AutoCloner

Multiple sequence alignment - TraesCS6D01G124700

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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	TraesCS6D01G124700	chr6D	100.000	4676	0	0	1	4676	89155269	89159944	0.000000e+00	8636
1	TraesCS6D01G124700	chr6D	79.428	2552	465	40	1215	3749	89166894	89169402	0.000000e+00	1749
2	TraesCS6D01G124700	chr6D	78.539	2395	473	30	996	3374	89068451	89070820	0.000000e+00	1537
3	TraesCS6D01G124700	chr6D	79.454	1465	262	29	1529	2978	89301360	89302800	0.000000e+00	1002
4	TraesCS6D01G124700	chr6D	78.210	514	102	10	1040	1548	89299574	89300082	2.100000e-83	320
5	TraesCS6D01G124700	chr6B	95.288	4669	189	16	9	4673	171181731	171186372	0.000000e+00	7374
6	TraesCS6D01G124700	chr6B	79.461	2707	483	46	992	3675	171029191	171031847	0.000000e+00	1851
7	TraesCS6D01G124700	chr6B	78.743	2658	491	59	904	3525	171699945	171702564	0.000000e+00	1711
8	TraesCS6D01G124700	chr6B	78.169	2075	402	35	1349	3405	171704818	171706859	0.000000e+00	1275
9	TraesCS6D01G124700	chr6B	80.127	1731	302	25	2003	3725	171206063	171207759	0.000000e+00	1253
10	TraesCS6D01G124700	chr6A	96.903	3164	93	4	819	3979	107243201	107246362	0.000000e+00	5295
11	TraesCS6D01G124700	chr6A	79.023	2703	497	45	995	3675	107214452	107217106	0.000000e+00	1786
12	TraesCS6D01G124700	chr6A	79.445	1839	338	25	1981	3807	107270589	107272399	0.000000e+00	1266
13	TraesCS6D01G124700	chr6A	84.427	777	64	15	1	724	107242357	107243129	0.000000e+00	712
14	TraesCS6D01G124700	chr6A	89.394	330	26	7	4345	4673	107246393	107246714	1.570000e-109	407
15	TraesCS6D01G124700	chr7A	78.291	1990	397	25	1676	3646	732158011	732156038	0.000000e+00	1249
16	TraesCS6D01G124700	chrUn	78.316	1877	354	41	904	2758	335904524	335906369	0.000000e+00	1162
17	TraesCS6D01G124700	chrUn	78.316	1877	354	41	904	2758	335907206	335909051	0.000000e+00	1162
18	TraesCS6D01G124700	chrUn	79.218	1689	308	33	1307	2978	325921070	325919408	0.000000e+00	1134
19	TraesCS6D01G124700	chrUn	78.466	1486	279	31	1289	2758	394420116	394421576	0.000000e+00	933
20	TraesCS6D01G124700	chrUn	82.039	206	33	3	904	1107	458178172	458178375	6.220000e-39	172
21	TraesCS6D01G124700	chr7D	78.594	1565	291	31	2088	3637	634088405	634089940	0.000000e+00	994
22	TraesCS6D01G124700	chr7B	82.271	361	64	0	1011	1371	742417693	742418053	3.510000e-81	313
