AutoCloner

Multiple sequence alignment - TraesCS3B01G247100

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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	TraesCS3B01G247100	chr3B	100.000	3398	0	0	1	3398	393192016	393195413	0.000000e+00	6276.0
1	TraesCS3B01G247100	chr4B	94.319	3415	154	31	1	3398	443187667	443184276	0.000000e+00	5195.0
2	TraesCS3B01G247100	chr6B	94.085	3415	159	30	1	3398	440006972	440010360	0.000000e+00	5147.0
3	TraesCS3B01G247100	chr6B	91.546	2212	163	18	1	2194	356445492	356447697	0.000000e+00	3027.0
4	TraesCS3B01G247100	chr6D	93.993	3313	164	24	1	3298	283636546	283633254	0.000000e+00	4983.0
5	TraesCS3B01G247100	chr4A	93.297	3312	188	26	1	3298	500275895	500272604	0.000000e+00	4855.0
6	TraesCS3B01G247100	chr4A	93.237	3312	183	28	1	3298	500281252	500277968	0.000000e+00	4837.0
7	TraesCS3B01G247100	chr1B	94.457	3121	130	26	295	3398	524764070	524767164	0.000000e+00	4765.0
8	TraesCS3B01G247100	chr1B	90.018	3406	283	40	1	3379	106886648	106890023	0.000000e+00	4353.0
9	TraesCS3B01G247100	chr1B	94.090	2521	142	5	1	2518	593273255	593270739	0.000000e+00	3823.0
10	TraesCS3B01G247100	chr1B	98.148	54	1	0	3345	3398	102610435	102610382	1.000000e-15	95.3
11	TraesCS3B01G247100	chr2B	90.120	3421	286	37	1	3398	330762439	330765830	0.000000e+00	4397.0
12	TraesCS3B01G247100	chr2B	90.723	3320	262	27	1	3298	550080266	550076971	0.000000e+00	4383.0
13	TraesCS3B01G247100	chr2B	85.925	1151	122	28	2262	3398	357090096	357088972	0.000000e+00	1192.0
14	TraesCS3B01G247100	chr4D	89.163	3359	284	44	1	3342	272407425	272410720	0.000000e+00	4113.0
15	TraesCS3B01G247100	chr3A	90.629	2209	193	12	1	2200	392544790	392546993	0.000000e+00	2920.0
16	TraesCS3B01G247100	chr3A	87.342	79	8	2	1	78	408446392	408446469	4.670000e-14	89.8

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	TraesCS3B01G247100	chr3B	393192016	393195413	3397	False	6276	6276	100.000	1	3398	1	chr3B.!!$F1	3397
1	TraesCS3B01G247100	chr4B	443184276	443187667	3391	True	5195	5195	94.319	1	3398	1	chr4B.!!$R1	3397
2	TraesCS3B01G247100	chr6B	440006972	440010360	3388	False	5147	5147	94.085	1	3398	1	chr6B.!!$F2	3397
3	TraesCS3B01G247100	chr6B	356445492	356447697	2205	False	3027	3027	91.546	1	2194	1	chr6B.!!$F1	2193
4	TraesCS3B01G247100	chr6D	283633254	283636546	3292	True	4983	4983	93.993	1	3298	1	chr6D.!!$R1	3297
5	TraesCS3B01G247100	chr4A	500272604	500281252	8648	True	4846	4855	93.267	1	3298	2	chr4A.!!$R1	3297
6	TraesCS3B01G247100	chr1B	524764070	524767164	3094	False	4765	4765	94.457	295	3398	1	chr1B.!!$F2	3103
7	TraesCS3B01G247100	chr1B	106886648	106890023	3375	False	4353	4353	90.018	1	3379	1	chr1B.!!$F1	3378
