AutoCloner

Multiple sequence alignment - TraesCS5D01G207100

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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	TraesCS5D01G207100	chr5D	100.000	3107	0	0	1	3107	313280197	313283303	0.000000e+00	5738.0
1	TraesCS5D01G207100	chr5D	86.761	846	85	12	2284	3107	313329223	313330063	0.000000e+00	917.0
2	TraesCS5D01G207100	chr5D	81.038	559	80	18	2102	2654	313205381	313205919	3.700000e-114	422.0
3	TraesCS5D01G207100	chr5B	91.626	2257	122	35	896	3107	360875482	360877716	0.000000e+00	3059.0
4	TraesCS5D01G207100	chr5B	93.766	770	25	8	1	749	360874106	360874873	0.000000e+00	1134.0
5	TraesCS5D01G207100	chr5B	92.707	617	27	6	158	757	360854051	360854666	0.000000e+00	874.0
6	TraesCS5D01G207100	chr5B	95.210	167	8	0	1	167	360844270	360844436	6.610000e-67	265.0
7	TraesCS5D01G207100	chr5B	92.513	187	8	5	896	1077	360856539	360856724	2.380000e-66	263.0
8	TraesCS5D01G207100	chr5B	84.733	131	9	7	762	890	360875314	360875435	1.510000e-23	121.0
9	TraesCS5D01G207100	chr5B	83.969	131	10	7	762	890	360856371	360856492	7.040000e-22	115.0
10	TraesCS5D01G207100	chr5B	89.796	49	4	1	2743	2791	354301772	354301725	9.300000e-06	62.1
11	TraesCS5D01G207100	chr5A	94.087	778	44	1	1478	2255	407149175	407149950	0.000000e+00	1181.0
12	TraesCS5D01G207100	chr5A	97.138	629	16	1	1	629	407147379	407148005	0.000000e+00	1061.0
13	TraesCS5D01G207100	chr5A	89.623	742	53	11	680	1418	407148133	407148853	0.000000e+00	922.0
14	TraesCS5D01G207100	chr5A	74.772	329	65	13	2362	2687	547504882	547505195	6.990000e-27	132.0
15	TraesCS5D01G207100	chr4D	76.261	337	69	6	2338	2673	399731101	399730775	5.330000e-38	169.0
16	TraesCS5D01G207100	chr4B	76.753	271	54	2	2396	2666	666069548	666069287	3.230000e-30	143.0
17	TraesCS5D01G207100	chr3D	83.221	149	23	2	2954	3101	394925133	394924986	5.400000e-28	135.0
18	TraesCS5D01G207100	chr6D	85.393	89	13	0	3000	3088	137790831	137790743	3.300000e-15	93.5
19	TraesCS5D01G207100	chr3A	92.500	40	3	0	3061	3100	25898411	25898372	1.200000e-04	58.4

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	TraesCS5D01G207100	chr5D	313280197	313283303	3106	False	5738.000000	5738	100.000000	1	3107	1	chr5D.!!$F2	3106
1	TraesCS5D01G207100	chr5D	313329223	313330063	840	False	917.000000	917	86.761000	2284	3107	1	chr5D.!!$F3	823
2	TraesCS5D01G207100	chr5D	313205381	313205919	538	False	422.000000	422	81.038000	2102	2654	1	chr5D.!!$F1	552
