AutoCloner

Multiple sequence alignment - TraesCS2B01G263100

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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	TraesCS2B01G263100	chr2B	100.000	3173	0	0	1	3173	352282711	352279539	0.000000e+00	5860.0
1	TraesCS2B01G263100	chr2D	97.650	1404	13	5	1019	2402	295807092	295808495	0.000000e+00	2392.0
2	TraesCS2B01G263100	chr2D	98.249	1028	14	2	1	1026	295806113	295807138	0.000000e+00	1796.0
3	TraesCS2B01G263100	chr2A	98.320	1250	21	0	1019	2268	364480893	364482142	0.000000e+00	2193.0
4	TraesCS2B01G263100	chr2A	95.644	1033	15	5	1	1026	364479930	364480939	0.000000e+00	1631.0
5	TraesCS2B01G263100	chr2A	95.862	145	4	1	2260	2402	364482860	364483004	1.900000e-57	233.0
6	TraesCS2B01G263100	chr2A	86.364	132	16	1	2220	2351	777680588	777680717	3.300000e-30	143.0
7	TraesCS2B01G263100	chr3B	94.961	774	22	3	2400	3173	684369445	684368689	0.000000e+00	1197.0
8	TraesCS2B01G263100	chr3B	74.830	294	60	11	1418	1701	141735636	141735925	1.550000e-23	121.0
9	TraesCS2B01G263100	chr6D	95.333	450	18	2	1	449	437412721	437413168	0.000000e+00	712.0
10	TraesCS2B01G263100	chr6B	94.222	450	23	2	1	449	662169013	662169460	0.000000e+00	684.0
11	TraesCS2B01G263100	chr6B	92.177	294	21	1	129	422	662235932	662236223	6.330000e-112	414.0
12	TraesCS2B01G263100	chr6B	96.947	131	4	0	1	131	662223458	662223588	1.480000e-53	220.0
13	TraesCS2B01G263100	chr6B	100.000	29	0	0	436	464	662180829	662180857	2.000000e-03	54.7
14	TraesCS2B01G263100	chr6A	94.000	450	23	3	1	449	585797971	585798417	0.000000e+00	678.0
15	TraesCS2B01G263100	chr3D	82.353	187	22	5	2223	2400	571901822	571902006	5.480000e-33	152.0
16	TraesCS2B01G263100	chr3D	95.833	48	2	0	1526	1573	91696365	91696412	9.440000e-11	78.7
17	TraesCS2B01G263100	chr4B	83.333	156	14	10	739	888	49740259	49740408	1.990000e-27	134.0
18	TraesCS2B01G263100	chr4B	82.482	137	18	5	755	887	438375334	438375200	7.190000e-22	115.0
19	TraesCS2B01G263100	chr7A	81.212	165	22	7	754	912	427814849	427815010	1.200000e-24	124.0
20	TraesCS2B01G263100	chr5D	83.088	136	18	3	753	884	220683187	220683321	5.560000e-23	119.0
21	TraesCS2B01G263100	chr3A	80.000	160	28	4	1418	1575	545257734	545257891	7.190000e-22	115.0
22	TraesCS2B01G263100	chr4A	81.884	138	17	7	751	884	136431368	136431501	3.350000e-20	110.0
23	TraesCS2B01G263100	chr7B	82.171	129	19	3	762	887	369872865	369872738	1.200000e-19	108.0
24	TraesCS2B01G263100	chr4D	81.752	137	18	6	755	887	442168736	442168603	1.200000e-19	108.0