8	TraesCS3B01G247100	chr1B	593270739	593273255	2516	True	3823	3823	94.090	1	2518	1	chr1B.!!$R2	2517
9	TraesCS3B01G247100	chr2B	330762439	330765830	3391	False	4397	4397	90.120	1	3398	1	chr2B.!!$F1	3397
10	TraesCS3B01G247100	chr2B	550076971	550080266	3295	True	4383	4383	90.723	1	3298	1	chr2B.!!$R2	3297
11	TraesCS3B01G247100	chr2B	357088972	357090096	1124	True	1192	1192	85.925	2262	3398	1	chr2B.!!$R1	1136
12	TraesCS3B01G247100	chr4D	272407425	272410720	3295	False	4113	4113	89.163	1	3342	1	chr4D.!!$F1	3341
13	TraesCS3B01G247100	chr3A	392544790	392546993	2203	False	2920	2920	90.629	1	2200	1	chr3A.!!$F1	2199

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
245	249	0.865769	GTTTGTGAGCGTGTGTAGGG	59.134	55.0	0.0	0.0	0.0	3.53	F
1415	1446	0.889994	GCTCCACCAAATCATGCACA	59.110	50.0	0.0	0.0	0.0	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1824	1868	2.102578	TGTTCGAGCTCTGGATCATCA	58.897	47.619	12.85	0.0	0.0	3.07	R
2427	2481	1.004394	TCTCCTCTTCACCGTGCTCTA	59.996	52.381	0.00	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
22	23	2.946762	GACACTCGCAGTTTGGGC	59.053	61.111	0.00	0.00	0.00	5.36
46	49	5.445010	CGTAAAAATCCCGCTGTACTTACAC	60.445	44.000	0.00	0.00	31.93	2.90
245	249	0.865769	GTTTGTGAGCGTGTGTAGGG	59.134	55.000	0.00	0.00	0.00	3.53
389	393	5.358922	CAAAAATTTTGAGTTGAGGCCTGA	58.641	37.500	12.00	0.00	0.00	3.86
545	551	7.171508	GTGTATGTTGTTCACATTCTCTCTCAA	59.828	37.037	0.00	0.00	44.40	3.02
717	748	1.064166	AGCTTGTATGCAGCTTGGGAT	60.064	47.619	0.00	0.00	35.02	3.85
848	879	1.537202	GTCAGCTGGTGGAACAATCAC	59.463	52.381	15.13	0.00	44.16	3.06
871	902	1.071471	AAGACCGTTGAGGGTGCAG	59.929	57.895	0.00	0.00	46.96	4.41
932	963	3.288092	GGGGTTATGAAAGGCCTAGTTG	58.712	50.000	5.16	0.00	0.00	3.16
983	1014	4.065088	TCAGAAGCTGTGTGTTCCATAAC	58.935	43.478	0.00	0.00	33.01	1.89
1005	1036	6.065976	ACTGAACAGAAATCATCCATGGTA	57.934	37.500	12.58	0.00	0.00	3.25
1282	1313	6.045318	GCTAAGTTGAGACAGCAAGATATGA	58.955	40.000	0.00	0.00	34.13	2.15
1369	1400	6.926826	CCACACTTGTGTTACAACTGTATCTA	59.073	38.462	8.52	0.00	44.21	1.98
1406	1437	6.248433	AGAAGAAATCATTAGCTCCACCAAA	58.752	36.000	0.00	0.00	0.00	3.28
1407	1438	6.894103	AGAAGAAATCATTAGCTCCACCAAAT	59.106	34.615	0.00	0.00	0.00	2.32
1409	1440	6.189859	AGAAATCATTAGCTCCACCAAATCA	58.810	36.000	0.00	0.00	0.00	2.57
1413	1444	2.804986	TAGCTCCACCAAATCATGCA	57.195	45.000	0.00	0.00	0.00	3.96
1414	1445	1.180029	AGCTCCACCAAATCATGCAC	58.820	50.000	0.00	0.00	0.00	4.57
1415	1446	0.889994	GCTCCACCAAATCATGCACA	59.110	50.000	0.00	0.00	0.00	4.57
1420	1454	4.085009	TCCACCAAATCATGCACATACAA	58.915	39.130	0.00	0.00	0.00	2.41
