AutoCloner

Multiple sequence alignment - TraesCS3B01G362700

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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	TraesCS3B01G362700	chr3B	100.000	5181	0	0	1	5181	574339894	574334714	0.000000e+00	9568.0
1	TraesCS3B01G362700	chr3B	92.028	577	34	9	1	569	574378230	574377658	0.000000e+00	800.0
2	TraesCS3B01G362700	chr3B	93.933	445	12	3	4180	4609	440880729	440881173	0.000000e+00	658.0
3	TraesCS3B01G362700	chr3B	81.519	395	47	20	567	939	735233173	735233563	8.430000e-78	302.0
4	TraesCS3B01G362700	chr3B	90.361	83	5	2	1322	1404	792049501	792049422	7.100000e-19	106.0
5	TraesCS3B01G362700	chr5D	86.064	2167	243	42	1443	3565	442702415	442700264	0.000000e+00	2274.0
6	TraesCS3B01G362700	chr5B	85.156	2176	239	46	1447	3565	539075598	539073450	0.000000e+00	2152.0
7	TraesCS3B01G362700	chr5B	92.601	419	30	1	2823	3241	381073943	381074360	7.420000e-168	601.0
8	TraesCS3B01G362700	chr5A	85.167	2009	237	40	1443	3408	559015686	559013696	0.000000e+00	2002.0
9	TraesCS3B01G362700	chr5A	89.936	467	25	8	601	1047	605319393	605318929	2.690000e-162	582.0
10	TraesCS3B01G362700	chr5A	80.153	655	102	17	2631	3267	595920570	595919926	1.020000e-126	464.0
11	TraesCS3B01G362700	chr5A	82.353	170	7	9	926	1078	412513475	412513638	5.450000e-25	126.0
12	TraesCS3B01G362700	chr3A	93.083	506	18	5	4180	4669	460820752	460820248	0.000000e+00	725.0
13	TraesCS3B01G362700	chr3A	91.810	232	16	1	338	569	577076319	577076091	2.330000e-83	320.0
14	TraesCS3B01G362700	chr3A	81.818	176	7	11	922	1078	108884905	108885074	1.960000e-24	124.0
15	TraesCS3B01G362700	chr1B	91.585	511	29	9	4679	5181	540112429	540112933	0.000000e+00	693.0
16	TraesCS3B01G362700	chr1B	85.207	507	48	8	594	1074	566405037	566404532	3.600000e-136	496.0
17	TraesCS3B01G362700	chr1B	91.233	365	24	4	567	925	500417490	500417852	1.680000e-134	490.0
18	TraesCS3B01G362700	chr1B	82.192	584	81	10	2737	3305	55345200	55345775	1.010000e-131	481.0
19	TraesCS3B01G362700	chr1B	80.988	405	49	20	568	950	16938697	16938299	3.920000e-76	296.0
20	TraesCS3B01G362700	chr2B	88.435	588	38	16	568	1127	648909357	648909942	0.000000e+00	682.0
21	TraesCS3B01G362700	chr2B	88.261	230	18	7	3956	4185	773926487	773926707	3.080000e-67	267.0
22	TraesCS3B01G362700	chr2B	85.047	214	24	7	1235	1440	468671831	468672044	1.460000e-50	211.0
23	TraesCS3B01G362700	chr2B	81.218	197	23	9	4682	4867	707254799	707254992	4.180000e-31	147.0
24	TraesCS3B01G362700	chr2B	83.140	172	10	9	926	1078	37327056	37326885	7.000000e-29	139.0
