AutoCloner

Multiple sequence alignment - TraesCS3D01G458200

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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	TraesCS3D01G458200	chr3D	100.000	3326	0	0	1	3326	563597296	563593971	0.000000e+00	6143.0
1	TraesCS3D01G458200	chr3D	84.167	840	107	15	1754	2574	563446569	563445737	0.000000e+00	791.0
2	TraesCS3D01G458200	chr3D	86.207	464	41	12	877	1338	563447438	563446996	6.450000e-132	481.0
3	TraesCS3D01G458200	chr3D	90.878	296	27	0	1286	1581	563447000	563446705	6.690000e-107	398.0
4	TraesCS3D01G458200	chr3D	82.873	362	38	16	2968	3326	563445319	563444979	1.500000e-78	303.0
5	TraesCS3D01G458200	chr3D	90.045	221	22	0	1109	1329	563435829	563435609	1.510000e-73	287.0
6	TraesCS3D01G458200	chr3D	76.867	549	92	23	1062	1582	577028950	577029491	9.090000e-71	278.0
7	TraesCS3D01G458200	chr3D	76.531	294	63	5	1963	2254	568012516	568012805	4.440000e-34	156.0
8	TraesCS3D01G458200	chr3D	86.331	139	18	1	2347	2484	563433856	563433718	2.070000e-32	150.0
9	TraesCS3D01G458200	chr3D	86.667	105	12	2	2347	2450	563432832	563432729	7.540000e-22	115.0
10	TraesCS3D01G458200	chr3D	98.462	65	1	0	2527	2591	563594705	563594641	7.540000e-22	115.0
11	TraesCS3D01G458200	chr3D	98.462	65	1	0	2592	2656	563594770	563594706	7.540000e-22	115.0
12	TraesCS3D01G458200	chr3D	87.500	64	8	0	2189	2252	7596510	7596573	1.280000e-09	75.0
13	TraesCS3D01G458200	chr3B	95.308	2387	86	9	214	2591	751015903	751013534	0.000000e+00	3764.0
14	TraesCS3D01G458200	chr3B	95.257	738	30	3	2592	3326	751013598	751012863	0.000000e+00	1164.0
15	TraesCS3D01G458200	chr3B	79.279	444	86	6	1868	2309	750901067	750900628	4.170000e-79	305.0
16	TraesCS3D01G458200	chr3B	81.723	383	51	6	866	1229	751842880	751843262	5.390000e-78	302.0
17	TraesCS3D01G458200	chr3B	91.549	213	17	1	1	212	751016159	751015947	3.250000e-75	292.0
18	TraesCS3D01G458200	chr3B	78.412	403	68	10	1141	1526	751511284	751510884	9.220000e-61	244.0
19	TraesCS3D01G458200	chr3B	77.816	293	60	3	1957	2248	751166772	751167060	3.410000e-40	176.0
20	TraesCS3D01G458200	chr3A	95.480	2102	74	8	214	2314	698169652	698167571	0.000000e+00	3336.0
21	TraesCS3D01G458200	chr3A	96.216	740	21	4	2592	3326	698167275	698166538	0.000000e+00	1205.0
22	TraesCS3D01G458200	chr3A	98.940	283	1	2	2310	2591	698167492	698167211	3.830000e-139	505.0
23	TraesCS3D01G458200	chr3A	86.825	463	40	5	877	1338	698146645	698146203	6.410000e-137	497.0
24	TraesCS3D01G458200	chr3A	90.203	296	29	0	1286	1581	698146207	698145912	1.450000e-103	387.0
25	TraesCS3D01G458200	chr3A	96.226	212	7	1	1	212	698169906	698169696	2.460000e-91	346.0
