AutoCloner

Multiple sequence alignment - TraesCS1D01G203900

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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	TraesCS1D01G203900	chr1D	100.000	3446	0	0	1	3446	288894639	288891194	0.000000e+00	6364.0
1	TraesCS1D01G203900	chr1B	95.192	3390	83	24	1	3348	390382776	390379425	0.000000e+00	5284.0
2	TraesCS1D01G203900	chr1B	97.000	100	3	0	3345	3444	390379388	390379289	5.910000e-38	169.0
3	TraesCS1D01G203900	chr1A	90.627	2710	122	58	414	3089	361175532	361172921	0.000000e+00	3476.0
4	TraesCS1D01G203900	chr1A	83.229	477	62	13	17	489	361176024	361175562	4.110000e-114	422.0
5	TraesCS1D01G203900	chr1A	88.593	263	21	8	3087	3348	361172882	361172628	9.290000e-81	311.0
6	TraesCS1D01G203900	chr1A	93.396	106	3	1	3345	3446	361172591	361172486	1.660000e-33	154.0
7	TraesCS1D01G203900	chr5A	81.588	277	35	11	1640	1914	665079587	665079325	7.490000e-52	215.0
8	TraesCS1D01G203900	chr5A	83.590	195	29	3	1786	1980	685432556	685432747	2.730000e-41	180.0
9	TraesCS1D01G203900	chr5A	81.333	75	6	6	337	410	667933720	667933787	2.000000e-03	54.7
10	TraesCS1D01G203900	chr3D	80.268	299	42	14	1631	1928	362069952	362069670	3.480000e-50	209.0
11	TraesCS1D01G203900	chrUn	80.488	287	40	12	1630	1914	270382315	270382043	4.510000e-49	206.0
12	TraesCS1D01G203900	chrUn	84.043	94	11	4	382	472	328115651	328115559	1.700000e-13	87.9
13	TraesCS1D01G203900	chr3A	80.488	287	40	12	1630	1914	30997360	30997632	4.510000e-49	206.0
14	TraesCS1D01G203900	chr3A	79.933	299	43	14	1631	1928	482184058	482183776	1.620000e-48	204.0
15	TraesCS1D01G203900	chr4D	81.863	204	30	6	1786	1986	502396865	502397064	7.650000e-37	165.0
16	TraesCS1D01G203900	chr7D	80.769	78	13	2	382	459	138037767	138037692	3.710000e-05	60.2
17	TraesCS1D01G203900	chr7B	85.714	56	5	3	377	431	451072916	451072969	4.800000e-04	56.5
18	TraesCS1D01G203900	chr6D	100.000	28	0	0	383	410	324740193	324740166	6.000000e-03	52.8
19	TraesCS1D01G203900	chr4B	100.000	28	0	0	383	410	405388101	405388074	6.000000e-03	52.8
20	TraesCS1D01G203900	chr3B	91.892	37	3	0	383	419	367052688	367052652	6.000000e-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	TraesCS1D01G203900	chr1D	288891194	288894639	3445	True	6364.00	6364	100.00000	1	3446	1	chr1D.!!$R1	3445
1	TraesCS1D01G203900	chr1B	390379289	390382776	3487	True	2726.50	5284	96.09600	1	3444	2	chr1B.!!$R1	3443
2	TraesCS1D01G203900	chr1A	361172486	361176024	3538	True	1090.75	3476	88.96125	17	3446	4	chr1A.!!$R1	3429

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
950	1093	0.107654	GGGGTTACCACAGCTAGCAG	60.108	60.0	18.83	12.15	39.85	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2706	2888	1.949525	AGCCATAATCCGTGTGAATGC	59.05	47.619	0.0	0.0	0.0	3.56	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
164	169	6.685527	TTTGATGGTAGTTAATTGCGCATA	57.314	33.333	12.75	0.00	0.00	3.14
237	242	0.822811	GCATCTCAGTCTCTCTGGCA	59.177	55.000	0.00	0.00	43.76	4.92
238	243	1.413445	GCATCTCAGTCTCTCTGGCAT	59.587	52.381	0.00	0.00	43.76	4.40
318	323	1.123077	CCACCTACATGCAGCTAGGA	58.877	55.000	21.20	0.00	34.60	2.94
326	331	5.641209	CCTACATGCAGCTAGGATTAACATC	59.359	44.000	12.38	0.00	32.46	3.06
