AutoCloner

Multiple sequence alignment - TraesCS4A01G345500

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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	TraesCS4A01G345500	chr4A	100.000	5593	0	0	1	5593	624938337	624932745	0.000000e+00	10329
1	TraesCS4A01G345500	chr1A	98.705	5561	33	12	61	5593	570141329	570146878	0.000000e+00	9834
2	TraesCS4A01G345500	chr5B	89.700	3738	210	79	1298	4929	687801487	687797819	0.000000e+00	4608
3	TraesCS4A01G345500	chr5B	88.347	1210	79	27	84	1257	687802800	687801617	0.000000e+00	1397
4	TraesCS4A01G345500	chr5B	80.631	919	99	41	2468	3318	639964192	639965099	6.110000e-179	638
5	TraesCS4A01G345500	chr5B	89.637	386	34	4	1665	2048	639977673	639978054	2.340000e-133	486
6	TraesCS4A01G345500	chr5B	78.114	594	77	29	3294	3838	639968040	639968629	1.500000e-85	327
7	TraesCS4A01G345500	chr5B	85.197	304	27	15	3490	3775	639965321	639965624	4.240000e-76	296
8	TraesCS4A01G345500	chr5B	85.197	304	27	15	3490	3775	639974884	639975187	4.240000e-76	296
9	TraesCS4A01G345500	chr5B	80.816	245	23	15	3536	3770	639974176	639974406	2.680000e-38	171
10	TraesCS4A01G345500	chr5B	92.473	93	3	1	1965	2053	639973659	639973751	4.550000e-26	130
11	TraesCS4A01G345500	chr5D	86.757	2658	216	71	2192	4778	545213663	545211071	0.000000e+00	2833
12	TraesCS4A01G345500	chr5D	92.719	1346	80	5	830	2165	545215088	545213751	0.000000e+00	1927
13	TraesCS4A01G345500	chr5D	87.565	579	44	13	1599	2165	509435774	509436336	0.000000e+00	645
14	TraesCS4A01G345500	chr5D	83.802	747	44	42	84	782	545215820	545215103	6.110000e-179	638
15	TraesCS4A01G345500	chr5D	79.243	925	102	39	2468	3318	509428288	509429196	3.780000e-156	562
16	TraesCS4A01G345500	chr5D	90.349	373	32	3	1665	2034	509444457	509444828	2.340000e-133	486
17	TraesCS4A01G345500	chr5D	86.761	355	24	13	4516	4851	545169134	545168784	1.900000e-99	374
18	TraesCS4A01G345500	chr5D	84.715	386	18	17	4914	5262	545168148	545167767	1.150000e-91	348
19	TraesCS4A01G345500	chr5D	79.074	540	63	27	3631	4140	545171361	545170842	5.400000e-85	326
20	TraesCS4A01G345500	chr5D	79.765	425	63	15	3432	3838	509432631	509433050	2.550000e-73	287
21	TraesCS4A01G345500	chr5A	87.109	512	53	7	1665	2165	636638769	636639278	8.130000e-158	568
22	TraesCS4A01G345500	chr5A	82.429	387	35	21	2877	3252	636640650	636641014	1.960000e-79	307
23	TraesCS4A01G345500	chr5A	84.026	313	34	11	3490	3786	636630973	636631285	2.550000e-73	287