1824	1868	0.613260	TACTCGAAGCCAAGGCACAT	59.387	50.000	14.40	0.00	44.88	3.21
1862	1906	4.675114	CGAACAACCAAGTAATCAAGTTGC	59.325	41.667	0.00	0.00	41.12	4.17
1896	1949	8.031864	TCATCTACTACTCTTGAAGAAGCAAAG	58.968	37.037	0.00	0.00	0.00	2.77
1967	2020	2.296190	TCACACAAGAGCGTGATGTAGT	59.704	45.455	0.00	0.00	39.34	2.73
1976	2029	5.833082	AGAGCGTGATGTAGTAGGTTTATG	58.167	41.667	0.00	0.00	0.00	1.90
2205	2259	9.050601	ACTAGTCTTGAGCTTAATGATAAATGC	57.949	33.333	0.00	0.00	0.00	3.56
2301	2355	3.849911	TGGACACTCGATTGATGACTTC	58.150	45.455	10.04	0.00	0.00	3.01
2395	2449	2.158623	TCACTTCATGCTGACCAGGTTT	60.159	45.455	0.00	0.00	0.00	3.27
2427	2481	1.386772	TTGGGACCCTGGTGGACTT	60.387	57.895	13.00	0.00	38.00	3.01
2520	2579	3.177228	AGAAGCAAAAGGAGAGGAGCTA	58.823	45.455	0.00	0.00	0.00	3.32
2534	2593	3.954904	GAGGAGCTACAGTTGGTGAGATA	59.045	47.826	0.00	0.00	0.00	1.98
2590	2654	7.099120	AGCTATTTCATGACCCATTTTGAAAC	58.901	34.615	0.00	0.00	39.94	2.78
2597	2662	6.666980	TCATGACCCATTTTGAAACCATCATA	59.333	34.615	0.00	0.00	38.03	2.15
2644	2710	0.881118	TTTGGGTCGCTTGAGCAATC	59.119	50.000	3.65	0.00	41.93	2.67
2728	2796	3.815401	ACTGAGTGTTGAATGCCTTGTAC	59.185	43.478	0.00	0.00	0.00	2.90
2791	2860	6.003950	TGAAAGCTATTAGTTTGGAGTGCTT	58.996	36.000	0.00	0.00	40.59	3.91
2806	2875	5.665812	TGGAGTGCTTAAATCCCTAGTACAT	59.334	40.000	0.00	0.00	31.73	2.29
2915	2984	4.574674	TTGAGAGCAATCACCTAACCAT	57.425	40.909	0.00	0.00	0.00	3.55
2930	2999	6.716628	CACCTAACCATTATGGATTAGCATGT	59.283	38.462	19.23	11.38	40.96	3.21
2941	3010	6.508030	TGGATTAGCATGTTATGTTCCCTA	57.492	37.500	9.65	0.00	0.00	3.53
3172	3325	4.202326	GGTGTATACCATGTTCTCGGGATT	60.202	45.833	3.35	0.00	46.71	3.01
3189	3342	4.626771	CGGGATTGGTGGTATGTTCCTTTA	60.627	45.833	0.00	0.00	0.00	1.85
3195	8633	3.118000	GGTGGTATGTTCCTTTAGGGAGG	60.118	52.174	0.00	0.00	46.01	4.30
3388	8833	5.761165	TTAAGTTCTTTTTGTTCTCGGGG	57.239	39.130	0.00	0.00	0.00	5.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	4.626604	TGTAAGTACAGCGGGATTTTTACG	59.373	41.667	0.00	0.00	0.00	3.18
23	24	5.640783	AGTGTAAGTACAGCGGGATTTTTAC	59.359	40.000	0.00	0.00	36.78	2.01
24	25	5.797051	AGTGTAAGTACAGCGGGATTTTTA	58.203	37.500	0.00	0.00	36.78	1.52
46	49	0.171007	ACGGCGCCAAAATGATCAAG	59.829	50.000	28.98	7.69	0.00	3.02
89	93	4.582656	AGCCTAGTCTATAGCTTCACACAG	59.417	45.833	0.00	0.00	29.27	3.66
245	249	9.982651	TCAATGAGCCTACAAATAGTAAGATAC	57.017	33.333	0.00	0.00	30.92	2.24
367	371	5.612725	TCAGGCCTCAACTCAAAATTTTT	57.387	34.783	0.00	0.00	0.00	1.94
389	393	5.065914	TCTGCAAGACAAGAGCAATAAGTT	58.934	37.500	0.00	0.00	38.67	2.66
545	551	1.912043	ACCAGTCCTTAGCAGCATCTT	59.088	47.619	0.00	0.00	0.00	2.40
848	879	0.249741	ACCCTCAACGGTCTTGTTCG	60.250	55.000	0.00	0.00	0.00	3.95
