AutoCloner

Multiple sequence alignment - TraesCS4B01G192400

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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	TraesCS4B01G192400	chr4B	100.000	5788	0	0	1	5788	415376015	415370228	0.000000e+00	10689.0
1	TraesCS4B01G192400	chr6B	98.853	5753	57	4	44	5788	707368105	707373856	0.000000e+00	10250.0
2	TraesCS4B01G192400	chr6B	98.201	5725	90	10	43	5759	428711528	428717247	0.000000e+00	9989.0
3	TraesCS4B01G192400	chr6B	99.180	5120	35	6	614	5729	429210662	429215778	0.000000e+00	9215.0
4	TraesCS4B01G192400	chr3A	98.831	5646	62	4	43	5686	652786271	652791914	0.000000e+00	10057.0
5	TraesCS4B01G192400	chr3A	94.549	587	28	3	5204	5788	197148513	197147929	0.000000e+00	904.0
6	TraesCS4B01G192400	chr3A	92.143	560	33	8	5237	5788	504452539	504453095	0.000000e+00	780.0
7	TraesCS4B01G192400	chr3A	94.758	496	22	3	5296	5788	652793054	652793548	0.000000e+00	769.0
8	TraesCS4B01G192400	chr3A	90.134	598	46	11	5195	5788	445855878	445856466	0.000000e+00	765.0
9	TraesCS4B01G192400	chr7A	99.078	5423	45	5	44	5464	550293808	550288389	0.000000e+00	9732.0
10	TraesCS4B01G192400	chrUn	98.169	5298	95	2	389	5686	56613426	56618721	0.000000e+00	9245.0
11	TraesCS4B01G192400	chr3B	97.667	5315	117	7	44	5354	471527881	471533192	0.000000e+00	9121.0
12	TraesCS4B01G192400	chr3B	90.172	814	64	13	4983	5788	396473551	396474356	0.000000e+00	1046.0
13	TraesCS4B01G192400	chr3B	89.571	815	67	14	4983	5788	565550068	565549263	0.000000e+00	1018.0
14	TraesCS4B01G192400	chr4A	97.615	5284	123	3	44	5324	542631328	542636611	0.000000e+00	9057.0
15	TraesCS4B01G192400	chr1B	94.921	5729	270	16	43	5759	417083621	417077902	0.000000e+00	8948.0
16	TraesCS4B01G192400	chr2A	92.373	826	38	9	4983	5788	513890665	513891485	0.000000e+00	1158.0
17	TraesCS4B01G192400	chr2A	94.889	587	27	2	5202	5788	573510531	573511114	0.000000e+00	915.0
18	TraesCS4B01G192400	chr2B	92.576	660	44	5	5130	5788	211780986	211781641	0.000000e+00	942.0
19	TraesCS4B01G192400	chr1D	97.727	44	1	0	1	44	407633336	407633293	6.220000e-10	76.8
20	TraesCS4B01G192400	chr7D	97.619	42	1	0	1	42	429615182	429615223	8.050000e-09	73.1
21	TraesCS4B01G192400	chr7B	97.619	42	1	0	1	42	188628802	188628761	8.050000e-09	73.1
22	TraesCS4B01G192400	chr7B	97.619	42	1	0	1	42	393971199	393971158	8.050000e-09	73.1
23	TraesCS4B01G192400	chr7B	97.619	42	1	0	1	42	455971125	455971084	8.050000e-09	73.1
24	TraesCS4B01G192400	chr7B	97.619	42	1	0	1	42	455973304	455973263	8.050000e-09	73.1
25	TraesCS4B01G192400	chr5B	97.619	42	1	0	1	42	88972181	88972140	8.050000e-09	73.1
26	TraesCS4B01G192400	chr3D	97.619	42	1	0	1	42	299735907	299735866	8.050000e-09	73.1
27	TraesCS4B01G192400	chr2D	97.619	42	1	0	1	42	387452679	387452720	8.050000e-09	73.1

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	TraesCS4B01G192400	chr4B	415370228	415376015	5787	True	10689	10689	100.0000	1	5788	1	chr4B.!!$R1	5787
