AutoCloner

Multiple sequence alignment - TraesCS6D01G326900

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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	TraesCS6D01G326900	chr6D	100.000	3481	0	0	1	3481	431923261	431919781	0.000000e+00	6429
1	TraesCS6D01G326900	chr6D	88.579	753	56	9	1	725	67785801	67785051	0.000000e+00	887
2	TraesCS6D01G326900	chr7D	92.559	3521	189	32	1	3481	475990109	475986622	0.000000e+00	4983
3	TraesCS6D01G326900	chr5B	91.151	3458	246	34	59	3481	636511295	636514727	0.000000e+00	4636
4	TraesCS6D01G326900	chr2D	90.380	3503	250	43	6	3481	594644854	594641412	0.000000e+00	4521
5	TraesCS6D01G326900	chr2D	96.804	219	7	0	3263	3481	343544476	343544694	1.970000e-97	366
6	TraesCS6D01G326900	chr3B	90.500	3158	258	28	345	3481	532747365	532744229	0.000000e+00	4132
7	TraesCS6D01G326900	chr3B	90.886	3083	237	33	431	3481	657695264	657692194	0.000000e+00	4096
8	TraesCS6D01G326900	chr3B	89.818	658	44	8	2826	3481	36814409	36813773	0.000000e+00	822
9	TraesCS6D01G326900	chr3B	93.911	427	25	1	3055	3481	722571968	722571543	0.000000e+00	643
10	TraesCS6D01G326900	chr4B	89.542	3299	282	44	227	3481	99428793	99425514	0.000000e+00	4122
11	TraesCS6D01G326900	chr4B	91.027	3087	223	34	431	3481	553948312	553945244	0.000000e+00	4117
12	TraesCS6D01G326900	chr4B	90.814	3059	242	26	222	3257	212139491	212136449	0.000000e+00	4056
13	TraesCS6D01G326900	chr4B	90.579	3057	246	29	222	3257	212110340	212107305	0.000000e+00	4012
14	TraesCS6D01G326900	chr1B	90.694	3084	234	36	431	3481	50150802	50147739	0.000000e+00	4056
15	TraesCS6D01G326900	chr6B	90.506	3086	239	38	431	3481	420671253	420674319	0.000000e+00	4026
16	TraesCS6D01G326900	chr1D	89.787	3006	221	43	6	2983	479088433	479085486	0.000000e+00	3771
17	TraesCS6D01G326900	chr1D	87.759	1013	73	25	6	1001	218906036	218907014	0.000000e+00	1136
18	TraesCS6D01G326900	chr6A	87.527	922	66	30	6	910	107466729	107465840	0.000000e+00	1020
19	TraesCS6D01G326900	chr3D	88.631	862	60	13	4	837	537586705	537585854	0.000000e+00	1014

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	TraesCS6D01G326900	chr6D	431919781	431923261	3480	True	6429	6429	100.000	1	3481	1	chr6D.!!$R2	3480
1	TraesCS6D01G326900	chr6D	67785051	67785801	750	True	887	887	88.579	1	725	1	chr6D.!!$R1	724
2	TraesCS6D01G326900	chr7D	475986622	475990109	3487	True	4983	4983	92.559	1	3481	1	chr7D.!!$R1	3480
3	TraesCS6D01G326900	chr5B	636511295	636514727	3432	False	4636	4636	91.151	59	3481	1	chr5B.!!$F1	3422
4	TraesCS6D01G326900	chr2D	594641412	594644854	3442	True	4521	4521	90.380	6	3481	1	chr2D.!!$R1	3475
