AutoCloner

Multiple sequence alignment - TraesCS4B01G119400

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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	TraesCS4B01G119400	chr4B	100.000	3568	0	0	1	3568	139741989	139745556	0.000000e+00	6589
1	TraesCS4B01G119400	chr4B	97.555	2577	51	2	636	3201	2598690	2601265	0.000000e+00	4399
2	TraesCS4B01G119400	chr5A	99.149	2936	25	0	633	3568	346306294	346309229	0.000000e+00	5284
3	TraesCS4B01G119400	chr3A	99.010	2930	29	0	637	3566	199412059	199414988	0.000000e+00	5251
4	TraesCS4B01G119400	chr7B	98.336	2944	35	3	634	3566	554160474	554163414	0.000000e+00	5153
5	TraesCS4B01G119400	chr1A	99.104	2568	23	0	636	3203	63763700	63761133	0.000000e+00	4615
6	TraesCS4B01G119400	chr1A	97.895	475	9	1	3095	3568	320477403	320476929	0.000000e+00	821
7	TraesCS4B01G119400	chr1B	99.218	2556	20	0	635	3190	167930127	167927572	0.000000e+00	4610
8	TraesCS4B01G119400	chr1B	98.109	476	7	2	3095	3568	167927765	167927290	0.000000e+00	828
9	TraesCS4B01G119400	chr3B	98.269	2600	44	1	634	3233	681202911	681200313	0.000000e+00	4551
10	TraesCS4B01G119400	chr3B	98.084	2609	37	3	637	3233	731127043	731129650	0.000000e+00	4529
11	TraesCS4B01G119400	chr3B	95.506	267	8	3	636	899	681197388	681197653	1.180000e-114	424
12	TraesCS4B01G119400	chr3B	87.500	392	18	20	629	1004	731133886	731133510	1.180000e-114	424
13	TraesCS4B01G119400	chr2A	98.827	2387	28	0	636	3022	672536852	672539238	0.000000e+00	4253
14	TraesCS4B01G119400	chr4D	91.264	641	44	9	1	634	98300050	98300685	0.000000e+00	863
15	TraesCS4B01G119400	chr5B	99.134	462	4	0	3107	3568	56908667	56909128	0.000000e+00	832
16	TraesCS4B01G119400	chr4A	98.316	475	7	1	3095	3568	683249681	683249207	0.000000e+00	832
17	TraesCS4B01G119400	chr2B	98.105	475	8	1	3095	3568	652847488	652847014	0.000000e+00	826
18	TraesCS4B01G119400	chr2B	87.080	387	19	20	634	1004	652842528	652842899	3.320000e-110	409

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	TraesCS4B01G119400	chr4B	139741989	139745556	3567	False	6589	6589	100.0000	1	3568	1	chr4B.!!$F2	3567
1	TraesCS4B01G119400	chr4B	2598690	2601265	2575	False	4399	4399	97.5550	636	3201	1	chr4B.!!$F1	2565
2	TraesCS4B01G119400	chr5A	346306294	346309229	2935	False	5284	5284	99.1490	633	3568	1	chr5A.!!$F1	2935
3	TraesCS4B01G119400	chr3A	199412059	199414988	2929	False	5251	5251	99.0100	637	3566	1	chr3A.!!$F1	2929
4	TraesCS4B01G119400	chr7B	554160474	554163414	2940	False	5153	5153	98.3360	634	3566	1	chr7B.!!$F1	2932
5	TraesCS4B01G119400	chr1A	63761133	63763700	2567	True	4615	4615	99.1040	636	3203	1	chr1A.!!$R1	2567
6	TraesCS4B01G119400	chr1B	167927290	167930127	2837	True	2719	4610	98.6635	635	3568	2	chr1B.!!$R1	2933
