AutoCloner

Multiple sequence alignment - TraesCS5D01G162800

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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	TraesCS5D01G162800	chr5D	100.000	2667	0	0	1	2667	254520726	254518060	0.000000e+00	4926
1	TraesCS5D01G162800	chr5D	96.703	728	21	2	1938	2665	242125870	242126594	0.000000e+00	1208
2	TraesCS5D01G162800	chr5D	96.149	727	26	2	1941	2667	220436997	220437721	0.000000e+00	1186
3	TraesCS5D01G162800	chr5D	96.281	726	22	4	1941	2665	337721969	337721248	0.000000e+00	1186
4	TraesCS5D01G162800	chr5D	95.251	737	33	2	1929	2665	292021547	292022281	0.000000e+00	1166
5	TraesCS5D01G162800	chr5A	92.863	1205	59	13	832	2023	337820848	337819658	0.000000e+00	1724
6	TraesCS5D01G162800	chr5A	95.173	663	18	3	185	839	337821538	337820882	0.000000e+00	1035
7	TraesCS5D01G162800	chr5B	92.561	1062	43	16	832	1869	288329464	288330513	0.000000e+00	1491
8	TraesCS5D01G162800	chr5B	95.606	842	25	4	1	839	288328594	288329426	0.000000e+00	1339
9	TraesCS5D01G162800	chr6D	96.966	725	20	2	1941	2665	65485626	65486348	0.000000e+00	1216
10	TraesCS5D01G162800	chr6D	96.000	725	27	2	1941	2665	451812836	451812114	0.000000e+00	1177
11	TraesCS5D01G162800	chrUn	96.281	726	25	2	1940	2665	94204823	94204100	0.000000e+00	1190
12	TraesCS5D01G162800	chr2D	96.011	727	27	2	1939	2665	249398805	249398081	0.000000e+00	1181
13	TraesCS5D01G162800	chr1A	95.492	732	30	3	1937	2667	99178739	99179468	0.000000e+00	1166
14	TraesCS5D01G162800	chr4B	81.046	306	25	24	1387	1680	182674914	182675198	2.080000e-51	213
15	TraesCS5D01G162800	chr4A	81.126	302	22	23	1390	1679	450794376	450794654	2.690000e-50	209
16	TraesCS5D01G162800	chr4D	79.470	302	23	22	1390	1680	119826734	119827007	7.590000e-41	178

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	TraesCS5D01G162800	chr5D	254518060	254520726	2666	True	4926.0	4926	100.0000	1	2667	1	chr5D.!!$R1	2666
1	TraesCS5D01G162800	chr5D	242125870	242126594	724	False	1208.0	1208	96.7030	1938	2665	1	chr5D.!!$F2	727
2	TraesCS5D01G162800	chr5D	220436997	220437721	724	False	1186.0	1186	96.1490	1941	2667	1	chr5D.!!$F1	726
3	TraesCS5D01G162800	chr5D	337721248	337721969	721	True	1186.0	1186	96.2810	1941	2665	1	chr5D.!!$R2	724
4	TraesCS5D01G162800	chr5D	292021547	292022281	734	False	1166.0	1166	95.2510	1929	2665	1	chr5D.!!$F3	736
5	TraesCS5D01G162800	chr5A	337819658	337821538	1880	True	1379.5	1724	94.0180	185	2023	2	chr5A.!!$R1	1838