23	TraesCS6D01G124700	chr1B	77.566	419	94	0	3224	3642	660467247	660467665	2.160000e-63	254

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	TraesCS6D01G124700	chr6D	89155269	89159944	4675	False	8636	8636	100.000000	1	4676	1	chr6D.!!$F2	4675
1	TraesCS6D01G124700	chr6D	89166894	89169402	2508	False	1749	1749	79.428000	1215	3749	1	chr6D.!!$F3	2534
2	TraesCS6D01G124700	chr6D	89068451	89070820	2369	False	1537	1537	78.539000	996	3374	1	chr6D.!!$F1	2378
3	TraesCS6D01G124700	chr6D	89299574	89302800	3226	False	661	1002	78.832000	1040	2978	2	chr6D.!!$F4	1938
4	TraesCS6D01G124700	chr6B	171181731	171186372	4641	False	7374	7374	95.288000	9	4673	1	chr6B.!!$F2	4664
5	TraesCS6D01G124700	chr6B	171029191	171031847	2656	False	1851	1851	79.461000	992	3675	1	chr6B.!!$F1	2683
6	TraesCS6D01G124700	chr6B	171699945	171706859	6914	False	1493	1711	78.456000	904	3525	2	chr6B.!!$F4	2621
7	TraesCS6D01G124700	chr6B	171206063	171207759	1696	False	1253	1253	80.127000	2003	3725	1	chr6B.!!$F3	1722
8	TraesCS6D01G124700	chr6A	107242357	107246714	4357	False	2138	5295	90.241333	1	4673	3	chr6A.!!$F3	4672
9	TraesCS6D01G124700	chr6A	107214452	107217106	2654	False	1786	1786	79.023000	995	3675	1	chr6A.!!$F1	2680
10	TraesCS6D01G124700	chr6A	107270589	107272399	1810	False	1266	1266	79.445000	1981	3807	1	chr6A.!!$F2	1826
11	TraesCS6D01G124700	chr7A	732156038	732158011	1973	True	1249	1249	78.291000	1676	3646	1	chr7A.!!$R1	1970
12	TraesCS6D01G124700	chrUn	335904524	335909051	4527	False	1162	1162	78.316000	904	2758	2	chrUn.!!$F3	1854
13	TraesCS6D01G124700	chrUn	325919408	325921070	1662	True	1134	1134	79.218000	1307	2978	1	chrUn.!!$R1	1671
14	TraesCS6D01G124700	chrUn	394420116	394421576	1460	False	933	933	78.466000	1289	2758	1	chrUn.!!$F1	1469
15	TraesCS6D01G124700	chr7D	634088405	634089940	1535	False	994	994	78.594000	2088	3637	1	chr7D.!!$F1	1549

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
698	774	1.066858	AGGCACCGTGAACTGACATAG	60.067	52.381	1.65	0.0	0.00	2.23	F
2343	3730	0.403271	AGCTTCCTGCAACCATGTCT	59.597	50.000	0.00	0.0	45.94	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2500	3908	2.260844	TCCAAGAGTTGCAGAAGTGG	57.739	50.0	0.0	0.0	0.0	4.00	R
4218	7735	0.035317	GCATGTCCTGGTGTGACAGA	59.965	55.0	0.0	0.0	45.2	3.41	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
163	167	5.682862	CGTCTTCTTTTCCAAAGTCACAATG	59.317	40.000	0.00	0.00	0.00	2.82
