AutoCloner

Multiple sequence alignment - TraesCS6D01G208000

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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	TraesCS6D01G208000	chr6D	100.000	2405	0	0	1	2405	293318906	293321310	0.000000e+00	4442.0
1	TraesCS6D01G208000	chr6A	89.263	2198	131	37	247	2405	427448656	427446525	0.000000e+00	2654.0
2	TraesCS6D01G208000	chr6A	88.934	244	23	2	1	242	427449002	427448761	5.030000e-77	298.0
3	TraesCS6D01G208000	chr6A	77.262	409	80	9	389	788	64252782	64253186	6.690000e-56	228.0
4	TraesCS6D01G208000	chr6B	91.997	1562	71	19	856	2405	457877479	457878998	0.000000e+00	2143.0
5	TraesCS6D01G208000	chr4A	87.849	609	64	9	188	788	578106117	578106723	0.000000e+00	706.0
6	TraesCS6D01G208000	chr5D	87.889	611	58	8	188	788	324369019	324368415	0.000000e+00	704.0
7	TraesCS6D01G208000	chr5D	87.070	611	69	9	188	790	295080374	295079766	0.000000e+00	682.0
8	TraesCS6D01G208000	chr5D	83.478	460	51	16	345	788	526430961	526430511	2.880000e-109	405.0
9	TraesCS6D01G208000	chr5D	81.024	332	53	7	404	730	348514240	348514566	3.070000e-64	255.0
10	TraesCS6D01G208000	chr5D	94.444	36	1	1	98	132	221880386	221880421	1.000000e-03	54.7
11	TraesCS6D01G208000	chr4D	88.715	576	52	6	188	753	414043872	414044444	0.000000e+00	691.0
12	TraesCS6D01G208000	chr5B	87.336	608	68	8	188	788	375796456	375795851	0.000000e+00	688.0
13	TraesCS6D01G208000	chr3B	86.379	602	70	5	188	781	650063210	650063807	0.000000e+00	647.0
14	TraesCS6D01G208000	chr3B	95.000	40	1	1	94	132	534275767	534275806	7.180000e-06	62.1
15	TraesCS6D01G208000	chr2D	83.882	608	91	4	188	788	474994630	474995237	7.460000e-160	573.0
16	TraesCS6D01G208000	chr1B	83.468	617	85	13	188	792	604833847	604833236	2.090000e-155	558.0
17	TraesCS6D01G208000	chr1B	84.310	478	54	12	188	651	506150095	506150565	4.720000e-122	448.0
18	TraesCS6D01G208000	chr1D	80.813	615	96	13	188	786	110503361	110502753	1.680000e-126	462.0
19	TraesCS6D01G208000	chr1D	79.310	551	77	16	240	777	64147035	64146509	3.800000e-93	351.0
20	TraesCS6D01G208000	chr1A	82.986	288	39	9	512	791	347675176	347674891	3.970000e-63	252.0
21	TraesCS6D01G208000	chr2A	95.000	40	1	1	94	132	565154337	565154298	7.180000e-06	62.1
22	TraesCS6D01G208000	chr2B	94.444	36	2	0	91	126	361289178	361289213	3.340000e-04	56.5
23	TraesCS6D01G208000	chr4B	100.000	28	0	0	99	126	15932229	15932202	4.000000e-03	52.8
