AutoCloner

Multiple sequence alignment - TraesCS7D01G104400

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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	TraesCS7D01G104400	chr7D	100.000	3803	0	0	1	3803	63486600	63482798	0.000000e+00	7023.0
1	TraesCS7D01G104400	chr7D	92.647	68	5	0	3563	3630	556214253	556214320	8.690000e-17	99.0
2	TraesCS7D01G104400	chr7D	92.647	68	5	0	3563	3630	556214369	556214436	8.690000e-17	99.0
3	TraesCS7D01G104400	chr7A	89.553	2527	141	55	662	3126	66285158	66282693	0.000000e+00	3090.0
4	TraesCS7D01G104400	chr7A	91.146	576	48	1	7	582	66285727	66285155	0.000000e+00	778.0
5	TraesCS7D01G104400	chr7B	89.017	2422	165	45	775	3126	3896805	3894415	0.000000e+00	2905.0
6	TraesCS7D01G104400	chr7B	96.154	52	2	0	684	735	3896869	3896818	6.770000e-13	86.1
7	TraesCS7D01G104400	chr4A	90.143	1116	89	17	1183	2291	690206740	690207841	0.000000e+00	1432.0
8	TraesCS7D01G104400	chr4A	88.241	1080	99	19	1194	2261	713186841	713187904	0.000000e+00	1266.0
9	TraesCS7D01G104400	chr4A	87.990	408	48	1	7	414	105029563	105029157	7.390000e-132	481.0
10	TraesCS7D01G104400	chr4A	86.124	418	39	11	2637	3039	713188408	713188821	2.100000e-117	433.0
11	TraesCS7D01G104400	chr4A	85.646	418	33	12	2637	3039	690208342	690208747	7.600000e-112	414.0
12	TraesCS7D01G104400	chr4A	84.868	304	27	12	2298	2590	690207913	690208208	4.810000e-74	289.0
13	TraesCS7D01G104400	chr4A	82.237	304	35	13	2298	2590	713187979	713188274	1.060000e-60	244.0
14	TraesCS7D01G104400	chr2B	87.088	1092	113	20	1183	2261	55411455	55412531	0.000000e+00	1210.0
15	TraesCS7D01G104400	chr2B	85.612	417	41	10	2637	3038	55413033	55413445	1.630000e-113	420.0
16	TraesCS7D01G104400	chr2B	81.908	304	31	13	2298	2590	55412608	55412898	6.350000e-58	235.0
17	TraesCS7D01G104400	chr3B	85.481	978	116	20	1183	2153	624661269	624660311	0.000000e+00	996.0
18	TraesCS7D01G104400	chr3B	96.923	65	2	0	3563	3627	568667474	568667538	4.020000e-20	110.0
19	TraesCS7D01G104400	chr3B	95.312	64	3	0	3565	3628	568933187	568933250	6.720000e-18	102.0
20	TraesCS7D01G104400	chr3B	84.375	96	14	1	535	630	5896304	5896210	4.040000e-15	93.5
21	TraesCS7D01G104400	chr4D	90.749	454	42	0	7	460	359842976	359843429	1.170000e-169	606.0
22	TraesCS7D01G104400	chr1B	91.724	145	12	0	7	151	328880113	328880257	6.440000e-48	202.0
23	TraesCS7D01G104400	chr1B	88.235	68	8	0	3563	3630	128847993	128847926	8.760000e-12	82.4
24	TraesCS7D01G104400	chr2D	84.024	169	24	3	300	468	7216151	7215986	3.930000e-35	159.0
25	TraesCS7D01G104400	chr2D	86.747	83	10	1	555	637	615146678	615146597	1.450000e-14	91.6
26	TraesCS7D01G104400	chr2D	91.837	49	4	0	19	67	7216619	7216571	6.820000e-08	69.4
27	TraesCS7D01G104400	chrUn	85.833	120	14	3	535	654	340767718	340767602	1.430000e-24	124.0
28	TraesCS7D01G104400	chr5B	92.222	90	4	3	3562	3649	7019566	7019654	1.430000e-24	124.0
29	TraesCS7D01G104400	chr5B	85.366	123	15	3	532	654	440549689	440549808	1.430000e-24	124.0
30	TraesCS7D01G104400	chr5B	85.366	123	15	3	532	654	440560498	440560617	1.430000e-24	124.0
31	TraesCS7D01G104400	chr5B	100.000	31	0	0	3136	3166	684076308	684076338	1.480000e-04	58.4
32	TraesCS7D01G104400	chr5D	83.607	122	15	5	535	654	371017363	371017245	4.020000e-20	110.0
33	TraesCS7D01G104400	chr5D	82.787	122	19	2	532	653	371280386	371280505	1.440000e-19	108.0
34	TraesCS7D01G104400	chr3A	84.685	111	14	3	525	634	8931963	8932071	1.440000e-19	108.0
35	TraesCS7D01G104400	chr6D	95.455	66	3	0	3563	3628	218382634	218382569	5.200000e-19	106.0
36	TraesCS7D01G104400	chr5A	84.848	99	13	2	529	626	90931221	90931318	8.690000e-17	99.0
37	TraesCS7D01G104400	chr3D	80.000	100	14	4	3548	3643	102648137	102648040	6.820000e-08	69.4