204	208	1.110518	TTTGGTTGTTCTTCCCGCCC	61.111	55.000	0.00	0.00	0.00	6.13
227	231	9.141400	GCCCGATTAGTATCTGTAATTCTAAAG	57.859	37.037	0.00	0.00	0.00	1.85
411	463	2.358125	CGTGGTCGATGGCCAACA	60.358	61.111	10.96	0.82	37.81	3.33
465	517	2.048503	GCCGTCGGCTGTGTTACT	60.049	61.111	28.98	0.00	46.69	2.24
559	611	8.696410	TCAACCTAAACAAAAACAATCTTGTC	57.304	30.769	0.00	0.00	41.31	3.18
698	774	1.066858	AGGCACCGTGAACTGACATAG	60.067	52.381	1.65	0.00	0.00	2.23
717	793	5.239744	ACATAGACATAGTCAGTCATCGGTC	59.760	44.000	0.00	0.00	38.46	4.79
869	947	2.365617	ACCCATATACCTGTTCAGCGAG	59.634	50.000	0.00	0.00	0.00	5.03
920	998	8.140628	TGTGCAATTATGTATTTGTTCTGTGTT	58.859	29.630	0.00	0.00	0.00	3.32
974	1055	1.217244	CCCTGCAGCTTGCCATTTC	59.783	57.895	8.66	0.00	44.23	2.17
1311	1399	0.680921	ATCTTGTTGGCACCATCCCG	60.681	55.000	0.00	0.00	0.00	5.14
1445	1533	8.525290	AATCTGGGAAATAACCAATTGACTAG	57.475	34.615	7.12	0.00	37.59	2.57
1454	1542	4.322057	ACCAATTGACTAGCCCAGAATT	57.678	40.909	7.12	0.00	0.00	2.17
1466	1554	4.218312	AGCCCAGAATTTGACAAGTTCTT	58.782	39.130	19.93	6.42	30.19	2.52
1797	3182	2.890808	TGCGAGTTCTTTCACTGAGT	57.109	45.000	0.00	0.00	0.00	3.41
2033	3419	9.020731	TGTACATGACAACTATATCGATGGTAT	57.979	33.333	8.54	0.00	34.15	2.73
2343	3730	0.403271	AGCTTCCTGCAACCATGTCT	59.597	50.000	0.00	0.00	45.94	3.41
2455	3854	4.447389	CCAAGGTGGCAAAAGATAAAAACG	59.553	41.667	0.00	0.00	0.00	3.60
2500	3908	3.366374	GCCATCTGCCTTTTGTCAGTTAC	60.366	47.826	0.00	0.00	0.00	2.50
3157	5882	6.721318	ACAAATCTTAGAGGCATCCAGTTAA	58.279	36.000	0.00	0.00	0.00	2.01
3309	6682	6.560304	TGATATTCCTCAGCTCCCTTAATCTT	59.440	38.462	0.00	0.00	0.00	2.40
3409	6782	0.607489	CCTGGGACTTTGTGGCTCTG	60.607	60.000	0.00	0.00	0.00	3.35
3829	7223	5.143376	TGTGTAGCTTTAGTCAGGGTAAC	57.857	43.478	0.00	0.00	0.00	2.50
3851	7245	2.096218	GGTTTGTGTCTCGCTCATGTTC	60.096	50.000	0.00	0.00	0.00	3.18
3902	7296	7.408756	AATATTTCTGAAGCCTATTGTGCAA	57.591	32.000	0.00	0.00	0.00	4.08
3979	7496	1.114119	CCTTCGAGCCTACCTACCCC	61.114	65.000	0.00	0.00	0.00	4.95
4043	7560	4.944930	CCATATCCTAGTACTTCTCCCGAG	59.055	50.000	0.00	0.00	0.00	4.63
4044	7561	3.512219	ATCCTAGTACTTCTCCCGAGG	57.488	52.381	0.00	0.00	0.00	4.63
4046	7563	1.133730	CCTAGTACTTCTCCCGAGGCT	60.134	57.143	0.00	0.00	0.00	4.58
4061	7578	2.223900	CGAGGCTGCATCTGTATCAAGA	60.224	50.000	12.78	0.00	0.00	3.02
