AutoCloner

Multiple sequence alignment - TraesCS1B01G336800

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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	TraesCS1B01G336800	chr1B	100.000	2965	0	0	1	2965	563786343	563789307	0.000000e+00	5476.0
1	TraesCS1B01G336800	chr1B	90.484	1156	52	22	263	1384	563846617	563847748	0.000000e+00	1472.0
2	TraesCS1B01G336800	chr1B	89.879	988	67	16	1426	2396	563847838	563848809	0.000000e+00	1240.0
3	TraesCS1B01G336800	chr1B	84.354	588	50	17	2386	2965	563849090	563849643	3.360000e-149	538.0
4	TraesCS1B01G336800	chr1B	86.145	498	48	11	1441	1917	560788616	560788119	4.380000e-143	518.0
5	TraesCS1B01G336800	chr1B	85.010	507	50	12	1435	1928	561256355	561255862	2.660000e-135	492.0
6	TraesCS1B01G336800	chr1B	78.922	835	72	60	674	1462	561257572	561256796	3.460000e-129	472.0
7	TraesCS1B01G336800	chr1B	76.471	782	83	53	694	1442	561158147	561157434	6.130000e-87	331.0
8	TraesCS1B01G336800	chr1B	84.014	294	25	6	487	769	560789689	560789407	2.270000e-66	263.0
9	TraesCS1B01G336800	chr1B	95.000	80	4	0	1313	1392	561257002	561256923	3.100000e-25	126.0
10	TraesCS1B01G336800	chr1B	92.500	80	6	0	1313	1392	561157623	561157544	6.720000e-22	115.0
11	TraesCS1B01G336800	chrUn	93.383	2403	114	26	1	2389	305657433	305659804	0.000000e+00	3515.0
12	TraesCS1B01G336800	chrUn	94.098	1169	55	8	4	1161	394107542	394106377	0.000000e+00	1764.0
13	TraesCS1B01G336800	chrUn	91.357	914	51	17	1479	2389	342934773	342935661	0.000000e+00	1225.0
14	TraesCS1B01G336800	chrUn	86.124	418	41	11	2557	2965	7340209	7339800	4.540000e-118	435.0
15	TraesCS1B01G336800	chrUn	87.705	122	7	4	2386	2506	305660090	305660204	5.150000e-28	135.0
16	TraesCS1B01G336800	chrUn	87.705	122	7	4	2386	2506	342935947	342936061	5.150000e-28	135.0
17	TraesCS1B01G336800	chr1A	93.333	1545	80	13	1433	2965	514257494	514259027	0.000000e+00	2261.0
18	TraesCS1B01G336800	chr1A	88.417	1459	110	27	1	1442	514256024	514257440	0.000000e+00	1703.0
19	TraesCS1B01G336800	chr1A	88.595	491	43	7	1435	1912	512461177	512460687	4.260000e-163	584.0
20	TraesCS1B01G336800	chr1A	85.396	493	50	10	1441	1914	512039632	512039143	2.660000e-135	492.0
21	TraesCS1B01G336800	chr1A	76.786	840	80	67	648	1462	512462368	512461619	6.040000e-97	364.0
22	TraesCS1B01G336800	chr1A	84.965	286	22	10	487	762	511790997	511790723	1.350000e-68	270.0
23	TraesCS1B01G336800	chr1A	89.899	198	20	0	489	686	511636603	511636406	3.790000e-64	255.0
