AutoCloner

Multiple sequence alignment - TraesCS3B01G282700

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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	TraesCS3B01G282700	chr3B	100.000	4014	0	0	1	4014	452858268	452862281	0.000000e+00	7413.0
1	TraesCS3B01G282700	chr4B	96.230	1857	51	12	1983	3824	24569343	24567491	0.000000e+00	3024.0
2	TraesCS3B01G282700	chr4B	91.066	1276	43	21	748	1983	24570618	24569374	0.000000e+00	1659.0
3	TraesCS3B01G282700	chr4B	88.934	488	41	6	144	619	24571110	24570624	1.240000e-164	590.0
4	TraesCS3B01G282700	chr4B	89.912	456	40	5	11	462	24571566	24571113	2.080000e-162	582.0
5	TraesCS3B01G282700	chr4B	94.059	202	8	2	3817	4014	24566719	24566518	1.810000e-78	303.0
6	TraesCS3B01G282700	chr4D	88.840	2025	124	35	1	1983	14670464	14668500	0.000000e+00	2394.0
7	TraesCS3B01G282700	chr4D	89.152	1945	123	35	46	1952	14604011	14605905	0.000000e+00	2342.0
8	TraesCS3B01G282700	chr4D	94.897	1313	55	7	1983	3288	14605968	14607275	0.000000e+00	2043.0
9	TraesCS3B01G282700	chr4D	91.494	1399	88	15	1984	3354	14668468	14667073	0.000000e+00	1895.0
10	TraesCS3B01G282700	chr4D	81.870	353	42	11	3450	3786	14607355	14607701	1.100000e-70	278.0
11	TraesCS3B01G282700	chr4D	80.114	352	44	13	3451	3786	14667045	14666704	5.180000e-59	239.0
12	TraesCS3B01G282700	chr4D	97.222	36	1	0	2000	2035	14605798	14605833	1.200000e-05	62.1
13	TraesCS3B01G282700	chr4D	97.222	36	1	0	2000	2035	14668645	14668610	1.200000e-05	62.1
14	TraesCS3B01G282700	chr4A	89.132	1785	98	38	845	2586	456479685	456481416	0.000000e+00	2134.0
15	TraesCS3B01G282700	chr4A	88.330	1808	115	41	845	2586	586730941	586732718	0.000000e+00	2082.0
16	TraesCS3B01G282700	chr4A	92.041	1269	88	8	2092	3354	586733305	586734566	0.000000e+00	1772.0
17	TraesCS3B01G282700	chr4A	90.701	1269	85	14	2092	3354	574193618	574194859	0.000000e+00	1659.0
18	TraesCS3B01G282700	chr4A	85.961	1332	125	33	2062	3354	456481431	456482739	0.000000e+00	1367.0
19	TraesCS3B01G282700	chr4A	81.301	369	43	14	2356	2710	574193264	574193620	3.950000e-70	276.0
20	TraesCS3B01G282700	chr4A	80.508	354	46	15	3451	3786	456482767	456483115	2.400000e-62	250.0
21	TraesCS3B01G282700	chr4A	86.473	207	20	7	3812	4014	456483600	456483802	1.880000e-53	220.0
22	TraesCS3B01G282700	chr4A	79.023	348	45	15	2378	2710	586732973	586733307	3.140000e-51	213.0
23	TraesCS3B01G282700	chr4A	94.444	36	2	0	2000	2035	586731971	586732006	5.600000e-04	56.5
24	TraesCS3B01G282700	chr1B	100.000	30	0	0	1364	1393	322421574	322421603	5.600000e-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	TraesCS3B01G282700	chr3B	452858268	452862281	4013	False	7413.000	7413	100.00000	1	4014	1	chr3B.!!$F1	4013