871	902	5.298777	AGGCAATGCTCTCAATGAGAATAAC	59.701	40.000	14.44	5.07	40.14	1.89
932	963	3.243401	ACAACTTGCAACCTTCGGATTTC	60.243	43.478	0.00	0.00	0.00	2.17
983	1014	5.297776	GGTACCATGGATGATTTCTGTTCAG	59.702	44.000	21.47	0.00	0.00	3.02
1005	1036	7.480760	AACATGCTGGTTTTGAATATTAGGT	57.519	32.000	0.00	0.00	0.00	3.08
1191	1222	8.675705	TTGACTCATTCTGAACAGTTTCATTA	57.324	30.769	5.55	0.00	41.05	1.90
1221	1252	5.561679	GGTTCCTCATAAACCTCTTCTTGT	58.438	41.667	0.00	0.00	42.42	3.16
1282	1313	6.543831	AGCTGACTAACACAAGTGAATTTCTT	59.456	34.615	7.28	0.00	0.00	2.52
1406	1437	8.743085	ACTCTCTTTAATTGTATGTGCATGAT	57.257	30.769	0.00	0.00	0.00	2.45
1407	1438	9.836864	ATACTCTCTTTAATTGTATGTGCATGA	57.163	29.630	0.00	0.00	0.00	3.07
1499	1534	5.147032	CCTCTTGTATCTCTCTCCTTGGAT	58.853	45.833	0.00	0.00	0.00	3.41
1737	1772	5.411669	GCTACTACCAGCAACACTTAATTGT	59.588	40.000	0.00	0.00	41.40	2.71
1824	1868	2.102578	TGTTCGAGCTCTGGATCATCA	58.897	47.619	12.85	0.00	0.00	3.07
1862	1906	7.800155	TCAAGAGTAGTAGATGATGAGTCTG	57.200	40.000	0.00	0.00	0.00	3.51
1896	1949	3.258971	AGTTCATCTACAGCAGCTTCC	57.741	47.619	0.00	0.00	0.00	3.46
1967	2020	8.988060	TGTCATCAAGAGGATTACATAAACCTA	58.012	33.333	0.76	0.00	38.41	3.08
1976	2029	5.988561	GGACTCATGTCATCAAGAGGATTAC	59.011	44.000	0.00	0.00	44.61	1.89
2205	2259	3.941483	GGTCAACACTAACATGAGGATGG	59.059	47.826	0.00	0.00	33.39	3.51
2395	2449	1.351017	GTCCCAAGGAATGTCACCTCA	59.649	52.381	0.00	0.00	36.67	3.86
2427	2481	1.004394	TCTCCTCTTCACCGTGCTCTA	59.996	52.381	0.00	0.00	0.00	2.43
2520	2579	3.735208	CGCTCGATTATCTCACCAACTGT	60.735	47.826	0.00	0.00	0.00	3.55
2597	2662	9.565090	AGCAGTTGATTACATCATGTATAATGT	57.435	29.630	0.00	3.55	39.39	2.71
2609	2675	5.296780	CGACCCAAATAGCAGTTGATTACAT	59.703	40.000	0.00	0.00	0.00	2.29
2644	2710	8.438676	AAATTCAGTGGGACGATATTTAAGAG	57.561	34.615	0.00	0.00	0.00	2.85
2728	2796	6.341880	CAAGCATTGTGTAGATCACTAGTG	57.658	41.667	17.17	17.17	46.27	2.74
2915	2984	7.526041	AGGGAACATAACATGCTAATCCATAA	58.474	34.615	0.00	0.00	0.00	1.90
2930	2999	4.476297	TGCTACCGATCTAGGGAACATAA	58.524	43.478	0.00	0.00	35.02	1.90
2941	3010	1.831106	TGGTTCACATGCTACCGATCT	59.169	47.619	0.00	0.00	34.62	2.75
2974	3043	3.128589	ACGCATAAGCACAAAAATCGGAT	59.871	39.130	0.00	0.00	42.27	4.18
2978	3053	5.174761	TGAACAACGCATAAGCACAAAAATC	59.825	36.000	0.00	0.00	42.27	2.17
3129	3213	6.817184	ACACCTAGTTCGACAATTATAGCAT	58.183	36.000	0.00	0.00	0.00	3.79
3147	3231	3.893200	CCCGAGAACATGGTATACACCTA	59.107	47.826	5.01	0.00	45.98	3.08
3172	3325	3.521937	CTCCCTAAAGGAACATACCACCA	59.478	47.826	0.00	0.00	46.94	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.