AutoCloner

Multiple sequence alignment - TraesCS1A01G214900

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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	TraesCS1A01G214900	chr1A	100.000	2402	0	0	1	2402	379615881	379618282	0.000000e+00	4436
1	TraesCS1A01G214900	chr1A	95.916	1004	37	2	1400	2402	57483540	57482540	0.000000e+00	1624
2	TraesCS1A01G214900	chr1A	95.518	1004	41	2	1400	2402	358951332	358952332	0.000000e+00	1602
3	TraesCS1A01G214900	chr1A	95.423	1005	42	2	1399	2402	57501095	57500094	0.000000e+00	1598
4	TraesCS1A01G214900	chr1A	95.423	1005	42	3	1400	2402	80003007	80002005	0.000000e+00	1598
5	TraesCS1A01G214900	chr1A	95.788	926	38	1	474	1398	379138794	379137869	0.000000e+00	1493
6	TraesCS1A01G214900	chr1A	94.416	394	20	2	466	857	379146376	379145983	2.640000e-169	604
7	TraesCS1A01G214900	chr1A	89.693	456	45	1	1	454	379142514	379142059	4.450000e-162	580
8	TraesCS1A01G214900	chr1A	93.243	148	9	1	1257	1404	379145986	379145840	1.450000e-52	217
9	TraesCS1A01G214900	chr7A	95.721	1005	38	2	1399	2402	605065757	605064757	0.000000e+00	1613
10	TraesCS1A01G214900	chr7A	95.622	1005	39	2	1399	2402	404573897	404572897	0.000000e+00	1607
11	TraesCS1A01G214900	chr7A	85.301	449	59	5	12	453	232820787	232820339	7.830000e-125	457
12	TraesCS1A01G214900	chr3A	95.626	1006	41	3	1399	2402	20253778	20254782	0.000000e+00	1611
13	TraesCS1A01G214900	chr5A	95.522	1005	38	3	1400	2402	299534113	299533114	0.000000e+00	1600
14	TraesCS1A01G214900	chr4A	95.423	1005	44	2	1400	2402	33152599	33153603	0.000000e+00	1600
15	TraesCS1A01G214900	chr1B	92.038	942	68	7	466	1404	402502852	402503789	0.000000e+00	1317
16	TraesCS1A01G214900	chr2B	86.192	449	53	4	13	453	424760053	424759606	6.010000e-131	477
17	TraesCS1A01G214900	chr7B	85.746	449	55	6	12	452	303574151	303574598	1.300000e-127	466
18	TraesCS1A01G214900	chr7D	85.011	467	58	6	12	468	269490684	269491148	4.680000e-127	464
19	TraesCS1A01G214900	chr6A	84.501	471	68	4	1	468	262429478	262429010	6.050000e-126	460
20	TraesCS1A01G214900	chr6B	84.648	469	62	6	9	468	561220299	561219832	2.180000e-125	459
21	TraesCS1A01G214900	chr3D	84.922	451	58	5	12	453	399532631	399533080	4.710000e-122	448
22	TraesCS1A01G214900	chr5B	84.855	449	61	4	12	453	33201319	33201767	1.690000e-121	446

