AutoCloner

Multiple sequence alignment - TraesCS3B01G277800

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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	TraesCS3B01G277800	chr3B	100.000	5257	0	0	1	5257	447978120	447972864	0.000000e+00	9708.0
1	TraesCS3B01G277800	chr3B	82.375	522	51	22	3729	4213	53959053	53959570	2.930000e-112	416.0
2	TraesCS3B01G277800	chr3B	87.542	297	19	10	3729	4011	54315304	54315596	1.410000e-85	327.0
3	TraesCS3B01G277800	chr3B	83.030	165	27	1	487	651	527711099	527711262	1.180000e-31	148.0
4	TraesCS3B01G277800	chr3B	91.379	58	5	0	4124	4181	54315720	54315777	4.360000e-11	80.5
5	TraesCS3B01G277800	chr3D	93.209	3858	121	41	780	4523	348152938	348149108	0.000000e+00	5542.0
6	TraesCS3B01G277800	chr3D	87.467	750	81	11	1	747	348155148	348154409	0.000000e+00	852.0
7	TraesCS3B01G277800	chr3D	86.087	575	49	6	4702	5257	125686633	125686071	1.630000e-164	590.0
8	TraesCS3B01G277800	chr3D	79.861	576	67	24	3729	4267	31802636	31803199	4.970000e-100	375.0
9	TraesCS3B01G277800	chr3D	85.256	312	21	10	3729	4028	31966711	31966413	1.110000e-76	298.0
10	TraesCS3B01G277800	chr3D	80.726	358	51	9	3187	3530	496503345	496502992	4.040000e-66	263.0
11	TraesCS3B01G277800	chr3D	89.256	121	8	2	4520	4635	561469615	561469735	4.240000e-31	147.0
12	TraesCS3B01G277800	chr3D	94.118	85	4	1	705	788	348154422	348154338	1.540000e-25	128.0
13	TraesCS3B01G277800	chr3D	84.746	118	13	2	4523	4635	208583202	208583085	4.300000e-21	113.0
14	TraesCS3B01G277800	chr3D	94.030	67	4	0	4705	4771	361801934	361802000	9.310000e-18	102.0
15	TraesCS3B01G277800	chr3A	95.105	2247	62	15	1254	3456	467098929	467096687	0.000000e+00	3496.0
16	TraesCS3B01G277800	chr3A	92.527	1017	34	9	3542	4523	467096622	467095613	0.000000e+00	1419.0
17	TraesCS3B01G277800	chr3A	96.907	485	11	1	775	1255	467099495	467099011	0.000000e+00	809.0
18	TraesCS3B01G277800	chr3A	81.297	663	63	20	4646	5257	141011512	141012164	1.020000e-131	481.0
19	TraesCS3B01G277800	chr3A	86.792	318	27	7	3175	3480	662791211	662791525	1.810000e-89	340.0
20	TraesCS3B01G277800	chr3A	82.482	137	18	3	4514	4645	727911888	727912023	1.200000e-21	115.0
21	TraesCS3B01G277800	chr6A	87.230	556	39	6	4704	5257	7716023	7715498	5.820000e-169	604.0
22	TraesCS3B01G277800	chr2D	82.111	777	65	27	4536	5257	79529546	79528789	9.740000e-167	597.0
23	TraesCS3B01G277800	chr2D	82.317	164	22	4	462	625	140340161	140340317	9.180000e-28	135.0
24	TraesCS3B01G277800	chr2D	82.812	128	17	2	4523	4645	37231685	37231558	5.570000e-20	110.0
25	TraesCS3B01G277800	chr2B	83.852	514	39	17	4766	5257	165096180	165095689	2.890000e-122	449.0
26	TraesCS3B01G277800	chr2B	79.819	332	49	11	3216	3532	531050160	531050488	5.300000e-55	226.0
27	TraesCS3B01G277800	chr2B	81.152	191	31	5	462	650	697985742	697985555	1.180000e-31	148.0
28	TraesCS3B01G277800	chr2B	87.603	121	10	2	4520	4635	165096547	165096427	9.180000e-28	135.0
29	TraesCS3B01G277800	chr4D	86.059	373	41	8	3175	3536	394409287	394409659	1.780000e-104	390.0
