AutoCloner

Multiple sequence alignment - TraesCS6B01G072900

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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	TraesCS6B01G072900	chr6B	100.000	2468	0	0	1	2468	49416177	49413710	0.000000e+00	4558.0
1	TraesCS6B01G072900	chr6B	90.648	1636	124	16	27	1651	49761971	49763588	0.000000e+00	2146.0
2	TraesCS6B01G072900	chr6B	89.049	694	46	11	1778	2465	49763592	49764261	0.000000e+00	833.0
3	TraesCS6B01G072900	chr6B	82.055	691	99	18	989	1664	49664239	49664919	1.280000e-157	566.0
4	TraesCS6B01G072900	chr6B	89.423	312	32	1	226	536	630345864	630345553	2.300000e-105	392.0
5	TraesCS6B01G072900	chr6B	84.615	195	12	5	637	814	630345488	630345295	7.010000e-41	178.0
6	TraesCS6B01G072900	chr6B	85.227	88	13	0	1944	2031	49880701	49880788	9.400000e-15	91.6
7	TraesCS6B01G072900	chr6B	87.838	74	8	1	2317	2389	49881087	49881160	4.370000e-13	86.1
8	TraesCS6B01G072900	chr6B	85.135	74	10	1	2317	2389	48540584	48540657	9.470000e-10	75.0
9	TraesCS6B01G072900	chr6A	91.438	2476	167	21	10	2465	28429214	28431664	0.000000e+00	3356.0
10	TraesCS6B01G072900	chr6A	77.434	226	32	12	2045	2265	31119848	31119637	1.550000e-22	117.0
11	TraesCS6B01G072900	chr6A	96.774	31	1	0	2434	2464	27549036	27549066	4.000000e-03	52.8
12	TraesCS6B01G072900	chr6D	92.006	1914	121	13	10	1905	27117919	27119818	0.000000e+00	2658.0
13	TraesCS6B01G072900	chr6D	81.014	848	127	24	968	1796	27201917	27202749	0.000000e+00	643.0
14	TraesCS6B01G072900	chr6D	90.331	393	19	9	2075	2465	27120610	27120985	4.740000e-137	497.0
15	TraesCS6B01G072900	chr6D	78.222	225	31	12	2045	2265	27179932	27180142	7.160000e-26	128.0
16	TraesCS6B01G072900	chr6D	77.674	215	26	14	2038	2247	27304989	27305186	7.210000e-21	111.0
17	TraesCS6B01G072900	chr6D	73.926	326	57	18	1944	2265	27204100	27204401	3.360000e-19	106.0
18	TraesCS6B01G072900	chr5A	89.206	315	33	1	223	536	6377686	6378000	2.300000e-105	392.0
19	TraesCS6B01G072900	chr5A	84.184	196	12	5	637	814	6378065	6378259	3.260000e-39	172.0
20	TraesCS6B01G072900	chr5A	96.552	58	2	0	637	694	6378002	6378059	2.020000e-16	97.1
21	TraesCS6B01G072900	chr5B	84.615	195	12	8	637	814	549535472	549535279	7.010000e-41	178.0
22	TraesCS6B01G072900	chrUn	81.152	191	24	7	2204	2391	241644929	241644748	2.560000e-30	143.0
23	TraesCS6B01G072900	chrUn	81.152	191	24	7	2204	2391	297911260	297911441	2.560000e-30	143.0
