AutoCloner

Multiple sequence alignment - TraesCS3A01G173400

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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	TraesCS3A01G173400	chr3A	100.000	2512	0	0	1	2512	191743853	191746364	0.000000e+00	4639
1	TraesCS3A01G173400	chr1A	95.156	2436	99	14	1	2427	517446951	517444526	0.000000e+00	3827
2	TraesCS3A01G173400	chr1A	94.670	2439	108	16	1	2427	257591381	257588953	0.000000e+00	3764
3	TraesCS3A01G173400	chr1A	89.189	111	4	1	2402	2512	517444482	517444380	5.640000e-27	132
4	TraesCS3A01G173400	chr6A	94.003	2518	116	18	4	2512	356473981	356471490	0.000000e+00	3781
5	TraesCS3A01G173400	chr6A	94.661	2435	110	15	1	2427	468224299	468226721	0.000000e+00	3759
6	TraesCS3A01G173400	chr6A	94.572	2432	115	13	1	2427	251355325	251352906	0.000000e+00	3744
7	TraesCS3A01G173400	chr6A	94.451	2433	111	14	1	2427	357526639	357524225	0.000000e+00	3723
8	TraesCS3A01G173400	chr7A	94.696	2432	110	12	1	2427	165281045	165283462	0.000000e+00	3759
9	TraesCS3A01G173400	chr4A	94.586	2438	111	14	1	2427	9466886	9469313	0.000000e+00	3751
10	TraesCS3A01G173400	chr5A	94.463	2438	113	16	1	2427	639808006	639810432	0.000000e+00	3735
11	TraesCS3A01G173400	chr2B	89.189	111	6	4	2402	2512	192844251	192844355	1.570000e-27	134
12	TraesCS3A01G173400	chrUn	89.189	111	4	1	2402	2512	130606834	130606936	5.640000e-27	132
13	TraesCS3A01G173400	chr7B	89.189	111	4	1	2402	2512	39502137	39502035	5.640000e-27	132
14	TraesCS3A01G173400	chr7B	89.189	111	4	1	2402	2512	524001186	524001288	5.640000e-27	132
15	TraesCS3A01G173400	chr5B	89.189	111	4	1	2402	2512	264711666	264711564	5.640000e-27	132
16	TraesCS3A01G173400	chr4B	89.189	111	4	1	2402	2512	147305513	147305615	5.640000e-27	132
17	TraesCS3A01G173400	chr4B	89.189	111	4	1	2402	2512	178223296	178223398	5.640000e-27	132

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	TraesCS3A01G173400	chr3A	191743853	191746364	2511	False	4639.0	4639	100.0000	1	2512	1	chr3A.!!$F1	2511
1	TraesCS3A01G173400	chr1A	257588953	257591381	2428	True	3764.0	3764	94.6700	1	2427	1	chr1A.!!$R1	2426
2	TraesCS3A01G173400	chr1A	517444380	517446951	2571	True	1979.5	3827	92.1725	1	2512	2	chr1A.!!$R2	2511
3	TraesCS3A01G173400	chr6A	356471490	356473981	2491	True	3781.0	3781	94.0030	4	2512	1	chr6A.!!$R2	2508
4	TraesCS3A01G173400	chr6A	468224299	468226721	2422	False	3759.0	3759	94.6610	1	2427	1	chr6A.!!$F1	2426
5	TraesCS3A01G173400	chr6A	251352906	251355325	2419	True	3744.0	3744	94.5720	1	2427	1	chr6A.!!$R1	2426
6	TraesCS3A01G173400	chr6A	357524225	357526639	2414	True	3723.0	3723	94.4510	1	2427	1	chr6A.!!$R3	2426