1	TraesCS4B01G192400	chr6B	707368105	707373856	5751	False	10250	10250	98.8530	44	5788	1	chr6B.!!$F3	5744
2	TraesCS4B01G192400	chr6B	428711528	428717247	5719	False	9989	9989	98.2010	43	5759	1	chr6B.!!$F1	5716
3	TraesCS4B01G192400	chr6B	429210662	429215778	5116	False	9215	9215	99.1800	614	5729	1	chr6B.!!$F2	5115
4	TraesCS4B01G192400	chr3A	652786271	652793548	7277	False	5413	10057	96.7945	43	5788	2	chr3A.!!$F3	5745
5	TraesCS4B01G192400	chr3A	197147929	197148513	584	True	904	904	94.5490	5204	5788	1	chr3A.!!$R1	584
6	TraesCS4B01G192400	chr3A	504452539	504453095	556	False	780	780	92.1430	5237	5788	1	chr3A.!!$F2	551
7	TraesCS4B01G192400	chr3A	445855878	445856466	588	False	765	765	90.1340	5195	5788	1	chr3A.!!$F1	593
8	TraesCS4B01G192400	chr7A	550288389	550293808	5419	True	9732	9732	99.0780	44	5464	1	chr7A.!!$R1	5420
9	TraesCS4B01G192400	chrUn	56613426	56618721	5295	False	9245	9245	98.1690	389	5686	1	chrUn.!!$F1	5297
10	TraesCS4B01G192400	chr3B	471527881	471533192	5311	False	9121	9121	97.6670	44	5354	1	chr3B.!!$F2	5310
11	TraesCS4B01G192400	chr3B	396473551	396474356	805	False	1046	1046	90.1720	4983	5788	1	chr3B.!!$F1	805
12	TraesCS4B01G192400	chr3B	565549263	565550068	805	True	1018	1018	89.5710	4983	5788	1	chr3B.!!$R1	805
13	TraesCS4B01G192400	chr4A	542631328	542636611	5283	False	9057	9057	97.6150	44	5324	1	chr4A.!!$F1	5280
14	TraesCS4B01G192400	chr1B	417077902	417083621	5719	True	8948	8948	94.9210	43	5759	1	chr1B.!!$R1	5716
15	TraesCS4B01G192400	chr2A	513890665	513891485	820	False	1158	1158	92.3730	4983	5788	1	chr2A.!!$F1	805
16	TraesCS4B01G192400	chr2A	573510531	573511114	583	False	915	915	94.8890	5202	5788	1	chr2A.!!$F2	586
17	TraesCS4B01G192400	chr2B	211780986	211781641	655	False	942	942	92.5760	5130	5788	1	chr2B.!!$F1	658

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
26	27	0.110486	AGGCATCACAGGAACGGTTT	59.890	50.0	0.00	0.0	31.98	3.27	F
27	28	0.958822	GGCATCACAGGAACGGTTTT	59.041	50.0	0.00	0.0	31.98	2.43	F
1599	1602	0.885150	TCACGTGTCGCTCTCAGACT	60.885	55.0	16.51	0.0	39.24	3.24	F
2945	2948	0.108585	ATGAAGAACCACTGGCACGT	59.891	50.0	0.00	0.0	0.00	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1599	1602	0.615331	CTGGGCTAGCCTTCTTCACA	59.385	55.000	32.18	18.55	36.10	3.58	R
2945	2948	1.067354	GGCGTTTTCCGACTCTTCCTA	60.067	52.381	0.00	0.00	43.06	2.94	R
4487	4500	3.368948	GGTCATTCTGAAGTGTCTCCTCC	60.369	52.174	0.00	0.00	0.00	4.30	R
5030	5044	5.617252	ACAAAAATCCTACCGAGTGAAGAA	58.383	37.500	0.00	0.00	0.00	2.52	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
18	19	3.955145	TTGGTGTAGGCATCACAGG	57.045	52.632	12.54	0.00	35.10	4.00
19	20	1.357137	TTGGTGTAGGCATCACAGGA	58.643	50.000	12.54	0.00	35.10	3.86
20	21	1.357137	TGGTGTAGGCATCACAGGAA	58.643	50.000	12.54	0.00	37.52	3.36
21	22	1.003118	TGGTGTAGGCATCACAGGAAC	59.997	52.381	12.54	0.00	37.52	3.62
22	23	1.359848	GTGTAGGCATCACAGGAACG	58.640	55.000	7.09	0.00	36.05	3.95
