AutoCloner

Multiple sequence alignment - TraesCS2B01G028500

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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	TraesCS2B01G028500	chr2B	100.000	2609	0	0	1	2609	13239585	13236977	0.000000e+00	4819
1	TraesCS2B01G028500	chr2B	94.231	1976	45	22	676	2609	13166805	13164857	0.000000e+00	2953
2	TraesCS2B01G028500	chr2B	95.421	677	25	6	1	673	13169151	13168477	0.000000e+00	1074
3	TraesCS2B01G028500	chr2B	78.365	624	100	25	993	1609	151628154	151627559	3.170000e-99	372
4	TraesCS2B01G028500	chr2B	78.719	531	92	15	1082	1610	150948504	150947993	4.160000e-88	335
5	TraesCS2B01G028500	chr2B	90.000	210	21	0	2333	2542	610601337	610601546	3.310000e-69	272
6	TraesCS2B01G028500	chr2B	91.463	82	7	0	1086	1167	150985312	150985231	2.120000e-21	113
7	TraesCS2B01G028500	chr2D	84.980	506	48	12	2059	2542	637374030	637373531	3.020000e-134	488
8	TraesCS2B01G028500	chr2D	83.789	512	55	14	2053	2542	639296891	639297396	6.580000e-126	460
9	TraesCS2B01G028500	chr2D	82.353	527	83	8	1086	1610	99683453	99683971	1.420000e-122	449
10	TraesCS2B01G028500	chr2D	81.321	530	89	8	1080	1607	99703701	99704222	3.100000e-114	422
11	TraesCS2B01G028500	chr2D	79.092	617	98	18	998	1609	99737329	99736739	1.880000e-106	396
12	TraesCS2B01G028500	chr2D	77.673	636	105	19	982	1610	99723344	99723949	1.150000e-93	353
13	TraesCS2B01G028500	chr2A	80.713	617	104	15	997	1609	98603420	98604025	1.410000e-127	466
14	TraesCS2B01G028500	chr2A	80.935	535	88	12	1080	1610	98908049	98908573	6.720000e-111	411
15	TraesCS2B01G028500	chr2A	78.905	621	105	14	993	1609	99159800	99159202	5.230000e-107	398
16	TraesCS2B01G028500	chr2A	78.357	633	112	19	986	1610	98903061	98903676	1.130000e-103	387
17	TraesCS2B01G028500	chr3B	84.024	507	53	13	2059	2542	693647650	693648151	1.830000e-126	462
18	TraesCS2B01G028500	chr3B	82.051	507	64	19	2054	2542	141706879	141706382	8.690000e-110	407
19	TraesCS2B01G028500	chr6B	81.818	594	59	21	2059	2609	308517797	308517210	1.100000e-123	453
20	TraesCS2B01G028500	chr6B	86.337	344	47	0	2199	2542	32088523	32088866	2.450000e-100	375
21	TraesCS2B01G028500	chr6A	82.524	515	61	15	2051	2542	54007267	54007775	2.400000e-115	425
22	TraesCS2B01G028500	chr5A	82.617	512	59	16	2054	2542	709419406	709419910	2.400000e-115	425
23	TraesCS2B01G028500	chr5A	82.387	511	62	14	2054	2542	709416329	709415825	1.120000e-113	420
24	TraesCS2B01G028500	chr7B	82.087	508	60	10	2059	2542	13804946	13804446	3.130000e-109	405