1	TraesCS3B01G282700	chr4B	24566518	24571566	5048	True	1231.600	3024	92.04020	11	4014	5	chr4B.!!$R1	4003
2	TraesCS3B01G282700	chr4D	14604011	14607701	3690	False	1181.275	2342	90.78525	46	3786	4	chr4D.!!$F1	3740
3	TraesCS3B01G282700	chr4D	14666704	14670464	3760	True	1147.525	2394	89.41750	1	3786	4	chr4D.!!$R1	3785
4	TraesCS3B01G282700	chr4A	586730941	586734566	3625	False	1030.875	2082	88.45950	845	3354	4	chr4A.!!$F3	2509
5	TraesCS3B01G282700	chr4A	456479685	456483802	4117	False	992.750	2134	85.51850	845	4014	4	chr4A.!!$F1	3169
6	TraesCS3B01G282700	chr4A	574193264	574194859	1595	False	967.500	1659	86.00100	2092	3354	2	chr4A.!!$F2	1262

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	Hairpin	End Stability	Orientation
584	920	0.177141	TAATTTCCTCTGCCCGTCCG	59.823	55.0	0.00	0.00	4.79	F
685	1023	0.463833	CCGGGGTTGGAATCTAGCAC	60.464	60.0	0.00	0.00	4.40	F
950	1317	0.618981	AAACCCATCCGGACTCTTCC	59.381	55.0	6.12	38.77	3.46	F
1776	2206	0.742281	CTGAGGTGCTGCGTAATGCT	60.742	55.0	0.00	46.63	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1543	1959	0.603707	TCAAACAGCTCAAGAGGGCG	60.604	55.000	0.00	0.00	6.13	R
1691	2118	0.721718	GAAAGATCACAAGTCGCCCG	59.278	55.000	0.00	0.00	6.13	R
1943	2386	1.542492	ACTACCAGTCTACCACACGG	58.458	55.000	0.00	38.77	4.94	R
3305	5453	1.880027	CAAAAGGAAACGGAGTCCAGG	59.120	52.381	10.49	45.00	4.45	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
42	44	3.294079	GCTTTTGCATGCACCTTGT	57.706	47.368	22.58	0.00	46.58	3.16
54	56	2.154462	GCACCTTGTAGTCACTTGCAT	58.846	47.619	0.00	0.00	0.00	3.96
114	116	2.571212	AGCCTTCACAACAATTGTCGA	58.429	42.857	12.39	6.39	43.23	4.20
276	281	2.276309	ATTGACTAGCCCTGCCCTGC	62.276	60.000	0.00	0.00	0.00	4.85
328	333	8.969267	GTTTACATGAATCTTAGACGGTATCTG	58.031	37.037	0.00	0.00	38.49	2.90
358	363	3.378399	GAGTCCTCCTGGAAGCCGC	62.378	68.421	0.00	0.00	45.18	6.53
428	433	2.737544	CCACATGTGGGATCATGGAAA	58.262	47.619	33.56	0.00	46.39	3.13
437	773	1.616725	GGATCATGGAAAGGGTGCACA	60.617	52.381	20.43	0.00	0.00	4.57
471	807	3.781307	CGAACCGGCCTGATGGGA	61.781	66.667	0.00	0.00	37.23	4.37
584	920	0.177141	TAATTTCCTCTGCCCGTCCG	59.823	55.000	0.00	0.00	0.00	4.79
593	930	3.845259	GCCCGTCCGCCACTATCA	61.845	66.667	0.00	0.00	0.00	2.15
630	967	3.566523	CAACGTAGTCACCACTCTTCTC	58.433	50.000	0.00	0.00	45.00	2.87
634	971	1.249407	AGTCACCACTCTTCTCGACC	58.751	55.000	0.00	0.00	0.00	4.79
646	983	3.056250	TCTTCTCGACCGTAGTGTCTACT	60.056	47.826	5.58	0.00	40.99	2.57
664	1001	8.221766	GTGTCTACTGTGAACTTTTAGTAATGC	58.778	37.037	0.00	0.00	0.00	3.56
685	1023	0.463833	CCGGGGTTGGAATCTAGCAC	60.464	60.000	0.00	0.00	0.00	4.40
689	1027	1.429148	GGTTGGAATCTAGCACGGCG	61.429	60.000	4.80	4.80	0.00	6.46
719	1057	7.501225	AGCATTGTACTAACACTGTTACCTTTT	59.499	33.333	0.00	0.00	38.26	2.27
