AutoCloner

Multiple sequence alignment - TraesCS1A01G118300

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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	TraesCS1A01G118300	chr1A	100.000	3047	0	0	1	3047	126859513	126856467	0.000000e+00	5627.0
1	TraesCS1A01G118300	chr1A	100.000	1115	0	0	3294	4408	126856220	126855106	0.000000e+00	2060.0
2	TraesCS1A01G118300	chr1A	90.000	70	6	1	300	368	242698732	242698801	6.070000e-14	89.8
3	TraesCS1A01G118300	chr1D	96.084	2707	65	12	373	3047	115578811	115576114	0.000000e+00	4373.0
4	TraesCS1A01G118300	chr1D	96.682	1115	35	1	3294	4406	115575736	115574622	0.000000e+00	1853.0
5	TraesCS1A01G118300	chr1D	78.061	392	65	13	5	378	38249106	38249494	1.230000e-55	228.0
6	TraesCS1A01G118300	chr1B	95.266	2197	74	12	4	2175	177003192	177001001	0.000000e+00	3454.0
7	TraesCS1A01G118300	chr1B	94.813	1041	33	2	3368	4406	176999709	176998688	0.000000e+00	1604.0
8	TraesCS1A01G118300	chr1B	95.128	862	30	6	2185	3034	177000911	177000050	0.000000e+00	1349.0
9	TraesCS1A01G118300	chr1B	100.000	45	0	0	3301	3345	176999750	176999706	2.830000e-12	84.2
10	TraesCS1A01G118300	chr3D	81.896	939	162	5	1156	2093	81364229	81365160	0.000000e+00	785.0
11	TraesCS1A01G118300	chr3D	80.201	298	51	6	3	297	399674405	399674113	2.670000e-52	217.0
12	TraesCS1A01G118300	chr3D	88.000	75	6	3	295	368	104126744	104126816	7.860000e-13	86.1
13	TraesCS1A01G118300	chr3B	81.197	952	170	6	1156	2106	127290014	127290957	0.000000e+00	758.0
14	TraesCS1A01G118300	chr3A	81.363	939	167	6	1156	2093	95527724	95528655	0.000000e+00	758.0
15	TraesCS1A01G118300	chr5D	87.468	391	28	13	1	371	360408893	360408504	8.760000e-117	431.0
16	TraesCS1A01G118300	chr5D	81.250	304	45	11	1	297	441216389	441216091	7.370000e-58	235.0
17	TraesCS1A01G118300	chr5D	87.324	71	8	1	303	372	397874666	397874596	3.650000e-11	80.5
18	TraesCS1A01G118300	chr7D	81.544	298	43	10	5	297	76596992	76597282	7.370000e-58	235.0
19	TraesCS1A01G118300	chr7D	80.921	304	46	11	1	297	575677087	575676789	3.430000e-56	230.0
20	TraesCS1A01G118300	chr7D	86.076	79	6	4	295	370	136982803	136982879	3.650000e-11	80.5
21	TraesCS1A01G118300	chr2B	78.010	382	66	12	3	368	572262987	572263366	1.600000e-54	224.0
22	TraesCS1A01G118300	chr6B	80.135	297	52	6	5	297	644489392	644489685	9.600000e-52	215.0
23	TraesCS1A01G118300	chr2A	86.250	80	7	4	295	373	613475975	613476051	2.830000e-12	84.2

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	TraesCS1A01G118300	chr1A	126855106	126859513	4407	True	3843.5	5627	100.00000	1	4408	2	chr1A.!!$R1	4407
