AutoCloner

Multiple sequence alignment - TraesCS2A01G325100

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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	TraesCS2A01G325100	chr2A	100.000	3694	0	0	1	3694	554832737	554836430	0.000000e+00	6822.0
1	TraesCS2A01G325100	chr2A	95.588	68	2	1	2307	2373	688579312	688579245	1.400000e-19	108.0
2	TraesCS2A01G325100	chr2D	93.260	1988	67	25	1046	2998	431503643	431501688	0.000000e+00	2867.0
3	TraesCS2A01G325100	chr2D	94.860	428	22	0	3057	3484	431501681	431501254	0.000000e+00	669.0
4	TraesCS2A01G325100	chr2B	95.721	1776	58	8	1023	2794	510395222	510393461	0.000000e+00	2843.0
5	TraesCS2A01G325100	chr2B	98.535	1024	15	0	1	1024	367677244	367676221	0.000000e+00	1808.0
6	TraesCS2A01G325100	chr2B	98.535	1024	15	0	1	1024	382238904	382237881	0.000000e+00	1808.0
7	TraesCS2A01G325100	chr2B	94.069	843	39	3	2858	3694	510393304	510392467	0.000000e+00	1269.0
8	TraesCS2A01G325100	chr1A	98.927	1025	11	0	1	1025	557473899	557474923	0.000000e+00	1832.0
9	TraesCS2A01G325100	chr3B	98.829	1025	12	0	1	1025	276483164	276482140	0.000000e+00	1827.0
10	TraesCS2A01G325100	chr4B	98.633	1024	14	0	1	1024	311355419	311354396	0.000000e+00	1814.0
11	TraesCS2A01G325100	chr4B	98.439	1025	16	0	1	1025	322665827	322666851	0.000000e+00	1805.0
12	TraesCS2A01G325100	chr4A	98.633	1024	14	0	1	1024	540075800	540076823	0.000000e+00	1814.0
13	TraesCS2A01G325100	chr4A	98.346	1028	15	2	1	1026	551210288	551209261	0.000000e+00	1803.0
14	TraesCS2A01G325100	chr4A	96.429	56	2	0	2491	2546	677971122	677971067	3.930000e-15	93.5
15	TraesCS2A01G325100	chr6A	98.535	1024	15	0	1	1024	387982433	387983456	0.000000e+00	1808.0
16	TraesCS2A01G325100	chr5D	80.233	172	28	6	1185	1355	377297567	377297401	1.390000e-24	124.0
17	TraesCS2A01G325100	chr3A	92.857	56	4	0	2491	2546	624835458	624835403	8.500000e-12	82.4
18	TraesCS2A01G325100	chr1D	86.765	68	8	1	1185	1252	163767457	163767523	1.420000e-09	75.0

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	TraesCS2A01G325100	chr2A	554832737	554836430	3693	False	6822	6822	100.000	1	3694	1	chr2A.!!$F1	3693
1	TraesCS2A01G325100	chr2D	431501254	431503643	2389	True	1768	2867	94.060	1046	3484	2	chr2D.!!$R1	2438
2	TraesCS2A01G325100	chr2B	510392467	510395222	2755	True	2056	2843	94.895	1023	3694	2	chr2B.!!$R3	2671
3	TraesCS2A01G325100	chr2B	367676221	367677244	1023	True	1808	1808	98.535	1	1024	1	chr2B.!!$R1	1023
4	TraesCS2A01G325100	chr2B	382237881	382238904	1023	True	1808	1808	98.535	1	1024	1	chr2B.!!$R2	1023
5	TraesCS2A01G325100	chr1A	557473899	557474923	1024	False	1832	1832	98.927	1	1025	1	chr1A.!!$F1	1024
6	TraesCS2A01G325100	chr3B	276482140	276483164	1024	True	1827	1827	98.829	1	1025	1	chr3B.!!$R1	1024
