGGTGAATCGAACCAC	60.068	52.381	10.88	10.88	38.77	4.16
3190	6552	5.480642	ACATATCGAGCATCATCCTCTTT	57.519	39.130	0.00	0.00	33.17	2.52
3560	6922	1.572085	CTTCAACAGTGAGGCGCCAG	61.572	60.000	31.54	14.95	34.49	4.85
3736	7099	3.578978	TGACCTGTTCTACTGGGTTGTA	58.421	45.455	7.51	0.00	41.00	2.41
4003	9461	8.285776	GTAGTTCAGTTAACTGCGTTTAACTA	57.714	34.615	26.93	26.93	46.15	2.24
4026	9484	1.151668	CGCAACAGAAAGAGAGTGGG	58.848	55.000	0.00	0.00	0.00	4.61
4133	9596	1.655484	CAATGTGTGAGGCAGCGATA	58.345	50.000	0.00	0.00	0.00	2.92
4171	10393	0.678048	CCTTTCCCCTTCTCCAAGCG	60.678	60.000	0.00	0.00	0.00	4.68
4304	11653	0.390492	CTGCCGCTGATCTCATACCA	59.610	55.000	0.00	0.00	0.00	3.25
4364	11713	4.292178	CTCCGATGAGCTCGCCCC	62.292	72.222	9.64	0.00	46.25	5.80
4500	11850	0.603569	ACTTGCTCGAGACGGTCATT	59.396	50.000	18.75	0.00	0.00	2.57
4625	11989	1.555075	GACCTCACCCAAGCAGATGTA	59.445	52.381	0.00	0.00	0.00	2.29
4669	12033	4.324991	GGTCGACCCCACCGCTTT	62.325	66.667	24.75	0.00	0.00	3.51
4718	12339	0.460284	GCATTCTGATGACGACGGGT	60.460	55.000	0.00	0.00	35.16	5.28
4792	12419	1.390565	CCACTACCCCTCTACACGAG	58.609	60.000	0.00	0.00	39.57	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	8.918202	ACACAAAGACTTATATTTCAGGTTCA	57.082	30.769	0.00	0.00	0.00	3.18
96	97	7.030768	CAGTGTGCAATCAAAATCATGTGATA	58.969	34.615	0.00	0.00	33.31	2.15
140	141	5.397559	GCATTAACCACCCTGAGTACCTAAT	60.398	44.000	0.00	0.00	0.00	1.73
150	151	2.738743	AGATTGGCATTAACCACCCTG	58.261	47.619	0.00	0.00	40.19	4.45
177	374	1.115467	CTCCTCGTATCCCTGCTTGT	58.885	55.000	0.00	0.00	0.00	3.16
265	462	1.303799	ACAAGATGCCTGCTTGCTCG	61.304	55.000	9.40	0.00	45.00	5.03
374	571	2.939103	GAGCCGAGCTTGATTTGTATGT	59.061	45.455	1.22	0.00	39.88	2.29
394	591	1.000771	CGGAGACAGTGAGGGAGGA	60.001	63.158	0.00	0.00	0.00	3.71
656	1060	7.393841	TTTTGCTATCAATGTGTCATCATCA	57.606	32.000	0.00	0.00	31.33	3.07
686	1093	5.575218	CCACAAGTACCAACAAGTCAAAAAC	59.425	40.000	0.00	0.00	0.00	2.43
687	1094	5.477291	TCCACAAGTACCAACAAGTCAAAAA	59.523	36.000	0.00	0.00	0.00	1.94
688	1095	5.010933	TCCACAAGTACCAACAAGTCAAAA	58.989	37.500	0.00	0.00	0.00	2.44
689	1096	4.590918	TCCACAAGTACCAACAAGTCAAA	58.409	39.130	0.00	0.00	0.00	2.69
690	1097	4.223556	TCCACAAGTACCAACAAGTCAA	57.776	40.909	0.00	0.00	0.00	3.18
691	1098	3.916359	TCCACAAGTACCAACAAGTCA	57.084	42.857	0.00	0.00	0.00	3.41
692	1099	5.767816	AAATCCACAAGTACCAACAAGTC	57.232	39.130	0.00	0.00	0.00	3.01
693	1100	6.538945	AAAAATCCACAAGTACCAACAAGT	57.461	33.333	0.00	0.00	0.00	3.16