24	TraesCS1B01G336800	chr1A	89.500	200	21	0	487	686	512040681	512040482	1.360000e-63	254.0
25	TraesCS1B01G336800	chr1A	84.074	270	26	5	487	749	512018870	512018611	8.210000e-61	244.0
26	TraesCS1B01G336800	chr1A	95.000	80	4	0	1313	1392	512461825	512461746	3.100000e-25	126.0
27	TraesCS1B01G336800	chr1A	97.059	34	0	1	822	855	511636333	511636301	4.130000e-04	56.5
28	TraesCS1B01G336800	chr1D	91.607	1549	99	19	1433	2965	416986066	416987599	0.000000e+00	2111.0
29	TraesCS1B01G336800	chr1D	90.585	1487	87	19	1	1462	416930591	416932049	0.000000e+00	1921.0
30	TraesCS1B01G336800	chr1D	91.937	893	49	12	2085	2965	416933045	416933926	0.000000e+00	1229.0
31	TraesCS1B01G336800	chr1D	90.378	582	37	4	873	1442	416985438	416986012	0.000000e+00	747.0
32	TraesCS1B01G336800	chr1D	87.652	494	44	7	1433	1917	415145509	415145024	2.580000e-155	558.0
33	TraesCS1B01G336800	chr1D	86.056	502	48	13	1441	1920	415053228	415052727	1.220000e-143	520.0
34	TraesCS1B01G336800	chr1D	80.349	458	42	31	952	1395	414941847	414941424	1.340000e-78	303.0
35	TraesCS1B01G336800	chr1D	80.392	459	40	27	952	1395	415053888	415053465	1.340000e-78	303.0
36	TraesCS1B01G336800	chr1D	82.517	286	28	9	487	762	415059390	415059117	6.390000e-57	231.0
37	TraesCS1B01G336800	chr1D	74.510	459	67	26	952	1395	415058977	415058554	1.420000e-33	154.0
38	TraesCS1B01G336800	chr1D	86.207	145	11	5	694	829	415146668	415146524	6.620000e-32	148.0
39	TraesCS1B01G336800	chr1D	91.566	83	7	0	1313	1395	415146157	415146075	6.720000e-22	115.0
40	TraesCS1B01G336800	chr1D	93.220	59	4	0	1433	1491	416932086	416932144	1.460000e-13	87.9
41	TraesCS1B01G336800	chr1D	96.970	33	1	0	823	855	415053999	415053967	4.130000e-04	56.5

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	TraesCS1B01G336800	chr1B	563786343	563789307	2964	False	5476.000000	5476	100.000000	1	2965	1	chr1B.!!$F1	2964
1	TraesCS1B01G336800	chr1B	563846617	563849643	3026	False	1083.333333	1472	88.239000	263	2965	3	chr1B.!!$F2	2702
2	TraesCS1B01G336800	chr1B	560788119	560789689	1570	True	390.500000	518	85.079500	487	1917	2	chr1B.!!$R1	1430
3	TraesCS1B01G336800	chr1B	561255862	561257572	1710	True	363.333333	492	86.310667	674	1928	3	chr1B.!!$R3	1254
4	TraesCS1B01G336800	chr1B	561157434	561158147	713	True	223.000000	331	84.485500	694	1442	2	chr1B.!!$R2	748
5	TraesCS1B01G336800	chrUn	305657433	305660204	2771	False	1825.000000	3515	90.544000	1	2506	2	chrUn.!!$F1	2505