3	TraesCS5D01G207100	chr5B	360874106	360877716	3610	False	1438.000000	3059	90.041667	1	3107	3	chr5B.!!$F3	3106
4	TraesCS5D01G207100	chr5B	360854051	360856724	2673	False	417.333333	874	89.729667	158	1077	3	chr5B.!!$F2	919
5	TraesCS5D01G207100	chr5A	407147379	407149950	2571	False	1054.666667	1181	93.616000	1	2255	3	chr5A.!!$F2	2254

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
798	2585	0.739813	ACCAAGCGGATTCGTAGTGC	60.740	55.0	0.0	0.0	38.89	4.40	F
1653	3798	0.693622	TTGGGGGAATGTTCTACGCA	59.306	50.0	0.0	0.0	0.00	5.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1953	4098	0.452122	CGCAGTTCCGCTTTAAACCG	60.452	55.000	0.0	0.0	0.00	4.44	R
2610	4761	1.062002	GATGTTGTGTACGAATGGCGG	59.938	52.381	0.0	0.0	46.49	6.13	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
70	71	1.185618	AGCGGGCGATTCCTAGCATA	61.186	55.000	0.00	0.00	39.61	3.14
189	190	2.507992	CAAGAGCTGGGCGTCGAG	60.508	66.667	0.00	0.00	0.00	4.04
454	455	0.977627	ACCACCGCAGATGATCCAGA	60.978	55.000	0.00	0.00	0.00	3.86
599	608	1.405661	CGGTGTTTCTCTAGGGAAGCC	60.406	57.143	15.75	12.96	0.00	4.35
753	840	1.009900	CGTCCATCTCTACGCGGTC	60.010	63.158	12.47	0.00	31.66	4.79
778	2565	1.263356	TCAGAACGGGGACTTCGATT	58.737	50.000	0.00	0.00	0.00	3.34
781	2568	1.479730	AGAACGGGGACTTCGATTACC	59.520	52.381	0.00	0.00	0.00	2.85
798	2585	0.739813	ACCAAGCGGATTCGTAGTGC	60.740	55.000	0.00	0.00	38.89	4.40
801	2588	1.108776	AAGCGGATTCGTAGTGCCTA	58.891	50.000	0.00	0.00	38.89	3.93
802	2589	1.329256	AGCGGATTCGTAGTGCCTAT	58.671	50.000	0.00	0.00	38.89	2.57
803	2590	2.511659	AGCGGATTCGTAGTGCCTATA	58.488	47.619	0.00	0.00	38.89	1.31
804	2591	3.090037	AGCGGATTCGTAGTGCCTATAT	58.910	45.455	0.00	0.00	38.89	0.86
805	2592	4.267536	AGCGGATTCGTAGTGCCTATATA	58.732	43.478	0.00	0.00	38.89	0.86
872	2660	1.201647	GTGTAGGAGCAGTTCGTAGCA	59.798	52.381	0.00	0.00	0.00	3.49
891	2679	4.020617	CGCCTGCAGGGAACTCCA	62.021	66.667	33.46	0.00	40.21	3.86
892	2680	2.360475	GCCTGCAGGGAACTCCAC	60.360	66.667	33.46	10.92	40.21	4.02
894	2682	2.528818	CCTGCAGGGAACTCCACCA	61.529	63.158	26.14	0.00	40.21	4.17
977	2811	2.303022	AGAAGCTGAAGGAATCCGTTCA	59.697	45.455	11.66	11.66	42.70	3.18
984	2818	2.736682	GGAATCCGTTCACGCACCG	61.737	63.158	0.00	0.00	36.01	4.94
1021	2858	1.359459	GGCGACGAAAGGAAGCGAAT	61.359	55.000	0.00	0.00	0.00	3.34
1234	3110	0.809241	GACTGAGGAGGCAAGCGATG	60.809	60.000	0.00	0.00	0.00	3.84