24	TraesCS4A01G345500	chr2B	88.772	285	29	2	1351	1633	702722554	702722271	4.150000e-91	346
25	TraesCS4A01G345500	chr2D	87.719	285	32	2	1351	1633	583228795	583228512	4.180000e-86	329

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	TraesCS4A01G345500	chr4A	624932745	624938337	5592	True	10329.000000	10329	100.000000	1	5593	1	chr4A.!!$R1	5592
1	TraesCS4A01G345500	chr1A	570141329	570146878	5549	False	9834.000000	9834	98.705000	61	5593	1	chr1A.!!$F1	5532
2	TraesCS4A01G345500	chr5B	687797819	687802800	4981	True	3002.500000	4608	89.023500	84	4929	2	chr5B.!!$R1	4845
3	TraesCS4A01G345500	chr5B	639964192	639968629	4437	False	420.333333	638	81.314000	2468	3838	3	chr5B.!!$F1	1370
4	TraesCS4A01G345500	chr5B	639973659	639978054	4395	False	270.750000	486	87.030750	1665	3775	4	chr5B.!!$F2	2110
5	TraesCS4A01G345500	chr5D	545211071	545215820	4749	True	1799.333333	2833	87.759333	84	4778	3	chr5D.!!$R2	4694
6	TraesCS4A01G345500	chr5D	509428288	509436336	8048	False	498.000000	645	82.191000	1599	3838	3	chr5D.!!$F2	2239
7	TraesCS4A01G345500	chr5D	545167767	545171361	3594	True	349.333333	374	83.516667	3631	5262	3	chr5D.!!$R1	1631
8	TraesCS4A01G345500	chr5A	636638769	636641014	2245	False	437.500000	568	84.769000	1665	3252	2	chr5A.!!$F2	1587

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
42	43	1.428869	AACCTCTCACCTTGCTCACT	58.571	50.000	0.00	0.00	0.00	3.41	F
44	45	1.771255	ACCTCTCACCTTGCTCACTTT	59.229	47.619	0.00	0.00	0.00	2.66	F
46	47	2.038295	CCTCTCACCTTGCTCACTTTCT	59.962	50.000	0.00	0.00	0.00	2.52	F
56	57	2.172505	TGCTCACTTTCTTTCTGGGTCA	59.827	45.455	0.00	0.00	0.00	4.02	F
106	107	2.947652	CCATCCATCAGTCAATCCACAC	59.052	50.000	0.00	0.00	0.00	3.82	F
1560	1745	4.202524	TGCCTAAACAGGTAAAGGTGATGT	60.203	41.667	0.00	0.00	0.00	3.06	F
2091	2285	4.558860	GGCAGTTAATTTTCTGAACGATGC	59.441	41.667	11.89	4.49	34.02	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1307	1489	2.972348	TCCCAGGTTCTAGAACACACT	58.028	47.619	31.30	19.21	42.85	3.55	R
1645	1833	3.760738	TCCAACCACATGTTCAGCAATA	58.239	40.909	0.00	0.00	34.00	1.90	R
1707	1895	4.134563	AGACCAGTTTAGACAACGCAAAT	58.865	39.130	0.00	0.00	0.00	2.32	R
2091	2285	4.418392	GAGGACAATTGTGCAAAGCATAG	58.582	43.478	28.72	0.00	41.91	2.23	R
2683	2996	7.217200	ACTACAAAGAGCAAACAGATTACAGA	58.783	34.615	0.00	0.00	0.00	3.41	R
3255	4269	2.038033	TGTCTTGGTAGGTTACTGGCAC	59.962	50.000	0.00	0.00	0.00	5.01	R
4602	12221	0.826256	GCGAAAAACAAGGGGAGGGT	60.826	55.000	0.00	0.00	0.00	4.34	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
