AutoCloner

Multiple sequence alignment - TraesCS3D01G500500

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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	TraesCS3D01G500500	chr3D	100.000	3303	0	0	1	3303	589695125	589698427	0.000000e+00	6100.0
1	TraesCS3D01G500500	chr3D	85.805	472	40	18	2735	3202	438059517	438059965	2.980000e-130	475.0
2	TraesCS3D01G500500	chr3D	91.837	245	19	1	2460	2703	581828093	581827849	1.140000e-89	340.0
3	TraesCS3D01G500500	chr2D	98.032	3150	22	4	177	3303	19545690	19542558	0.000000e+00	5437.0
4	TraesCS3D01G500500	chr2D	87.045	1482	160	20	952	2411	10310167	10311638	0.000000e+00	1644.0
5	TraesCS3D01G500500	chr2D	89.921	1141	106	5	1249	2382	19245524	19244386	0.000000e+00	1461.0
6	TraesCS3D01G500500	chr2D	90.272	514	42	4	697	1208	19246322	19245815	0.000000e+00	665.0
7	TraesCS3D01G500500	chr2D	95.679	162	2	2	1	161	19545835	19545678	4.230000e-64	255.0
8	TraesCS3D01G500500	chr2D	86.667	75	7	1	200	274	19246866	19246795	2.730000e-11	80.5
9	TraesCS3D01G500500	chrUn	89.127	1821	149	34	658	2458	169570502	169572293	0.000000e+00	2220.0
10	TraesCS3D01G500500	chrUn	84.375	1024	148	5	1292	2303	150939697	150940720	0.000000e+00	994.0
11	TraesCS3D01G500500	chrUn	85.586	888	83	33	658	1528	391746266	391747125	0.000000e+00	889.0
12	TraesCS3D01G500500	chrUn	86.486	185	25	0	1019	1203	2685	2501	1.550000e-48	204.0
13	TraesCS3D01G500500	chr1B	89.127	1821	149	34	658	2458	44790418	44788627	0.000000e+00	2220.0
14	TraesCS3D01G500500	chr1B	94.444	72	3	1	2457	2527	603538206	603538135	3.480000e-20	110.0
15	TraesCS3D01G500500	chr2A	87.536	1396	146	15	975	2353	10465043	10466427	0.000000e+00	1589.0
16	TraesCS3D01G500500	chr2B	87.034	1396	147	24	943	2326	38841490	38842863	0.000000e+00	1544.0
17	TraesCS3D01G500500	chr2B	86.328	1397	164	23	986	2369	4482064	4483446	0.000000e+00	1496.0
18	TraesCS3D01G500500	chr2B	89.194	583	41	12	2735	3303	212571180	212571754	0.000000e+00	708.0
19	TraesCS3D01G500500	chr2B	84.672	137	9	3	2567	2703	212570520	212570644	3.460000e-25	126.0
20	TraesCS3D01G500500	chr4D	91.424	583	28	12	2735	3303	437821415	437821989	0.000000e+00	780.0
21	TraesCS3D01G500500	chr4D	91.081	583	28	11	2735	3303	497693902	497693330	0.000000e+00	767.0
22	TraesCS3D01G500500	chr4D	91.803	244	14	4	2460	2703	497695152	497694915	5.280000e-88	335.0
23	TraesCS3D01G500500	chr4D	89.051	274	18	4	2460	2729	437820204	437820469	2.460000e-86	329.0
24	TraesCS3D01G500500	chr6D	90.862	580	32	11	2735	3300	111021119	111021691	0.000000e+00	758.0
25	TraesCS3D01G500500	chr6D	91.837	245	14	4	2460	2703	111019850	111020089	1.470000e-88	337.0
26	TraesCS3D01G500500	chr5D	89.428	577	42	10	2739	3303	542466443	542465874	0.000000e+00	710.0
27	TraesCS3D01G500500	chr5D	88.908	586	34	18	2735	3303	384481912	384481341	0.000000e+00	693.0
28	TraesCS3D01G500500	chr5D	85.864	573	55	20	2735	3303	480152997	480153547	1.320000e-163	586.0
29	TraesCS3D01G500500	chr5D	90.842	273	18	4	2460	2728	542467694	542467425	3.130000e-95	359.0
30	TraesCS3D01G500500	chr1A	89.057	594	35	17	2735	3303	35134155	35134743	0.000000e+00	710.0
31	TraesCS3D01G500500	chr1A	89.381	113	11	1	2459	2571	559046021	559046132	1.240000e-29	141.0
32	TraesCS3D01G500500	chr6B	88.205	585	43	13	2741	3303	719333773	719333193	0.000000e+00	675.0
