AutoCloner

Multiple sequence alignment - TraesCS3A01G529400

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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	TraesCS3A01G529400	chr3A	100.000	2978	0	0	1	2978	742927946	742930923	0.000000e+00	5500.0
1	TraesCS3A01G529400	chr3A	84.573	901	105	17	996	1895	742955107	742955974	0.000000e+00	863.0
2	TraesCS3A01G529400	chr3A	88.288	222	26	0	2260	2481	742962573	742962794	1.760000e-67	267.0
3	TraesCS3A01G529400	chr3D	94.062	2021	86	19	964	2977	609363785	609365778	0.000000e+00	3037.0
4	TraesCS3A01G529400	chr3D	91.813	965	54	9	1	965	609362818	609363757	0.000000e+00	1321.0
5	TraesCS3A01G529400	chr3D	82.812	128	9	7	542	664	609368711	609368830	5.250000e-18	102.0
6	TraesCS3A01G529400	chr3B	87.174	1996	218	17	996	2978	820178971	820177001	0.000000e+00	2233.0
7	TraesCS3A01G529400	chr3B	92.032	1481	115	3	970	2448	820185903	820184424	0.000000e+00	2078.0
8	TraesCS3A01G529400	chr3B	89.638	1573	153	8	978	2543	819991977	819990408	0.000000e+00	1993.0
9	TraesCS3A01G529400	chr3B	91.776	1447	78	15	1520	2951	820114801	820116221	0.000000e+00	1975.0
10	TraesCS3A01G529400	chr3B	86.551	1554	200	7	996	2543	820122919	820124469	0.000000e+00	1703.0
11	TraesCS3A01G529400	chr3B	92.565	807	36	2	611	1393	820113997	820114803	0.000000e+00	1136.0
12	TraesCS3A01G529400	chr3B	88.943	615	61	5	1	612	820112284	820112894	0.000000e+00	752.0
13	TraesCS3A01G529400	chr3B	91.830	306	21	3	585	888	820187616	820187313	9.870000e-115	424.0
14	TraesCS3A01G529400	chr3B	90.722	291	22	3	306	596	820187923	820187638	1.670000e-102	383.0
15	TraesCS3A01G529400	chr3B	88.235	102	7	3	2691	2791	820090784	820090881	1.880000e-22	117.0
16	TraesCS3A01G529400	chr1A	85.405	1480	202	8	978	2453	578941159	578939690	0.000000e+00	1524.0
17	TraesCS3A01G529400	chr1D	86.214	972	125	5	978	1949	482243482	482242520	0.000000e+00	1044.0
18	TraesCS3A01G529400	chr2A	75.543	184	38	7	2019	2198	763333057	763332877	1.900000e-12	84.2
19	TraesCS3A01G529400	chr2D	87.500	64	8	0	2092	2155	568410234	568410297	1.140000e-09	75.0
20	TraesCS3A01G529400	chr2D	88.525	61	7	0	2095	2155	568727372	568727432	1.140000e-09	75.0

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	TraesCS3A01G529400	chr3A	742927946	742930923	2977	False	5500.000000	5500	100.000000	1	2978	1	chr3A.!!$F1	2977
1	TraesCS3A01G529400	chr3A	742955107	742955974	867	False	863.000000	863	84.573000	996	1895	1	chr3A.!!$F2	899
