AutoCloner

Multiple sequence alignment - TraesCS3B01G027500

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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	TraesCS3B01G027500	chr3B	100.000	3192	0	0	1	3192	11926748	11929939	0.000000e+00	5895
1	TraesCS3B01G027500	chr3B	90.633	790	69	5	1434	2220	11958358	11957571	0.000000e+00	1044
2	TraesCS3B01G027500	chr3B	94.549	587	30	2	1	587	150272511	150271927	0.000000e+00	905
3	TraesCS3B01G027500	chr3B	94.378	587	32	1	1	587	155596409	155596994	0.000000e+00	900
4	TraesCS3B01G027500	chr3B	93.898	590	34	2	1	590	154443139	154442552	0.000000e+00	889
5	TraesCS3B01G027500	chr3B	89.896	386	24	4	585	969	11959249	11958878	1.720000e-132	483
6	TraesCS3B01G027500	chrUn	96.748	2460	74	3	1	2455	36297690	36295232	0.000000e+00	4095
7	TraesCS3B01G027500	chrUn	90.339	797	67	4	1434	2220	36477680	36478476	0.000000e+00	1037
8	TraesCS3B01G027500	chrUn	94.208	587	32	2	1	587	233141548	233140964	0.000000e+00	894
9	TraesCS3B01G027500	chrUn	91.860	602	38	8	1787	2385	368221870	368221277	0.000000e+00	830
10	TraesCS3B01G027500	chrUn	90.323	620	41	9	585	1202	35514308	35514910	0.000000e+00	795
11	TraesCS3B01G027500	chrUn	88.986	572	55	8	803	1370	32300196	32299629	0.000000e+00	701
12	TraesCS3B01G027500	chrUn	83.182	660	57	21	2467	3097	35839794	35839160	3.600000e-154	555
13	TraesCS3B01G027500	chrUn	86.381	536	35	11	2465	2975	419490206	419489684	4.650000e-153	551
14	TraesCS3B01G027500	chrUn	91.729	399	21	2	1933	2319	32299031	32298633	7.790000e-151	544
15	TraesCS3B01G027500	chrUn	91.919	396	20	2	1933	2316	267483420	267483815	7.790000e-151	544
16	TraesCS3B01G027500	chrUn	86.248	509	45	11	2593	3097	32297989	32297502	2.180000e-146	529
17	TraesCS3B01G027500	chrUn	86.364	506	44	11	2593	3094	267484462	267484946	2.180000e-146	529
18	TraesCS3B01G027500	chrUn	88.489	417	41	7	958	1370	267482409	267482822	6.150000e-137	497
19	TraesCS3B01G027500	chrUn	89.896	386	24	4	585	969	36476810	36477181	1.720000e-132	483
20	TraesCS3B01G027500	chrUn	92.342	222	16	1	2971	3192	36441686	36441466	6.650000e-82	315
21	TraesCS3B01G027500	chrUn	86.772	189	22	3	3001	3187	36482336	36482523	1.160000e-49	207
22	TraesCS3B01G027500	chrUn	84.932	146	17	3	2793	2937	36482083	36482224	3.320000e-30	143
23	TraesCS3B01G027500	chrUn	86.290	124	12	3	2275	2393	36478607	36478730	2.580000e-26	130
24	TraesCS3B01G027500	chrUn	94.203	69	4	0	2386	2454	32298618	32298550	4.350000e-19	106
25	TraesCS3B01G027500	chrUn	93.056	72	5	0	2383	2454	267483830	267483901	4.350000e-19	106
26	TraesCS3B01G027500	chr3D	93.364	1085	54	4	1378	2461	5813366	5812299	0.000000e+00	1589
27	TraesCS3B01G027500	chr3D	89.924	794	62	9	585	1375	5814183	5813405	0.000000e+00	1007
28	TraesCS3B01G027500	chr3D	84.625	761	103	9	1442	2192	5862572	5863328	0.000000e+00	745
29	TraesCS3B01G027500	chr3D	83.939	660	54	25	2468	3097	5811920	5811283	4.590000e-163	584
