AutoCloner

Multiple sequence alignment - TraesCS2B01G028900

Loading Multiple Alignment...

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	TraesCS2B01G028900	chr2B	100.000	3711	0	0	1	3711	13357498	13361208	0.000000e+00	6854
1	TraesCS2B01G028900	chr2B	99.416	1883	9	2	737	2619	13388843	13390723	0.000000e+00	3415
2	TraesCS2B01G028900	chr2B	94.891	2192	88	6	428	2619	13337872	13340039	0.000000e+00	3406
3	TraesCS2B01G028900	chr2B	94.279	2150	108	7	472	2619	13201680	13203816	0.000000e+00	3275
4	TraesCS2B01G028900	chr2B	98.920	741	6	1	1	739	13378814	13379554	0.000000e+00	1323
5	TraesCS2B01G028900	chr2B	97.716	394	9	0	2226	2619	13144730	13145123	0.000000e+00	678
6	TraesCS2B01G028900	chr2B	95.116	430	17	2	1	429	13327355	13327781	0.000000e+00	675
7	TraesCS2B01G028900	chr2B	85.185	459	40	18	29	470	13197606	13198053	2.630000e-121	446
8	TraesCS2B01G028900	chr2D	91.891	2639	173	17	5	2619	9856051	9858672	0.000000e+00	3650
9	TraesCS2B01G028900	chr2A	90.916	2631	205	22	1	2619	9939902	9937294	0.000000e+00	3504
10	TraesCS2B01G028900	chr3D	87.097	1085	132	7	2631	3711	588943503	588944583	0.000000e+00	1221
11	TraesCS2B01G028900	chr3D	78.208	491	98	7	2133	2619	32586045	32586530	4.660000e-79	305
12	TraesCS2B01G028900	chr6B	86.588	1096	129	9	2625	3711	387224232	387225318	0.000000e+00	1194
13	TraesCS2B01G028900	chr7B	86.560	997	122	10	2646	3634	13332588	13331596	0.000000e+00	1088
14	TraesCS2B01G028900	chr7B	80.730	1069	196	9	2648	3711	615126134	615125071	0.000000e+00	824
15	TraesCS2B01G028900	chr3B	87.343	956	114	5	2631	3583	418309716	418310667	0.000000e+00	1088
16	TraesCS2B01G028900	chr3B	81.584	1086	190	9	2631	3711	820757813	820758893	0.000000e+00	889
17	TraesCS2B01G028900	chr3B	87.129	101	13	0	3611	3711	418310976	418311076	8.420000e-22	115
18	TraesCS2B01G028900	chr1A	84.516	1085	143	16	2632	3705	152377719	152378789	0.000000e+00	1050
19	TraesCS2B01G028900	chr4A	84.158	1092	151	14	2631	3711	103329085	103330165	0.000000e+00	1038
20	TraesCS2B01G028900	chr4B	82.396	1085	180	7	2631	3711	550440255	550439178	0.000000e+00	935
21	TraesCS2B01G028900	chr5A	82.150	1070	159	11	2646	3711	555931994	555930953	0.000000e+00	889
22	TraesCS2B01G028900	chrUn	100.000	426	0	0	2041	2466	476519406	476519831	0.000000e+00	787
23	TraesCS2B01G028900	chrUn	100.000	397	0	0	816	1212	479131598	479131994	0.000000e+00	734
24	TraesCS2B01G028900	chr7A	81.466	955	165	10	2759	3710	165215031	165215976	0.000000e+00	773
25	TraesCS2B01G028900	chr1B	78.543	494	98	5	2133	2619	548198291	548197799	5.980000e-83	318