2	TraesCS3A01G529400	chr3D	609362818	609368830	6012	False	1486.666667	3037	89.562333	1	2977	3	chr3D.!!$F1	2976
3	TraesCS3A01G529400	chr3B	820177001	820178971	1970	True	2233.000000	2233	87.174000	996	2978	1	chr3B.!!$R2	1982
4	TraesCS3A01G529400	chr3B	819990408	819991977	1569	True	1993.000000	1993	89.638000	978	2543	1	chr3B.!!$R1	1565
5	TraesCS3A01G529400	chr3B	820122919	820124469	1550	False	1703.000000	1703	86.551000	996	2543	1	chr3B.!!$F2	1547
6	TraesCS3A01G529400	chr3B	820112284	820116221	3937	False	1287.666667	1975	91.094667	1	2951	3	chr3B.!!$F3	2950
7	TraesCS3A01G529400	chr3B	820184424	820187923	3499	True	961.666667	2078	91.528000	306	2448	3	chr3B.!!$R3	2142
8	TraesCS3A01G529400	chr1A	578939690	578941159	1469	True	1524.000000	1524	85.405000	978	2453	1	chr1A.!!$R1	1475
9	TraesCS3A01G529400	chr1D	482242520	482243482	962	True	1044.000000	1044	86.214000	978	1949	1	chr1D.!!$R1	971

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
134	135	0.036010	CCACCAGATTCGAGTTGCCT	60.036	55.000	0.00	0.00	4.75	F
824	1965	0.323178	AAGAATGGCTGGCTGGACAG	60.323	55.000	2.00	41.41	3.51	F
1333	3828	1.071699	ACCGGAAAAGCTTGCACTCTA	59.928	47.619	9.46	0.00	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1395	3890	0.038892	TCCCTGCGAAGAACGTGTAC	60.039	55.0	0.00	44.60	2.90	R
1856	4354	0.108233	CTCCTTCAGCTGCTCTGTCC	60.108	60.0	9.47	43.32	4.02	R
2830	5337	0.397941	CTCTTGGCTGACTGTTGGGA	59.602	55.0	0.00	0.00	4.37	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
30	31	1.550130	CGCCAGGGACCTCCTTAACA	61.550	60.000	0.00	0.00	45.47	2.41
76	77	2.997315	CTGACCGCCAGGACCTCA	60.997	66.667	0.00	0.00	41.02	3.86
91	92	4.578898	TCACGTCCAAGCACGCGT	62.579	61.111	5.58	5.58	43.93	6.01
134	135	0.036010	CCACCAGATTCGAGTTGCCT	60.036	55.000	0.00	0.00	0.00	4.75
149	150	0.756294	TGCCTCCACGAGAAGAAACA	59.244	50.000	0.00	0.00	0.00	2.83
195	196	4.208686	CACTAGGCGGCGTCCTCC	62.209	72.222	22.70	9.49	37.66	4.30
237	238	3.346734	GGGAGGAATGGTGGGGCA	61.347	66.667	0.00	0.00	0.00	5.36
304	306	0.454957	CCGAGCATGTTTTTCGCAGG	60.455	55.000	0.00	0.00	33.25	4.85
488	490	9.620660	GTGAAGTATGTTCCACGAAATTTAAAT	57.379	29.630	0.00	0.00	0.00	1.40
824	1965	0.323178	AAGAATGGCTGGCTGGACAG	60.323	55.000	2.00	0.00	41.41	3.51
879	2020	5.657745	TCCAGTTTCCACTATATAACGTCCA	59.342	40.000	0.00	0.00	0.00	4.02
899	3343	3.549827	CCACATATCTCTGAGTCGTGAGC	60.550	52.174	4.32	0.00	0.00	4.26
942	3386	2.483877	CTCAAGGCAGTTACAATTCGCA	59.516	45.455	0.00	0.00	0.00	5.10
