AutoCloner

Multiple sequence alignment - TraesCS2A01G100100

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	TraesCS2A01G100100	chr2A	100.000	3779	0	0	1	3779	52756126	52759904	0.000000e+00	6979.0
1	TraesCS2A01G100100	chr2A	86.491	2354	297	18	397	2737	52573270	52570925	0.000000e+00	2566.0
2	TraesCS2A01G100100	chr2A	83.914	2095	316	13	588	2671	52427833	52425749	0.000000e+00	1982.0
3	TraesCS2A01G100100	chr2A	81.808	1726	278	25	407	2116	52540934	52539229	0.000000e+00	1415.0
4	TraesCS2A01G100100	chr2A	92.647	68	3	2	334	400	52756524	52756590	3.110000e-16	97.1
5	TraesCS2A01G100100	chr2D	96.089	3759	102	21	55	3779	51252787	51256534	0.000000e+00	6085.0
6	TraesCS2A01G100100	chr2D	86.188	2353	297	17	397	2737	51160287	51157951	0.000000e+00	2519.0
7	TraesCS2A01G100100	chr2D	87.111	675	76	8	413	1076	51137879	51137205	0.000000e+00	754.0
8	TraesCS2A01G100100	chr2D	95.714	70	2	1	397	466	51253090	51253158	1.110000e-20	111.0
9	TraesCS2A01G100100	chr2D	95.312	64	3	0	337	400	51253158	51253221	6.680000e-18	102.0
10	TraesCS2A01G100100	chr2B	94.722	3221	112	23	55	3236	80200073	80203274	0.000000e+00	4953.0
11	TraesCS2A01G100100	chr2B	86.060	2353	309	15	397	2737	79709220	79706875	0.000000e+00	2510.0
12	TraesCS2A01G100100	chr2B	83.951	2293	338	21	397	2671	79671883	79669603	0.000000e+00	2169.0
13	TraesCS2A01G100100	chr2B	88.669	556	24	13	3233	3779	80203337	80203862	3.180000e-180	641.0
14	TraesCS2A01G100100	chr2B	83.914	373	28	14	3379	3719	79706384	79706012	1.010000e-85	327.0
15	TraesCS2A01G100100	chr2B	92.188	64	5	0	337	400	80200442	80200505	1.450000e-14	91.6
16	TraesCS2A01G100100	chr7D	82.397	2403	393	24	402	2793	76396825	76399208	0.000000e+00	2067.0
17	TraesCS2A01G100100	chr7A	81.913	2405	402	26	402	2793	80313788	80316172	0.000000e+00	2001.0
18	TraesCS2A01G100100	chr7A	82.386	2112	353	13	712	2820	82155452	82153357	0.000000e+00	1821.0
19	TraesCS2A01G100100	chr7A	100.000	32	0	0	26	57	260012929	260012898	4.080000e-05	60.2

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	TraesCS2A01G100100	chr2A	52756126	52759904	3778	False	3538.050000	6979	96.323500	1	3779	2	chr2A.!!$F1	3778
1	TraesCS2A01G100100	chr2A	52570925	52573270	2345	True	2566.000000	2566	86.491000	397	2737	1	chr2A.!!$R3	2340
2	TraesCS2A01G100100	chr2A	52425749	52427833	2084	True	1982.000000	1982	83.914000	588	2671	1	chr2A.!!$R1	2083