7	TraesCS3A01G173400	chr7A	165281045	165283462	2417	False	3759.0	3759	94.6960	1	2427	1	chr7A.!!$F1	2426
8	TraesCS3A01G173400	chr4A	9466886	9469313	2427	False	3751.0	3751	94.5860	1	2427	1	chr4A.!!$F1	2426
9	TraesCS3A01G173400	chr5A	639808006	639810432	2426	False	3735.0	3735	94.4630	1	2427	1	chr5A.!!$F1	2426

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
752	774	1.890876	TGACCACCACATGTTAGTGC	58.109	50.0	16.92	7.88	38.18	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1838	1863	0.251033	GGGCCCGTGAACTAGGTTTT	60.251	55.0	5.69	0.0	0.0	2.43	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
47	49	7.752239	TCAAAACCGTCAAATAACACGTTTTAA	59.248	29.630	0.00	0.00	30.46	1.52
122	124	8.464404	TGAAGCTATGGAGATTTTTCTGATTTG	58.536	33.333	0.00	0.00	29.33	2.32
182	189	4.716794	TCTCTCCCTATTCTACGAACTCC	58.283	47.826	0.00	0.00	0.00	3.85
186	193	3.629398	TCCCTATTCTACGAACTCCGAAC	59.371	47.826	0.00	0.00	41.76	3.95
219	226	4.437930	GGTGATAGCTCATTTGTGTGAAGC	60.438	45.833	0.00	0.00	32.98	3.86
523	542	6.373216	TGAAATCTGGTCAAACCCTAATAACG	59.627	38.462	0.00	0.00	37.50	3.18
618	638	2.122167	GCCAAACACCACCCGTCAA	61.122	57.895	0.00	0.00	0.00	3.18
752	774	1.890876	TGACCACCACATGTTAGTGC	58.109	50.000	16.92	7.88	38.18	4.40
759	781	3.372206	CACCACATGTTAGTGCTAAGAGC	59.628	47.826	11.73	0.00	42.82	4.09
803	826	6.682746	ACAAAATACAATGTGGCAAATCGTA	58.317	32.000	0.00	0.00	0.00	3.43
872	895	2.559440	GAGCAGATCGAGCAATTCCTT	58.441	47.619	2.38	0.00	0.00	3.36
873	896	2.286872	AGCAGATCGAGCAATTCCTTG	58.713	47.619	2.38	0.00	35.36	3.61
882	905	4.023193	TCGAGCAATTCCTTGGTTTCTTTC	60.023	41.667	0.00	0.00	42.91	2.62
937	960	3.156288	TCCTCTGTTTCTTCCTCTCGA	57.844	47.619	0.00	0.00	0.00	4.04
997	1020	1.980052	CCGGTGTATGGTCCAGTGT	59.020	57.895	0.00	0.00	0.00	3.55
1032	1055	4.314440	GACTGCCCACGGACTGCA	62.314	66.667	0.00	0.00	0.00	4.41
1053	1076	2.104281	ACCACTAAAGCGGTTGACTTCT	59.896	45.455	0.00	0.00	28.43	2.85
1082	1105	2.158325	AGAAGAATGGGAACTTTGGGCA	60.158	45.455	0.00	0.00	0.00	5.36
1104	1127	2.596452	GAGTTCGTCAAATGCGAGAGA	58.404	47.619	0.00	0.00	39.61	3.10
1109	1132	1.728971	CGTCAAATGCGAGAGAAAGCT	59.271	47.619	0.00	0.00	0.00	3.74
1118	1141	2.124942	GAGAAAGCTGGAGGGGCG	60.125	66.667	0.00	0.00	34.52	6.13
1338	1362	1.450848	CATGACAGTGCCGCTCCAT	60.451	57.895	0.00	0.00	0.00	3.41
1397	1421	6.878317	AGATGTCGAACTGAAGATGGAATTA	58.122	36.000	0.00	0.00	0.00	1.40
1483	1507	7.048512	GCTTTAGGAATACTTGCTCTAGGAAA	58.951	38.462	0.00	0.00	31.99	3.13
1651	1676	2.614057	ACACTTTCAGTTTCGGCAGAAG	59.386	45.455	0.00	0.00	37.70	2.85
