AutoCloner

Multiple sequence alignment - TraesCS5A01G017600

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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	TraesCS5A01G017600	chr5A	100.000	2820	0	0	1	2820	14027116	14029935	0.000000e+00	5208.0
1	TraesCS5A01G017600	chr1B	95.312	2773	120	9	1	2767	10716344	10713576	0.000000e+00	4392.0
2	TraesCS5A01G017600	chr1B	95.245	2776	119	11	1	2768	594965517	594962747	0.000000e+00	4383.0
3	TraesCS5A01G017600	chr1A	94.998	2779	115	17	1	2768	475635512	475638277	0.000000e+00	4340.0
4	TraesCS5A01G017600	chr1A	93.662	142	9	0	1158	1299	287275149	287275008	2.200000e-51	213.0
5	TraesCS5A01G017600	chr1A	96.296	54	2	0	2767	2820	148061179	148061232	3.870000e-14	89.8
6	TraesCS5A01G017600	chr1A	96.296	54	2	0	2767	2820	359819909	359819962	3.870000e-14	89.8
7	TraesCS5A01G017600	chr1A	96.296	54	2	0	2767	2820	419331713	419331766	3.870000e-14	89.8
8	TraesCS5A01G017600	chr3A	94.710	2779	123	18	1	2768	43479714	43476949	0.000000e+00	4296.0
9	TraesCS5A01G017600	chr3A	94.710	2779	124	17	1	2768	44063995	44061229	0.000000e+00	4296.0
10	TraesCS5A01G017600	chr2B	94.420	2778	129	16	1	2768	756008178	756010939	0.000000e+00	4248.0
11	TraesCS5A01G017600	chr4A	94.563	2722	125	12	52	2768	528832613	528835316	0.000000e+00	4185.0
12	TraesCS5A01G017600	chr2A	94.084	2451	108	14	322	2768	762831526	762833943	0.000000e+00	3688.0
13	TraesCS5A01G017600	chr2A	94.771	1530	74	4	1242	2768	81144492	81146018	0.000000e+00	2377.0
14	TraesCS5A01G017600	chr2A	95.304	1235	49	5	1	1227	81142486	81143719	0.000000e+00	1951.0
15	TraesCS5A01G017600	chr7A	95.646	1493	57	6	1253	2743	28406822	28408308	0.000000e+00	2390.0
16	TraesCS5A01G017600	chr7A	95.910	1198	47	2	1	1196	28405623	28406820	0.000000e+00	1940.0
17	TraesCS5A01G017600	chr7D	94.737	133	7	0	1168	1300	266214252	266214384	1.020000e-49	207.0
18	TraesCS5A01G017600	chr3D	93.007	143	9	1	1157	1299	351086613	351086754	1.020000e-49	207.0
19	TraesCS5A01G017600	chr3D	96.296	54	2	0	2767	2820	173521579	173521632	3.870000e-14	89.8
20	TraesCS5A01G017600	chr3D	96.296	54	2	0	2767	2820	349427076	349427129	3.870000e-14	89.8
21	TraesCS5A01G017600	chr3B	98.305	118	2	0	1180	1297	749091009	749090892	1.020000e-49	207.0
22	TraesCS5A01G017600	chr5B	94.118	136	7	1	1163	1297	148500203	148500068	3.680000e-49	206.0
