AutoCloner

Multiple sequence alignment - TraesCS6B01G372600

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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	TraesCS6B01G372600	chr6B	100.000	3841	0	0	1	3841	646100958	646104798	0.000000e+00	7094
1	TraesCS6B01G372600	chr6B	96.753	616	20	0	3226	3841	55636244	55635629	0.000000e+00	1027
2	TraesCS6B01G372600	chr4D	95.645	3146	127	7	1	3144	502618753	502621890	0.000000e+00	5042
3	TraesCS6B01G372600	chr4D	96.429	616	21	1	3226	3841	502622446	502623060	0.000000e+00	1014
4	TraesCS6B01G372600	chr3D	95.613	3146	128	7	1	3144	579344618	579347755	0.000000e+00	5036
5	TraesCS6B01G372600	chr3D	96.916	616	18	1	3226	3841	579348310	579348924	0.000000e+00	1031
6	TraesCS6B01G372600	chr2D	95.583	3147	128	7	1	3144	82250617	82247479	0.000000e+00	5031
7	TraesCS6B01G372600	chr2D	96.916	616	18	1	3226	3841	82246923	82246309	0.000000e+00	1031
8	TraesCS6B01G372600	chrUn	95.550	3146	130	7	1	3144	134333756	134330619	0.000000e+00	5025
9	TraesCS6B01G372600	chrUn	96.916	616	18	1	3226	3841	134330064	134329450	0.000000e+00	1031
10	TraesCS6B01G372600	chr3B	95.058	3197	149	6	1	3196	728851297	728854485	0.000000e+00	5020
11	TraesCS6B01G372600	chr1A	94.234	2584	142	5	476	3058	394485024	394487601	0.000000e+00	3940
12	TraesCS6B01G372600	chr1A	94.210	2349	128	7	711	3058	394415106	394417447	0.000000e+00	3578
13	TraesCS6B01G372600	chr5A	93.176	2550	166	6	476	3023	542029676	542027133	0.000000e+00	3738
14	TraesCS6B01G372600	chr4B	93.194	2101	126	12	909	3006	524149752	524147666	0.000000e+00	3072
15	TraesCS6B01G372600	chr4B	95.942	616	25	0	3226	3841	669391919	669391304	0.000000e+00	1000
16	TraesCS6B01G372600	chr4B	95.942	616	25	0	3226	3841	669430765	669431380	0.000000e+00	1000
17	TraesCS6B01G372600	chr4A	93.960	1755	103	3	1	1753	687964162	687962409	0.000000e+00	2651
18	TraesCS6B01G372600	chr5D	96.591	616	20	1	3226	3841	531438034	531437420	0.000000e+00	1020
19	TraesCS6B01G372600	chr5D	95.213	188	8	1	2957	3144	531438775	531438589	2.900000e-76	296
20	TraesCS6B01G372600	chr7D	96.429	616	20	2	3226	3841	109458785	109459398	0.000000e+00	1014

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	TraesCS6B01G372600	chr6B	646100958	646104798	3840	False	7094.0	7094	100.0000	1	3841	1	chr6B.!!$F1	3840
1	TraesCS6B01G372600	chr6B	55635629	55636244	615	True	1027.0	1027	96.7530	3226	3841	1	chr6B.!!$R1	615