25	26	8.767944	CGTTAATTGATATGCAGGTAAGAAAC	57.232	34.615	0.00	0.00	0.00	2.78
37	38	3.075148	GGTAAGAAACCTCTCACCTTGC	58.925	50.000	0.00	0.00	45.75	4.01
38	39	3.244596	GGTAAGAAACCTCTCACCTTGCT	60.245	47.826	0.00	0.00	45.75	3.91
39	40	2.849294	AGAAACCTCTCACCTTGCTC	57.151	50.000	0.00	0.00	0.00	4.26
40	41	2.050144	AGAAACCTCTCACCTTGCTCA	58.950	47.619	0.00	0.00	0.00	4.26
41	42	2.147150	GAAACCTCTCACCTTGCTCAC	58.853	52.381	0.00	0.00	0.00	3.51
42	43	1.428869	AACCTCTCACCTTGCTCACT	58.571	50.000	0.00	0.00	0.00	3.41
43	44	1.428869	ACCTCTCACCTTGCTCACTT	58.571	50.000	0.00	0.00	0.00	3.16
44	45	1.771255	ACCTCTCACCTTGCTCACTTT	59.229	47.619	0.00	0.00	0.00	2.66
45	46	2.224402	ACCTCTCACCTTGCTCACTTTC	60.224	50.000	0.00	0.00	0.00	2.62
46	47	2.038295	CCTCTCACCTTGCTCACTTTCT	59.962	50.000	0.00	0.00	0.00	2.52
47	48	3.495806	CCTCTCACCTTGCTCACTTTCTT	60.496	47.826	0.00	0.00	0.00	2.52
48	49	4.133078	CTCTCACCTTGCTCACTTTCTTT	58.867	43.478	0.00	0.00	0.00	2.52
49	50	4.130118	TCTCACCTTGCTCACTTTCTTTC	58.870	43.478	0.00	0.00	0.00	2.62
50	51	4.133078	CTCACCTTGCTCACTTTCTTTCT	58.867	43.478	0.00	0.00	0.00	2.52
51	52	3.879295	TCACCTTGCTCACTTTCTTTCTG	59.121	43.478	0.00	0.00	0.00	3.02
52	53	3.004106	CACCTTGCTCACTTTCTTTCTGG	59.996	47.826	0.00	0.00	0.00	3.86
53	54	2.555757	CCTTGCTCACTTTCTTTCTGGG	59.444	50.000	0.00	0.00	0.00	4.45
54	55	3.217626	CTTGCTCACTTTCTTTCTGGGT	58.782	45.455	0.00	0.00	0.00	4.51
55	56	2.851195	TGCTCACTTTCTTTCTGGGTC	58.149	47.619	0.00	0.00	0.00	4.46
56	57	2.172505	TGCTCACTTTCTTTCTGGGTCA	59.827	45.455	0.00	0.00	0.00	4.02
57	58	3.181440	TGCTCACTTTCTTTCTGGGTCAT	60.181	43.478	0.00	0.00	0.00	3.06
58	59	3.823304	GCTCACTTTCTTTCTGGGTCATT	59.177	43.478	0.00	0.00	0.00	2.57
59	60	4.279420	GCTCACTTTCTTTCTGGGTCATTT	59.721	41.667	0.00	0.00	0.00	2.32
63	64	7.461749	TCACTTTCTTTCTGGGTCATTTATCT	58.538	34.615	0.00	0.00	0.00	1.98
106	107	2.947652	CCATCCATCAGTCAATCCACAC	59.052	50.000	0.00	0.00	0.00	3.82
995	1080	6.064060	CCATTAATTCCTCACCAATCAGCTA	58.936	40.000	0.00	0.00	0.00	3.32
1560	1745	4.202524	TGCCTAAACAGGTAAAGGTGATGT	60.203	41.667	0.00	0.00	0.00	3.06
1645	1833	6.370718	GGTTAATGAAACAGTCCGTCAGTTAT	59.629	38.462	0.00	0.00	40.08	1.89
1707	1895	5.626142	TGTATTTCAGGTAAACTTCTGGCA	58.374	37.500	0.00	0.00	0.00	4.92
2091	2285	4.558860	GGCAGTTAATTTTCTGAACGATGC	59.441	41.667	11.89	4.49	34.02	3.91
2812	3159	9.491675	TTTACAAGTCGTCTAATTATTGTTCCA	57.508	29.630	5.47	0.00	33.31	3.53