23	TraesCS5A01G017600	chr5B	93.382	136	9	0	1165	1300	705034259	705034124	4.760000e-48	202.0
24	TraesCS5A01G017600	chr6D	91.837	147	10	2	1154	1300	183707738	183707594	1.320000e-48	204.0
25	TraesCS5A01G017600	chr4B	94.615	130	7	0	1169	1298	70814110	70813981	4.760000e-48	202.0
26	TraesCS5A01G017600	chr2D	94.615	130	7	0	1169	1298	183209474	183209345	4.760000e-48	202.0
27	TraesCS5A01G017600	chr2D	98.148	54	1	0	2767	2820	143292620	143292567	8.320000e-16	95.3
28	TraesCS5A01G017600	chr6A	96.296	54	2	0	2767	2820	352772006	352771953	3.870000e-14	89.8
29	TraesCS5A01G017600	chr6A	96.296	54	2	0	2767	2820	352804051	352803998	3.870000e-14	89.8
30	TraesCS5A01G017600	chr1D	96.296	54	2	0	2767	2820	246748270	246748323	3.870000e-14	89.8

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	TraesCS5A01G017600	chr5A	14027116	14029935	2819	False	5208	5208	100.0000	1	2820	1	chr5A.!!$F1	2819
1	TraesCS5A01G017600	chr1B	10713576	10716344	2768	True	4392	4392	95.3120	1	2767	1	chr1B.!!$R1	2766
2	TraesCS5A01G017600	chr1B	594962747	594965517	2770	True	4383	4383	95.2450	1	2768	1	chr1B.!!$R2	2767
3	TraesCS5A01G017600	chr1A	475635512	475638277	2765	False	4340	4340	94.9980	1	2768	1	chr1A.!!$F4	2767
4	TraesCS5A01G017600	chr3A	43476949	43479714	2765	True	4296	4296	94.7100	1	2768	1	chr3A.!!$R1	2767
5	TraesCS5A01G017600	chr3A	44061229	44063995	2766	True	4296	4296	94.7100	1	2768	1	chr3A.!!$R2	2767
6	TraesCS5A01G017600	chr2B	756008178	756010939	2761	False	4248	4248	94.4200	1	2768	1	chr2B.!!$F1	2767
7	TraesCS5A01G017600	chr4A	528832613	528835316	2703	False	4185	4185	94.5630	52	2768	1	chr4A.!!$F1	2716
8	TraesCS5A01G017600	chr2A	762831526	762833943	2417	False	3688	3688	94.0840	322	2768	1	chr2A.!!$F1	2446
9	TraesCS5A01G017600	chr2A	81142486	81146018	3532	False	2164	2377	95.0375	1	2768	2	chr2A.!!$F2	2767
10	TraesCS5A01G017600	chr7A	28405623	28408308	2685	False	2165	2390	95.7780	1	2743	2	chr7A.!!$F1	2742

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
115	122	0.829182	CAGCTTCAGGCCCTTGGTTT	60.829	55.000	0.0	0.0	43.05	3.27	F
360	371	1.544246	CCACCCACCTTTTCCGATTTC	59.456	52.381	0.0	0.0	0.00	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1632	2403	0.441533	GTTGTGACTCGATGCAGCAG	59.558	55.000	1.53	1.06	0.0	4.24	R
1953	2727	1.877443	GATCTAGAGTCCAGTCGAGCC	59.123	57.143	0.00	0.00	0.0	4.70	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