25	TraesCS2B01G028500	chr3A	87.079	356	43	3	2185	2539	507598100	507598453	1.450000e-107	399
26	TraesCS2B01G028500	chr3D	83.939	330	32	8	2234	2542	519601721	519602050	1.960000e-76	296
27	TraesCS2B01G028500	chr3D	80.919	283	44	10	255	531	33209985	33209707	5.660000e-52	215
28	TraesCS2B01G028500	chr4A	81.329	316	55	4	219	531	512543183	512543497	1.200000e-63	254
29	TraesCS2B01G028500	chr5D	81.350	311	55	3	223	531	114976674	114976365	1.550000e-62	250
30	TraesCS2B01G028500	chr5D	79.743	311	55	7	220	525	354279861	354279554	4.370000e-53	219
31	TraesCS2B01G028500	chr4D	80.380	316	58	4	219	531	75046612	75046298	1.210000e-58	237
32	TraesCS2B01G028500	chr1A	81.034	290	49	6	221	508	533144705	533144990	2.610000e-55	226
33	TraesCS2B01G028500	chr1B	81.004	279	47	6	256	532	589068118	589068392	1.570000e-52	217
34	TraesCS2B01G028500	chr4B	78.914	313	61	5	222	531	107453331	107453021	9.460000e-50	207

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	TraesCS2B01G028500	chr2B	13236977	13239585	2608	True	4819.0	4819	100.000	1	2609	1	chr2B.!!$R1	2608
1	TraesCS2B01G028500	chr2B	13164857	13169151	4294	True	2013.5	2953	94.826	1	2609	2	chr2B.!!$R5	2608
2	TraesCS2B01G028500	chr2B	151627559	151628154	595	True	372.0	372	78.365	993	1609	1	chr2B.!!$R4	616
3	TraesCS2B01G028500	chr2B	150947993	150948504	511	True	335.0	335	78.719	1082	1610	1	chr2B.!!$R2	528
4	TraesCS2B01G028500	chr2D	639296891	639297396	505	False	460.0	460	83.789	2053	2542	1	chr2D.!!$F4	489
5	TraesCS2B01G028500	chr2D	99683453	99683971	518	False	449.0	449	82.353	1086	1610	1	chr2D.!!$F1	524
6	TraesCS2B01G028500	chr2D	99703701	99704222	521	False	422.0	422	81.321	1080	1607	1	chr2D.!!$F2	527
7	TraesCS2B01G028500	chr2D	99736739	99737329	590	True	396.0	396	79.092	998	1609	1	chr2D.!!$R1	611
8	TraesCS2B01G028500	chr2D	99723344	99723949	605	False	353.0	353	77.673	982	1610	1	chr2D.!!$F3	628
9	TraesCS2B01G028500	chr2A	98603420	98604025	605	False	466.0	466	80.713	997	1609	1	chr2A.!!$F1	612
10	TraesCS2B01G028500	chr2A	98908049	98908573	524	False	411.0	411	80.935	1080	1610	1	chr2A.!!$F3	530
11	TraesCS2B01G028500	chr2A	99159202	99159800	598	True	398.0	398	78.905	993	1609	1	chr2A.!!$R1	616
12	TraesCS2B01G028500	chr2A	98903061	98903676	615	False	387.0	387	78.357	986	1610	1	chr2A.!!$F2	624
13	TraesCS2B01G028500	chr3B	693647650	693648151	501	False	462.0	462	84.024	2059	2542	1	chr3B.!!$F1	483
14	TraesCS2B01G028500	chr6B	308517210	308517797	587	True	453.0	453	81.818	2059	2609	1	chr6B.!!$R1	550