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	TraesCS2B01G263100	chr2B	352279539	352282711	3172	True	5860.000000	5860	100.000000	1	3173	1	chr2B.!!$R1	3172
1	TraesCS2B01G263100	chr2D	295806113	295808495	2382	False	2094.000000	2392	97.949500	1	2402	2	chr2D.!!$F1	2401
2	TraesCS2B01G263100	chr2A	364479930	364483004	3074	False	1352.333333	2193	96.608667	1	2402	3	chr2A.!!$F2	2401
3	TraesCS2B01G263100	chr3B	684368689	684369445	756	True	1197.000000	1197	94.961000	2400	3173	1	chr3B.!!$R1	773

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
514	515	0.333993	TACAGCCTTACCCGAGGACT	59.666	55.000	0.00	0.0	39.25	3.85	F
1007	1017	2.040544	GGACACCGTTGATGGCCTG	61.041	63.158	3.32	0.0	42.62	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2046	2061	1.539124	GAACTCCCTCACCCCCACT	60.539	63.158	0.0	0.0	0.00	4.00	R
2983	3742	0.394488	TGACCTCTCTGGCTCTACCG	60.394	60.000	0.0	0.0	43.94	4.02	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
315	316	1.279496	CTGGGGATGGAGTCACTGAA	58.721	55.000	0.00	0.00	0.00	3.02
406	407	0.667487	ACGTCTGCATCTGACCAACG	60.667	55.000	0.00	0.00	35.00	4.10
514	515	0.333993	TACAGCCTTACCCGAGGACT	59.666	55.000	0.00	0.00	39.25	3.85
740	748	4.677584	AGCGTTCTTGCTCTATACTCTTG	58.322	43.478	0.00	0.00	42.95	3.02
760	768	9.302345	ACTCTTGTTGTAACAGTCATATATTCG	57.698	33.333	0.00	0.00	40.50	3.34
823	831	4.753233	TGGACCAAACACAAACTGAAATG	58.247	39.130	0.00	0.00	0.00	2.32
849	857	7.322664	AGTGAACAAACACACTGAAATGAAAT	58.677	30.769	0.00	0.00	44.18	2.17
891	899	8.747538	AAAAAGTTACAACATCTTGTAGGAGT	57.252	30.769	0.00	0.00	42.56	3.85
892	900	9.841295	AAAAAGTTACAACATCTTGTAGGAGTA	57.159	29.630	0.00	0.00	42.56	2.59
1001	1011	4.752879	CCGCCGGACACCGTTGAT	62.753	66.667	5.05	0.00	46.80	2.57
1002	1012	3.487202	CGCCGGACACCGTTGATG	61.487	66.667	5.05	0.00	46.80	3.07
1003	1013	3.124921	GCCGGACACCGTTGATGG	61.125	66.667	5.05	0.00	46.80	3.51
1004	1014	3.124921	CCGGACACCGTTGATGGC	61.125	66.667	0.00	0.00	46.80	4.40
1005	1015	3.124921	CGGACACCGTTGATGGCC	61.125	66.667	0.00	0.00	42.73	5.36
1006	1016	2.351276	GGACACCGTTGATGGCCT	59.649	61.111	3.32	0.00	42.62	5.19
1007	1017	2.040544	GGACACCGTTGATGGCCTG	61.041	63.158	3.32	0.00	42.62	4.85
1008	1018	2.672996	ACACCGTTGATGGCCTGC	60.673	61.111	3.32	0.00	0.00	4.85
1009	1019	2.672651	CACCGTTGATGGCCTGCA	60.673	61.111	3.32	0.00	0.00	4.41
1010	1020	2.672996	ACCGTTGATGGCCTGCAC	60.673	61.111	3.32	0.00	0.00	4.57
1011	1021	3.443045	CCGTTGATGGCCTGCACC	61.443	66.667	3.32	0.00	0.00	5.01
1012	1022	2.672651	CGTTGATGGCCTGCACCA	60.673	61.111	3.32	0.00	45.82	4.17