6	TraesCS1B01G336800	chrUn	394106377	394107542	1165	True	1764.000000	1764	94.098000	4	1161	1	chrUn.!!$R2	1157
7	TraesCS1B01G336800	chrUn	342934773	342936061	1288	False	680.000000	1225	89.531000	1479	2506	2	chrUn.!!$F2	1027
8	TraesCS1B01G336800	chr1A	514256024	514259027	3003	False	1982.000000	2261	90.875000	1	2965	2	chr1A.!!$F1	2964
9	TraesCS1B01G336800	chr1A	512039143	512040681	1538	True	373.000000	492	87.448000	487	1914	2	chr1A.!!$R4	1427
10	TraesCS1B01G336800	chr1A	512460687	512462368	1681	True	358.000000	584	86.793667	648	1912	3	chr1A.!!$R5	1264
11	TraesCS1B01G336800	chr1D	416985438	416987599	2161	False	1429.000000	2111	90.992500	873	2965	2	chr1D.!!$F2	2092
12	TraesCS1B01G336800	chr1D	416930591	416933926	3335	False	1079.300000	1921	91.914000	1	2965	3	chr1D.!!$F1	2964
13	TraesCS1B01G336800	chr1D	415052727	415053999	1272	True	293.166667	520	87.806000	823	1920	3	chr1D.!!$R2	1097
14	TraesCS1B01G336800	chr1D	415145024	415146668	1644	True	273.666667	558	88.475000	694	1917	3	chr1D.!!$R4	1223

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
469	510	0.107017	AGCCACTATGCGCCTGATTT	60.107	50.0	4.18	0.0	36.02	2.17	F
470	511	0.740737	GCCACTATGCGCCTGATTTT	59.259	50.0	4.18	0.0	0.00	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1462	2333	0.604073	TGTCCGCGAGATTGTGGTTA	59.396	50.0	8.23	0.00	40.48	2.85	R
2427	4270	0.693049	TGCCCCAAGAGAAGTTCTCC	59.307	55.0	25.93	12.27	44.42	3.71	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
113	114	4.712829	TCATTAACGGGTCAACTATGAGGA	59.287	41.667	0.00	0.00	35.88	3.71
173	176	8.827177	TTTAGCTAGAGAAAGATCGTCAAAAA	57.173	30.769	0.00	0.00	0.00	1.94
287	296	2.425592	GCAACCAGGCCCCAAAAC	59.574	61.111	0.00	0.00	0.00	2.43
293	311	0.407918	CCAGGCCCCAAAACTTAGGA	59.592	55.000	0.00	0.00	0.00	2.94
307	325	2.644798	ACTTAGGAAGCCAATCCAGTGT	59.355	45.455	3.88	0.00	42.27	3.55
350	368	3.190953	GTCCTTAGCGCCGAATACTATCT	59.809	47.826	2.29	0.00	0.00	1.98
353	371	1.617322	AGCGCCGAATACTATCTGGA	58.383	50.000	2.29	0.00	0.00	3.86
354	372	2.171840	AGCGCCGAATACTATCTGGAT	58.828	47.619	2.29	0.00	0.00	3.41
367	391	1.348064	TCTGGATGACGACCAAAGGT	58.652	50.000	0.00	0.00	39.44	3.50
467	508	0.319728	CTAGCCACTATGCGCCTGAT	59.680	55.000	4.18	0.00	36.02	2.90
468	509	0.758734	TAGCCACTATGCGCCTGATT	59.241	50.000	4.18	0.00	36.02	2.57
469	510	0.107017	AGCCACTATGCGCCTGATTT	60.107	50.000	4.18	0.00	36.02	2.17
470	511	0.740737	GCCACTATGCGCCTGATTTT	59.259	50.000	4.18	0.00	0.00	1.82
499	543	5.862924	TTTTGAAACGGAGATGCTCTTAG	57.137	39.130	0.00	0.00	0.00	2.18
