AutoCloner

Multiple sequence alignment - TraesCS3A01G101800

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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	TraesCS3A01G101800	chr3A	100.000	4019	0	0	1	4019	66061365	66065383	0.000000e+00	7422
1	TraesCS3A01G101800	chr3B	88.626	3675	285	68	1	3600	89355363	89351747	0.000000e+00	4348
2	TraesCS3A01G101800	chr3B	91.686	3019	190	22	594	3600	89092640	89095609	0.000000e+00	4128
3	TraesCS3A01G101800	chr3B	73.715	1537	366	33	1109	2617	576020773	576022299	2.100000e-157	566
4	TraesCS3A01G101800	chr3B	89.080	348	20	4	21	359	89065985	89066323	2.230000e-112	416
5	TraesCS3A01G101800	chr3D	89.723	3036	201	42	350	3287	56687735	56684713	0.000000e+00	3775
6	TraesCS3A01G101800	chr3D	90.256	390	36	2	3620	4009	360593323	360592936	3.580000e-140	508
7	TraesCS3A01G101800	chr3D	89.500	400	41	1	3620	4019	31975428	31975030	4.640000e-139	505
8	TraesCS3A01G101800	chr3D	90.728	151	10	2	1	148	56688326	56688177	8.810000e-47	198
9	TraesCS3A01G101800	chr3D	90.476	84	8	0	735	818	56689275	56689192	1.180000e-20	111
10	TraesCS3A01G101800	chr6D	90.274	401	36	3	3620	4019	192100797	192100399	4.600000e-144	521
11	TraesCS3A01G101800	chr6D	88.974	390	34	7	3212	3600	18949902	18950283	1.310000e-129	473
12	TraesCS3A01G101800	chr2A	89.950	398	34	3	3620	4017	235312402	235312011	3.580000e-140	508
13	TraesCS3A01G101800	chr6B	90.415	386	35	2	3620	4004	662252449	662252065	1.290000e-139	507
14	TraesCS3A01G101800	chr5A	89.526	401	39	3	3620	4019	454198760	454198362	4.640000e-139	505
15	TraesCS3A01G101800	chr4A	89.250	400	37	4	3620	4017	30813801	30813406	2.790000e-136	496
16	TraesCS3A01G101800	chr4A	88.750	400	45	0	3620	4019	602940600	602940201	1.300000e-134	490
17	TraesCS3A01G101800	chr7D	89.870	385	35	2	3620	4004	4357475	4357855	3.610000e-135	492
18	TraesCS3A01G101800	chr7D	88.974	390	34	7	3212	3600	124864788	124865169	1.310000e-129	473
19	TraesCS3A01G101800	chr7D	88.974	390	34	7	3212	3600	429090944	429091325	1.310000e-129	473
20	TraesCS3A01G101800	chr5D	88.974	390	34	7	3212	3600	53887709	53887328	1.310000e-129	473
21	TraesCS3A01G101800	chr1D	88.974	390	33	8	3212	3600	266861272	266860892	1.310000e-129	473
22	TraesCS3A01G101800	chr1D	88.974	390	34	7	3212	3600	394221868	394221487	1.310000e-129	473
23	TraesCS3A01G101800	chr4D	88.718	390	35	7	3212	3600	27891680	27891299	6.080000e-128	468

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	TraesCS3A01G101800	chr3A	66061365	66065383	4018	False	7422.000000	7422	100.000	1	4019	1	chr3A.!!$F1	4018
1	TraesCS3A01G101800	chr3B	89351747	89355363	3616	True	4348.000000	4348	88.626	1	3600	1	chr3B.!!$R1	3599
2	TraesCS3A01G101800	chr3B	89092640	89095609	2969	False	4128.000000	4128	91.686	594	3600	1	chr3B.!!$F2	3006
3	TraesCS3A01G101800	chr3B	576020773	576022299	1526	False	566.000000	566	73.715	1109	2617	1	chr3B.!!$F3	1508
4	TraesCS3A01G101800	chr3D	56684713	56689275	4562	True	1361.333333	3775	90.309	1	3287	3	chr3D.!!$R3	3286

