AutoCloner

Multiple sequence alignment - TraesCS5D01G151000

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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	TraesCS5D01G151000	chr5D	100.000	2129	0	0	1	2129	240131741	240133869	0.000000e+00	3932
1	TraesCS5D01G151000	chr5D	98.793	1409	16	1	721	2129	6206514	6205107	0.000000e+00	2507
2	TraesCS5D01G151000	chr5D	98.663	673	8	1	1	673	326758862	326758191	0.000000e+00	1192
3	TraesCS5D01G151000	chr5D	98.366	673	10	1	1	673	199932908	199932237	0.000000e+00	1181
4	TraesCS5D01G151000	chrUn	99.359	1403	8	1	721	2123	317471877	317470476	0.000000e+00	2540
5	TraesCS5D01G151000	chrUn	100.000	1313	0	0	772	2084	412876642	412877954	0.000000e+00	2425
6	TraesCS5D01G151000	chr3D	99.219	1409	9	2	721	2129	21898848	21900254	0.000000e+00	2540
7	TraesCS5D01G151000	chr3D	98.366	673	11	0	1	673	548652262	548652934	0.000000e+00	1182
8	TraesCS5D01G151000	chr3D	98.217	673	12	0	1	673	503660661	503659989	0.000000e+00	1177
9	TraesCS5D01G151000	chr1D	99.219	1409	10	1	721	2129	483921649	483920242	0.000000e+00	2540
10	TraesCS5D01G151000	chr1D	98.936	1410	11	3	721	2129	254490971	254492377	0.000000e+00	2518
11	TraesCS5D01G151000	chr1D	98.220	674	11	1	1	673	300987194	300986521	0.000000e+00	1177
12	TraesCS5D01G151000	chr1D	98.217	673	12	0	1	673	400713257	400712585	0.000000e+00	1177
13	TraesCS5D01G151000	chr3B	98.297	1409	22	2	721	2129	201507887	201509293	0.000000e+00	2468
14	TraesCS5D01G151000	chr3B	98.347	121	2	0	2008	2128	820706588	820706468	1.650000e-51	213
15	TraesCS5D01G151000	chr3B	96.694	121	4	0	2008	2128	820577610	820577490	3.580000e-48	202
16	TraesCS5D01G151000	chr4D	96.806	1409	28	9	721	2129	19911272	19912663	0.000000e+00	2337
17	TraesCS5D01G151000	chr2D	95.969	1439	24	7	721	2129	334227225	334228659	0.000000e+00	2305
18	TraesCS5D01G151000	chr7D	98.366	673	11	0	1	673	220063163	220063835	0.000000e+00	1182
19	TraesCS5D01G151000	chr6D	98.217	673	12	0	1	673	78601843	78602515	0.000000e+00	1177
20	TraesCS5D01G151000	chr6D	98.217	673	12	0	1	673	306176919	306177591	0.000000e+00	1177
21	TraesCS5D01G151000	chr2A	97.279	588	7	2	1542	2129	42773842	42773264	0.000000e+00	989
22	TraesCS5D01G151000	chr2B	96.491	114	4	0	1920	2033	171456012	171456125	2.790000e-44	189

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	TraesCS5D01G151000	chr5D	240131741	240133869	2128	False	3932	3932	100.000	1	2129	1	chr5D.!!$F1	2128
1	TraesCS5D01G151000	chr5D	6205107	6206514	1407	True	2507	2507	98.793	721	2129	1	chr5D.!!$R1	1408
2	TraesCS5D01G151000	chr5D	326758191	326758862	671	True	1192	1192	98.663	1	673	1	chr5D.!!$R3	672
3	TraesCS5D01G151000	chr5D	199932237	199932908	671	True	1181	1181	98.366	1	673	1	chr5D.!!$R2	672
