AutoCloner

Multiple sequence alignment - TraesCS3B01G070900

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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	TraesCS3B01G070900	chr3B	100.000	2141	0	0	1	2141	42708358	42706218	0.000000e+00	3954.0
1	TraesCS3B01G070900	chr3B	79.178	754	100	29	612	1343	42715053	42714335	8.950000e-129	470.0
2	TraesCS3B01G070900	chr3B	78.891	649	65	48	852	1487	42701263	42700674	7.210000e-100	374.0
3	TraesCS3B01G070900	chr3B	83.210	405	45	16	838	1225	42690342	42689944	1.220000e-92	350.0
4	TraesCS3B01G070900	chr3B	88.514	148	15	2	1279	1425	42689926	42689780	6.070000e-41	178.0
5	TraesCS3B01G070900	chr3B	83.523	176	18	9	610	781	42701453	42701285	1.020000e-33	154.0
6	TraesCS3B01G070900	chr3B	85.981	107	6	5	2041	2138	42713612	42713506	2.910000e-19	106.0
7	TraesCS3B01G070900	chr3D	93.189	1292	54	10	561	1839	25161472	25160202	0.000000e+00	1868.0
8	TraesCS3B01G070900	chr3D	90.718	571	40	9	1	567	25162076	25161515	0.000000e+00	749.0
9	TraesCS3B01G070900	chr3D	81.784	807	74	28	587	1366	25190857	25190097	1.820000e-170	608.0
10	TraesCS3B01G070900	chr3D	94.510	255	7	1	1887	2141	25160188	25159941	9.270000e-104	387.0
11	TraesCS3B01G070900	chr3D	87.755	98	6	3	1286	1383	25150937	25150846	2.250000e-20	110.0
12	TraesCS3B01G070900	chr3D	83.636	110	8	5	2041	2141	25189240	25189132	6.290000e-16	95.3
13	TraesCS3B01G070900	chr3A	90.737	1371	74	29	581	1937	34583690	34582359	0.000000e+00	1779.0
14	TraesCS3B01G070900	chr3A	89.649	570	46	9	1	567	34584299	34583740	0.000000e+00	713.0
15	TraesCS3B01G070900	chr3A	80.774	801	75	38	587	1366	34593683	34592941	8.630000e-154	553.0
16	TraesCS3B01G070900	chr3A	81.591	440	34	28	992	1424	34580318	34579919	9.530000e-84	320.0
17	TraesCS3B01G070900	chr3A	96.988	166	5	0	1973	2138	34582362	34582197	1.620000e-71	279.0
18	TraesCS3B01G070900	chr3A	82.883	222	16	10	579	781	34580603	34580385	1.690000e-41	180.0
19	TraesCS3B01G070900	chr3A	85.455	110	7	7	2041	2141	34592271	34592162	2.910000e-19	106.0
20	TraesCS3B01G070900	chr3A	97.436	39	1	0	2103	2141	34539780	34539742	1.370000e-07	67.6
21	TraesCS3B01G070900	chr1A	79.889	542	55	32	896	1418	548454416	548454922	4.370000e-92	348.0
22	TraesCS3B01G070900	chr1D	76.731	722	86	53	785	1476	453573449	453574118	5.700000e-86	327.0
23	TraesCS3B01G070900	chr1B	77.226	685	66	59	785	1430	624018866	624019499	3.430000e-83	318.0
24	TraesCS3B01G070900	chr1B	97.500	40	1	0	2099	2138	624020540	624020579	3.810000e-08	69.4
25	TraesCS3B01G070900	chr1B	95.000	40	2	0	2099	2138	623993628	623993667	1.770000e-06	63.9