15	TraesCS2B01G028500	chr6A	54007267	54007775	508	False	425.0	425	82.524	2051	2542	1	chr6A.!!$F1	491
16	TraesCS2B01G028500	chr5A	709419406	709419910	504	False	425.0	425	82.617	2054	2542	1	chr5A.!!$F1	488
17	TraesCS2B01G028500	chr5A	709415825	709416329	504	True	420.0	420	82.387	2054	2542	1	chr5A.!!$R1	488
18	TraesCS2B01G028500	chr7B	13804446	13804946	500	True	405.0	405	82.087	2059	2542	1	chr7B.!!$R1	483

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
547	552	0.179045	ATAGCAGATTCCGCACCCAC	60.179	55.0	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2026	3765	0.241213	GCAAAGCTTTCGGGAACTCC	59.759	55.0	9.23	0.0	0.0	3.85	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
80	83	4.154918	GCTCTGAAATTCAGTGATTTCGGT	59.845	41.667	24.06	4.40	45.85	4.69
194	199	9.888878	ATCGAAATTGCTGATATATTTTGACAG	57.111	29.630	0.00	0.00	35.56	3.51
249	254	0.250467	ACTCTGCGCCTTGTTGTGAT	60.250	50.000	4.18	0.00	0.00	3.06
253	258	3.867857	TCTGCGCCTTGTTGTGATAATA	58.132	40.909	4.18	0.00	0.00	0.98
254	259	4.257731	TCTGCGCCTTGTTGTGATAATAA	58.742	39.130	4.18	0.00	0.00	1.40
410	415	1.407936	TGGTTGAATGTTGTGGTGGG	58.592	50.000	0.00	0.00	0.00	4.61
448	453	2.153645	TGCATGTTAAGGTGAGCACTG	58.846	47.619	0.16	0.00	0.00	3.66
546	551	1.419381	TATAGCAGATTCCGCACCCA	58.581	50.000	0.00	0.00	0.00	4.51
547	552	0.179045	ATAGCAGATTCCGCACCCAC	60.179	55.000	0.00	0.00	0.00	4.61
666	671	3.660865	AGACGTGCGAAATACTTCCTTT	58.339	40.909	0.00	0.00	0.00	3.11
673	678	6.129457	CGTGCGAAATACTTCCTTTTCTTTTG	60.129	38.462	0.00	0.00	31.20	2.44
674	679	6.695713	GTGCGAAATACTTCCTTTTCTTTTGT	59.304	34.615	0.00	0.00	31.20	2.83
687	2361	6.865726	CCTTTTCTTTTGTTTTGTTTTTGGGG	59.134	34.615	0.00	0.00	0.00	4.96
706	2380	4.263905	TGGGGAAGATACTTTGCTTGTCAT	60.264	41.667	0.00	0.00	0.00	3.06
731	2405	1.018910	CAAACACCCGGTCGTTTTCT	58.981	50.000	14.06	0.00	33.14	2.52
732	2406	1.402613	CAAACACCCGGTCGTTTTCTT	59.597	47.619	14.06	0.00	33.14	2.52
733	2407	1.753930	AACACCCGGTCGTTTTCTTT	58.246	45.000	0.00	0.00	0.00	2.52
734	2408	2.618442	ACACCCGGTCGTTTTCTTTA	57.382	45.000	0.00	0.00	0.00	1.85
735	2409	2.916640	ACACCCGGTCGTTTTCTTTAA	58.083	42.857	0.00	0.00	0.00	1.52
736	2410	3.277715	ACACCCGGTCGTTTTCTTTAAA	58.722	40.909	0.00	0.00	0.00	1.52
737	2411	3.884693	ACACCCGGTCGTTTTCTTTAAAT	59.115	39.130	0.00	0.00	0.00	1.40
738	2412	4.338964	ACACCCGGTCGTTTTCTTTAAATT	59.661	37.500	0.00	0.00	0.00	1.82
739	2413	5.163530	ACACCCGGTCGTTTTCTTTAAATTT	60.164	36.000	0.00	0.00	0.00	1.82
740	2414	5.749588	CACCCGGTCGTTTTCTTTAAATTTT	59.250	36.000	0.00	0.00	0.00	1.82
