AutoCloner

Multiple sequence alignment - TraesCS5D01G423900

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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	TraesCS5D01G423900	chr5D	100.000	2270	0	0	1	2270	483659945	483657676	0.000000e+00	4193.0
1	TraesCS5D01G423900	chr5D	85.621	153	14	7	37	185	157451658	157451806	1.090000e-33	154.0
2	TraesCS5D01G423900	chr5A	92.277	1243	76	9	224	1456	605144753	605143521	0.000000e+00	1746.0
3	TraesCS5D01G423900	chr5A	89.150	682	42	14	1612	2270	605140876	605140204	0.000000e+00	821.0
4	TraesCS5D01G423900	chr5A	82.759	203	19	11	186	383	663403794	663403603	1.390000e-37	167.0
5	TraesCS5D01G423900	chr5A	79.221	154	19	10	2128	2270	605698346	605698195	6.680000e-16	95.3
6	TraesCS5D01G423900	chr5B	89.496	1409	70	28	182	1560	594760767	594759407	0.000000e+00	1711.0
7	TraesCS5D01G423900	chr5B	85.760	625	55	16	1574	2171	594759358	594758741	4.110000e-177	630.0
8	TraesCS5D01G423900	chr5B	88.108	185	19	2	3	185	510513940	510513757	1.370000e-52	217.0
9	TraesCS5D01G423900	chr5B	89.583	48	2	3	1392	1439	212631059	212631103	8.760000e-05	58.4
10	TraesCS5D01G423900	chr4D	79.075	411	51	20	893	1290	483448576	483448188	1.350000e-62	250.0
11	TraesCS5D01G423900	chr4D	83.744	203	16	11	186	383	483449727	483449537	2.320000e-40	176.0
12	TraesCS5D01G423900	chr4D	78.095	315	35	21	197	503	483461882	483461594	3.880000e-38	169.0
13	TraesCS5D01G423900	chr4A	90.909	187	11	5	1	185	713286181	713285999	1.740000e-61	246.0
14	TraesCS5D01G423900	chr3B	87.831	189	16	6	1	185	782683576	782683391	4.910000e-52	215.0
15	TraesCS5D01G423900	chr3B	86.170	188	20	6	1	185	782685208	782685024	4.950000e-47	198.0
16	TraesCS5D01G423900	chr7B	88.268	179	18	2	1	177	510721894	510721717	6.350000e-51	211.0
17	TraesCS5D01G423900	chr1B	86.364	176	22	2	10	185	594860384	594860211	8.280000e-45	191.0
18	TraesCS5D01G423900	chr7D	80.156	257	38	10	2026	2270	613765050	613764795	1.790000e-41	180.0
19	TraesCS5D01G423900	chr4B	83.254	209	16	12	182	383	613710662	613710858	8.330000e-40	174.0
20	TraesCS5D01G423900	chr6D	82.587	201	18	9	2081	2270	122522303	122522497	6.490000e-36	161.0
21	TraesCS5D01G423900	chr7A	81.407	199	21	9	2084	2270	37851799	37851605	5.050000e-32	148.0
22	TraesCS5D01G423900	chr1D	83.099	142	13	6	2135	2270	228041548	228041684	3.960000e-23	119.0
23	TraesCS5D01G423900	chr1A	81.333	150	13	9	2135	2270	517388566	517388714	8.570000e-20	108.0
24	TraesCS5D01G423900	chrUn	79.355	155	16	12	2130	2270	308646341	308646189	6.680000e-16	95.3
25	TraesCS5D01G423900	chr6A	79.355	155	16	12	2130	2270	607138756	607138604	6.680000e-16	95.3
26	TraesCS5D01G423900	chr6B	93.182	44	2	1	70	113	82199257	82199299	1.880000e-06	63.9
27	TraesCS5D01G423900	chr6B	93.182	44	2	1	70	113	82218411	82218453	1.880000e-06	63.9
28	TraesCS5D01G423900	chr2A	95.000	40	1	1	1398	1437	203719570	203719532	6.770000e-06	62.1