789	1127	3.309193	GCCTTCCTCCATTTCTTAGGGTT	60.309	47.826	0.00	0.00	0.00	4.11
794	1132	5.959512	TCCTCCATTTCTTAGGGTTCAAAA	58.040	37.500	0.00	0.00	0.00	2.44
894	1255	3.068590	CACAGCTTGGAGAACCACAATTT	59.931	43.478	0.00	0.00	46.80	1.82
950	1317	0.618981	AAACCCATCCGGACTCTTCC	59.381	55.000	6.12	0.00	38.77	3.46
967	1336	4.599041	TCTTCCAGAGAGAGAGAAAGAGG	58.401	47.826	0.00	0.00	0.00	3.69
1568	1986	4.320788	CCCTCTTGAGCTGTTTGATTGAAC	60.321	45.833	0.00	0.00	0.00	3.18
1589	2007	2.490509	CCCCACGGGTTACTGAATTTTC	59.509	50.000	0.41	0.00	38.25	2.29
1676	2101	8.804688	ATTAAGCTGTCGATTCATCTTAGTAC	57.195	34.615	0.00	0.00	31.05	2.73
1691	2118	5.947443	TCTTAGTACCACTCTTAGTTTCGC	58.053	41.667	0.00	0.00	0.00	4.70
1739	2169	2.841442	ACTCCAGTGGTAGTTTGCTC	57.159	50.000	9.54	0.00	0.00	4.26
1776	2206	0.742281	CTGAGGTGCTGCGTAATGCT	60.742	55.000	0.00	0.00	46.63	3.79
1777	2207	1.020861	TGAGGTGCTGCGTAATGCTG	61.021	55.000	0.00	0.00	46.63	4.41
1815	2245	0.824759	ATAGTCGCCTCCTGTGTTCC	59.175	55.000	0.00	0.00	0.00	3.62
1881	2324	1.216178	GCATGTGTGGTTGCATCCC	59.784	57.895	11.33	3.66	38.72	3.85
2044	2551	4.626042	TGTGTGTTTGCATAAATTGACCC	58.374	39.130	0.00	0.00	0.00	4.46
2113	2622	2.267324	GAGGCTCACTCCAGTGGC	59.733	66.667	10.25	8.80	45.65	5.01
2431	4004	4.286032	AGCAGGTTGGTATTCAAGTCAGTA	59.714	41.667	0.00	0.00	35.80	2.74
2850	4992	5.692613	ATTTCAAAAATGTTGCACATGGG	57.307	34.783	0.00	0.00	37.97	4.00
2851	4993	3.123157	TCAAAAATGTTGCACATGGGG	57.877	42.857	0.00	0.00	37.97	4.96
3133	5277	4.780815	TCCAATCATCCCTGTTGATACAC	58.219	43.478	0.00	0.00	33.52	2.90
3219	5364	6.990798	TGGATCTATTGCTATGACTGAAGAG	58.009	40.000	0.00	0.00	0.00	2.85
3231	5376	9.766277	GCTATGACTGAAGAGACATTTTTAAAG	57.234	33.333	0.00	0.00	36.26	1.85
3235	5380	9.173021	TGACTGAAGAGACATTTTTAAAGTGAA	57.827	29.630	7.19	0.00	0.00	3.18
3305	5453	5.241662	ACTACAGAGAACCTTGCAGATTTC	58.758	41.667	0.00	0.00	0.00	2.17
3375	5523	3.253921	CACTGACAAACATGGATCTGCAA	59.746	43.478	0.00	0.00	0.00	4.08
3382	5530	5.769662	ACAAACATGGATCTGCAAACTTCTA	59.230	36.000	0.00	0.00	0.00	2.10
3391	5539	7.094805	TGGATCTGCAAACTTCTATGTTTACAC	60.095	37.037	0.00	0.00	37.98	2.90
3392	5540	7.119846	GGATCTGCAAACTTCTATGTTTACACT	59.880	37.037	0.00	0.00	37.98	3.55
3395	5543	7.715249	TCTGCAAACTTCTATGTTTACACTCTT	59.285	33.333	0.00	0.00	37.98	2.85
3786	5958	6.183360	GCTTTTTACACCCTCATTTTAATGCG	60.183	38.462	0.00	0.00	36.36	4.73
3805	5993	3.003275	TGCGAAGTGTGTCCTGATTTTTC	59.997	43.478	0.00	0.00	0.00	2.29
3809	5997	6.265577	CGAAGTGTGTCCTGATTTTTCTTTT	58.734	36.000	0.00	0.00	0.00	2.27
3887	6856	2.346766	TTCAGCTCAACCTTTCTGCA	57.653	45.000	0.00	0.00	0.00	4.41
3888	6857	2.574006	TCAGCTCAACCTTTCTGCAT	57.426	45.000	0.00	0.00	0.00	3.96