2	TraesCS6B01G372600	chr4D	502618753	502623060	4307	False	3028.0	5042	96.0370	1	3841	2	chr4D.!!$F1	3840
3	TraesCS6B01G372600	chr3D	579344618	579348924	4306	False	3033.5	5036	96.2645	1	3841	2	chr3D.!!$F1	3840
4	TraesCS6B01G372600	chr2D	82246309	82250617	4308	True	3031.0	5031	96.2495	1	3841	2	chr2D.!!$R1	3840
5	TraesCS6B01G372600	chrUn	134329450	134333756	4306	True	3028.0	5025	96.2330	1	3841	2	chrUn.!!$R1	3840
6	TraesCS6B01G372600	chr3B	728851297	728854485	3188	False	5020.0	5020	95.0580	1	3196	1	chr3B.!!$F1	3195
7	TraesCS6B01G372600	chr1A	394485024	394487601	2577	False	3940.0	3940	94.2340	476	3058	1	chr1A.!!$F2	2582
8	TraesCS6B01G372600	chr1A	394415106	394417447	2341	False	3578.0	3578	94.2100	711	3058	1	chr1A.!!$F1	2347
9	TraesCS6B01G372600	chr5A	542027133	542029676	2543	True	3738.0	3738	93.1760	476	3023	1	chr5A.!!$R1	2547
10	TraesCS6B01G372600	chr4B	524147666	524149752	2086	True	3072.0	3072	93.1940	909	3006	1	chr4B.!!$R1	2097
11	TraesCS6B01G372600	chr4B	669391304	669391919	615	True	1000.0	1000	95.9420	3226	3841	1	chr4B.!!$R2	615
12	TraesCS6B01G372600	chr4B	669430765	669431380	615	False	1000.0	1000	95.9420	3226	3841	1	chr4B.!!$F1	615
13	TraesCS6B01G372600	chr4A	687962409	687964162	1753	True	2651.0	2651	93.9600	1	1753	1	chr4A.!!$R1	1752
14	TraesCS6B01G372600	chr5D	531437420	531438775	1355	True	658.0	1020	95.9020	2957	3841	2	chr5D.!!$R1	884
15	TraesCS6B01G372600	chr7D	109458785	109459398	613	False	1014.0	1014	96.4290	3226	3841	1	chr7D.!!$F1	615

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
509	511	0.613260	TGCTGTAGTTGTAGCCAGGG	59.387	55.0	39.15	4.45	F
834	838	0.660595	GATCTGATACGCCACCGTCG	60.661	60.0	46.39	5.12	F
1194	1200	0.846427	ATCTTCTGCCCCCACCAAGA	60.846	55.0	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	End Stability	Orientation
1316	1322	1.137513	GTCTGTTGTGCACGACCTAC	58.862	55.0	30.04	23.56	3.18	R
1867	1875	1.189752	TCTGAGCCTGCTTTCGATCT	58.810	50.0	0.00	0.00	2.75	R
3009	3017	0.384309	ACGTCAGACAAACAGAGCGA	59.616	50.0	0.41	0.00	4.93	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
28	29	4.463186	GTGGGAATCAGTATATAGACGGCT	59.537	45.833	0.00	0.00	0.00	5.52
44	45	1.335872	CGGCTGGTCCATTTTGTTGAC	60.336	52.381	0.00	0.00	34.01	3.18
206	207	1.539496	GCTGGTCGTCACTTGTACCAA	60.539	52.381	0.00	0.00	41.30	3.67
231	232	6.691754	TGTAGAGCACTGAAAATTTGTTCA	57.308	33.333	0.00	0.00	36.15	3.18