30	TraesCS3B01G277800	chr4D	84.302	344	26	10	4934	5255	481970200	481970537	1.420000e-80	311.0
31	TraesCS3B01G277800	chr4D	87.379	103	13	0	1493	1595	475149645	475149543	9.250000e-23	119.0
32	TraesCS3B01G277800	chr4D	82.836	134	18	2	4517	4645	450013683	450013816	1.200000e-21	115.0
33	TraesCS3B01G277800	chr1D	86.464	362	37	6	3175	3529	427426507	427426863	2.300000e-103	387.0
34	TraesCS3B01G277800	chr1D	83.380	361	37	11	3176	3536	345238559	345238896	3.950000e-81	313.0
35	TraesCS3B01G277800	chr1D	78.261	230	42	6	465	693	112625704	112625926	1.970000e-29	141.0
36	TraesCS3B01G277800	chr7A	86.761	355	33	8	3171	3514	617691879	617692230	2.970000e-102	383.0
37	TraesCS3B01G277800	chr7A	94.366	71	3	1	4702	4771	232391375	232391305	2.000000e-19	108.0
38	TraesCS3B01G277800	chr6D	83.407	452	30	13	4702	5112	463616089	463615642	1.380000e-100	377.0
39	TraesCS3B01G277800	chr6D	88.889	198	10	3	5064	5255	470393611	470393420	3.170000e-57	233.0
40	TraesCS3B01G277800	chr6D	94.030	134	7	1	5125	5257	463583650	463583517	8.930000e-48	202.0
41	TraesCS3B01G277800	chr6D	82.119	151	22	2	4500	4645	447243488	447243638	1.990000e-24	124.0
42	TraesCS3B01G277800	chr6D	94.203	69	3	1	4702	4769	448160757	448160825	2.590000e-18	104.0
43	TraesCS3B01G277800	chr7D	87.975	316	25	7	3176	3480	47847423	47847736	1.390000e-95	361.0
44	TraesCS3B01G277800	chr7D	83.082	331	28	11	3174	3479	22860542	22860869	5.190000e-70	276.0
45	TraesCS3B01G277800	chr7D	77.273	374	56	11	3171	3532	606790449	606790093	5.370000e-45	193.0
46	TraesCS3B01G277800	chr2A	86.538	312	20	9	3729	4028	528108499	528108198	1.830000e-84	324.0
47	TraesCS3B01G277800	chr2A	80.617	227	31	4	5033	5257	32374433	32374218	4.210000e-36	163.0
48	TraesCS3B01G277800	chr2A	79.111	225	42	2	465	689	160780737	160780518	3.280000e-32	150.0
49	TraesCS3B01G277800	chr4A	91.204	216	8	1	3174	3378	706659854	706659639	3.100000e-72	283.0
50	TraesCS3B01G277800	chr4A	81.564	179	29	4	483	659	578561730	578561906	1.530000e-30	145.0
51	TraesCS3B01G277800	chr4A	89.320	103	11	0	1493	1595	681906784	681906682	4.270000e-26	130.0
52	TraesCS3B01G277800	chr4A	92.958	71	4	1	4702	4771	473307066	473306996	9.310000e-18	102.0
53	TraesCS3B01G277800	chr5B	83.283	329	27	10	4948	5254	648739765	648739443	1.440000e-70	278.0
54	TraesCS3B01G277800	chr1A	80.546	293	34	9	3261	3537	587804273	587803988	2.480000e-48	204.0
55	TraesCS3B01G277800	chr1A	80.617	227	37	4	465	689	103647410	103647189	9.050000e-38	169.0
56	TraesCS3B01G277800	chr6B	82.511	223	31	4	5033	5254	81648548	81648763	6.950000e-44	189.0
57	TraesCS3B01G277800	chr4B	76.894	264	50	8	432	691	39020188	39019932	7.100000e-29	139.0
58	TraesCS3B01G277800	chr5A	94.366	71	3	1	4702	4771	482683044	482683114	2.000000e-19	108.0
59	TraesCS3B01G277800	chr1B	82.114	123	17	2	4518	4635	564890438	564890316	3.350000e-17	100.0
60	TraesCS3B01G277800	chr1B	81.301	123	17	3	4519	4635	684911318	684911196	1.560000e-15	95.3
