AutoCloner

Multiple sequence alignment - TraesCS1B01G020000

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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	TraesCS1B01G020000	chr1B	100.000	2929	0	0	1	2929	9416508	9413580	0.000000e+00	5409.0
1	TraesCS1B01G020000	chr1B	83.838	297	48	0	2554	2850	468510558	468510854	1.720000e-72	283.0
2	TraesCS1B01G020000	chr1B	78.744	207	42	2	2644	2849	637594625	637594420	1.420000e-28	137.0
3	TraesCS1B01G020000	chr1B	95.556	45	2	0	1177	1221	491083440	491083396	4.050000e-09	73.1
4	TraesCS1B01G020000	chr1D	92.897	2520	130	11	1	2479	7130980	7128469	0.000000e+00	3616.0
5	TraesCS1B01G020000	chr1D	90.008	1251	59	13	7	1204	7652132	7653369	0.000000e+00	1557.0
6	TraesCS1B01G020000	chr1D	88.495	930	68	19	1233	2143	7653369	7654278	0.000000e+00	1088.0
7	TraesCS1B01G020000	chr1D	95.098	408	20	0	2522	2929	7128470	7128063	0.000000e+00	643.0
8	TraesCS1B01G020000	chr1D	84.848	297	45	0	2554	2850	347409381	347409677	1.710000e-77	300.0
9	TraesCS1B01G020000	chr1D	93.333	45	3	0	1177	1221	466370175	466370219	1.880000e-07	67.6
10	TraesCS1B01G020000	chr1A	90.625	992	65	12	696	1687	8677822	8676859	0.000000e+00	1291.0
11	TraesCS1B01G020000	chr1A	88.465	1049	75	18	1679	2684	8675624	8674579	0.000000e+00	1225.0
12	TraesCS1B01G020000	chr1A	94.276	297	14	2	1	297	8678321	8678028	4.450000e-123	451.0
13	TraesCS1B01G020000	chr1A	83.838	297	48	0	2554	2850	448034393	448034689	1.720000e-72	283.0
14	TraesCS1B01G020000	chr1A	85.833	120	14	2	2744	2863	8674581	8674465	1.100000e-24	124.0
15	TraesCS1B01G020000	chr2B	73.529	646	142	24	1292	1925	761707136	761707764	4.910000e-53	219.0
16	TraesCS1B01G020000	chr2D	72.835	589	139	18	1320	1899	620812257	620812833	6.450000e-42	182.0
17	TraesCS1B01G020000	chr3B	92.308	52	3	1	1167	1217	420417298	420417247	4.050000e-09	73.1
18	TraesCS1B01G020000	chr6B	93.023	43	3	0	1175	1217	508613007	508613049	2.440000e-06	63.9
19	TraesCS1B01G020000	chr3D	93.182	44	2	1	1174	1217	557459142	557459100	2.440000e-06	63.9
20	TraesCS1B01G020000	chr3A	97.297	37	1	0	1181	1217	434000930	434000894	2.440000e-06	63.9
21	TraesCS1B01G020000	chr3A	85.965	57	6	2	1163	1217	710863526	710863582	3.150000e-05	60.2

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	TraesCS1B01G020000	chr1B	9413580	9416508	2928	True	5409.00	5409	100.00000	1	2929	1	chr1B.!!$R1	2928
1	TraesCS1B01G020000	chr1D	7128063	7130980	2917	True	2129.50	3616	93.99750	1	2929	2	chr1D.!!$R1	2928
2	TraesCS1B01G020000	chr1D	7652132	7654278	2146	False	1322.50	1557	89.25150	7	2143	2	chr1D.!!$F3	2136
3	TraesCS1B01G020000	chr1A	8674465	8678321	3856	True	772.75	1291	89.79975	1	2863	4	chr1A.!!$R1	2862