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	TraesCS7D01G104400	chr7D	63482798	63486600	3802	True	7023.000000	7023	100.000000	1	3803	1	chr7D.!!$R1	3802
1	TraesCS7D01G104400	chr7A	66282693	66285727	3034	True	1934.000000	3090	90.349500	7	3126	2	chr7A.!!$R1	3119
2	TraesCS7D01G104400	chr7B	3894415	3896869	2454	True	1495.550000	2905	92.585500	684	3126	2	chr7B.!!$R1	2442
3	TraesCS7D01G104400	chr4A	690206740	690208747	2007	False	711.666667	1432	86.885667	1183	3039	3	chr4A.!!$F1	1856
4	TraesCS7D01G104400	chr4A	713186841	713188821	1980	False	647.666667	1266	85.534000	1194	3039	3	chr4A.!!$F2	1845
5	TraesCS7D01G104400	chr2B	55411455	55413445	1990	False	621.666667	1210	84.869333	1183	3038	3	chr2B.!!$F1	1855
6	TraesCS7D01G104400	chr3B	624660311	624661269	958	True	996.000000	996	85.481000	1183	2153	1	chr3B.!!$R2	970

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
305	306	0.109532	TCATCCGTTTTGCCACCTCA	59.890	50.0	0.00	0.0	0.00	3.86	F
799	800	0.314935	TCAAACGTACTCCGGGACAC	59.685	55.0	0.00	0.0	42.24	3.67	F
850	852	0.530650	CAGACGAACCAGGCGCATAT	60.531	55.0	10.83	0.0	0.00	1.78	F
2031	2084	0.610174	CTCCTACAAGGTCAGCAGCA	59.390	55.0	0.00	0.0	36.53	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1822	1875	0.249868	TCAGGCAAAGACAGTGACGG	60.250	55.000	0.00	0.0	0.00	4.79	R
2122	2181	0.890542	TGCCGTTCTGCAGAGCAATT	60.891	50.000	27.22	0.0	38.41	2.32	R
2123	2182	1.302752	TGCCGTTCTGCAGAGCAAT	60.303	52.632	27.22	0.0	38.41	3.56	R
3473	3738	0.034059	CCTCCCTTATTGCTCGCGAT	59.966	55.000	10.36	0.0	0.00	4.58	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
39	40	3.548770	GAACATGATCTGCTCCCAATCA	58.451	45.455	0.00	0.00	34.17	2.57
68	69	0.459489	GAAGCCTGCACCACAAACAA	59.541	50.000	0.00	0.00	0.00	2.83
82	83	1.596727	CAAACAAATTGGCACCAACCG	59.403	47.619	3.77	0.00	38.88	4.44
103	104	2.892425	GGAATCTCACCGGCTGCG	60.892	66.667	0.00	0.00	0.00	5.18
140	141	0.179215	CGCATGTCCTTGAAGAACGC	60.179	55.000	0.00	0.00	0.00	4.84
147	148	0.512952	CCTTGAAGAACGCCGACTTG	59.487	55.000	0.00	0.00	0.00	3.16
149	150	0.531974	TTGAAGAACGCCGACTTGCT	60.532	50.000	0.00	0.00	0.00	3.91
187	188	2.825836	CCCGAGCAAGTGCCATCC	60.826	66.667	0.00	0.00	43.38	3.51
194	195	1.097547	GCAAGTGCCATCCAGCGTAT	61.098	55.000	0.00	0.00	34.65	3.06
218	219	4.096984	GCGGTCATTGATCTCTGGAATTTT	59.903	41.667	0.00	0.00	0.00	1.82
224	225	8.738106	GTCATTGATCTCTGGAATTTTCTCTTT	58.262	33.333	0.00	0.00	0.00	2.52
230	231	9.122779	GATCTCTGGAATTTTCTCTTTGATCAT	57.877	33.333	0.00	0.00	0.00	2.45
264	265	1.280421	ACCTCATCTTCTGGGTCAAGC	59.720	52.381	0.00	0.00	0.00	4.01
280	281	0.329596	AAGCTGCCCGAAGAAATCCT	59.670	50.000	0.00	0.00	0.00	3.24
293	294	3.917300	AGAAATCCTCTAGGTCATCCGT	58.083	45.455	0.00	0.00	39.05	4.69
305	306	0.109532	TCATCCGTTTTGCCACCTCA	59.890	50.000	0.00	0.00	0.00	3.86
341	342	3.777925	CGAGCGTGCGTCCAAAGG	61.778	66.667	0.00	0.00	0.00	3.11
352	353	2.227757	TCCAAAGGGGTCGCCATCA	61.228	57.895	8.89	0.00	38.11	3.07
355	356	1.002134	AAAGGGGTCGCCATCACAG	60.002	57.895	8.89	0.00	0.00	3.66
356	357	3.628646	AAGGGGTCGCCATCACAGC	62.629	63.158	8.89	0.00	0.00	4.40
364	365	1.078848	GCCATCACAGCTTCCGTCT	60.079	57.895	0.00	0.00	0.00	4.18
367	368	1.354040	CATCACAGCTTCCGTCTCAC	58.646	55.000	0.00	0.00	0.00	3.51
380	381	1.155042	GTCTCACAGAAGCCTTGCAG	58.845	55.000	0.00	0.00	0.00	4.41
385	386	1.023513	ACAGAAGCCTTGCAGATCGC	61.024	55.000	3.07	3.07	42.89	4.58
389	390	2.124983	GCCTTGCAGATCGCTGGA	60.125	61.111	18.00	0.00	42.53	3.86