1	TraesCS1A01G118300	chr1D	115574622	115578811	4189	True	3113.0	4373	96.38300	373	4406	2	chr1D.!!$R1	4033
2	TraesCS1A01G118300	chr1B	176998688	177003192	4504	True	1622.8	3454	96.30175	4	4406	4	chr1B.!!$R1	4402
3	TraesCS1A01G118300	chr3D	81364229	81365160	931	False	785.0	785	81.89600	1156	2093	1	chr3D.!!$F1	937
4	TraesCS1A01G118300	chr3B	127290014	127290957	943	False	758.0	758	81.19700	1156	2106	1	chr3B.!!$F1	950
5	TraesCS1A01G118300	chr3A	95527724	95528655	931	False	758.0	758	81.36300	1156	2093	1	chr3A.!!$F1	937

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
968	995	0.251832	ATGGGTGTCTGACTCGAGGT	60.252	55.000	18.41	1.94	0.00	3.85	F
1362	1390	1.573829	CGGCCTGTGTGCGTATGTTT	61.574	55.000	0.00	0.00	0.00	2.83	F
2892	3014	1.981495	AGGCTTATATGGGAGCACCTC	59.019	52.381	0.00	0.00	40.63	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2897	3019	0.106569	TGGATGGAATGCGGCATTCT	60.107	50.000	39.19	28.10	46.47	2.40	R
3359	3612	6.654161	AGAAAGAAATGTCCATCACTTGAGAG	59.346	38.462	0.00	0.00	0.00	3.20	R
4023	4278	2.551459	GAGAAATGTGCACTGAGCTTGT	59.449	45.455	19.41	2.62	45.94	3.16	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
28	29	2.266689	GGTGCCGACGGTAATGGT	59.733	61.111	16.73	0.00	0.00	3.55
33	34	0.457035	GCCGACGGTAATGGTGTCTA	59.543	55.000	16.73	0.00	0.00	2.59
74	75	1.991099	GAGGTACCGTCGTGGAGCTC	61.991	65.000	4.71	4.71	42.00	4.09
110	111	1.306141	ATGGCTTGAGGTCTCCGGA	60.306	57.895	2.93	2.93	0.00	5.14
119	120	0.618981	AGGTCTCCGGATGAAAACCC	59.381	55.000	3.57	2.60	0.00	4.11
120	121	0.326927	GGTCTCCGGATGAAAACCCA	59.673	55.000	3.57	0.00	0.00	4.51
131	132	1.342819	TGAAAACCCAAAATCAGGCCG	59.657	47.619	0.00	0.00	0.00	6.13
148	149	2.509336	GTGCCAGATCGGGTGACG	60.509	66.667	13.75	0.00	46.11	4.35
212	213	0.681733	AGACCCGATGATGGATTCCG	59.318	55.000	0.00	0.00	0.00	4.30
216	217	1.081892	CCGATGATGGATTCCGATGC	58.918	55.000	0.00	0.00	0.00	3.91
225	226	0.652592	GATTCCGATGCTGTTCACGG	59.347	55.000	0.00	0.00	45.61	4.94
234	235	1.010125	CTGTTCACGGTTGTTGGCG	60.010	57.895	0.00	0.00	0.00	5.69
251	252	2.897350	GGAGCTTCGGATTGCGGG	60.897	66.667	0.00	0.00	0.00	6.13
270	279	1.271217	GGGGTGCCGACTAGTCTTTTT	60.271	52.381	20.34	0.00	0.00	1.94
292	301	6.902224	TTTTTCTTTTCCTTTTGCACTAGC	57.098	33.333	0.00	0.00	42.57	3.42
293	302	5.852282	TTTCTTTTCCTTTTGCACTAGCT	57.148	34.783	0.00	0.00	42.74	3.32
295	304	4.718961	TCTTTTCCTTTTGCACTAGCTCT	58.281	39.130	0.00	0.00	42.74	4.09
323	332	4.762251	AGGTGTTCTTGTAATGCCTCTTTC	59.238	41.667	0.00	0.00	0.00	2.62
346	355	7.630242	TCTGATCAATGAATTTGGTAACTCC	57.370	36.000	0.00	0.00	35.92	3.85