24	TraesCS6B01G072900	chrUn	95.312	64	3	0	2316	2379	76835674	76835611	4.340000e-18	102.0
25	TraesCS6B01G072900	chrUn	95.312	64	3	0	2316	2379	241639751	241639688	4.340000e-18	102.0

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	TraesCS6B01G072900	chr6B	49413710	49416177	2467	True	4558.000000	4558	100.000000	1	2468	1	chr6B.!!$R1	2467
1	TraesCS6B01G072900	chr6B	49761971	49764261	2290	False	1489.500000	2146	89.848500	27	2465	2	chr6B.!!$F3	2438
2	TraesCS6B01G072900	chr6B	49664239	49664919	680	False	566.000000	566	82.055000	989	1664	1	chr6B.!!$F2	675
3	TraesCS6B01G072900	chr6B	630345295	630345864	569	True	285.000000	392	87.019000	226	814	2	chr6B.!!$R2	588
4	TraesCS6B01G072900	chr6A	28429214	28431664	2450	False	3356.000000	3356	91.438000	10	2465	1	chr6A.!!$F2	2455
5	TraesCS6B01G072900	chr6D	27117919	27120985	3066	False	1577.500000	2658	91.168500	10	2465	2	chr6D.!!$F3	2455
6	TraesCS6B01G072900	chr6D	27201917	27204401	2484	False	374.500000	643	77.470000	968	2265	2	chr6D.!!$F4	1297
7	TraesCS6B01G072900	chr5A	6377686	6378259	573	False	220.366667	392	89.980667	223	814	3	chr5A.!!$F1	591

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
184	185	0.600782	AGCAAAAATTGGCGGCACAG	60.601	50.0	12.92	0.0	34.54	3.66	F
1204	1257	0.393077	CAACAAGGACCCTGTCGTCT	59.607	55.0	0.00	0.0	32.65	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1291	1352	1.342174	TCTACCGACAGACCCACAAAC	59.658	52.381	0.0	0.0	0.0	2.93	R
2376	4350	0.758685	TTTGCCCAGACAACCCCTTG	60.759	55.000	0.0	0.0	0.0	3.61	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
79	80	4.810491	GTGTTGAATTGTTGAAATGCAGGT	59.190	37.500	0.00	0.00	0.00	4.00
82	83	5.273674	TGAATTGTTGAAATGCAGGTGAA	57.726	34.783	0.00	0.00	0.00	3.18
93	94	1.604378	CAGGTGAAGGGAAGCGGAT	59.396	57.895	0.00	0.00	0.00	4.18
114	115	3.165058	TCGATTGCTGAAGCGACTTAT	57.835	42.857	0.00	0.00	44.66	1.73
146	147	3.660959	AGATGGGGGCATGAATCAAAAT	58.339	40.909	0.00	0.00	0.00	1.82
154	155	7.038017	TGGGGGCATGAATCAAAATAAAAGTAA	60.038	33.333	0.00	0.00	0.00	2.24
184	185	0.600782	AGCAAAAATTGGCGGCACAG	60.601	50.000	12.92	0.00	34.54	3.66
195	203	1.153745	CGGCACAGTAGGAGCACTC	60.154	63.158	0.00	0.00	0.00	3.51
207	215	2.234661	AGGAGCACTCGATGTTGATCAA	59.765	45.455	3.38	3.38	0.00	2.57
212	220	5.237815	AGCACTCGATGTTGATCAACTAAA	58.762	37.500	32.57	17.75	41.67	1.85
219	227	6.485313	TCGATGTTGATCAACTAAAAAGTGGT	59.515	34.615	32.57	10.72	41.67	4.16
224	232	7.069331	TGTTGATCAACTAAAAAGTGGTGGATT	59.931	33.333	32.57	0.00	41.67	3.01