5	TraesCS6D01G326900	chr3B	532744229	532747365	3136	True	4132	4132	90.500	345	3481	1	chr3B.!!$R2	3136
6	TraesCS6D01G326900	chr3B	657692194	657695264	3070	True	4096	4096	90.886	431	3481	1	chr3B.!!$R3	3050
7	TraesCS6D01G326900	chr3B	36813773	36814409	636	True	822	822	89.818	2826	3481	1	chr3B.!!$R1	655
8	TraesCS6D01G326900	chr4B	99425514	99428793	3279	True	4122	4122	89.542	227	3481	1	chr4B.!!$R1	3254
9	TraesCS6D01G326900	chr4B	553945244	553948312	3068	True	4117	4117	91.027	431	3481	1	chr4B.!!$R4	3050
10	TraesCS6D01G326900	chr4B	212136449	212139491	3042	True	4056	4056	90.814	222	3257	1	chr4B.!!$R3	3035
11	TraesCS6D01G326900	chr4B	212107305	212110340	3035	True	4012	4012	90.579	222	3257	1	chr4B.!!$R2	3035
12	TraesCS6D01G326900	chr1B	50147739	50150802	3063	True	4056	4056	90.694	431	3481	1	chr1B.!!$R1	3050
13	TraesCS6D01G326900	chr6B	420671253	420674319	3066	False	4026	4026	90.506	431	3481	1	chr6B.!!$F1	3050
14	TraesCS6D01G326900	chr1D	479085486	479088433	2947	True	3771	3771	89.787	6	2983	1	chr1D.!!$R1	2977
15	TraesCS6D01G326900	chr1D	218906036	218907014	978	False	1136	1136	87.759	6	1001	1	chr1D.!!$F1	995
16	TraesCS6D01G326900	chr6A	107465840	107466729	889	True	1020	1020	87.527	6	910	1	chr6A.!!$R1	904
17	TraesCS6D01G326900	chr3D	537585854	537586705	851	True	1014	1014	88.631	4	837	1	chr3D.!!$R1	833

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
149	176	2.030007	GCATGCTAGGCAAACTGAACAA	60.030	45.455	11.37	43.62	2.83	F
271	313	2.557056	CTGAATATGCATCCTGGCCAAG	59.443	50.000	7.01	0.00	3.61	F
1240	1336	1.271379	CCCCTGTAGTGGTGTCTTTGG	60.271	57.143	0.00	0.00	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1155	1251	0.250597	GGTTAGGCCCACGACTTGTT	60.251	55.0	0.00	0.00	2.83	R
2180	2298	0.039798	CACACATCCAGCTGCACAAC	60.040	55.0	8.66	0.00	3.32	R
2628	2761	0.678048	AAAGCTCGATGCCAACTCCC	60.678	55.0	0.00	44.23	4.30	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
149	176	2.030007	GCATGCTAGGCAAACTGAACAA	60.030	45.455	11.37	0.00	43.62	2.83
231	266	4.584638	AAACATGTATCCTGGCCAACTA	57.415	40.909	7.01	0.00	0.00	2.24
271	313	2.557056	CTGAATATGCATCCTGGCCAAG	59.443	50.000	7.01	0.00	0.00	3.61
288	330	6.480763	TGGCCAAGTGAAACATCTATTCTAA	58.519	36.000	0.61	0.00	41.43	2.10
372	415	3.875727	CTGGCCAACTGAGACATCTATTG	59.124	47.826	7.01	0.00	0.00	1.90
441	506	8.409358	AACTTTTGTCCATAGCTAATGAAACT	57.591	30.769	0.00	0.00	37.86	2.66
498	565	8.275187	TCTTATCCCACACATATATTCTGGTT	57.725	34.615	0.00	0.00	0.00	3.67
673	743	9.887629	ATCAAATTATGTCCAAATTATGTGCAA	57.112	25.926	0.00	0.00	0.00	4.08
675	745	9.757859	CAAATTATGTCCAAATTATGTGCAAAC	57.242	29.630	0.00	0.00	0.00	2.93