26	TraesCS2B01G028900	chr5B	78.208	491	102	4	2133	2619	549549574	549550063	3.600000e-80	309

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	TraesCS2B01G028900	chr2B	13357498	13361208	3710	False	6854.0	6854	100.000	1	3711	1	chr2B.!!$F4	3710
1	TraesCS2B01G028900	chr2B	13388843	13390723	1880	False	3415.0	3415	99.416	737	2619	1	chr2B.!!$F6	1882
2	TraesCS2B01G028900	chr2B	13337872	13340039	2167	False	3406.0	3406	94.891	428	2619	1	chr2B.!!$F3	2191
3	TraesCS2B01G028900	chr2B	13197606	13203816	6210	False	1860.5	3275	89.732	29	2619	2	chr2B.!!$F7	2590
4	TraesCS2B01G028900	chr2B	13378814	13379554	740	False	1323.0	1323	98.920	1	739	1	chr2B.!!$F5	738
5	TraesCS2B01G028900	chr2D	9856051	9858672	2621	False	3650.0	3650	91.891	5	2619	1	chr2D.!!$F1	2614
6	TraesCS2B01G028900	chr2A	9937294	9939902	2608	True	3504.0	3504	90.916	1	2619	1	chr2A.!!$R1	2618
7	TraesCS2B01G028900	chr3D	588943503	588944583	1080	False	1221.0	1221	87.097	2631	3711	1	chr3D.!!$F2	1080
8	TraesCS2B01G028900	chr6B	387224232	387225318	1086	False	1194.0	1194	86.588	2625	3711	1	chr6B.!!$F1	1086
9	TraesCS2B01G028900	chr7B	13331596	13332588	992	True	1088.0	1088	86.560	2646	3634	1	chr7B.!!$R1	988
10	TraesCS2B01G028900	chr7B	615125071	615126134	1063	True	824.0	824	80.730	2648	3711	1	chr7B.!!$R2	1063
11	TraesCS2B01G028900	chr3B	820757813	820758893	1080	False	889.0	889	81.584	2631	3711	1	chr3B.!!$F1	1080
12	TraesCS2B01G028900	chr3B	418309716	418311076	1360	False	601.5	1088	87.236	2631	3711	2	chr3B.!!$F2	1080
13	TraesCS2B01G028900	chr1A	152377719	152378789	1070	False	1050.0	1050	84.516	2632	3705	1	chr1A.!!$F1	1073
14	TraesCS2B01G028900	chr4A	103329085	103330165	1080	False	1038.0	1038	84.158	2631	3711	1	chr4A.!!$F1	1080
15	TraesCS2B01G028900	chr4B	550439178	550440255	1077	True	935.0	935	82.396	2631	3711	1	chr4B.!!$R1	1080
16	TraesCS2B01G028900	chr5A	555930953	555931994	1041	True	889.0	889	82.150	2646	3711	1	chr5A.!!$R1	1065
17	TraesCS2B01G028900	chr7A	165215031	165215976	945	False	773.0	773	81.466	2759	3710	1	chr7A.!!$F1	951

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
679	4363	1.002868	GAAGGCCAAGAGCTCAGCA	60.003	57.895	17.77	0.00	43.05	4.41	F
1212	4896	0.618680	ACTGCATGGAGCTAGACCCA	60.619	55.000	14.95	6.07	45.94	4.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2043	5727	2.158667	TGAGAACACCACTTCCTTTCCC	60.159	50.0	0.00	0.0	0.0	3.97	R
3194	6901	0.034896	CGTTGCTTCTGGTACCCACT	59.965	55.0	10.07	0.0	0.0	4.00	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