547	591	6.536582	CAGCTAGGCATTGGACATATATACAC	59.463	42.308	0.00	0.00	0.00	2.90
554	598	4.465632	TGGACATATATACACGGGCATC	57.534	45.455	0.00	0.00	0.00	3.91
561	605	9.464714	GACATATATACACGGGCATCTATTTAG	57.535	37.037	0.00	0.00	0.00	1.85
571	615	7.387673	CACGGGCATCTATTTAGAACATGATTA	59.612	37.037	0.00	0.00	35.69	1.75
1024	1162	1.441729	GTCGATCGCCATCTTCCCA	59.558	57.895	11.09	0.00	0.00	4.37
1075	1213	2.134933	GCCCTACTTCCTCCTCGGG	61.135	68.421	0.00	0.00	34.79	5.14
1462	2333	0.102481	CCAACGCGCCATACTACTCT	59.898	55.000	5.73	0.00	0.00	3.24
1477	2354	2.279582	ACTCTAACCACAATCTCGCG	57.720	50.000	0.00	0.00	0.00	5.87
1672	3184	0.386113	GGAGATCGAGTTCTTCCCGG	59.614	60.000	0.00	0.00	0.00	5.73
1820	3342	1.210413	CTCCGATCAGTATCCGGCG	59.790	63.158	0.00	0.00	0.00	6.46
2007	3552	9.699703	CCCGTTTCTTTCCTTTTTAATTCATTA	57.300	29.630	0.00	0.00	0.00	1.90
2272	3819	1.841450	TTTGTTTTAACCGGCAAGCG	58.159	45.000	0.00	0.00	0.00	4.68
2431	4274	4.039092	GCAAGGGGCTGCAGGAGA	62.039	66.667	17.12	0.00	42.17	3.71
2432	4275	2.759114	CAAGGGGCTGCAGGAGAA	59.241	61.111	17.12	0.00	0.00	2.87
2435	4278	1.430369	AAGGGGCTGCAGGAGAACTT	61.430	55.000	17.12	0.00	0.00	2.66
2436	4279	1.377856	GGGGCTGCAGGAGAACTTC	60.378	63.158	17.12	0.00	0.00	3.01
2462	4307	1.069358	GGGCATAGTGAGTAGGACTGC	59.931	57.143	0.00	0.00	0.00	4.40
2476	4321	3.362706	AGGACTGCAGGAGAACGTAATA	58.637	45.455	19.93	0.00	0.00	0.98
2478	4323	4.406003	AGGACTGCAGGAGAACGTAATAAT	59.594	41.667	19.93	0.00	0.00	1.28
2487	4332	7.466050	GCAGGAGAACGTAATAATCTCAAAAGG	60.466	40.741	14.40	2.52	41.06	3.11
2507	4352	4.494591	AGGAAAAGTGAGTAGGAGGACTT	58.505	43.478	0.00	0.00	0.00	3.01
2532	4377	6.597672	TGGTGTCAGTGTGCTAAATAATAAGG	59.402	38.462	0.00	0.00	0.00	2.69
2681	4529	3.102097	GCTCCAAAATCGAGCCCG	58.898	61.111	0.00	0.00	45.76	6.13
2697	4545	1.502231	CCCGTAGCTTCATGGAATCG	58.498	55.000	0.00	0.00	0.00	3.34
2713	4561	5.483811	TGGAATCGCAAAGTGTAGTCATAA	58.516	37.500	0.00	0.00	0.00	1.90
2714	4562	6.112734	TGGAATCGCAAAGTGTAGTCATAAT	58.887	36.000	0.00	0.00	0.00	1.28
2715	4563	7.269316	TGGAATCGCAAAGTGTAGTCATAATA	58.731	34.615	0.00	0.00	0.00	0.98
2739	4594	7.138692	AGAAATGTCTCTTTTTCGAGAATGG	57.861	36.000	2.35	0.00	41.38	3.16
2772	4627	5.709164	CCCATGTGAGTTTCTTGATCTTTCT	59.291	40.000	0.00	0.00	0.00	2.52
2778	4633	7.331934	TGTGAGTTTCTTGATCTTTCTATTCCG	59.668	37.037	0.00	0.00	0.00	4.30
2780	4635	6.116126	AGTTTCTTGATCTTTCTATTCCGGG	58.884	40.000	0.00	0.00	0.00	5.73