30	TraesCS3B01G027500	chr3A	93.836	1022	46	3	1434	2455	15432050	15433054	0.000000e+00	1522
31	TraesCS3B01G027500	chr3A	88.611	799	68	13	585	1376	15430862	15431644	0.000000e+00	950
32	TraesCS3B01G027500	chr3A	94.530	585	30	2	1	585	646114530	646113948	0.000000e+00	902
33	TraesCS3B01G027500	chr3A	88.062	645	57	10	730	1370	12175370	12174742	0.000000e+00	747
34	TraesCS3B01G027500	chr3A	91.729	399	21	2	1933	2319	12174144	12173746	7.790000e-151	544
35	TraesCS3B01G027500	chr3A	86.248	509	45	11	2593	3097	12173102	12172615	2.180000e-146	529
36	TraesCS3B01G027500	chr3A	94.718	284	15	0	2909	3192	15434142	15434425	2.920000e-120	442
37	TraesCS3B01G027500	chr3A	90.647	278	20	3	2593	2864	15433870	15434147	6.510000e-97	364
38	TraesCS3B01G027500	chr3A	93.464	153	9	1	585	737	12175850	12175699	3.200000e-55	226
39	TraesCS3B01G027500	chr3A	92.771	83	3	2	2460	2542	15433443	15433522	2.010000e-22	117
40	TraesCS3B01G027500	chr3A	94.203	69	4	0	2386	2454	12173731	12173663	4.350000e-19	106
41	TraesCS3B01G027500	chr7D	93.237	1035	42	6	1434	2458	42194795	42193779	0.000000e+00	1498
42	TraesCS3B01G027500	chr7D	90.691	666	44	9	713	1376	42195566	42194917	0.000000e+00	870
43	TraesCS3B01G027500	chr7D	87.059	510	40	12	2593	3097	42193222	42192734	1.290000e-153	553
44	TraesCS3B01G027500	chr7D	77.114	402	49	25	2828	3191	560284907	560284511	3.250000e-45	193
45	TraesCS3B01G027500	chr1B	94.397	589	32	1	1	589	272894372	272894959	0.000000e+00	904
46	TraesCS3B01G027500	chr7B	94.530	585	31	1	1	585	47731524	47732107	0.000000e+00	902
47	TraesCS3B01G027500	chr7B	94.017	585	32	3	1	585	189489368	189489949	0.000000e+00	883
48	TraesCS3B01G027500	chr7B	84.928	763	106	6	1447	2206	40287313	40286557	0.000000e+00	763
49	TraesCS3B01G027500	chr7B	77.282	471	74	26	850	1291	608301756	608301290	2.460000e-61	246
50	TraesCS3B01G027500	chr7A	84.231	761	103	9	1446	2196	90481088	90480335	0.000000e+00	725

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	TraesCS3B01G027500	chr3B	11926748	11929939	3191	False	5895.000000	5895	100.000000	1	3192	1	chr3B.!!$F1	3191
1	TraesCS3B01G027500	chr3B	150271927	150272511	584	True	905.000000	905	94.549000	1	587	1	chr3B.!!$R1	586
2	TraesCS3B01G027500	chr3B	155596409	155596994	585	False	900.000000	900	94.378000	1	587	1	chr3B.!!$F2	586
3	TraesCS3B01G027500	chr3B	154442552	154443139	587	True	889.000000	889	93.898000	1	590	1	chr3B.!!$R2	589
4	TraesCS3B01G027500	chr3B	11957571	11959249	1678	True	763.500000	1044	90.264500	585	2220	2	chr3B.!!$R3	1635
5	TraesCS3B01G027500	chrUn	36295232	36297690	2458	True	4095.000000	4095	96.748000	1	2455	1	chrUn.!!$R2	2454
6	TraesCS3B01G027500	chrUn	233140964	233141548	584	True	894.000000	894	94.208000	1	587	1	chrUn.!!$R4	586
7	TraesCS3B01G027500	chrUn	368221277	368221870	593	True	830.000000	830	91.860000	1787	2385	1	chrUn.!!$R5	598
8	TraesCS3B01G027500	chrUn	35514308	35514910	602	False	795.000000	795	90.323000	585	1202	1	chrUn.!!$F1	617