45	46	7.213678	GGATTTTGGTGGATTTGAACTAAACA	58.786	34.615	0.00	0.00	0.00	2.83
115	122	0.829182	CAGCTTCAGGCCCTTGGTTT	60.829	55.000	0.00	0.00	43.05	3.27
202	209	8.726988	GTTGTTGTCTCCATTGCTATTTTACTA	58.273	33.333	0.00	0.00	0.00	1.82
271	278	8.355169	ACGTGTCTCAGTTCTTAATTTAGTGTA	58.645	33.333	0.00	0.00	0.00	2.90
360	371	1.544246	CCACCCACCTTTTCCGATTTC	59.456	52.381	0.00	0.00	0.00	2.17
485	497	6.645003	GGCTTTGTCGATTGGAAAAATAGTTT	59.355	34.615	0.00	0.00	31.50	2.66
583	595	9.139174	CCCAACTACTTTATTTTATGCTTTGTG	57.861	33.333	0.00	0.00	0.00	3.33
602	614	7.522073	GCTTTGTGACTGTAATCTCCAATTTCA	60.522	37.037	0.00	0.00	0.00	2.69
745	757	8.292444	TGAAAAGATATGGGTGGAATTAACAG	57.708	34.615	0.00	0.00	0.00	3.16
747	759	9.136323	GAAAAGATATGGGTGGAATTAACAGAT	57.864	33.333	0.00	0.00	0.00	2.90
867	879	4.433304	CGTTTCGTTGTTTTAGCTGAGTTG	59.567	41.667	0.00	0.00	0.00	3.16
932	944	4.731313	AGGAGGAACTTGAAGAATTGGT	57.269	40.909	0.00	0.00	41.55	3.67
1185	1199	5.699097	TTGTAATACTTGCTTTGTCCCAC	57.301	39.130	0.00	0.00	0.00	4.61
1237	1251	8.792831	ACGGATGTATCTAATACTAAAACGTG	57.207	34.615	0.00	0.00	36.70	4.49
1239	1253	8.899776	CGGATGTATCTAATACTAAAACGTGAC	58.100	37.037	0.00	0.00	36.70	3.67
1315	2086	5.479306	AGTATTAGTCAAGACGTGCATTGT	58.521	37.500	0.00	0.00	36.20	2.71
1483	2254	7.041107	GGCTAATTGTTATTTCTCCAAATGCA	58.959	34.615	0.00	0.00	33.95	3.96
1632	2403	3.565482	TCTTCTCTTTCACCATGTGTTGC	59.435	43.478	0.00	0.00	34.79	4.17
1816	2587	3.264193	TGATCCCTCAGTTACATGCTTGT	59.736	43.478	10.40	10.40	39.98	3.16
1829	2600	5.112220	ACATGCTTGTTGACACAGTATTG	57.888	39.130	0.00	0.00	33.22	1.90
1953	2727	3.760151	TGATTGCAGGATCCAAAGAACTG	59.240	43.478	15.82	2.22	35.36	3.16
2170	2952	1.967066	CCCACTTTTGGTTGCCACATA	59.033	47.619	0.00	0.00	42.10	2.29
2173	2955	3.995705	CCACTTTTGGTTGCCACATATTG	59.004	43.478	0.00	0.00	38.23	1.90
2198	2980	6.809196	GGCACCACGAAAATTTTATATTGTCA	59.191	34.615	2.75	0.00	0.00	3.58
2231	3013	1.529865	GCTACAAACAGTTCACCCGTC	59.470	52.381	0.00	0.00	0.00	4.79
2283	3067	6.267496	AGTATGTTGCAATTTCCTGTTACC	57.733	37.500	0.59	0.00	0.00	2.85
2364	3148	1.067915	GCCTAATGCCACGAAAGCAAA	60.068	47.619	3.16	0.00	44.83	3.68
2657	3444	3.199880	ACCTATTAGCATGTGTCCAGC	57.800	47.619	0.00	0.00	0.00	4.85
2675	3462	2.393557	CCGCAACGGCTATCAACAT	58.606	52.632	0.00	0.00	41.17	2.71