782	2456	3.319137	TCTGGTAAGCCGATGATATGC	57.681	47.619	0.00	0.00	37.67	3.14
807	2497	1.955080	AGTATCTAGCTACCACGCACC	59.045	52.381	0.10	0.00	0.00	5.01
866	2556	1.482593	CTACGATTCTCAAGGCACCCT	59.517	52.381	0.00	0.00	33.87	4.34
878	2568	0.820871	GGCACCCTACTCTCTGTCTG	59.179	60.000	0.00	0.00	0.00	3.51
885	2575	3.199946	CCCTACTCTCTGTCTGTCTCTCT	59.800	52.174	0.00	0.00	0.00	3.10
886	2576	4.191544	CCTACTCTCTGTCTGTCTCTCTG	58.808	52.174	0.00	0.00	0.00	3.35
887	2577	3.788227	ACTCTCTGTCTGTCTCTCTGT	57.212	47.619	0.00	0.00	0.00	3.41
888	2578	3.674997	ACTCTCTGTCTGTCTCTCTGTC	58.325	50.000	0.00	0.00	0.00	3.51
1114	2825	1.620739	GGTCATCTCCAGCAGCTCCA	61.621	60.000	0.00	0.00	0.00	3.86
1627	3363	8.598041	ACATCTGATAACTTACTCCTCAAGTTT	58.402	33.333	5.85	0.00	42.18	2.66
1665	3404	0.944386	GAGTGATGTGCCGTTGTTGT	59.056	50.000	0.00	0.00	0.00	3.32
1666	3405	1.333619	GAGTGATGTGCCGTTGTTGTT	59.666	47.619	0.00	0.00	0.00	2.83
1667	3406	1.065401	AGTGATGTGCCGTTGTTGTTG	59.935	47.619	0.00	0.00	0.00	3.33
1687	3426	2.203294	AAAGCACGGGCCTTCGTT	60.203	55.556	5.73	0.00	41.86	3.85
1708	3447	1.742268	TGGATTGTGTGTGTGTGTGTG	59.258	47.619	0.00	0.00	0.00	3.82
1709	3448	1.742831	GGATTGTGTGTGTGTGTGTGT	59.257	47.619	0.00	0.00	0.00	3.72
1776	3515	3.054434	AGCTTCTATGTGTGCCCATAACA	60.054	43.478	0.00	0.00	0.00	2.41
2022	3761	9.557061	TCAATATCTCTTCCAGAATCAAATCAG	57.443	33.333	0.00	0.00	33.62	2.90
2026	3765	6.882656	TCTCTTCCAGAATCAAATCAGGTAG	58.117	40.000	0.00	0.00	0.00	3.18
2375	4139	0.030807	TCCTGGATCAGATCTGGGCA	60.031	55.000	22.42	3.84	32.44	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
236	241	7.416817	TCATCAATTATTATCACAACAAGGCG	58.583	34.615	0.00	0.00	0.00	5.52
249	254	9.598517	GTCAGCCCAAATTTTCATCAATTATTA	57.401	29.630	0.00	0.00	0.00	0.98
253	258	5.867330	TGTCAGCCCAAATTTTCATCAATT	58.133	33.333	0.00	0.00	0.00	2.32
254	259	5.486735	TGTCAGCCCAAATTTTCATCAAT	57.513	34.783	0.00	0.00	0.00	2.57
438	443	1.882912	TGAATGTGACAGTGCTCACC	58.117	50.000	17.58	7.84	40.02	4.02
509	514	8.700051	TCTGCTATATCTAAGAGAATAATGGCC	58.300	37.037	0.00	0.00	0.00	5.36
597	602	0.249699	TTTGAGCGAAACCTCAGCGA	60.250	50.000	0.00	0.00	42.34	4.93
598	603	0.164647	CTTTGAGCGAAACCTCAGCG	59.835	55.000	0.00	0.00	42.34	5.18
599	604	0.110010	GCTTTGAGCGAAACCTCAGC	60.110	55.000	0.00	0.00	42.34	4.26
600	605	1.229428	TGCTTTGAGCGAAACCTCAG	58.771	50.000	0.00	0.00	46.26	3.35
666	671	6.998673	TCTTCCCCAAAAACAAAACAAAAGAA	59.001	30.769	0.00	0.00	0.00	2.52
673	678	7.466725	GCAAAGTATCTTCCCCAAAAACAAAAC	60.467	37.037	0.00	0.00	0.00	2.43