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	TraesCS1A01G214900	chr1A	379615881	379618282	2401	False	4436.0	4436	100.000	1	2402	1	chr1A.!!$F2	2401
1	TraesCS1A01G214900	chr1A	57482540	57483540	1000	True	1624.0	1624	95.916	1400	2402	1	chr1A.!!$R1	1002
2	TraesCS1A01G214900	chr1A	358951332	358952332	1000	False	1602.0	1602	95.518	1400	2402	1	chr1A.!!$F1	1002
3	TraesCS1A01G214900	chr1A	57500094	57501095	1001	True	1598.0	1598	95.423	1399	2402	1	chr1A.!!$R2	1003
4	TraesCS1A01G214900	chr1A	80002005	80003007	1002	True	1598.0	1598	95.423	1400	2402	1	chr1A.!!$R3	1002
5	TraesCS1A01G214900	chr1A	379137869	379146376	8507	True	723.5	1493	93.285	1	1404	4	chr1A.!!$R4	1403
6	TraesCS1A01G214900	chr7A	605064757	605065757	1000	True	1613.0	1613	95.721	1399	2402	1	chr7A.!!$R3	1003
7	TraesCS1A01G214900	chr7A	404572897	404573897	1000	True	1607.0	1607	95.622	1399	2402	1	chr7A.!!$R2	1003
8	TraesCS1A01G214900	chr3A	20253778	20254782	1004	False	1611.0	1611	95.626	1399	2402	1	chr3A.!!$F1	1003
9	TraesCS1A01G214900	chr5A	299533114	299534113	999	True	1600.0	1600	95.522	1400	2402	1	chr5A.!!$R1	1002
10	TraesCS1A01G214900	chr4A	33152599	33153603	1004	False	1600.0	1600	95.423	1400	2402	1	chr4A.!!$F1	1002
11	TraesCS1A01G214900	chr1B	402502852	402503789	937	False	1317.0	1317	92.038	466	1404	1	chr1B.!!$F1	938

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
400	4265	0.112025	TGACCACATTCACCATGCCA	59.888	50.0	0.0	0.0	36.14	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1788	8905	1.000163	ACGTACAACTGAGACAGCAGG	60.0	52.381	0.0	0.0	40.2	4.85	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	3886	0.323725	GGCAGGTGTTGGATGGACAT	60.324	55.000	0.00	0.00	0.00	3.06
24	3887	1.098050	GCAGGTGTTGGATGGACATC	58.902	55.000	3.72	3.72	37.11	3.06
30	3893	1.134936	TGTTGGATGGACATCGTACGG	60.135	52.381	16.52	2.32	38.69	4.02
32	3895	0.742505	TGGATGGACATCGTACGGTC	59.257	55.000	16.52	15.10	38.69	4.79
37	3900	2.202570	ACATCGTACGGTCGCTGC	60.203	61.111	16.52	0.00	31.47	5.25
48	3911	0.179100	GGTCGCTGCAGCTAGAATCA	60.179	55.000	34.22	8.12	39.32	2.57
52	3915	3.064545	GTCGCTGCAGCTAGAATCATTTT	59.935	43.478	34.22	0.00	39.32	1.82
78	3941	6.691754	TTGACTAAGTTGACAAATCTTGCA	57.308	33.333	0.00	0.00	0.00	4.08
84	3947	1.462616	TGACAAATCTTGCATCCCCG	58.537	50.000	0.00	0.00	0.00	5.73
97	3960	0.252197	ATCCCCGTCAACTTAGTGGC	59.748	55.000	0.00	0.00	0.00	5.01
139	4002	6.642733	AATATGGTGGGTAATAGCTAGCAT	57.357	37.500	20.61	20.61	44.96	3.79