2785	4640	4.777463	TGATCTTTCTATTCCGGGTTTCC	58.223	43.478	0.00	0.00	0.00	3.13
2928	4787	2.929641	TGGAGTTGTGTCATCTTGCAA	58.070	42.857	0.00	0.00	0.00	4.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.197282	CGTACTTATACTACGACTTCGAGTGA	59.803	42.308	5.47	0.00	43.02	3.41
8	9	6.188175	CCACACGTACTTATACTACGACTTC	58.812	44.000	13.59	0.00	39.50	3.01
93	94	5.687166	ATTCCTCATAGTTGACCCGTTAA	57.313	39.130	0.00	0.00	0.00	2.01
127	128	6.750660	AAAATTCCAATGCATCATATCCCA	57.249	33.333	0.00	0.00	0.00	4.37
173	176	1.726248	GGCGCGCTCAATTTGAAATTT	59.274	42.857	32.29	0.00	0.00	1.82
176	183	1.441849	CGGCGCGCTCAATTTGAAA	60.442	52.632	32.29	0.00	0.00	2.69
279	288	2.302587	TGGCTTCCTAAGTTTTGGGG	57.697	50.000	0.00	0.00	31.20	4.96
280	289	3.195610	GGATTGGCTTCCTAAGTTTTGGG	59.804	47.826	0.47	0.00	32.68	4.12
283	292	4.524328	CACTGGATTGGCTTCCTAAGTTTT	59.476	41.667	8.24	0.00	36.68	2.43
287	296	3.012518	CACACTGGATTGGCTTCCTAAG	58.987	50.000	8.24	2.02	36.68	2.18
293	311	1.321474	CACACACACTGGATTGGCTT	58.679	50.000	0.00	0.00	0.00	4.35
350	368	1.052617	TCACCTTTGGTCGTCATCCA	58.947	50.000	0.00	0.00	31.02	3.41
353	371	1.508632	CGTTCACCTTTGGTCGTCAT	58.491	50.000	0.00	0.00	31.02	3.06
354	372	1.155424	GCGTTCACCTTTGGTCGTCA	61.155	55.000	0.00	0.00	31.02	4.35
417	442	1.737838	CTTTGCAGTGCGGAGGATTA	58.262	50.000	11.20	0.00	0.00	1.75
499	543	4.549458	CAAAATCAACTGTGGATGTGGTC	58.451	43.478	0.00	0.00	0.00	4.02
547	591	6.808008	AATCATGTTCTAAATAGATGCCCG	57.192	37.500	0.00	0.00	31.40	6.13
561	605	6.915544	TGACTCAGAAGCATAATCATGTTC	57.084	37.500	0.00	0.00	34.40	3.18
1024	1162	0.565674	GGGAGGGAAGGAGAGGAGAT	59.434	60.000	0.00	0.00	0.00	2.75
1290	1464	2.284405	GGGTCCTCCTGGTCGGAA	60.284	66.667	8.64	0.00	42.53	4.30
1291	1465	4.393778	GGGGTCCTCCTGGTCGGA	62.394	72.222	3.85	3.85	40.30	4.55
1295	1469	2.606826	GTTCGGGGTCCTCCTGGT	60.607	66.667	0.00	0.00	42.31	4.00
1445	2316	2.223665	GGTTAGAGTAGTATGGCGCGTT	60.224	50.000	8.43	0.00	0.00	4.84
1446	2317	1.336125	GGTTAGAGTAGTATGGCGCGT	59.664	52.381	8.43	0.00	0.00	6.01
1447	2318	1.335810	TGGTTAGAGTAGTATGGCGCG	59.664	52.381	0.00	0.00	0.00	6.86
1462	2333	0.604073	TGTCCGCGAGATTGTGGTTA	59.396	50.000	8.23	0.00	40.48	2.85
1820	3342	4.657436	AGAACTCGTTCATGGATCTACC	57.343	45.455	11.90	0.00	41.84	3.18
2113	3659	7.083858	ACATACACATGAATTGAAAAGGTTCG	58.916	34.615	0.00	0.00	34.86	3.95
2166	3712	2.230266	CCCAATTTCCGAAAATGACCGT	59.770	45.455	10.03	0.00	35.27	4.83
2256	3803	3.837093	GCGCTTGCCGGTTAAAAC	58.163	55.556	1.90	0.00	37.44	2.43