61	TraesCS3B01G277800	chr7B	93.878	49	3	0	4932	4980	388162339	388162387	2.030000e-09	75.0

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	TraesCS3B01G277800	chr3B	447972864	447978120	5256	True	9708	9708	100.000000	1	5257	1	chr3B.!!$R1	5256
1	TraesCS3B01G277800	chr3B	53959053	53959570	517	False	416	416	82.375000	3729	4213	1	chr3B.!!$F1	484
2	TraesCS3B01G277800	chr3D	348149108	348155148	6040	True	2174	5542	91.598000	1	4523	3	chr3D.!!$R5	4522
3	TraesCS3B01G277800	chr3D	125686071	125686633	562	True	590	590	86.087000	4702	5257	1	chr3D.!!$R2	555
4	TraesCS3B01G277800	chr3D	31802636	31803199	563	False	375	375	79.861000	3729	4267	1	chr3D.!!$F1	538
5	TraesCS3B01G277800	chr3A	467095613	467099495	3882	True	1908	3496	94.846333	775	4523	3	chr3A.!!$R1	3748
6	TraesCS3B01G277800	chr3A	141011512	141012164	652	False	481	481	81.297000	4646	5257	1	chr3A.!!$F1	611
7	TraesCS3B01G277800	chr6A	7715498	7716023	525	True	604	604	87.230000	4704	5257	1	chr6A.!!$R1	553
8	TraesCS3B01G277800	chr2D	79528789	79529546	757	True	597	597	82.111000	4536	5257	1	chr2D.!!$R2	721
9	TraesCS3B01G277800	chr2B	165095689	165096547	858	True	292	449	85.727500	4520	5257	2	chr2B.!!$R2	737

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
508	511	0.037326	CACACACGCACATCCTACCT	60.037	55.000	0.00	0.00	0.00	3.08	F
603	606	0.039798	CGACGAAAACGTCTCCTCCA	60.040	55.000	17.92	0.00	36.81	3.86	F
892	2350	1.040339	CCCTCACTCTCCTTCCCTCG	61.040	65.000	0.00	0.00	0.00	4.63	F
1290	2831	1.134818	TCACCGAATCCGTGGATTGAG	60.135	52.381	18.49	11.44	43.98	3.02	F
2990	4577	0.735471	GCAGCCTAGCAAGGTAAAGC	59.265	55.000	0.00	0.00	45.64	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1704	3248	1.110442	CACAGGTGGCAAAAGTTGGA	58.890	50.000	0.00	3.53	R
2586	4173	1.569548	TCCTCTACAATCCTCCGGACT	59.430	52.381	32.98	3.85	R
2801	4388	6.313744	TGCAAGTTCCTTACTTCTTAAAGC	57.686	37.500	45.29	3.51	R
3249	4837	0.320247	GGATGGTATGCAGGCTCTCG	60.320	60.000	0.00	4.04	R
4946	6743	0.107831	AAGCTACAACCGGCACTCAA	59.892	50.000	0.00	3.02	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
33	34	5.278907	CCAATATTGATATTGCGCCTTTCCA	60.279	40.000	17.23	0.00	45.11	3.53
36	37	2.929641	TGATATTGCGCCTTTCCATCA	58.070	42.857	4.18	2.51	0.00	3.07
38	39	1.024271	TATTGCGCCTTTCCATCAGC	58.976	50.000	4.18	0.00	0.00	4.26
43	44	2.124151	CCTTTCCATCAGCCGGGG	60.124	66.667	2.18	0.00	0.00	5.73
71	72	3.820590	CCACACTGGCGACACAAA	58.179	55.556	0.00	0.00	35.60	2.83
72	73	1.355210	CCACACTGGCGACACAAAC	59.645	57.895	0.00	0.00	35.60	2.93
73	74	1.095228	CCACACTGGCGACACAAACT	61.095	55.000	0.00	0.00	35.60	2.66
75	76	1.937223	CACACTGGCGACACAAACTAA	59.063	47.619	0.00	0.00	35.60	2.24
76	77	1.937899	ACACTGGCGACACAAACTAAC	59.062	47.619	0.00	0.00	35.60	2.34
77	78	1.070843	CACTGGCGACACAAACTAACG	60.071	52.381	0.00	0.00	35.60	3.18
78	79	1.202440	ACTGGCGACACAAACTAACGA	60.202	47.619	0.00	0.00	35.60	3.85
79	80	1.191647	CTGGCGACACAAACTAACGAC	59.808	52.381	0.00	0.00	35.60	4.34
90	91	3.659089	CTAACGACCGTGGGCCAGG	62.659	68.421	19.14	19.14	0.00	4.45