141	4004	3.045634	TGGTGGGTAATAGCTAGCATGT	58.954	45.455	18.83	3.26	29.94	3.21
146	4009	4.039245	TGGGTAATAGCTAGCATGTGAGTC	59.961	45.833	18.83	0.70	0.00	3.36
206	4071	4.021925	GCTGGTGGGTCCGAGCTT	62.022	66.667	4.63	0.00	37.37	3.74
211	4076	1.371558	GTGGGTCCGAGCTTTCAGT	59.628	57.895	0.00	0.00	0.00	3.41
212	4077	0.250338	GTGGGTCCGAGCTTTCAGTT	60.250	55.000	0.00	0.00	0.00	3.16
250	4115	3.117888	TCATGAAATACAGAGGCCCTTCC	60.118	47.826	0.00	0.00	0.00	3.46
252	4117	0.546598	AAATACAGAGGCCCTTCCGG	59.453	55.000	0.00	0.00	40.77	5.14
253	4118	0.620700	AATACAGAGGCCCTTCCGGT	60.621	55.000	0.00	0.00	40.77	5.28
254	4119	1.338136	ATACAGAGGCCCTTCCGGTG	61.338	60.000	0.00	0.00	40.77	4.94
256	4121	4.332543	AGAGGCCCTTCCGGTGGA	62.333	66.667	15.90	0.00	40.77	4.02
269	4134	1.078426	GGTGGATCCCCGTTGTCAG	60.078	63.158	9.90	0.00	34.29	3.51
297	4162	5.885881	AGGAATCATTATTTTGCGCGTAAA	58.114	33.333	18.59	18.59	0.00	2.01
320	4185	2.571653	AGGAGGCACTTACTTGCATACA	59.428	45.455	0.00	0.00	39.71	2.29
321	4186	3.009033	AGGAGGCACTTACTTGCATACAA	59.991	43.478	0.00	0.00	39.71	2.41
334	4199	1.406887	GCATACAATCGTGGACCCAGT	60.407	52.381	0.00	0.00	0.00	4.00
338	4203	1.156736	CAATCGTGGACCCAGTTGTC	58.843	55.000	0.00	0.00	34.42	3.18
344	4209	1.003233	GGACCCAGTTGTCAGCCTC	60.003	63.158	0.00	0.00	36.97	4.70
396	4261	2.559698	TCGTTGACCACATTCACCAT	57.440	45.000	0.00	0.00	0.00	3.55
400	4265	0.112025	TGACCACATTCACCATGCCA	59.888	50.000	0.00	0.00	36.14	4.92
402	4267	1.243342	ACCACATTCACCATGCCACG	61.243	55.000	0.00	0.00	36.14	4.94
436	4301	1.524621	CGGTGGATGATGGTGAGGC	60.525	63.158	0.00	0.00	0.00	4.70
443	4308	1.622811	GATGATGGTGAGGCCTAGGAG	59.377	57.143	14.75	0.00	38.35	3.69
454	4319	1.001248	CCTAGGAGGGGAACGACCA	59.999	63.158	1.05	0.00	41.20	4.02
455	4320	0.616679	CCTAGGAGGGGAACGACCAA	60.617	60.000	1.05	0.00	41.20	3.67
459	4324	1.192803	GGAGGGGAACGACCAAGAGT	61.193	60.000	0.00	0.00	41.20	3.24
460	4325	0.685660	GAGGGGAACGACCAAGAGTT	59.314	55.000	0.00	0.00	41.20	3.01
547	7657	5.834239	AAGTATGTTGTCTCGTTAAACGG	57.166	39.130	0.00	0.00	42.81	4.44
783	7894	7.452880	ACACAACTAATGCATTCTACATGTT	57.547	32.000	16.86	9.54	0.00	2.71
804	7915	7.372451	TGTTTGAGGTGCTATTAATACACAC	57.628	36.000	20.21	16.69	36.00	3.82
918	8029	9.705103	AAATATGCATCAATAGGCACCTATATT	57.295	29.630	0.19	1.31	46.61	1.28