229	237	7.488322	TCAACTAAAAAGTGGTGGATTCTTTG	58.512	34.615	0.00	0.00	32.74	2.77
232	240	4.751767	AAAAGTGGTGGATTCTTTGCAA	57.248	36.364	0.00	0.00	32.74	4.08
373	384	7.366513	CCTCTTCTTCCTTTCAAGACAAAATC	58.633	38.462	0.00	0.00	31.88	2.17
434	445	8.703604	TTTTCATGTTCGGTTGAAACAAATTA	57.296	26.923	0.00	0.00	40.51	1.40
468	479	2.275134	TCATCTTTTGGCTGCTGTGA	57.725	45.000	0.00	0.00	0.00	3.58
494	505	4.191544	ACATTGGACATGAACGATCGAAT	58.808	39.130	24.34	10.21	0.00	3.34
543	558	3.130633	TCTGTCACAAATGGTCGAACAG	58.869	45.455	9.97	5.51	0.00	3.16
578	593	6.127952	TGTCATCAATGCGAATTCTTGAATCA	60.128	34.615	11.35	8.71	33.03	2.57
582	597	4.548991	ATGCGAATTCTTGAATCAGCTC	57.451	40.909	17.23	4.55	0.00	4.09
583	598	3.337358	TGCGAATTCTTGAATCAGCTCA	58.663	40.909	17.23	3.58	0.00	4.26
746	761	2.498905	CATGCATTCAGTTGTCGTTCG	58.501	47.619	0.00	0.00	0.00	3.95
752	800	2.445453	TCAGTTGTCGTTCGCAAAAC	57.555	45.000	4.39	0.00	0.00	2.43
897	945	1.759445	ACAGTCACACAGCAGTTCTCT	59.241	47.619	0.00	0.00	0.00	3.10
943	991	4.459330	TGAATGAACAGTCACCATTCACA	58.541	39.130	16.08	3.08	46.28	3.58
953	1001	1.264020	CACCATTCACAACTCACCACG	59.736	52.381	0.00	0.00	0.00	4.94
1073	1126	0.738975	CTCATGCTGTCAAGGCCATG	59.261	55.000	5.01	2.45	0.00	3.66
1161	1214	1.377725	CCCGATGCTCTGCAAGGTT	60.378	57.895	13.39	0.00	43.62	3.50
1204	1257	0.393077	CAACAAGGACCCTGTCGTCT	59.607	55.000	0.00	0.00	32.65	4.18
1291	1352	3.226682	GTAGAGGACCTACCACCCTAG	57.773	57.143	0.00	0.00	41.45	3.02
1306	1367	1.337823	CCCTAGTTTGTGGGTCTGTCG	60.338	57.143	0.00	0.00	38.65	4.35
1660	1735	0.038166	TTCCCCTGTCCAGATTGCAC	59.962	55.000	0.00	0.00	0.00	4.57
1702	1777	4.792068	TCTTTTTGTGAGGTGGAAGTGAT	58.208	39.130	0.00	0.00	0.00	3.06
1773	1849	0.890683	CAAGCCTTGTGTGAATCCCC	59.109	55.000	0.00	0.00	0.00	4.81
1941	3412	6.783892	AAATGAGCACACGCAAAATAAAAT	57.216	29.167	0.00	0.00	42.27	1.82
1943	3414	7.881643	AATGAGCACACGCAAAATAAAATAA	57.118	28.000	0.00	0.00	42.27	1.40
1946	3417	6.697455	TGAGCACACGCAAAATAAAATAAACA	59.303	30.769	0.00	0.00	42.27	2.83
1947	3418	6.872608	AGCACACGCAAAATAAAATAAACAC	58.127	32.000	0.00	0.00	42.27	3.32
1948	3419	6.477033	AGCACACGCAAAATAAAATAAACACA	59.523	30.769	0.00	0.00	42.27	3.72
1949	3420	7.010552	AGCACACGCAAAATAAAATAAACACAA	59.989	29.630	0.00	0.00	42.27	3.33
1966	3437	2.483877	CACAACATGTACCTGCATCGTT	59.516	45.455	0.00	0.00	0.00	3.85
2036	3533	0.035439	ACAGGCCCGTGTATGAAAGG	60.035	55.000	0.00	0.00	0.00	3.11