33	TraesCS3D01G500500	chr5B	88.153	574	38	25	2735	3301	11304082	11304632	0.000000e+00	656.0
34	TraesCS3D01G500500	chr5B	84.426	244	20	3	2460	2703	686436965	686436740	1.190000e-54	224.0
35	TraesCS3D01G500500	chr3A	86.632	576	51	20	2735	3303	549912259	549911703	6.060000e-172	614.0
36	TraesCS3D01G500500	chr1D	89.152	507	24	12	2735	3224	218326287	218326779	1.310000e-168	603.0
37	TraesCS3D01G500500	chr5A	90.000	250	13	4	2735	2973	662524079	662523831	2.470000e-81	313.0
38	TraesCS3D01G500500	chr6A	87.719	114	4	4	2624	2728	445616011	445615899	1.240000e-24	124.0

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	TraesCS3D01G500500	chr3D	589695125	589698427	3302	False	6100.0	6100	100.000000	1	3303	1	chr3D.!!$F2	3302
1	TraesCS3D01G500500	chr2D	19542558	19545835	3277	True	2846.0	5437	96.855500	1	3303	2	chr2D.!!$R2	3302
2	TraesCS3D01G500500	chr2D	10310167	10311638	1471	False	1644.0	1644	87.045000	952	2411	1	chr2D.!!$F1	1459
3	TraesCS3D01G500500	chr2D	19244386	19246866	2480	True	735.5	1461	88.953333	200	2382	3	chr2D.!!$R1	2182
4	TraesCS3D01G500500	chrUn	169570502	169572293	1791	False	2220.0	2220	89.127000	658	2458	1	chrUn.!!$F2	1800
5	TraesCS3D01G500500	chrUn	150939697	150940720	1023	False	994.0	994	84.375000	1292	2303	1	chrUn.!!$F1	1011
6	TraesCS3D01G500500	chrUn	391746266	391747125	859	False	889.0	889	85.586000	658	1528	1	chrUn.!!$F3	870
7	TraesCS3D01G500500	chr1B	44788627	44790418	1791	True	2220.0	2220	89.127000	658	2458	1	chr1B.!!$R1	1800
8	TraesCS3D01G500500	chr2A	10465043	10466427	1384	False	1589.0	1589	87.536000	975	2353	1	chr2A.!!$F1	1378
9	TraesCS3D01G500500	chr2B	38841490	38842863	1373	False	1544.0	1544	87.034000	943	2326	1	chr2B.!!$F2	1383
10	TraesCS3D01G500500	chr2B	4482064	4483446	1382	False	1496.0	1496	86.328000	986	2369	1	chr2B.!!$F1	1383
11	TraesCS3D01G500500	chr2B	212570520	212571754	1234	False	417.0	708	86.933000	2567	3303	2	chr2B.!!$F3	736
12	TraesCS3D01G500500	chr4D	437820204	437821989	1785	False	554.5	780	90.237500	2460	3303	2	chr4D.!!$F1	843
13	TraesCS3D01G500500	chr4D	497693330	497695152	1822	True	551.0	767	91.442000	2460	3303	2	chr4D.!!$R1	843
14	TraesCS3D01G500500	chr6D	111019850	111021691	1841	False	547.5	758	91.349500	2460	3300	2	chr6D.!!$F1	840
15	TraesCS3D01G500500	chr5D	384481341	384481912	571	True	693.0	693	88.908000	2735	3303	1	chr5D.!!$R1	568
16	TraesCS3D01G500500	chr5D	480152997	480153547	550	False	586.0	586	85.864000	2735	3303	1	chr5D.!!$F1	568
17	TraesCS3D01G500500	chr5D	542465874	542467694	1820	True	534.5	710	90.135000	2460	3303	2	chr5D.!!$R2	843
18	TraesCS3D01G500500	chr1A	35134155	35134743	588	False	710.0	710	89.057000	2735	3303	1	chr1A.!!$F1	568
19	TraesCS3D01G500500	chr6B	719333193	719333773	580	True	675.0	675	88.205000	2741	3303	1	chr6B.!!$R1	562
20	TraesCS3D01G500500	chr5B	11304082	11304632	550	False	656.0	656	88.153000	2735	3301	1	chr5B.!!$F1	566
21	TraesCS3D01G500500	chr3A	549911703	549912259	556	True	614.0	614	86.632000	2735	3303	1	chr3A.!!$R1	568

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
155	157	0.113190	TGGTCAGCACAGGAGAGAGA	59.887	55.0	0.0	0.0	0.0	3.1	F