938	8049	5.668558	ATTAACACCGTCAAAGTGAACTC	57.331	39.130	0.00	0.00	38.63	3.01
940	8051	4.395959	AACACCGTCAAAGTGAACTCTA	57.604	40.909	0.00	0.00	38.63	2.43
950	8061	6.704493	GTCAAAGTGAACTCTATAACACACCA	59.296	38.462	0.00	0.00	35.97	4.17
1142	8253	9.105844	TGAATCCCCAAAATGGAACTTTATTTA	57.894	29.630	0.00	0.00	40.96	1.40
1143	8254	9.952030	GAATCCCCAAAATGGAACTTTATTTAA	57.048	29.630	0.00	0.00	40.96	1.52
1313	8424	6.599638	AGTTGCTATCCAATGAAGTTTCCTAC	59.400	38.462	0.00	0.00	35.55	3.18
1367	8478	3.736224	CCCCAGAGGCCACTGCAT	61.736	66.667	23.46	0.00	40.13	3.96
1405	8516	2.642311	TGTTGCCCTATGGACTGAAAGA	59.358	45.455	0.00	0.00	37.43	2.52
1453	8569	5.048713	GGGGTGAATAGGCGATTTTTATGAG	60.049	44.000	0.00	0.00	0.00	2.90
1482	8598	0.960364	TGAGGAATTTGCCGGTGAGC	60.960	55.000	1.90	0.00	0.00	4.26
1494	8610	2.711542	CCGGTGAGCAAATTCCTTAGT	58.288	47.619	0.00	0.00	0.00	2.24
1579	8695	3.972133	TCATGATGAAATGAAGGCAGGT	58.028	40.909	0.00	0.00	33.63	4.00
1595	8712	3.399330	GCAGGTACAAAGTACAGAAGCA	58.601	45.455	9.27	0.00	0.00	3.91
1684	8801	6.917217	AGTCTTCAGTCAAAGTCTTCAAAG	57.083	37.500	0.00	0.00	0.00	2.77
1744	8861	7.281999	GGAAATGGAAGAGTTGAGGAAATAGAG	59.718	40.741	0.00	0.00	0.00	2.43
1759	8876	4.576330	AATAGAGCCAGTAAGCTTGGTT	57.424	40.909	9.86	0.00	45.15	3.67
1907	9024	1.137086	CCCAGTCCTCACCGTATTCTG	59.863	57.143	0.00	0.00	0.00	3.02
1995	9114	2.431419	TCACAAACTTGGTCACTCGGTA	59.569	45.455	0.00	0.00	0.00	4.02
2114	9233	4.934001	TCAATCTCTTCAGTGATGCTCAAC	59.066	41.667	0.00	0.00	0.00	3.18
2245	9364	0.322008	GAGCAGCCAACCAGCTAGTT	60.322	55.000	0.00	0.00	42.61	2.24
2314	9433	8.537728	TGATAAGACATAAATGCCCTTCAATT	57.462	30.769	2.65	0.00	0.00	2.32
2323	9442	8.805175	CATAAATGCCCTTCAATTATATGACCA	58.195	33.333	0.00	0.00	30.96	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.034066	CCATCCAACACCTGCCGT	59.966	61.111	0.00	0.00	0.00	5.68
3	4	2.040544	GTCCATCCAACACCTGCCG	61.041	63.158	0.00	0.00	0.00	5.69
4	5	0.323725	ATGTCCATCCAACACCTGCC	60.324	55.000	0.00	0.00	0.00	4.85
5	6	1.098050	GATGTCCATCCAACACCTGC	58.902	55.000	0.00	0.00	31.76	4.85
6	7	1.339055	ACGATGTCCATCCAACACCTG	60.339	52.381	1.84	0.00	34.40	4.00
7	8	0.984230	ACGATGTCCATCCAACACCT	59.016	50.000	1.84	0.00	34.40	4.00
23	3886	4.771356	GCTGCAGCGACCGTACGA	62.771	66.667	25.23	0.00	35.09	3.43
52	3915	8.845227	TGCAAGATTTGTCAACTTAGTCAATAA	58.155	29.630	0.00	0.00	0.00	1.40