679	4363	1.002868	GAAGGCCAAGAGCTCAGCA	60.003	57.895	17.77	0.00	43.05	4.41
1212	4896	0.618680	ACTGCATGGAGCTAGACCCA	60.619	55.000	14.95	6.07	45.94	4.51
2019	5703	2.097791	GTGTGCTTTCGGTTTGTTGGTA	59.902	45.455	0.00	0.00	0.00	3.25
2043	5727	3.160269	GCTATTGATGATTTGGAGGGGG	58.840	50.000	0.00	0.00	0.00	5.40
2504	6188	5.589452	TGTCATGACTGCATAATACATTGCA	59.411	36.000	25.55	0.00	46.03	4.08
2619	6303	5.004448	TCGAGTTCTGACTACAATGAGAGT	58.996	41.667	0.00	0.00	35.88	3.24
2620	6304	5.473846	TCGAGTTCTGACTACAATGAGAGTT	59.526	40.000	0.00	0.00	35.88	3.01
2621	6305	5.797934	CGAGTTCTGACTACAATGAGAGTTC	59.202	44.000	0.00	0.00	35.88	3.01
2622	6306	6.348950	CGAGTTCTGACTACAATGAGAGTTCT	60.349	42.308	0.00	0.00	35.88	3.01
2623	6307	6.686630	AGTTCTGACTACAATGAGAGTTCTG	58.313	40.000	0.00	0.00	33.32	3.02
2624	6308	6.491745	AGTTCTGACTACAATGAGAGTTCTGA	59.508	38.462	0.00	0.00	33.32	3.27
2625	6309	6.260870	TCTGACTACAATGAGAGTTCTGAC	57.739	41.667	0.00	0.00	0.00	3.51
2626	6310	6.007076	TCTGACTACAATGAGAGTTCTGACT	58.993	40.000	0.00	0.00	39.32	3.41
2627	6311	7.168905	TCTGACTACAATGAGAGTTCTGACTA	58.831	38.462	0.00	0.00	35.88	2.59
2628	6312	7.119992	TCTGACTACAATGAGAGTTCTGACTAC	59.880	40.741	0.00	0.00	35.88	2.73
2629	6313	6.715264	TGACTACAATGAGAGTTCTGACTACA	59.285	38.462	0.00	0.00	35.88	2.74
2665	6349	3.812053	GACAGACCATCATAGTTCCATGC	59.188	47.826	0.00	0.00	0.00	4.06
2674	6358	8.825774	ACCATCATAGTTCCATGCTACATAATA	58.174	33.333	0.00	0.00	0.00	0.98
2748	6432	4.327357	GCACACGAGTATATGGCATATCAC	59.673	45.833	22.63	17.48	0.00	3.06
2911	6595	4.623932	ACTCAAGAATACACTTGCTCCA	57.376	40.909	0.00	0.00	44.52	3.86
2935	6619	2.936993	GCACCCTACTGATTCCACACTG	60.937	54.545	0.00	0.00	0.00	3.66
2980	6664	6.068735	TCTCTCCTAGGGAACTCAACTCTATT	60.069	42.308	9.46	0.00	43.67	1.73
3003	6687	2.848694	ACCTGATCCTCCAACATGACAT	59.151	45.455	0.00	0.00	0.00	3.06
3022	6706	5.070446	TGACATGTGACTAGTGGAAAGACTT	59.930	40.000	1.15	0.00	0.00	3.01
3035	6719	1.809684	AAGACTTAGAAACCAGCCGC	58.190	50.000	0.00	0.00	0.00	6.53
3047	6731	2.670934	AGCCGCTTGAGTTGCTGG	60.671	61.111	0.00	0.00	31.70	4.85
3112	6796	3.054802	AGACCAAATTTCGAGCTCTCCAT	60.055	43.478	12.85	0.00	0.00	3.41
3141	6825	3.187700	GTCACCAAGATCATACGTGGAC	58.812	50.000	0.00	0.00	40.77	4.02
3145	6829	3.131223	ACCAAGATCATACGTGGACTCTG	59.869	47.826	0.00	0.00	40.77	3.35
3157	6864	3.927142	CGTGGACTCTGGAAGAACATAAC	59.073	47.826	0.00	0.00	46.34	1.89
3161	6868	5.073144	TGGACTCTGGAAGAACATAACCTTT	59.927	40.000	0.00	0.00	46.34	3.11