1236	3112	2.249413	CTGAGGAGGCAAGCGATGGT	62.249	60.000	0.00	0.00	0.00	3.55
1280	3156	2.202440	GCAGCAATCACAGCGCAG	60.202	61.111	11.47	3.33	37.01	5.18
1418	3298	2.910360	CCTGCCATCGGGTCATCA	59.090	61.111	0.00	0.00	36.17	3.07
1419	3299	1.227764	CCTGCCATCGGGTCATCAG	60.228	63.158	0.00	0.00	36.17	2.90
1420	3300	1.689243	CCTGCCATCGGGTCATCAGA	61.689	60.000	0.00	0.00	36.17	3.27
1564	3706	2.378038	GAGCCCAATGGTTTGAGCATA	58.622	47.619	0.00	0.00	38.91	3.14
1653	3798	0.693622	TTGGGGGAATGTTCTACGCA	59.306	50.000	0.00	0.00	0.00	5.24
1774	3919	4.142315	CGGAATTTCAGCTGTTGGAATCAT	60.142	41.667	14.67	0.00	33.69	2.45
1793	3938	1.809209	GCGGAGAGCTGTTCAGAGC	60.809	63.158	0.00	0.00	44.04	4.09
1846	3991	0.953727	TCTGCATGTTGGTGTTCAGC	59.046	50.000	0.00	0.00	0.00	4.26
1885	4030	1.529244	GCCTGGGTGAAAGTGCACT	60.529	57.895	15.25	15.25	38.78	4.40
1908	4053	2.391926	TGGGTGACAGAGTGTTCCTA	57.608	50.000	0.00	0.00	0.00	2.94
1953	4098	1.079503	CACTAAGTGCGGAAGAAGCC	58.920	55.000	0.00	0.00	0.00	4.35
2001	4146	0.757561	TGAGACACGGTGACAAGGGA	60.758	55.000	16.29	0.00	0.00	4.20
2004	4149	2.232941	GAGACACGGTGACAAGGGATTA	59.767	50.000	16.29	0.00	0.00	1.75
2043	4188	0.539051	GAGGCACCACTACTCTGCAT	59.461	55.000	0.00	0.00	32.20	3.96
2064	4209	0.392998	ATCCCGGTCAACATCTGCAC	60.393	55.000	0.00	0.00	0.00	4.57
2097	4242	5.067674	GGCTGCTGAAATATTGTTGATACCA	59.932	40.000	0.00	0.00	0.00	3.25
2098	4243	6.405731	GGCTGCTGAAATATTGTTGATACCAA	60.406	38.462	0.00	0.00	0.00	3.67
2256	4403	8.840833	TGATACCACATTGTAACGCAATATAT	57.159	30.769	0.00	0.00	45.33	0.86
2336	4485	1.783365	AGTGAAAGCCTTTCTCCCCTT	59.217	47.619	17.51	0.00	40.32	3.95
2355	4504	1.327690	TAATCTCCGCCGGTGAGCTT	61.328	55.000	18.79	15.71	0.00	3.74
2362	4511	2.109126	GCCGGTGAGCTTGTGGATC	61.109	63.158	1.90	0.00	0.00	3.36
2408	4558	3.637273	GCTCGTTGTGGGGAGGGT	61.637	66.667	0.00	0.00	0.00	4.34
2459	4610	9.670442	AGTAGATAGGTATGGTTTTAATCCTCA	57.330	33.333	0.00	0.00	0.00	3.86
2580	4731	1.592669	CCAGCGTAGATTCCTGCCG	60.593	63.158	0.00	0.00	0.00	5.69
2586	4737	1.382557	TAGATTCCTGCCGGCTCCA	60.383	57.895	29.70	6.34	0.00	3.86
2610	4761	1.284715	CGGCGAAGTTGGGTTTTCC	59.715	57.895	0.00	0.00	39.75	3.13
2623	4774	1.158434	GTTTTCCCGCCATTCGTACA	58.842	50.000	0.00	0.00	36.19	2.90
2657	4808	8.261492	AGATTTAGTGTCATGTTCTTCACATC	57.739	34.615	0.00	0.00	43.17	3.06
2732	4899	0.606401	ATGGTTGTTCGGTGCTCCAG	60.606	55.000	5.52	0.00	0.00	3.86
2789	4957	5.508200	TTTGTACTTGCGGTGAATCTTTT	57.492	34.783	0.00	0.00	0.00	2.27