4	TraesCS5D01G151000	chrUn	317470476	317471877	1401	True	2540	2540	99.359	721	2123	1	chrUn.!!$R1	1402
5	TraesCS5D01G151000	chrUn	412876642	412877954	1312	False	2425	2425	100.000	772	2084	1	chrUn.!!$F1	1312
6	TraesCS5D01G151000	chr3D	21898848	21900254	1406	False	2540	2540	99.219	721	2129	1	chr3D.!!$F1	1408
7	TraesCS5D01G151000	chr3D	548652262	548652934	672	False	1182	1182	98.366	1	673	1	chr3D.!!$F2	672
8	TraesCS5D01G151000	chr3D	503659989	503660661	672	True	1177	1177	98.217	1	673	1	chr3D.!!$R1	672
9	TraesCS5D01G151000	chr1D	483920242	483921649	1407	True	2540	2540	99.219	721	2129	1	chr1D.!!$R3	1408
10	TraesCS5D01G151000	chr1D	254490971	254492377	1406	False	2518	2518	98.936	721	2129	1	chr1D.!!$F1	1408
11	TraesCS5D01G151000	chr1D	300986521	300987194	673	True	1177	1177	98.220	1	673	1	chr1D.!!$R1	672
12	TraesCS5D01G151000	chr1D	400712585	400713257	672	True	1177	1177	98.217	1	673	1	chr1D.!!$R2	672
13	TraesCS5D01G151000	chr3B	201507887	201509293	1406	False	2468	2468	98.297	721	2129	1	chr3B.!!$F1	1408
14	TraesCS5D01G151000	chr4D	19911272	19912663	1391	False	2337	2337	96.806	721	2129	1	chr4D.!!$F1	1408
15	TraesCS5D01G151000	chr2D	334227225	334228659	1434	False	2305	2305	95.969	721	2129	1	chr2D.!!$F1	1408
16	TraesCS5D01G151000	chr7D	220063163	220063835	672	False	1182	1182	98.366	1	673	1	chr7D.!!$F1	672
17	TraesCS5D01G151000	chr6D	78601843	78602515	672	False	1177	1177	98.217	1	673	1	chr6D.!!$F1	672
18	TraesCS5D01G151000	chr6D	306176919	306177591	672	False	1177	1177	98.217	1	673	1	chr6D.!!$F2	672
19	TraesCS5D01G151000	chr2A	42773264	42773842	578	True	989	989	97.279	1542	2129	1	chr2A.!!$R1	587

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
688	690	0.546598	GAAATCCCCTCCCATCGTGT	59.453	55.0	0.0	0.0	0.0	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1720	1726	3.05857	TGCTTGCGACAATAACGACAAAT	60.059	39.13	0.0	0.0	0.0	2.32	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
39	40	2.299582	CTCAATGCATTTCCACCACCAA	59.700	45.455	9.83	0.00	0.00	3.67
246	247	5.981315	GTCGTGCTATAACTACCAATGCTAA	59.019	40.000	0.00	0.00	0.00	3.09
419	421	3.303351	AGGTGGGGCTTATGATTTGAG	57.697	47.619	0.00	0.00	0.00	3.02
674	676	9.213799	AGTCACTTGTTGAAATCTCTAGAAATC	57.786	33.333	0.00	0.00	35.39	2.17
675	677	8.447053	GTCACTTGTTGAAATCTCTAGAAATCC	58.553	37.037	0.00	0.00	35.39	3.01
676	678	7.607991	TCACTTGTTGAAATCTCTAGAAATCCC	59.392	37.037	0.00	0.00	0.00	3.85
677	679	6.887002	ACTTGTTGAAATCTCTAGAAATCCCC	59.113	38.462	0.00	0.00	0.00	4.81
678	680	6.642733	TGTTGAAATCTCTAGAAATCCCCT	57.357	37.500	0.00	0.00	0.00	4.79
679	681	6.653989	TGTTGAAATCTCTAGAAATCCCCTC	58.346	40.000	0.00	0.00	0.00	4.30
680	682	5.896073	TGAAATCTCTAGAAATCCCCTCC	57.104	43.478	0.00	0.00	0.00	4.30