24	TraesCS6D01G208000	chr4B	100.000	28	0	0	99	126	15995663	15995636	4.000000e-03	52.8

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	TraesCS6D01G208000	chr6D	293318906	293321310	2404	False	4442	4442	100.0000	1	2405	1	chr6D.!!$F1	2404
1	TraesCS6D01G208000	chr6A	427446525	427449002	2477	True	1476	2654	89.0985	1	2405	2	chr6A.!!$R1	2404
2	TraesCS6D01G208000	chr6B	457877479	457878998	1519	False	2143	2143	91.9970	856	2405	1	chr6B.!!$F1	1549
3	TraesCS6D01G208000	chr4A	578106117	578106723	606	False	706	706	87.8490	188	788	1	chr4A.!!$F1	600
4	TraesCS6D01G208000	chr5D	324368415	324369019	604	True	704	704	87.8890	188	788	1	chr5D.!!$R2	600
5	TraesCS6D01G208000	chr5D	295079766	295080374	608	True	682	682	87.0700	188	790	1	chr5D.!!$R1	602
6	TraesCS6D01G208000	chr4D	414043872	414044444	572	False	691	691	88.7150	188	753	1	chr4D.!!$F1	565
7	TraesCS6D01G208000	chr5B	375795851	375796456	605	True	688	688	87.3360	188	788	1	chr5B.!!$R1	600
8	TraesCS6D01G208000	chr3B	650063210	650063807	597	False	647	647	86.3790	188	781	1	chr3B.!!$F2	593
9	TraesCS6D01G208000	chr2D	474994630	474995237	607	False	573	573	83.8820	188	788	1	chr2D.!!$F1	600
10	TraesCS6D01G208000	chr1B	604833236	604833847	611	True	558	558	83.4680	188	792	1	chr1B.!!$R1	604
11	TraesCS6D01G208000	chr1D	110502753	110503361	608	True	462	462	80.8130	188	786	1	chr1D.!!$R2	598
12	TraesCS6D01G208000	chr1D	64146509	64147035	526	True	351	351	79.3100	240	777	1	chr1D.!!$R1	537

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
821	967	0.319641	AGTTCAAAGAGGCGACGTCC	60.32	55.0	10.58	2.55	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1950	2114	4.096231	CCCTGTGTTTATTTGCGATGATGA	59.904	41.667	0.0	0.0	0.0	2.92	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
80	81	1.418264	TGATTGAAACCGGGAGACACA	59.582	47.619	6.32	0.00	0.00	3.72
81	82	1.804748	GATTGAAACCGGGAGACACAC	59.195	52.381	6.32	0.00	0.00	3.82
95	96	5.057149	GGAGACACACATCCAATATGGTAC	58.943	45.833	0.00	0.00	39.03	3.34
96	97	5.036117	AGACACACATCCAATATGGTACC	57.964	43.478	4.43	4.43	39.03	3.34
101	102	2.986728	ACATCCAATATGGTACCCCCTC	59.013	50.000	10.07	0.00	39.03	4.30
102	103	2.127651	TCCAATATGGTACCCCCTCC	57.872	55.000	10.07	0.00	39.03	4.30
103	104	0.690762	CCAATATGGTACCCCCTCCG	59.309	60.000	10.07	0.00	31.35	4.63