101	102	2.356667	GGCCAGGGGAGGTCAAAG	59.643	66.667	0.00	0.00	32.13	2.77
104	105	1.779061	GCCAGGGGAGGTCAAAGACA	61.779	60.000	0.00	0.00	33.68	3.41
127	128	0.323302	TGACATAAGGCGCCTTCACA	59.677	50.000	43.34	31.40	37.47	3.58
144	145	1.262417	CACATGTATAGCAAGCGCCTG	59.738	52.381	2.29	1.24	39.83	4.85
193	194	8.560355	CCAAATTCTAAAATAACTTTTGGGGG	57.440	34.615	0.00	0.00	36.09	5.40
194	195	8.160765	CCAAATTCTAAAATAACTTTTGGGGGT	58.839	33.333	0.00	0.00	36.09	4.95
199	200	8.873186	TCTAAAATAACTTTTGGGGGTAAGAG	57.127	34.615	0.00	0.00	36.09	2.85
202	203	6.464530	AATAACTTTTGGGGGTAAGAGAGT	57.535	37.500	0.00	0.00	0.00	3.24
205	206	2.426431	TTTGGGGGTAAGAGAGTGGA	57.574	50.000	0.00	0.00	0.00	4.02
226	227	5.015178	TGGATTAAGTTTCTTGGAGGGTCAT	59.985	40.000	0.00	0.00	0.00	3.06
232	233	5.316987	AGTTTCTTGGAGGGTCATTTAGTG	58.683	41.667	0.00	0.00	0.00	2.74
267	268	3.407967	GCATCCGTTCCCCTCCCA	61.408	66.667	0.00	0.00	0.00	4.37

Showing 1 to 25 of 133 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.681025	GGCGCAATATCAATATTGGTTGTG	59.319	41.667	23.35	23.35	46.03	3.33
9	10	5.163513	GGAAAGGCGCAATATCAATATTGG	58.836	41.667	19.32	12.65	46.03	3.16
15	16	3.286353	TGATGGAAAGGCGCAATATCAA	58.714	40.909	10.83	0.00	0.00	2.57
22	23	2.751436	GGCTGATGGAAAGGCGCA	60.751	61.111	10.83	0.00	0.00	6.09
33	34	1.224592	CTTACTTGCCCCGGCTGAT	59.775	57.895	7.35	0.00	42.51	2.90
36	37	2.351276	CACTTACTTGCCCCGGCT	59.649	61.111	7.35	0.00	42.51	5.52
43	44	0.593128	CCAGTGTGGCACTTACTTGC	59.407	55.000	19.83	0.70	42.59	4.01
68	69	1.571215	GGCCCACGGTCGTTAGTTTG	61.571	60.000	0.00	0.00	0.00	2.93
71	72	2.918802	TGGCCCACGGTCGTTAGT	60.919	61.111	0.00	0.00	0.00	2.24
72	73	2.125673	CTGGCCCACGGTCGTTAG	60.126	66.667	0.00	0.00	0.00	2.34
73	74	3.697747	CCTGGCCCACGGTCGTTA	61.698	66.667	0.00	0.00	0.00	3.18
90	91	1.420138	TCAAGGTGTCTTTGACCTCCC	59.580	52.381	0.00	0.00	43.42	4.30
101	102	0.727398	GCGCCTTATGTCAAGGTGTC	59.273	55.000	15.81	6.80	46.74	3.67
104	105	0.328258	AAGGCGCCTTATGTCAAGGT	59.672	50.000	39.65	12.55	39.60	3.50
127	128	2.420642	CATCAGGCGCTTGCTATACAT	58.579	47.619	15.68	0.00	39.13	2.29
144	145	2.689983	CCCTCATTTGCACCTAACCATC	59.310	50.000	0.00	0.00	0.00	3.51
193	194	8.095169	TCCAAGAAACTTAATCCACTCTCTTAC	58.905	37.037	0.00	0.00	0.00	2.34
194	195	8.202461	TCCAAGAAACTTAATCCACTCTCTTA	57.798	34.615	0.00	0.00	0.00	2.10
196	197	6.296145	CCTCCAAGAAACTTAATCCACTCTCT	60.296	42.308	0.00	0.00	0.00	3.10
197	198	5.877564	CCTCCAAGAAACTTAATCCACTCTC	59.122	44.000	0.00	0.00	0.00	3.20
199	200	4.944317	CCCTCCAAGAAACTTAATCCACTC	59.056	45.833	0.00	0.00	0.00	3.51
202	203	4.352595	TGACCCTCCAAGAAACTTAATCCA	59.647	41.667	0.00	0.00	0.00	3.41
205	206	8.170730	ACTAAATGACCCTCCAAGAAACTTAAT	58.829	33.333	0.00	0.00	0.00	1.40
226	227	7.553402	TGCGGCCTAGTATTTATTTTCACTAAA	59.447	33.333	0.00	0.00	0.00	1.85
232	233	5.390567	CGGATGCGGCCTAGTATTTATTTTC	60.391	44.000	0.00	0.00	0.00	2.29

Showing 1 to 25 of 147 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.