AutoCloner

Multiple sequence alignment - TraesCS2B01G063000

Loading Multiple Alignment...

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	TraesCS2B01G063000	chr2B	100.000	2641	0	0	1	2641	30161299	30158659	0.000000e+00	4878
1	TraesCS2B01G063000	chr2B	92.629	1818	108	17	1	1800	30230907	30229098	0.000000e+00	2591
2	TraesCS2B01G063000	chr2B	90.984	1453	95	24	375	1800	30174272	30172829	0.000000e+00	1925
3	TraesCS2B01G063000	chr2B	90.984	1453	95	21	375	1800	30187991	30186548	0.000000e+00	1925
4	TraesCS2B01G063000	chr2B	90.709	1453	97	18	375	1800	30209503	30208062	0.000000e+00	1901
5	TraesCS2B01G063000	chr2B	95.361	388	14	4	1	386	30174684	30174299	4.830000e-172	614
6	TraesCS2B01G063000	chr2B	95.116	389	15	4	1	386	30188405	30188018	6.250000e-171	610
7	TraesCS2B01G063000	chr2B	94.845	388	14	5	1	385	30209915	30209531	3.760000e-168	601
8	TraesCS2B01G063000	chr2B	83.154	279	43	4	2365	2641	70876269	70876545	4.360000e-63	252
9	TraesCS2B01G063000	chr2B	90.411	146	6	3	1662	1800	30233212	30233068	4.490000e-43	185
10	TraesCS2B01G063000	chrUn	92.849	1818	103	18	1	1800	178510481	178512289	0.000000e+00	2612
11	TraesCS2B01G063000	chrUn	90.154	1818	114	26	1	1800	178493755	178495525	0.000000e+00	2305
12	TraesCS2B01G063000	chrUn	90.645	1101	79	15	716	1800	178476272	178477364	0.000000e+00	1441
13	TraesCS2B01G063000	chrUn	92.399	671	36	5	1699	2369	12594428	12593773	0.000000e+00	942
14	TraesCS2B01G063000	chrUn	94.402	393	14	5	1	386	178475563	178475954	4.870000e-167	597
15	TraesCS2B01G063000	chrUn	94.203	276	14	2	2366	2641	12593713	12593440	1.130000e-113	420
16	TraesCS2B01G063000	chrUn	94.000	250	13	2	375	622	178475981	178476230	6.900000e-101	377
17	TraesCS2B01G063000	chr2D	90.391	1561	100	23	829	2369	18235379	18233849	0.000000e+00	2006
18	TraesCS2B01G063000	chr2D	89.130	276	27	3	2366	2641	18233789	18233517	9.050000e-90	340
19	TraesCS2B01G063000	chr3B	94.802	885	32	7	987	1867	557608607	557609481	0.000000e+00	1367
20	TraesCS2B01G063000	chr1B	95.172	725	28	5	987	1708	624495762	624495042	0.000000e+00	1138
21	TraesCS2B01G063000	chr1B	92.638	163	5	3	1706	1867	624486242	624486086	7.350000e-56	228
22	TraesCS2B01G063000	chr2A	83.304	563	62	23	830	1370	19375458	19374906	8.490000e-135	490
23	TraesCS2B01G063000	chr1A	90.572	297	20	7	538	829	525024591	525024884	1.150000e-103	387
24	TraesCS2B01G063000	chr6B	89.831	295	25	5	538	828	233671701	233671408	8.930000e-100	374
25	TraesCS2B01G063000	chr5B	89.562	297	24	4	538	827	711278304	711278600	1.150000e-98	370

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	TraesCS2B01G063000	chr2B	30158659	30161299	2640	True	4878.0	4878	100.000000	1	2641	1	chr2B.!!$R1	2640
1	TraesCS2B01G063000	chr2B	30229098	30233212	4114	True	1388.0	2591	91.520000	1	1800	2	chr2B.!!$R5	1799
2	TraesCS2B01G063000	chr2B	30172829	30174684	1855	True	1269.5	1925	93.172500	1	1800	2	chr2B.!!$R2	1799