26	TraesCS3D01G458200	chr3A	92.488	213	16	0	1109	1321	698032330	698032118	4.170000e-79	305.0
27	TraesCS3D01G458200	chr3A	83.099	142	19	3	2348	2484	698029859	698029718	1.250000e-24	124.0
28	TraesCS3D01G458200	chr6B	77.363	402	68	14	1135	1517	704550467	704550070	2.010000e-52	217.0
29	TraesCS3D01G458200	chr6A	73.383	402	81	14	1137	1522	115504994	115504603	3.480000e-25	126.0
30	TraesCS3D01G458200	chr4B	79.348	92	19	0	242	333	14537896	14537805	7.700000e-07	65.8
31	TraesCS3D01G458200	chr5B	97.143	35	1	0	299	333	567677695	567677661	3.580000e-05	60.2

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	TraesCS3D01G458200	chr3D	563593971	563597296	3325	True	2124.333333	6143	98.974667	1	3326	3	chr3D.!!$R3	3325
1	TraesCS3D01G458200	chr3D	563444979	563447438	2459	True	493.250000	791	86.031250	877	3326	4	chr3D.!!$R2	2449
2	TraesCS3D01G458200	chr3D	577028950	577029491	541	False	278.000000	278	76.867000	1062	1582	1	chr3D.!!$F3	520
3	TraesCS3D01G458200	chr3B	751012863	751016159	3296	True	1740.000000	3764	94.038000	1	3326	3	chr3B.!!$R3	3325
4	TraesCS3D01G458200	chr3A	698166538	698169906	3368	True	1348.000000	3336	96.715500	1	3326	4	chr3A.!!$R3	3325
5	TraesCS3D01G458200	chr3A	698145912	698146645	733	True	442.000000	497	88.514000	877	1581	2	chr3A.!!$R2	704
6	TraesCS3D01G458200	chr3A	698029718	698032330	2612	True	214.500000	305	87.793500	1109	2484	2	chr3A.!!$R1	1375

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
564	612	0.537188	TTTCAGTCTCCTCATCGGCC	59.463	55.0	0.0	0.0	0.0	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2539	3619	0.03392	ACAACAGAGAGACGCATGCA	59.966	50.0	19.57	0.0	0.0	3.96	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
260	304	2.121538	CCTCCGAGATGAGCACCGA	61.122	63.158	0.00	0.00	0.00	4.69
284	328	7.467811	CGAAAGAATCATCTTCAACCTATTGGG	60.468	40.741	0.00	0.00	45.19	4.12
337	381	7.478520	ACATTGCAAAGACTAATCGGTATAC	57.521	36.000	8.96	0.00	0.00	1.47
439	487	2.819984	AATCACGAACTGCCCCGCAT	62.820	55.000	0.00	0.00	38.13	4.73
456	504	3.692101	CCGCATACCTCATGTTTTACCAA	59.308	43.478	0.00	0.00	36.95	3.67
550	598	1.593196	TTGGAACAGCGAGGTTTCAG	58.407	50.000	1.61	0.00	42.39	3.02
564	612	0.537188	TTTCAGTCTCCTCATCGGCC	59.463	55.000	0.00	0.00	0.00	6.13
569	617	1.133325	AGTCTCCTCATCGGCCATAGT	60.133	52.381	2.24	0.00	0.00	2.12
665	713	2.978156	TCCATCAGAGGCAAAAAGGT	57.022	45.000	0.00	0.00	0.00	3.50
670	718	3.708563	TCAGAGGCAAAAAGGTTTTCG	57.291	42.857	0.00	0.00	0.00	3.46
846	899	1.562783	CTCCGTCTCTCCCCTTCTTT	58.437	55.000	0.00	0.00	0.00	2.52
852	905	2.640332	GTCTCTCCCCTTCTTTGGTTCT	59.360	50.000	0.00	0.00	0.00	3.01
887	940	5.633830	ATTTATCCACTCTGCTTGTGTTG	57.366	39.130	0.00	0.00	33.92	3.33