4	TraesCS1B01G020000	chr2B	761707136	761707764	628	False	219.00	219	73.52900	1292	1925	1	chr2B.!!$F1	633

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
938	996	0.700564	AGGGACCACAAGATGCATGT	59.299	50.0	2.46	0.0	0.0	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1930	3231	0.392998	ACCAAGATGTGCCATCCGAC	60.393	55.0	10.46	0.0	0.0	4.79	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
51	52	3.001838	TGAACATATATCCAAACGTGCGC	59.998	43.478	0.00	0.00	0.00	6.09
80	82	6.489022	AGAACCTTGTTTAAGCCTACGATTTT	59.511	34.615	0.00	0.00	32.40	1.82
233	235	4.230657	TGTTTTCCACTTTTCACGTTGTG	58.769	39.130	0.00	0.00	34.45	3.33
235	237	5.048921	TGTTTTCCACTTTTCACGTTGTGTA	60.049	36.000	0.00	0.00	34.79	2.90
405	449	5.216566	TCATAAATCTCGTTTTCTTGCCG	57.783	39.130	0.00	0.00	0.00	5.69
507	554	3.181487	GGCATATGTTTCGTCCAGCATTT	60.181	43.478	4.29	0.00	0.00	2.32
622	669	1.270147	ACCTACGCCCATCGCTTAATC	60.270	52.381	0.00	0.00	43.23	1.75
624	671	1.000955	CTACGCCCATCGCTTAATCCT	59.999	52.381	0.00	0.00	43.23	3.24
873	928	7.518188	ACCTGACAGGGTTATATTAAGATTGG	58.482	38.462	25.34	0.00	40.58	3.16
889	947	8.792830	TTAAGATTGGTCATGAGGTTTCTTAG	57.207	34.615	0.00	0.00	0.00	2.18
905	963	9.220767	AGGTTTCTTAGAATCAAGTATGTTGTC	57.779	33.333	0.00	0.00	0.00	3.18
937	995	1.100510	CAGGGACCACAAGATGCATG	58.899	55.000	2.46	0.00	0.00	4.06
938	996	0.700564	AGGGACCACAAGATGCATGT	59.299	50.000	2.46	0.00	0.00	3.21
939	997	1.098050	GGGACCACAAGATGCATGTC	58.902	55.000	2.46	3.74	0.00	3.06
991	1049	2.886523	CACATTGCTCTTGGTCTTGGAA	59.113	45.455	0.00	0.00	0.00	3.53
993	1051	3.760684	ACATTGCTCTTGGTCTTGGAATC	59.239	43.478	0.00	0.00	0.00	2.52
1005	1063	4.518211	GGTCTTGGAATCTGGCATATGAAG	59.482	45.833	6.97	3.14	0.00	3.02
1037	1095	1.208052	GCATGCTGAGAAGTCTACCCA	59.792	52.381	11.37	0.00	0.00	4.51
1052	1110	0.325671	ACCCACCCATCAGAGATCGT	60.326	55.000	0.00	0.00	0.00	3.73
1157	1215	4.953269	TGTGTTTGAATTCGCTCGATTAC	58.047	39.130	0.04	0.00	0.00	1.89
1163	1221	8.132995	TGTTTGAATTCGCTCGATTACTAGATA	58.867	33.333	0.00	0.00	0.00	1.98
1231	1289	6.981559	CAGAGGTAGTAGTTTATTTCCTGCTC	59.018	42.308	0.00	0.00	0.00	4.26
1467	1525	1.676014	GCAACGGTGGCTACTCTCAAT	60.676	52.381	0.90	0.00	0.00	2.57
1568	1626	0.321122	GCCAGAGGGACAAGACAGTG	60.321	60.000	0.00	0.00	35.59	3.66
1575	1633	0.819259	GGACAAGACAGTGGCAGCAA	60.819	55.000	0.00	0.00	0.00	3.91
1587	1645	1.801771	TGGCAGCAACAACACGTATAC	59.198	47.619	0.00	0.00	0.00	1.47
1600	1658	4.752146	ACACGTATACTAGGCTTTTGGTC	58.248	43.478	0.00	0.00	0.00	4.02
1673	1731	1.888512	GTTGTCCGTCTACAGGGTACA	59.111	52.381	0.00	0.00	0.00	2.90