1013	1023	2.693762	CGTTGATGGCCTGCACCAG	61.694	63.158	3.32	0.00	44.71	4.00
1014	1024	2.677524	TTGATGGCCTGCACCAGC	60.678	61.111	3.32	4.71	46.52	4.85
1632	1647	2.358615	GGCGACACATGGCTGACA	60.359	61.111	0.00	0.00	0.00	3.58
2100	2115	1.084370	GCTTCTTCACCATCGACCCG	61.084	60.000	0.00	0.00	0.00	5.28
2486	3245	2.265683	GACCGTCCGATGGTTTTACTC	58.734	52.381	13.71	0.00	37.69	2.59
2505	3264	2.863137	CTCCTGAACGAATTAGCTGCTC	59.137	50.000	4.91	0.00	0.00	4.26
2655	3414	0.611200	TTACTGTGTGGGGACGATGG	59.389	55.000	0.00	0.00	0.00	3.51
2695	3454	0.917333	TCAACCAGTCCCCCATACCC	60.917	60.000	0.00	0.00	0.00	3.69
2696	3455	1.621514	AACCAGTCCCCCATACCCC	60.622	63.158	0.00	0.00	0.00	4.95
2732	3491	3.775654	CCGCTCCCCACTCTCCAC	61.776	72.222	0.00	0.00	0.00	4.02
2733	3492	4.135153	CGCTCCCCACTCTCCACG	62.135	72.222	0.00	0.00	0.00	4.94
2734	3493	3.775654	GCTCCCCACTCTCCACGG	61.776	72.222	0.00	0.00	0.00	4.94
2735	3494	3.775654	CTCCCCACTCTCCACGGC	61.776	72.222	0.00	0.00	0.00	5.68
2736	3495	4.316823	TCCCCACTCTCCACGGCT	62.317	66.667	0.00	0.00	0.00	5.52
2737	3496	3.775654	CCCCACTCTCCACGGCTC	61.776	72.222	0.00	0.00	0.00	4.70
2738	3497	3.775654	CCCACTCTCCACGGCTCC	61.776	72.222	0.00	0.00	0.00	4.70
2739	3498	3.775654	CCACTCTCCACGGCTCCC	61.776	72.222	0.00	0.00	0.00	4.30
2795	3554	3.626924	AGAACCGCAGCTCCCGTT	61.627	61.111	3.00	0.00	0.00	4.44
2831	3590	2.696125	GAGGAGCCCCCATCCCAA	60.696	66.667	0.00	0.00	37.57	4.12
2916	3675	0.688087	GATCGAGGAGGGAGGGTGTT	60.688	60.000	0.00	0.00	0.00	3.32
2944	3703	1.152715	GAGAGGGGAGACGTAGGGG	60.153	68.421	0.00	0.00	0.00	4.79
2960	3719	3.017581	GGGGTGGAGGTCAGGCAT	61.018	66.667	0.00	0.00	0.00	4.40
2963	3722	2.359169	GGTGGAGGTCAGGCATCGA	61.359	63.158	0.00	0.00	0.00	3.59
2966	3725	0.977627	TGGAGGTCAGGCATCGACAT	60.978	55.000	0.00	0.00	34.97	3.06
3003	3762	1.398692	GGTAGAGCCAGAGAGGTCAG	58.601	60.000	0.00	0.00	40.61	3.51
3025	3784	1.524621	GGTCGGCATGGATGTCCTG	60.525	63.158	0.09	0.00	36.82	3.86
3028	3787	2.599597	GGCATGGATGTCCTGCCT	59.400	61.111	23.65	0.00	46.97	4.75
3094	3853	1.417592	CGTCGAAGTGCAGCATCAC	59.582	57.895	0.00	0.67	37.24	3.06
3121	3880	6.150140	GTGATGTGTATGGCTTCTCTCTTTTT	59.850	38.462	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
315	316	4.200092	GGCCTTTATCCTTTTCATCGTCT	58.800	43.478	0.00	0.00	0.00	4.18
514	515	7.234661	TGTAACTCATGTAGTATGTGTTGGA	57.765	36.000	14.17	2.47	37.50	3.53
740	748	6.129168	CGGAGCGAATATATGACTGTTACAAC	60.129	42.308	0.00	0.00	0.00	3.32