435	440	3.289836	CCATACATGCCACCTCATCAAA	58.710	45.455	0.00	0.00	0.00	2.69
443	448	3.202818	TGCCACCTCATCAAATCCACTAT	59.797	43.478	0.00	0.00	0.00	2.12
830	973	6.313519	TGAGGACCTGTGATAAAAAGCTAT	57.686	37.500	0.00	0.00	0.00	2.97
885	1028	2.039480	ACCCATCGATCCATCCATTCTG	59.961	50.000	0.00	0.00	0.00	3.02
950	1093	0.107654	GGGGTTACCACAGCTAGCAG	60.108	60.000	18.83	12.15	39.85	4.24
982	1126	8.473219	TCAGAATCACACATCCATATATAGAGC	58.527	37.037	0.00	0.00	0.00	4.09
983	1127	8.476447	CAGAATCACACATCCATATATAGAGCT	58.524	37.037	0.00	0.00	0.00	4.09
984	1128	8.476447	AGAATCACACATCCATATATAGAGCTG	58.524	37.037	0.00	0.00	0.00	4.24
985	1129	7.968014	ATCACACATCCATATATAGAGCTGA	57.032	36.000	0.00	0.00	0.00	4.26
986	1130	7.163001	TCACACATCCATATATAGAGCTGAC	57.837	40.000	0.00	0.00	0.00	3.51
987	1131	6.153510	TCACACATCCATATATAGAGCTGACC	59.846	42.308	0.00	0.00	0.00	4.02
988	1132	5.126222	ACACATCCATATATAGAGCTGACCG	59.874	44.000	0.00	0.00	0.00	4.79
989	1133	5.358160	CACATCCATATATAGAGCTGACCGA	59.642	44.000	0.00	0.00	0.00	4.69
990	1134	6.040278	CACATCCATATATAGAGCTGACCGAT	59.960	42.308	0.00	0.00	0.00	4.18
991	1135	6.264292	ACATCCATATATAGAGCTGACCGATC	59.736	42.308	0.00	0.00	0.00	3.69
992	1136	5.755849	TCCATATATAGAGCTGACCGATCA	58.244	41.667	0.00	0.00	0.00	2.92
1084	1228	2.291043	GGACCCCACACGTCCTCAT	61.291	63.158	0.00	0.00	45.41	2.90
1240	1401	2.807967	CCACTACACACACACCAAGATG	59.192	50.000	0.00	0.00	0.00	2.90
1333	1498	3.186909	TGGCATAATCGCATATCGTAGC	58.813	45.455	0.00	0.00	39.67	3.58
1334	1499	3.186909	GGCATAATCGCATATCGTAGCA	58.813	45.455	0.00	0.00	39.67	3.49
1335	1500	3.000322	GGCATAATCGCATATCGTAGCAC	60.000	47.826	0.00	0.00	39.67	4.40
1346	1511	2.064573	TCGTAGCACACACACATCTG	57.935	50.000	0.00	0.00	0.00	2.90
1860	2036	0.173481	GCCAGAGCTACGTGATGACA	59.827	55.000	0.00	0.00	35.50	3.58
2115	2291	4.692475	GGCACCACCTACGGCGTT	62.692	66.667	21.24	0.00	34.51	4.84
2497	2678	2.110967	CCAGAGAGGCAATGCGTGG	61.111	63.158	4.75	0.00	0.00	4.94
2669	2851	6.039717	TGAGTTTTTCCCTTGACAATGAAGAG	59.960	38.462	0.00	0.00	0.00	2.85
2770	2952	4.563140	TTTATGGCTTCCCTTCGTTAGT	57.437	40.909	0.00	0.00	0.00	2.24
2780	2962	7.420002	GCTTCCCTTCGTTAGTAAAAGAAAAA	58.580	34.615	4.33	0.71	33.56	1.94
2826	3008	8.406172	TCGCAAAAGAAAAATATTTATGGCTC	57.594	30.769	0.01	0.00	0.00	4.70
2860	3053	1.887198	ACACTACAGTCTCGTTCCCTG	59.113	52.381	0.00	0.00	0.00	4.45
3086	3283	3.183172	CGATCGGCTATGAACATTGTCTG	59.817	47.826	7.38	0.00	0.00	3.51
3262	3501	5.157940	AGCCAAGTAGCCATATCATGTAG	57.842	43.478	0.00	0.00	0.00	2.74
3299	3543	8.848474	AGTAATACTGTTATGAAGCTTTGTGT	57.152	30.769	0.00	0.00	0.00	3.72
3300	3544	8.721478	AGTAATACTGTTATGAAGCTTTGTGTG	58.279	33.333	0.00	0.00	0.00	3.82
3416	3700	1.461127	CCTTGCTCTTCTACGTTGTGC	59.539	52.381	0.00	0.00	0.00	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	6.920569	AAGACACAAATAAAGAGTCGTTGT	57.079	33.333	1.17	0.00	32.82	3.32
11	12	7.186804	ACAAAGACACAAATAAAGAGTCGTTG	58.813	34.615	14.65	14.65	44.57	4.10
12	13	7.316544	ACAAAGACACAAATAAAGAGTCGTT	57.683	32.000	0.00	0.00	32.82	3.85
14	15	8.523464	CAAAACAAAGACACAAATAAAGAGTCG	58.477	33.333	0.00	0.00	32.82	4.18