1667	1692	4.127171	GCAGAAGACAACTACCAGTTCAA	58.873	43.478	0.00	0.00	36.03	2.69
1674	1699	7.482169	AGACAACTACCAGTTCAATGATAGA	57.518	36.000	0.00	0.00	36.03	1.98
1675	1700	8.083828	AGACAACTACCAGTTCAATGATAGAT	57.916	34.615	0.00	0.00	36.03	1.98
1723	1748	3.388024	GTGTTGGATCATACCCTAGCTCA	59.612	47.826	0.00	0.00	0.00	4.26
1727	1752	4.492646	TGGATCATACCCTAGCTCATCAA	58.507	43.478	0.00	0.00	0.00	2.57
1739	1764	6.426328	CCCTAGCTCATCAAATGACAGTAATC	59.574	42.308	0.00	0.00	35.06	1.75
1832	1857	2.159824	TCGAGTTCGTCAGTTCTGCTAG	59.840	50.000	1.07	0.00	40.80	3.42
1863	1889	0.766131	TAGTTCACGGGCCCAAAGAA	59.234	50.000	24.92	18.92	0.00	2.52
2007	2034	3.694043	TTTTGGCTTTCCTTTATGGGC	57.306	42.857	0.00	0.00	36.20	5.36
2082	2109	5.490139	AGCGAACCAATACTTCATGATTG	57.510	39.130	0.00	0.00	33.63	2.67
2095	2123	5.478332	ACTTCATGATTGGAAAAAGAGGTCC	59.522	40.000	0.00	0.00	0.00	4.46
2359	2390	1.628846	AGCCGTGTCTAAACTTGGGAT	59.371	47.619	0.00	0.00	0.00	3.85
2463	2563	5.163343	ACACACCAAACTCACACTACATAGT	60.163	40.000	0.00	0.00	36.90	2.12
2464	2564	6.041182	ACACACCAAACTCACACTACATAGTA	59.959	38.462	0.00	0.00	34.13	1.82
2465	2565	6.586463	CACACCAAACTCACACTACATAGTAG	59.414	42.308	2.79	2.79	34.13	2.57
2466	2566	6.492429	ACACCAAACTCACACTACATAGTAGA	59.508	38.462	10.87	0.10	34.13	2.59
2467	2567	7.178628	ACACCAAACTCACACTACATAGTAGAT	59.821	37.037	10.87	0.00	34.13	1.98
2468	2568	8.683615	CACCAAACTCACACTACATAGTAGATA	58.316	37.037	10.87	0.00	34.13	1.98
2469	2569	8.904834	ACCAAACTCACACTACATAGTAGATAG	58.095	37.037	10.87	5.22	34.13	2.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
73	75	8.884124	TCATTTTGGAGTGAATAAGAAGGATT	57.116	30.769	0.00	0.00	0.00	3.01
84	86	5.569355	TCCATAGCTTCATTTTGGAGTGAA	58.431	37.500	0.00	0.00	32.80	3.18
182	189	5.292765	AGCTATCACCTATGAACATGTTCG	58.707	41.667	28.55	18.64	42.28	3.95
186	193	7.228108	ACAAATGAGCTATCACCTATGAACATG	59.772	37.037	0.00	0.00	38.57	3.21
288	296	3.270027	TGTAATTCTTGCGCACATAGCT	58.730	40.909	11.12	0.00	42.61	3.32
523	542	2.541556	GGTTATGAGAGAGTCAACGGC	58.458	52.381	0.00	0.00	39.19	5.68
586	606	0.618458	TTTGGCGCTTGGTAGGATCT	59.382	50.000	7.64	0.00	0.00	2.75
618	638	1.453745	CGCATGCCTACCCCACATT	60.454	57.895	13.15	0.00	0.00	2.71
650	670	1.839354	TGCAGTAGCCAATCAGGATGA	59.161	47.619	0.00	0.00	46.53	2.92
752	774	8.734386	AGTTTGAATATTTGAACCAGCTCTTAG	58.266	33.333	9.82	0.00	0.00	2.18
803	826	5.481644	AGAGGAGAAGGGGAAGCTATATTT	58.518	41.667	0.00	0.00	0.00	1.40
872	895	2.721906	AGAAGATGGGGGAAAGAAACCA	59.278	45.455	0.00	0.00	37.41	3.67