1751	3052	1.801983	CGCAACTACATGGCATGCA	59.198	52.632	26.70	14.01	36.84	3.96
1752	3053	0.382873	CGCAACTACATGGCATGCAT	59.617	50.000	26.70	11.46	36.84	3.96
1854	3155	2.645604	GGGGGATTTGGGAGGATCA	58.354	57.895	0.00	0.00	36.25	2.92
2021	3330	0.525668	CACTAGCTACTTGACCGCCG	60.526	60.000	0.00	0.00	0.00	6.46
2126	3444	2.082231	CACATCTTGAGCTTGTCTGGG	58.918	52.381	0.00	0.00	0.00	4.45
2230	3548	2.125350	CTTGGCGAGGCTCCTGAC	60.125	66.667	9.32	0.00	0.00	3.51
2266	3602	2.969827	GGGTTGCCGAAACATGGG	59.030	61.111	0.00	0.00	40.86	4.00
2291	3627	4.954118	ACGGTGACCCTGAGGCCA	62.954	66.667	5.01	0.00	36.11	5.36
2378	3714	0.617820	GGGCTACCCTCTCAACCTCA	60.618	60.000	0.00	0.00	41.34	3.86
2392	3728	1.794714	ACCTCAATCATAGTCCCGCT	58.205	50.000	0.00	0.00	0.00	5.52
2397	3733	4.191544	CTCAATCATAGTCCCGCTTTTGA	58.808	43.478	0.00	0.00	0.00	2.69
2451	3804	3.426191	CGCAGCTTTAGTGTACGTTGTAA	59.574	43.478	0.00	0.00	0.00	2.41
2452	3805	4.432503	CGCAGCTTTAGTGTACGTTGTAAG	60.433	45.833	0.00	0.00	0.00	2.34
2483	3837	4.291783	GTCGACTAATTTGGATCTCGGAG	58.708	47.826	8.70	0.00	0.00	4.63
2497	3851	2.824341	TCTCGGAGGGAGTAGTTTGTTC	59.176	50.000	4.96	0.00	43.60	3.18
2500	3854	2.353803	CGGAGGGAGTAGTTTGTTCCTG	60.354	54.545	0.00	0.00	0.00	3.86
2519	3873	7.451255	TGTTCCTGGAGTTATGTTGATTGATTT	59.549	33.333	0.00	0.00	0.00	2.17
2608	3965	3.945436	GACACCGATGTCGTTGCA	58.055	55.556	0.00	0.00	45.66	4.08
2687	4044	2.049433	AACAACTCGGCCTCGTCG	60.049	61.111	0.00	0.00	37.69	5.12
2735	4092	0.109597	GGCAAGCCATGAAAGTCACG	60.110	55.000	6.14	0.00	35.81	4.35
2774	4131	2.185867	GGCCCATTAGCGTCGACA	59.814	61.111	17.16	0.00	0.00	4.35
2785	4142	2.741092	GTCGACAAGCTCCACCCA	59.259	61.111	11.55	0.00	0.00	4.51
2920	4277	8.780846	TTGATATACCGGCGATTTTACATATT	57.219	30.769	9.30	0.00	0.00	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	4.830826	AGGCTTAAACAAGGTTCTTTCG	57.169	40.909	0.00	0.00	0.00	3.46
405	449	1.379309	AGGAGGAGGACGAGTGCTC	60.379	63.158	15.07	15.07	45.76	4.26
407	451	2.419739	GGAGGAGGAGGACGAGTGC	61.420	68.421	0.00	0.00	0.00	4.40
622	669	3.004734	GTCACCAATGGTTGAAAGACAGG	59.995	47.826	0.16	0.00	31.02	4.00
624	671	2.955660	GGTCACCAATGGTTGAAAGACA	59.044	45.455	17.79	0.00	31.02	3.41
804	859	2.853594	CCATGATGCACGTTTACATTGC	59.146	45.455	0.00	0.00	36.76	3.56
866	921	7.020827	TCTAAGAAACCTCATGACCAATCTT	57.979	36.000	11.58	11.58	0.00	2.40
873	928	7.913674	ACTTGATTCTAAGAAACCTCATGAC	57.086	36.000	0.00	0.00	0.00	3.06
889	947	4.032900	ACGATGCGACAACATACTTGATTC	59.967	41.667	0.00	0.00	0.00	2.52
905	963	0.168128	GTCCCTGGAAAAACGATGCG	59.832	55.000	0.00	0.00	0.00	4.73
937	995	0.664767	GCAGGGATCGCTATGACGAC	60.665	60.000	12.54	0.00	46.28	4.34
