AutoCloner

Multiple sequence alignment - TraesCS1A01G360700

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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	TraesCS1A01G360700	chr1A	100.000	4152	0	0	1	4152	541769317	541773468	0.000000e+00	7668.0
1	TraesCS1A01G360700	chr1A	81.381	333	29	15	275	579	541729636	541729963	1.490000e-59	241.0
2	TraesCS1A01G360700	chr1A	75.884	311	58	13	2816	3116	77074558	77074255	4.330000e-30	143.0
3	TraesCS1A01G360700	chr1A	75.079	317	53	20	1111	1411	56337494	56337800	1.570000e-24	124.0
4	TraesCS1A01G360700	chr1A	98.039	51	1	0	4102	4152	369275749	369275699	5.720000e-14	89.8
5	TraesCS1A01G360700	chr1D	89.145	3602	174	70	336	3864	445587809	445591266	0.000000e+00	4285.0
6	TraesCS1A01G360700	chr1D	84.940	166	17	6	476	636	445586564	445586726	1.190000e-35	161.0
7	TraesCS1A01G360700	chr1D	76.000	300	56	13	2814	3103	76456616	76456323	1.560000e-29	141.0
8	TraesCS1A01G360700	chr1B	89.958	3067	140	71	822	3811	608949548	608952523	0.000000e+00	3803.0
9	TraesCS1A01G360700	chr1B	82.250	569	37	24	276	795	608949000	608949553	2.290000e-117	433.0
10	TraesCS1A01G360700	chr1B	93.190	279	17	2	1	278	128454976	128455253	3.860000e-110	409.0
11	TraesCS1A01G360700	chr1B	91.429	280	21	3	1	278	648177623	648177901	8.420000e-102	381.0
12	TraesCS1A01G360700	chr1B	75.503	298	55	15	2817	3103	119773033	119772743	3.370000e-26	130.0
13	TraesCS1A01G360700	chr1B	78.607	201	35	7	1310	1503	91882036	91881837	4.360000e-25	126.0
14	TraesCS1A01G360700	chr2A	93.662	284	16	2	1	282	413075787	413076070	1.380000e-114	424.0
15	TraesCS1A01G360700	chr4B	91.519	283	21	3	1	281	360059507	360059226	1.810000e-103	387.0
16	TraesCS1A01G360700	chr7A	90.941	287	24	2	1	285	184440335	184440049	6.510000e-103	385.0
17	TraesCS1A01G360700	chr7A	89.091	165	16	2	1671	1834	166751795	166751632	1.960000e-48	204.0
18	TraesCS1A01G360700	chr7A	80.349	229	36	7	1301	1522	457867107	457866881	9.230000e-37	165.0
19	TraesCS1A01G360700	chr7A	97.917	48	1	0	4105	4152	271158944	271158897	2.660000e-12	84.2
20	TraesCS1A01G360700	chr6B	91.429	280	21	3	1	278	140814155	140814433	8.420000e-102	381.0
21	TraesCS1A01G360700	chr6B	91.429	280	21	3	1	278	259980849	259981127	8.420000e-102	381.0
22	TraesCS1A01G360700	chr6B	85.938	192	23	4	1650	1839	574715520	574715709	7.040000e-48	202.0
23	TraesCS1A01G360700	chr5D	91.166	283	22	3	1	281	455340196	455339915	8.420000e-102	381.0
24	TraesCS1A01G360700	chr4A	90.657	289	24	3	1	287	222565530	222565243	8.420000e-102	381.0
25	TraesCS1A01G360700	chr7D	88.172	186	20	2	1650	1834	164874339	164874155	1.940000e-53	220.0
26	TraesCS1A01G360700	chr7D	80.000	230	35	9	1301	1522	400171056	400170830	4.300000e-35	159.0
27	TraesCS1A01G360700	chr7D	76.190	336	55	16	1057	1377	164874804	164874479	2.000000e-33	154.0
28	TraesCS1A01G360700	chr7D	80.628	191	34	3	1646	1834	400170840	400170651	1.200000e-30	145.0
29	TraesCS1A01G360700	chr7D	98.039	51	1	0	4102	4152	611008346	611008396	5.720000e-14	89.8
30	TraesCS1A01G360700	chr7D	96.078	51	2	0	4102	4152	536460039	536460089	2.660000e-12	84.2
31	TraesCS1A01G360700	chr6A	85.938	192	23	4	1650	1839	529019291	529019480	7.040000e-48	202.0
32	TraesCS1A01G360700	chr6A	98.148	54	1	0	4099	4152	212328125	212328178	1.230000e-15	95.3
33	TraesCS1A01G360700	chr6D	85.417	192	24	4	1650	1839	384439335	384439524	3.270000e-46	196.0
34	TraesCS1A01G360700	chr7B	80.349	229	36	7	1301	1522	409712047	409711821	9.230000e-37	165.0
35	TraesCS1A01G360700	chr7B	75.224	335	60	20	1057	1379	128308749	128308426	2.010000e-28	137.0
36	TraesCS1A01G360700	chr7B	98.000	50	1	0	4103	4152	353969487	353969536	2.060000e-13	87.9
37	TraesCS1A01G360700	chr5B	83.146	178	26	4	1650	1825	314193483	314193308	4.300000e-35	159.0
38	TraesCS1A01G360700	chr3D	79.897	194	26	11	1309	1492	120148562	120148372	3.370000e-26	130.0
39	TraesCS1A01G360700	chr3A	79.275	193	27	11	1310	1492	127090469	127090280	5.640000e-24	122.0
40	TraesCS1A01G360700	chr3A	100.000	50	0	0	4103	4152	7653095	7653046	4.420000e-15	93.5
41	TraesCS1A01G360700	chr5A	100.000	50	0	0	4103	4152	69549063	69549014	4.420000e-15	93.5
42	TraesCS1A01G360700	chr3B	98.113	53	1	0	4100	4152	693739323	693739375	4.420000e-15	93.5