74	3937	1.349688	ACTAAGTTGACGGGGATGCAA	59.650	47.619	0.00	0.00	0.00	4.08
78	3941	0.252197	GCCACTAAGTTGACGGGGAT	59.748	55.000	0.00	0.00	0.00	3.85
84	3947	0.109723	TGTGGGGCCACTAAGTTGAC	59.890	55.000	6.53	0.00	46.30	3.18
97	3960	0.625316	TTGGAGGATGACATGTGGGG	59.375	55.000	1.15	0.00	0.00	4.96
128	3991	6.093219	CACAAAAGACTCACATGCTAGCTATT	59.907	38.462	17.23	0.00	0.00	1.73
129	3992	5.583854	CACAAAAGACTCACATGCTAGCTAT	59.416	40.000	17.23	5.06	0.00	2.97
130	3993	4.931601	CACAAAAGACTCACATGCTAGCTA	59.068	41.667	17.23	2.58	0.00	3.32
139	4002	6.934645	CCTCCTTATTACACAAAAGACTCACA	59.065	38.462	0.00	0.00	0.00	3.58
141	4004	5.938125	GCCTCCTTATTACACAAAAGACTCA	59.062	40.000	0.00	0.00	0.00	3.41
146	4009	6.349363	GGAAGTGCCTCCTTATTACACAAAAG	60.349	42.308	0.00	0.00	33.69	2.27
175	4040	2.054363	CACCAGCTATATCTTCGCACG	58.946	52.381	0.00	0.00	0.00	5.34
180	4045	2.028930	CGGACCCACCAGCTATATCTTC	60.029	54.545	0.00	0.00	38.90	2.87
230	4095	2.158755	CGGAAGGGCCTCTGTATTTCAT	60.159	50.000	6.46	0.00	0.00	2.57
252	4117	1.078426	CCTGACAACGGGGATCCAC	60.078	63.158	15.23	9.60	38.80	4.02
253	4118	1.537889	ACCTGACAACGGGGATCCA	60.538	57.895	15.23	0.00	46.20	3.41
254	4119	1.078426	CACCTGACAACGGGGATCC	60.078	63.158	1.92	1.92	46.20	3.36
256	4121	1.537889	TCCACCTGACAACGGGGAT	60.538	57.895	0.00	0.00	46.20	3.85
269	4134	4.610945	CGCAAAATAATGATTCCTCCACC	58.389	43.478	0.00	0.00	0.00	4.61
297	4162	2.656947	TGCAAGTAAGTGCCTCCTTT	57.343	45.000	0.00	0.00	44.26	3.11
320	4185	0.762418	TGACAACTGGGTCCACGATT	59.238	50.000	0.00	0.00	36.97	3.34
321	4186	0.321671	CTGACAACTGGGTCCACGAT	59.678	55.000	0.00	0.00	36.97	3.73
334	4199	0.601558	GTACGTGGAGAGGCTGACAA	59.398	55.000	0.00	0.00	0.00	3.18
338	4203	1.471676	GGATTGTACGTGGAGAGGCTG	60.472	57.143	0.00	0.00	0.00	4.85
344	4209	5.578005	TTAGAAGAGGATTGTACGTGGAG	57.422	43.478	0.00	0.00	0.00	3.86
396	4261	4.830765	GGTGCTATCGGCGTGGCA	62.831	66.667	14.19	14.19	45.43	4.92
400	4265	3.849951	CCCTGGTGCTATCGGCGT	61.850	66.667	6.85	0.00	45.43	5.68
425	4290	0.399091	CCTCCTAGGCCTCACCATCA	60.399	60.000	9.68	0.00	43.14	3.07
436	4301	0.616679	TTGGTCGTTCCCCTCCTAGG	60.617	60.000	0.82	0.82	34.77	3.02
443	4308	0.605589	CCAACTCTTGGTCGTTCCCC	60.606	60.000	0.00	0.00	45.93	4.81
484	7594	6.128035	GGCACATGACGGATGCATTATTTATA	60.128	38.462	0.00	0.00	41.27	0.98
486	7596	4.023279	GGCACATGACGGATGCATTATTTA	60.023	41.667	0.00	0.00	41.27	1.40