2695	3482	6.449635	ACATATGTTGTTTCGTGGCAATAT	57.550	33.333	1.41	0.00	33.74	1.28
2725	3512	4.195416	TCGCCACAAATCAGCATGTATTA	58.805	39.130	0.00	0.00	37.40	0.98
2743	3530	7.559835	TGTATTACGACGAACGATTTTGTTA	57.440	32.000	0.00	0.00	45.77	2.41
2768	3555	1.207329	AGACCCGAATCCTTGTAGTGC	59.793	52.381	0.00	0.00	0.00	4.40
2769	3556	0.252197	ACCCGAATCCTTGTAGTGCC	59.748	55.000	0.00	0.00	0.00	5.01
2770	3557	0.463833	CCCGAATCCTTGTAGTGCCC	60.464	60.000	0.00	0.00	0.00	5.36
2771	3558	0.463833	CCGAATCCTTGTAGTGCCCC	60.464	60.000	0.00	0.00	0.00	5.80
2772	3559	0.463833	CGAATCCTTGTAGTGCCCCC	60.464	60.000	0.00	0.00	0.00	5.40
2773	3560	0.623723	GAATCCTTGTAGTGCCCCCA	59.376	55.000	0.00	0.00	0.00	4.96
2774	3561	0.625849	AATCCTTGTAGTGCCCCCAG	59.374	55.000	0.00	0.00	0.00	4.45
2775	3562	1.281925	ATCCTTGTAGTGCCCCCAGG	61.282	60.000	0.00	0.00	0.00	4.45
2788	3575	3.350163	CCAGGGGTCTTGGGCCAT	61.350	66.667	7.26	0.00	0.00	4.40
2789	3576	2.276740	CAGGGGTCTTGGGCCATC	59.723	66.667	7.26	0.65	0.00	3.51
2790	3577	3.411517	AGGGGTCTTGGGCCATCG	61.412	66.667	7.26	1.25	0.00	3.84
2801	3588	4.115199	GCCATCGCCCTGGGAACT	62.115	66.667	19.27	0.00	36.75	3.01
2802	3589	2.190578	CCATCGCCCTGGGAACTC	59.809	66.667	19.27	0.00	32.28	3.01
2803	3590	2.190578	CATCGCCCTGGGAACTCC	59.809	66.667	19.27	0.00	0.00	3.85
2804	3591	2.041265	ATCGCCCTGGGAACTCCT	59.959	61.111	19.27	0.00	36.20	3.69
2805	3592	1.616628	ATCGCCCTGGGAACTCCTT	60.617	57.895	19.27	0.00	36.20	3.36
2806	3593	1.627297	ATCGCCCTGGGAACTCCTTC	61.627	60.000	19.27	0.00	36.20	3.46
2807	3594	2.592993	CGCCCTGGGAACTCCTTCA	61.593	63.158	19.27	0.00	36.20	3.02
2808	3595	1.002011	GCCCTGGGAACTCCTTCAC	60.002	63.158	19.27	0.00	36.20	3.18
2809	3596	1.296715	CCCTGGGAACTCCTTCACG	59.703	63.158	7.01	0.00	31.63	4.35
2810	3597	1.481056	CCCTGGGAACTCCTTCACGT	61.481	60.000	7.01	0.00	31.63	4.49
2811	3598	0.396811	CCTGGGAACTCCTTCACGTT	59.603	55.000	0.00	0.00	31.63	3.99
2812	3599	1.512926	CTGGGAACTCCTTCACGTTG	58.487	55.000	0.00	0.00	31.63	4.10
2813	3600	0.534203	TGGGAACTCCTTCACGTTGC	60.534	55.000	0.00	0.00	31.63	4.17
2814	3601	1.566018	GGGAACTCCTTCACGTTGCG	61.566	60.000	0.00	0.00	33.03	4.85
2815	3602	0.878961	GGAACTCCTTCACGTTGCGT	60.879	55.000	0.00	0.00	42.36	5.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	4.000988	AGCACGATTCAGTTAAAACGGAT	58.999	39.130	0.00	0.00	33.29	4.18
115	122	5.356470	TGCATCCGAATAAATCATCAACACA	59.644	36.000	0.00	0.00	0.00	3.72