119	120	3.442977	CCCTCCGTCCCGTAATATAAGAG	59.557	52.174	0.00	0.00	0.00	2.85
126	129	6.347402	CCGTCCCGTAATATAAGAGCATTTTG	60.347	42.308	0.00	0.00	0.00	2.44
155	158	9.401058	ACTTTAGGGAATGTAATTTGAGATCTG	57.599	33.333	0.00	0.00	36.07	2.90
156	159	8.752005	TTTAGGGAATGTAATTTGAGATCTGG	57.248	34.615	0.00	0.00	36.07	3.86
157	160	5.699143	AGGGAATGTAATTTGAGATCTGGG	58.301	41.667	0.00	0.00	36.07	4.45
163	166	5.324409	TGTAATTTGAGATCTGGGCAAAGT	58.676	37.500	0.00	6.76	35.29	2.66
164	167	5.415701	TGTAATTTGAGATCTGGGCAAAGTC	59.584	40.000	10.48	6.17	35.29	3.01
165	168	2.099141	TTGAGATCTGGGCAAAGTCG	57.901	50.000	0.00	0.00	0.00	4.18
176	179	2.287608	GGGCAAAGTCGAAGAAACAAGG	60.288	50.000	0.00	0.00	39.69	3.61
182	185	5.485662	AAGTCGAAGAAACAAGGTTCAAG	57.514	39.130	0.17	0.00	39.69	3.02
281	386	2.527875	GAGGATCTCGGCCCCCAT	60.528	66.667	0.00	0.00	0.00	4.00
317	423	2.662156	GCGTTCTCGTTCTTGTTAGAGG	59.338	50.000	0.00	0.00	39.49	3.69
398	504	1.755393	ATGTTCTATCCCCGTCCCGC	61.755	60.000	0.00	0.00	0.00	6.13
478	584	1.179152	TTCGGTCGATGCTGGTCTTA	58.821	50.000	0.00	0.00	0.00	2.10
493	599	5.163301	GCTGGTCTTAGGTGGATCTATTTGA	60.163	44.000	0.00	0.00	0.00	2.69
603	746	2.056577	GGTCCTTAACACGACGACTTG	58.943	52.381	0.00	0.00	0.00	3.16
712	857	1.604308	TCGTCGCTAGGTGGTCCAA	60.604	57.895	0.00	0.00	35.89	3.53
818	964	3.334272	AAAAAGTTCAAAGAGGCGACG	57.666	42.857	0.00	0.00	0.00	5.12
819	965	1.949465	AAAGTTCAAAGAGGCGACGT	58.051	45.000	0.00	0.00	0.00	4.34
820	966	1.499049	AAGTTCAAAGAGGCGACGTC	58.501	50.000	5.18	5.18	0.00	4.34
821	967	0.319641	AGTTCAAAGAGGCGACGTCC	60.320	55.000	10.58	2.55	0.00	4.79
822	968	1.005394	TTCAAAGAGGCGACGTCCC	60.005	57.895	10.58	12.26	0.00	4.46
823	969	2.758770	TTCAAAGAGGCGACGTCCCG	62.759	60.000	10.58	0.24	0.00	5.14
824	970	4.065281	AAAGAGGCGACGTCCCGG	62.065	66.667	10.58	0.00	0.00	5.73
854	1000	1.168407	ACACCGTCGTCTCTTCCGAA	61.168	55.000	0.00	0.00	35.89	4.30
858	1004	1.068748	CCGTCGTCTCTTCCGAAGAAA	60.069	52.381	11.94	0.00	37.02	2.52
896	1046	4.477975	CAGCGTCTCCGTCCGTCC	62.478	72.222	0.00	0.00	36.15	4.79
1108	1258	1.304952	CCCGGCCAAAACCCTATCA	59.695	57.895	2.24	0.00	0.00	2.15
1119	1269	0.469518	ACCCTATCAGCTACGTCCCC	60.470	60.000	0.00	0.00	0.00	4.81
1433	1583	4.201950	GCGTCTTCCGGTACTAGTAATGAA	60.202	45.833	3.61	6.95	36.94	2.57
1456	1611	0.314302	GGGAGGTCGTCGATATGGTG	59.686	60.000	0.00	0.00	0.00	4.17