23	24	0.249120	TGTAGGCATCACAGGAACGG	59.751	55.000	0.00	0.00	0.00	4.44
24	25	0.249398	GTAGGCATCACAGGAACGGT	59.751	55.000	0.00	0.00	37.10	4.83
25	26	0.981183	TAGGCATCACAGGAACGGTT	59.019	50.000	0.00	0.00	31.98	4.44
26	27	0.110486	AGGCATCACAGGAACGGTTT	59.890	50.000	0.00	0.00	31.98	3.27
27	28	0.958822	GGCATCACAGGAACGGTTTT	59.041	50.000	0.00	0.00	31.98	2.43
28	29	2.156098	GGCATCACAGGAACGGTTTTA	58.844	47.619	0.00	0.00	31.98	1.52
29	30	2.752903	GGCATCACAGGAACGGTTTTAT	59.247	45.455	0.00	0.00	31.98	1.40
30	31	3.427503	GGCATCACAGGAACGGTTTTATG	60.428	47.826	0.00	0.00	31.98	1.90
31	32	3.190535	GCATCACAGGAACGGTTTTATGT	59.809	43.478	0.00	0.00	31.98	2.29
32	33	4.722194	CATCACAGGAACGGTTTTATGTG	58.278	43.478	19.48	19.48	39.44	3.21
33	34	4.074627	TCACAGGAACGGTTTTATGTGA	57.925	40.909	22.09	22.09	43.33	3.58
34	35	4.647611	TCACAGGAACGGTTTTATGTGAT	58.352	39.130	22.09	0.00	41.37	3.06
35	36	4.454161	TCACAGGAACGGTTTTATGTGATG	59.546	41.667	22.09	7.59	41.37	3.07
36	37	4.215399	CACAGGAACGGTTTTATGTGATGT	59.785	41.667	20.28	5.72	40.27	3.06
37	38	4.215399	ACAGGAACGGTTTTATGTGATGTG	59.785	41.667	0.00	0.00	27.95	3.21
38	39	3.190535	AGGAACGGTTTTATGTGATGTGC	59.809	43.478	0.00	0.00	0.00	4.57
39	40	3.190535	GGAACGGTTTTATGTGATGTGCT	59.809	43.478	0.00	0.00	0.00	4.40
40	41	4.393680	GGAACGGTTTTATGTGATGTGCTA	59.606	41.667	0.00	0.00	0.00	3.49
41	42	4.939509	ACGGTTTTATGTGATGTGCTAC	57.060	40.909	0.00	0.00	0.00	3.58
267	269	5.162870	TGGAGGAAGGTGGCTTATATAGAGA	60.163	44.000	0.00	0.00	0.00	3.10
602	604	2.038426	TGGATTGAGGCTTCGAGTGAAA	59.962	45.455	0.00	0.00	32.66	2.69
924	927	1.084289	GCCTTTTTCGCCACGTATCT	58.916	50.000	0.00	0.00	0.00	1.98
1108	1111	1.376037	CCTCCGCACCACTTTCCTC	60.376	63.158	0.00	0.00	0.00	3.71
1111	1114	2.030562	CGCACCACTTTCCTCCGT	59.969	61.111	0.00	0.00	0.00	4.69
1599	1602	0.885150	TCACGTGTCGCTCTCAGACT	60.885	55.000	16.51	0.00	39.24	3.24
2945	2948	0.108585	ATGAAGAACCACTGGCACGT	59.891	50.000	0.00	0.00	0.00	4.49
4487	4500	4.838486	GACTCGACGCTCTGGCCG	62.838	72.222	0.00	0.00	34.44	6.13
5030	5044	1.377463	CTCCGAGTGAGAGGGTCGT	60.377	63.158	0.00	0.00	44.42	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.357137	TCCTGTGATGCCTACACCAA	58.643	50.000	0.00	0.00	37.45	3.67
1	2	1.003118	GTTCCTGTGATGCCTACACCA	59.997	52.381	0.00	0.00	37.45	4.17
2	3	1.739067	GTTCCTGTGATGCCTACACC	58.261	55.000	0.00	0.00	37.45	4.16
3	4	1.359848	CGTTCCTGTGATGCCTACAC	58.640	55.000	0.00	0.00	38.55	2.90
4	5	0.249120	CCGTTCCTGTGATGCCTACA	59.751	55.000	0.00	0.00	0.00	2.74
5	6	0.249398	ACCGTTCCTGTGATGCCTAC	59.751	55.000	0.00	0.00	0.00	3.18
6	7	0.981183	AACCGTTCCTGTGATGCCTA	59.019	50.000	0.00	0.00	0.00	3.93
7	8	0.110486	AAACCGTTCCTGTGATGCCT	59.890	50.000	0.00	0.00	0.00	4.75
8	9	0.958822	AAAACCGTTCCTGTGATGCC	59.041	50.000	0.00	0.00	0.00	4.40
9	10	3.190535	ACATAAAACCGTTCCTGTGATGC	59.809	43.478	0.00	0.00	0.00	3.91
10	11	4.454161	TCACATAAAACCGTTCCTGTGATG	59.546	41.667	14.65	0.09	38.36	3.07