3	TraesCS2B01G063000	chr2B	30186548	30188405	1857	True	1267.5	1925	93.050000	1	1800	2	chr2B.!!$R3	1799
4	TraesCS2B01G063000	chr2B	30208062	30209915	1853	True	1251.0	1901	92.777000	1	1800	2	chr2B.!!$R4	1799
5	TraesCS2B01G063000	chrUn	178510481	178512289	1808	False	2612.0	2612	92.849000	1	1800	1	chrUn.!!$F2	1799
6	TraesCS2B01G063000	chrUn	178493755	178495525	1770	False	2305.0	2305	90.154000	1	1800	1	chrUn.!!$F1	1799
7	TraesCS2B01G063000	chrUn	178475563	178477364	1801	False	805.0	1441	93.015667	1	1800	3	chrUn.!!$F3	1799
8	TraesCS2B01G063000	chrUn	12593440	12594428	988	True	681.0	942	93.301000	1699	2641	2	chrUn.!!$R1	942
9	TraesCS2B01G063000	chr2D	18233517	18235379	1862	True	1173.0	2006	89.760500	829	2641	2	chr2D.!!$R1	1812
10	TraesCS2B01G063000	chr3B	557608607	557609481	874	False	1367.0	1367	94.802000	987	1867	1	chr3B.!!$F1	880
11	TraesCS2B01G063000	chr1B	624495042	624495762	720	True	1138.0	1138	95.172000	987	1708	1	chr1B.!!$R2	721
12	TraesCS2B01G063000	chr2A	19374906	19375458	552	True	490.0	490	83.304000	830	1370	1	chr2A.!!$R1	540

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
312	2624	1.13458	CGTCATGATGAAGCCCAGAGT	60.135	52.381	9.46	0.0	0.0	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1940	4345	0.02877	CTCCGTCTGATCGAGCTGTC	59.971	60.0	0.9	0.0	0.0	3.51	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
312	2624	1.134580	CGTCATGATGAAGCCCAGAGT	60.135	52.381	9.46	0.00	0.00	3.24
394	2745	2.188062	ACTAATTTTGTTCGGGCCGA	57.812	45.000	27.46	27.46	0.00	5.54
423	2774	9.418045	CTAATTTTGTTTCCCACGACAATATTT	57.582	29.630	9.13	0.06	37.98	1.40
457	2808	1.843368	TCCCTCGTACCGAACTTCAT	58.157	50.000	0.00	0.00	34.74	2.57
575	2928	4.053983	CAGACACAAGCGCTCATATACAT	58.946	43.478	12.06	0.00	0.00	2.29
637	3001	1.379176	CCTCCGAGAGACTGAGCCA	60.379	63.158	0.00	0.00	0.00	4.75
690	3054	3.872728	CGCCTCGTCGTCGATGGA	61.873	66.667	14.28	6.69	45.21	3.41
699	3063	1.135746	GTCGTCGATGGAAACGTCTCT	60.136	52.381	4.48	0.00	44.51	3.10
711	3075	4.277423	GGAAACGTCTCTTCCCATTGAAAA	59.723	41.667	6.27	0.00	37.03	2.29
850	3214	9.644993	TCGCATTATACATTCAAATTCGTTTAG	57.355	29.630	0.00	0.00	0.00	1.85
996	3364	2.160205	TCGAGTCGGACAGAGAAACAT	58.840	47.619	13.54	0.00	0.00	2.71
1043	3414	0.393267	CTCTCTCCTCCGTCCTCGTT	60.393	60.000	0.00	0.00	35.01	3.85
1145	3531	0.522180	CGCAGGACTACGACTTCTGT	59.478	55.000	0.00	0.00	0.00	3.41
1613	3999	2.736347	CCTTCTTCTACCTCCGGAAGA	58.264	52.381	7.17	3.27	43.89	2.87
1694	4090	5.544650	ACTTGCAAAATTTCCAATGGAGAG	58.455	37.500	0.86	0.00	31.21	3.20
1708	4111	1.067142	TGGAGAGCGATGTGGTGTAAC	60.067	52.381	0.00	0.00	0.00	2.50
1790	4195	2.366916	CAGATCAGGCGAGGAAGGTTAT	59.633	50.000	0.00	0.00	0.00	1.89
1837	4242	8.973182	CAATCCTACTCTTACTCTAGACCTTTT	58.027	37.037	0.00	0.00	0.00	2.27