873	896	3.357203	GAGAAGATGGGGGAAAGAAACC	58.643	50.000	0.00	0.00	0.00	3.27
882	905	1.834263	AGAAGAACGAGAAGATGGGGG	59.166	52.381	0.00	0.00	0.00	5.40
1053	1076	4.699994	AGTTCCCATTCTTCTCCTCCTTA	58.300	43.478	0.00	0.00	0.00	2.69
1104	1127	1.279025	TAATCCGCCCCTCCAGCTTT	61.279	55.000	0.00	0.00	0.00	3.51
1109	1132	0.191064	AGATCTAATCCGCCCCTCCA	59.809	55.000	0.00	0.00	0.00	3.86
1118	1141	4.747605	GCGAGGAAAACTCAGATCTAATCC	59.252	45.833	0.00	0.00	46.98	3.01
1260	1284	0.178924	AGCAAGCCCAACCCTTGAAT	60.179	50.000	5.41	0.00	41.64	2.57
1305	1329	2.225091	TGTCATGGGGCAGATTGAACTT	60.225	45.455	0.00	0.00	0.00	2.66
1309	1333	0.994247	ACTGTCATGGGGCAGATTGA	59.006	50.000	15.97	0.00	36.62	2.57
1338	1362	2.435410	CGGATGCACTGCTGCTGA	60.435	61.111	13.69	0.00	44.57	4.26
1397	1421	7.148018	TGCTTGAAGTTCTTGTTCATCTTCTTT	60.148	33.333	4.17	0.00	36.49	2.52
1433	1457	8.074972	GCTATTAGATTGGATTGCTTCTTCAAG	58.925	37.037	0.00	0.00	0.00	3.02
1483	1507	5.297776	CGAGAGATGGCCATCAAGTAAAAAT	59.702	40.000	40.05	21.13	40.22	1.82
1651	1676	8.723942	AATCTATCATTGAACTGGTAGTTGTC	57.276	34.615	0.00	0.00	38.80	3.18
1699	1724	4.040755	AGCTAGGGTATGATCCAACACTT	58.959	43.478	4.77	0.00	30.36	3.16
1723	1748	9.376075	CTCAAGTACTGATTACTGTCATTTGAT	57.624	33.333	0.00	0.00	40.44	2.57
1727	1752	6.701340	TGCTCAAGTACTGATTACTGTCATT	58.299	36.000	0.00	0.00	40.44	2.57
1739	1764	1.802960	CCTTGTGCTGCTCAAGTACTG	59.197	52.381	30.85	18.37	41.72	2.74
1798	1823	3.554731	ACGAACTCGAGGACAAAAGTTTC	59.445	43.478	18.41	6.95	43.02	2.78
1838	1863	0.251033	GGGCCCGTGAACTAGGTTTT	60.251	55.000	5.69	0.00	0.00	2.43
1839	1864	1.377612	GGGCCCGTGAACTAGGTTT	59.622	57.895	5.69	0.00	0.00	3.27
1840	1865	1.420532	TTGGGCCCGTGAACTAGGTT	61.421	55.000	19.37	0.00	0.00	3.50
1841	1866	1.420532	TTTGGGCCCGTGAACTAGGT	61.421	55.000	19.37	0.00	0.00	3.08
1850	1876	1.745890	GCTTTTTCTTTGGGCCCGT	59.254	52.632	19.37	0.00	0.00	5.28
1863	1889	1.398692	TCGCTTGTTTCTGGGCTTTT	58.601	45.000	0.00	0.00	0.00	2.27
2082	2109	2.677542	AGGGTTGGACCTCTTTTTCC	57.322	50.000	0.00	0.00	38.64	3.13
2311	2342	4.373527	GCGTGGGAAAAATTAACCAAAGT	58.626	39.130	0.00	0.00	34.26	2.66
2312	2343	3.743911	GGCGTGGGAAAAATTAACCAAAG	59.256	43.478	0.00	0.00	34.26	2.77
2466	2566	9.346515	CCCTAGCTACCCTATCTATCTATCTAT	57.653	40.741	0.00	0.00	0.00	1.98
2467	2567	7.238096	GCCCTAGCTACCCTATCTATCTATCTA	59.762	44.444	0.00	0.00	35.50	1.98
2468	2568	6.045106	GCCCTAGCTACCCTATCTATCTATCT	59.955	46.154	0.00	0.00	35.50	1.98
2469	2569	6.183361	TGCCCTAGCTACCCTATCTATCTATC	60.183	46.154	0.00	0.00	40.80	2.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.