760	768	5.641209	AGCATCTCATATTTATGAACGGAGC	59.359	40.000	2.18	3.13	41.72	4.70
823	831	5.879237	TCATTTCAGTGTGTTTGTTCACTC	58.121	37.500	0.00	0.00	42.05	3.51
993	1003	2.672996	GTGCAGGCCATCAACGGT	60.673	61.111	5.01	0.00	0.00	4.83
994	1004	3.443045	GGTGCAGGCCATCAACGG	61.443	66.667	5.01	0.00	0.00	4.44
995	1005	2.672651	TGGTGCAGGCCATCAACG	60.673	61.111	5.01	0.00	29.80	4.10
996	1006	2.998279	GCTGGTGCAGGCCATCAAC	61.998	63.158	5.01	5.27	37.96	3.18
997	1007	2.677524	GCTGGTGCAGGCCATCAA	60.678	61.111	5.01	0.00	37.96	2.57
998	1008	3.969119	TGCTGGTGCAGGCCATCA	61.969	61.111	5.01	0.00	45.31	3.07
1028	1038	3.771160	AGGCCATCGACGGTGTCC	61.771	66.667	5.01	3.19	0.00	4.02
1029	1039	2.509336	CAGGCCATCGACGGTGTC	60.509	66.667	5.01	0.00	0.00	3.67
1030	1040	4.760047	GCAGGCCATCGACGGTGT	62.760	66.667	5.01	0.00	0.00	4.16
1031	1041	4.758251	TGCAGGCCATCGACGGTG	62.758	66.667	5.01	0.00	0.00	4.94
1032	1042	4.760047	GTGCAGGCCATCGACGGT	62.760	66.667	5.01	0.00	0.00	4.83
1106	1121	1.002250	CAGTGGAGTACGTGACGTGC	61.002	60.000	22.16	20.15	41.39	5.34
1632	1647	1.946475	GAGTAAAGTCGGCGGCCTCT	61.946	60.000	18.34	12.28	0.00	3.69
2046	2061	1.539124	GAACTCCCTCACCCCCACT	60.539	63.158	0.00	0.00	0.00	4.00
2486	3245	1.590238	CGAGCAGCTAATTCGTTCAGG	59.410	52.381	0.00	0.00	0.00	3.86
2655	3414	3.754068	GGTTTCACCCCACGTTCC	58.246	61.111	0.00	0.00	30.04	3.62
2695	3454	3.917760	GAGGAGGATGGACGCGGG	61.918	72.222	12.47	0.00	0.00	6.13
2696	3455	3.917760	GGAGGAGGATGGACGCGG	61.918	72.222	12.47	0.00	0.00	6.46
2849	3608	1.139853	GATCCTTTCCTCTCATGCCGT	59.860	52.381	0.00	0.00	0.00	5.68
2916	3675	2.363018	CCCCTCTCCTCTGCGACA	60.363	66.667	0.00	0.00	0.00	4.35
2944	3703	2.592308	GATGCCTGACCTCCACCC	59.408	66.667	0.00	0.00	0.00	4.61
2960	3719	1.095807	ATCTGCGTCTCCGATGTCGA	61.096	55.000	3.62	0.00	43.02	4.20
2963	3722	1.736586	GGATCTGCGTCTCCGATGT	59.263	57.895	0.00	0.00	35.63	3.06
2983	3742	0.394488	TGACCTCTCTGGCTCTACCG	60.394	60.000	0.00	0.00	43.94	4.02
3006	3765	2.588877	GGACATCCATGCCGACCG	60.589	66.667	0.00	0.00	35.64	4.79
3015	3774	1.303561	GCACAAGGCAGGACATCCA	60.304	57.895	0.00	0.00	43.97	3.41
3025	3784	1.294659	CTTCTCCTCGTGCACAAGGC	61.295	60.000	19.57	0.00	45.13	4.35
3028	3787	1.371183	CCCTTCTCCTCGTGCACAA	59.629	57.895	18.64	0.00	0.00	3.33
3062	3821	1.939785	CGACGGTCGTGCATAGAGC	60.940	63.158	21.68	12.46	45.96	4.09
3094	3853	4.118410	GAGAGAAGCCATACACATCACAG	58.882	47.826	0.00	0.00	0.00	3.66
3121	3880	9.273016	CAGTTTGTAAAATTAGGAACAGAGAGA	57.727	33.333	0.00	0.00	0.00	3.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.