255	260	4.428615	TGTAGGAATTAAAACTTGCCGC	57.571	40.909	0.00	0.00	0.00	6.53
293	298	2.305927	AGCTGCATGTAGGTGGTTACTT	59.694	45.455	15.01	0.00	0.00	2.24
553	670	6.928979	TTTCGTTGAGATTTGGTTGTCTAA	57.071	33.333	0.00	0.00	0.00	2.10
555	672	7.687941	ATATTTCGTTGAGATTTGGTTGTCT	57.312	32.000	0.00	0.00	0.00	3.41
641	758	3.736740	GCGGGTGAACATGTGTTTCTTTT	60.737	43.478	0.00	0.00	38.56	2.27
732	875	8.506140	AATTCGTCATTTGACACTACAAATTG	57.494	30.769	11.02	0.00	44.63	2.32
830	973	3.936453	GTGTGGGCACGATATTTTCTACA	59.064	43.478	0.00	0.00	35.75	2.74
885	1028	4.492160	TGGCACGAGCGATCGGTC	62.492	66.667	31.90	31.90	43.41	4.79
950	1093	4.264253	TGGATGTGTGATTCTGATTGGTC	58.736	43.478	0.00	0.00	0.00	4.02
982	1126	1.864565	TTGTGTGTGTGATCGGTCAG	58.135	50.000	0.00	0.00	34.36	3.51
983	1127	2.542020	ATTGTGTGTGTGATCGGTCA	57.458	45.000	0.00	0.00	0.00	4.02
984	1128	2.095768	CCAATTGTGTGTGTGATCGGTC	60.096	50.000	4.43	0.00	0.00	4.79
985	1129	1.879380	CCAATTGTGTGTGTGATCGGT	59.121	47.619	4.43	0.00	0.00	4.69
986	1130	1.199789	CCCAATTGTGTGTGTGATCGG	59.800	52.381	4.43	0.00	0.00	4.18
987	1131	1.879380	ACCCAATTGTGTGTGTGATCG	59.121	47.619	4.43	0.00	0.00	3.69
988	1132	2.095768	CGACCCAATTGTGTGTGTGATC	60.096	50.000	0.00	0.00	0.00	2.92
989	1133	1.879380	CGACCCAATTGTGTGTGTGAT	59.121	47.619	0.00	0.00	0.00	3.06
990	1134	1.304254	CGACCCAATTGTGTGTGTGA	58.696	50.000	0.00	0.00	0.00	3.58
991	1135	1.021202	ACGACCCAATTGTGTGTGTG	58.979	50.000	0.00	0.00	0.00	3.82
992	1136	1.403679	CAACGACCCAATTGTGTGTGT	59.596	47.619	0.00	0.00	0.00	3.72
1084	1228	1.427368	GAGGAGGGAGAGAGATGGCTA	59.573	57.143	0.00	0.00	0.00	3.93
1240	1401	2.352127	GGAGCACAATGAAGGTTCTTGC	60.352	50.000	0.00	0.00	0.00	4.01
1346	1511	3.756434	TCGGATGATTGGAAAACTGGAAC	59.244	43.478	0.00	0.00	0.00	3.62
1449	1615	3.361158	CGGGATGGCACGCAACAA	61.361	61.111	0.00	0.00	32.17	2.83
1983	2159	3.195698	CTGTAAGCTTCGGCCGGC	61.196	66.667	27.83	21.18	43.01	6.13
2007	2183	4.770874	GGCGGCGGGAAAGCTACA	62.771	66.667	9.78	0.00	37.29	2.74
2497	2678	4.715523	TACGCAGGCTGCCCCAAC	62.716	66.667	32.08	5.68	41.12	3.77
2578	2759	5.810525	AGCAAATAATCATACGTGCAAGAC	58.189	37.500	6.65	0.00	34.44	3.01
2669	2851	5.046950	AGAGGTTCAGAGAGGTTTGATACAC	60.047	44.000	0.00	0.00	0.00	2.90
2706	2888	1.949525	AGCCATAATCCGTGTGAATGC	59.050	47.619	0.00	0.00	0.00	3.56
2737	2919	6.497259	AGGGAAGCCATAAATCTATAGAACGA	59.503	38.462	6.52	0.00	0.00	3.85
2770	2952	9.500701	AGGGGAGCCATAAATATTTTTCTTTTA	57.499	29.630	5.91	0.00	0.00	1.52
2780	2962	5.256474	CGAATGAAGGGGAGCCATAAATAT	58.744	41.667	0.00	0.00	0.00	1.28
2792	2974	3.658757	TTTCTTTTGCGAATGAAGGGG	57.341	42.857	13.14	0.00	32.55	4.79
2826	3008	6.154706	AGACTGTAGTGTAAGTGATAAAGGGG	59.845	42.308	0.00	0.00	0.00	4.79
2860	3053	3.423539	TGTTATCATATGCAGGGAGCC	57.576	47.619	0.00	0.00	44.83	4.70
3104	3343	4.056740	AGCGCATCAGAAATCAGTAGATG	58.943	43.478	11.47	0.00	39.17	2.90
3105	3344	4.333913	AGCGCATCAGAAATCAGTAGAT	57.666	40.909	11.47	0.00	35.53	1.98
3299	3543	1.003959	TGGTTGCACGATAGCAGCA	60.004	52.632	14.81	0.00	46.00	4.41
3300	3544	1.425428	GTGGTTGCACGATAGCAGC	59.575	57.895	0.00	0.00	46.54	5.25

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.