3170	6877	7.504238	TGGAAGAACATAACCTTTGTGTTGTAT	59.496	33.333	5.85	0.00	43.64	2.29
3226	6933	0.670546	AGCAACGGACAATCGTCAGG	60.671	55.000	0.00	0.00	44.54	3.86
3234	6941	2.230508	GGACAATCGTCAGGTGAGTGTA	59.769	50.000	0.00	0.00	43.83	2.90
3237	6944	3.258372	ACAATCGTCAGGTGAGTGTACAT	59.742	43.478	0.00	0.00	42.23	2.29
3348	7056	1.522806	CGTGCCGCCTTATTAGCCA	60.523	57.895	0.00	0.00	0.00	4.75
3372	7080	8.461222	CCATCATATTTTCAGCTTTGTCACTAA	58.539	33.333	0.00	0.00	0.00	2.24
3396	7104	0.599728	GTCGCTCATCCCATCTCTGC	60.600	60.000	0.00	0.00	0.00	4.26
3427	7135	2.793160	ATCGTGGCCAGCACTGACAG	62.793	60.000	5.11	0.00	0.00	3.51
3464	7174	2.125431	GCCGCCATTGCAGCATTT	60.125	55.556	0.00	0.00	40.71	2.32
3486	7196	2.622436	GCAGAGAAGCCGTTGAAGTAT	58.378	47.619	0.00	0.00	0.00	2.12
3495	7205	2.883574	CCGTTGAAGTATAAGCCACGA	58.116	47.619	0.00	0.00	0.00	4.35
3496	7206	2.601763	CCGTTGAAGTATAAGCCACGAC	59.398	50.000	0.00	0.00	0.00	4.34
3500	7210	4.054780	TGAAGTATAAGCCACGACCATC	57.945	45.455	0.00	0.00	0.00	3.51
3501	7211	3.704566	TGAAGTATAAGCCACGACCATCT	59.295	43.478	0.00	0.00	0.00	2.90
3502	7212	4.161565	TGAAGTATAAGCCACGACCATCTT	59.838	41.667	0.00	0.00	0.00	2.40
3508	7218	3.554692	CACGACCATCTTCGCCGC	61.555	66.667	0.00	0.00	43.06	6.53
3607	7598	2.522367	GGGGGTTCCAGTCGTTCCA	61.522	63.158	0.00	0.00	35.00	3.53
3662	7653	1.671379	GGCACCCTCGACAAACTCC	60.671	63.158	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
648	4332	0.833287	GGCCTTCTGTCAGGATGCTA	59.167	55.000	8.16	0.00	35.71	3.49
679	4363	2.437359	GATGAGCCTGTTGCCGCT	60.437	61.111	0.00	0.00	42.71	5.52
1212	4896	3.350219	AAGTATTGCGGATCACCAGTT	57.650	42.857	0.00	0.00	35.59	3.16
2019	5703	4.836736	CCCCTCCAAATCATCAATAGCATT	59.163	41.667	0.00	0.00	0.00	3.56
2043	5727	2.158667	TGAGAACACCACTTCCTTTCCC	60.159	50.000	0.00	0.00	0.00	3.97
2619	6303	8.346300	GTCTTATGATCTCGATTGTAGTCAGAA	58.654	37.037	0.00	0.00	0.00	3.02
2620	6304	7.499232	TGTCTTATGATCTCGATTGTAGTCAGA	59.501	37.037	0.00	0.00	0.00	3.27
2621	6305	7.643579	TGTCTTATGATCTCGATTGTAGTCAG	58.356	38.462	0.00	0.00	0.00	3.51
2622	6306	7.499232	TCTGTCTTATGATCTCGATTGTAGTCA	59.501	37.037	0.00	0.00	0.00	3.41
2623	6307	7.801315	GTCTGTCTTATGATCTCGATTGTAGTC	59.199	40.741	0.00	0.00	0.00	2.59
2624	6308	7.255312	GGTCTGTCTTATGATCTCGATTGTAGT	60.255	40.741	0.00	0.00	0.00	2.73
2625	6309	7.081349	GGTCTGTCTTATGATCTCGATTGTAG	58.919	42.308	0.00	0.00	0.00	2.74
2626	6310	6.546034	TGGTCTGTCTTATGATCTCGATTGTA	59.454	38.462	0.00	0.00	0.00	2.41
2627	6311	5.360999	TGGTCTGTCTTATGATCTCGATTGT	59.639	40.000	0.00	0.00	0.00	2.71