479	481	5.907197	AATGACACTTGACGAAACACTAG	57.093	39.130	0.00	0.00	0.00	2.57
509	511	0.613260	TGCTGTAGTTGTAGCCAGGG	59.387	55.000	0.00	0.00	39.15	4.45
828	832	3.300388	AGGAGAAAGATCTGATACGCCA	58.700	45.455	0.00	0.00	35.54	5.69
834	838	0.660595	GATCTGATACGCCACCGTCG	60.661	60.000	0.00	0.00	46.39	5.12
884	888	9.100554	TCATCTACGTCTTAAAAACAACTTGAA	57.899	29.630	0.00	0.00	0.00	2.69
965	971	3.009723	ACATCCTAATTGCCAAGACACG	58.990	45.455	0.00	0.00	0.00	4.49
969	975	2.811431	CCTAATTGCCAAGACACGTCAA	59.189	45.455	0.00	0.00	0.00	3.18
1117	1123	2.677228	CCGACCCCAATGAGGCTT	59.323	61.111	0.00	0.00	35.39	4.35
1171	1177	3.645268	GAGGATTTGCCCGCACCCT	62.645	63.158	4.65	4.65	37.37	4.34
1194	1200	0.846427	ATCTTCTGCCCCCACCAAGA	60.846	55.000	0.00	0.00	0.00	3.02
1224	1230	6.424812	TCGTGGAAGATGCACTTGAATATATG	59.575	38.462	6.31	0.00	36.50	1.78
1230	1236	6.291377	AGATGCACTTGAATATATGTTCGGT	58.709	36.000	7.59	6.34	0.00	4.69
1241	1247	9.315525	TGAATATATGTTCGGTTTTATGAACGA	57.684	29.630	7.59	0.00	45.75	3.85
1325	1331	7.484975	AGAAATCTCATTAGAAGTAGGTCGTG	58.515	38.462	0.00	0.00	34.73	4.35
1408	1414	9.435688	GATTAAATCTTACTTTTTGTGGCCATT	57.564	29.630	9.72	0.00	0.00	3.16
1862	1870	3.958147	TCTGGATAAGAAGCGATACACCA	59.042	43.478	0.00	0.00	29.54	4.17
1867	1875	5.279306	GGATAAGAAGCGATACACCATACCA	60.279	44.000	0.00	0.00	0.00	3.25
1876	1884	4.917998	CGATACACCATACCAGATCGAAAG	59.082	45.833	0.00	0.00	38.71	2.62
1880	1888	2.158900	ACCATACCAGATCGAAAGCAGG	60.159	50.000	0.00	0.00	0.00	4.85
1926	1934	3.328382	TTGTAACGTCAGCAAGCCTAT	57.672	42.857	0.00	0.00	0.00	2.57
1994	2002	0.979709	TAGAGAGGCATGCAGGCACT	60.980	55.000	26.25	22.12	46.01	4.40
2070	2078	4.561752	AGCTCTAAGGTATTCCTGGATGT	58.438	43.478	0.00	0.00	44.35	3.06
2156	2164	5.825151	TGATGTGTTCAACTCCACAATTGTA	59.175	36.000	11.53	0.00	44.10	2.41
2157	2165	6.319911	TGATGTGTTCAACTCCACAATTGTAA	59.680	34.615	11.53	1.62	44.10	2.41
2158	2166	6.130298	TGTGTTCAACTCCACAATTGTAAG	57.870	37.500	11.53	13.83	38.56	2.34
2225	2233	3.366052	AACCTGTGTTGACCTTCTGTT	57.634	42.857	0.00	0.00	32.13	3.16
2250	2258	3.972133	TCTACTTCCGTTGTCTATCCCA	58.028	45.455	0.00	0.00	0.00	4.37
2267	2275	1.000163	CCCAGATTCCTCGTATGGTCG	60.000	57.143	0.00	0.00	0.00	4.79
2411	2419	3.213206	ACTCAATGAAGTGTTGCAGGA	57.787	42.857	0.00	0.00	0.00	3.86
2481	2489	3.190327	ACATGTCATTCAATTTTCGGCGA	59.810	39.130	4.99	4.99	0.00	5.54