4073	7590	8.596380	GCATCTGTATCAAGACTTTAACTACAC	58.404	37.037	0.00	0.00	0.00	2.90
4093	7610	2.761208	ACGTAGTGATCTTCAAGGGGAG	59.239	50.000	0.00	0.00	42.51	4.30
4099	7616	1.003580	GATCTTCAAGGGGAGCACACA	59.996	52.381	0.00	0.00	0.00	3.72
4102	7619	0.179020	TTCAAGGGGAGCACACACTG	60.179	55.000	0.00	0.00	0.00	3.66
4113	7630	1.862815	GCACACACTGCTTCTTGCTTG	60.863	52.381	0.00	0.00	43.33	4.01
4115	7632	2.094675	ACACACTGCTTCTTGCTTGTT	58.905	42.857	0.00	0.00	43.37	2.83
4142	7659	1.075601	TCCCTGGAGAAAATGGTGCT	58.924	50.000	0.00	0.00	0.00	4.40
4167	7684	1.000739	CTGGCAATGACACCCCCAT	59.999	57.895	0.00	0.00	0.00	4.00
4171	7688	0.323725	GCAATGACACCCCCATGACT	60.324	55.000	0.00	0.00	0.00	3.41
4179	7696	1.004745	CACCCCCATGACTACAGCTTT	59.995	52.381	0.00	0.00	0.00	3.51
4181	7698	1.561542	CCCCCATGACTACAGCTTTCT	59.438	52.381	0.00	0.00	0.00	2.52
4218	7735	4.451900	ACGACTTTCTTCCAGTCATTTGT	58.548	39.130	0.00	0.00	40.78	2.83
4273	8006	4.956075	TCTCAGTGCTACATGTTCCTATGA	59.044	41.667	2.30	3.21	0.00	2.15
4279	8012	4.129380	GCTACATGTTCCTATGATGTGCA	58.871	43.478	2.30	0.00	32.59	4.57
4330	8064	5.486526	AGTGAGAACCTTAAGAGCATTCAG	58.513	41.667	3.36	0.00	0.00	3.02
4331	8065	5.012561	AGTGAGAACCTTAAGAGCATTCAGT	59.987	40.000	3.36	1.90	0.00	3.41
4341	8365	4.126208	AGAGCATTCAGTGATGTCTCAG	57.874	45.455	14.48	0.00	35.01	3.35
4342	8366	2.608546	GAGCATTCAGTGATGTCTCAGC	59.391	50.000	0.00	0.00	33.88	4.26
4389	11061	2.863740	TCGAGTGAATGTGTGTGTGTTC	59.136	45.455	0.00	0.00	0.00	3.18
4455	11127	9.202273	TCACAAAATAAAAAGCAATCCATACAC	57.798	29.630	0.00	0.00	0.00	2.90
4459	11132	3.874392	AAAAGCAATCCATACACTGGC	57.126	42.857	0.00	0.00	45.52	4.85
4500	11173	9.508642	AACCTGAACTTGGAAAAACAAATTAAA	57.491	25.926	0.00	0.00	0.00	1.52
4607	11280	6.976636	TTACGTGCTTGATTTGTCATATGA	57.023	33.333	0.00	0.00	0.00	2.15
4608	11281	7.552458	TTACGTGCTTGATTTGTCATATGAT	57.448	32.000	9.02	0.00	0.00	2.45
4645	11318	8.139989	GGAAAAGTTACAGTTCTGTACTAGTCA	58.860	37.037	11.54	0.00	34.56	3.41
4667	11340	8.478877	AGTCATAGTAGGAAATAGACAACCAAG	58.521	37.037	0.00	0.00	0.00	3.61
4673	11346	5.690865	AGGAAATAGACAACCAAGTCAACA	58.309	37.500	0.00	0.00	40.98	3.33
4674	11347	6.126409	AGGAAATAGACAACCAAGTCAACAA	58.874	36.000	0.00	0.00	40.98	2.83
4675	11348	6.777580	AGGAAATAGACAACCAAGTCAACAAT	59.222	34.615	0.00	0.00	40.98	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