25	TraesCS3B01G362700	chr2B	84.270	89	10	4	999	1083	774748248	774748336	3.320000e-12	84.2
26	TraesCS3B01G362700	chr3D	94.318	440	15	6	4180	4609	342107058	342107497	0.000000e+00	665.0
27	TraesCS3B01G362700	chr3D	90.000	230	19	2	341	569	438542483	438542257	1.410000e-75	294.0
28	TraesCS3B01G362700	chr3D	80.711	197	24	9	4682	4867	449733422	449733229	1.950000e-29	141.0
29	TraesCS3B01G362700	chr6B	88.029	543	41	8	564	1083	673625148	673625689	5.700000e-174	621.0
30	TraesCS3B01G362700	chr6B	89.800	451	32	9	4682	5125	646580112	646579669	2.710000e-157	566.0
31	TraesCS3B01G362700	chr6B	84.630	540	49	16	567	1079	564645409	564645941	1.660000e-139	507.0
32	TraesCS3B01G362700	chr6B	88.182	220	18	4	3966	4185	452049594	452049383	6.660000e-64	255.0
33	TraesCS3B01G362700	chr6B	86.147	231	22	9	3956	4185	63976989	63977210	1.860000e-59	241.0
34	TraesCS3B01G362700	chr6D	82.148	717	99	13	2607	3305	427064313	427065018	5.780000e-164	588.0
35	TraesCS3B01G362700	chr6D	80.203	197	25	9	4682	4867	428456464	428456271	9.050000e-28	135.0
36	TraesCS3B01G362700	chr4A	83.045	578	47	21	2994	3565	669816108	669816640	1.310000e-130	477.0
37	TraesCS3B01G362700	chr4A	83.807	352	37	15	1	338	591249930	591249585	3.010000e-82	316.0
38	TraesCS3B01G362700	chr4A	82.222	225	29	10	1230	1443	222146828	222147052	3.190000e-42	183.0
39	TraesCS3B01G362700	chr4B	81.633	588	83	10	2737	3308	636709179	636708601	1.020000e-126	464.0
40	TraesCS3B01G362700	chr4B	96.855	159	5	0	4511	4669	109320129	109320287	3.080000e-67	267.0
41	TraesCS3B01G362700	chr4B	93.082	159	8	1	4180	4335	14189138	14188980	4.040000e-56	230.0
42	TraesCS3B01G362700	chr4B	88.764	178	8	2	4264	4429	109319943	109320120	1.890000e-49	207.0
43	TraesCS3B01G362700	chrUn	85.321	327	39	8	1	322	281651281	281651603	3.870000e-86	329.0
44	TraesCS3B01G362700	chrUn	85.321	327	39	8	1	322	333801754	333801432	3.870000e-86	329.0
45	TraesCS3B01G362700	chrUn	85.321	327	39	8	1	322	433723428	433723106	3.870000e-86	329.0
46	TraesCS3B01G362700	chr7A	85.061	328	40	7	1	322	56980239	56979915	5.000000e-85	326.0
47	TraesCS3B01G362700	chr2D	84.136	353	38	14	1	338	560397911	560397562	5.000000e-85	326.0
48	TraesCS3B01G362700	chr2D	88.696	230	18	6	3956	4185	59159692	59159913	1.840000e-69	274.0
49	TraesCS3B01G362700	chr2D	87.013	231	21	7	3956	4185	650378704	650378926	8.610000e-63	252.0
50	TraesCS3B01G362700	chr2D	78.680	197	26	11	4682	4867	585069429	585069620	3.280000e-22	117.0
51	TraesCS3B01G362700	chr1D	85.152	330	34	13	1	322	119296579	119296257	1.800000e-84	324.0