7	TraesCS2A01G325100	chr4B	311354396	311355419	1023	True	1814	1814	98.633	1	1024	1	chr4B.!!$R1	1023
8	TraesCS2A01G325100	chr4B	322665827	322666851	1024	False	1805	1805	98.439	1	1025	1	chr4B.!!$F1	1024
9	TraesCS2A01G325100	chr4A	540075800	540076823	1023	False	1814	1814	98.633	1	1024	1	chr4A.!!$F1	1023
10	TraesCS2A01G325100	chr4A	551209261	551210288	1027	True	1803	1803	98.346	1	1026	1	chr4A.!!$R1	1025
11	TraesCS2A01G325100	chr6A	387982433	387983456	1023	False	1808	1808	98.535	1	1024	1	chr6A.!!$F1	1023

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
870	873	1.236628	CTGGCATCTTAGCAGCATCC	58.763	55.0	0.00	0.0	35.83	3.51	F
1830	1833	0.670854	GGAACTTCCACCAGCTCGAC	60.671	60.0	2.62	0.0	36.28	4.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2610	2613	0.967887	TTCTCCTCCTCAGCGTCCAG	60.968	60.0	0.0	0.0	0.00	3.86	R
3076	3214	0.098200	TCATAGACGCTTCCGACGTG	59.902	55.0	0.0	0.0	45.24	4.49	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
673	674	2.352421	CCCACAAGACGACGTACAAGAT	60.352	50.000	0.00	0.00	0.00	2.40
696	697	6.857083	TTTAGGGGGAGAATGATGGATAAA	57.143	37.500	0.00	0.00	0.00	1.40
870	873	1.236628	CTGGCATCTTAGCAGCATCC	58.763	55.000	0.00	0.00	35.83	3.51
923	926	4.469469	AAATATGTATCCCCAACCCCTG	57.531	45.455	0.00	0.00	0.00	4.45
1007	1010	5.938710	GTCATCCACATCTATCAATGCTCAT	59.061	40.000	0.00	0.00	0.00	2.90
1015	1018	6.320418	ACATCTATCAATGCTCATGCTGAAAA	59.680	34.615	0.00	0.00	40.48	2.29
1039	1042	4.101790	CAATCCGCACCACCACGC	62.102	66.667	0.00	0.00	0.00	5.34
1095	1098	2.249413	CTCCCGAGCTCTTGGCATGT	62.249	60.000	12.85	0.00	44.79	3.21
1167	1170	4.443266	AGCAAGAGACGCTCCGCC	62.443	66.667	12.16	0.46	33.35	6.13
1168	1171	4.443266	GCAAGAGACGCTCCGCCT	62.443	66.667	3.66	0.00	0.00	5.52
1169	1172	2.202676	CAAGAGACGCTCCGCCTC	60.203	66.667	3.66	0.00	0.00	4.70
1644	1647	2.401195	GCCGCGAGCAACAAGATC	59.599	61.111	8.23	0.00	42.97	2.75
1830	1833	0.670854	GGAACTTCCACCAGCTCGAC	60.671	60.000	2.62	0.00	36.28	4.20
1994	1997	0.981183	AAAGGCATCCTCACGGTACA	59.019	50.000	0.00	0.00	30.89	2.90
2006	2009	1.135489	CACGGTACATACTCGTGCACT	60.135	52.381	16.19	0.00	37.83	4.40
2008	2011	1.917955	CGGTACATACTCGTGCACTTG	59.082	52.381	16.19	9.74	0.00	3.16
2051	2054	4.025813	GCACACAAGCATTTCGTTGAAAAT	60.026	37.500	0.00	0.00	35.11	1.82
2053	2056	6.122125	CACACAAGCATTTCGTTGAAAATTC	58.878	36.000	0.00	0.00	35.11	2.17
2325	2328	4.758251	CCACCGAGCCATGCACGA	62.758	66.667	7.46	0.00	44.57	4.35
2682	2685	3.573489	CTGTTCGCGAAACCACGGC	62.573	63.158	25.24	9.84	37.03	5.68
2689	2692	3.419759	GAAACCACGGCGATGCGT	61.420	61.111	16.62	5.91	0.00	5.24
2730	2736	5.491070	TCTATGTGCAGCAAATAAGTGACT	58.509	37.500	6.73	0.00	0.00	3.41