1838	4243	9.549984	AATCCTACTCTTACTCTAGACCTTTTT	57.450	33.333	0.00	0.00	0.00	1.94
1878	4283	3.500343	ACCAAAATTCTACTGCTTGGCT	58.500	40.909	3.27	0.00	40.20	4.75
1881	4286	4.240096	CAAAATTCTACTGCTTGGCTTGG	58.760	43.478	0.00	0.00	0.00	3.61
1882	4287	1.467920	ATTCTACTGCTTGGCTTGGC	58.532	50.000	0.00	0.00	0.00	4.52
1895	4300	1.174712	GCTTGGCCTGAACTGAAGCA	61.175	55.000	14.89	0.00	39.09	3.91
1896	4301	1.321474	CTTGGCCTGAACTGAAGCAA	58.679	50.000	3.32	0.00	0.00	3.91
1897	4302	1.682854	CTTGGCCTGAACTGAAGCAAA	59.317	47.619	3.32	0.00	0.00	3.68
1938	4343	4.123506	GGCCTGAAGAGAGCTTTACATAC	58.876	47.826	0.00	0.00	33.61	2.39
1939	4344	4.383118	GGCCTGAAGAGAGCTTTACATACA	60.383	45.833	0.00	0.00	33.61	2.29
1940	4345	4.808364	GCCTGAAGAGAGCTTTACATACAG	59.192	45.833	0.00	0.00	33.61	2.74
1941	4346	5.394663	GCCTGAAGAGAGCTTTACATACAGA	60.395	44.000	0.00	0.00	33.61	3.41
2262	4667	3.997021	CCTGCAGAATCGACAAACTACTT	59.003	43.478	17.39	0.00	0.00	2.24
2267	4672	6.926826	TGCAGAATCGACAAACTACTTTAAGA	59.073	34.615	0.00	0.00	0.00	2.10
2332	4737	8.507524	AATCCTGAAAAGTACTAAGTATTGCC	57.492	34.615	0.00	0.00	0.00	4.52
2335	4741	5.503002	TGAAAAGTACTAAGTATTGCCCCC	58.497	41.667	0.00	0.00	0.00	5.40
2351	4757	1.152881	CCCCACATCCTTAGGCTGC	60.153	63.158	1.55	0.00	0.00	5.25
2354	4760	1.616725	CCCACATCCTTAGGCTGCAAA	60.617	52.381	1.55	0.00	0.00	3.68
2355	4761	2.170166	CCACATCCTTAGGCTGCAAAA	58.830	47.619	1.55	0.00	0.00	2.44
2364	4770	6.186957	TCCTTAGGCTGCAAAATTATTCAGA	58.813	36.000	0.50	0.00	0.00	3.27
2371	4839	7.340232	AGGCTGCAAAATTATTCAGACAGATAA	59.660	33.333	0.50	0.00	37.05	1.75
2390	4858	7.663081	ACAGATAAAGATAATCATGCGTGGAAT	59.337	33.333	5.98	0.00	0.00	3.01
2391	4859	9.154847	CAGATAAAGATAATCATGCGTGGAATA	57.845	33.333	5.98	0.00	0.00	1.75
2417	4885	6.759497	ACCATTATCAGGTTAGTTTTCTGC	57.241	37.500	0.00	0.00	35.33	4.26
2420	4888	7.553044	ACCATTATCAGGTTAGTTTTCTGCTAC	59.447	37.037	0.00	0.00	35.33	3.58
2492	4960	9.337396	TCAACCCATTAACATATTGATGTCTAC	57.663	33.333	0.00	0.00	45.93	2.59
2496	4964	7.119699	CCCATTAACATATTGATGTCTACGCAT	59.880	37.037	0.00	0.00	45.93	4.73
2631	5099	3.473647	CCCTCCTCGATGGCTGCA	61.474	66.667	0.50	0.00	35.26	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
312	2624	8.634335	TCTTCTCATTAACCAATTGACATTCA	57.366	30.769	7.12	0.00	0.00	2.57
394	2745	6.210287	TGTCGTGGGAAACAAAATTAGTTT	57.790	33.333	8.24	8.24	41.53	2.66
423	2774	6.534793	GGTACGAGGGAAAATATTGTCGTTTA	59.465	38.462	12.39	0.00	40.79	2.01
424	2775	5.352293	GGTACGAGGGAAAATATTGTCGTTT	59.648	40.000	12.39	0.00	40.79	3.60
485	2836	2.230508	GGACCTCGATATATGCCGAACA	59.769	50.000	0.00	0.00	34.17	3.18
550	2903	2.680312	ATGAGCGCTTGTGTCTGTAT	57.320	45.000	13.26	0.00	0.00	2.29
575	2928	0.973496	TAGGGGTGAGTGTATGCGCA	60.973	55.000	14.96	14.96	0.00	6.09
637	3001	8.204836	ACTTCGTAATTCTTAAGATGGTATGCT	58.795	33.333	5.89	0.00	0.00	3.79
687	3051	2.370519	TCAATGGGAAGAGACGTTTCCA	59.629	45.455	17.12	3.73	44.77	3.53