Showing 1 to 25 of 436 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	0.339162	TTCCATGTTCCATGGGCCAT	59.661	50.000	14.78	14.78	39.60	4.40
2	3	0.614415	GTTCCATGTTCCATGGGCCA	60.614	55.000	20.13	9.61	39.60	5.36
4	5	1.137479	CATGTTCCATGTTCCATGGGC	59.863	52.381	20.13	14.50	39.60	5.36
116	117	1.651240	CTTCAAGGACATGCGGGCAG	61.651	60.000	0.00	0.00	0.00	4.85
119	120	0.804989	GTTCTTCAAGGACATGCGGG	59.195	55.000	0.00	0.00	0.00	6.13
120	121	0.443869	CGTTCTTCAAGGACATGCGG	59.556	55.000	0.00	0.00	0.00	5.69
121	122	0.179215	GCGTTCTTCAAGGACATGCG	60.179	55.000	0.00	0.00	0.00	4.73
140	141	2.743636	TAAGACCTTCAGCAAGTCGG	57.256	50.000	0.00	0.00	0.00	4.79
147	148	2.675348	GCACACTGATAAGACCTTCAGC	59.325	50.000	0.06	0.00	42.51	4.26
149	150	3.557054	GGTGCACACTGATAAGACCTTCA	60.557	47.826	20.43	0.00	0.00	3.02
180	181	2.588596	CGCATACGCTGGATGGCA	60.589	61.111	0.00	0.00	35.30	4.92
187	188	1.193203	GATCAATGACCGCATACGCTG	59.807	52.381	0.00	0.00	38.22	5.18
194	195	1.194218	TCCAGAGATCAATGACCGCA	58.806	50.000	0.00	0.00	0.00	5.69
230	231	3.956848	AGATGAGGTGTTCGATGATCTGA	59.043	43.478	0.00	0.00	0.00	3.27
239	240	1.276421	ACCCAGAAGATGAGGTGTTCG	59.724	52.381	0.00	0.00	35.38	3.95
264	265	2.224161	CCTAGAGGATTTCTTCGGGCAG	60.224	54.545	0.00	0.00	37.36	4.85
280	281	1.626321	TGGCAAAACGGATGACCTAGA	59.374	47.619	0.00	0.00	0.00	2.43
293	294	0.821711	CGGGTCTTGAGGTGGCAAAA	60.822	55.000	0.00	0.00	0.00	2.44
341	342	2.045926	AAGCTGTGATGGCGACCC	60.046	61.111	0.00	0.00	34.52	4.46
352	353	1.040646	TTCTGTGAGACGGAAGCTGT	58.959	50.000	0.00	0.00	38.47	4.40
364	365	1.673923	CGATCTGCAAGGCTTCTGTGA	60.674	52.381	0.00	0.00	0.00	3.58
367	368	1.720301	GCGATCTGCAAGGCTTCTG	59.280	57.895	0.00	0.00	45.45	3.02
380	381	1.611491	CCTACCTTCTCTCCAGCGATC	59.389	57.143	0.00	0.00	0.00	3.69
385	386	3.287222	CTGAGTCCTACCTTCTCTCCAG	58.713	54.545	0.00	0.00	0.00	3.86
389	390	1.683629	CCGCTGAGTCCTACCTTCTCT	60.684	57.143	0.00	0.00	0.00	3.10

Showing 1 to 25 of 433 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.