6	TraesCS5D01G162800	chr5B	288328594	288330513	1919	False	1415.0	1491	94.0835	1	1869	2	chr5B.!!$F1	1868
7	TraesCS5D01G162800	chr6D	65485626	65486348	722	False	1216.0	1216	96.9660	1941	2665	1	chr6D.!!$F1	724
8	TraesCS5D01G162800	chr6D	451812114	451812836	722	True	1177.0	1177	96.0000	1941	2665	1	chr6D.!!$R1	724
9	TraesCS5D01G162800	chrUn	94204100	94204823	723	True	1190.0	1190	96.2810	1940	2665	1	chrUn.!!$R1	725
10	TraesCS5D01G162800	chr2D	249398081	249398805	724	True	1181.0	1181	96.0110	1939	2665	1	chr2D.!!$R1	726
11	TraesCS5D01G162800	chr1A	99178739	99179468	729	False	1166.0	1166	95.4920	1937	2667	1	chr1A.!!$F1	730

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
904	959	0.03779	AGGCGAGAGTTGACTTGCTC	60.038	55.0	0.0	0.0	44.18	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2382	2482	0.547954	AACTCCAGAACTCCCCTCCC	60.548	60.0	0.0	0.0	0.0	4.3	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
27	28	5.195185	TGACGGTAATCATAGTAGTGGACA	58.805	41.667	0.00	0.00	0.00	4.02
51	52	2.983402	CACATCAGGTGCTGTCTTTG	57.017	50.000	0.00	0.00	41.36	2.77
84	85	7.436376	GCATTTTTAGCTTCTAATCACCATTCC	59.564	37.037	0.00	0.00	0.00	3.01
98	99	1.467920	CATTCCTGGGAAGTTCCTGC	58.532	55.000	21.25	6.54	37.56	4.85
120	121	4.797933	GCGCATCTTTGTTTTCCCCTTTTA	60.798	41.667	0.30	0.00	0.00	1.52
159	160	6.209986	TGATTTGTTTCATCATCTCTTTGCCT	59.790	34.615	0.00	0.00	0.00	4.75
167	168	5.302568	TCATCATCTCTTTGCCTTTGTGTTT	59.697	36.000	0.00	0.00	0.00	2.83
168	169	4.935702	TCATCTCTTTGCCTTTGTGTTTG	58.064	39.130	0.00	0.00	0.00	2.93
212	213	8.897752	ACTAAGAAATGATTAGCTTGGAATCAC	58.102	33.333	11.64	1.81	44.03	3.06
215	216	4.524802	ATGATTAGCTTGGAATCACCCA	57.475	40.909	11.64	0.00	44.03	4.51
223	224	4.082245	AGCTTGGAATCACCCAAAAATACG	60.082	41.667	0.00	0.00	44.78	3.06
236	237	7.277539	CACCCAAAAATACGTACTTACCGATAA	59.722	37.037	0.00	0.00	0.00	1.75
246	247	2.970640	ACTTACCGATAATCCTGACCCC	59.029	50.000	0.00	0.00	0.00	4.95
325	326	1.123928	ATAGTGCCTGTAGAGGTGCC	58.876	55.000	7.90	0.00	42.15	5.01
374	375	2.625617	GGGGCATGGTTTAAGGATTCCA	60.626	50.000	5.29	0.00	0.00	3.53
771	780	0.608130	GGACTTTGGGTTGGCATTCC	59.392	55.000	0.00	0.00	0.00	3.01
801	810	4.284490	TCTCTGGCTACTGTTTGATTGAGT	59.716	41.667	0.00	0.00	0.00	3.41
817	826	4.397481	TTGAGTATGTGGCTCAGATGAG	57.603	45.455	5.45	5.45	42.95	2.90
818	827	3.635591	TGAGTATGTGGCTCAGATGAGA	58.364	45.455	13.98	0.00	44.74	3.27