183	187	2.164338	GGCGGGAAGAACAACCAAATA	58.836	47.619	0.00	0.00	0.00	1.40
227	231	9.586150	CTGATAAAACAATGATATCGTAGCAAC	57.414	33.333	0.00	0.00	0.00	4.17
411	463	2.611473	CGCTGAACCATGAAGACAGAGT	60.611	50.000	0.00	0.00	0.00	3.24
465	517	3.764434	GAGGCGGATGTTAGGATATCTCA	59.236	47.826	2.05	0.00	0.00	3.27
559	611	1.578583	AAGTTTTCAGGGACGACACG	58.421	50.000	0.00	0.00	0.00	4.49
600	653	5.127194	CCTGTGGATGTGAGCTTAAGTACTA	59.873	44.000	4.02	0.00	0.00	1.82
698	774	4.036852	TCATGACCGATGACTGACTATGTC	59.963	45.833	0.00	0.00	36.06	3.06
717	793	3.288964	AGTAGTCTCCGGTAAGGTCATG	58.711	50.000	0.00	0.00	41.99	3.07
728	804	2.944349	GGGAAGTGACTAGTAGTCTCCG	59.056	54.545	26.60	0.00	45.27	4.63
920	998	8.623903	CATTGCATTTGGAAATAGCTAGAGTAA	58.376	33.333	0.00	0.00	0.00	2.24
974	1055	4.876107	CAGCAGGTTATAGTGTTGGTAAGG	59.124	45.833	0.00	0.00	0.00	2.69
1006	1094	3.406764	AGATGTGGAAGAGTTTCTGCAC	58.593	45.455	0.00	0.00	33.68	4.57
1445	1533	4.301628	CAAGAACTTGTCAAATTCTGGGC	58.698	43.478	9.89	0.00	35.92	5.36
1454	1542	5.129634	TGAACATAGGCAAGAACTTGTCAA	58.870	37.500	18.95	5.06	46.84	3.18
1466	1554	2.086869	GCTTCAAGCTGAACATAGGCA	58.913	47.619	0.71	0.00	38.45	4.75
1797	3182	2.746279	ACCCACCAAGTGAATTGTCA	57.254	45.000	0.00	0.00	37.17	3.58
2033	3419	3.260632	TGAAAACATCTCTGACGGGATGA	59.739	43.478	15.56	0.00	41.05	2.92
2343	3730	6.151480	TGAGAGCAACAAGATTTATCAATGCA	59.849	34.615	0.00	0.00	0.00	3.96
2432	3819	4.447389	CGTTTTTATCTTTTGCCACCTTGG	59.553	41.667	0.00	0.00	41.55	3.61
2455	3854	2.479566	TCTCCCATGAAGCTGTTGTC	57.520	50.000	0.00	0.00	0.00	3.18
2500	3908	2.260844	TCCAAGAGTTGCAGAAGTGG	57.739	50.000	0.00	0.00	0.00	4.00
2636	4044	4.876679	GGGACCTTAGTGAAGAATTACAGC	59.123	45.833	0.00	0.00	34.25	4.40
3309	6682	2.562738	TCCTGACAGAAGATTGCTCGAA	59.437	45.455	3.32	0.00	0.00	3.71
3676	7068	4.801891	CTTCATCTTCATTTGGTGTGGTG	58.198	43.478	0.00	0.00	0.00	4.17
3829	7223	0.439985	CATGAGCGAGACACAAACCG	59.560	55.000	0.00	0.00	0.00	4.44
3887	7281	5.578336	GGAAAAATCTTGCACAATAGGCTTC	59.422	40.000	0.00	0.00	0.00	3.86
3902	7296	6.603201	TCAACTCTGAACAACAGGAAAAATCT	59.397	34.615	0.00	0.00	45.76	2.40
3979	7496	4.761739	TGCTGGAGGTTTCACTATTTGAAG	59.238	41.667	0.00	0.00	45.22	3.02
4043	7560	3.191078	AGTCTTGATACAGATGCAGCC	57.809	47.619	0.00	0.00	0.00	4.85
4044	7561	6.314896	AGTTAAAGTCTTGATACAGATGCAGC	59.685	38.462	0.00	0.00	0.00	5.25
4046	7563	8.311109	TGTAGTTAAAGTCTTGATACAGATGCA	58.689	33.333	0.00	0.00	0.00	3.96