3	TraesCS2A01G100100	chr2A	52539229	52540934	1705	True	1415.000000	1415	81.808000	407	2116	1	chr2A.!!$R2	1709
4	TraesCS2A01G100100	chr2D	51157951	51160287	2336	True	2519.000000	2519	86.188000	397	2737	1	chr2D.!!$R2	2340
5	TraesCS2A01G100100	chr2D	51252787	51256534	3747	False	2099.333333	6085	95.705000	55	3779	3	chr2D.!!$F1	3724
6	TraesCS2A01G100100	chr2D	51137205	51137879	674	True	754.000000	754	87.111000	413	1076	1	chr2D.!!$R1	663
7	TraesCS2A01G100100	chr2B	79669603	79671883	2280	True	2169.000000	2169	83.951000	397	2671	1	chr2B.!!$R1	2274
8	TraesCS2A01G100100	chr2B	80200073	80203862	3789	False	1895.200000	4953	91.859667	55	3779	3	chr2B.!!$F1	3724
9	TraesCS2A01G100100	chr2B	79706012	79709220	3208	True	1418.500000	2510	84.987000	397	3719	2	chr2B.!!$R2	3322
10	TraesCS2A01G100100	chr7D	76396825	76399208	2383	False	2067.000000	2067	82.397000	402	2793	1	chr7D.!!$F1	2391
11	TraesCS2A01G100100	chr7A	80313788	80316172	2384	False	2001.000000	2001	81.913000	402	2793	1	chr7A.!!$F1	2391
12	TraesCS2A01G100100	chr7A	82153357	82155452	2095	True	1821.000000	1821	82.386000	712	2820	1	chr7A.!!$R1	2108

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	Hairpin	End Stability	Orientation
35	36	0.036105	TTGATGCTCCAGCGACATGT	60.036	50.000	45.83	3.21	F
264	278	0.179073	CGTTCCTGCCATCCCAGTAG	60.179	60.000	0.00	2.57	F
1025	1064	0.400213	TGCACCCTTCCTTTGACGAT	59.600	50.000	0.00	3.73	F
1113	1152	1.079819	ATCGGTGCCAAGTCACTCG	60.080	57.895	37.16	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1006	1045	0.400213	ATCGTCAAAGGAAGGGTGCA	59.600	50.000	0.00	0.00	0.00	4.57	R
1286	1329	1.209128	CGGTAGATTGCTTACAGCGG	58.791	55.000	0.00	0.00	46.26	5.52	R
1838	1890	2.507102	CCGCGCTCACCTGTACAG	60.507	66.667	16.34	16.34	0.00	2.74	R
3073	3208	1.135199	CAATTGCAGATGGCCTGTGAC	60.135	52.381	3.32	0.00	44.71	3.67	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
29	30	1.647629	GCAGATTGATGCTCCAGCG	59.352	57.895	0.00	0.00	45.83	5.18
30	31	0.812811	GCAGATTGATGCTCCAGCGA	60.813	55.000	0.00	0.00	45.83	4.93
31	32	0.935898	CAGATTGATGCTCCAGCGAC	59.064	55.000	0.00	0.00	45.83	5.19
32	33	0.538584	AGATTGATGCTCCAGCGACA	59.461	50.000	0.00	0.00	45.83	4.35
33	34	1.140452	AGATTGATGCTCCAGCGACAT	59.860	47.619	0.00	0.00	45.83	3.06
34	35	1.263484	GATTGATGCTCCAGCGACATG	59.737	52.381	0.00	0.00	45.83	3.21
35	36	0.036105	TTGATGCTCCAGCGACATGT	60.036	50.000	0.00	0.00	45.83	3.21
36	37	0.823460	TGATGCTCCAGCGACATGTA	59.177	50.000	0.00	0.00	45.83	2.29