819	828	4.221530	TGAGTATGTGGCTCAGATGAGAT	58.778	43.478	13.98	1.03	44.74	2.75
820	829	4.038883	TGAGTATGTGGCTCAGATGAGATG	59.961	45.833	13.98	0.00	44.74	2.90
821	830	4.221530	AGTATGTGGCTCAGATGAGATGA	58.778	43.478	13.98	0.00	44.74	2.92
904	959	0.037790	AGGCGAGAGTTGACTTGCTC	60.038	55.000	0.00	0.00	44.18	4.26
935	990	3.367932	CGTATAAATACATGGCCGCTGAG	59.632	47.826	11.80	0.00	32.87	3.35
1023	1081	4.155709	TGTATCATCATCACTCCTCCTCC	58.844	47.826	0.00	0.00	0.00	4.30
1024	1082	3.634218	ATCATCATCACTCCTCCTCCT	57.366	47.619	0.00	0.00	0.00	3.69
1025	1083	2.956132	TCATCATCACTCCTCCTCCTC	58.044	52.381	0.00	0.00	0.00	3.71
1026	1084	2.517553	TCATCATCACTCCTCCTCCTCT	59.482	50.000	0.00	0.00	0.00	3.69
1027	1085	3.052262	TCATCATCACTCCTCCTCCTCTT	60.052	47.826	0.00	0.00	0.00	2.85
1028	1086	3.025322	TCATCACTCCTCCTCCTCTTC	57.975	52.381	0.00	0.00	0.00	2.87
1029	1087	2.584965	TCATCACTCCTCCTCCTCTTCT	59.415	50.000	0.00	0.00	0.00	2.85
1030	1088	3.012274	TCATCACTCCTCCTCCTCTTCTT	59.988	47.826	0.00	0.00	0.00	2.52
1031	1089	3.094484	TCACTCCTCCTCCTCTTCTTC	57.906	52.381	0.00	0.00	0.00	2.87
1041	1099	5.398236	TCCTCCTCTTCTTCTTCTTCTTCA	58.602	41.667	0.00	0.00	0.00	3.02
1144	1205	2.952978	CACTGCTACTACTACTCCCAGG	59.047	54.545	0.00	0.00	0.00	4.45
1148	1209	2.158579	GCTACTACTACTCCCAGGAGCT	60.159	54.545	13.78	4.10	45.54	4.09
1188	1249	4.374702	CGCCGTGTGCTGAGCAAC	62.375	66.667	9.51	9.11	41.47	4.17
1338	1409	2.708255	GTACGTCTCCTCGCTCGG	59.292	66.667	0.00	0.00	0.00	4.63
1339	1410	2.513204	TACGTCTCCTCGCTCGGG	60.513	66.667	0.00	0.00	0.00	5.14
1657	1731	1.043116	TCGCCGTCTCCTCCATCAAT	61.043	55.000	0.00	0.00	0.00	2.57
1750	1824	3.567164	CCCATATCCTGTTGCATCAACTC	59.433	47.826	10.52	0.00	43.85	3.01
1767	1841	3.795623	ACTCAAACTACGACGCCATAT	57.204	42.857	0.00	0.00	0.00	1.78
1806	1894	1.608283	GGACCGGACACCTTCTTCTTG	60.608	57.143	9.46	0.00	0.00	3.02
1811	1899	2.802816	CGGACACCTTCTTCTTGTTCTG	59.197	50.000	0.00	0.00	0.00	3.02
1814	1902	5.365619	GGACACCTTCTTCTTGTTCTGTTA	58.634	41.667	0.00	0.00	0.00	2.41
1828	1916	7.444183	TCTTGTTCTGTTAATTAGTTGGAGTGG	59.556	37.037	0.00	0.00	0.00	4.00
1920	2011	1.618861	CGTCTACTCTGTCCGCAAAG	58.381	55.000	0.00	0.00	0.00	2.77
2053	2150	6.746120	AGTCACATAACGAGAAGTACAAAGT	58.254	36.000	0.00	0.00	0.00	2.66
2054	2151	7.208080	AGTCACATAACGAGAAGTACAAAGTT	58.792	34.615	0.00	0.00	0.00	2.66
2185	2283	2.892425	GGCCATCGAGCGAAGGTG	60.892	66.667	14.55	1.10	39.88	4.00