9	TraesCS3B01G027500	chrUn	35839160	35839794	634	True	555.000000	555	83.182000	2467	3097	1	chrUn.!!$R1	630
10	TraesCS3B01G027500	chrUn	419489684	419490206	522	True	551.000000	551	86.381000	2465	2975	1	chrUn.!!$R6	510
11	TraesCS3B01G027500	chrUn	32297502	32300196	2694	True	470.000000	701	90.291500	803	3097	4	chrUn.!!$R7	2294
12	TraesCS3B01G027500	chrUn	267482409	267484946	2537	False	419.000000	544	89.957000	958	3094	4	chrUn.!!$F3	2136
13	TraesCS3B01G027500	chrUn	36476810	36482523	5713	False	400.000000	1037	87.645800	585	3187	5	chrUn.!!$F2	2602
14	TraesCS3B01G027500	chr3D	5811283	5814183	2900	True	1060.000000	1589	89.075667	585	3097	3	chr3D.!!$R1	2512
15	TraesCS3B01G027500	chr3D	5862572	5863328	756	False	745.000000	745	84.625000	1442	2192	1	chr3D.!!$F1	750
16	TraesCS3B01G027500	chr3A	646113948	646114530	582	True	902.000000	902	94.530000	1	585	1	chr3A.!!$R1	584
17	TraesCS3B01G027500	chr3A	15430862	15434425	3563	False	679.000000	1522	92.116600	585	3192	5	chr3A.!!$F1	2607
18	TraesCS3B01G027500	chr3A	12172615	12175850	3235	True	430.400000	747	90.741200	585	3097	5	chr3A.!!$R2	2512
19	TraesCS3B01G027500	chr7D	42192734	42195566	2832	True	973.666667	1498	90.329000	713	3097	3	chr7D.!!$R2	2384
20	TraesCS3B01G027500	chr1B	272894372	272894959	587	False	904.000000	904	94.397000	1	589	1	chr1B.!!$F1	588
21	TraesCS3B01G027500	chr7B	47731524	47732107	583	False	902.000000	902	94.530000	1	585	1	chr7B.!!$F1	584
22	TraesCS3B01G027500	chr7B	189489368	189489949	581	False	883.000000	883	94.017000	1	585	1	chr7B.!!$F2	584
23	TraesCS3B01G027500	chr7B	40286557	40287313	756	True	763.000000	763	84.928000	1447	2206	1	chr7B.!!$R1	759
24	TraesCS3B01G027500	chr7A	90480335	90481088	753	True	725.000000	725	84.231000	1446	2196	1	chr7A.!!$R1	750

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
1697	2556	2.358615	AGTCCGCATGCGCTTTCA	60.359	55.556	34.0	11.84	38.24	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2733	7220	0.464554	GTAACCCAGGCCTCTGCATC	60.465	60.0	0.0	0.0	39.61	3.91	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
1697	2556	2.358615	AGTCCGCATGCGCTTTCA	60.359	55.556	34.00	11.84	38.24	2.69
1863	2731	2.043450	CCTCGTCTCCCTCTGCCT	60.043	66.667	0.00	0.00	0.00	4.75
2094	2964	4.521062	GCTGCTCTCCGGCGACAT	62.521	66.667	9.30	0.00	35.83	3.06
2297	3260	2.892852	ACCACACATGTGCAAGCTAATT	59.107	40.909	25.68	0.00	44.34	1.40
2355	3323	8.311836	TCAGTAGTAATTTAACTAAGCAGCAGT	58.688	33.333	0.00	0.00	33.85	4.40
2357	3325	8.311836	AGTAGTAATTTAACTAAGCAGCAGTGA	58.688	33.333	0.00	0.00	33.85	3.41
2358	3326	7.979444	AGTAATTTAACTAAGCAGCAGTGAA	57.021	32.000	0.00	0.00	0.00	3.18
2359	3327	8.034058	AGTAATTTAACTAAGCAGCAGTGAAG	57.966	34.615	0.00	0.00	0.00	3.02
2360	3328	5.886960	ATTTAACTAAGCAGCAGTGAAGG	57.113	39.130	0.00	0.00	0.00	3.46
2361	3329	4.617253	TTAACTAAGCAGCAGTGAAGGA	57.383	40.909	0.00	0.00	0.00	3.36
2362	3330	3.710209	AACTAAGCAGCAGTGAAGGAT	57.290	42.857	0.00	0.00	0.00	3.24