37	38	1.413812	TGATGCTCCAGCGACATGTAT	59.586	47.619	0.00	0.00	45.83	2.29
38	39	2.158914	TGATGCTCCAGCGACATGTATT	60.159	45.455	0.00	0.00	45.83	1.89
39	40	2.401583	TGCTCCAGCGACATGTATTT	57.598	45.000	0.00	0.00	45.83	1.40
40	41	2.279741	TGCTCCAGCGACATGTATTTC	58.720	47.619	0.00	0.00	45.83	2.17
41	42	1.258982	GCTCCAGCGACATGTATTTCG	59.741	52.381	0.00	0.00	38.31	3.46
42	43	1.860950	CTCCAGCGACATGTATTTCGG	59.139	52.381	0.00	0.00	35.73	4.30
43	44	1.206132	TCCAGCGACATGTATTTCGGT	59.794	47.619	0.00	0.07	46.29	4.69
44	45	2.427812	TCCAGCGACATGTATTTCGGTA	59.572	45.455	8.74	0.00	43.70	4.02
45	46	3.069016	TCCAGCGACATGTATTTCGGTAT	59.931	43.478	8.74	0.00	43.70	2.73
46	47	4.278919	TCCAGCGACATGTATTTCGGTATA	59.721	41.667	8.74	0.00	43.70	1.47
47	48	4.621460	CCAGCGACATGTATTTCGGTATAG	59.379	45.833	8.74	0.00	43.70	1.31
48	49	5.458015	CAGCGACATGTATTTCGGTATAGA	58.542	41.667	8.74	0.00	43.70	1.98
49	50	5.569441	CAGCGACATGTATTTCGGTATAGAG	59.431	44.000	8.74	0.00	43.70	2.43
50	51	4.857588	GCGACATGTATTTCGGTATAGAGG	59.142	45.833	0.00	0.00	35.73	3.69
51	52	5.399858	CGACATGTATTTCGGTATAGAGGG	58.600	45.833	0.00	0.00	0.00	4.30
52	53	5.182570	CGACATGTATTTCGGTATAGAGGGA	59.817	44.000	0.00	0.00	0.00	4.20
53	54	6.591750	ACATGTATTTCGGTATAGAGGGAG	57.408	41.667	0.00	0.00	0.00	4.30
264	278	0.179073	CGTTCCTGCCATCCCAGTAG	60.179	60.000	0.00	0.00	0.00	2.57
314	329	8.855279	GCGCAAATTAAAGTCATTAATGTGTTA	58.145	29.630	14.97	9.07	45.34	2.41
339	365	5.334414	CCAAGATGCGCTGGATTTATCTAAC	60.334	44.000	9.73	0.00	0.00	2.34
400	426	5.179555	GCTGTATAAAGATTTCCCGGTGATC	59.820	44.000	0.00	0.42	0.00	2.92
566	605	1.669115	GCCACTTCTCTTGCTCGCA	60.669	57.895	0.00	0.00	0.00	5.10
585	624	2.159028	GCAATCCTCTTTCCTACGCTCT	60.159	50.000	0.00	0.00	0.00	4.09
636	675	1.665735	GCGTACACCAAAATGCCACAG	60.666	52.381	0.00	0.00	0.00	3.66
642	681	1.545582	ACCAAAATGCCACAGAATCCG	59.454	47.619	0.00	0.00	0.00	4.18
1006	1045	0.669077	GACACCGGTCTCTATGCGAT	59.331	55.000	2.59	0.00	40.99	4.58
1025	1064	0.400213	TGCACCCTTCCTTTGACGAT	59.600	50.000	0.00	0.00	0.00	3.73
1113	1152	1.079819	ATCGGTGCCAAGTCACTCG	60.080	57.895	0.00	0.00	37.16	4.18
1286	1329	1.308998	ACAAGGTATGCGCCAATAGC	58.691	50.000	4.18	6.90	38.52	2.97
1838	1890	3.334583	TCAGGATTACAACTCCAGTGC	57.665	47.619	0.00	0.00	35.08	4.40
2323	2376	2.270205	CCGCAGATCCTGGCTTGT	59.730	61.111	0.00	0.00	31.21	3.16
3073	3208	0.108615	AAGAGAGGCGATTGTGTCCG	60.109	55.000	0.00	0.00	0.00	4.79