1482	1640	7.015389	GCTGGTGGTCTATCTAGTTAGGTTATT	59.985	40.741	7.79	0.00	0.00	1.40
1483	1641	9.584008	CTGGTGGTCTATCTAGTTAGGTTATTA	57.416	37.037	7.79	0.00	0.00	0.98
1503	1661	8.837389	GTTATTATGGGTGAGGTGAAACTATTC	58.163	37.037	0.00	0.00	36.74	1.75
1540	1698	4.192317	ACCTTTCGGTGATCAATCTAAGC	58.808	43.478	0.00	0.00	43.51	3.09
1603	1761	8.526667	TGGTTAATATATGCAAGTGCCTTAAA	57.473	30.769	0.00	0.00	41.18	1.52
1655	1813	7.914346	CGAGGTTCTCTTTAATAGTACGATTGT	59.086	37.037	11.06	0.00	0.00	2.71
1706	1864	2.014010	ATTGTGGCTGTGTTGGGAAT	57.986	45.000	0.00	0.00	0.00	3.01
1819	1980	8.653036	ACATTAGGCTACTAGGGATACTTAAG	57.347	38.462	0.00	0.00	0.00	1.85
1836	1997	8.794335	ATACTTAAGTCCCAAATCTCTTTGAC	57.206	34.615	12.39	0.00	43.71	3.18
1843	2004	5.946377	GTCCCAAATCTCTTTGACCATAGTT	59.054	40.000	0.00	0.00	43.71	2.24
1875	2036	8.558700	GGTATGCAATTTTAGCCATTTTATTGG	58.441	33.333	0.00	0.00	39.94	3.16
1880	2041	7.765819	GCAATTTTAGCCATTTTATTGGAGACT	59.234	33.333	0.00	0.00	39.25	3.24
1928	2092	3.439476	GCACTCTTTGATCAGCAGTGATT	59.561	43.478	24.38	3.51	43.92	2.57
1949	2113	5.815233	TTTTGCACTGGGAAATCCAATTA	57.185	34.783	1.22	0.00	46.51	1.40
1950	2114	6.371595	TTTTGCACTGGGAAATCCAATTAT	57.628	33.333	1.22	0.00	46.51	1.28
1951	2115	5.596836	TTGCACTGGGAAATCCAATTATC	57.403	39.130	1.22	0.00	46.51	1.75
1979	2143	3.613671	CGCAAATAAACACAGGGAATGCA	60.614	43.478	0.00	0.00	0.00	3.96
2009	2173	7.054124	TGGAACTTCAGTGAACTCTTATTGTT	58.946	34.615	0.08	2.09	0.00	2.83
2132	2300	3.304928	GCAATATGCCCTTGATTTCCTCG	60.305	47.826	0.00	0.00	37.42	4.63
2134	2302	4.647564	ATATGCCCTTGATTTCCTCGAT	57.352	40.909	0.00	0.00	0.00	3.59
2206	2374	4.543692	CAAGGCACATTCTATTAGCATGC	58.456	43.478	10.51	10.51	0.00	4.06
2243	2411	9.709495	CCCTCTTCTTTGAAATCATCTCTATAG	57.291	37.037	0.00	0.00	0.00	1.31

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	9.938670	TGTGTGTACACTAAACAAACAATTATC	57.061	29.630	25.60	0.0	41.09	1.75
69	70	0.253044	ATTGGATGTGTGTCTCCCGG	59.747	55.000	0.00	0.0	0.00	5.73
103	104	7.225931	TGTCAAAATGCTCTTATATTACGGGAC	59.774	37.037	0.00	0.0	0.00	4.46
119	120	5.783111	ACATTCCCTAAAGTGTCAAAATGC	58.217	37.500	0.00	0.0	0.00	3.56
126	129	8.561738	TCTCAAATTACATTCCCTAAAGTGTC	57.438	34.615	0.00	0.0	0.00	3.67
134	137	5.699143	CCCAGATCTCAAATTACATTCCCT	58.301	41.667	0.00	0.0	0.00	4.20
135	138	4.279420	GCCCAGATCTCAAATTACATTCCC	59.721	45.833	0.00	0.0	0.00	3.97