2289	2387	4.849329	CGTCAGTAGCCCGCCGAC	62.849	72.222	0.00	0.00	0.00	4.79
2382	2482	1.447643	CTAATGTGGCGAGAGGGGG	59.552	63.158	0.00	0.00	0.00	5.40
2611	2712	2.711311	CGCAGATCCATTGCCACG	59.289	61.111	0.26	0.00	38.31	4.94
2656	2757	1.969064	CGGATGGACCAAACCGCAA	60.969	57.895	23.65	0.00	38.98	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	6.570692	ACTTTGTCCACTACTATGATTACCG	58.429	40.000	0.00	0.00	0.00	4.02
51	52	4.790765	AGAAGCTAAAAATGCAAGTCCC	57.209	40.909	0.00	0.00	0.00	4.46
84	85	1.372087	GATGCGCAGGAACTTCCCAG	61.372	60.000	18.32	0.00	37.19	4.45
98	99	3.385193	AAAGGGGAAAACAAAGATGCG	57.615	42.857	0.00	0.00	0.00	4.73
139	140	5.302568	ACAAAGGCAAAGAGATGATGAAACA	59.697	36.000	0.00	0.00	0.00	2.83
143	144	4.401022	ACACAAAGGCAAAGAGATGATGA	58.599	39.130	0.00	0.00	0.00	2.92
144	145	4.778534	ACACAAAGGCAAAGAGATGATG	57.221	40.909	0.00	0.00	0.00	3.07
145	146	5.069516	ACAAACACAAAGGCAAAGAGATGAT	59.930	36.000	0.00	0.00	0.00	2.45
159	160	1.786937	ATGGGGAGCACAAACACAAA	58.213	45.000	0.00	0.00	0.00	2.83
167	168	2.359850	GCGACAATGGGGAGCACA	60.360	61.111	0.00	0.00	0.00	4.57
168	169	1.971167	TTGCGACAATGGGGAGCAC	60.971	57.895	0.00	0.00	37.57	4.40
212	213	7.769272	TTATCGGTAAGTACGTATTTTTGGG	57.231	36.000	8.72	0.00	0.00	4.12
215	216	9.252962	CAGGATTATCGGTAAGTACGTATTTTT	57.747	33.333	8.72	2.37	0.00	1.94
223	224	4.021632	GGGGTCAGGATTATCGGTAAGTAC	60.022	50.000	0.00	0.00	0.00	2.73
236	237	1.635817	CCATGAACCGGGGTCAGGAT	61.636	60.000	27.11	4.41	0.00	3.24
246	247	1.953686	ACCACTTTGTTCCATGAACCG	59.046	47.619	0.00	0.00	41.35	4.44
325	326	2.005451	CAGGAGATGTGCCTTTTCTCG	58.995	52.381	0.00	0.00	37.38	4.04
374	375	3.767711	GGAAATCTCCCACTTTTCCACT	58.232	45.455	8.41	0.00	45.02	4.00
621	622	0.316689	CACGACCAAACCTCGCAAAC	60.317	55.000	0.00	0.00	34.34	2.93
771	780	1.337260	ACAGTAGCCAGAGAAACTGCG	60.337	52.381	1.43	0.00	44.52	5.18
801	810	3.323115	GGTCATCTCATCTGAGCCACATA	59.677	47.826	2.21	0.00	41.80	2.29
817	826	2.000447	GACGGCACTAACAAGGTCATC	59.000	52.381	0.00	0.00	0.00	2.92
818	827	1.346395	TGACGGCACTAACAAGGTCAT	59.654	47.619	0.00	0.00	30.20	3.06
819	828	0.753867	TGACGGCACTAACAAGGTCA	59.246	50.000	0.00	0.00	32.51	4.02
820	829	1.732259	CATGACGGCACTAACAAGGTC	59.268	52.381	0.00	0.00	0.00	3.85
821	830	1.610624	CCATGACGGCACTAACAAGGT	60.611	52.381	0.00	0.00	0.00	3.50
904	959	1.733758	TATTTATACGCGCCGGCCG	60.734	57.895	28.27	28.27	40.75	6.13
935	990	4.389992	AGTGATGAATGATTGACGTGTGTC	59.610	41.667	0.00	0.00	45.71	3.67