681	683	4.660771	TGAAATCTCTAGAAATCCCCTCCC	59.339	45.833	0.00	0.00	0.00	4.30
682	684	4.302004	AATCTCTAGAAATCCCCTCCCA	57.698	45.455	0.00	0.00	0.00	4.37
683	685	4.516953	ATCTCTAGAAATCCCCTCCCAT	57.483	45.455	0.00	0.00	0.00	4.00
684	686	3.863086	TCTCTAGAAATCCCCTCCCATC	58.137	50.000	0.00	0.00	0.00	3.51
685	687	2.564947	CTCTAGAAATCCCCTCCCATCG	59.435	54.545	0.00	0.00	0.00	3.84
686	688	2.090719	TCTAGAAATCCCCTCCCATCGT	60.091	50.000	0.00	0.00	0.00	3.73
687	689	0.839946	AGAAATCCCCTCCCATCGTG	59.160	55.000	0.00	0.00	0.00	4.35
688	690	0.546598	GAAATCCCCTCCCATCGTGT	59.453	55.000	0.00	0.00	0.00	4.49
689	691	1.766496	GAAATCCCCTCCCATCGTGTA	59.234	52.381	0.00	0.00	0.00	2.90
690	692	2.118403	AATCCCCTCCCATCGTGTAT	57.882	50.000	0.00	0.00	0.00	2.29
691	693	3.269592	AATCCCCTCCCATCGTGTATA	57.730	47.619	0.00	0.00	0.00	1.47
692	694	3.491766	ATCCCCTCCCATCGTGTATAT	57.508	47.619	0.00	0.00	0.00	0.86
693	695	4.620086	ATCCCCTCCCATCGTGTATATA	57.380	45.455	0.00	0.00	0.00	0.86
694	696	4.620086	TCCCCTCCCATCGTGTATATAT	57.380	45.455	0.00	0.00	0.00	0.86
695	697	5.737437	TCCCCTCCCATCGTGTATATATA	57.263	43.478	0.00	0.00	0.00	0.86
696	698	5.452255	TCCCCTCCCATCGTGTATATATAC	58.548	45.833	14.86	14.86	0.00	1.47
697	699	5.043956	TCCCCTCCCATCGTGTATATATACA	60.044	44.000	19.51	19.51	40.69	2.29
698	700	5.839063	CCCCTCCCATCGTGTATATATACAT	59.161	44.000	24.67	9.70	44.25	2.29
699	701	6.015350	CCCCTCCCATCGTGTATATATACATC	60.015	46.154	24.67	17.50	44.25	3.06
700	702	6.015350	CCCTCCCATCGTGTATATATACATCC	60.015	46.154	24.67	14.02	44.25	3.51
701	703	6.294010	CCTCCCATCGTGTATATATACATCCG	60.294	46.154	24.67	22.76	44.25	4.18
702	704	6.124340	TCCCATCGTGTATATATACATCCGT	58.876	40.000	24.67	13.65	44.25	4.69
703	705	6.261603	TCCCATCGTGTATATATACATCCGTC	59.738	42.308	24.67	12.81	44.25	4.79
704	706	6.436261	CCATCGTGTATATATACATCCGTCC	58.564	44.000	24.67	12.21	44.25	4.79
705	707	5.723492	TCGTGTATATATACATCCGTCCG	57.277	43.478	24.67	21.04	44.25	4.79
706	708	5.178061	TCGTGTATATATACATCCGTCCGT	58.822	41.667	24.67	0.00	44.25	4.69
707	709	5.063817	TCGTGTATATATACATCCGTCCGTG	59.936	44.000	24.67	9.49	44.25	4.94
708	710	5.032863	GTGTATATATACATCCGTCCGTGC	58.967	45.833	24.67	7.68	44.25	5.34
709	711	2.905959	TATATACATCCGTCCGTGCG	57.094	50.000	0.00	0.00	0.00	5.34
710	712	4.787563	GTATATATACATCCGTCCGTGCGG	60.788	50.000	16.50	3.94	41.62	5.69
711	713	7.157641	GTATATATACATCCGTCCGTGCGGT	62.158	48.000	16.50	0.00	41.34	5.68
770	772	4.884668	AGAACCCTCGTGTCATTTCTTA	57.115	40.909	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	40	3.057734	CCAAACGCGTCTAAAGTCTCTT	58.942	45.455	14.44	0.00	0.00	2.85
246	247	1.139058	ACTAGCGATCGGCCTGAAAAT	59.861	47.619	18.30	0.00	45.17	1.82