2815	4983	7.932120	AATAGATCGGATTCTGTTCGTAAAG	57.068	36.000	0.00	0.00	0.00	1.85
2864	5032	2.203337	GAAGGTGTGCACTGCCCA	60.203	61.111	19.41	0.00	0.00	5.36
2874	5042	1.613630	CACTGCCCACCCTACTCCT	60.614	63.158	0.00	0.00	0.00	3.69
3024	5198	7.724061	AGAGTTTTACAAGTAACCCACAATCAT	59.276	33.333	0.00	0.00	0.00	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	71	2.235016	CGTCGACACGCAGTTTGGT	61.235	57.895	17.16	0.00	41.61	3.67
104	105	2.995482	CGTTGTCTATGACGGCGC	59.005	61.111	6.90	0.00	34.95	6.53
151	152	3.807538	GGCGACGTCCACGAGCTA	61.808	66.667	10.58	0.00	42.38	3.32
478	479	2.001812	CACGTGATTGGTCCTCTCTG	57.998	55.000	10.90	0.00	0.00	3.35
510	511	4.944372	CGTACGGGATGGAGGCGC	62.944	72.222	7.57	0.00	0.00	6.53
741	828	2.548480	CTGATGTATGACCGCGTAGAGA	59.452	50.000	4.92	0.00	0.00	3.10
753	840	3.458189	GAAGTCCCCGTTCTGATGTATG	58.542	50.000	0.00	0.00	0.00	2.39
778	2565	1.470285	GCACTACGAATCCGCTTGGTA	60.470	52.381	0.00	0.00	39.95	3.25
781	2568	0.460284	AGGCACTACGAATCCGCTTG	60.460	55.000	0.00	0.00	36.02	4.01
798	2585	5.228012	CGATGCGCGCACATATATATATAGG	59.772	44.000	39.05	11.87	0.00	2.57
801	2588	4.546570	ACGATGCGCGCACATATATATAT	58.453	39.130	39.05	17.15	46.04	0.86
802	2589	3.959943	ACGATGCGCGCACATATATATA	58.040	40.909	39.05	9.89	46.04	0.86
803	2590	2.789339	GACGATGCGCGCACATATATAT	59.211	45.455	39.05	18.93	46.04	0.86
804	2591	2.159435	AGACGATGCGCGCACATATATA	60.159	45.455	39.05	11.72	46.04	0.86
805	2592	0.992072	GACGATGCGCGCACATATAT	59.008	50.000	39.05	20.73	46.04	0.86
872	2660	4.400961	GAGTTCCCTGCAGGCGCT	62.401	66.667	28.39	22.29	39.64	5.92
890	2678	1.597742	CTCCAACAAGTGTCCTGGTG	58.402	55.000	0.00	0.00	30.09	4.17
891	2679	0.474184	CCTCCAACAAGTGTCCTGGT	59.526	55.000	0.00	0.00	30.09	4.00
892	2680	0.250901	CCCTCCAACAAGTGTCCTGG	60.251	60.000	0.00	0.00	0.00	4.45
894	2682	1.059913	CTCCCTCCAACAAGTGTCCT	58.940	55.000	0.00	0.00	0.00	3.85
977	2811	0.949105	GTTGTGATTCTCCGGTGCGT	60.949	55.000	0.00	0.00	0.00	5.24
984	2818	1.668419	CCATCGGGTTGTGATTCTCC	58.332	55.000	0.00	0.00	0.00	3.71
1021	2858	1.133294	TGGATCCGGTGGAGCTGTATA	60.133	52.381	7.39	0.00	38.31	1.47
1234	3110	3.386768	TGTGCTGTACAAGAAGAGACC	57.613	47.619	0.00	0.00	36.06	3.85
1259	3135	1.138047	GCGCTGTGATTGCTGCATTC	61.138	55.000	15.58	15.58	33.72	2.67
1280	3156	1.511613	TTCCAGATCATCCAGTCCCC	58.488	55.000	0.00	0.00	0.00	4.81
1329	3209	2.032376	TGTCGCATGAGCAGCCAA	59.968	55.556	0.00	0.00	42.27	4.52