347	356	6.603201	TCTGATCAATGAATTTGGTAACTCCC	59.397	38.462	0.00	0.00	35.92	4.30
356	365	6.272792	TGAATTTGGTAACTCCCCTACTAACA	59.727	38.462	0.00	0.00	34.77	2.41
359	368	5.945144	TGGTAACTCCCCTACTAACATTC	57.055	43.478	0.00	0.00	34.77	2.67
361	370	4.646492	GGTAACTCCCCTACTAACATTCGA	59.354	45.833	0.00	0.00	0.00	3.71
396	405	3.503827	TCTCATTGTTCGTGCGTAGAT	57.496	42.857	0.00	0.00	0.00	1.98
443	453	2.106566	TGACATGGCAACCAACTTTGT	58.893	42.857	0.00	0.00	36.95	2.83
445	455	3.055530	TGACATGGCAACCAACTTTGTTT	60.056	39.130	0.00	0.00	36.95	2.83
450	460	3.259374	TGGCAACCAACTTTGTTTCAAGA	59.741	39.130	0.00	0.00	0.00	3.02
504	514	5.904941	TGTGATTTTGCAGACTTGTGAATT	58.095	33.333	0.00	0.00	0.00	2.17
505	515	5.978919	TGTGATTTTGCAGACTTGTGAATTC	59.021	36.000	0.00	0.00	0.00	2.17
506	516	5.116074	GTGATTTTGCAGACTTGTGAATTCG	59.884	40.000	0.04	0.00	0.00	3.34
962	989	2.711009	TCCTTGAAATGGGTGTCTGACT	59.289	45.455	9.51	0.00	0.00	3.41
968	995	0.251832	ATGGGTGTCTGACTCGAGGT	60.252	55.000	18.41	1.94	0.00	3.85
1091	1119	4.759205	GCCGCCCAAGTCCCCAAT	62.759	66.667	0.00	0.00	0.00	3.16
1362	1390	1.573829	CGGCCTGTGTGCGTATGTTT	61.574	55.000	0.00	0.00	0.00	2.83
1554	1582	3.006940	TCGCAAGTACATGGACAATTCC	58.993	45.455	11.55	0.00	39.90	3.01
2106	2134	7.069826	TCTCATTTTCAGGTGAAATTTTGTCCT	59.930	33.333	5.99	0.00	42.83	3.85
2150	2180	4.507388	CCTATTGCCAGTGTTTGTTGTTTG	59.493	41.667	0.00	0.00	0.00	2.93
2156	2186	6.166279	TGCCAGTGTTTGTTGTTTGATTAAA	58.834	32.000	0.00	0.00	0.00	1.52
2191	2301	6.095947	GCTTATAGCGCATATAGTTGGTTC	57.904	41.667	11.47	0.00	0.00	3.62
2211	2321	7.732025	TGGTTCTCAGAACACTCATTTAGTTA	58.268	34.615	19.37	0.00	35.76	2.24
2219	2329	7.332182	CAGAACACTCATTTAGTTAAGGGAGTC	59.668	40.741	0.00	0.00	35.76	3.36
2256	2378	6.307776	TCTTGTGGGTGGTATTTGTATTTCA	58.692	36.000	0.00	0.00	0.00	2.69
2260	2382	6.551601	TGTGGGTGGTATTTGTATTTCAAACT	59.448	34.615	0.00	0.00	46.77	2.66
2294	2416	4.481368	ACCGCCAAGATATGTTCTGTTA	57.519	40.909	0.00	0.00	33.93	2.41
2430	2552	8.785946	CCAATGCAAAATACATTCTTTCCTTTT	58.214	29.630	0.00	0.00	35.58	2.27
2555	2677	6.692486	ACCTGTTGTTTTTGTTTGTGACATA	58.308	32.000	0.00	0.00	38.26	2.29
2892	3014	1.981495	AGGCTTATATGGGAGCACCTC	59.019	52.381	0.00	0.00	40.63	3.85
2897	3019	2.088104	ATATGGGAGCACCTCGAGAA	57.912	50.000	15.71	0.00	41.11	2.87
3401	3654	6.182039	TCTTTCTTTGACAAGATAATGCCG	57.818	37.500	0.00	0.00	38.89	5.69
3446	3701	3.591527	ACAACTTTGGATATGGGAGGTCA	59.408	43.478	0.00	0.00	0.00	4.02
3671	3926	4.397103	ACATGTTCTGGTATTGCACATCTG	59.603	41.667	0.00	0.00	0.00	2.90