52	TraesCS3B01G362700	chr7D	85.015	327	38	9	1	322	26832668	26832988	6.470000e-84	322.0
53	TraesCS3B01G362700	chr7B	78.759	532	65	37	567	1075	511944647	511945153	3.900000e-81	313.0
54	TraesCS3B01G362700	chr7B	88.845	251	20	4	565	808	39113432	39113183	8.430000e-78	302.0
55	TraesCS3B01G362700	chr4D	88.696	230	18	6	3956	4185	372982192	372981971	1.840000e-69	274.0
56	TraesCS3B01G362700	chr4D	86.957	230	21	7	3956	4185	6929389	6929169	3.100000e-62	250.0
57	TraesCS3B01G362700	chr1A	87.773	229	18	7	3956	4184	302019335	302019117	5.150000e-65	259.0
58	TraesCS3B01G362700	chr2A	87.391	230	19	7	3956	4185	569291199	569290980	6.660000e-64	255.0

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	TraesCS3B01G362700	chr3B	574334714	574339894	5180	True	9568	9568	100.000	1	5181	1	chr3B.!!$R1	5180
1	TraesCS3B01G362700	chr3B	574377658	574378230	572	True	800	800	92.028	1	569	1	chr3B.!!$R2	568
2	TraesCS3B01G362700	chr5D	442700264	442702415	2151	True	2274	2274	86.064	1443	3565	1	chr5D.!!$R1	2122
3	TraesCS3B01G362700	chr5B	539073450	539075598	2148	True	2152	2152	85.156	1447	3565	1	chr5B.!!$R1	2118
4	TraesCS3B01G362700	chr5A	559013696	559015686	1990	True	2002	2002	85.167	1443	3408	1	chr5A.!!$R1	1965
5	TraesCS3B01G362700	chr5A	595919926	595920570	644	True	464	464	80.153	2631	3267	1	chr5A.!!$R2	636
6	TraesCS3B01G362700	chr3A	460820248	460820752	504	True	725	725	93.083	4180	4669	1	chr3A.!!$R1	489
7	TraesCS3B01G362700	chr1B	540112429	540112933	504	False	693	693	91.585	4679	5181	1	chr1B.!!$F3	502
8	TraesCS3B01G362700	chr1B	566404532	566405037	505	True	496	496	85.207	594	1074	1	chr1B.!!$R2	480
9	TraesCS3B01G362700	chr1B	55345200	55345775	575	False	481	481	82.192	2737	3305	1	chr1B.!!$F1	568
10	TraesCS3B01G362700	chr2B	648909357	648909942	585	False	682	682	88.435	568	1127	1	chr2B.!!$F2	559
11	TraesCS3B01G362700	chr6B	673625148	673625689	541	False	621	621	88.029	564	1083	1	chr6B.!!$F3	519
12	TraesCS3B01G362700	chr6B	564645409	564645941	532	False	507	507	84.630	567	1079	1	chr6B.!!$F2	512
13	TraesCS3B01G362700	chr6D	427064313	427065018	705	False	588	588	82.148	2607	3305	1	chr6D.!!$F1	698
14	TraesCS3B01G362700	chr4A	669816108	669816640	532	False	477	477	83.045	2994	3565	1	chr4A.!!$F2	571
15	TraesCS3B01G362700	chr4B	636708601	636709179	578	True	464	464	81.633	2737	3308	1	chr4B.!!$R2	571
16	TraesCS3B01G362700	chr7B	511944647	511945153	506	False	313	313	78.759	567	1075	1	chr7B.!!$F1	508

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