2363	3331	3.710209	ACTAAGCAGCAGTGAAGGATT	57.290	42.857	0.00	0.00	0.00	3.01
2364	3332	4.826274	ACTAAGCAGCAGTGAAGGATTA	57.174	40.909	0.00	0.00	0.00	1.75
2365	3333	4.508662	ACTAAGCAGCAGTGAAGGATTAC	58.491	43.478	0.00	0.00	0.00	1.89
2366	3334	3.710209	AAGCAGCAGTGAAGGATTACT	57.290	42.857	0.00	0.00	0.00	2.24
2367	3335	4.826274	AAGCAGCAGTGAAGGATTACTA	57.174	40.909	0.00	0.00	0.00	1.82
2368	3336	4.130286	AGCAGCAGTGAAGGATTACTAC	57.870	45.455	0.00	0.00	0.00	2.73
2369	3337	3.772025	AGCAGCAGTGAAGGATTACTACT	59.228	43.478	0.00	0.00	0.00	2.57
2370	3338	3.868077	GCAGCAGTGAAGGATTACTACTG	59.132	47.826	0.00	0.00	39.95	2.74
2371	3339	4.437239	CAGCAGTGAAGGATTACTACTGG	58.563	47.826	0.00	0.00	35.58	4.00
2372	3340	3.118592	AGCAGTGAAGGATTACTACTGGC	60.119	47.826	0.00	0.00	36.06	4.85
2373	3341	3.118592	GCAGTGAAGGATTACTACTGGCT	60.119	47.826	0.00	0.00	36.06	4.75
2440	3427	6.833416	TGGTTAAGCTGTTTAGGCAATATCAT	59.167	34.615	6.19	0.00	0.00	2.45
2545	3944	0.320683	TGCCATTGTGGACAGAGTCG	60.321	55.000	0.00	0.00	40.96	4.18
2619	4315	6.364435	GGATCATGCTTCTTTCAAAGTTTGTC	59.636	38.462	15.08	1.16	0.00	3.18
2687	4383	5.175859	TGGTATTCGATGACTTGGAACTTC	58.824	41.667	0.00	0.00	0.00	3.01
2734	7221	4.638304	CATCACATGATGTAGATGCCTGA	58.362	43.478	18.14	3.66	45.10	3.86
2735	7222	4.968971	TCACATGATGTAGATGCCTGAT	57.031	40.909	0.00	0.00	0.00	2.90
2736	7223	4.638304	TCACATGATGTAGATGCCTGATG	58.362	43.478	0.00	0.00	0.00	3.07
2737	7224	3.188667	CACATGATGTAGATGCCTGATGC	59.811	47.826	0.00	0.00	41.77	3.91
2738	7225	8.653328	ATCACATGATGTAGATGCCTGATGCA	62.653	42.308	0.00	0.00	43.53	3.96
2747	7234	2.192443	CCTGATGCAGAGGCCTGG	59.808	66.667	12.00	2.48	40.72	4.45
2748	7235	2.192443	CTGATGCAGAGGCCTGGG	59.808	66.667	12.00	2.01	40.72	4.45
2749	7236	2.611800	TGATGCAGAGGCCTGGGT	60.612	61.111	12.00	0.00	40.72	4.51
2750	7237	2.207501	CTGATGCAGAGGCCTGGGTT	62.208	60.000	12.00	0.00	40.72	4.11
2751	7238	0.913934	TGATGCAGAGGCCTGGGTTA	60.914	55.000	12.00	0.00	40.72	2.85
2752	7239	0.464554	GATGCAGAGGCCTGGGTTAC	60.465	60.000	12.00	0.00	40.72	2.50
2753	7240	1.926426	ATGCAGAGGCCTGGGTTACC	61.926	60.000	12.00	0.00	40.72	2.85
2754	7241	2.998949	CAGAGGCCTGGGTTACCC	59.001	66.667	12.00	14.66	45.71	3.69
2809	7303	2.746904	CCATTGTCCAACATAGCGTCAA	59.253	45.455	0.00	0.00	0.00	3.18
2922	7421	3.663995	TTTCACAATGCAATGGACCTG	57.336	42.857	6.73	0.00	0.00	4.00
2996	7522	2.957402	TCTCAAGTCCCAAACTGCAT	57.043	45.000	0.00	0.00	38.58	3.96
3002	7528	5.626142	TCAAGTCCCAAACTGCATAAACTA	58.374	37.500	0.00	0.00	38.58	2.24
3055	7603	4.501559	CACCTGATAATGCGCATTCAAAAG	59.498	41.667	36.99	26.71	32.50	2.27
3085	7634	6.975197	TCGCAATCTTTTTGTGACATTTAACA	59.025	30.769	0.00	0.00	34.42	2.41
3187	7736	4.925054	ACATTGTATGCAACACAAAGATGC	59.075	37.500	20.14	0.00	45.38	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
498	501	1.302192	CAATGGGGTCGTGTCCGTT	60.302	57.895	0.00	0.00	35.01	4.44