4061	7578	7.879070	TGAAGATCACTACGTGTAGTTAAAGT	58.121	34.615	9.88	0.00	43.35	2.66
4073	7590	2.482142	GCTCCCCTTGAAGATCACTACG	60.482	54.545	0.00	0.00	0.00	3.51
4078	7595	1.003580	GTGTGCTCCCCTTGAAGATCA	59.996	52.381	0.00	0.00	0.00	2.92
4080	7597	1.067295	TGTGTGCTCCCCTTGAAGAT	58.933	50.000	0.00	0.00	0.00	2.40
4102	7619	5.177511	GGGAACAATTTAACAAGCAAGAAGC	59.822	40.000	0.00	0.00	46.19	3.86
4103	7620	6.421801	CAGGGAACAATTTAACAAGCAAGAAG	59.578	38.462	0.00	0.00	0.00	2.85
4104	7621	6.279882	CAGGGAACAATTTAACAAGCAAGAA	58.720	36.000	0.00	0.00	0.00	2.52
4106	7623	4.990426	CCAGGGAACAATTTAACAAGCAAG	59.010	41.667	0.00	0.00	0.00	4.01
4108	7625	4.219115	TCCAGGGAACAATTTAACAAGCA	58.781	39.130	0.00	0.00	0.00	3.91
4109	7626	4.522789	TCTCCAGGGAACAATTTAACAAGC	59.477	41.667	0.00	0.00	0.00	4.01
4113	7630	6.873605	CCATTTTCTCCAGGGAACAATTTAAC	59.126	38.462	0.00	0.00	0.00	2.01
4115	7632	6.014669	CACCATTTTCTCCAGGGAACAATTTA	60.015	38.462	0.00	0.00	0.00	1.40
4142	7659	0.883153	GTGTCATTGCCAGTGATGCA	59.117	50.000	0.00	0.00	36.84	3.96
4171	7688	8.429607	GTCAGGTTTGATGTACAGAAAGCTGTA	61.430	40.741	34.01	25.97	43.59	2.74
4179	7696	3.572682	AGTCGTCAGGTTTGATGTACAGA	59.427	43.478	0.33	0.00	40.52	3.41
4181	7698	4.330944	AAGTCGTCAGGTTTGATGTACA	57.669	40.909	0.00	0.00	40.52	2.90
4189	7706	3.118371	ACTGGAAGAAAGTCGTCAGGTTT	60.118	43.478	0.00	0.00	37.43	3.27
4218	7735	0.035317	GCATGTCCTGGTGTGACAGA	59.965	55.000	0.00	0.00	45.20	3.41
4273	8006	2.236146	TCGAGGAACCTTGTATGCACAT	59.764	45.455	7.83	0.00	33.76	3.21
4279	8012	2.640826	TGGGTTTCGAGGAACCTTGTAT	59.359	45.455	16.58	0.00	46.63	2.29
4330	8064	1.337260	ACTTCACCGCTGAGACATCAC	60.337	52.381	0.00	0.00	0.00	3.06
4331	8065	0.969149	ACTTCACCGCTGAGACATCA	59.031	50.000	0.00	0.00	0.00	3.07
4341	8365	3.712881	GGTCGCACACTTCACCGC	61.713	66.667	0.00	0.00	0.00	5.68
4342	8366	2.279851	TGGTCGCACACTTCACCG	60.280	61.111	0.00	0.00	0.00	4.94
4389	11061	1.063006	GCACACGCATGCATACCAG	59.937	57.895	19.57	2.13	45.39	4.00
4415	11087	4.764050	TTTTGTGACTACAGGGAAGACA	57.236	40.909	0.00	0.00	38.23	3.41
4607	11280	2.367947	ACTTTTCCCTCTCCCTCCAT	57.632	50.000	0.00	0.00	0.00	3.41
4608	11281	2.133858	AACTTTTCCCTCTCCCTCCA	57.866	50.000	0.00	0.00	0.00	3.86
4645	11318	8.375493	TGACTTGGTTGTCTATTTCCTACTAT	57.625	34.615	0.00	0.00	37.79	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.