7	TraesCS4B01G119400	chr3B	681200313	681202911	2598	True	4551	4551	98.2690	634	3233	1	chr3B.!!$R1	2599
8	TraesCS4B01G119400	chr3B	731127043	731129650	2607	False	4529	4529	98.0840	637	3233	1	chr3B.!!$F2	2596
9	TraesCS4B01G119400	chr2A	672536852	672539238	2386	False	4253	4253	98.8270	636	3022	1	chr2A.!!$F1	2386
10	TraesCS4B01G119400	chr4D	98300050	98300685	635	False	863	863	91.2640	1	634	1	chr4D.!!$F1	633

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
309	315	0.033504	ATACCGGGCTTAGCATCACG	59.966	55.0	6.32	4.77	0.00	4.35	F
1083	1103	0.179009	CCACCGATGGGCTCAATCAT	60.179	55.0	0.00	0.00	43.04	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2016	2036	1.203162	TGCATTCTCCATTGTTGGGGT	60.203	47.619	0.0	0.0	44.67	4.95	R
2882	2902	8.950210	CAAATGATACTAACTGGAGTTCAACAT	58.050	33.333	0.0	0.0	39.31	2.71	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
76	77	3.739209	CGACTCCATTGCATAGAAGCTCA	60.739	47.826	0.00	0.00	34.99	4.26
108	109	7.549147	AAGTGGGTCTTAGTACAAGTTCATA	57.451	36.000	0.00	0.00	34.23	2.15
120	121	3.310227	ACAAGTTCATACAAAACACGCGA	59.690	39.130	15.93	0.00	0.00	5.87
134	135	1.539827	CACGCGAAAAAGGAAGGGAAT	59.460	47.619	15.93	0.00	0.00	3.01
139	140	3.611766	GCGAAAAAGGAAGGGAATGACAC	60.612	47.826	0.00	0.00	0.00	3.67
140	141	3.568007	CGAAAAAGGAAGGGAATGACACA	59.432	43.478	0.00	0.00	0.00	3.72
172	178	4.268884	CAGAGAGCGCTCCAAACTTATTAC	59.731	45.833	32.94	4.68	42.30	1.89
195	201	1.822506	GTGGAACTCAGGCTAAACCC	58.177	55.000	0.00	0.00	40.58	4.11
197	203	0.611714	GGAACTCAGGCTAAACCCGA	59.388	55.000	0.00	0.00	40.58	5.14
204	210	2.399356	GGCTAAACCCGAGCAGTGC	61.399	63.158	7.13	7.13	41.98	4.40
217	223	3.968724	CGAGCAGTGCAGAAAAGTAAAAC	59.031	43.478	19.20	0.00	0.00	2.43
222	228	5.507985	GCAGTGCAGAAAAGTAAAACCAGAT	60.508	40.000	11.09	0.00	0.00	2.90
262	268	3.930504	GCTGAAGAGCATTGGGGG	58.069	61.111	0.00	0.00	45.46	5.40
291	297	1.807814	AGGGGATTTCCAGCGTAGAT	58.192	50.000	0.00	0.00	37.91	1.98
294	300	2.289506	GGGGATTTCCAGCGTAGATACC	60.290	54.545	0.00	0.00	37.91	2.73
295	301	2.609737	GGGATTTCCAGCGTAGATACCG	60.610	54.545	0.00	0.00	37.91	4.02
302	308	1.068472	CAGCGTAGATACCGGGCTTAG	60.068	57.143	6.32	0.00	0.00	2.18
309	315	0.033504	ATACCGGGCTTAGCATCACG	59.966	55.000	6.32	4.77	0.00	4.35
334	340	6.702282	GCTCACACTCTATTTATCCCTACAAC	59.298	42.308	0.00	0.00	0.00	3.32
360	366	5.170021	TGGATAAGCAACAACAATCAATGC	58.830	37.500	0.00	0.00	37.28	3.56
385	391	7.227512	GCTACTGATATGGTAAATTTGACAGCT	59.772	37.037	0.00	0.00	0.00	4.24
386	392	9.764363	CTACTGATATGGTAAATTTGACAGCTA	57.236	33.333	0.00	0.00	0.00	3.32
440	446	7.770801	TTGATCATCATAAGTAAGACAACCG	57.229	36.000	0.00	0.00	0.00	4.44