2272	3819	3.120511	CGCTCCACTGTTTTCTTTCTAGC	60.121	47.826	0.00	0.00	0.00	3.42
2427	4270	0.693049	TGCCCCAAGAGAAGTTCTCC	59.307	55.000	25.93	12.27	44.42	3.71
2431	4274	2.912956	TCACTATGCCCCAAGAGAAGTT	59.087	45.455	0.00	0.00	0.00	2.66
2432	4275	2.503356	CTCACTATGCCCCAAGAGAAGT	59.497	50.000	0.00	0.00	0.00	3.01
2435	4278	2.254152	ACTCACTATGCCCCAAGAGA	57.746	50.000	0.00	0.00	0.00	3.10
2436	4279	2.366916	CCTACTCACTATGCCCCAAGAG	59.633	54.545	0.00	0.00	0.00	2.85
2462	4307	7.764443	TCCTTTTGAGATTATTACGTTCTCCTG	59.236	37.037	10.81	0.87	35.99	3.86
2476	4321	7.518188	TCCTACTCACTTTTCCTTTTGAGATT	58.482	34.615	4.51	0.00	38.19	2.40
2478	4323	6.464465	CCTCCTACTCACTTTTCCTTTTGAGA	60.464	42.308	4.51	0.00	38.19	3.27
2487	4332	4.040584	ACCAAGTCCTCCTACTCACTTTTC	59.959	45.833	0.00	0.00	0.00	2.29
2507	4352	6.597672	CCTTATTATTTAGCACACTGACACCA	59.402	38.462	0.00	0.00	0.00	4.17
2532	4377	4.319118	GCAAATGCTAGAATCGCTCTTACC	60.319	45.833	0.00	0.00	38.21	2.85
2583	4430	6.154203	TCATGTGTTCACCAAAAATAGCAA	57.846	33.333	0.37	0.00	0.00	3.91
2593	4440	5.320277	TGGTATCATTTCATGTGTTCACCA	58.680	37.500	0.37	0.00	0.00	4.17
2595	4442	7.134815	GCTATGGTATCATTTCATGTGTTCAC	58.865	38.462	0.00	0.00	34.96	3.18
2596	4443	6.827762	TGCTATGGTATCATTTCATGTGTTCA	59.172	34.615	0.00	0.00	34.96	3.18
2597	4444	7.227314	TCTGCTATGGTATCATTTCATGTGTTC	59.773	37.037	0.00	0.00	34.96	3.18
2681	4529	3.375299	ACTTTGCGATTCCATGAAGCTAC	59.625	43.478	0.00	0.00	0.00	3.58
2690	4538	3.394674	TGACTACACTTTGCGATTCCA	57.605	42.857	0.00	0.00	0.00	3.53
2697	4545	9.922305	GACATTTCTATTATGACTACACTTTGC	57.078	33.333	0.00	0.00	0.00	3.68
2713	4561	8.887717	CCATTCTCGAAAAAGAGACATTTCTAT	58.112	33.333	0.00	0.00	45.88	1.98
2714	4562	7.334421	CCCATTCTCGAAAAAGAGACATTTCTA	59.666	37.037	0.00	0.00	45.88	2.10
2715	4563	6.150140	CCCATTCTCGAAAAAGAGACATTTCT	59.850	38.462	0.00	0.00	45.88	2.52
2726	4574	4.324267	GAGAGTTCCCCATTCTCGAAAAA	58.676	43.478	0.00	0.00	33.96	1.94
2795	4652	4.928020	CGAGGATTGATACATGTGAGATGG	59.072	45.833	9.11	0.00	0.00	3.51
2848	4706	9.522804	AATAGAAAAACAATGCGACTACAAAAA	57.477	25.926	0.00	0.00	0.00	1.94
2889	4748	2.289195	CCAAACCGAGGTAGCTACAACA	60.289	50.000	24.75	0.00	0.00	3.33
2891	4750	2.232941	CTCCAAACCGAGGTAGCTACAA	59.767	50.000	24.75	0.00	0.00	2.41
2900	4759	1.226746	GACACAACTCCAAACCGAGG	58.773	55.000	0.00	0.00	33.93	4.63
2928	4787	8.737168	TCAAATTAGATGTCGAGGAAATGAAT	57.263	30.769	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.