AutoCloner

Multiple sequence alignment - TraesCS6D01G282600

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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	TraesCS6D01G282600	chr6D	100.000	5155	0	0	1	5155	389970279	389975433	0.000000e+00	9520.0
1	TraesCS6D01G282600	chr6D	87.437	199	17	3	3223	3421	445766140	445765950	6.720000e-54	222.0
2	TraesCS6D01G282600	chr6A	91.802	1842	95	21	2145	3957	536252653	536254467	0.000000e+00	2514.0
3	TraesCS6D01G282600	chr6A	92.222	720	38	10	895	1600	536251476	536252191	0.000000e+00	1003.0
4	TraesCS6D01G282600	chr6A	83.882	881	72	34	4312	5155	536254821	536255668	0.000000e+00	776.0
5	TraesCS6D01G282600	chr6A	91.989	362	11	3	4000	4352	536254466	536254818	4.640000e-135	492.0
6	TraesCS6D01G282600	chr6A	78.378	111	13	5	85	192	558992969	558992867	1.550000e-05	62.1
7	TraesCS6D01G282600	chr6B	91.898	938	60	7	1938	2871	583613125	583614050	0.000000e+00	1297.0
8	TraesCS6D01G282600	chr6B	92.201	718	43	10	893	1603	583612110	583612821	0.000000e+00	1003.0
9	TraesCS6D01G282600	chr6B	94.424	538	20	4	3648	4177	583614554	583615089	0.000000e+00	819.0
10	TraesCS6D01G282600	chr6B	90.681	558	25	17	4602	5155	584310862	584310328	0.000000e+00	717.0
11	TraesCS6D01G282600	chr6B	89.614	337	19	7	2887	3223	583614161	583614481	1.030000e-111	414.0
12	TraesCS6D01G282600	chr6B	80.952	441	35	16	4199	4623	584311357	584310950	2.330000e-78	303.0
13	TraesCS6D01G282600	chr6B	86.441	236	21	6	3223	3457	672366444	672366219	1.110000e-61	248.0
14	TraesCS6D01G282600	chr2D	92.659	899	36	5	1	898	498318939	498318070	0.000000e+00	1267.0
15	TraesCS6D01G282600	chr2D	77.778	198	37	6	658	849	459315992	459315796	1.170000e-21	115.0
16	TraesCS6D01G282600	chr2A	95.789	475	19	1	1	475	181837086	181836613	0.000000e+00	765.0
17	TraesCS6D01G282600	chr2A	92.701	411	28	2	484	894	181815407	181814999	4.450000e-165	592.0
18	TraesCS6D01G282600	chr7B	88.756	587	53	12	324	907	135982278	135981702	0.000000e+00	706.0
19	TraesCS6D01G282600	chr7B	92.331	326	20	3	1	325	135982694	135982373	4.700000e-125	459.0
20	TraesCS6D01G282600	chr3B	86.806	576	47	8	324	872	66472903	66473476	2.640000e-172	616.0
21	TraesCS6D01G282600	chr3B	92.923	325	23	0	1	325	66472537	66472861	1.680000e-129	473.0
22	TraesCS6D01G282600	chr3B	93.103	116	8	0	3306	3421	812340196	812340311	2.470000e-38	171.0
23	TraesCS6D01G282600	chr3B	79.412	238	43	6	615	849	237112993	237112759	4.130000e-36	163.0
24	TraesCS6D01G282600	chr2B	85.366	574	47	20	324	894	604325096	604324557	1.250000e-155	560.0
25	TraesCS6D01G282600	chr2B	94.462	325	18	0	1	325	604325566	604325242	7.710000e-138	501.0
26	TraesCS6D01G282600	chr2B	87.202	336	37	4	555	890	604324422	604324093	1.350000e-100	377.0
27	TraesCS6D01G282600	chr5A	88.811	286	25	6	1	281	324467041	324466758	1.370000e-90	344.0
28	TraesCS6D01G282600	chr5A	91.000	200	15	3	79	276	469132221	469132023	3.060000e-67	267.0
29	TraesCS6D01G282600	chr5A	85.128	195	27	1	3226	3420	330196273	330196081	1.130000e-46	198.0
30	TraesCS6D01G282600	chr3A	89.140	221	22	1	3225	3445	455780260	455780042	1.830000e-69	274.0
31	TraesCS6D01G282600	chr3A	89.950	199	17	2	3226	3421	182637175	182637373	2.380000e-63	254.0
32	TraesCS6D01G282600	chr3A	91.057	123	11	0	3306	3428	734786096	734786218	3.190000e-37	167.0
33	TraesCS6D01G282600	chr7A	91.195	159	12	1	1219	1375	137763680	137763838	1.120000e-51	215.0
34	TraesCS6D01G282600	chr7D	92.908	141	10	0	1235	1375	137555468	137555608	6.770000e-49	206.0
35	TraesCS6D01G282600	chr7D	80.000	205	35	6	693	894	25280062	25279861	4.160000e-31	147.0
36	TraesCS6D01G282600	chr5D	83.249	197	30	3	3226	3421	242123599	242123793	1.470000e-40	178.0
37	TraesCS6D01G282600	chr3D	87.603	121	13	1	3225	3345	337952838	337952720	6.960000e-29	139.0