453	459	2.597510	AACCGGCTTGTCCTTGGC	60.598	61.111	0.00	0.00	0.00	4.52
481	487	3.788227	AGGATTAGGTCACTTGTTGCA	57.212	42.857	0.00	0.00	0.00	4.08
497	503	8.583765	CACTTGTTGCACTCTTTTACTTTTTAC	58.416	33.333	0.00	0.00	0.00	2.01
516	522	3.120321	ACTGTTGCTCACGTTCCATTA	57.880	42.857	0.00	0.00	0.00	1.90
517	523	3.674997	ACTGTTGCTCACGTTCCATTAT	58.325	40.909	0.00	0.00	0.00	1.28
548	554	7.455641	ACACCCATGAAACATAAAACGATTA	57.544	32.000	0.00	0.00	0.00	1.75
555	561	9.490663	CATGAAACATAAAACGATTAGACCTTC	57.509	33.333	0.00	0.00	0.00	3.46
575	581	5.221461	CCTTCTTGTACTTGTAGTGACACCT	60.221	44.000	0.84	0.00	34.48	4.00
627	635	5.957771	AACTAGTGGGATCAATGCTCTTA	57.042	39.130	0.00	0.00	0.00	2.10
857	876	4.671590	TGACTGGGACGAGGCCGA	62.672	66.667	0.00	0.00	39.50	5.54
953	973	2.676822	TTCTCTCTGCCTCGCCGT	60.677	61.111	0.00	0.00	0.00	5.68
1083	1103	0.179009	CCACCGATGGGCTCAATCAT	60.179	55.000	0.00	0.00	43.04	2.45
2016	2036	0.036732	GTGGGTTGATGAGCAGTGGA	59.963	55.000	0.00	0.00	0.00	4.02
2565	2585	6.059787	ACCATAAAGAAGAGAAGCAGATGT	57.940	37.500	0.00	0.00	0.00	3.06
3265	3285	1.707989	TGATGGCTTTAGGTGGTTCCA	59.292	47.619	0.00	0.00	39.02	3.53
3411	3432	6.830324	TCCAAGCTTGCATAATCAATAACTCT	59.170	34.615	21.43	0.00	0.00	3.24
3433	3454	9.099071	ACTCTAGCATATCAAGATAGTCCATTT	57.901	33.333	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	0.915364	GAAGCCCTCCCTGTTGATCT	59.085	55.000	0.00	0.00	0.00	2.75
47	48	2.115291	GCAATGGAGTCGGGGAAGC	61.115	63.158	0.00	0.00	0.00	3.86
84	85	5.881923	TGAACTTGTACTAAGACCCACTT	57.118	39.130	10.71	0.00	42.04	3.16
108	109	2.923605	TCCTTTTTCGCGTGTTTTGT	57.076	40.000	5.77	0.00	0.00	2.83
120	121	5.221702	CCATTGTGTCATTCCCTTCCTTTTT	60.222	40.000	0.00	0.00	0.00	1.94
139	140	1.364626	GCGCTCTCTGGACACCATTG	61.365	60.000	0.00	0.00	30.82	2.82
140	141	1.078848	GCGCTCTCTGGACACCATT	60.079	57.895	0.00	0.00	30.82	3.16
149	155	2.370281	TAAGTTTGGAGCGCTCTCTG	57.630	50.000	34.46	0.00	39.31	3.35
172	178	3.330267	GTTTAGCCTGAGTTCCACTCTG	58.670	50.000	5.53	4.87	45.27	3.35
185	191	1.296715	CACTGCTCGGGTTTAGCCT	59.703	57.895	0.00	0.00	39.30	4.58
192	198	0.886490	CTTTTCTGCACTGCTCGGGT	60.886	55.000	1.98	0.00	0.00	5.28
194	200	1.795768	TACTTTTCTGCACTGCTCGG	58.204	50.000	1.98	0.00	0.00	4.63
195	201	3.878086	TTTACTTTTCTGCACTGCTCG	57.122	42.857	1.98	0.00	0.00	5.03
197	203	3.699038	TGGTTTTACTTTTCTGCACTGCT	59.301	39.130	1.98	0.00	0.00	4.24
204	210	6.084277	GCGGTTATCTGGTTTTACTTTTCTG	58.916	40.000	0.00	0.00	0.00	3.02
217	223	3.749981	GCCATGGCGGTTATCTGG	58.250	61.111	23.48	0.00	36.97	3.86
222	228	1.554583	TGGTGTAGCCATGGCGGTTA	61.555	55.000	30.50	15.43	43.61	2.85
256	262	1.196104	CCCTACTCAACGACCCCCAA	61.196	60.000	0.00	0.00	0.00	4.12