976	3467	5.393461	GCCAACTATTTCCTCCAATTCTGTG	60.393	44.000	0.00	0.00	0.00	3.66
1333	3828	1.071699	ACCGGAAAAGCTTGCACTCTA	59.928	47.619	9.46	0.00	0.00	2.43
1389	3884	1.135689	GTTTGCATGAATCTCGGCGTT	60.136	47.619	6.85	0.00	0.00	4.84
1516	4011	2.387445	CCGCTCAATTTCGTCGGCA	61.387	57.895	0.00	0.00	33.36	5.69
1737	4232	2.669229	TACTGCGTCGGTCCGTCA	60.669	61.111	11.88	7.25	0.00	4.35
1842	4340	2.745152	CGTGTTCTTCTGTTTGGGGAGT	60.745	50.000	0.00	0.00	0.00	3.85
1856	4354	1.153549	GGAGTAAGGGCACGCTCTG	60.154	63.158	0.00	0.00	0.00	3.35
1999	4497	1.214589	GGAACTTGACGCGCTCCTA	59.785	57.895	5.73	0.00	0.00	2.94
2048	4547	3.229697	GCAGGGGCCTATTATCAAGTT	57.770	47.619	0.84	0.00	0.00	2.66
2125	4624	0.174845	CTGCGGATGGAACTCGGTAA	59.825	55.000	0.00	0.00	0.00	2.85
2379	4878	2.935481	CTGGAGGAAGGTGGCCCA	60.935	66.667	0.00	0.00	0.00	5.36
2415	4914	3.476552	TGTCCAGTTTCTGTTGGATGTC	58.523	45.455	0.00	0.00	44.74	3.06
2418	4917	3.138304	CCAGTTTCTGTTGGATGTCGAA	58.862	45.455	0.00	0.00	36.55	3.71
2494	4996	1.825090	CATGTTGCTAGTCCAAGCCA	58.175	50.000	0.00	0.00	42.05	4.75
2511	5013	3.313791	AGCCACCCCTGTTTACATTTTT	58.686	40.909	0.00	0.00	0.00	1.94
2521	5023	6.102663	CCTGTTTACATTTTTGTTGTGTGGA	58.897	36.000	0.00	0.00	0.00	4.02
2522	5024	6.760770	CCTGTTTACATTTTTGTTGTGTGGAT	59.239	34.615	0.00	0.00	0.00	3.41
2551	5053	2.021355	AGTCACTACTACCTCCGTCG	57.979	55.000	0.00	0.00	32.84	5.12
2618	5120	8.439971	ACTAGGCACATTATTCATAGATTTGGA	58.560	33.333	0.00	0.00	0.00	3.53
2667	5169	5.779771	AGTCCATCCTTTATTGCCAGAAAAA	59.220	36.000	0.00	0.00	0.00	1.94
2669	5171	5.187576	TCCATCCTTTATTGCCAGAAAAAGG	59.812	40.000	6.39	6.39	46.14	3.11
2847	5354	1.691196	TTTCCCAACAGTCAGCCAAG	58.309	50.000	0.00	0.00	0.00	3.61
2850	5357	0.109342	CCCAACAGTCAGCCAAGAGT	59.891	55.000	0.00	0.00	0.00	3.24
2870	5377	1.189752	CTGCTGGTCAGGAAGCTAGA	58.810	55.000	0.00	0.00	40.21	2.43
2895	5414	3.569194	TTGTCCAACCAGCTTTCAGTA	57.431	42.857	0.00	0.00	0.00	2.74
2919	5438	2.621998	AGAATGCTTGGCACAGATATGC	59.378	45.455	0.00	0.00	43.04	3.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	0.759959	TGGCTGGACGTTGTTAAGGA	59.240	50.000	0.00	0.00	0.00	3.36
60	61	3.311110	GTGAGGTCCTGGCGGTCA	61.311	66.667	0.00	0.00	0.00	4.02
134	135	0.599204	GCGGTGTTTCTTCTCGTGGA	60.599	55.000	0.00	0.00	0.00	4.02
202	203	4.704103	TCCTCCTCCTGCCGTGCT	62.704	66.667	0.00	0.00	0.00	4.40
237	238	0.395448	GGGCGTGACTCTACCCTAGT	60.395	60.000	0.00	0.00	39.42	2.57