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	TraesCS1A01G360700	chr1A	541769317	541773468	4151	False	7668	7668	100.0000	1	4152	1	chr1A.!!$F3	4151
1	TraesCS1A01G360700	chr1D	445586564	445591266	4702	False	2223	4285	87.0425	336	3864	2	chr1D.!!$F1	3528
2	TraesCS1A01G360700	chr1B	608949000	608952523	3523	False	2118	3803	86.1040	276	3811	2	chr1B.!!$F3	3535

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
325	326	0.251165	GGCTCCCCAAACTAAGCACA	60.251	55.0	0.0	0.0	36.47	4.57	F
1298	2279	0.184692	TGGCTGACATGTTGTTGGGA	59.815	50.0	0.0	0.0	0.00	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1318	2299	0.107508	TCGTAGTACCCTCCGGTCAG	60.108	60.0	0.00	0.0	43.29	3.51	R
3269	4287	0.108138	ATCAAGACCCACTAGTGCGC	60.108	55.0	17.86	0.0	0.00	6.09	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	6.455360	CATCTATACAAAGCCACCAACATT	57.545	37.500	0.00	0.00	0.00	2.71
24	25	7.566760	CATCTATACAAAGCCACCAACATTA	57.433	36.000	0.00	0.00	0.00	1.90
25	26	7.995289	CATCTATACAAAGCCACCAACATTAA	58.005	34.615	0.00	0.00	0.00	1.40
26	27	8.632679	CATCTATACAAAGCCACCAACATTAAT	58.367	33.333	0.00	0.00	0.00	1.40
27	28	8.220755	TCTATACAAAGCCACCAACATTAATC	57.779	34.615	0.00	0.00	0.00	1.75
30	31	5.540911	ACAAAGCCACCAACATTAATCAAG	58.459	37.500	0.00	0.00	0.00	3.02
31	32	5.070313	ACAAAGCCACCAACATTAATCAAGT	59.930	36.000	0.00	0.00	0.00	3.16
33	34	4.406456	AGCCACCAACATTAATCAAGTCA	58.594	39.130	0.00	0.00	0.00	3.41
34	35	4.832266	AGCCACCAACATTAATCAAGTCAA	59.168	37.500	0.00	0.00	0.00	3.18
35	36	5.304101	AGCCACCAACATTAATCAAGTCAAA	59.696	36.000	0.00	0.00	0.00	2.69
37	38	7.178274	AGCCACCAACATTAATCAAGTCAAATA	59.822	33.333	0.00	0.00	0.00	1.40
70	71	9.784531	ATGTTTTCTCATACTAGTAATCCATGG	57.215	33.333	4.97	4.97	0.00	3.66
71	72	7.715249	TGTTTTCTCATACTAGTAATCCATGGC	59.285	37.037	6.96	0.00	0.00	4.40
72	73	7.618019	TTTCTCATACTAGTAATCCATGGCT	57.382	36.000	6.96	0.14	0.00	4.75
73	74	7.618019	TTCTCATACTAGTAATCCATGGCTT	57.382	36.000	6.96	6.44	0.00	4.35
75	76	8.721133	TCTCATACTAGTAATCCATGGCTTAA	57.279	34.615	9.59	0.00	0.00	1.85
77	78	9.950496	CTCATACTAGTAATCCATGGCTTAATT	57.050	33.333	12.99	7.51	0.00	1.40
83	84	9.372369	CTAGTAATCCATGGCTTAATTACTAGC	57.628	37.037	32.63	14.59	46.96	3.42
84	85	7.745717	AGTAATCCATGGCTTAATTACTAGCA	58.254	34.615	24.68	0.00	41.04	3.49
86	87	7.458409	AATCCATGGCTTAATTACTAGCATG	57.542	36.000	6.96	10.84	39.15	4.06
87	88	4.761739	TCCATGGCTTAATTACTAGCATGC	59.238	41.667	10.51	10.51	39.15	4.06
89	90	5.184479	CCATGGCTTAATTACTAGCATGCAT	59.816	40.000	21.98	7.44	39.15	3.96
90	91	5.694231	TGGCTTAATTACTAGCATGCATG	57.306	39.130	22.70	22.70	39.15	4.06
91	92	5.132502	TGGCTTAATTACTAGCATGCATGT	58.867	37.500	26.79	19.24	39.15	3.21
93	94	6.427853	TGGCTTAATTACTAGCATGCATGTAG	59.572	38.462	26.79	24.73	39.15	2.74