2730	2738	7.452880	TTGTTTCATTGTTTCTAGGATCCAG	57.547	36.000	15.82	9.58	0.00	3.86
2765	2773	2.026822	CCAAGTGGTAGTCCAGATGCTT	60.027	50.000	0.00	0.00	45.24	3.91
2989	2997	1.602377	ACTACAAGTTGGTTTCGCTGC	59.398	47.619	7.96	0.00	0.00	5.25
2995	3003	5.424757	ACAAGTTGGTTTCGCTGCTATATA	58.575	37.500	7.96	0.00	0.00	0.86
3006	3014	7.546778	TTCGCTGCTATATATGTTGTTTTGA	57.453	32.000	0.00	0.00	0.00	2.69
3009	3017	9.435688	TCGCTGCTATATATGTTGTTTTGATAT	57.564	29.630	0.00	0.00	0.00	1.63
3010	3018	9.694520	CGCTGCTATATATGTTGTTTTGATATC	57.305	33.333	0.00	0.00	0.00	1.63
3011	3019	9.694520	GCTGCTATATATGTTGTTTTGATATCG	57.305	33.333	0.00	0.00	0.00	2.92
3012	3020	9.694520	CTGCTATATATGTTGTTTTGATATCGC	57.305	33.333	0.00	0.00	0.00	4.58
3192	3200	3.332034	ACATGCCGAAAACCTACTACAC	58.668	45.455	0.00	0.00	0.00	2.90
3196	3204	4.497300	TGCCGAAAACCTACTACACATAC	58.503	43.478	0.00	0.00	0.00	2.39
3197	3205	4.021280	TGCCGAAAACCTACTACACATACA	60.021	41.667	0.00	0.00	0.00	2.29
3198	3206	5.114081	GCCGAAAACCTACTACACATACAT	58.886	41.667	0.00	0.00	0.00	2.29
3199	3207	5.583457	GCCGAAAACCTACTACACATACATT	59.417	40.000	0.00	0.00	0.00	2.71
3200	3208	6.456449	GCCGAAAACCTACTACACATACATTG	60.456	42.308	0.00	0.00	0.00	2.82
3201	3209	6.592607	CCGAAAACCTACTACACATACATTGT	59.407	38.462	0.00	0.00	39.91	2.71
3216	3224	8.284945	ACATACATTGTGATAGAAATTGCTGT	57.715	30.769	0.00	0.00	37.11	4.40
3292	3774	5.086104	ACGATGTATACTTTCAAGCCAGT	57.914	39.130	4.17	0.00	0.00	4.00
3298	3780	6.636705	TGTATACTTTCAAGCCAGTAATCGT	58.363	36.000	4.17	0.00	0.00	3.73
3457	3939	0.462375	GTCCCCGCCAAAGTGTTTTT	59.538	50.000	0.00	0.00	0.00	1.94
3458	3940	0.461961	TCCCCGCCAAAGTGTTTTTG	59.538	50.000	0.00	0.00	0.00	2.44
3488	3970	7.450634	TGACTACATAAAGTACAAGTCTGTCCT	59.549	37.037	0.00	0.00	35.38	3.85
3670	4153	7.280205	CAGAATAGACATGTGGGGTAAGTAAAC	59.720	40.741	1.15	0.00	0.00	2.01
3694	4177	7.813645	ACTTAAATTAAAAGAGGCACTAACGG	58.186	34.615	7.31	0.00	41.55	4.44
3819	4302	4.079253	TCCTCCTATTTTTCTGGCACAAC	58.921	43.478	0.00	0.00	38.70	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	4.017808	GGACCAGCCGTCTATATACTGAT	58.982	47.826	1.90	0.00	41.64	2.90
28	29	3.509575	GCCTATGTCAACAAAATGGACCA	59.490	43.478	0.00	0.00	0.00	4.02
44	45	5.443185	ACCGAAAATTCATGATGCCTATG	57.557	39.130	0.00	0.00	0.00	2.23
115	116	6.949352	AAAGATATGTTGATGGTAGGCAAG	57.051	37.500	0.00	0.00	0.00	4.01