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	TraesCS5D01G423900	chr5D	483657676	483659945	2269	True	4193.0	4193	100.0000	1	2270	1	chr5D.!!$R1	2269
1	TraesCS5D01G423900	chr5A	605140204	605144753	4549	True	1283.5	1746	90.7135	224	2270	2	chr5A.!!$R3	2046
2	TraesCS5D01G423900	chr5B	594758741	594760767	2026	True	1170.5	1711	87.6280	182	2171	2	chr5B.!!$R2	1989
3	TraesCS5D01G423900	chr4D	483448188	483449727	1539	True	213.0	250	81.4095	186	1290	2	chr4D.!!$R2	1104
4	TraesCS5D01G423900	chr3B	782683391	782685208	1817	True	206.5	215	87.0005	1	185	2	chr3B.!!$R1	184

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
886	2204	1.000283	CCTAGGCCTAGTCTTCATGCG	60.0	57.143	33.0	14.38	0.0	4.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1758	6027	0.681175	ATTGGCCCAAGAAGTGTTGC	59.319	50.0	1.16	0.0	0.0	4.17	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
106	107	2.871633	GGAACAGCCAACCAATTTTGTG	59.128	45.455	0.00	0.00	36.34	3.33
170	172	5.801380	ACCTAACCTGTAATGTGGTAGTTG	58.199	41.667	0.00	0.00	35.17	3.16
177	179	5.431420	TGTAATGTGGTAGTTGTTTGCTG	57.569	39.130	0.00	0.00	0.00	4.41
358	1120	4.813161	ACTTGAATGTGACTGTGAGTGAAG	59.187	41.667	0.00	0.00	0.00	3.02
462	1225	1.449070	CTCTTTAACCCCCGCGGAC	60.449	63.158	30.73	0.00	34.64	4.79
463	1226	2.816520	CTTTAACCCCCGCGGACG	60.817	66.667	30.73	18.68	39.67	4.79
464	1227	3.299524	CTTTAACCCCCGCGGACGA	62.300	63.158	30.73	3.57	43.93	4.20
465	1228	2.582734	CTTTAACCCCCGCGGACGAT	62.583	60.000	30.73	13.15	43.93	3.73
532	1295	6.841755	AGTATAATCTCACCTGAGCCTAACTT	59.158	38.462	0.00	0.00	41.80	2.66
539	1302	6.096987	TCTCACCTGAGCCTAACTTATACAAG	59.903	42.308	0.00	0.00	41.80	3.16
628	1500	2.484287	AAACCCCATCAGGCAGGACG	62.484	60.000	0.00	0.00	0.00	4.79
675	1834	3.391049	AGAAAGTCGAAGAAAACGGAGG	58.609	45.455	0.00	0.00	39.69	4.30
878	2196	3.130227	CACCGCCTAGGCCTAGTC	58.870	66.667	33.00	23.34	46.52	2.59
886	2204	1.000283	CCTAGGCCTAGTCTTCATGCG	60.000	57.143	33.00	14.38	0.00	4.73
922	2240	3.447586	TGCTCGTCTCCTGCTAATTAACT	59.552	43.478	0.00	0.00	0.00	2.24
956	2282	3.499048	CATTACGGCAGTATAGGTAGCG	58.501	50.000	0.00	0.00	32.12	4.26
957	2283	1.527034	TACGGCAGTATAGGTAGCGG	58.473	55.000	0.00	0.00	0.00	5.52
981	2307	5.517770	GCCATTTGCAGATCAACTAATCAAC	59.482	40.000	0.00	0.00	40.77	3.18
983	2309	6.971184	CCATTTGCAGATCAACTAATCAACTC	59.029	38.462	0.00	0.00	33.73	3.01
991	2317	3.119388	TCAACTAATCAACTCCGTACGGG	60.119	47.826	32.80	24.55	35.59	5.28
998	2324	4.253257	CTCCGTACGGGCGAGCTC	62.253	72.222	32.80	2.73	34.94	4.09
1008	2334	1.139734	GGCGAGCTCAATGACGAGA	59.860	57.895	15.40	0.00	34.79	4.04
1035	2361	1.136690	CGTGCTTCTGCGTCTGTTTA	58.863	50.000	0.00	0.00	43.34	2.01
1044	2370	1.338973	TGCGTCTGTTTAGTCGTCCTT	59.661	47.619	0.00	0.00	37.69	3.36
1062	2388	2.441901	CTCCTCGCTGGCTCCTCT	60.442	66.667	0.00	0.00	35.26	3.69
1203	2840	2.956964	CCGCAAGAGATCGCCGAC	60.957	66.667	0.00	0.00	43.02	4.79
1312	3032	1.412710	TGATAAGGTGTCCATCGGCTC	59.587	52.381	0.00	0.00	0.00	4.70