910	995	5.918426	TGATTGTCATAATGGTGTGCAAT	57.082	34.783	0.00	0.00	32.81	3.56
1076	1172	3.134262	CCTCCTGATCTCAATGAGCTTCA	59.866	47.826	5.18	9.95	31.32	3.02
1155	1251	2.664568	GCGATCTGTTTACTACACGCAA	59.335	45.455	0.00	0.00	44.47	4.85
1240	1336	1.271379	CCCCTGTAGTGGTGTCTTTGG	60.271	57.143	0.00	0.00	0.00	3.28
1401	1497	2.092429	GGAACCCTATGTTGGCATGAGA	60.092	50.000	0.00	0.00	37.29	3.27
1504	1600	1.680487	CGGACACCCCACACCAATA	59.320	57.895	0.00	0.00	34.14	1.90
1603	1699	5.459831	CCTGTCCTGGACCCTATACTAGATT	60.460	48.000	23.42	0.00	0.00	2.40
1716	1815	2.875080	AACGCGAGACAATAAAGCAC	57.125	45.000	15.93	0.00	0.00	4.40
1734	1833	2.400399	CACACTCAATGCAAGGCAAAG	58.600	47.619	0.00	0.00	43.62	2.77
1838	1937	6.149474	CCTTCGTTGTCCAAATACTTGAGATT	59.851	38.462	0.00	0.00	34.14	2.40
1866	1965	4.581309	AGGCATCTCTCCTGATGAAAAA	57.419	40.909	8.46	0.00	44.71	1.94
1896	1998	5.220586	GCGCATCTTGTATAACTGCAACTTA	60.221	40.000	0.30	0.00	33.13	2.24
1941	2052	6.481643	TCCCTTACAGAATTAAGTTTCCCTG	58.518	40.000	0.00	0.00	0.00	4.45
1953	2064	1.282157	GTTTCCCTGTAGGCAGTCCAT	59.718	52.381	0.00	0.00	41.02	3.41
2016	2127	2.838736	AGTGTGCAACTAGTGTCCAAG	58.161	47.619	0.00	0.00	37.36	3.61
2044	2155	7.775093	TCCCATCCAGTTTTCTATATCACTTTG	59.225	37.037	0.00	0.00	0.00	2.77
2045	2156	7.420800	CCATCCAGTTTTCTATATCACTTTGC	58.579	38.462	0.00	0.00	0.00	3.68
2046	2157	7.284034	CCATCCAGTTTTCTATATCACTTTGCT	59.716	37.037	0.00	0.00	0.00	3.91
2047	2158	7.615582	TCCAGTTTTCTATATCACTTTGCTG	57.384	36.000	0.00	0.00	0.00	4.41
2048	2159	6.094048	TCCAGTTTTCTATATCACTTTGCTGC	59.906	38.462	0.00	0.00	0.00	5.25
2057	2168	4.916983	ATCACTTTGCTGCTTTGTTGTA	57.083	36.364	0.00	0.00	0.00	2.41
2064	2175	5.568685	TTGCTGCTTTGTTGTACAACTAA	57.431	34.783	32.58	29.36	37.90	2.24
2080	2191	7.988599	TGTACAACTAAATTACCTTCACTGTGT	59.011	33.333	7.79	0.00	0.00	3.72
2094	2205	7.602644	ACCTTCACTGTGTAACTACATAATGTG	59.397	37.037	7.79	0.00	38.63	3.21
2101	2212	9.198837	CTGTGTAACTACATAATGTGTTGTGTA	57.801	33.333	0.00	0.00	44.24	2.90
2119	2237	5.533482	TGTGTACAAAGTGCAAGTGTTTTT	58.467	33.333	0.00	0.00	28.81	1.94
2156	2274	3.620488	TGTCCATTTCCTGCAACTATCC	58.380	45.455	0.00	0.00	0.00	2.59
2421	2552	3.336138	AAACCGATCCAGACTTCTTCC	57.664	47.619	0.00	0.00	0.00	3.46
2626	2759	2.713154	GGTTGCGCGTTTGTGAGT	59.287	55.556	8.43	0.00	0.00	3.41
2628	2761	1.717728	GTTGCGCGTTTGTGAGTCG	60.718	57.895	8.43	0.00	0.00	4.18
2681	2814	2.822561	CGAGCATTCCTAGAGGCTATGA	59.177	50.000	12.20	0.00	36.59	2.15
2713	2846	4.868734	CCTCCTAACAACTTCATAACCGAC	59.131	45.833	0.00	0.00	0.00	4.79
2745	2878	4.280425	TGCAATGAGGCAGTCAATACAAAA	59.720	37.500	0.00	0.00	39.19	2.44
2778	2911	2.316867	CCGTGCATCGCTGTTGTCA	61.317	57.895	0.00	0.00	38.35	3.58