156	158	0.817013	GGTCAGCACAGGAGAGAGAG	59.183	60.0	0.0	0.0	0.0	3.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1099	1269	3.357079	CTGGGACACGCAGTTGGC	61.357	66.667	7.49	0.0	41.61	4.52	R
2373	2843	7.711339	AGAGAGAAAGTTCTACAATTTGAACGT	59.289	33.333	2.79	0.0	44.95	3.99	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
59	61	6.305399	CCATGTTGAACAACTAGTTTATTGCG	59.695	38.462	5.07	0.00	41.51	4.85
141	143	5.869649	TTCTCTATCGATTGGATTGGTCA	57.130	39.130	1.71	0.00	36.55	4.02
143	145	3.993081	CTCTATCGATTGGATTGGTCAGC	59.007	47.826	1.71	0.00	36.55	4.26
144	146	2.715749	ATCGATTGGATTGGTCAGCA	57.284	45.000	0.00	0.00	28.32	4.41
145	147	1.737838	TCGATTGGATTGGTCAGCAC	58.262	50.000	0.00	0.00	0.00	4.40
146	148	1.003003	TCGATTGGATTGGTCAGCACA	59.997	47.619	0.00	0.00	0.00	4.57
147	149	1.399440	CGATTGGATTGGTCAGCACAG	59.601	52.381	0.00	0.00	0.00	3.66
148	150	1.747355	GATTGGATTGGTCAGCACAGG	59.253	52.381	0.00	0.00	0.00	4.00
149	151	0.770499	TTGGATTGGTCAGCACAGGA	59.230	50.000	0.00	0.00	0.00	3.86
150	152	0.325933	TGGATTGGTCAGCACAGGAG	59.674	55.000	0.00	0.00	0.00	3.69
151	153	0.615331	GGATTGGTCAGCACAGGAGA	59.385	55.000	0.00	0.00	0.00	3.71
152	154	1.406614	GGATTGGTCAGCACAGGAGAG	60.407	57.143	0.00	0.00	0.00	3.20
153	155	1.552337	GATTGGTCAGCACAGGAGAGA	59.448	52.381	0.00	0.00	0.00	3.10
154	156	0.972134	TTGGTCAGCACAGGAGAGAG	59.028	55.000	0.00	0.00	0.00	3.20
155	157	0.113190	TGGTCAGCACAGGAGAGAGA	59.887	55.000	0.00	0.00	0.00	3.10
156	158	0.817013	GGTCAGCACAGGAGAGAGAG	59.183	60.000	0.00	0.00	0.00	3.20
157	159	1.615651	GGTCAGCACAGGAGAGAGAGA	60.616	57.143	0.00	0.00	0.00	3.10
158	160	1.745087	GTCAGCACAGGAGAGAGAGAG	59.255	57.143	0.00	0.00	0.00	3.20
159	161	1.632920	TCAGCACAGGAGAGAGAGAGA	59.367	52.381	0.00	0.00	0.00	3.10
160	162	2.019249	CAGCACAGGAGAGAGAGAGAG	58.981	57.143	0.00	0.00	0.00	3.20
161	163	1.915489	AGCACAGGAGAGAGAGAGAGA	59.085	52.381	0.00	0.00	0.00	3.10
162	164	2.092753	AGCACAGGAGAGAGAGAGAGAG	60.093	54.545	0.00	0.00	0.00	3.20
163	165	2.092968	GCACAGGAGAGAGAGAGAGAGA	60.093	54.545	0.00	0.00	0.00	3.10
164	166	3.801698	CACAGGAGAGAGAGAGAGAGAG	58.198	54.545	0.00	0.00	0.00	3.20
165	167	3.452264	CACAGGAGAGAGAGAGAGAGAGA	59.548	52.174	0.00	0.00	0.00	3.10
166	168	3.708631	ACAGGAGAGAGAGAGAGAGAGAG	59.291	52.174	0.00	0.00	0.00	3.20
167	169	3.963374	CAGGAGAGAGAGAGAGAGAGAGA	59.037	52.174	0.00	0.00	0.00	3.10
168	170	4.039004	CAGGAGAGAGAGAGAGAGAGAGAG	59.961	54.167	0.00	0.00	0.00	3.20
169	171	4.078922	AGGAGAGAGAGAGAGAGAGAGAGA	60.079	50.000	0.00	0.00	0.00	3.10
170	172	4.280677	GGAGAGAGAGAGAGAGAGAGAGAG	59.719	54.167	0.00	0.00	0.00	3.20
171	173	5.136068	AGAGAGAGAGAGAGAGAGAGAGA	57.864	47.826	0.00	0.00	0.00	3.10
172	174	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
173	175	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
174	176	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
175	177	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
189	191	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
193	195	7.786943	AGAGAGAGAGAGAGAGAGAGAGAATTA	59.213	40.741	0.00	0.00	0.00	1.40
862	1029	3.188460	TCGGTTGCTTTGCATCTTTCTAC	59.812	43.478	0.00	0.00	38.76	2.59
2393	2863	9.843334	TTACAAACGTTCAAATTGTAGAACTTT	57.157	25.926	0.00	9.42	41.40	2.66