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	TraesCS6D01G282600	chr6D	389970279	389975433	5154	False	9520.000000	9520	100.00000	1	5155	1	chr6D.!!$F1	5154
1	TraesCS6D01G282600	chr6A	536251476	536255668	4192	False	1196.250000	2514	89.97375	895	5155	4	chr6A.!!$F1	4260
2	TraesCS6D01G282600	chr6B	583612110	583615089	2979	False	883.250000	1297	92.03425	893	4177	4	chr6B.!!$F1	3284
3	TraesCS6D01G282600	chr6B	584310328	584311357	1029	True	510.000000	717	85.81650	4199	5155	2	chr6B.!!$R2	956
4	TraesCS6D01G282600	chr2D	498318070	498318939	869	True	1267.000000	1267	92.65900	1	898	1	chr2D.!!$R2	897
5	TraesCS6D01G282600	chr7B	135981702	135982694	992	True	582.500000	706	90.54350	1	907	2	chr7B.!!$R1	906
6	TraesCS6D01G282600	chr3B	66472537	66473476	939	False	544.500000	616	89.86450	1	872	2	chr3B.!!$F2	871
7	TraesCS6D01G282600	chr2B	604324093	604325566	1473	True	479.333333	560	89.01000	1	894	3	chr2B.!!$R1	893

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
600	1197	0.937304	CGATACTTGGCGTCCCATTG	59.063	55.0	0.00	0.0	41.78	2.82	F
1473	2085	0.251033	TCTGTTGCTCTTGCTGCCAT	60.251	50.0	0.00	0.0	40.48	4.40	F
1639	2263	0.035317	TGACACATGACTGCTGTCCC	59.965	55.0	19.64	0.0	42.28	4.46	F
1685	2309	0.036105	ACTGCTGCATCATTCGGACA	60.036	50.0	1.31	0.0	0.00	4.02	F
2224	2915	0.040204	AGCCCCCAGAAACAATCAGG	59.960	55.0	0.00	0.0	34.56	3.86	F
3280	4129	0.447801	GCATGACAAATCGAACGCCT	59.552	50.0	0.00	0.0	0.00	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1620	2244	0.035317	GGGACAGCAGTCATGTGTCA	59.965	55.000	11.67	0.0	46.80	3.58	R
2981	3781	0.034476	CTGGCTCAGCACAGAGTTCA	59.966	55.000	8.98	0.0	37.94	3.18	R
3302	4151	1.106285	AAGGAAATTGCCATCCTCGC	58.894	50.000	4.92	0.0	45.33	5.03	R
3303	4152	4.157656	TGTTAAAGGAAATTGCCATCCTCG	59.842	41.667	4.92	0.0	45.33	4.63	R
3983	4841	0.698238	CAGTCCCACCAGATTCCCAA	59.302	55.000	0.00	0.0	0.00	4.12	R
5127	6206	0.400670	CTAAAGAGGGGAGGAGGGGG	60.401	65.000	0.00	0.0	0.00	5.40	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
422	573	3.022406	GGTAGTGGGTAGGTCTGTACTG	58.978	54.545	0.00	0.00	0.00	2.74
465	616	4.124851	ACCTGACGGTCTCAATACATTC	57.875	45.455	9.88	0.00	40.27	2.67
600	1197	0.937304	CGATACTTGGCGTCCCATTG	59.063	55.000	0.00	0.00	41.78	2.82
732	1332	2.501128	GACTAGCGCCATCAGCCA	59.499	61.111	2.29	0.00	38.78	4.75
812	1412	3.818387	CACGCTCGAGTCAAGTTAAGTA	58.182	45.455	15.13	0.00	0.00	2.24
820	1420	6.220930	TCGAGTCAAGTTAAGTAACTGCAAT	58.779	36.000	4.52	0.00	45.17	3.56
823	1423	7.095607	CGAGTCAAGTTAAGTAACTGCAATTCT	60.096	37.037	4.52	0.00	45.17	2.40
861	1461	8.403236	GTTCTAACACCAAACTAAACATTGAGT	58.597	33.333	0.00	0.00	0.00	3.41
862	1462	9.616156	TTCTAACACCAAACTAAACATTGAGTA	57.384	29.630	0.00	0.00	0.00	2.59
863	1463	9.616156	TCTAACACCAAACTAAACATTGAGTAA	57.384	29.630	0.00	0.00	0.00	2.24
1016	1616	1.978580	TCTGTTTGTCTTCTCCCTCCC	59.021	52.381	0.00	0.00	0.00	4.30
1022	1622	2.692741	CTTCTCCCTCCCCCACCC	60.693	72.222	0.00	0.00	0.00	4.61
1023	1623	3.216371	TTCTCCCTCCCCCACCCT	61.216	66.667	0.00	0.00	0.00	4.34
1138	1741	2.690778	GCCGATTTGCGTGGCTTCT	61.691	57.895	0.00	0.00	45.40	2.85
1193	1796	2.812619	GGCCTCTCGGATCTTGGGG	61.813	68.421	0.00	0.00	0.00	4.96
1210	1820	2.035783	GGGAAGAAGGTGGGTGGC	59.964	66.667	0.00	0.00	0.00	5.01
1429	2040	0.449388	CCTGATCCGCTTGCTTGAAC	59.551	55.000	0.00	0.00	0.00	3.18
1459	2071	1.237285	AAAAGATGCGCGCCTCTGTT	61.237	50.000	34.23	31.58	0.00	3.16
1473	2085	0.251033	TCTGTTGCTCTTGCTGCCAT	60.251	50.000	0.00	0.00	40.48	4.40
1475	2087	1.214589	GTTGCTCTTGCTGCCATGG	59.785	57.895	7.63	7.63	40.48	3.66
1486	2105	2.440247	GCCATGGAGTTTCGGGGG	60.440	66.667	18.40	0.00	0.00	5.40
1500	2119	1.968493	TCGGGGGTCATGTATAGCTTC	59.032	52.381	0.00	0.00	0.00	3.86
1548	2172	2.255316	GCTCGTGCAGTTCTAGTCTTC	58.745	52.381	4.26	0.00	39.41	2.87
1549	2173	2.510874	CTCGTGCAGTTCTAGTCTTCG	58.489	52.381	0.00	0.00	0.00	3.79
1552	2176	2.350484	CGTGCAGTTCTAGTCTTCGTCA	60.350	50.000	0.00	0.00	0.00	4.35