206	207	7.715657	TGAACAAATTTTCAGTGCTCTACAAT	58.284	30.769	0.00	0.00	31.68	2.71
240	241	6.389906	GGTTTACCTGTATGTACGTAACTGT	58.610	40.000	0.00	0.00	0.00	3.55
495	497	3.589735	TCCATTTTCCCTGGCTACAACTA	59.410	43.478	0.00	0.00	33.56	2.24
509	511	7.440523	ACAAAGTCATCTACTGTCCATTTTC	57.559	36.000	0.00	0.00	38.88	2.29
609	611	9.173939	CACACTTTAACAGAAATGATTGTTCTC	57.826	33.333	0.00	0.00	38.41	2.87
678	680	7.675270	AAGTACGCGTACAGAAAATACATAG	57.325	36.000	41.10	0.00	38.48	2.23
689	692	2.785477	CCCGAATTAAGTACGCGTACAG	59.215	50.000	41.10	24.75	38.48	2.74
877	881	4.888326	TGCCTGCCAAATATTTCAAGTT	57.112	36.364	0.00	0.00	0.00	2.66
884	888	6.179040	TGCTTTTTATTGCCTGCCAAATATT	58.821	32.000	0.00	0.00	36.92	1.28
932	938	2.445565	TAGGATGTCGATGCAGCATC	57.554	50.000	23.63	23.63	38.51	3.91
965	971	3.542875	CGCATGAGTGATCGTTCATTGAC	60.543	47.826	8.56	2.85	33.56	3.18
969	975	2.299993	ACGCATGAGTGATCGTTCAT	57.700	45.000	0.00	6.06	33.56	2.57
1117	1123	2.060383	CATCGTGGAGCTGGAGGGA	61.060	63.158	0.00	0.00	0.00	4.20
1194	1200	2.783135	AGTGCATCTTCCACGAAATGT	58.217	42.857	0.00	0.00	38.22	2.71
1224	1230	3.776043	ACGTCGTTCATAAAACCGAAC	57.224	42.857	0.00	0.00	38.50	3.95
1241	1247	2.028658	AGTGTCTGCTCATCATGAACGT	60.029	45.455	0.00	0.00	0.00	3.99
1297	1303	9.372369	CGACCTACTTCTAATGAGATTTCTTTT	57.628	33.333	0.00	0.00	0.00	2.27
1316	1322	1.137513	GTCTGTTGTGCACGACCTAC	58.862	55.000	30.04	23.56	0.00	3.18
1349	1355	7.944729	AACAAATCAAGCAATACCATACTCT	57.055	32.000	0.00	0.00	0.00	3.24
1671	1678	2.276732	TTTTGCAGCACCTTCTAGCT	57.723	45.000	0.00	0.00	42.94	3.32
1825	1833	3.189618	TCCAGATTGAGCTGCATGTAG	57.810	47.619	6.42	6.42	34.56	2.74
1829	1837	4.701651	TCTTATCCAGATTGAGCTGCAT	57.298	40.909	1.02	0.00	34.56	3.96
1862	1870	1.765314	AGCCTGCTTTCGATCTGGTAT	59.235	47.619	0.00	0.00	0.00	2.73
1867	1875	1.189752	TCTGAGCCTGCTTTCGATCT	58.810	50.000	0.00	0.00	0.00	2.75
1876	1884	4.631773	TCAGCATTCTGAGCCTGC	57.368	55.556	0.00	0.00	43.95	4.85
1994	2002	8.429237	AATAATGTTTTCCTCCAACCATGTTA	57.571	30.769	0.00	0.00	0.00	2.41
2250	2258	2.933573	AGTCGACCATACGAGGAATCT	58.066	47.619	13.01	0.00	42.88	2.40
2267	2275	3.871594	CCTCATCCGATTTACCACAAGTC	59.128	47.826	0.00	0.00	0.00	3.01
2411	2419	2.509964	GTGTTCCATCCAAGGACCCTAT	59.490	50.000	0.00	0.00	37.42	2.57
2455	2463	5.177327	GCCGAAAATTGAATGACATGTTGTT	59.823	36.000	0.00	0.00	0.00	2.83