3750	4005	8.843262	CATGATAAATATCAAAGTCTTGGCTCA	58.157	33.333	7.17	0.00	44.96	4.26
3761	4016	5.192327	AGTCTTGGCTCAACATTGAAAAG	57.808	39.130	0.00	1.49	36.64	2.27
3860	4115	5.065218	CCTTCATTGTCAGCAGTGGTATTAC	59.935	44.000	0.00	0.00	33.75	1.89
4023	4278	8.447200	TCAATGGTAATCAATTCCATCCATCTA	58.553	33.333	0.00	0.00	40.52	1.98
4111	4366	5.621193	ACGGATTTAGTCCCATCCAATTAG	58.379	41.667	0.00	0.00	44.77	1.73
4283	4538	8.192774	TGAAGAATTTCCTATGCTGCTATTTTG	58.807	33.333	0.00	0.00	32.09	2.44
4291	4546	7.505258	TCCTATGCTGCTATTTTGTGTACATA	58.495	34.615	0.00	0.00	0.00	2.29
4398	4653	2.632028	TGCCACAGTTACGTTTACCCTA	59.368	45.455	0.00	0.00	0.00	3.53
4406	4661	6.183360	ACAGTTACGTTTACCCTAGTCAAGTT	60.183	38.462	0.00	0.00	0.00	2.66
4407	4662	6.364435	CAGTTACGTTTACCCTAGTCAAGTTC	59.636	42.308	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	1.214589	CCACGACGGTACCTCCAAG	59.785	63.158	10.90	0.00	35.57	3.61
74	75	0.179000	ATGGGGTAAGAAGAGCAGCG	59.821	55.000	0.00	0.00	0.00	5.18
110	111	2.028203	CGGCCTGATTTTGGGTTTTCAT	60.028	45.455	0.00	0.00	0.00	2.57
131	132	2.509336	CGTCACCCGATCTGGCAC	60.509	66.667	2.58	0.00	39.56	5.01
141	142	3.236003	GAGGACACCACCGTCACCC	62.236	68.421	0.00	0.00	37.66	4.61
212	213	1.334960	CCAACAACCGTGAACAGCATC	60.335	52.381	0.00	0.00	0.00	3.91
216	217	1.010125	CGCCAACAACCGTGAACAG	60.010	57.895	0.00	0.00	0.00	3.16
225	226	2.556287	CGAAGCTCCGCCAACAAC	59.444	61.111	0.00	0.00	0.00	3.32
234	235	2.897350	CCCGCAATCCGAAGCTCC	60.897	66.667	0.00	0.00	40.02	4.70
251	252	2.180432	AAAAAGACTAGTCGGCACCC	57.820	50.000	17.07	0.00	34.09	4.61
270	279	6.096846	AGAGCTAGTGCAAAAGGAAAAGAAAA	59.903	34.615	0.00	0.00	42.74	2.29
280	289	2.670414	CTCCGAAGAGCTAGTGCAAAAG	59.330	50.000	0.00	0.00	42.74	2.27
292	301	2.821991	ACAAGAACACCTCCGAAGAG	57.178	50.000	0.00	0.00	40.09	2.85
293	302	4.566004	CATTACAAGAACACCTCCGAAGA	58.434	43.478	0.00	0.00	0.00	2.87
295	304	3.071479	GCATTACAAGAACACCTCCGAA	58.929	45.455	0.00	0.00	0.00	4.30
323	332	6.183360	GGGGAGTTACCAAATTCATTGATCAG	60.183	42.308	0.00	0.00	41.85	2.90
368	377	7.940178	ACGCACGAACAATGAGATATAATTA	57.060	32.000	0.00	0.00	0.00	1.40
396	405	5.452078	AAAAATCATTCGCAAGGAAGTGA	57.548	34.783	0.00	0.00	38.24	3.41
443	453	5.940192	AATGTAGTGCACGAATCTTGAAA	57.060	34.783	12.01	0.00	0.00	2.69
445	455	5.120674	CAGAAATGTAGTGCACGAATCTTGA	59.879	40.000	12.01	0.00	0.00	3.02
450	460	5.689383	AAACAGAAATGTAGTGCACGAAT	57.311	34.783	12.01	3.59	0.00	3.34
504	514	4.766891	AGAAAATGCCAATCCTTCTTTCGA	59.233	37.500	0.00	0.00	0.00	3.71
505	515	5.064441	AGAAAATGCCAATCCTTCTTTCG	57.936	39.130	0.00	0.00	0.00	3.46