3889	6858	2.156917	TCAGCTCAACCTTTCTGCATG	58.843	47.619	0.00	0.00	0.00	4.06
3890	6859	2.156917	CAGCTCAACCTTTCTGCATGA	58.843	47.619	0.00	0.00	0.00	3.07
3892	6861	2.555757	AGCTCAACCTTTCTGCATGAAC	59.444	45.455	0.00	0.00	33.88	3.18
3893	6862	2.294233	GCTCAACCTTTCTGCATGAACA	59.706	45.455	0.00	0.00	33.88	3.18
3895	6864	4.543692	CTCAACCTTTCTGCATGAACAAG	58.456	43.478	0.00	0.00	33.88	3.16
3903	6876	0.528924	TGCATGAACAAGCCATCAGC	59.471	50.000	0.00	0.00	44.25	4.26
3914	6887	1.789078	GCCATCAGCGATGCCGAATT	61.789	55.000	11.51	0.00	38.59	2.17
3915	6888	0.040692	CCATCAGCGATGCCGAATTG	60.041	55.000	11.51	0.00	38.59	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	5.007528	GTGCATGCAAAAGCTTAAAGGAAAA	59.992	36.000	24.58	0.00	0.00	2.29
42	44	2.591923	TGCCCAAAATGCAAGTGACTA	58.408	42.857	0.00	0.00	35.40	2.59
54	56	7.564660	AGATCTTAACATATTCCATGCCCAAAA	59.435	33.333	0.00	0.00	0.00	2.44
103	105	5.065218	GCTGGAATCTACATCGACAATTGTT	59.935	40.000	13.36	0.00	0.00	2.83
114	116	0.759346	GGGTCCGCTGGAATCTACAT	59.241	55.000	0.00	0.00	31.38	2.29
165	167	9.149225	CAATCAATATAATCAGAGCTGGAGTAC	57.851	37.037	0.00	0.00	0.00	2.73
254	259	1.062121	AGGGCAGGGCTAGTCAATAGA	60.062	52.381	0.00	0.00	32.76	1.98
328	333	1.950973	GAGGACTCCTCCACCGCTTC	61.951	65.000	13.65	0.00	44.36	3.86
361	366	3.525268	ACTTGAAGCACAAAACAAGGG	57.475	42.857	0.00	0.00	42.39	3.95
471	807	0.243636	GTTATGGCGCCAAAAGCTGT	59.756	50.000	36.33	18.17	40.39	4.40
584	920	1.815421	CGGCTGTGGTGATAGTGGC	60.815	63.158	0.00	0.00	0.00	5.01
613	950	2.162008	GGTCGAGAAGAGTGGTGACTAC	59.838	54.545	0.00	0.00	30.16	2.73
630	967	2.071540	TCACAGTAGACACTACGGTCG	58.928	52.381	10.61	7.88	42.62	4.79
634	971	7.137426	ACTAAAAGTTCACAGTAGACACTACG	58.863	38.462	0.00	0.00	32.21	3.51
646	983	3.754323	CGGGGCATTACTAAAAGTTCACA	59.246	43.478	0.00	0.00	0.00	3.58
662	999	4.055227	GATTCCAACCCCGGGGCA	62.055	66.667	40.67	18.60	39.32	5.36
664	1001	1.837090	CTAGATTCCAACCCCGGGG	59.163	63.158	39.18	39.18	42.03	5.73
685	1023	3.368539	TGTTAGTACAATGCTTAACGCCG	59.631	43.478	0.00	0.00	38.05	6.46
723	1061	4.979815	CCGGCATTAAACGTTTTCTCTTTT	59.020	37.500	20.19	0.00	0.00	2.27
730	1068	2.510768	TTGCCGGCATTAAACGTTTT	57.489	40.000	33.25	0.00	0.00	2.43
732	1070	2.510768	TTTTGCCGGCATTAAACGTT	57.489	40.000	33.25	0.00	0.00	3.99
769	1107	5.179452	TGAACCCTAAGAAATGGAGGAAG	57.821	43.478	0.00	0.00	31.45	3.46
789	1127	8.352201	CCTCAAATCTGTGTAAAGATGTTTTGA	58.648	33.333	0.00	0.00	36.99	2.69
794	1132	5.182001	GTGCCTCAAATCTGTGTAAAGATGT	59.818	40.000	0.00	0.00	36.99	3.06
894	1255	2.828520	TGGTCAACTGGTTTGCTTTTCA	59.171	40.909	0.00	0.00	34.88	2.69
950	1317	2.364632	TCGCCTCTTTCTCTCTCTCTG	58.635	52.381	0.00	0.00	0.00	3.35