2734	2740	5.042593	TGTGCAGCAAATAAGTGACTTTTG	58.957	37.500	1.97	4.21	34.30	2.44
2800	2825	9.301153	AGTTTTGCTGTTTTGAAATACTAACAG	57.699	29.630	0.00	0.00	0.00	3.16
2808	2833	8.956426	TGTTTTGAAATACTAACAGATCCATCC	58.044	33.333	0.00	0.00	0.00	3.51
2945	3083	6.863275	TGATAGTAACTTTGCGAGATTGAGA	58.137	36.000	0.00	0.00	0.00	3.27
2990	3128	3.373748	TGCAAGCGTCCAAACATATGTAG	59.626	43.478	9.21	5.04	0.00	2.74
3015	3153	2.492484	CAACTCTAGCACGTCTTAGGGT	59.508	50.000	3.15	3.15	0.00	4.34
3024	3162	2.496070	CACGTCTTAGGGTCCTGATTGA	59.504	50.000	0.00	0.00	0.00	2.57
3025	3163	3.133003	CACGTCTTAGGGTCCTGATTGAT	59.867	47.826	0.00	0.00	0.00	2.57
3031	3169	6.708054	GTCTTAGGGTCCTGATTGATGTAATG	59.292	42.308	0.00	0.00	0.00	1.90
3037	3175	5.220854	GGTCCTGATTGATGTAATGAAACCG	60.221	44.000	0.00	0.00	0.00	4.44
3157	3295	9.956640	ATGATGAAGAGAAGTAGAAGTTGAAAT	57.043	29.630	0.00	0.00	0.00	2.17
3207	3345	8.908903	TGACATGGGTCCAATATGTAATAAAAC	58.091	33.333	0.00	0.00	43.65	2.43
3315	3453	6.378564	GGATCAATATATCGACAAGAGGGAGA	59.621	42.308	0.00	0.00	0.00	3.71
3325	3463	2.191400	CAAGAGGGAGAGGGTGAATGA	58.809	52.381	0.00	0.00	0.00	2.57
3461	3605	1.508088	CATGCGGCTCAAAACTCCC	59.492	57.895	0.00	0.00	0.00	4.30
3470	3614	1.071699	CTCAAAACTCCCGTGGAAGGA	59.928	52.381	0.00	0.00	0.00	3.36
3555	3699	3.323243	AGCAAATGCACTTGAGAATTGC	58.677	40.909	12.91	7.92	45.16	3.56
3633	3777	4.495679	GCAAAGTCTTGACAACAATCACGA	60.496	41.667	3.49	0.00	35.37	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
673	674	6.857083	TTTATCCATCATTCTCCCCCTAAA	57.143	37.500	0.00	0.00	0.00	1.85
696	697	3.769844	CACAAGGACCCTAGTACACAGAT	59.230	47.826	0.00	0.00	0.00	2.90
734	735	1.561542	CCTCCTAACTGCCACAAGGAT	59.438	52.381	0.00	0.00	37.50	3.24
870	873	1.531423	CCAGCCAAGGCATATGCTAG	58.469	55.000	26.12	15.72	44.88	3.42
923	926	0.108520	CACAATGCCATGCCAACCTC	60.109	55.000	0.00	0.00	0.00	3.85
1007	1010	3.188460	GCGGATTGTTAGACTTTTCAGCA	59.812	43.478	0.00	0.00	0.00	4.41
1015	1018	1.338769	GGTGGTGCGGATTGTTAGACT	60.339	52.381	0.00	0.00	0.00	3.24
1039	1042	2.593436	AAACTGTTGTCGCGGGGG	60.593	61.111	6.13	0.00	0.00	5.40
1041	1044	2.051345	GCAAACTGTTGTCGCGGG	60.051	61.111	6.13	0.00	37.06	6.13
1043	1046	0.998226	CATGGCAAACTGTTGTCGCG	60.998	55.000	0.00	0.00	42.60	5.87
1095	1098	3.485431	GCGACGACGACGAGGAGA	61.485	66.667	22.94	0.00	42.66	3.71
1994	1997	6.163476	TGTTCTTATTCAAGTGCACGAGTAT	58.837	36.000	12.01	9.70	33.20	2.12
2006	2009	6.853872	GTGCGTGTGTATTTGTTCTTATTCAA	59.146	34.615	0.00	0.00	0.00	2.69
2008	2011	6.302313	GTGTGCGTGTGTATTTGTTCTTATTC	59.698	38.462	0.00	0.00	0.00	1.75
2051	2054	6.148811	CCTTCAAAGATACGTAAAAGCCAGAA	59.851	38.462	0.00	0.00	0.00	3.02