Showing 1 to 25 of 518 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.455360	AATGTTGGTGGCTTTGTATAGATG	57.545	37.500	0.00	0.00	0.00	2.90
1	2	8.766994	ATTAATGTTGGTGGCTTTGTATAGAT	57.233	30.769	0.00	0.00	0.00	1.98
2	3	7.831690	TGATTAATGTTGGTGGCTTTGTATAGA	59.168	33.333	0.00	0.00	0.00	1.98
3	4	7.995289	TGATTAATGTTGGTGGCTTTGTATAG	58.005	34.615	0.00	0.00	0.00	1.31
5	6	6.849085	TGATTAATGTTGGTGGCTTTGTAT	57.151	33.333	0.00	0.00	0.00	2.29
7	8	5.070313	ACTTGATTAATGTTGGTGGCTTTGT	59.930	36.000	0.00	0.00	0.00	2.83
9	10	5.304101	TGACTTGATTAATGTTGGTGGCTTT	59.696	36.000	0.00	0.00	0.00	3.51
10	11	4.832266	TGACTTGATTAATGTTGGTGGCTT	59.168	37.500	0.00	0.00	0.00	4.35
11	12	4.406456	TGACTTGATTAATGTTGGTGGCT	58.594	39.130	0.00	0.00	0.00	4.75
44	45	9.784531	CCATGGATTACTAGTATGAGAAAACAT	57.215	33.333	5.56	0.00	0.00	2.71
45	46	7.715249	GCCATGGATTACTAGTATGAGAAAACA	59.285	37.037	18.40	0.00	0.00	2.83
47	48	8.034313	AGCCATGGATTACTAGTATGAGAAAA	57.966	34.615	18.40	0.00	0.00	2.29
48	49	7.618019	AGCCATGGATTACTAGTATGAGAAA	57.382	36.000	18.40	0.00	0.00	2.52
49	50	7.618019	AAGCCATGGATTACTAGTATGAGAA	57.382	36.000	15.01	0.00	0.00	2.87
51	52	9.950496	AATTAAGCCATGGATTACTAGTATGAG	57.050	33.333	21.83	0.00	0.00	2.90
58	59	8.876181	TGCTAGTAATTAAGCCATGGATTACTA	58.124	33.333	26.62	26.62	42.30	1.82
60	61	7.979444	TGCTAGTAATTAAGCCATGGATTAC	57.021	36.000	21.83	20.37	37.97	1.89
61	62	7.121168	GCATGCTAGTAATTAAGCCATGGATTA	59.879	37.037	18.43	18.43	37.97	1.75
62	63	6.071728	GCATGCTAGTAATTAAGCCATGGATT	60.072	38.462	20.80	20.80	37.97	3.01
64	65	4.761739	GCATGCTAGTAATTAAGCCATGGA	59.238	41.667	18.40	0.00	37.97	3.41
65	66	4.520111	TGCATGCTAGTAATTAAGCCATGG	59.480	41.667	20.33	7.63	37.97	3.66
66	67	5.694231	TGCATGCTAGTAATTAAGCCATG	57.306	39.130	20.33	10.17	37.97	3.66
67	68	5.771666	ACATGCATGCTAGTAATTAAGCCAT	59.228	36.000	26.53	0.00	37.97	4.40
69	70	5.695851	ACATGCATGCTAGTAATTAAGCC	57.304	39.130	26.53	0.00	37.97	4.35
70	71	7.171508	TCACTACATGCATGCTAGTAATTAAGC	59.828	37.037	26.98	2.70	39.25	3.09

Showing 1 to 25 of 489 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.