271	278	5.853572	TTTTGTATCCCTGGTTACTTCCT	57.146	39.130	6.10	0.00	0.00	3.36
332	343	3.239449	GAAAAGGTGGGTGGATTTCCTT	58.761	45.455	0.00	0.00	39.75	3.36
360	371	9.748708	TTGTCCAAAATCATCTTAAACTTTCAG	57.251	29.630	0.00	0.00	0.00	3.02
453	464	2.154462	CAATCGACAAAGCCCAAGTCT	58.846	47.619	0.00	0.00	0.00	3.24
485	497	6.539173	AGACTACATGGTGTTTGTTTGGATA	58.461	36.000	0.00	0.00	0.00	2.59
534	546	3.624861	CGCAAGAGAAAAGCTCCACATAT	59.375	43.478	0.00	0.00	45.10	1.78
583	595	6.603201	TGGGAATGAAATTGGAGATTACAGTC	59.397	38.462	0.00	0.00	36.07	3.51
602	614	7.510675	CCATAGTAATGGTATACCTGGGAAT	57.489	40.000	22.41	4.70	46.68	3.01
702	714	6.980978	TCTTTTCAACGCACCAATATTTCAAA	59.019	30.769	0.00	0.00	0.00	2.69
745	757	9.294030	GAATTTGTTTCATATGTCCAGTCAATC	57.706	33.333	1.90	0.00	34.27	2.67
747	759	8.081633	GTGAATTTGTTTCATATGTCCAGTCAA	58.918	33.333	1.90	0.00	45.77	3.18
886	898	4.586421	TGGTTAATCCTGCACATTTTGTGA	59.414	37.500	11.63	0.00	42.96	3.58
932	944	1.484653	ACAAGACACACACTGCTACCA	59.515	47.619	0.00	0.00	0.00	3.25
1024	1038	3.334691	CCTGGTCATAGCGAAGTTTCAA	58.665	45.455	0.00	0.00	0.00	2.69
1106	1120	6.691754	ACGTGCACCATTGAATTAATCATA	57.308	33.333	12.15	0.00	38.03	2.15
1173	1187	3.731652	CAAGAATTGTGGGACAAAGCA	57.268	42.857	0.00	0.00	44.16	3.91
1225	1239	8.255206	TGGATGTATCAAGTCACGTTTTAGTAT	58.745	33.333	0.00	0.00	0.00	2.12
1227	1241	6.460781	TGGATGTATCAAGTCACGTTTTAGT	58.539	36.000	0.00	0.00	0.00	2.24
1228	1242	6.961359	TGGATGTATCAAGTCACGTTTTAG	57.039	37.500	0.00	0.00	0.00	1.85
1229	1243	9.607988	AATATGGATGTATCAAGTCACGTTTTA	57.392	29.630	0.00	0.00	0.00	1.52
1232	1246	9.261180	CTAAATATGGATGTATCAAGTCACGTT	57.739	33.333	0.00	0.00	0.00	3.99
1233	1247	8.638873	TCTAAATATGGATGTATCAAGTCACGT	58.361	33.333	0.00	0.00	0.00	4.49
1234	1248	8.916654	GTCTAAATATGGATGTATCAAGTCACG	58.083	37.037	0.00	0.00	0.00	4.35
1315	2086	7.768582	AGCAATGTACTAGTAAATGTGCATGTA	59.231	33.333	25.62	0.00	38.95	2.29
1363	2134	4.590918	TCTCAATCCTCTTCGTAGTCACT	58.409	43.478	0.00	0.00	0.00	3.41
1444	2215	4.288626	ACAATTAGCCTTCCACCTTGAGTA	59.711	41.667	0.00	0.00	0.00	2.59
1483	2254	7.986085	ATTCTTTGTTGTAGCTTGTATGAGT	57.014	32.000	0.00	0.00	0.00	3.41
1632	2403	0.441533	GTTGTGACTCGATGCAGCAG	59.558	55.000	1.53	1.06	0.00	4.24
1816	2587	3.769739	ACTGGAGCAATACTGTGTCAA	57.230	42.857	0.00	0.00	0.00	3.18