1426	3151	3.002246	GCTGCGTCAATTAATTCGGATCA	59.998	43.478	10.27	3.68	0.00	2.92
1502	3227	4.397420	ACATGTGCCAACTATGTTTCTCA	58.603	39.130	0.00	0.00	31.38	3.27
1532	3265	3.057315	CCGTTTGGAATGCTGAAACTGAT	60.057	43.478	0.00	0.00	37.49	2.90
1555	3288	4.897076	TCAATACCGGCCTTGTCTAATCTA	59.103	41.667	14.31	0.00	0.00	1.98
1683	5952	5.860182	TCGTTTACTAACCAATCGACTGAAG	59.140	40.000	0.00	0.00	0.00	3.02
1734	6003	7.963465	GTCTTATAGCACAACTTAAGCCTTTTC	59.037	37.037	1.29	0.00	0.00	2.29
1750	6019	3.305744	CCTTTTCCCCATACAAACCAACG	60.306	47.826	0.00	0.00	0.00	4.10
1758	6027	1.787057	TACAAACCAACGCAAGCCCG	61.787	55.000	0.00	0.00	45.62	6.13
1790	6059	1.603326	GGGCCAATGCAAAACAACAAG	59.397	47.619	4.39	0.00	40.13	3.16
1809	6080	7.714377	ACAACAAGCCATTGATGAACAATTTTA	59.286	29.630	5.41	0.00	45.60	1.52
2124	6414	9.716556	AATGGATTAGAGATATCGGTATTACCT	57.283	33.333	11.05	0.00	35.66	3.08
2192	6483	8.816640	TGAAGTTTAAGGAAGAATGAATTTGC	57.183	30.769	0.00	0.00	0.00	3.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.421248	CCCGCCCCTAAATAAACCGTTA	60.421	50.000	0.00	0.00	0.00	3.18
32	33	7.781324	AAATTGATCTGGTTTATGACAGGTT	57.219	32.000	0.00	0.00	35.47	3.50
86	87	2.871633	CCACAAAATTGGTTGGCTGTTC	59.128	45.455	0.00	0.00	32.50	3.18
96	97	8.887717	TGTTTCAAAAATCTACCACAAAATTGG	58.112	29.630	0.00	0.00	43.04	3.16
147	149	5.308759	ACAACTACCACATTACAGGTTAGGT	59.691	40.000	0.00	0.00	39.31	3.08
148	150	5.801380	ACAACTACCACATTACAGGTTAGG	58.199	41.667	0.00	0.00	39.31	2.69
149	151	7.581476	CAAACAACTACCACATTACAGGTTAG	58.419	38.462	0.00	0.00	39.31	2.34
152	154	4.277423	GCAAACAACTACCACATTACAGGT	59.723	41.667	0.00	0.00	41.89	4.00
155	157	4.884744	ACAGCAAACAACTACCACATTACA	59.115	37.500	0.00	0.00	0.00	2.41
170	172	4.211374	CCCTAATGCGAGTATACAGCAAAC	59.789	45.833	23.45	1.89	44.51	2.93
177	179	1.403780	CCGGCCCTAATGCGAGTATAC	60.404	57.143	0.00	0.00	0.00	1.47
201	957	3.259876	ACGGGAATATTATAAGCTCGGCA	59.740	43.478	0.00	0.00	0.00	5.69
358	1120	3.959293	TGGGTCATGGATGATCATATGC	58.041	45.455	8.54	6.32	39.68	3.14
462	1225	3.104470	CGATAATGATGGAGCTCGATCG	58.896	50.000	27.18	16.04	34.37	3.69
463	1226	4.103365	ACGATAATGATGGAGCTCGATC	57.897	45.455	26.66	26.66	0.00	3.69
464	1227	4.527509	AACGATAATGATGGAGCTCGAT	57.472	40.909	11.42	11.42	0.00	3.59
465	1228	4.322080	AAACGATAATGATGGAGCTCGA	57.678	40.909	7.83	3.70	0.00	4.04
471	1234	8.426881	TGTTCGATTAAAACGATAATGATGGA	57.573	30.769	8.49	0.00	39.45	3.41
509	1272	8.958060	ATAAGTTAGGCTCAGGTGAGATTATA	57.042	34.615	11.29	0.00	44.74	0.98
517	1280	6.222038	TCTTGTATAAGTTAGGCTCAGGTG	57.778	41.667	0.00	0.00	35.38	4.00
532	1295	7.044181	GCTATATGCATTGAGCCTCTTGTATA	58.956	38.462	17.55	7.88	44.83	1.47
675	1834	3.085010	CACGCGACGCACTTTTGC	61.085	61.111	21.35	0.00	46.21	3.68
873	2191	3.786635	AGGCTAAACGCATGAAGACTAG	58.213	45.455	0.00	0.00	41.67	2.57
878	2196	5.853282	GCATTTATAGGCTAAACGCATGAAG	59.147	40.000	0.00	0.00	41.67	3.02