960	1329	4.800971	GCGTTTATTTTTCGCCTCTTTC	57.199	40.909	0.00	0.00	43.41	2.62
984	1354	0.463833	GCATCGGGGACTCGGAAATT	60.464	55.000	0.00	0.00	0.00	1.82
1543	1959	0.603707	TCAAACAGCTCAAGAGGGCG	60.604	55.000	0.00	0.00	0.00	6.13
1589	2007	5.196341	TGCTAGTATCCATCCAGTAAACG	57.804	43.478	0.00	0.00	0.00	3.60
1676	2101	1.359459	GCCCGCGAAACTAAGAGTGG	61.359	60.000	8.23	0.00	0.00	4.00
1691	2118	0.721718	GAAAGATCACAAGTCGCCCG	59.278	55.000	0.00	0.00	0.00	6.13
1739	2169	7.413438	GCACCTCAGAAATGTACATTTAGTCAG	60.413	40.741	29.07	21.21	40.77	3.51
1776	2206	5.827797	ACTATCAGCTTGTTTTTCCTTCACA	59.172	36.000	0.00	0.00	0.00	3.58
1777	2207	6.319141	ACTATCAGCTTGTTTTTCCTTCAC	57.681	37.500	0.00	0.00	0.00	3.18
1815	2245	9.236691	CCATCTATCGTTTTCCATGTAAAATTG	57.763	33.333	0.00	0.00	31.43	2.32
1881	2324	2.029828	ACCACTCTAGAGAACTTGCACG	60.030	50.000	26.57	4.36	0.00	5.34
1943	2386	1.542492	ACTACCAGTCTACCACACGG	58.458	55.000	0.00	0.00	38.77	4.94
2044	2551	4.039151	AGAGTGCTACGATGAACTGATG	57.961	45.455	0.00	0.00	0.00	3.07
2219	2728	8.359642	GCTAATCTGCAATTAAATATGTCCCAA	58.640	33.333	0.00	0.00	0.00	4.12
2850	4992	2.290641	CCAACCGCATTATCTACAAGCC	59.709	50.000	0.00	0.00	0.00	4.35
2851	4993	2.943033	ACCAACCGCATTATCTACAAGC	59.057	45.455	0.00	0.00	0.00	4.01
3231	5376	9.638239	TGCCTCTCAAATATAATTTTTGTTCAC	57.362	29.630	2.01	0.00	35.90	3.18
3268	5415	6.942532	TCTCTGTAGTTTGAAACAGCAAAT	57.057	33.333	11.02	0.00	42.31	2.32
3305	5453	1.880027	CAAAAGGAAACGGAGTCCAGG	59.120	52.381	10.49	0.00	45.00	4.45
3341	5489	4.153986	GTTTGTCAGTGATCAAGAATGCG	58.846	43.478	0.00	0.00	0.00	4.73
3425	5575	7.122048	CAGGTCTCTATATAGGGATGTCATCA	58.878	42.308	15.43	0.00	34.86	3.07
3641	5798	5.301551	ACTTGATGTGTTCAATGCCTAACAA	59.698	36.000	0.00	0.00	43.30	2.83
3786	5958	7.433425	CAGAAAAGAAAAATCAGGACACACTTC	59.567	37.037	0.00	0.00	0.00	3.01
3805	5993	1.961793	TCCGACCACCAACAGAAAAG	58.038	50.000	0.00	0.00	0.00	2.27
3809	5997	0.834612	AGTTTCCGACCACCAACAGA	59.165	50.000	0.00	0.00	0.00	3.41
3887	6856	1.674441	CATCGCTGATGGCTTGTTCAT	59.326	47.619	9.73	0.00	36.51	2.57
3888	6857	1.089112	CATCGCTGATGGCTTGTTCA	58.911	50.000	9.73	0.00	36.51	3.18
3889	6858	0.248377	GCATCGCTGATGGCTTGTTC	60.248	55.000	16.56	0.00	40.10	3.18
3890	6859	1.805254	GCATCGCTGATGGCTTGTT	59.195	52.632	16.56	0.00	40.10	2.83
3903	6876	0.248215	GGTTGAGCAATTCGGCATCG	60.248	55.000	0.00	0.00	35.83	3.84
3909	6882	4.155826	TGTGAAATAGGGTTGAGCAATTCG	59.844	41.667	0.00	0.00	0.00	3.34
3914	6887	4.922206	AGAATGTGAAATAGGGTTGAGCA	58.078	39.130	0.00	0.00	0.00	4.26
3915	6888	4.943705	TGAGAATGTGAAATAGGGTTGAGC	59.056	41.667	0.00	0.00	0.00	4.26
3990	6963	3.062466	CTCCGTGAGCCGAGGTCA	61.062	66.667	2.27	2.27	39.56	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.