260	266	1.201424	AATCCCCTACTCAACGACCC	58.799	55.000	0.00	0.00	0.00	4.46
262	268	2.235402	TGGAAATCCCCTACTCAACGAC	59.765	50.000	0.00	0.00	34.29	4.34
291	297	1.440060	CGTGATGCTAAGCCCGGTA	59.560	57.895	0.00	0.00	0.00	4.02
302	308	2.215907	ATAGAGTGTGAGCGTGATGC	57.784	50.000	0.00	0.00	46.98	3.91
309	315	6.406692	TGTAGGGATAAATAGAGTGTGAGC	57.593	41.667	0.00	0.00	0.00	4.26
334	340	7.675403	GCATTGATTGTTGTTGCTTATCCAATG	60.675	37.037	0.00	0.00	0.00	2.82
360	366	8.668510	AGCTGTCAAATTTACCATATCAGTAG	57.331	34.615	0.00	0.00	0.00	2.57
385	391	5.664665	TGAGGATGGAGGGATAATGACATA	58.335	41.667	0.00	0.00	0.00	2.29
386	392	4.506354	TGAGGATGGAGGGATAATGACAT	58.494	43.478	0.00	0.00	0.00	3.06
398	404	7.812690	TGATCAAACATTATTGAGGATGGAG	57.187	36.000	0.00	0.00	42.21	3.86
399	405	8.000127	TGATGATCAAACATTATTGAGGATGGA	59.000	33.333	0.00	0.00	42.21	3.41
440	446	2.378038	TGATATTGCCAAGGACAAGCC	58.622	47.619	0.00	0.00	0.00	4.35
453	459	8.400947	CAACAAGTGACCTAATCCTTGATATTG	58.599	37.037	5.34	0.00	38.23	1.90
467	473	2.717639	AAGAGTGCAACAAGTGACCT	57.282	45.000	0.00	0.00	41.43	3.85
481	487	8.182227	GTGAGCAACAGTAAAAAGTAAAAGAGT	58.818	33.333	0.00	0.00	0.00	3.24
497	503	4.685169	AATAATGGAACGTGAGCAACAG	57.315	40.909	0.00	0.00	0.00	3.16
517	523	9.482627	GTTTTATGTTTCATGGGTGTAATGAAA	57.517	29.630	7.33	7.33	46.55	2.69
548	554	5.597182	TGTCACTACAAGTACAAGAAGGTCT	59.403	40.000	0.00	0.00	30.91	3.85
555	561	5.277345	GCAAAGGTGTCACTACAAGTACAAG	60.277	44.000	2.35	0.00	37.36	3.16
575	581	9.810545	AAAAAGTACTAAGCACAAAATAGCAAA	57.189	25.926	0.00	0.00	0.00	3.68
603	609	5.283457	AGAGCATTGATCCCACTAGTTAC	57.717	43.478	0.00	0.00	0.00	2.50
604	610	5.957771	AAGAGCATTGATCCCACTAGTTA	57.042	39.130	0.00	0.00	0.00	2.24
605	611	4.851639	AAGAGCATTGATCCCACTAGTT	57.148	40.909	0.00	0.00	0.00	2.24
606	612	5.604231	TGATAAGAGCATTGATCCCACTAGT	59.396	40.000	0.00	0.00	0.00	2.57
620	628	7.176515	TGCAATTTACTCCTTTTGATAAGAGCA	59.823	33.333	0.00	0.00	0.00	4.26
621	629	7.486232	GTGCAATTTACTCCTTTTGATAAGAGC	59.514	37.037	0.00	0.00	0.00	4.09
627	635	6.899393	TCTGTGCAATTTACTCCTTTTGAT	57.101	33.333	0.00	0.00	0.00	2.57
857	876	2.264794	CGCGCCCTAAACAGGAGT	59.735	61.111	0.00	0.00	0.00	3.85
2016	2036	1.203162	TGCATTCTCCATTGTTGGGGT	60.203	47.619	0.00	0.00	44.67	4.95
2565	2585	9.809096	CATGAGCTCAGTAATCTTAAACTCTTA	57.191	33.333	22.96	0.00	0.00	2.10
2882	2902	8.950210	CAAATGATACTAACTGGAGTTCAACAT	58.050	33.333	0.00	0.00	39.31	2.71
2936	2956	9.836076	CATATGTAACTATTCCTCAAATGCATG	57.164	33.333	0.00	0.00	0.00	4.06
3411	3432	8.316946	CCTGAAATGGACTATCTTGATATGCTA	58.683	37.037	0.00	0.00	0.00	3.49
3433	3454	3.691118	GCAACTTATGAGTGAATGCCTGA	59.309	43.478	2.21	0.00	35.91	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.