694	1101	7.712797	ACTAAAAATCCACAAGTACCAACAAG	58.287	34.615	0.00	0.00	0.00	3.16
732	1144	7.977853	GGATACACTAACATCGAGGTAGAAAAA	59.022	37.037	1.83	0.00	40.09	1.94
741	1153	5.575606	ACAAAACGGATACACTAACATCGAG	59.424	40.000	0.00	0.00	0.00	4.04
831	1368	6.663523	CCTATTTTATCCCATCATTACCCACC	59.336	42.308	0.00	0.00	0.00	4.61
1013	1559	2.603075	TCCCCTCCAATTCACAAAGG	57.397	50.000	0.00	0.00	0.00	3.11
1222	1769	2.933906	CACGTTTGTTACCACAGTCAGT	59.066	45.455	0.00	0.00	33.22	3.41
1325	1872	1.472480	GGCGCCAAAGAAATTAGCAGA	59.528	47.619	24.80	0.00	0.00	4.26
1514	2606	7.103641	TCTGTTATTGGCTGGTTCTAGTTAAG	58.896	38.462	0.00	0.00	0.00	1.85
1719	4746	6.041865	TCCATCAAATTTGTTGAGACCACATT	59.958	34.615	24.43	0.00	31.23	2.71
1726	4753	6.713762	ACACTTCCATCAAATTTGTTGAGA	57.286	33.333	24.43	17.93	31.23	3.27
1731	4758	6.275335	CAGACAACACTTCCATCAAATTTGT	58.725	36.000	17.47	3.04	0.00	2.83
1790	4842	7.660030	AATAAATGTATCCCAAGTTCCCAAG	57.340	36.000	0.00	0.00	0.00	3.61
1860	4912	9.891535	CTTCTTCTTTTCAAACAATTTTTCTCG	57.108	29.630	0.00	0.00	0.00	4.04
1866	4918	9.942850	TTTCCTCTTCTTCTTTTCAAACAATTT	57.057	25.926	0.00	0.00	0.00	1.82
1923	4975	8.818057	GCTTATGGTTTGTGTCTATTACAGTAG	58.182	37.037	0.00	0.00	39.29	2.57
2063	5116	6.913170	ACATGACAAGTTATAAGGCAGTTTG	58.087	36.000	0.00	0.00	0.00	2.93
2255	5348	3.404224	TGCACAAATCAATGCATGGTT	57.596	38.095	0.00	0.00	46.63	3.67
2266	5359	3.567164	CAGTCCATATCCCTGCACAAATC	59.433	47.826	0.00	0.00	0.00	2.17
2894	6229	7.954788	ACTTCAGACTATTTGTTTGAGAGAC	57.045	36.000	0.00	0.00	40.25	3.36
3190	6552	1.218875	CTTGCTGCACCGTGAACGTA	61.219	55.000	0.00	0.00	37.74	3.57
3560	6922	1.595382	CGATCGACTTCATGCCCCC	60.595	63.158	10.26	0.00	0.00	5.40
3736	7099	1.016130	CGAGCAATCCGACAACAGCT	61.016	55.000	0.00	0.00	34.61	4.24
4003	9461	2.614057	CACTCTCTTTCTGTTGCGGTTT	59.386	45.455	0.00	0.00	0.00	3.27
4026	9484	2.983592	CCTTCGGCCCAACACACC	60.984	66.667	0.00	0.00	0.00	4.16
4133	9596	7.834681	GGGAAAGGGAAACTAGTTGATATTTCT	59.165	37.037	22.55	4.83	32.72	2.52
4171	10393	3.188786	CAGGTTAGGTGAGCGCGC	61.189	66.667	26.66	26.66	0.00	6.86
4304	11653	2.609737	GGATTTTACCGGCGATCGAGAT	60.610	50.000	21.57	0.42	42.43	2.75
4646	12010	4.692475	GTGGGGTCGACCGTTGGG	62.692	72.222	27.68	0.00	41.60	4.12
4667	12031	4.560856	GCGGCGGTGTTGTGCAAA	62.561	61.111	9.78	0.00	0.00	3.68
4708	12072	3.367743	CGGAGGAACCCGTCGTCA	61.368	66.667	0.00	0.00	44.23	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.