2538	3009	4.590918	TGTTTATGATTCTTTGGGCGGTA	58.409	39.130	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	61	0.602638	TCAGACCGCCACATGTCAAC	60.603	55.000	0.00	0.00	33.89	3.18
141	143	1.915489	TCTCTCTCTCTCTCCTGTGCT	59.085	52.381	0.00	0.00	0.00	4.40
143	145	3.452264	TCTCTCTCTCTCTCTCTCCTGTG	59.548	52.174	0.00	0.00	0.00	3.66
144	146	3.708631	CTCTCTCTCTCTCTCTCTCCTGT	59.291	52.174	0.00	0.00	0.00	4.00
145	147	3.963374	TCTCTCTCTCTCTCTCTCTCCTG	59.037	52.174	0.00	0.00	0.00	3.86
146	148	4.078922	TCTCTCTCTCTCTCTCTCTCTCCT	60.079	50.000	0.00	0.00	0.00	3.69
147	149	4.219115	TCTCTCTCTCTCTCTCTCTCTCC	58.781	52.174	0.00	0.00	0.00	3.71
148	150	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
149	151	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
150	152	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
151	153	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
152	154	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
153	155	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
154	156	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
155	157	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
156	158	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
157	159	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
158	160	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
159	161	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
160	162	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
161	163	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
162	164	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
163	165	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
164	166	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
165	167	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
166	168	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
167	169	5.136068	TCTCTCTCTCTCTCTCTCTCTCT	57.864	47.826	0.00	0.00	0.00	3.10
168	170	5.860941	TTCTCTCTCTCTCTCTCTCTCTC	57.139	47.826	0.00	0.00	0.00	3.20
169	171	6.821616	AATTCTCTCTCTCTCTCTCTCTCT	57.178	41.667	0.00	0.00	0.00	3.10
170	172	8.997323	CAATAATTCTCTCTCTCTCTCTCTCTC	58.003	40.741	0.00	0.00	0.00	3.20
171	173	7.941238	CCAATAATTCTCTCTCTCTCTCTCTCT	59.059	40.741	0.00	0.00	0.00	3.10
172	174	7.721399	ACCAATAATTCTCTCTCTCTCTCTCTC	59.279	40.741	0.00	0.00	0.00	3.20
173	175	7.586349	ACCAATAATTCTCTCTCTCTCTCTCT	58.414	38.462	0.00	0.00	0.00	3.10
174	176	7.040409	GGACCAATAATTCTCTCTCTCTCTCTC	60.040	44.444	0.00	0.00	0.00	3.20
175	177	6.777580	GGACCAATAATTCTCTCTCTCTCTCT	59.222	42.308	0.00	0.00	0.00	3.10
189	191	5.602561	GGCATAAAAGGGAGGACCAATAATT	59.397	40.000	0.00	0.00	43.89	1.40
193	195	2.314549	TGGCATAAAAGGGAGGACCAAT	59.685	45.455	0.00	0.00	43.89	3.16
862	1029	7.446001	AACTAGGCTCATTTGAGAAAGAAAG	57.554	36.000	11.70	2.54	44.74	2.62
1099	1269	3.357079	CTGGGACACGCAGTTGGC	61.357	66.667	7.49	0.00	41.61	4.52
2373	2843	7.711339	AGAGAGAAAGTTCTACAATTTGAACGT	59.289	33.333	2.79	0.00	44.95	3.99
2387	2857	4.081420	TGTGATGCCCTAGAGAGAAAGTTC	60.081	45.833	0.00	0.00	0.00	3.01
2393	2863	6.560003	TTTTATTGTGATGCCCTAGAGAGA	57.440	37.500	0.00	0.00	0.00	3.10
2538	3009	2.365582	GGCGTTACTCATCCAATGGTT	58.634	47.619	0.00	0.00	0.00	3.67
3092	4627	9.271828	CTTTCTTTTGTGGGTATTTTGCTTTAT	57.728	29.630	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.