2628	6312	5.836347	TGGTCTGTCTTATGATCTCGATTG	58.164	41.667	0.00	0.00	0.00	2.67
2629	6313	6.266330	TGATGGTCTGTCTTATGATCTCGATT	59.734	38.462	0.00	0.00	0.00	3.34
2748	6432	3.735591	TGTTCGGTAAAACAGAGAAGGG	58.264	45.455	0.00	0.00	34.31	3.95
2771	6455	1.601166	TTGTCTCGAGTCTCGGTTCA	58.399	50.000	21.63	14.33	40.88	3.18
2980	6664	3.843619	TGTCATGTTGGAGGATCAGGTAA	59.156	43.478	0.00	0.00	36.25	2.85
3003	6687	6.971726	TTCTAAGTCTTTCCACTAGTCACA	57.028	37.500	0.00	0.00	0.00	3.58
3022	6706	0.685097	ACTCAAGCGGCTGGTTTCTA	59.315	50.000	7.38	0.00	32.39	2.10
3035	6719	0.820891	AGGTGTGCCAGCAACTCAAG	60.821	55.000	0.00	0.00	28.85	3.02
3047	6731	0.106708	TGACAGAGGAACAGGTGTGC	59.893	55.000	0.00	0.00	0.00	4.57
3112	6796	0.918983	GATCTTGGTGACCCCCATGA	59.081	55.000	0.00	0.00	41.35	3.07
3141	6825	5.765182	ACACAAAGGTTATGTTCTTCCAGAG	59.235	40.000	0.00	0.00	0.00	3.35
3145	6829	6.144078	ACAACACAAAGGTTATGTTCTTCC	57.856	37.500	0.00	0.00	34.36	3.46
3187	6894	2.984435	TCTGGTACCCACTACTGTCA	57.016	50.000	10.07	0.00	0.00	3.58
3193	6900	1.274167	CGTTGCTTCTGGTACCCACTA	59.726	52.381	10.07	0.00	0.00	2.74
3194	6901	0.034896	CGTTGCTTCTGGTACCCACT	59.965	55.000	10.07	0.00	0.00	4.00
3226	6933	3.461946	GCTTGAAGCATGTACACTCAC	57.538	47.619	13.09	0.00	41.89	3.51
3348	7056	9.236006	AGTTAGTGACAAAGCTGAAAATATGAT	57.764	29.630	0.00	0.00	0.00	2.45
3372	7080	1.556911	AGATGGGATGAGCGACAAAGT	59.443	47.619	0.00	0.00	0.00	2.66
3396	7104	1.300931	CCACGATGCCTACCGATGG	60.301	63.158	0.00	0.00	0.00	3.51
3438	7146	4.397832	AATGGCGGCGGTTACGGT	62.398	61.111	9.78	0.00	41.36	4.83
3479	7189	3.704566	AGATGGTCGTGGCTTATACTTCA	59.295	43.478	0.00	0.00	0.00	3.02
3486	7196	0.459585	GCGAAGATGGTCGTGGCTTA	60.460	55.000	0.00	0.00	43.06	3.09
3495	7205	4.814294	GGTCGCGGCGAAGATGGT	62.814	66.667	28.14	0.00	37.72	3.55
3496	7206	4.812476	TGGTCGCGGCGAAGATGG	62.812	66.667	28.14	0.00	37.72	3.51
3508	7218	2.343758	CTGACAGTGGGGTGGTCG	59.656	66.667	0.00	0.00	34.32	4.79
3509	7219	1.122019	AGACTGACAGTGGGGTGGTC	61.122	60.000	14.14	0.00	0.00	4.02
3596	7312	2.186903	CGGGGATGGAACGACTGG	59.813	66.667	0.00	0.00	0.00	4.00
3602	7593	1.148498	GGGATGTCGGGGATGGAAC	59.852	63.158	0.00	0.00	0.00	3.62
3604	7595	2.447765	GGGGATGTCGGGGATGGA	60.448	66.667	0.00	0.00	0.00	3.41
3607	7598	4.880426	AGCGGGGATGTCGGGGAT	62.880	66.667	0.00	0.00	0.00	3.85
3626	7617	0.877071	CCACATGGCCTCATTATCGC	59.123	55.000	3.32	0.00	0.00	4.58
3640	7631	0.889186	GTTTGTCGAGGGTGCCACAT	60.889	55.000	0.00	0.00	0.00	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.