2765	2773	5.104776	AGCAGCTAGATTGTCTTTCACCATA	60.105	40.000	0.00	0.00	0.00	2.74
2829	2837	8.615211	TGCATAGAAGCATATTTAGTTGTTCAG	58.385	33.333	0.00	0.00	40.11	3.02
2955	2963	6.145048	CCAACTTGTAGTAGTACCAAAACTCG	59.855	42.308	5.26	0.00	0.00	4.18
2995	3003	6.500684	AACAGAGCGATATCAAAACAACAT	57.499	33.333	3.12	0.00	0.00	2.71
3006	3014	3.119459	ACGTCAGACAAACAGAGCGATAT	60.119	43.478	0.41	0.00	0.00	1.63
3009	3017	0.384309	ACGTCAGACAAACAGAGCGA	59.616	50.000	0.41	0.00	0.00	4.93
3010	3018	0.778815	GACGTCAGACAAACAGAGCG	59.221	55.000	11.55	0.00	0.00	5.03
3011	3019	1.852942	TGACGTCAGACAAACAGAGC	58.147	50.000	15.76	0.00	0.00	4.09
3012	3020	4.051237	TCATTGACGTCAGACAAACAGAG	58.949	43.478	19.11	0.00	35.84	3.35
3174	3182	3.688694	ATGTGTAGTAGGTTTTCGGCA	57.311	42.857	0.00	0.00	0.00	5.69
3199	3207	9.665719	TGAAGTTATACAGCAATTTCTATCACA	57.334	29.630	0.00	0.00	0.00	3.58
3204	3212	9.249457	CGAGATGAAGTTATACAGCAATTTCTA	57.751	33.333	0.00	0.00	0.00	2.10
3205	3213	7.766278	ACGAGATGAAGTTATACAGCAATTTCT	59.234	33.333	0.00	0.00	0.00	2.52
3206	3214	7.910304	ACGAGATGAAGTTATACAGCAATTTC	58.090	34.615	0.00	0.00	0.00	2.17
3207	3215	7.849804	ACGAGATGAAGTTATACAGCAATTT	57.150	32.000	0.00	0.00	0.00	1.82
3208	3216	9.197694	GATACGAGATGAAGTTATACAGCAATT	57.802	33.333	0.00	0.00	0.00	2.32
3209	3217	7.539022	CGATACGAGATGAAGTTATACAGCAAT	59.461	37.037	0.00	0.00	0.00	3.56
3210	3218	6.856426	CGATACGAGATGAAGTTATACAGCAA	59.144	38.462	0.00	0.00	0.00	3.91
3211	3219	6.017357	ACGATACGAGATGAAGTTATACAGCA	60.017	38.462	0.00	0.00	0.00	4.41
3212	3220	6.372185	ACGATACGAGATGAAGTTATACAGC	58.628	40.000	0.00	0.00	0.00	4.40
3219	3227	8.618677	TGAAGTTATACGATACGAGATGAAGTT	58.381	33.333	0.00	0.00	0.00	2.66
3220	3228	8.151141	TGAAGTTATACGATACGAGATGAAGT	57.849	34.615	0.00	0.00	0.00	3.01
3222	3230	8.235226	GGATGAAGTTATACGATACGAGATGAA	58.765	37.037	0.00	0.00	0.00	2.57
3223	3231	7.389607	TGGATGAAGTTATACGATACGAGATGA	59.610	37.037	0.00	0.00	0.00	2.92
3292	3774	4.038282	ACGTGCCTTATGACCATACGATTA	59.962	41.667	8.63	0.00	0.00	1.75
3298	3780	3.302161	AGGTACGTGCCTTATGACCATA	58.698	45.455	20.57	0.00	34.71	2.74
3488	3970	8.145767	ACGAATAATAATTGTCGGAACATCCTA	58.854	33.333	0.00	0.00	34.73	2.94
3563	4045	3.029570	GACGTGACTCCCTTAGGGTAAT	58.970	50.000	18.01	3.73	44.74	1.89
3670	4153	8.036273	TCCGTTAGTGCCTCTTTTAATTTAAG	57.964	34.615	0.00	0.00	0.00	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.