506	516	7.442062	TGAAAAGAAAATGCCAATCCTTCTTTC	59.558	33.333	8.17	4.37	42.55	2.62
516	526	4.161189	TGTGGTCTGAAAAGAAAATGCCAA	59.839	37.500	0.00	0.00	0.00	4.52
519	529	3.730715	CGTGTGGTCTGAAAAGAAAATGC	59.269	43.478	0.00	0.00	0.00	3.56
920	932	0.459585	CCATGGACGAACCCACTACG	60.460	60.000	5.56	0.00	39.34	3.51
1091	1119	1.819903	TCCCATTCACGTCATACGACA	59.180	47.619	6.44	0.00	46.05	4.35
1362	1390	3.344703	CCTGAACAGGTTGATGGCA	57.655	52.632	12.21	0.00	43.61	4.92
1554	1582	1.065636	TCAAGCAGCCTGGAGATGAAG	60.066	52.381	0.00	0.00	0.00	3.02
2156	2186	9.877178	ATATGCGCTATAAGCTAGTAAAGAAAT	57.123	29.630	9.73	0.00	39.60	2.17
2179	2209	7.482169	TGAGTGTTCTGAGAACCAACTATAT	57.518	36.000	21.45	0.00	0.00	0.86
2191	2301	7.386851	TCCCTTAACTAAATGAGTGTTCTGAG	58.613	38.462	0.00	0.00	38.87	3.35
2211	2321	7.234166	ACAAGAATCAATTGAAATGACTCCCTT	59.766	33.333	13.09	0.00	0.00	3.95
2219	2329	5.640357	CCACCCACAAGAATCAATTGAAATG	59.360	40.000	13.09	11.15	0.00	2.32
2256	2378	3.377172	GGCGGTAAATGTGATGCTAGTTT	59.623	43.478	0.00	0.00	0.00	2.66
2260	2382	2.700722	TGGCGGTAAATGTGATGCTA	57.299	45.000	0.00	0.00	0.00	3.49
2430	2552	7.595819	AATCTCCAACAAACAACATAAGGAA	57.404	32.000	0.00	0.00	0.00	3.36
2469	2591	8.934697	TCCACATCTGTAAAGCTTTATATAGGT	58.065	33.333	21.28	15.59	0.00	3.08
2492	2614	0.323302	TGGCGCATAGAAGTGTTCCA	59.677	50.000	10.83	0.00	0.00	3.53
2571	2693	8.721479	TCTTAGTTTCTAGGCTAGGAGTGTATA	58.279	37.037	20.92	3.73	0.00	1.47
2892	3014	0.305922	GGAATGCGGCATTCTTCTCG	59.694	55.000	39.19	2.87	46.47	4.04
2897	3019	0.106569	TGGATGGAATGCGGCATTCT	60.107	50.000	39.19	28.10	46.47	2.40
3359	3612	6.654161	AGAAAGAAATGTCCATCACTTGAGAG	59.346	38.462	0.00	0.00	0.00	3.20
3401	3654	6.200286	TGTTTCACAGAACAATCGACTAGAAC	59.800	38.462	0.00	0.00	36.64	3.01
3524	3779	3.145286	TGTTTGCTCGTCCATCAAATCA	58.855	40.909	0.00	0.00	33.08	2.57
3683	3938	6.019318	CCTTAATTATGCAGCAATGTTCTTGC	60.019	38.462	0.00	1.78	45.22	4.01
3761	4016	8.483307	TCCAGACGTTAAAAATATAAGGACAC	57.517	34.615	0.00	0.00	0.00	3.67
3860	4115	8.315391	ACATCATCCATGATAACAGTTAATCG	57.685	34.615	1.64	0.00	45.23	3.34
4023	4278	2.551459	GAGAAATGTGCACTGAGCTTGT	59.449	45.455	19.41	2.62	45.94	3.16
4111	4366	6.100714	TGGGGATAACTAGACAGGTTAAATCC	59.899	42.308	0.00	0.00	33.99	3.01
4218	4473	8.473358	TGTATTTCTAGATCCTTGAATCGGTA	57.527	34.615	0.00	0.00	0.00	4.02
4251	4506	8.193438	AGCAGCATAGGAAATTCTTCATTTTAC	58.807	33.333	0.00	0.00	35.02	2.01
4283	4538	8.780249	ACAGTTTGTTCAATAAGGTATGTACAC	58.220	33.333	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.