2230	4196	4.018960	ACTTCACATCTCCAGGCACTTAAT	60.019	41.667	0.00	0.00	34.60	1.40
2376	4350	0.959372	ATCAGCACAGGCAGCTTCAC	60.959	55.000	0.00	0.00	44.61	3.18
2453	4427	5.865552	CAGGTTATTTTTCTGGCATGAACTG	59.134	40.000	0.00	0.00	0.00	3.16
2465	4439	3.084039	GCATGAACTGTTCCATTGGAGA	58.916	45.455	17.26	0.00	31.21	3.71
2466	4440	3.698040	GCATGAACTGTTCCATTGGAGAT	59.302	43.478	17.26	0.00	31.21	2.75
2467	4441	4.883585	GCATGAACTGTTCCATTGGAGATA	59.116	41.667	17.26	0.00	31.21	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.481952	GCTTCAAGCACACGAAATCTCT	59.518	45.455	3.89	0.00	41.89	3.10
1	2	2.844281	GCTTCAAGCACACGAAATCTC	58.156	47.619	3.89	0.00	41.89	2.75
2	3	2.977405	GCTTCAAGCACACGAAATCT	57.023	45.000	3.89	0.00	41.89	2.40
18	19	2.071778	TTGCCTCCTTTCTGTTGCTT	57.928	45.000	0.00	0.00	0.00	3.91
79	80	0.830648	ATCGAATCCGCTTCCCTTCA	59.169	50.000	0.00	0.00	35.37	3.02
82	83	0.815615	GCAATCGAATCCGCTTCCCT	60.816	55.000	0.00	0.00	35.37	4.20
93	94	1.795768	AAGTCGCTTCAGCAATCGAA	58.204	45.000	0.00	0.00	42.21	3.71
114	115	0.704076	CCCCCATCTTTTCACCTGGA	59.296	55.000	0.00	0.00	0.00	3.86
154	155	6.200808	CGCCAATTTTTGCTTGAAGAAAAAT	58.799	32.000	11.63	14.14	41.39	1.82
160	161	1.195222	GCCGCCAATTTTTGCTTGAAG	59.805	47.619	0.00	0.00	0.00	3.02
161	162	1.224965	GCCGCCAATTTTTGCTTGAA	58.775	45.000	0.00	0.00	0.00	2.69
173	174	2.662596	CTCCTACTGTGCCGCCAA	59.337	61.111	0.00	0.00	0.00	4.52
184	185	2.941453	TCAACATCGAGTGCTCCTAC	57.059	50.000	0.00	0.00	0.00	3.18
195	203	6.578545	CACCACTTTTTAGTTGATCAACATCG	59.421	38.462	33.92	19.75	43.47	3.84
207	215	5.362430	TGCAAAGAATCCACCACTTTTTAGT	59.638	36.000	0.00	0.00	32.59	2.24
229	237	3.338249	TGAATCTTACACCTCTGCTTGC	58.662	45.455	0.00	0.00	0.00	4.01
232	240	3.834813	TCACTGAATCTTACACCTCTGCT	59.165	43.478	0.00	0.00	0.00	4.24
347	356	4.357918	TGTCTTGAAAGGAAGAAGAGGG	57.642	45.455	0.00	0.00	33.73	4.30
394	405	7.706179	CGAACATGAAAATATTGCAGGGTTAAT	59.294	33.333	0.00	0.00	0.00	1.40
434	445	7.603784	GCCAAAAGATGATTCCAACAAAACTAT	59.396	33.333	0.00	0.00	0.00	2.12
468	479	5.049060	TCGATCGTTCATGTCCAATGTTTTT	60.049	36.000	15.94	0.00	0.00	1.94
494	505	4.517075	TCCGTTGCAACATACTGAAATTGA	59.483	37.500	28.01	2.45	0.00	2.57
543	558	4.100529	CGCATTGATGACAACTGGAAATC	58.899	43.478	0.00	0.00	38.90	2.17
578	593	4.395542	GCAGAAGAAGTTGATCAATGAGCT	59.604	41.667	12.12	0.60	0.00	4.09
582	597	4.675190	ACGCAGAAGAAGTTGATCAATG	57.325	40.909	12.12	5.03	0.00	2.82