Showing 1 to 25 of 306 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
422	573	1.358759	CAACCCAAGACAACACGCC	59.641	57.895	0.00	0.00	0.00	5.68
766	1366	8.026026	TGCACATACGATCACAAAATACATTTT	58.974	29.630	0.00	0.00	40.37	1.82
782	1382	1.226295	CTCGAGCGTGCACATACGA	60.226	57.895	18.64	20.33	46.46	3.43
841	1441	8.745590	ACTTTTACTCAATGTTTAGTTTGGTGT	58.254	29.630	0.00	0.00	0.00	4.16
861	1461	6.288941	TCACCGGTCATCATAGAACTTTTA	57.711	37.500	2.59	0.00	0.00	1.52
862	1462	5.160607	TCACCGGTCATCATAGAACTTTT	57.839	39.130	2.59	0.00	0.00	2.27
863	1463	4.819105	TCACCGGTCATCATAGAACTTT	57.181	40.909	2.59	0.00	0.00	2.66
876	1476	4.100498	TGAAAGGAGGTAATATCACCGGTC	59.900	45.833	2.59	0.00	43.84	4.79
952	1552	3.556423	CCTCGGTACTTTAACTGGTGCTT	60.556	47.826	0.00	0.00	0.00	3.91
1079	1682	0.802494	GAATTCTTGCTTTCGCCCGA	59.198	50.000	0.00	0.00	34.43	5.14
1080	1683	0.179163	GGAATTCTTGCTTTCGCCCG	60.179	55.000	5.23	0.00	34.43	6.13
1083	1686	1.791914	GCGAGGAATTCTTGCTTTCGC	60.792	52.381	5.23	12.22	46.85	4.70
1134	1737	1.302832	AGAAAGGGCCGCACAGAAG	60.303	57.895	0.00	0.00	0.00	2.85
1193	1796	2.035783	GCCACCCACCTTCTTCCC	59.964	66.667	0.00	0.00	0.00	3.97
1459	2071	1.378119	CTCCATGGCAGCAAGAGCA	60.378	57.895	6.96	0.00	45.49	4.26
1473	2085	1.131303	ACATGACCCCCGAAACTCCA	61.131	55.000	0.00	0.00	0.00	3.86
1475	2087	3.802675	GCTATACATGACCCCCGAAACTC	60.803	52.174	0.00	0.00	0.00	3.01
1507	2126	0.111001	CCACGCAACGACCGTAAAAG	60.111	55.000	0.00	0.00	37.12	2.27
1517	2141	4.354212	CACGAGCACCACGCAACG	62.354	66.667	0.00	0.00	46.13	4.10
1544	2168	0.815095	TTATCTGCCGCTGACGAAGA	59.185	50.000	1.57	0.00	43.93	2.87
1548	2172	1.290203	ACAATTATCTGCCGCTGACG	58.710	50.000	1.57	0.00	39.67	4.35
1549	2173	3.871594	AGTAACAATTATCTGCCGCTGAC	59.128	43.478	1.57	0.00	0.00	3.51
1552	2176	3.206150	CCAGTAACAATTATCTGCCGCT	58.794	45.455	0.00	0.00	0.00	5.52
1564	2188	2.949177	ATCAGGCACACCAGTAACAA	57.051	45.000	0.00	0.00	39.06	2.83
1569	2193	2.664402	AGAAAATCAGGCACACCAGT	57.336	45.000	0.00	0.00	39.06	4.00

Showing 1 to 25 of 286 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.