136	139	4.889409	TGCCCAGATCTCAAATTACATTCC	59.111	41.667	0.00	0.0	0.00	3.01
155	158	2.287608	CCTTGTTTCTTCGACTTTGCCC	60.288	50.000	0.00	0.0	0.00	5.36
156	159	2.357952	ACCTTGTTTCTTCGACTTTGCC	59.642	45.455	0.00	0.0	0.00	4.52
157	160	3.692791	ACCTTGTTTCTTCGACTTTGC	57.307	42.857	0.00	0.0	0.00	3.68
163	166	4.127171	CCTCTTGAACCTTGTTTCTTCGA	58.873	43.478	0.00	0.0	0.00	3.71
164	167	3.304057	GCCTCTTGAACCTTGTTTCTTCG	60.304	47.826	0.00	0.0	0.00	3.79
165	168	3.632145	TGCCTCTTGAACCTTGTTTCTTC	59.368	43.478	0.00	0.0	0.00	2.87
176	179	3.145286	AGAGCTTTTCTGCCTCTTGAAC	58.855	45.455	0.00	0.0	33.93	3.18
182	185	2.027285	AGGAGAAGAGCTTTTCTGCCTC	60.027	50.000	27.75	13.3	43.95	4.70
296	402	2.662156	CCTCTAACAAGAACGAGAACGC	59.338	50.000	0.00	0.0	43.96	4.84
317	423	3.365265	CCCCAACCAAGACGCTGC	61.365	66.667	0.00	0.0	0.00	5.25
360	466	6.986817	AGAACATGGGAGACATTATTCTTACG	59.013	38.462	0.00	0.0	38.43	3.18
445	551	1.338136	ACCGAATCCCGCAAGATCCT	61.338	55.000	0.00	0.0	43.02	3.24
478	584	3.716872	ACCGGATTCAAATAGATCCACCT	59.283	43.478	9.46	0.0	32.91	4.00
493	599	2.301009	ACACCTAAACGAAGACCGGATT	59.699	45.455	9.46	1.4	43.93	3.01
603	746	4.220163	ACCTTGTTGTAGTAGACAGTAGGC	59.780	45.833	0.00	0.0	39.88	3.93
803	949	1.289800	GGGACGTCGCCTCTTTGAAC	61.290	60.000	21.11	0.0	0.00	3.18
804	950	1.005394	GGGACGTCGCCTCTTTGAA	60.005	57.895	21.11	0.0	0.00	2.69
822	968	3.423154	GGTGTTCTTCCGCTGCCG	61.423	66.667	0.00	0.0	0.00	5.69
823	969	3.423154	CGGTGTTCTTCCGCTGCC	61.423	66.667	0.00	0.0	41.48	4.85
854	1000	4.968812	TTTCCTTTCGTTTTCCGTTTCT	57.031	36.364	0.00	0.0	37.94	2.52
858	1004	2.792196	GCGTTTTCCTTTCGTTTTCCGT	60.792	45.455	0.00	0.0	37.94	4.69
893	1043	5.564063	GCCCACGGCTTATTTTTATATGGAC	60.564	44.000	0.00	0.0	46.69	4.02
894	1044	4.521256	GCCCACGGCTTATTTTTATATGGA	59.479	41.667	0.00	0.0	46.69	3.41
895	1045	4.805219	GCCCACGGCTTATTTTTATATGG	58.195	43.478	0.00	0.0	46.69	2.74
937	1087	1.743996	GAGGGTTTGGAGATCTGTGC	58.256	55.000	0.00	0.0	0.00	4.57
938	1088	2.009042	GCGAGGGTTTGGAGATCTGTG	61.009	57.143	0.00	0.0	0.00	3.66
939	1089	0.250513	GCGAGGGTTTGGAGATCTGT	59.749	55.000	0.00	0.0	0.00	3.41
940	1090	0.250234	TGCGAGGGTTTGGAGATCTG	59.750	55.000	0.00	0.0	0.00	2.90
1433	1583	0.178987	ATATCGACGACCTCCCAGCT	60.179	55.000	0.00	0.0	0.00	4.24
1456	1611	4.216708	ACCTAACTAGATAGACCACCAGC	58.783	47.826	8.54	0.0	0.00	4.85