674	679	6.540551	GCAAAGTATCTTCCCCAAAAACAAAA	59.459	34.615	0.00	0.00	0.00	2.44
687	2361	7.442364	TGCCTATATGACAAGCAAAGTATCTTC	59.558	37.037	0.00	0.00	0.00	2.87
706	2380	0.176219	CGACCGGGTGTTTGCCTATA	59.824	55.000	3.30	0.00	0.00	1.31
731	2405	9.284968	TCAACCACACTTTTTCCAAAATTTAAA	57.715	25.926	0.00	0.00	0.00	1.52
732	2406	8.848474	TCAACCACACTTTTTCCAAAATTTAA	57.152	26.923	0.00	0.00	0.00	1.52
733	2407	9.454859	AATCAACCACACTTTTTCCAAAATTTA	57.545	25.926	0.00	0.00	0.00	1.40
734	2408	7.936496	ATCAACCACACTTTTTCCAAAATTT	57.064	28.000	0.00	0.00	0.00	1.82
735	2409	7.936496	AATCAACCACACTTTTTCCAAAATT	57.064	28.000	0.00	0.00	0.00	1.82
736	2410	7.936496	AAATCAACCACACTTTTTCCAAAAT	57.064	28.000	0.00	0.00	0.00	1.82
737	2411	7.751768	AAAATCAACCACACTTTTTCCAAAA	57.248	28.000	0.00	0.00	0.00	2.44
738	2412	7.663493	AGAAAAATCAACCACACTTTTTCCAAA	59.337	29.630	12.98	0.00	43.55	3.28
739	2413	7.118971	CAGAAAAATCAACCACACTTTTTCCAA	59.881	33.333	12.98	0.00	43.55	3.53
740	2414	6.593382	CAGAAAAATCAACCACACTTTTTCCA	59.407	34.615	12.98	0.00	43.55	3.53
782	2456	3.188873	GCGTGGTAGCTAGATACTGTAGG	59.811	52.174	17.18	10.68	0.00	3.18
833	2523	4.375272	AGAATCGTAGCACATCAATCAGG	58.625	43.478	0.00	0.00	0.00	3.86
866	2556	4.619628	CGACAGAGAGACAGACAGAGAGTA	60.620	50.000	0.00	0.00	0.00	2.59
878	2568	0.107116	TAGGGAGCCGACAGAGAGAC	60.107	60.000	0.00	0.00	0.00	3.36
885	2575	2.108168	GCCATATATAGGGAGCCGACA	58.892	52.381	17.56	0.00	0.00	4.35
886	2576	2.108168	TGCCATATATAGGGAGCCGAC	58.892	52.381	17.56	0.00	0.00	4.79
887	2577	2.543037	TGCCATATATAGGGAGCCGA	57.457	50.000	17.56	0.00	0.00	5.54
888	2578	2.808202	GCATGCCATATATAGGGAGCCG	60.808	54.545	17.56	3.34	0.00	5.52
1114	2825	0.034896	ATCTCCTTGCACGGTTCGTT	59.965	50.000	9.36	0.00	38.32	3.85
1627	3363	5.045942	TCACTCCTTATTGTGGCTCAATGTA	60.046	40.000	21.52	10.60	45.14	2.29
1667	3406	4.056125	GAAGGCCCGTGCTTTGCC	62.056	66.667	0.00	0.00	45.70	4.52
1687	3426	2.163211	CACACACACACACACAATCCAA	59.837	45.455	0.00	0.00	0.00	3.53
1708	3447	1.226831	CCCCGCAAAACACACACAC	60.227	57.895	0.00	0.00	0.00	3.82
1709	3448	0.753479	ATCCCCGCAAAACACACACA	60.753	50.000	0.00	0.00	0.00	3.72
1844	3583	3.069729	GTCACCTCACCTGTATATCACCC	59.930	52.174	0.00	0.00	0.00	4.61
2022	3761	0.903236	AGCTTTCGGGAACTCCTACC	59.097	55.000	0.00	0.00	35.95	3.18
2026	3765	0.241213	GCAAAGCTTTCGGGAACTCC	59.759	55.000	9.23	0.00	0.00	3.85
2493	4258	1.123928	GGATTCCATCCGTGAGACCT	58.876	55.000	0.00	0.00	40.13	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.