11	12	4.647611	TCACATAAAACCGTTCCTGTGAT	58.352	39.130	14.65	0.00	38.36	3.06
12	13	4.074627	TCACATAAAACCGTTCCTGTGA	57.925	40.909	14.65	14.65	40.29	3.58
13	14	4.215399	ACATCACATAAAACCGTTCCTGTG	59.785	41.667	11.68	11.68	36.27	3.66
14	15	4.215399	CACATCACATAAAACCGTTCCTGT	59.785	41.667	0.00	0.00	0.00	4.00
15	16	4.722194	CACATCACATAAAACCGTTCCTG	58.278	43.478	0.00	0.00	0.00	3.86
16	17	3.190535	GCACATCACATAAAACCGTTCCT	59.809	43.478	0.00	0.00	0.00	3.36
17	18	3.190535	AGCACATCACATAAAACCGTTCC	59.809	43.478	0.00	0.00	0.00	3.62
18	19	4.419522	AGCACATCACATAAAACCGTTC	57.580	40.909	0.00	0.00	0.00	3.95
19	20	4.155280	GGTAGCACATCACATAAAACCGTT	59.845	41.667	0.00	0.00	0.00	4.44
20	21	3.687698	GGTAGCACATCACATAAAACCGT	59.312	43.478	0.00	0.00	0.00	4.83
21	22	3.938963	AGGTAGCACATCACATAAAACCG	59.061	43.478	0.00	0.00	0.00	4.44
22	23	4.700213	ACAGGTAGCACATCACATAAAACC	59.300	41.667	0.00	0.00	0.00	3.27
23	24	5.445939	CGACAGGTAGCACATCACATAAAAC	60.446	44.000	0.00	0.00	0.00	2.43
24	25	4.629634	CGACAGGTAGCACATCACATAAAA	59.370	41.667	0.00	0.00	0.00	1.52
25	26	4.180817	CGACAGGTAGCACATCACATAAA	58.819	43.478	0.00	0.00	0.00	1.40
26	27	3.194755	ACGACAGGTAGCACATCACATAA	59.805	43.478	0.00	0.00	0.00	1.90
27	28	2.758423	ACGACAGGTAGCACATCACATA	59.242	45.455	0.00	0.00	0.00	2.29
28	29	1.550524	ACGACAGGTAGCACATCACAT	59.449	47.619	0.00	0.00	0.00	3.21
29	30	0.966179	ACGACAGGTAGCACATCACA	59.034	50.000	0.00	0.00	0.00	3.58
30	31	1.350193	CACGACAGGTAGCACATCAC	58.650	55.000	0.00	0.00	0.00	3.06
31	32	0.246360	CCACGACAGGTAGCACATCA	59.754	55.000	0.00	0.00	0.00	3.07
32	33	0.246635	ACCACGACAGGTAGCACATC	59.753	55.000	0.00	0.00	40.98	3.06
33	34	0.685097	AACCACGACAGGTAGCACAT	59.315	50.000	0.00	0.00	42.25	3.21
34	35	0.032952	GAACCACGACAGGTAGCACA	59.967	55.000	0.00	0.00	42.25	4.57
35	36	0.317479	AGAACCACGACAGGTAGCAC	59.683	55.000	0.00	0.00	42.25	4.40
36	37	1.913778	TAGAACCACGACAGGTAGCA	58.086	50.000	0.00	0.00	42.25	3.49
37	38	2.877335	CTTAGAACCACGACAGGTAGC	58.123	52.381	0.00	0.00	42.25	3.58
38	39	2.416972	GGCTTAGAACCACGACAGGTAG	60.417	54.545	0.00	0.00	42.25	3.18
39	40	1.547372	GGCTTAGAACCACGACAGGTA	59.453	52.381	0.00	0.00	42.25	3.08
40	41	0.320697	GGCTTAGAACCACGACAGGT	59.679	55.000	0.00	0.00	45.91	4.00
41	42	0.608640	AGGCTTAGAACCACGACAGG	59.391	55.000	0.00	0.00	0.00	4.00
250	252	2.494073	GCGCTCTCTATATAAGCCACCT	59.506	50.000	0.00	0.00	32.31	4.00
602	604	2.601266	CGAAAACGACATCAACGCCTTT	60.601	45.455	0.00	0.00	0.00	3.11
924	927	3.052869	TCTGGGAGCAGTTATGAGGACTA	60.053	47.826	0.00	0.00	0.00	2.59
1599	1602	0.615331	CTGGGCTAGCCTTCTTCACA	59.385	55.000	32.18	18.55	36.10	3.58
2945	2948	1.067354	GGCGTTTTCCGACTCTTCCTA	60.067	52.381	0.00	0.00	43.06	2.94
4487	4500	3.368948	GGTCATTCTGAAGTGTCTCCTCC	60.369	52.174	0.00	0.00	0.00	4.30
5030	5044	5.617252	ACAAAAATCCTACCGAGTGAAGAA	58.383	37.500	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.