922	975	3.567397	GTGAGCAATCCCTCCTCTACTA	58.433	50.000	0.00	0.00	0.00	1.82
1090	1158	1.557269	TTCTCCCTCCTGCCAGAAGC	61.557	60.000	0.00	0.00	44.14	3.86
1864	2825	1.738830	CGCAAACGACCATACCCGT	60.739	57.895	0.00	0.00	43.93	5.28
1901	2862	0.247460	CGGTGGAGAAGTGCTGATCA	59.753	55.000	0.00	0.00	0.00	2.92
2237	3198	2.840038	TCCAGCTACACCATCAATGTCT	59.160	45.455	0.00	0.00	0.00	3.41
2495	3575	5.512753	TGCTAGCAAATTTCAGTTCAACA	57.487	34.783	16.84	0.00	0.00	3.33
2536	3616	1.003118	AGCCCTGCAACTGAATCGTTA	59.997	47.619	0.00	0.00	0.00	3.18
2537	3617	1.810151	GCCCTGCAACTGAATCGTTAA	59.190	47.619	0.00	0.00	0.00	2.01
2538	3618	2.227865	GCCCTGCAACTGAATCGTTAAA	59.772	45.455	0.00	0.00	0.00	1.52
2539	3619	3.119495	GCCCTGCAACTGAATCGTTAAAT	60.119	43.478	0.00	0.00	0.00	1.40
2540	3620	4.414852	CCCTGCAACTGAATCGTTAAATG	58.585	43.478	0.00	0.00	0.00	2.32
2541	3621	3.853671	CCTGCAACTGAATCGTTAAATGC	59.146	43.478	0.00	0.00	0.00	3.56
2542	3622	4.475028	CTGCAACTGAATCGTTAAATGCA	58.525	39.130	0.00	0.00	0.00	3.96
2543	3623	5.058149	TGCAACTGAATCGTTAAATGCAT	57.942	34.783	0.00	0.00	0.00	3.96
2544	3624	4.858140	TGCAACTGAATCGTTAAATGCATG	59.142	37.500	0.00	0.00	0.00	4.06
2545	3625	4.259530	GCAACTGAATCGTTAAATGCATGC	60.260	41.667	11.82	11.82	0.00	4.06
2546	3626	3.683989	ACTGAATCGTTAAATGCATGCG	58.316	40.909	14.09	3.37	0.00	4.73
2547	3627	3.126858	ACTGAATCGTTAAATGCATGCGT	59.873	39.130	14.09	10.53	0.00	5.24
2548	3628	3.679725	TGAATCGTTAAATGCATGCGTC	58.320	40.909	13.95	0.00	0.00	5.19
2549	3629	3.373748	TGAATCGTTAAATGCATGCGTCT	59.626	39.130	13.95	0.79	0.00	4.18
2550	3630	3.592381	ATCGTTAAATGCATGCGTCTC	57.408	42.857	13.95	3.48	0.00	3.36
2551	3631	2.616960	TCGTTAAATGCATGCGTCTCT	58.383	42.857	13.95	3.65	0.00	3.10
2552	3632	2.603110	TCGTTAAATGCATGCGTCTCTC	59.397	45.455	13.95	4.18	0.00	3.20
2553	3633	2.604914	CGTTAAATGCATGCGTCTCTCT	59.395	45.455	13.95	0.00	0.00	3.10
2554	3634	3.542875	CGTTAAATGCATGCGTCTCTCTG	60.543	47.826	13.95	0.00	0.00	3.35
2555	3635	2.105006	AAATGCATGCGTCTCTCTGT	57.895	45.000	13.95	0.00	0.00	3.41
2556	3636	2.105006	AATGCATGCGTCTCTCTGTT	57.895	45.000	13.95	0.00	0.00	3.16
2557	3637	1.366679	ATGCATGCGTCTCTCTGTTG	58.633	50.000	14.09	0.00	0.00	3.33
2558	3638	0.033920	TGCATGCGTCTCTCTGTTGT	59.966	50.000	14.09	0.00	0.00	3.32
2559	3639	1.151668	GCATGCGTCTCTCTGTTGTT	58.848	50.000	0.00	0.00	0.00	2.83
2560	3640	1.532868	GCATGCGTCTCTCTGTTGTTT	59.467	47.619	0.00	0.00	0.00	2.83
2561	3641	2.412065	GCATGCGTCTCTCTGTTGTTTC	60.412	50.000	0.00	0.00	0.00	2.78
2562	3642	1.865865	TGCGTCTCTCTGTTGTTTCC	58.134	50.000	0.00	0.00	0.00	3.13
2563	3643	1.138069	TGCGTCTCTCTGTTGTTTCCA	59.862	47.619	0.00	0.00	0.00	3.53