2830	2963	2.039818	TTGGTTAGTTGTTGTGCCGA	57.960	45.000	0.00	0.00	0.00	5.54
2860	2993	5.190528	AGGGCTCTCTGATGATTTCAACTAA	59.809	40.000	0.00	0.00	32.78	2.24
2953	3098	4.509970	GCTATGACACACACACACACTTTA	59.490	41.667	0.00	0.00	0.00	1.85
3051	3196	1.066143	CAGCGTAGTGAGGGGTTCAAT	60.066	52.381	0.00	0.00	37.61	2.57
3207	3353	3.713826	TGGTCCAACTTCCCAATAGAC	57.286	47.619	0.00	0.00	0.00	2.59
3210	3356	3.263425	GGTCCAACTTCCCAATAGACAGA	59.737	47.826	0.00	0.00	0.00	3.41
3253	3400	1.162698	GGACCTTTACCGCAAGTTCC	58.837	55.000	0.00	0.00	29.05	3.62
3418	3565	1.750206	TGTGTGAGTGCTGCAAAATGT	59.250	42.857	2.77	0.00	0.00	2.71
3423	3570	4.037803	TGTGAGTGCTGCAAAATGTACAAT	59.962	37.500	2.77	0.00	0.00	2.71
3470	3617	4.567537	CCTCAAGGTGTTCACCCATATTGA	60.568	45.833	17.06	17.20	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	5.316167	TGGCTAGAATCATGTTTCAGTTGT	58.684	37.500	16.79	1.02	0.00	3.32
231	266	0.320946	GTTGGCCAGCATGCATGTTT	60.321	50.000	26.79	13.59	31.97	2.83
271	313	8.547967	TCAGTTGGTTAGAATAGATGTTTCAC	57.452	34.615	0.00	0.00	0.00	3.18
288	330	3.620488	ACAGTCAATGTGTTCAGTTGGT	58.380	40.909	0.00	0.00	41.91	3.67
372	415	6.745116	ACTACAGATTTTTGGTTTTGGCTAC	58.255	36.000	0.00	0.00	0.00	3.58
441	506	9.163899	TGCGTGACTATTTTAATATGGTTTGTA	57.836	29.630	0.00	0.00	0.00	2.41
477	544	5.372363	TGGAACCAGAATATATGTGTGGGAT	59.628	40.000	11.21	2.58	32.13	3.85
498	565	2.584835	AGCTTTGCAATAGGTGTGGA	57.415	45.000	0.00	0.00	0.00	4.02
673	743	4.082354	GCAAGGAGCTGATTCAGATTTGTT	60.082	41.667	17.87	3.56	41.15	2.83
675	745	3.181489	GGCAAGGAGCTGATTCAGATTTG	60.181	47.826	17.87	13.66	44.79	2.32
888	968	5.918426	ATTGCACACCATTATGACAATCA	57.082	34.783	0.00	0.00	29.77	2.57
1076	1172	4.569719	TGCTGCTGATCCATATCATGAT	57.430	40.909	13.81	13.81	41.29	2.45
1155	1251	0.250597	GGTTAGGCCCACGACTTGTT	60.251	55.000	0.00	0.00	0.00	2.83
1377	1473	2.142356	TGCCAACATAGGGTTCCATG	57.858	50.000	0.00	0.00	37.72	3.66
1603	1699	5.939883	CCTCATCACTGTCAATAGGTTTTGA	59.060	40.000	0.00	0.00	33.32	2.69
1716	1815	3.250744	CATCTTTGCCTTGCATTGAGTG	58.749	45.455	0.00	0.00	38.76	3.51
1734	1833	4.514441	CCATCTATCAGCTTCACCAACATC	59.486	45.833	0.00	0.00	0.00	3.06
1838	1937	0.252881	AGGAGAGATGCCTTGGTGGA	60.253	55.000	0.00	0.00	38.35	4.02
1866	1965	5.516339	GCAGTTATACAAGATGCGCAATTTT	59.484	36.000	17.11	8.44	0.00	1.82
1867	1966	5.036737	GCAGTTATACAAGATGCGCAATTT	58.963	37.500	17.11	9.32	0.00	1.82
1869	1968	3.627123	TGCAGTTATACAAGATGCGCAAT	59.373	39.130	17.11	4.38	39.74	3.56
1896	1998	6.672657	AGGGATATAGAAACACACCTGTAGTT	59.327	38.462	0.00	0.00	0.00	2.24
1941	2052	1.200020	GTTGCACAATGGACTGCCTAC	59.800	52.381	0.00	0.00	31.97	3.18