3157	3293	7.164662	GCTCAACAAAAGAAATGTGAAAATTGC	59.835	33.333	0.00	0.00	0.00	3.56
3367	3569	5.279406	CCATCACTTGGTATGGCAAAGAAAA	60.279	40.000	3.78	0.00	40.99	2.29
3623	3865	3.118261	GGCTCCTGTCTCATGGAAATGTA	60.118	47.826	0.00	0.00	31.23	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	0.812811	TCGCTGGAGCATCAATCTGC	60.813	55.000	0.00	0.00	42.21	4.26
12	13	0.935898	GTCGCTGGAGCATCAATCTG	59.064	55.000	0.00	0.00	42.21	2.90
13	14	0.538584	TGTCGCTGGAGCATCAATCT	59.461	50.000	0.00	0.00	42.21	2.40
14	15	1.263484	CATGTCGCTGGAGCATCAATC	59.737	52.381	0.00	0.00	42.21	2.67
15	16	1.306148	CATGTCGCTGGAGCATCAAT	58.694	50.000	0.00	0.00	42.21	2.57
16	17	0.036105	ACATGTCGCTGGAGCATCAA	60.036	50.000	0.00	0.00	42.21	2.57
17	18	0.823460	TACATGTCGCTGGAGCATCA	59.177	50.000	0.00	0.00	42.21	3.07
18	19	2.160822	ATACATGTCGCTGGAGCATC	57.839	50.000	0.00	0.00	42.21	3.91
19	20	2.627515	AATACATGTCGCTGGAGCAT	57.372	45.000	0.00	0.00	42.21	3.79
20	21	2.279741	GAAATACATGTCGCTGGAGCA	58.720	47.619	0.00	0.00	42.21	4.26
21	22	1.258982	CGAAATACATGTCGCTGGAGC	59.741	52.381	0.00	0.00	37.78	4.70
22	23	1.860950	CCGAAATACATGTCGCTGGAG	59.139	52.381	0.00	0.00	35.93	3.86
23	24	1.206132	ACCGAAATACATGTCGCTGGA	59.794	47.619	0.00	0.00	35.93	3.86
24	25	1.651987	ACCGAAATACATGTCGCTGG	58.348	50.000	0.00	1.83	35.93	4.85
25	26	5.458015	TCTATACCGAAATACATGTCGCTG	58.542	41.667	0.00	0.00	35.93	5.18
26	27	5.335740	CCTCTATACCGAAATACATGTCGCT	60.336	44.000	0.00	0.00	35.93	4.93
27	28	4.857588	CCTCTATACCGAAATACATGTCGC	59.142	45.833	0.00	0.00	35.93	5.19
28	29	5.182570	TCCCTCTATACCGAAATACATGTCG	59.817	44.000	0.00	0.00	37.01	4.35
29	30	6.208994	ACTCCCTCTATACCGAAATACATGTC	59.791	42.308	0.00	0.00	0.00	3.06
30	31	6.075984	ACTCCCTCTATACCGAAATACATGT	58.924	40.000	2.69	2.69	0.00	3.21
31	32	6.591750	ACTCCCTCTATACCGAAATACATG	57.408	41.667	0.00	0.00	0.00	3.21
32	33	7.468496	ACTACTCCCTCTATACCGAAATACAT	58.532	38.462	0.00	0.00	0.00	2.29
33	34	6.845908	ACTACTCCCTCTATACCGAAATACA	58.154	40.000	0.00	0.00	0.00	2.29
34	35	7.064016	CGTACTACTCCCTCTATACCGAAATAC	59.936	44.444	0.00	0.00	0.00	1.89
35	36	7.099764	CGTACTACTCCCTCTATACCGAAATA	58.900	42.308	0.00	0.00	0.00	1.40
36	37	5.936956	CGTACTACTCCCTCTATACCGAAAT	59.063	44.000	0.00	0.00	0.00	2.17
37	38	5.163301	ACGTACTACTCCCTCTATACCGAAA	60.163	44.000	0.00	0.00	0.00	3.46
38	39	4.345257	ACGTACTACTCCCTCTATACCGAA	59.655	45.833	0.00	0.00	0.00	4.30