2564	3644	2.224281	TGCGTCTCTCTGTTGTTTCCAT	60.224	45.455	0.00	0.00	0.00	3.41
2565	3645	2.808543	GCGTCTCTCTGTTGTTTCCATT	59.191	45.455	0.00	0.00	0.00	3.16
2566	3646	3.994392	GCGTCTCTCTGTTGTTTCCATTA	59.006	43.478	0.00	0.00	0.00	1.90
2567	3647	4.631813	GCGTCTCTCTGTTGTTTCCATTAT	59.368	41.667	0.00	0.00	0.00	1.28
2568	3648	5.810587	GCGTCTCTCTGTTGTTTCCATTATA	59.189	40.000	0.00	0.00	0.00	0.98
2569	3649	6.480320	GCGTCTCTCTGTTGTTTCCATTATAT	59.520	38.462	0.00	0.00	0.00	0.86
2570	3650	7.011482	GCGTCTCTCTGTTGTTTCCATTATATT	59.989	37.037	0.00	0.00	0.00	1.28
2571	3651	8.883731	CGTCTCTCTGTTGTTTCCATTATATTT	58.116	33.333	0.00	0.00	0.00	1.40
2743	3827	0.765519	ACCTGGTTGTTCCCCGTAGT	60.766	55.000	0.00	0.00	34.77	2.73
3014	4203	0.614415	TTGCTTGGTTATGCAGGGGG	60.614	55.000	0.00	0.00	38.10	5.40
3077	4269	8.431222	AGATACTAGGTGAGAGTACGTAGATTT	58.569	37.037	11.25	0.00	39.94	2.17
3181	4376	3.376234	GGCCTAATTGGACCGACTTTAAC	59.624	47.826	0.00	0.00	38.13	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	4.142038	GGTTTCTTTAGGTGCTTTCTCCA	58.858	43.478	0.00	0.00	0.00	3.86
78	80	2.103941	TGCGCCTATGTGGATTGACATA	59.896	45.455	4.18	0.00	37.70	2.29
198	200	1.742268	AGGCTCGTACGTAAGAGGAAC	59.258	52.381	30.85	18.67	43.62	3.62
260	304	6.097412	GCCCAATAGGTTGAAGATGATTCTTT	59.903	38.462	0.00	0.00	39.14	2.52
284	328	2.496828	GATTGCAACCAGGGTGCTGC	62.497	60.000	30.04	18.00	33.78	5.25
327	371	7.217200	AGCTGATGTTACAATGTATACCGATT	58.783	34.615	0.00	0.00	0.00	3.34
337	381	2.868583	CTCCGGAGCTGATGTTACAATG	59.131	50.000	20.67	0.00	0.00	2.82
439	487	3.998341	GCTCGTTGGTAAAACATGAGGTA	59.002	43.478	0.00	0.00	0.00	3.08
456	504	0.099613	CTATCAGCGTCACTGCTCGT	59.900	55.000	0.00	0.00	45.23	4.18
550	598	1.271102	GACTATGGCCGATGAGGAGAC	59.729	57.143	0.00	0.00	45.00	3.36
564	612	1.132453	TCCAAGCTCACGACGACTATG	59.868	52.381	0.00	0.00	0.00	2.23
569	617	0.039437	GAACTCCAAGCTCACGACGA	60.039	55.000	0.00	0.00	0.00	4.20
846	899	8.531146	GGATAAATTTGGAGAATTGAAGAACCA	58.469	33.333	0.00	0.00	0.00	3.67
852	905	8.742777	CAGAGTGGATAAATTTGGAGAATTGAA	58.257	33.333	0.00	0.00	0.00	2.69
887	940	0.461693	GCTCACCAGATCAGCAGACC	60.462	60.000	0.00	0.00	33.06	3.85
922	975	1.071071	TGGAAACAACGGAATCGACCT	59.929	47.619	0.00	0.00	37.44	3.85
1069	1134	1.544825	TTCTGGCAGGAGGGAGAACG	61.545	60.000	15.73	0.00	0.00	3.95
1090	1158	2.974698	GCCGGATCCGCATCCTTG	60.975	66.667	29.12	14.01	46.20	3.61
1638	1787	4.737649	GCACCTCCTTTTCTTGGAAACTTG	60.738	45.833	0.00	0.00	32.61	3.16
1743	2684	2.113139	CAGAAACCCCGTGCCTGT	59.887	61.111	0.00	0.00	0.00	4.00
1901	2862	0.945099	CATCGCTGCAGCTTGATGAT	59.055	50.000	34.79	26.85	39.59	2.45
2054	3015	0.733729	AGGCGCTCAACGTAGTAGAG	59.266	55.000	7.64	0.00	45.00	2.43