1418	3298	1.653918	TCTCTTCCAGGAATCCCCTCT	59.346	52.381	1.09	0.00	45.60	3.69
1419	3299	2.171659	GTTCTCTTCCAGGAATCCCCTC	59.828	54.545	1.09	0.00	45.60	4.30
1564	3706	0.680280	AGCATCCGTGAGTCGTACCT	60.680	55.000	0.00	0.00	37.94	3.08
1774	3919	1.588597	CTCTGAACAGCTCTCCGCA	59.411	57.895	0.00	0.00	42.61	5.69
1846	3991	4.717629	TTCAGCGACGTCCAGCCG	62.718	66.667	10.58	0.87	0.00	5.52
1906	4051	6.461788	GCCCTGAAGTACCTAGAATTGACTAG	60.462	46.154	0.00	0.00	39.40	2.57
1908	4053	4.162509	GCCCTGAAGTACCTAGAATTGACT	59.837	45.833	0.00	0.00	0.00	3.41
1927	4072	1.221840	CCGCACTTAGTGATGCCCT	59.778	57.895	17.40	0.00	38.69	5.19
1953	4098	0.452122	CGCAGTTCCGCTTTAAACCG	60.452	55.000	0.00	0.00	0.00	4.44
2043	4188	1.557371	TGCAGATGTTGACCGGGATTA	59.443	47.619	6.32	0.00	0.00	1.75
2064	4209	1.089112	TTTCAGCAGCCACATCATCG	58.911	50.000	0.00	0.00	0.00	3.84
2070	4215	3.825585	TCAACAATATTTCAGCAGCCACA	59.174	39.130	0.00	0.00	0.00	4.17
2097	4242	4.466015	ACACAAAACCACATTCAAGAGGTT	59.534	37.500	0.00	0.00	43.02	3.50
2098	4243	4.023291	ACACAAAACCACATTCAAGAGGT	58.977	39.130	0.00	0.00	33.70	3.85
2336	4485	1.327690	AAGCTCACCGGCGGAGATTA	61.328	55.000	35.78	8.13	39.06	1.75
2355	4504	4.414956	AGGGGAGGCGGATCCACA	62.415	66.667	13.41	0.00	46.03	4.17
2408	4558	1.686325	GAGCCGAGGCACCAGGAATA	61.686	60.000	17.18	0.00	44.88	1.75
2459	4610	2.201022	ATTCGAGCGCCGTCCCTAT	61.201	57.895	16.00	0.00	39.75	2.57
2586	4737	2.436646	CCAACTTCGCCGCTCCAT	60.437	61.111	0.00	0.00	0.00	3.41
2610	4761	1.062002	GATGTTGTGTACGAATGGCGG	59.938	52.381	0.00	0.00	46.49	6.13
2623	4774	6.166279	ACATGACACTAAATCTCGATGTTGT	58.834	36.000	0.00	0.00	0.00	3.32
2657	4808	6.827641	TCTTCGTTGTTGGATTCTTTAATCG	58.172	36.000	0.00	0.00	42.16	3.34
2732	4899	9.185680	ACATAATAAAAATTACAGACTGGTCCC	57.814	33.333	7.51	0.00	0.00	4.46
2789	4957	9.459640	CTTTACGAACAGAATCCGATCTATTAA	57.540	33.333	0.00	0.00	0.00	1.40
2806	4974	9.072294	CAATAATTCAACCCATTCTTTACGAAC	57.928	33.333	0.00	0.00	33.72	3.95
2815	4983	7.759433	CCACTGTTACAATAATTCAACCCATTC	59.241	37.037	0.00	0.00	0.00	2.67
2864	5032	2.590611	TGTAGGATGGAAGGAGTAGGGT	59.409	50.000	0.00	0.00	0.00	4.34
2934	5104	9.729023	CTCCATTTAAAACAATATTATGCACGA	57.271	29.630	0.00	0.00	0.00	4.35
2989	5163	9.924650	GGTTACTTGTAAAACTCTATTCTCTCA	57.075	33.333	0.00	0.00	0.00	3.27
3024	5198	3.354467	TGCATGAGTAATTGCCATGTCA	58.646	40.909	18.72	15.46	39.69	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.