1482	1640	4.141801	CGGAATAGTTTCACCTCACCCATA	60.142	45.833	0.00	0.0	33.23	2.74
1483	1641	3.370527	CGGAATAGTTTCACCTCACCCAT	60.371	47.826	0.00	0.0	33.23	4.00
1484	1642	2.027561	CGGAATAGTTTCACCTCACCCA	60.028	50.000	0.00	0.0	33.23	4.51
1485	1643	2.235402	TCGGAATAGTTTCACCTCACCC	59.765	50.000	0.00	0.0	33.23	4.61
1491	1649	2.396590	TGCCTCGGAATAGTTTCACC	57.603	50.000	0.00	0.0	33.23	4.02
1503	1661	1.333636	AAGGTCTCCAGATGCCTCGG	61.334	60.000	0.00	0.0	0.00	4.63
1555	1713	0.036010	AACACGAGATCCAAGGGCAG	60.036	55.000	0.00	0.0	0.00	4.85
1655	1813	9.420118	AGAAATAACATAGCACCAATCCATAAA	57.580	29.630	0.00	0.0	0.00	1.40
1666	1824	7.219535	CACAATTGAGCAGAAATAACATAGCAC	59.780	37.037	13.59	0.0	0.00	4.40
1741	1899	4.803088	GCAAGATAAACACACAACAGCAAA	59.197	37.500	0.00	0.0	0.00	3.68
1819	1980	5.501156	ACTATGGTCAAAGAGATTTGGGAC	58.499	41.667	1.24	0.0	32.99	4.46
1843	2004	6.782082	TGGCTAAAATTGCATACCAATACA	57.218	33.333	0.00	0.0	43.22	2.29
1880	2041	7.563724	AATTAAGGTGTCCCACTAGACTAAA	57.436	36.000	0.00	0.0	37.66	1.85
1891	2052	4.489306	AGAGTGCTAATTAAGGTGTCCC	57.511	45.455	0.00	0.0	0.00	4.46
1894	2055	7.168219	TGATCAAAGAGTGCTAATTAAGGTGT	58.832	34.615	0.00	0.0	0.00	4.16
1895	2056	7.615582	TGATCAAAGAGTGCTAATTAAGGTG	57.384	36.000	0.00	0.0	0.00	4.00
1896	2057	6.317391	GCTGATCAAAGAGTGCTAATTAAGGT	59.683	38.462	0.00	0.0	0.00	3.50
1897	2058	6.317140	TGCTGATCAAAGAGTGCTAATTAAGG	59.683	38.462	0.00	0.0	0.00	2.69
1938	2102	8.752766	ATTTGCGATGATGATAATTGGATTTC	57.247	30.769	0.00	0.0	0.00	2.17
1949	2113	5.221106	CCCTGTGTTTATTTGCGATGATGAT	60.221	40.000	0.00	0.0	0.00	2.45
1950	2114	4.096231	CCCTGTGTTTATTTGCGATGATGA	59.904	41.667	0.00	0.0	0.00	2.92
1951	2115	4.096231	TCCCTGTGTTTATTTGCGATGATG	59.904	41.667	0.00	0.0	0.00	3.07
1979	2143	4.530161	AGAGTTCACTGAAGTTCCAGCTAT	59.470	41.667	0.00	0.0	37.68	2.97
2009	2173	8.715191	AATCACTAATTGTGTTGCAAAGAAAA	57.285	26.923	0.00	0.0	46.27	2.29
2132	2300	5.698545	GGTTATCCTAGTGCATCAACTCATC	59.301	44.000	0.00	0.0	0.00	2.92
2134	2302	4.469586	TGGTTATCCTAGTGCATCAACTCA	59.530	41.667	0.00	0.0	34.23	3.41
2206	2374	6.160576	TCAAAGAAGAGGGGTTCAATTTTG	57.839	37.500	0.00	0.0	0.00	2.44
2288	2456	5.591877	AGAACAAAAGCAACTCACAGAGATT	59.408	36.000	0.31	0.0	33.32	2.40
2329	2497	8.467963	ACAACAAGCATATCCATAATCATTCA	57.532	30.769	0.00	0.0	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.