498	7608	1.518325	TAACACTTGGCACATGACGG	58.482	50.000	0.00	0.00	39.30	4.79
537	7647	4.327898	GCTATCACATCAACCGTTTAACGA	59.672	41.667	19.61	0.00	46.05	3.85
539	7649	5.796350	AGCTATCACATCAACCGTTTAAC	57.204	39.130	0.00	0.00	0.00	2.01
895	8006	9.613428	GTTAATATAGGTGCCTATTGATGCATA	57.387	33.333	15.12	0.00	40.07	3.14
918	8029	4.395959	AGAGTTCACTTTGACGGTGTTA	57.604	40.909	0.00	0.00	36.25	2.41
940	8051	8.856153	TGTTGTTCTAATATGTGGTGTGTTAT	57.144	30.769	0.00	0.00	0.00	1.89
1353	8464	1.140452	ACATCTATGCAGTGGCCTCTG	59.860	52.381	27.01	27.01	40.13	3.35
1354	8465	1.504912	ACATCTATGCAGTGGCCTCT	58.495	50.000	3.32	1.65	40.13	3.69
1367	8478	6.663093	AGGGCAACAACAATAATCAACATCTA	59.337	34.615	0.00	0.00	39.74	1.98
1405	8516	3.345414	CCCCTCTAGTCGATATAACGCT	58.655	50.000	0.00	1.68	0.00	5.07
1430	8546	5.763204	TCTCATAAAAATCGCCTATTCACCC	59.237	40.000	0.00	0.00	0.00	4.61
1431	8547	6.861065	TCTCATAAAAATCGCCTATTCACC	57.139	37.500	0.00	0.00	0.00	4.02
1432	8548	8.778358	AGAATCTCATAAAAATCGCCTATTCAC	58.222	33.333	0.00	0.00	0.00	3.18
1453	8569	4.437930	CGGCAAATTCCTCAGTGAAGAATC	60.438	45.833	15.70	5.54	30.06	2.52
1482	8598	8.874816	GCTAGTAGTTCTTCACTAAGGAATTTG	58.125	37.037	0.00	0.00	39.86	2.32
1494	8610	2.443416	TCCGCTGCTAGTAGTTCTTCA	58.557	47.619	9.73	0.00	0.00	3.02
1574	8690	3.399330	TGCTTCTGTACTTTGTACCTGC	58.601	45.455	5.55	5.43	0.00	4.85
1579	8695	6.227522	TGTGCTTATGCTTCTGTACTTTGTA	58.772	36.000	1.96	0.00	40.48	2.41
1595	8712	5.130975	TCATCCTGTGTTATCCTGTGCTTAT	59.869	40.000	0.00	0.00	0.00	1.73
1684	8801	5.049474	TGTTGTGTGCTTGTTCATATCTGTC	60.049	40.000	0.00	0.00	0.00	3.51
1744	8861	3.408634	TGTCTTAACCAAGCTTACTGGC	58.591	45.455	0.00	0.00	0.00	4.85
1759	8876	7.016153	ACTGGTCTACCAAATCATTGTCTTA	57.984	36.000	2.97	0.00	46.97	2.10
1788	8905	1.000163	ACGTACAACTGAGACAGCAGG	60.000	52.381	0.00	0.00	40.20	4.85
1907	9024	3.495001	GTCTGTGTGACCTTAGTTCAAGC	59.505	47.826	0.00	0.00	39.69	4.01
1995	9114	3.703052	GCATCCAAGAGGAATTGTGGATT	59.297	43.478	1.27	0.00	46.48	3.01
2055	9174	3.246699	CGACGCTTGTTACCTTTGAAGAA	59.753	43.478	0.00	0.00	0.00	2.52
2114	9233	1.133606	ACACCTACAAACCCCAAGTGG	60.134	52.381	0.00	0.00	0.00	4.00
2245	9364	1.276140	AATAGCCGCCCCCTACAACA	61.276	55.000	0.00	0.00	0.00	3.33
2323	9442	8.287904	TGTCCCAAAATATCTATCCACCTAAT	57.712	34.615	0.00	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.