583	598	6.166279	TCTAACGCAGAAGAAGTTGATCAAT	58.834	36.000	12.12	0.00	0.00	2.57
739	754	1.070376	GTACCCAGTTTTGCGAACGAC	60.070	52.381	0.00	0.00	0.00	4.34
746	761	1.607148	GTGTCCTGTACCCAGTTTTGC	59.393	52.381	0.00	0.00	36.95	3.68
752	800	1.002087	GGTTGAGTGTCCTGTACCCAG	59.998	57.143	0.00	0.00	38.50	4.45
897	945	5.777223	AGCCAGTGTGAGCTCTTATATATCA	59.223	40.000	16.19	0.00	32.71	2.15
943	991	0.249911	GAGAACTGCCGTGGTGAGTT	60.250	55.000	5.46	5.46	32.57	3.01
953	1001	4.535526	AGAGAAGAGAAAGAGAACTGCC	57.464	45.455	0.00	0.00	0.00	4.85
1073	1126	1.999071	ATCCGAGAGCTGCTGACGAC	61.999	60.000	20.89	2.41	0.00	4.34
1204	1257	4.783621	GCAGGCGACCATGCAGGA	62.784	66.667	0.00	0.00	42.11	3.86
1291	1352	1.342174	TCTACCGACAGACCCACAAAC	59.658	52.381	0.00	0.00	0.00	2.93
1306	1367	3.281727	TTCCATCAATGTGCCTCTACC	57.718	47.619	0.00	0.00	0.00	3.18
1343	1404	9.288576	ACAAGATCATGAGAACAAAATAACAGA	57.711	29.630	4.68	0.00	0.00	3.41
1660	1735	8.733857	AAAAGAAGATAAGACAATTTTGCTCG	57.266	30.769	0.00	0.00	0.00	5.03
1773	1849	9.947669	TGAATTTCAAATTATTTTGCCTTTGTG	57.052	25.926	0.00	0.00	41.66	3.33
1851	1936	3.802948	ATCCTACGTCGAATTTCTGCT	57.197	42.857	0.00	0.00	0.00	4.24
1907	2142	5.270083	CGTGTGCTCATTTTCACTGTTTTA	58.730	37.500	0.00	0.00	34.49	1.52
1941	3412	4.153296	CGATGCAGGTACATGTTGTGTTTA	59.847	41.667	2.30	0.00	42.29	2.01
1943	3414	2.483877	CGATGCAGGTACATGTTGTGTT	59.516	45.455	2.30	0.00	42.29	3.32
1946	3417	2.472695	ACGATGCAGGTACATGTTGT	57.527	45.000	2.30	0.00	0.00	3.32
1947	3418	2.741517	TGAACGATGCAGGTACATGTTG	59.258	45.455	2.30	0.00	0.00	3.33
1948	3419	3.052455	TGAACGATGCAGGTACATGTT	57.948	42.857	2.30	0.00	0.00	2.71
1949	3420	2.760634	TGAACGATGCAGGTACATGT	57.239	45.000	9.57	2.69	0.00	3.21
2036	3533	7.147976	AGTTGGCTAATGTTTGAACTTGAATC	58.852	34.615	0.00	0.00	0.00	2.52
2094	4059	4.199310	TGCAATGCTACTGGGATAGTTTC	58.801	43.478	6.82	0.00	40.89	2.78
2147	4112	6.255887	GCAACTACGCACTTCTATTACTCAAT	59.744	38.462	0.00	0.00	0.00	2.57
2150	4115	5.100259	TGCAACTACGCACTTCTATTACTC	58.900	41.667	0.00	0.00	36.86	2.59
2158	4124	2.748461	TGTTTGCAACTACGCACTTC	57.252	45.000	0.00	0.00	42.87	3.01
2230	4196	8.545472	AGTACTAGTAAGGGACAAATTGCAATA	58.455	33.333	13.39	0.00	0.00	1.90
2304	4275	9.958180	CATACAATACTGTTTATATGGGATGGA	57.042	33.333	0.00	0.00	36.96	3.41
2376	4350	0.758685	TTTGCCCAGACAACCCCTTG	60.759	55.000	0.00	0.00	0.00	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.