2237	3198	1.377202	GCGGCAGTTGAGAATCCCA	60.377	57.895	0.00	0.00	0.00	4.37
2536	3616	2.105006	ACAGAGAGACGCATGCATTT	57.895	45.000	19.57	0.00	0.00	2.32
2537	3617	1.736126	CAACAGAGAGACGCATGCATT	59.264	47.619	19.57	2.99	0.00	3.56
2538	3618	1.338484	ACAACAGAGAGACGCATGCAT	60.338	47.619	19.57	0.36	0.00	3.96
2539	3619	0.033920	ACAACAGAGAGACGCATGCA	59.966	50.000	19.57	0.00	0.00	3.96
2540	3620	1.151668	AACAACAGAGAGACGCATGC	58.848	50.000	7.91	7.91	0.00	4.06
2541	3621	2.158449	GGAAACAACAGAGAGACGCATG	59.842	50.000	0.00	0.00	0.00	4.06
2542	3622	2.224281	TGGAAACAACAGAGAGACGCAT	60.224	45.455	0.00	0.00	37.44	4.73
2543	3623	1.138069	TGGAAACAACAGAGAGACGCA	59.862	47.619	0.00	0.00	37.44	5.24
2544	3624	1.865865	TGGAAACAACAGAGAGACGC	58.134	50.000	0.00	0.00	37.44	5.19
2584	3664	4.201841	TGCATTCAACGATTCAGCATACTG	60.202	41.667	0.00	0.00	45.95	2.74
2585	3665	3.940852	TGCATTCAACGATTCAGCATACT	59.059	39.130	0.00	0.00	0.00	2.12
2586	3666	4.277257	TGCATTCAACGATTCAGCATAC	57.723	40.909	0.00	0.00	0.00	2.39
2587	3667	4.790444	GCATGCATTCAACGATTCAGCATA	60.790	41.667	14.21	0.00	39.00	3.14
2588	3668	3.702330	CATGCATTCAACGATTCAGCAT	58.298	40.909	0.00	0.00	41.42	3.79
2589	3669	2.732912	GCATGCATTCAACGATTCAGCA	60.733	45.455	14.21	0.00	34.78	4.41
2590	3670	1.850441	GCATGCATTCAACGATTCAGC	59.150	47.619	14.21	0.00	0.00	4.26
2591	3671	2.106418	CGCATGCATTCAACGATTCAG	58.894	47.619	19.57	0.00	0.00	3.02
2592	3672	1.468127	ACGCATGCATTCAACGATTCA	59.532	42.857	19.57	0.00	32.38	2.57
2593	3673	2.104144	GACGCATGCATTCAACGATTC	58.896	47.619	19.57	0.86	32.38	2.52
2594	3674	1.739466	AGACGCATGCATTCAACGATT	59.261	42.857	19.57	0.00	32.38	3.34
2595	3675	1.328680	GAGACGCATGCATTCAACGAT	59.671	47.619	19.57	0.00	32.38	3.73
2596	3676	0.721154	GAGACGCATGCATTCAACGA	59.279	50.000	19.57	0.00	32.38	3.85
2597	3677	0.723414	AGAGACGCATGCATTCAACG	59.277	50.000	19.57	1.17	33.67	4.10
2598	3678	2.005451	AGAGAGACGCATGCATTCAAC	58.995	47.619	19.57	11.02	0.00	3.18
2599	3679	2.004733	CAGAGAGACGCATGCATTCAA	58.995	47.619	19.57	0.00	0.00	2.69
2600	3680	1.066645	ACAGAGAGACGCATGCATTCA	60.067	47.619	19.57	0.00	0.00	2.57
2987	4176	5.316167	CTGCATAACCAAGCAATATCCCTA	58.684	41.667	0.00	0.00	40.73	3.53
2988	4177	4.147321	CTGCATAACCAAGCAATATCCCT	58.853	43.478	0.00	0.00	40.73	4.20
3014	4203	5.416947	ACGTATGAGTTTGATGTTACTCCC	58.583	41.667	0.00	0.00	40.00	4.30
3077	4269	5.715434	AAAACGGCTAGCAGGAAAAATAA	57.285	34.783	19.27	0.00	0.00	1.40
3114	4307	4.703897	TGTCTGAATACCCATTCGAATCC	58.296	43.478	7.92	0.00	43.06	3.01
3181	4376	6.038825	ACATTGCCAATATTCAAATTGCATGG	59.961	34.615	0.00	0.00	35.85	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.