285	287	0.454957	CCTGCGAAAAACATGCTCGG	60.455	55.000	0.00	0.00	33.23	4.63
291	293	1.617850	TGATTGCCCTGCGAAAAACAT	59.382	42.857	0.00	0.00	0.00	2.71
304	306	8.865590	TTTACTTGTCTTAAAAACTGATTGCC	57.134	30.769	0.00	0.00	0.00	4.52
451	453	8.443937	GTGGAACATACTTCACTCATTTCTTAC	58.556	37.037	0.00	0.00	44.52	2.34
452	454	7.330946	CGTGGAACATACTTCACTCATTTCTTA	59.669	37.037	0.00	0.00	44.52	2.10
453	455	6.147821	CGTGGAACATACTTCACTCATTTCTT	59.852	38.462	0.00	0.00	44.52	2.52
516	518	5.352569	CCTCACAGCGAGATCTTTAAAACAT	59.647	40.000	0.00	0.00	45.45	2.71
879	2020	3.550820	AGCTCACGACTCAGAGATATGT	58.449	45.455	3.79	0.00	33.74	2.29
899	3343	0.529378	GAGCAGTTTGGGCATGGAAG	59.471	55.000	0.00	0.00	0.00	3.46
976	3467	4.986467	CCTATGGAAGGTGGGTGC	57.014	61.111	0.00	0.00	40.94	5.01
1333	3828	2.289631	TGCAGAACATGTCGAGGACAAT	60.290	45.455	0.00	0.00	45.96	2.71
1389	3884	0.040157	CGAAGAACGTGTACACCGGA	60.040	55.000	20.11	0.00	37.22	5.14
1395	3890	0.038892	TCCCTGCGAAGAACGTGTAC	60.039	55.000	0.00	0.00	44.60	2.90
1789	4287	2.356313	CTGCACGTCGAGCCACTT	60.356	61.111	12.18	0.00	0.00	3.16
1842	4340	1.888436	CTGTCCAGAGCGTGCCCTTA	61.888	60.000	0.00	0.00	0.00	2.69
1856	4354	0.108233	CTCCTTCAGCTGCTCTGTCC	60.108	60.000	9.47	0.00	43.32	4.02
1957	4455	2.001269	AGGGCGCCCTTCCAAGTAT	61.001	57.895	42.84	18.14	45.70	2.12
2038	4536	1.102978	GGCGCCCACAACTTGATAAT	58.897	50.000	18.11	0.00	0.00	1.28
2041	4539	3.055719	CGGCGCCCACAACTTGAT	61.056	61.111	23.46	0.00	0.00	2.57
2396	4895	2.367241	TCGACATCCAACAGAAACTGGA	59.633	45.455	0.00	0.00	45.65	3.86
2415	4914	3.908382	CGAGTTGCTTTCCAAGATTTTCG	59.092	43.478	0.00	0.00	33.21	3.46
2418	4917	2.029918	GCCGAGTTGCTTTCCAAGATTT	60.030	45.455	0.00	0.00	33.21	2.17
2494	4996	5.046231	ACACAACAAAAATGTAAACAGGGGT	60.046	36.000	0.00	0.00	0.00	4.95
2511	5013	8.995220	GTGACTTAAGTTATTATCCACACAACA	58.005	33.333	10.02	0.00	0.00	3.33
2522	5024	9.113838	CGGAGGTAGTAGTGACTTAAGTTATTA	57.886	37.037	10.02	4.01	37.10	0.98
2551	5053	7.009179	TCCATATGGGTCATATTCTTGAGAC	57.991	40.000	21.78	0.00	35.18	3.36
2652	5154	7.504403	TGATGTTTCCTTTTTCTGGCAATAAA	58.496	30.769	0.00	0.00	0.00	1.40
2830	5337	0.397941	CTCTTGGCTGACTGTTGGGA	59.602	55.000	0.00	0.00	0.00	4.37
2870	5377	3.513515	TGAAAGCTGGTTGGACAAAACTT	59.486	39.130	0.00	0.00	0.00	2.66
2895	5414	3.641434	ATCTGTGCCAAGCATTCTAGT	57.359	42.857	0.00	0.00	41.91	2.57
2919	5438	6.801539	TTAAGATCAATTAATAGCCTGGCG	57.198	37.500	13.96	0.00	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.