419	421	6.346919	CCGCATTAATAGTGAGTAATGAGCAC	60.347	42.308	8.80	0.00	43.26	4.40
673	675	4.620086	ATATATACACGATGGGAGGGGA	57.380	45.455	0.00	0.00	0.00	4.81
674	676	5.205821	TGTATATATACACGATGGGAGGGG	58.794	45.833	19.51	0.00	38.28	4.79
675	677	6.015350	GGATGTATATATACACGATGGGAGGG	60.015	46.154	24.43	0.00	45.11	4.30
676	678	6.294010	CGGATGTATATATACACGATGGGAGG	60.294	46.154	24.43	6.29	45.11	4.30
677	679	6.262496	ACGGATGTATATATACACGATGGGAG	59.738	42.308	28.58	17.05	45.11	4.30
678	680	6.124340	ACGGATGTATATATACACGATGGGA	58.876	40.000	28.58	9.33	45.11	4.37
679	681	6.387041	ACGGATGTATATATACACGATGGG	57.613	41.667	28.58	17.67	45.11	4.00
680	682	6.436261	GGACGGATGTATATATACACGATGG	58.564	44.000	28.58	18.64	45.11	3.51
681	683	6.134061	CGGACGGATGTATATATACACGATG	58.866	44.000	28.58	20.24	45.11	3.84
682	684	5.819379	ACGGACGGATGTATATATACACGAT	59.181	40.000	28.58	16.23	45.11	3.73
683	685	5.063817	CACGGACGGATGTATATATACACGA	59.936	44.000	28.58	11.62	45.11	4.35
684	686	5.260900	CACGGACGGATGTATATATACACG	58.739	45.833	24.43	24.04	45.11	4.49
685	687	5.032863	GCACGGACGGATGTATATATACAC	58.967	45.833	24.43	17.86	45.11	2.90
686	688	4.201841	CGCACGGACGGATGTATATATACA	60.202	45.833	24.22	24.22	46.21	2.29
687	689	4.277258	CGCACGGACGGATGTATATATAC	58.723	47.826	14.86	14.86	0.00	1.47
688	690	4.541085	CGCACGGACGGATGTATATATA	57.459	45.455	0.00	0.00	0.00	0.86
689	691	3.416119	CGCACGGACGGATGTATATAT	57.584	47.619	0.00	0.00	0.00	0.86
690	692	2.905959	CGCACGGACGGATGTATATA	57.094	50.000	0.00	0.00	0.00	0.86
691	693	3.786809	CGCACGGACGGATGTATAT	57.213	52.632	0.00	0.00	0.00	0.86
705	707	3.836176	AAGACGTCGTCCACCGCAC	62.836	63.158	21.40	0.00	36.19	5.34
706	708	3.547249	GAAGACGTCGTCCACCGCA	62.547	63.158	21.40	0.00	36.19	5.69
707	709	2.744307	AAGAAGACGTCGTCCACCGC	62.744	60.000	24.90	7.04	36.19	5.68
708	710	0.728466	GAAGAAGACGTCGTCCACCG	60.728	60.000	24.90	0.00	32.18	4.94
709	711	0.597072	AGAAGAAGACGTCGTCCACC	59.403	55.000	24.90	15.19	35.52	4.61
710	712	2.418983	AAGAAGAAGACGTCGTCCAC	57.581	50.000	24.90	18.91	35.52	4.02
711	713	2.621998	AGAAAGAAGAAGACGTCGTCCA	59.378	45.455	24.90	0.00	35.52	4.02
712	714	3.285816	AGAAAGAAGAAGACGTCGTCC	57.714	47.619	24.90	12.70	35.52	4.79
713	715	4.977347	AGAAAGAAAGAAGAAGACGTCGTC	59.023	41.667	21.86	21.86	35.18	4.20
714	716	4.934515	AGAAAGAAAGAAGAAGACGTCGT	58.065	39.130	10.46	6.85	0.00	4.34
715	717	5.216648	AGAGAAAGAAAGAAGAAGACGTCG	58.783	41.667	10.46	0.00	0.00	5.12
716	718	8.241367	AGATAGAGAAAGAAAGAAGAAGACGTC	58.759	37.037	7.70	7.70	0.00	4.34
717	719	8.117813	AGATAGAGAAAGAAAGAAGAAGACGT	57.882	34.615	0.00	0.00	0.00	4.34
1720	1726	3.058570	TGCTTGCGACAATAACGACAAAT	60.059	39.130	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.