2053	2056	5.642063	TCCTTCAAAGATACGTAAAAGCCAG	59.358	40.000	0.00	0.00	0.00	4.85
2325	2328	1.364171	GTATCTCGCAGCCGTGGAT	59.636	57.895	0.00	0.00	34.53	3.41
2610	2613	0.967887	TTCTCCTCCTCAGCGTCCAG	60.968	60.000	0.00	0.00	0.00	3.86
2689	2692	7.193595	CACATAGATCACAACATCGTACTACA	58.806	38.462	0.00	0.00	0.00	2.74
2759	2767	6.639632	AGCAAAACTGATAATGTTGACTGT	57.360	33.333	0.00	0.00	0.00	3.55
2800	2825	6.766467	ACTTTAATGTTTAGGTCGGATGGATC	59.234	38.462	0.00	0.00	0.00	3.36
2852	2978	4.704540	ACATTGGCAGATGTCCGATAAAAA	59.295	37.500	8.77	0.00	35.39	1.94
2853	2979	4.269183	ACATTGGCAGATGTCCGATAAAA	58.731	39.130	8.77	0.00	35.39	1.52
2854	2980	3.876914	GACATTGGCAGATGTCCGATAAA	59.123	43.478	21.77	0.00	46.48	1.40
2855	2981	3.466836	GACATTGGCAGATGTCCGATAA	58.533	45.455	21.77	0.00	46.48	1.75
2856	2982	3.111853	GACATTGGCAGATGTCCGATA	57.888	47.619	21.77	0.00	46.48	2.92
2912	3050	6.966632	TCGCAAAGTTACTATCAAATGCAATC	59.033	34.615	0.00	0.00	33.00	2.67
2945	3083	0.250467	AGACAACACAGCCGCTCATT	60.250	50.000	0.00	0.00	0.00	2.57
2990	3128	0.528470	AGACGTGCTAGAGTTGCTCC	59.472	55.000	0.00	0.00	0.00	4.70
3015	3153	5.739959	TCGGTTTCATTACATCAATCAGGA	58.260	37.500	0.00	0.00	0.00	3.86
3024	3162	7.425606	GGCTAAAATCATCGGTTTCATTACAT	58.574	34.615	0.00	0.00	0.00	2.29
3025	3163	6.457663	CGGCTAAAATCATCGGTTTCATTACA	60.458	38.462	0.00	0.00	0.00	2.41
3031	3169	4.609691	TTCGGCTAAAATCATCGGTTTC	57.390	40.909	0.00	0.00	0.00	2.78
3037	3175	4.588278	CGACCTTTTCGGCTAAAATCATC	58.412	43.478	0.00	0.00	44.60	2.92
3075	3213	0.179171	CATAGACGCTTCCGACGTGT	60.179	55.000	0.00	0.00	45.24	4.49
3076	3214	0.098200	TCATAGACGCTTCCGACGTG	59.902	55.000	0.00	0.00	45.24	4.49
3081	3219	0.591741	GTCGGTCATAGACGCTTCCG	60.592	60.000	0.00	0.00	39.40	4.30
3207	3345	5.139435	TCGCCATATCTCAACCTTCATAG	57.861	43.478	0.00	0.00	0.00	2.23
3315	3453	5.471424	TCCATAGATTCTCTCATTCACCCT	58.529	41.667	0.00	0.00	0.00	4.34
3325	3463	9.103861	GTTTTCGAAGAATTCCATAGATTCTCT	57.896	33.333	0.65	0.00	43.81	3.10
3461	3605	2.544685	CACTCTTATGCTCCTTCCACG	58.455	52.381	0.00	0.00	0.00	4.94
3470	3614	0.745845	CTTGCCCGCACTCTTATGCT	60.746	55.000	0.00	0.00	43.80	3.79
3516	3660	6.509418	TTTGCTTGTTTGTTAGACTTGAGT	57.491	33.333	0.00	0.00	0.00	3.41
3528	3672	4.114073	TCTCAAGTGCATTTGCTTGTTTG	58.886	39.130	16.52	7.62	41.83	2.93
3555	3699	5.955488	TGCTTAGCTTTGTACTCTGTCTAG	58.045	41.667	5.60	0.00	0.00	2.43
3608	3752	5.284079	GTGATTGTTGTCAAGACTTTGCAT	58.716	37.500	1.53	0.00	36.97	3.96
3633	3777	6.598427	AGCTTTCCCCCTTATATCTTTCTT	57.402	37.500	0.00	0.00	0.00	2.52
3666	3810	9.262358	CACTGCTTTACTTTTAGTAGTTTCTCT	57.738	33.333	0.00	0.00	35.54	3.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.