317	318	0.178987	ACCCAATAACACCAACGGCA	60.179	50.0	0.00	0.00	0.00	5.69	F
648	657	0.986527	TGGATCTGGCTGCTTGAAGA	59.013	50.0	0.00	0.00	0.00	2.87	F
1205	1255	0.033894	GACCTTCTCCTCGTCTCCCT	60.034	60.0	0.00	0.00	0.00	4.20	F
1206	1256	0.033894	ACCTTCTCCTCGTCTCCCTC	60.034	60.0	0.00	0.00	0.00	4.30	F
1374	1424	0.037232	GGTGGCAGAGAGTGGTGTAC	60.037	60.0	0.00	0.00	0.00	2.90	F
2301	2385	0.108585	ATGCTCACACAAACTCCGGT	59.891	50.0	0.00	0.00	0.00	5.28	F
3798	3948	0.036105	TGAGGTGCATCGTGCTCATT	60.036	50.0	10.54	1.52	45.31	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1186	1236	0.033894	AGGGAGACGAGGAGAAGGTC	60.034	60.0	0.00	0.0	0.00	3.85	R
2267	2351	0.178068	AGCATCATACCCGCGAACTT	59.822	50.0	8.23	0.0	0.00	2.66	R
2528	2616	0.453950	CAGATGTCTTGCGCACTTGC	60.454	55.0	11.12	0.9	37.78	4.01	R
3119	3254	1.361668	CGCAGATCCAACACGAAGGG	61.362	60.0	0.00	0.0	0.00	3.95	R
3124	3259	1.934589	TATTCCGCAGATCCAACACG	58.065	50.0	0.00	0.0	0.00	4.49	R
3884	4034	0.249868	CAGTGTGCTGAAGTCCCGAA	60.250	55.0	0.00	0.0	45.28	4.30	R
4671	4837	0.466124	GATGGTCAGGAGGTAGTGCC	59.534	60.0	0.00	0.0	37.58	5.01	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
31	32	3.699038	TCACCTGCCAAACTAAATATGCC	59.301	43.478	0.00	0.00	0.00	4.40
33	34	4.099881	CACCTGCCAAACTAAATATGCCAT	59.900	41.667	0.00	0.00	0.00	4.40
41	42	7.499292	CCAAACTAAATATGCCATCAATTCCA	58.501	34.615	0.00	0.00	0.00	3.53
53	54	8.316497	TGCCATCAATTCCAAAAATATAAGGA	57.684	30.769	0.00	0.00	0.00	3.36
179	180	9.948964	TTTCATGATGAATCTAATCATACCGAT	57.051	29.630	8.90	0.00	41.71	4.18
315	316	2.888414	AGAAACCCAATAACACCAACGG	59.112	45.455	0.00	0.00	0.00	4.44
317	318	0.178987	ACCCAATAACACCAACGGCA	60.179	50.000	0.00	0.00	0.00	5.69
372	380	3.119495	CGGCTGTTTGGCTAAGCTAAATT	60.119	43.478	0.00	0.00	40.72	1.82
410	418	8.827177	TGTAAGAACAGTAATTTAGGTGACTG	57.173	34.615	2.87	2.87	43.88	3.51
561	570	8.973835	TGTTTTTGTTAAAGTTTGTAGTCTGG	57.026	30.769	0.00	0.00	0.00	3.86
617	626	2.817423	GCTCCTCAGCGATTTGGCG	61.817	63.158	0.00	0.00	35.39	5.69
646	655	1.538047	GTTGGATCTGGCTGCTTGAA	58.462	50.000	0.00	0.00	0.00	2.69
648	657	0.986527	TGGATCTGGCTGCTTGAAGA	59.013	50.000	0.00	0.00	0.00	2.87
753	762	5.987347	GCAGCAAAATGTAAATATCATGCCT	59.013	36.000	0.00	0.00	0.00	4.75
776	785	2.425668	CACCGGGGTATTTTGGTCATTC	59.574	50.000	6.32	0.00	30.72	2.67
829	844	1.686110	CAACCCTAGACGGCTCCCT	60.686	63.158	0.00	0.00	0.00	4.20
1053	1103	4.803426	GCCTCCTCCTCGCACACG	62.803	72.222	0.00	0.00	42.01	4.49
1079	1129	4.458829	TCCCTCGTCCTCCCGCAT	62.459	66.667	0.00	0.00	0.00	4.73
1080	1130	3.917760	CCCTCGTCCTCCCGCATC	61.918	72.222	0.00	0.00	0.00	3.91