886	2204	5.405873	GGAGACGAGCATTTATAGGCTAAAC	59.594	44.000	0.00	0.00	42.35	2.01
947	2267	0.182537	TGCAAATGGCCGCTACCTAT	59.817	50.000	0.00	0.00	43.89	2.57
956	2282	4.098349	TGATTAGTTGATCTGCAAATGGCC	59.902	41.667	0.00	0.00	43.89	5.36
957	2283	5.252969	TGATTAGTTGATCTGCAAATGGC	57.747	39.130	0.00	0.00	45.13	4.40
981	2307	4.253257	GAGCTCGCCCGTACGGAG	62.253	72.222	35.41	26.34	37.50	4.63
983	2309	3.426117	ATTGAGCTCGCCCGTACGG	62.426	63.158	27.68	27.68	0.00	4.02
991	2317	0.179150	AGTCTCGTCATTGAGCTCGC	60.179	55.000	9.64	0.00	35.90	5.03
998	2324	2.476873	CGGGAGTAGTCTCGTCATTG	57.523	55.000	11.87	0.00	42.18	2.82
1008	2334	1.592223	GCAGAAGCACGGGAGTAGT	59.408	57.895	0.00	0.00	44.67	2.73
1035	2361	1.001887	AGCGAGGAGAAGGACGACT	60.002	57.895	0.00	0.00	0.00	4.18
1044	2370	2.441164	GAGGAGCCAGCGAGGAGA	60.441	66.667	2.12	0.00	41.22	3.71
1092	2418	2.741092	CTACGGTGGTGGTGCAGT	59.259	61.111	0.00	0.00	0.00	4.40
1096	2422	2.047274	CTGCCTACGGTGGTGGTG	60.047	66.667	0.00	0.00	0.00	4.17
1097	2423	4.016706	GCTGCCTACGGTGGTGGT	62.017	66.667	0.00	0.00	0.00	4.16
1098	2424	3.665675	GAGCTGCCTACGGTGGTGG	62.666	68.421	0.00	0.00	0.00	4.61
1312	3032	3.938963	ACCGCAAACTGAAGTATACATGG	59.061	43.478	5.50	0.00	0.00	3.66
1399	3123	3.211045	GAATTAATTGACGCAGCCCCTA	58.789	45.455	5.17	0.00	0.00	3.53
1400	3124	2.024414	GAATTAATTGACGCAGCCCCT	58.976	47.619	5.17	0.00	0.00	4.79
1426	3151	0.251653	TTGACGGACTACAGCCCTCT	60.252	55.000	0.00	0.00	0.00	3.69
1532	3265	3.709653	AGATTAGACAAGGCCGGTATTGA	59.290	43.478	22.53	5.38	0.00	2.57
1601	5854	2.818130	TCTTGAACAATTTGCAGGGC	57.182	45.000	0.00	0.00	0.00	5.19
1603	5856	3.321682	TCCCTTCTTGAACAATTTGCAGG	59.678	43.478	0.00	0.00	0.00	4.85
1604	5857	4.038402	AGTCCCTTCTTGAACAATTTGCAG	59.962	41.667	0.00	0.00	0.00	4.41
1605	5858	3.960102	AGTCCCTTCTTGAACAATTTGCA	59.040	39.130	0.00	0.00	0.00	4.08
1606	5859	4.301628	CAGTCCCTTCTTGAACAATTTGC	58.698	43.478	0.00	0.00	0.00	3.68
1607	5860	4.797275	GCCAGTCCCTTCTTGAACAATTTG	60.797	45.833	0.00	0.00	0.00	2.32
1608	5861	3.321968	GCCAGTCCCTTCTTGAACAATTT	59.678	43.478	0.00	0.00	0.00	1.82
1609	5862	2.893489	GCCAGTCCCTTCTTGAACAATT	59.107	45.455	0.00	0.00	0.00	2.32
1610	5863	2.108952	AGCCAGTCCCTTCTTGAACAAT	59.891	45.455	0.00	0.00	0.00	2.71
1706	5975	6.712276	AGGCTTAAGTTGTGCTATAAGACTT	58.288	36.000	4.02	0.00	40.04	3.01
1710	5979	7.251281	GGAAAAGGCTTAAGTTGTGCTATAAG	58.749	38.462	0.00	0.00	0.00	1.73
1734	6003	0.962489	TTGCGTTGGTTTGTATGGGG	59.038	50.000	0.00	0.00	0.00	4.96
1750	6019	2.050077	GAAGTGTTGCGGGCTTGC	60.050	61.111	0.00	0.00	0.00	4.01
1758	6027	0.681175	ATTGGCCCAAGAAGTGTTGC	59.319	50.000	1.16	0.00	0.00	4.17
2192	6483	3.283751	TGAAAGGGTAATACCAATGCCG	58.716	45.455	12.03	0.00	41.02	5.69
2239	6530	9.201989	AGGGTTTCATTCTTTCTTAGAAAAACT	57.798	29.630	8.82	0.00	45.62	2.66
2240	6531	9.817809	AAGGGTTTCATTCTTTCTTAGAAAAAC	57.182	29.630	8.82	8.57	45.62	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.