690	3054	4.642885	TGTTTTCAATGGGAAGAGACGTTT	59.357	37.500	0.00	0.00	36.72	3.60
699	3063	2.029470	GGCGATGTGTTTTCAATGGGAA	60.029	45.455	0.00	0.00	0.00	3.97
711	3075	1.086696	CAGGATTTTCGGCGATGTGT	58.913	50.000	11.76	0.00	0.00	3.72
850	3214	6.716898	ACTCTTTTACTAATTACGCCACAC	57.283	37.500	0.00	0.00	0.00	3.82
996	3364	1.407656	GGGGCCATGGTCGTCTGATA	61.408	60.000	14.67	0.00	0.00	2.15
1043	3414	1.539560	GCTGTGTGAGGAGCAGGAGA	61.540	60.000	0.00	0.00	35.15	3.71
1145	3531	4.329545	GCCCCCAGCGTCTTCACA	62.330	66.667	0.00	0.00	0.00	3.58
1613	3999	5.711976	ACTGTCCGGAAAGATGATCATTTTT	59.288	36.000	28.93	20.77	0.00	1.94
1665	4061	9.213799	TCCATTGGAAATTTTGCAAGTTATTAC	57.786	29.630	18.84	0.00	44.23	1.89
1694	4090	2.373540	TACTGGTTACACCACATCGC	57.626	50.000	0.00	0.00	44.79	4.58
1734	4137	5.999600	TGTGAATCAGAGAAAATCTTCAGCA	59.000	36.000	0.00	0.00	35.47	4.41
1790	4195	2.845486	CCATTTTTGCGAATCGAACGA	58.155	42.857	6.91	0.00	0.00	3.85
1878	4283	1.774110	TTTGCTTCAGTTCAGGCCAA	58.226	45.000	5.01	0.00	0.00	4.52
1881	4286	3.930634	AGATTTTGCTTCAGTTCAGGC	57.069	42.857	0.00	0.00	0.00	4.85
1912	4317	1.271127	AAGCTCTCTTCAGGCCTCCC	61.271	60.000	0.00	0.00	0.00	4.30
1938	4343	0.248417	CCGTCTGATCGAGCTGTCTG	60.248	60.000	0.90	0.00	0.00	3.51
1939	4344	0.393132	TCCGTCTGATCGAGCTGTCT	60.393	55.000	0.90	0.00	0.00	3.41
1940	4345	0.028770	CTCCGTCTGATCGAGCTGTC	59.971	60.000	0.90	0.00	0.00	3.51
1941	4346	0.393132	TCTCCGTCTGATCGAGCTGT	60.393	55.000	0.90	0.00	0.00	4.40
2187	4592	3.327404	GCCGGAGTGGAAGGGGAA	61.327	66.667	5.05	0.00	42.00	3.97
2262	4667	7.658575	GGAATAACACCTGTGTACTGTTCTTAA	59.341	37.037	2.92	0.00	44.13	1.85
2267	4672	5.061179	GTGGAATAACACCTGTGTACTGTT	58.939	41.667	2.92	3.33	44.13	3.16
2306	4711	9.609346	GGCAATACTTAGTACTTTTCAGGATTA	57.391	33.333	0.00	0.00	0.00	1.75
2332	4737	1.533711	CAGCCTAAGGATGTGGGGG	59.466	63.158	0.00	0.00	34.00	5.40
2335	4741	1.838112	TTTGCAGCCTAAGGATGTGG	58.162	50.000	0.00	0.00	41.69	4.17
2347	4753	8.915871	TTTATCTGTCTGAATAATTTTGCAGC	57.084	30.769	0.00	0.00	0.00	5.25
2364	4770	6.524734	TCCACGCATGATTATCTTTATCTGT	58.475	36.000	0.00	0.00	0.00	3.41
2371	4839	7.882791	TGGTATTATTCCACGCATGATTATCTT	59.117	33.333	0.00	0.00	0.00	2.40
2375	4843	7.994425	AATGGTATTATTCCACGCATGATTA	57.006	32.000	0.00	0.00	37.81	1.75
2378	4846	7.164803	TGATAATGGTATTATTCCACGCATGA	58.835	34.615	0.00	0.00	37.81	3.07
2383	4851	7.979444	AACCTGATAATGGTATTATTCCACG	57.021	36.000	0.00	0.00	37.81	4.94
2391	4859	8.903820	GCAGAAAACTAACCTGATAATGGTATT	58.096	33.333	0.00	0.00	36.69	1.89
2417	4885	6.309712	CCAGATGGTAGAAATTGCATGTAG	57.690	41.667	0.00	0.00	0.00	2.74
2492	4960	4.333649	ACATCATTCAGAAGGTAACATGCG	59.666	41.667	0.00	0.00	41.41	4.73
2496	4964	4.937620	GCTGACATCATTCAGAAGGTAACA	59.062	41.667	4.29	0.00	45.19	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.