939	997	0.037882	ATGCAGGGATCGCTATGACG	60.038	55.000	12.54	0.76	0.00	4.35
991	1049	4.657504	TCCAGTCTTCTTCATATGCCAGAT	59.342	41.667	0.00	0.00	0.00	2.90
993	1051	4.100653	TCTCCAGTCTTCTTCATATGCCAG	59.899	45.833	0.00	0.00	0.00	4.85
1005	1063	1.206610	TCAGCATGCTCTCCAGTCTTC	59.793	52.381	19.68	0.00	34.76	2.87
1052	1110	4.069232	CGCCAGCTTCGACCCAGA	62.069	66.667	0.00	0.00	0.00	3.86
1467	1525	3.962063	TCCCGTATGTACTTGAAGGCATA	59.038	43.478	0.00	2.65	0.00	3.14
1568	1626	2.073816	AGTATACGTGTTGTTGCTGCC	58.926	47.619	0.00	0.00	0.00	4.85
1575	1633	4.933400	CCAAAAGCCTAGTATACGTGTTGT	59.067	41.667	0.00	0.00	0.00	3.32
1587	1645	0.245539	TCGACGGACCAAAAGCCTAG	59.754	55.000	0.00	0.00	0.00	3.02
1673	1731	8.487028	CCTCCTTTGTAGTTAAATAGATCAGGT	58.513	37.037	0.00	0.00	0.00	4.00
1751	3052	4.503714	ACCATAACCGACAATCAGGAAT	57.496	40.909	0.00	0.00	0.00	3.01
1752	3053	3.992943	ACCATAACCGACAATCAGGAA	57.007	42.857	0.00	0.00	0.00	3.36
1854	3155	1.372997	CGTCAGCAACGTGCCTACT	60.373	57.895	6.39	0.00	46.52	2.57
1876	3177	2.694616	AAACATACCCAAGGCACCTT	57.305	45.000	0.00	0.00	36.60	3.50
1930	3231	0.392998	ACCAAGATGTGCCATCCGAC	60.393	55.000	10.46	0.00	0.00	4.79
1998	3307	2.366533	CGGTCAAGTAGCTAGTGAGGA	58.633	52.381	0.73	0.00	0.00	3.71
2126	3444	6.235664	TCAGTCCCTCTTAATACAAACCAAC	58.764	40.000	0.00	0.00	0.00	3.77
2230	3548	0.508641	CGTTGGAACACGCTCTCTTG	59.491	55.000	0.00	0.00	39.29	3.02
2266	3602	2.183555	GGGTCACCGTCGTGGATC	59.816	66.667	3.47	0.00	42.00	3.36
2291	3627	2.441532	GTGGAGCAGCATGGCCAT	60.442	61.111	14.09	14.09	35.86	4.40
2373	3709	1.794714	AGCGGGACTATGATTGAGGT	58.205	50.000	0.00	0.00	0.00	3.85
2378	3714	2.936498	CGTCAAAAGCGGGACTATGATT	59.064	45.455	0.00	0.00	29.88	2.57
2451	3804	3.314541	AATTAGTCGACGCACCTTTCT	57.685	42.857	10.46	0.00	0.00	2.52
2452	3805	3.424433	CCAAATTAGTCGACGCACCTTTC	60.424	47.826	10.46	0.00	0.00	2.62
2483	3837	2.638363	ACTCCAGGAACAAACTACTCCC	59.362	50.000	0.00	0.00	0.00	4.30
2497	3851	8.511604	AGTAAATCAATCAACATAACTCCAGG	57.488	34.615	0.00	0.00	0.00	4.45
2601	3958	0.744281	TGCTATCCGAGATGCAACGA	59.256	50.000	11.69	0.00	32.12	3.85
2608	3965	2.896044	TCATGCTTCTGCTATCCGAGAT	59.104	45.455	0.00	0.00	40.48	2.75
2650	4007	3.490031	AACATGGTCGCCACTGCCA	62.490	57.895	0.00	0.00	35.80	4.92
2687	4044	1.819632	GGTCGTCATGGCCACATCC	60.820	63.158	8.16	1.07	34.35	3.51
2735	4092	1.139058	ACCCACTATGGAGCATTCGAC	59.861	52.381	0.00	0.00	40.96	4.20
2764	4121	1.211969	GTGGAGCTTGTCGACGCTA	59.788	57.895	16.49	1.45	36.45	4.26
2774	4131	1.152030	TGAGGACTGGGTGGAGCTT	60.152	57.895	0.00	0.00	0.00	3.74
2785	4142	1.187087	GGTGAGATTCGGTGAGGACT	58.813	55.000	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.