1083	1133	4.770362	TCGTCCTCCCGCATCCCA	62.770	66.667	0.00	0.00	0.00	4.37
1084	1134	4.227134	CGTCCTCCCGCATCCCAG	62.227	72.222	0.00	0.00	0.00	4.45
1112	1162	4.862823	CCCCCGACCTCTCCCTCC	62.863	77.778	0.00	0.00	0.00	4.30
1113	1163	4.862823	CCCCGACCTCTCCCTCCC	62.863	77.778	0.00	0.00	0.00	4.30
1114	1164	3.756783	CCCGACCTCTCCCTCCCT	61.757	72.222	0.00	0.00	0.00	4.20
1115	1165	2.123640	CCGACCTCTCCCTCCCTC	60.124	72.222	0.00	0.00	0.00	4.30

Showing 1 to 25 of 607 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
208	209	9.744468	ACCTTGTAAGTTTGATCAAATTTGTAC	57.256	29.630	29.09	22.53	33.31	2.90
304	305	2.248135	CGCTGTGCCGTTGGTGTTA	61.248	57.895	0.00	0.00	0.00	2.41
317	318	2.185310	CTAGAAGGGTTGGGCGCTGT	62.185	60.000	7.64	0.00	40.49	4.40
324	332	7.337184	GGAATAGAAAAAGACTAGAAGGGTTGG	59.663	40.741	0.00	0.00	0.00	3.77
383	391	9.490379	AGTCACCTAAATTACTGTTCTTACAAG	57.510	33.333	0.00	0.00	32.92	3.16
489	497	7.799081	ACTAGTGGGGTACTTATGAAAATACC	58.201	38.462	0.00	0.00	40.89	2.73
505	513	6.702716	TTAAAAGTTTGTGAACTAGTGGGG	57.297	37.500	0.00	0.00	45.18	4.96
545	553	8.212312	TGGATGTAAACCAGACTACAAACTTTA	58.788	33.333	0.00	0.00	31.77	1.85
617	626	1.026718	CAGATCCAACGGCCAGGAAC	61.027	60.000	12.10	9.79	37.48	3.62
646	655	1.838073	ATCGGACGGCCCAAAACTCT	61.838	55.000	0.00	0.00	34.14	3.24
648	657	1.376812	GATCGGACGGCCCAAAACT	60.377	57.895	0.00	0.00	34.14	2.66
753	762	0.328926	GACCAAAATACCCCGGTGGA	59.671	55.000	15.08	0.00	38.00	4.02
776	785	1.476291	GGCCCTTTTATACCCGAGTGG	60.476	57.143	0.00	0.00	41.37	4.00
807	822	2.669240	GCCGTCTAGGGTTGCCTT	59.331	61.111	0.00	0.00	41.48	4.35
1062	1112	4.458829	ATGCGGGAGGACGAGGGA	62.459	66.667	0.00	0.00	35.47	4.20
1064	1114	3.917760	GGATGCGGGAGGACGAGG	61.918	72.222	0.00	0.00	35.47	4.63
1068	1118	4.554036	GCTGGGATGCGGGAGGAC	62.554	72.222	0.00	0.00	0.00	3.85
1095	1145	4.862823	GGAGGGAGAGGTCGGGGG	62.863	77.778	0.00	0.00	0.00	5.40
1096	1146	4.862823	GGGAGGGAGAGGTCGGGG	62.863	77.778	0.00	0.00	0.00	5.73
1097	1147	3.742248	GAGGGAGGGAGAGGTCGGG	62.742	73.684	0.00	0.00	0.00	5.14
1098	1148	2.123640	GAGGGAGGGAGAGGTCGG	60.124	72.222	0.00	0.00	0.00	4.79
1099	1149	2.517402	CGAGGGAGGGAGAGGTCG	60.517	72.222	0.00	0.00	0.00	4.79
1100	1150	2.835895	GCGAGGGAGGGAGAGGTC	60.836	72.222	0.00	0.00	0.00	3.85
1101	1151	3.673597	TGCGAGGGAGGGAGAGGT	61.674	66.667	0.00	0.00	0.00	3.85
1102	1152	3.151022	GTGCGAGGGAGGGAGAGG	61.151	72.222	0.00	0.00	0.00	3.69

Showing 1 to 25 of 609 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.