1829	2600	5.523438	ACTATTGCTAGACTAACTGGAGC	57.477	43.478	0.00	0.00	32.57	4.70
1953	2727	1.877443	GATCTAGAGTCCAGTCGAGCC	59.123	57.143	0.00	0.00	0.00	4.70
2123	2905	8.208718	TGTGGTAATATTCTATTGCAACTGTC	57.791	34.615	0.00	0.00	0.00	3.51
2170	2952	7.821846	ACAATATAAAATTTTCGTGGTGCCAAT	59.178	29.630	6.72	0.00	0.00	3.16
2173	2955	6.809196	TGACAATATAAAATTTTCGTGGTGCC	59.191	34.615	6.72	0.00	0.00	5.01
2198	2980	5.989777	ACTGTTTGTAGCGAGAAACTATTGT	59.010	36.000	17.98	10.16	39.11	2.71
2645	3432	3.364441	TTGCGGCTGGACACATGC	61.364	61.111	0.00	0.00	0.00	4.06
2657	3444	6.031502	AACATATGTTGATAGCCGTTGCGG	62.032	45.833	20.19	2.85	42.74	5.69
2675	3462	5.888691	ACATATTGCCACGAAACAACATA	57.111	34.783	0.00	0.00	0.00	2.29
2695	3482	3.621268	GCTGATTTGTGGCGATAAGTACA	59.379	43.478	0.00	0.00	0.00	2.90
2725	3512	4.775440	TTGTAACAAAATCGTTCGTCGT	57.225	36.364	0.00	0.00	40.80	4.34
2743	3530	4.715297	ACTACAAGGATTCGGGTCTATTGT	59.285	41.667	12.52	12.52	34.63	2.71
2771	3558	3.350163	ATGGCCCAAGACCCCTGG	61.350	66.667	0.00	0.00	0.00	4.45
2772	3559	2.276740	GATGGCCCAAGACCCCTG	59.723	66.667	0.00	0.00	0.00	4.45
2773	3560	3.411517	CGATGGCCCAAGACCCCT	61.412	66.667	0.00	0.00	0.00	4.79
2784	3571	4.115199	AGTTCCCAGGGCGATGGC	62.115	66.667	0.00	0.00	39.17	4.40
2785	3572	2.190578	GAGTTCCCAGGGCGATGG	59.809	66.667	0.00	0.54	40.29	3.51
2786	3573	1.915078	AAGGAGTTCCCAGGGCGATG	61.915	60.000	0.00	0.00	37.41	3.84
2787	3574	1.616628	AAGGAGTTCCCAGGGCGAT	60.617	57.895	0.00	0.00	37.41	4.58
2788	3575	2.203938	AAGGAGTTCCCAGGGCGA	60.204	61.111	0.00	0.00	37.41	5.54
2789	3576	2.269241	GAAGGAGTTCCCAGGGCG	59.731	66.667	0.00	0.00	37.41	6.13
2790	3577	1.002011	GTGAAGGAGTTCCCAGGGC	60.002	63.158	0.00	0.00	37.41	5.19
2791	3578	1.296715	CGTGAAGGAGTTCCCAGGG	59.703	63.158	0.00	0.00	37.41	4.45
2792	3579	0.396811	AACGTGAAGGAGTTCCCAGG	59.603	55.000	0.00	0.00	37.41	4.45
2793	3580	1.512926	CAACGTGAAGGAGTTCCCAG	58.487	55.000	0.00	0.00	37.41	4.45
2794	3581	0.534203	GCAACGTGAAGGAGTTCCCA	60.534	55.000	0.00	0.00	37.41	4.37
2795	3582	1.566018	CGCAACGTGAAGGAGTTCCC	61.566	60.000	0.00	0.00	36.42	3.97
2796	3583	0.878961	ACGCAACGTGAAGGAGTTCC	60.879	55.000	0.00	0.00	39.18	3.62
2797	3584	2.601562	ACGCAACGTGAAGGAGTTC	58.398	52.632	0.00	0.00	39.18	3.01
2798	3585	4.848685	ACGCAACGTGAAGGAGTT	57.151	50.000	0.00	0.00	39.18	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.