4074	9965	0.962356	GCACTGCTGTAAGGCCACAT	60.962	55.000	5.01	0.00	0.00	3.21
4188	11669	0.387239	GCATGCACCCGTTCTTTGAC	60.387	55.000	14.21	0.00	0.00	3.18
4602	12221	0.733566	CCGCACCTAGTTTTCGCGTA	60.734	55.000	5.77	0.00	44.23	4.42
5434	15072	8.791675	ACACTTTTGTTTTGGAAAATGTGATTT	58.208	25.926	16.34	0.00	40.86	2.17
5435	15073	9.623350	CACTTTTGTTTTGGAAAATGTGATTTT	57.377	25.926	7.87	0.00	44.56	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.855904	GGTTTCTTACCTGCATATCAATTAACG	59.144	37.037	0.00	0.00	44.10	3.18
17	18	3.997681	GAGCAAGGTGAGAGGTTTCTTAC	59.002	47.826	0.00	0.00	38.77	2.34
18	19	3.646162	TGAGCAAGGTGAGAGGTTTCTTA	59.354	43.478	0.00	0.00	32.53	2.10
19	20	2.439507	TGAGCAAGGTGAGAGGTTTCTT	59.560	45.455	0.00	0.00	32.53	2.52
20	21	2.050144	TGAGCAAGGTGAGAGGTTTCT	58.950	47.619	0.00	0.00	36.01	2.52
21	22	2.147150	GTGAGCAAGGTGAGAGGTTTC	58.853	52.381	0.00	0.00	0.00	2.78
22	23	1.771255	AGTGAGCAAGGTGAGAGGTTT	59.229	47.619	0.00	0.00	0.00	3.27
23	24	1.428869	AGTGAGCAAGGTGAGAGGTT	58.571	50.000	0.00	0.00	0.00	3.50
24	25	1.428869	AAGTGAGCAAGGTGAGAGGT	58.571	50.000	0.00	0.00	0.00	3.85
25	26	2.038295	AGAAAGTGAGCAAGGTGAGAGG	59.962	50.000	0.00	0.00	0.00	3.69
26	27	3.399440	AGAAAGTGAGCAAGGTGAGAG	57.601	47.619	0.00	0.00	0.00	3.20
27	28	3.845781	AAGAAAGTGAGCAAGGTGAGA	57.154	42.857	0.00	0.00	0.00	3.27
28	29	4.024218	CAGAAAGAAAGTGAGCAAGGTGAG	60.024	45.833	0.00	0.00	0.00	3.51
29	30	3.879295	CAGAAAGAAAGTGAGCAAGGTGA	59.121	43.478	0.00	0.00	0.00	4.02
30	31	3.004106	CCAGAAAGAAAGTGAGCAAGGTG	59.996	47.826	0.00	0.00	0.00	4.00
31	32	3.217626	CCAGAAAGAAAGTGAGCAAGGT	58.782	45.455	0.00	0.00	0.00	3.50
32	33	2.555757	CCCAGAAAGAAAGTGAGCAAGG	59.444	50.000	0.00	0.00	0.00	3.61
33	34	3.217626	ACCCAGAAAGAAAGTGAGCAAG	58.782	45.455	0.00	0.00	0.00	4.01
34	35	3.214328	GACCCAGAAAGAAAGTGAGCAA	58.786	45.455	0.00	0.00	0.00	3.91
35	36	2.172505	TGACCCAGAAAGAAAGTGAGCA	59.827	45.455	0.00	0.00	0.00	4.26
36	37	2.851195	TGACCCAGAAAGAAAGTGAGC	58.149	47.619	0.00	0.00	0.00	4.26
37	38	7.609532	AGATAAATGACCCAGAAAGAAAGTGAG	59.390	37.037	0.00	0.00	0.00	3.51
38	39	7.461749	AGATAAATGACCCAGAAAGAAAGTGA	58.538	34.615	0.00	0.00	0.00	3.41
39	40	7.391554	TGAGATAAATGACCCAGAAAGAAAGTG	59.608	37.037	0.00	0.00	0.00	3.16
40	41	7.461749	TGAGATAAATGACCCAGAAAGAAAGT	58.538	34.615	0.00	0.00	0.00	2.66
41	42	7.928307	TGAGATAAATGACCCAGAAAGAAAG	57.072	36.000	0.00	0.00	0.00	2.62