499	502	2.345991	CAATGGGGTCGTGTCCGT	59.654	61.111	0.00	0.00	35.01	4.69
1118	1458	1.077787	GTCGGTGCCATGGATTCCA	60.078	57.895	18.40	8.08	38.19	3.53
2094	2964	3.695606	GGACGCTGAGGGTGAGCA	61.696	66.667	6.97	0.00	36.12	4.26
2177	3062	2.093973	ACTTACTTCACTGCATCCTCCG	60.094	50.000	0.00	0.00	0.00	4.63
2340	3303	4.617253	TCCTTCACTGCTGCTTAGTTAA	57.383	40.909	0.00	0.00	0.00	2.01
2355	3323	5.464069	TCCATAGCCAGTAGTAATCCTTCA	58.536	41.667	0.00	0.00	0.00	3.02
2357	3325	6.084738	TCATCCATAGCCAGTAGTAATCCTT	58.915	40.000	0.00	0.00	0.00	3.36
2358	3326	5.655394	TCATCCATAGCCAGTAGTAATCCT	58.345	41.667	0.00	0.00	0.00	3.24
2359	3327	6.552445	ATCATCCATAGCCAGTAGTAATCC	57.448	41.667	0.00	0.00	0.00	3.01
2360	3328	8.754080	ACTAATCATCCATAGCCAGTAGTAATC	58.246	37.037	0.00	0.00	0.00	1.75
2361	3329	8.671987	ACTAATCATCCATAGCCAGTAGTAAT	57.328	34.615	0.00	0.00	0.00	1.89
2362	3330	9.769677	ATACTAATCATCCATAGCCAGTAGTAA	57.230	33.333	0.00	0.00	0.00	2.24
2364	3332	9.769677	TTATACTAATCATCCATAGCCAGTAGT	57.230	33.333	0.00	0.00	0.00	2.73
2393	3378	7.464273	ACCATCAGATGCCAGAATAATCATAA	58.536	34.615	4.68	0.00	0.00	1.90
2473	3869	2.175322	GTCAAGCTTGCTCGCAGC	59.825	61.111	21.99	2.10	42.82	5.25
2477	3873	0.725686	CATCAGGTCAAGCTTGCTCG	59.274	55.000	21.99	9.76	0.00	5.03
2545	3944	3.664107	GGGGGAAAACTCTTTGAAATGC	58.336	45.455	0.00	0.00	0.00	3.56
2619	4315	5.653769	ACCAGGATTTATGTGAACCATGAAG	59.346	40.000	0.00	0.00	33.12	3.02
2687	4383	7.696035	TGCGCACAATCAGTTTATTAAACATAG	59.304	33.333	18.83	9.92	43.79	2.23
2730	7217	2.192443	CCAGGCCTCTGCATCAGG	59.808	66.667	0.00	7.38	39.61	3.86
2731	7218	2.192443	CCCAGGCCTCTGCATCAG	59.808	66.667	0.00	0.00	39.61	2.90
2732	7219	0.913934	TAACCCAGGCCTCTGCATCA	60.914	55.000	0.00	0.00	39.61	3.07
2733	7220	0.464554	GTAACCCAGGCCTCTGCATC	60.465	60.000	0.00	0.00	39.61	3.91
2734	7221	1.609783	GTAACCCAGGCCTCTGCAT	59.390	57.895	0.00	0.00	39.61	3.96
2735	7222	2.602676	GGTAACCCAGGCCTCTGCA	61.603	63.158	0.00	0.00	39.61	4.41
2736	7223	2.272471	GGTAACCCAGGCCTCTGC	59.728	66.667	0.00	0.00	39.61	4.26
2765	7252	6.099341	GGACACAACTGTTGTTCATCTTTTT	58.901	36.000	22.66	0.00	43.23	1.94
2766	7253	5.184864	TGGACACAACTGTTGTTCATCTTTT	59.815	36.000	22.66	0.00	43.23	2.27
2767	7254	4.704540	TGGACACAACTGTTGTTCATCTTT	59.295	37.500	22.66	2.62	43.23	2.52
2768	7255	4.269183	TGGACACAACTGTTGTTCATCTT	58.731	39.130	22.66	4.25	43.23	2.40
2769	7256	3.884895	TGGACACAACTGTTGTTCATCT	58.115	40.909	22.66	4.18	43.23	2.90
2770	7257	4.836125	ATGGACACAACTGTTGTTCATC	57.164	40.909	22.66	18.57	43.23	2.92
2771	7258	4.402155	ACAATGGACACAACTGTTGTTCAT	59.598	37.500	22.66	20.65	43.23	2.57
2922	7421	3.486383	TGGAGGTTGGACTGAATTTGTC	58.514	45.455	4.55	4.55	0.00	3.18
2996	7522	6.909550	AACTTGGGAAATGCACATAGTTTA	57.090	33.333	0.00	0.00	31.61	2.01
3002	7528	9.566432	TTTTAAATAAACTTGGGAAATGCACAT	57.434	25.926	0.00	0.00	0.00	3.21
3055	7603	3.975035	GTCACAAAAAGATTGCGAACCTC	59.025	43.478	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.