1028	1086	9.311916	CCTGACAAGTATATGAAGAAGAAGAAG	57.688	37.037	0.00	0.00	0.00	2.85
1029	1087	8.260818	CCCTGACAAGTATATGAAGAAGAAGAA	58.739	37.037	0.00	0.00	0.00	2.52
1030	1088	7.619698	TCCCTGACAAGTATATGAAGAAGAAGA	59.380	37.037	0.00	0.00	0.00	2.87
1031	1089	7.786030	TCCCTGACAAGTATATGAAGAAGAAG	58.214	38.462	0.00	0.00	0.00	2.85
1041	1099	5.380043	CCATTGCTTCCCTGACAAGTATAT	58.620	41.667	0.00	0.00	0.00	0.86
1074	1132	4.668118	GACGCCGACGGTTGGGAA	62.668	66.667	16.73	0.00	46.04	3.97
1092	1150	1.001974	TGCAACAGATCACCGTAGCTT	59.998	47.619	0.00	0.00	0.00	3.74
1175	1236	1.300931	TCTCCGTTGCTCAGCACAC	60.301	57.895	0.00	0.00	38.71	3.82
1320	1387	2.708255	CGAGCGAGGAGACGTACC	59.292	66.667	3.41	3.41	35.59	3.34
1338	1409	2.846693	CAAAATCGAACAAGTACGGCC	58.153	47.619	0.00	0.00	0.00	6.13
1339	1410	2.239201	GCAAAATCGAACAAGTACGGC	58.761	47.619	0.00	0.00	0.00	5.68
1463	1534	2.480244	GCTGATCTGTGACTGCATCGTA	60.480	50.000	1.27	0.00	0.00	3.43
1475	1546	0.247736	GTGAACTCCGGCTGATCTGT	59.752	55.000	0.00	0.00	0.00	3.41
1627	1701	0.525668	AGACGGCGATGTAAAGCTCG	60.526	55.000	16.62	0.00	37.92	5.03
1750	1824	3.305094	ACGAAATATGGCGTCGTAGTTTG	59.695	43.478	13.65	13.65	45.57	2.93
1767	1841	3.928375	GTCCGCCTCTAAACATTACGAAA	59.072	43.478	0.00	0.00	0.00	3.46
1806	1894	5.705905	AGCCACTCCAACTAATTAACAGAAC	59.294	40.000	0.00	0.00	0.00	3.01
1811	1899	5.449177	GCATGAGCCACTCCAACTAATTAAC	60.449	44.000	0.00	0.00	33.58	2.01
1814	1902	3.019564	GCATGAGCCACTCCAACTAATT	58.980	45.455	0.00	0.00	33.58	1.40
1901	1992	1.199327	TCTTTGCGGACAGAGTAGACG	59.801	52.381	0.00	0.00	30.16	4.18
1920	2011	9.309516	TCGGTAAAAGATGTTGAGTGTATATTC	57.690	33.333	0.00	0.00	0.00	1.75
1952	2049	2.922740	ATATAAAGCGGGGCGAAAGA	57.077	45.000	0.00	0.00	0.00	2.52
2164	2262	3.417275	CTTCGCTCGATGGCCGTCT	62.417	63.158	22.53	0.00	39.75	4.18
2185	2283	1.097547	CATCACCGCCTTCATCACCC	61.098	60.000	0.00	0.00	0.00	4.61
2285	2383	1.299165	CCAGCGTATTCCTCGTCGG	60.299	63.158	0.00	0.00	0.00	4.79
2289	2387	1.067060	TGTGATCCAGCGTATTCCTCG	59.933	52.381	0.00	0.00	0.00	4.63
2382	2482	0.547954	AACTCCAGAACTCCCCTCCC	60.548	60.000	0.00	0.00	0.00	4.30
2383	2483	0.906066	GAACTCCAGAACTCCCCTCC	59.094	60.000	0.00	0.00	0.00	4.30
2544	2645	4.431131	CGCAATGGCCCTGGGTCT	62.431	66.667	19.84	0.73	36.38	3.85
2611	2712	6.272318	TGCCATTGAAAATTCGGATATTCAC	58.728	36.000	0.00	0.00	31.96	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.