42	43	8.331740	AGATGAGATAAATGACCCAGAAAGAAA	58.668	33.333	0.00	0.00	0.00	2.52
43	44	7.865820	AGATGAGATAAATGACCCAGAAAGAA	58.134	34.615	0.00	0.00	0.00	2.52
44	45	7.443302	AGATGAGATAAATGACCCAGAAAGA	57.557	36.000	0.00	0.00	0.00	2.52
45	46	8.428063	ACTAGATGAGATAAATGACCCAGAAAG	58.572	37.037	0.00	0.00	0.00	2.62
46	47	8.324191	ACTAGATGAGATAAATGACCCAGAAA	57.676	34.615	0.00	0.00	0.00	2.52
47	48	7.921041	ACTAGATGAGATAAATGACCCAGAA	57.079	36.000	0.00	0.00	0.00	3.02
48	49	9.607333	AATACTAGATGAGATAAATGACCCAGA	57.393	33.333	0.00	0.00	0.00	3.86
63	64	9.152327	GATGGATGGATGGATAATACTAGATGA	57.848	37.037	0.00	0.00	0.00	2.92
79	80	4.263816	GGATTGACTGATGGATGGATGGAT	60.264	45.833	0.00	0.00	0.00	3.41
80	81	3.073503	GGATTGACTGATGGATGGATGGA	59.926	47.826	0.00	0.00	0.00	3.41
81	82	3.181437	TGGATTGACTGATGGATGGATGG	60.181	47.826	0.00	0.00	0.00	3.51
82	83	3.819337	GTGGATTGACTGATGGATGGATG	59.181	47.826	0.00	0.00	0.00	3.51
106	107	3.742369	AGTCAATTTGGCAGCGAAATTTG	59.258	39.130	21.69	17.12	31.38	2.32
995	1080	1.051812	CCCAGAATACGCCATCTCCT	58.948	55.000	0.00	0.00	0.00	3.69
1307	1489	2.972348	TCCCAGGTTCTAGAACACACT	58.028	47.619	31.30	19.21	42.85	3.55
1645	1833	3.760738	TCCAACCACATGTTCAGCAATA	58.239	40.909	0.00	0.00	34.00	1.90
1707	1895	4.134563	AGACCAGTTTAGACAACGCAAAT	58.865	39.130	0.00	0.00	0.00	2.32
2091	2285	4.418392	GAGGACAATTGTGCAAAGCATAG	58.582	43.478	28.72	0.00	41.91	2.23
2677	2990	7.840342	AGAGCAAACAGATTACAGATTACAG	57.160	36.000	0.00	0.00	0.00	2.74
2678	2991	8.506437	CAAAGAGCAAACAGATTACAGATTACA	58.494	33.333	0.00	0.00	0.00	2.41
2679	2992	8.507249	ACAAAGAGCAAACAGATTACAGATTAC	58.493	33.333	0.00	0.00	0.00	1.89
2680	2993	8.621532	ACAAAGAGCAAACAGATTACAGATTA	57.378	30.769	0.00	0.00	0.00	1.75
2681	2994	7.516198	ACAAAGAGCAAACAGATTACAGATT	57.484	32.000	0.00	0.00	0.00	2.40
2682	2995	7.880195	ACTACAAAGAGCAAACAGATTACAGAT	59.120	33.333	0.00	0.00	0.00	2.90
2683	2996	7.217200	ACTACAAAGAGCAAACAGATTACAGA	58.783	34.615	0.00	0.00	0.00	3.41
3255	4269	2.038033	TGTCTTGGTAGGTTACTGGCAC	59.962	50.000	0.00	0.00	0.00	5.01
4074	9965	6.436847	TGGAAGGCAACATAAGAAAATGATCA	59.563	34.615	0.00	0.00	41.41	2.92
4188	11669	2.996621	GGTGTTTGGATCTCTCAACTCG	59.003	50.000	0.00	0.00	0.00	4.18
4602	12221	0.826256	GCGAAAAACAAGGGGAGGGT	60.826	55.000	0.00	0.00	0.00	4.34
5516	15154	5.964477	TCTCCCACTGTCATCCTTTAGTAAT	59.036	40.000	0.00	0.00	0.00	1.89
5517	15155	5.338632	TCTCCCACTGTCATCCTTTAGTAA	58.661	41.667	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.