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
998	2377	0.392729	CCTTGCCAGAGAGCTCAAGG	60.393	60.0	17.77	15.24	46.33	3.61	F
1653	3050	0.034059	ACGTGTTCTTGGCTCCTCTG	59.966	55.0	0.00	0.00	0.00	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2781	4211	0.394899	GCCCTAGCTTCAGCACCAAT	60.395	55.0	0.75	0.0	45.16	3.16	R
3604	5070	0.822121	AGCGGACCCTTTTGTGGTTC	60.822	55.0	0.00	0.0	35.85	3.62	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
76	1026	0.609681	GTCTCCTCAGTGGACCGACT	60.610	60.000	4.40	0.00	40.56	4.18
78	1028	1.304217	TCCTCAGTGGACCGACTCC	60.304	63.158	0.00	0.00	40.56	3.85
83	1033	1.000646	AGTGGACCGACTCCTCTCC	60.001	63.158	1.34	0.00	38.32	3.71
114	1067	4.934075	TCGCTTTCACATTTCTCTCATG	57.066	40.909	0.00	0.00	0.00	3.07
122	1075	5.319453	TCACATTTCTCTCATGCTTTTCCT	58.681	37.500	0.00	0.00	0.00	3.36
123	1076	5.182570	TCACATTTCTCTCATGCTTTTCCTG	59.817	40.000	0.00	0.00	0.00	3.86
129	1082	4.999950	TCTCTCATGCTTTTCCTGAAACTC	59.000	41.667	0.00	0.00	0.00	3.01
145	1098	3.626996	CTCCAGCCATGCAACCGGA	62.627	63.158	9.46	0.00	0.00	5.14
151	1104	3.585990	CATGCAACCGGATCGCCC	61.586	66.667	9.46	0.00	0.00	6.13
165	1118	2.361230	GCCCTGGGTTAGCCACAC	60.361	66.667	15.56	0.00	36.17	3.82
174	1129	3.320541	TGGGTTAGCCACACAGAAAAATG	59.679	43.478	0.00	0.00	31.91	2.32
183	1138	1.001487	CACAGAAAAATGGCTGTCGCA	60.001	47.619	0.00	0.00	43.06	5.10
199	1154	5.638596	TGTCGCAGTAGACTTTTATCAGA	57.361	39.130	0.00	0.00	41.47	3.27
200	1155	5.641709	TGTCGCAGTAGACTTTTATCAGAG	58.358	41.667	0.00	0.00	41.47	3.35
202	1157	6.072119	TGTCGCAGTAGACTTTTATCAGAGAA	60.072	38.462	0.00	0.00	41.47	2.87
203	1158	6.975772	GTCGCAGTAGACTTTTATCAGAGAAT	59.024	38.462	0.00	0.00	38.09	2.40
213	1170	8.940768	ACTTTTATCAGAGAATAGACAAGCTC	57.059	34.615	2.62	0.00	0.00	4.09
217	1174	8.532186	TTATCAGAGAATAGACAAGCTCTTCT	57.468	34.615	2.79	2.79	41.26	2.85
228	1185	2.435586	CTCTTCTGCAGGCACCCG	60.436	66.667	15.13	0.00	0.00	5.28
259	1216	3.013921	ACAAACAACACGTCCATCAGTT	58.986	40.909	0.00	0.00	0.00	3.16
265	1222	1.156736	CACGTCCATCAGTTTGGGAC	58.843	55.000	0.00	0.00	46.01	4.46
267	1224	1.019278	CGTCCATCAGTTTGGGACCG	61.019	60.000	0.00	0.00	46.61	4.79
318	1275	1.731969	GTGTCCACCGTGTAGCGAC	60.732	63.158	0.00	0.00	44.77	5.19
338	1295	1.903404	GCCCAGTCCTTGGTGTTGG	60.903	63.158	0.00	0.00	46.25	3.77
352	1309	1.224592	GTTGGGCGGATGAGGATGT	59.775	57.895	0.00	0.00	0.00	3.06

Showing 1 to 25 of 456 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	964	5.830000	ACTTTGTAAGGTGGTTTCAAGAC	57.170	39.130	0.00	0.00	28.33	3.01
76	1026	1.939082	CGAAGGGAGGAGGGAGAGGA	61.939	65.000	0.00	0.00	0.00	3.71
78	1028	2.131067	GCGAAGGGAGGAGGGAGAG	61.131	68.421	0.00	0.00	0.00	3.20
83	1033	0.391793	GTGAAAGCGAAGGGAGGAGG	60.392	60.000	0.00	0.00	0.00	4.30
114	1067	1.270826	GGCTGGAGTTTCAGGAAAAGC	59.729	52.381	7.36	7.36	35.43	3.51
122	1075	0.961019	GTTGCATGGCTGGAGTTTCA	59.039	50.000	0.00	0.00	0.00	2.69
123	1076	0.244721	GGTTGCATGGCTGGAGTTTC	59.755	55.000	0.00	0.00	0.00	2.78
129	1082	2.440796	ATCCGGTTGCATGGCTGG	60.441	61.111	0.00	5.27	0.00	4.85
145	1098	2.690881	TGGCTAACCCAGGGCGAT	60.691	61.111	4.91	0.00	39.18	4.58
151	1104	2.270352	TTTCTGTGTGGCTAACCCAG	57.730	50.000	0.00	0.00	46.54	4.45
165	1118	1.267806	ACTGCGACAGCCATTTTTCTG	59.732	47.619	6.74	0.00	44.33	3.02
169	1124	2.076863	GTCTACTGCGACAGCCATTTT	58.923	47.619	6.74	0.00	44.33	1.82
174	1129	1.797025	AAAAGTCTACTGCGACAGCC	58.203	50.000	6.74	0.00	44.33	4.85
200	1155	3.870419	CCTGCAGAAGAGCTTGTCTATTC	59.130	47.826	17.39	0.00	41.96	1.75
202	1157	2.419851	GCCTGCAGAAGAGCTTGTCTAT	60.420	50.000	17.39	0.00	32.65	1.98
203	1158	1.066573	GCCTGCAGAAGAGCTTGTCTA	60.067	52.381	17.39	0.00	32.65	2.59
210	1167	2.749441	GGGTGCCTGCAGAAGAGC	60.749	66.667	17.39	10.73	0.00	4.09
213	1170	1.898574	AAACGGGTGCCTGCAGAAG	60.899	57.895	17.39	0.00	0.00	2.85
217	1174	2.904866	GTCAAACGGGTGCCTGCA	60.905	61.111	0.00	0.00	0.00	4.41
249	1206	0.036306	ACGGTCCCAAACTGATGGAC	59.964	55.000	0.00	0.00	46.31	4.02
259	1216	3.943691	CGGGTTGGACGGTCCCAA	61.944	66.667	23.81	14.82	43.42	4.12
265	1222	2.435938	CCATGTCGGGTTGGACGG	60.436	66.667	0.00	0.00	39.83	4.79
267	1224	0.391263	GTCTCCATGTCGGGTTGGAC	60.391	60.000	0.00	0.00	37.10	4.02
324	1281	2.113139	CGCCCAACACCAAGGACT	59.887	61.111	0.00	0.00	0.00	3.85
338	1295	3.555967	AGGACATCCTCATCCGCC	58.444	61.111	0.00	0.00	44.77	6.13

Showing 1 to 25 of 407 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.