39	40	3.898123	ACGTACTACTCCCTCTATACCGA	59.102	47.826	0.00	0.00	0.00	4.69
40	41	4.264460	ACGTACTACTCCCTCTATACCG	57.736	50.000	0.00	0.00	0.00	4.02
41	42	6.353404	AGTACGTACTACTCCCTCTATACC	57.647	45.833	26.36	0.00	34.13	2.73
148	149	5.950758	ATACTCCTACTGAAGTATCTGCG	57.049	43.478	0.00	0.00	0.00	5.18
206	207	1.068121	GGATAGGGGATGTGGGGAAG	58.932	60.000	0.00	0.00	0.00	3.46
314	329	2.418368	TAAATCCAGCGCATCTTGGT	57.582	45.000	11.47	0.00	0.00	3.67
339	365	4.143347	GCGTTGACTTATTTTTGGCATGTG	60.143	41.667	0.00	0.00	0.00	3.21
390	416	1.202758	GGCATGTATTGATCACCGGGA	60.203	52.381	6.32	0.00	0.00	5.14
566	605	3.131400	GTGAGAGCGTAGGAAAGAGGATT	59.869	47.826	0.00	0.00	0.00	3.01
585	624	6.573876	GCATCTGGATTGATATAGCAGAGTGA	60.574	42.308	0.00	0.00	0.00	3.41
636	675	0.095417	GCACGAGAAGCAACGGATTC	59.905	55.000	0.00	0.00	39.70	2.52
642	681	2.222596	CGATGTAAGCACGAGAAGCAAC	60.223	50.000	0.00	0.00	0.00	4.17
762	801	0.970937	TAGGAGTGGAGAAGGCGTGG	60.971	60.000	0.00	0.00	0.00	4.94
1006	1045	0.400213	ATCGTCAAAGGAAGGGTGCA	59.600	50.000	0.00	0.00	0.00	4.57
1025	1064	1.002624	GGGTGGCGAAACTCCATGA	60.003	57.895	0.00	0.00	35.81	3.07
1113	1152	2.415893	CGCCAAATTCATCACCCTGAAC	60.416	50.000	0.00	0.00	37.93	3.18
1286	1329	1.209128	CGGTAGATTGCTTACAGCGG	58.791	55.000	0.00	0.00	46.26	5.52
1302	1345	1.611261	TAGGCCTGCCAGTAACGGT	60.611	57.895	17.99	0.00	38.92	4.83
1306	1349	2.111384	CTCTTCTAGGCCTGCCAGTAA	58.889	52.381	17.99	0.99	38.92	2.24
1658	1707	1.541147	TGCCACTCTTGTAATTGCAGC	59.459	47.619	0.00	0.00	0.00	5.25
1838	1890	2.507102	CCGCGCTCACCTGTACAG	60.507	66.667	16.34	16.34	0.00	2.74
2874	2974	9.566432	TTTGAATGGCATAACCTAAAATTTTGT	57.434	25.926	13.76	0.88	40.22	2.83
3073	3208	1.135199	CAATTGCAGATGGCCTGTGAC	60.135	52.381	3.32	0.00	44.71	3.67
3114	3250	2.320781	GAGCACTTAGAGGGGCATCTA	58.679	52.381	0.00	0.00	0.00	1.98
3157	3293	6.089551	CAGACTTGTAACGAGATTTACACCAG	59.910	42.308	0.00	0.00	40.80	4.00
3300	3502	3.392882	TGCGCTTATATCACACATGGAG	58.607	45.455	9.73	0.00	0.00	3.86
3367	3569	5.221382	GGTGCTTGATGGAATGCATTCTAAT	60.221	40.000	32.48	26.21	37.76	1.73
3576	3816	5.092554	TGGAAACTCGGTAATAGAATGCA	57.907	39.130	0.00	0.00	0.00	3.96
3623	3865	3.054434	TGTGTGCCATAGTAGCCAAAGAT	60.054	43.478	0.00	0.00	0.00	2.40
3723	3966	8.133024	TCCCAAATACAATACAAATCAAAGCT	57.867	30.769	0.00	0.00	0.00	3.74
3736	3979	7.986889	GCCATATGAAAACTTCCCAAATACAAT	59.013	33.333	3.65	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.