1953	2064	3.818210	CCAGTACCATAACAGTTGCACAA	59.182	43.478	0.00	0.00	0.00	3.33
2016	2127	7.283329	AGTGATATAGAAAACTGGATGGGAAC	58.717	38.462	0.00	0.00	0.00	3.62
2044	2155	7.114388	GGTAATTTAGTTGTACAACAAAGCAGC	59.886	37.037	33.93	24.59	40.15	5.25
2045	2156	8.349983	AGGTAATTTAGTTGTACAACAAAGCAG	58.650	33.333	33.93	0.00	40.15	4.24
2046	2157	8.228035	AGGTAATTTAGTTGTACAACAAAGCA	57.772	30.769	33.93	20.54	40.15	3.91
2047	2158	9.177304	GAAGGTAATTTAGTTGTACAACAAAGC	57.823	33.333	33.93	22.79	40.15	3.51
2057	2168	8.833493	GTTACACAGTGAAGGTAATTTAGTTGT	58.167	33.333	7.81	0.00	30.56	3.32
2094	2205	4.091453	ACACTTGCACTTTGTACACAAC	57.909	40.909	0.00	0.00	35.28	3.32
2101	2212	6.147000	CACCTTTAAAAACACTTGCACTTTGT	59.853	34.615	0.00	0.00	0.00	2.83
2119	2237	2.370519	TGGACAACTAGCTGCACCTTTA	59.629	45.455	1.02	0.00	0.00	1.85
2180	2298	0.039798	CACACATCCAGCTGCACAAC	60.040	55.000	8.66	0.00	0.00	3.32
2223	2349	6.472163	CGTCCTGCATAATACAAAATGAAACC	59.528	38.462	0.00	0.00	0.00	3.27
2229	2356	8.506437	CATCATACGTCCTGCATAATACAAAAT	58.494	33.333	0.00	0.00	0.00	1.82
2496	2628	1.216977	CAATCGTGGTACGCCTCCA	59.783	57.895	0.00	0.00	42.21	3.86
2626	2759	2.892640	CTCGATGCCAACTCCCGA	59.107	61.111	0.00	0.00	0.00	5.14
2628	2761	0.678048	AAAGCTCGATGCCAACTCCC	60.678	55.000	0.00	0.00	44.23	4.30
2681	2814	3.844640	AGTTGTTAGGAGGTTTGCCATT	58.155	40.909	0.00	0.00	37.19	3.16
2713	2846	1.389609	GCCTCATTGCACCATCCTGG	61.390	60.000	0.00	0.00	45.02	4.45
2745	2878	1.604604	CACGGTGGTTGGAAAGATGT	58.395	50.000	0.00	0.00	0.00	3.06
2778	2911	3.262405	AGCCTTTTTCATGATGTGCCATT	59.738	39.130	0.00	0.00	0.00	3.16
2810	2943	2.577700	TCGGCACAACAACTAACCAAT	58.422	42.857	0.00	0.00	0.00	3.16
2817	2950	1.608590	CTGGATTTCGGCACAACAACT	59.391	47.619	0.00	0.00	0.00	3.16
2830	2963	2.485659	TCATCAGAGAGCCCTGGATTT	58.514	47.619	0.00	0.00	34.99	2.17
2860	2993	3.813443	AGTGAAGCTGAAGTCAACACAT	58.187	40.909	0.00	0.00	0.00	3.21
2953	3098	7.773690	AGTTGACCTGTATTTGTACAACTTCTT	59.226	33.333	8.07	0.00	41.95	2.52
3051	3196	6.592607	GGTTCACATATCTTTTTAGGACGACA	59.407	38.462	0.00	0.00	0.00	4.35
3207	3353	4.150098	GTGTAGGTTTCGTAAGCTTGTCTG	59.850	45.833	9.86	0.00	41.95	3.51
3210	3356	4.332428	AGTGTAGGTTTCGTAAGCTTGT	57.668	40.909	9.86	0.00	41.95	3.16
3253	3400	4.758674	TCCAATCAGCTCAAACTCTTCTTG	59.241	41.667	0.00	0.00	0.00	3.02
3355	3502	1.142870	TGCCTGCACCAAGTAGTTTCT	59.857	47.619	0.00	0.00	0.00	2.52
3418	3565	1.066215	ACAGAGCATGCCGTCATTGTA	60.066	47.619	15.66	0.00	0.00	2.41
3423	3570	2.327343	GCAACAGAGCATGCCGTCA	61.327	57.895	15.66	0.00	36.56	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.