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	TraesCS3B01G070900	chr3B	42706218	42708358	2140	True	3954.000000	3954	100.000000	1	2141	1	chr3B.!!$R1	2140
1	TraesCS3B01G070900	chr3B	42713506	42715053	1547	True	288.000000	470	82.579500	612	2138	2	chr3B.!!$R4	1526
2	TraesCS3B01G070900	chr3B	42689780	42690342	562	True	264.000000	350	85.862000	838	1425	2	chr3B.!!$R2	587
3	TraesCS3B01G070900	chr3B	42700674	42701453	779	True	264.000000	374	81.207000	610	1487	2	chr3B.!!$R3	877
4	TraesCS3B01G070900	chr3D	25159941	25162076	2135	True	1001.333333	1868	92.805667	1	2141	3	chr3D.!!$R2	2140
5	TraesCS3B01G070900	chr3D	25189132	25190857	1725	True	351.650000	608	82.710000	587	2141	2	chr3D.!!$R3	1554
6	TraesCS3B01G070900	chr3A	34579919	34584299	4380	True	654.200000	1779	88.369600	1	2138	5	chr3A.!!$R2	2137
7	TraesCS3B01G070900	chr3A	34592162	34593683	1521	True	329.500000	553	83.114500	587	2141	2	chr3A.!!$R3	1554
8	TraesCS3B01G070900	chr1A	548454416	548454922	506	False	348.000000	348	79.889000	896	1418	1	chr1A.!!$F1	522
9	TraesCS3B01G070900	chr1D	453573449	453574118	669	False	327.000000	327	76.731000	785	1476	1	chr1D.!!$F1	691

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
479	484	0.108709	CAATTGTGGTGGCATTCGGG	60.109	55.0	0.0	0.0	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2015	2463	1.063114	AGGTTGAGGCGAGTATACCCT	60.063	52.381	0.0	0.0	0.0	4.34	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
40	41	0.322098	CGTAAGATTGGCCACCACCA	60.322	55.000	3.88	0.00	43.02	4.17
55	56	2.421314	CCACACGTGCCAGAGTCA	59.579	61.111	17.22	0.00	0.00	3.41
63	64	2.032681	GCCAGAGTCACCGCCTTT	59.967	61.111	0.00	0.00	0.00	3.11
71	72	1.978080	TCACCGCCTTTGCATGCAT	60.978	52.632	23.37	0.58	37.32	3.96
142	145	6.250711	TGAGTTAGTCATCCACCTTGTAGTA	58.749	40.000	0.00	0.00	0.00	1.82
169	172	0.617820	TAGCCAGTGGTCCCTCCTTC	60.618	60.000	11.74	0.00	37.07	3.46
176	179	0.256752	TGGTCCCTCCTTCGTCGATA	59.743	55.000	0.00	0.00	37.07	2.92
198	201	4.227134	CCTGCCGCTACCATCGCT	62.227	66.667	0.00	0.00	0.00	4.93
215	218	2.601666	TGAGCGTGAGAGTGGGCT	60.602	61.111	0.00	0.00	38.70	5.19
216	219	2.125753	GAGCGTGAGAGTGGGCTG	60.126	66.667	0.00	0.00	35.54	4.85
217	220	3.655810	GAGCGTGAGAGTGGGCTGG	62.656	68.421	0.00	0.00	35.54	4.85
218	221	4.767255	GCGTGAGAGTGGGCTGGG	62.767	72.222	0.00	0.00	0.00	4.45
219	222	4.087892	CGTGAGAGTGGGCTGGGG	62.088	72.222	0.00	0.00	0.00	4.96
220	223	2.607750	GTGAGAGTGGGCTGGGGA	60.608	66.667	0.00	0.00	0.00	4.81
221	224	1.997874	GTGAGAGTGGGCTGGGGAT	60.998	63.158	0.00	0.00	0.00	3.85
253	256	2.564947	GGGAGAGAAAGCAAGACAGAGA	59.435	50.000	0.00	0.00	0.00	3.10
274	277	1.187087	GAGGTGGGAGACGAGTGAAT	58.813	55.000	0.00	0.00	0.00	2.57
290	293	5.504665	CGAGTGAATTGAAACAGTTGCTTCT	60.505	40.000	0.00	0.00	0.00	2.85
316	320	4.321452	CGAGCTAGGTAACAGTTGTAACCA	60.321	45.833	6.51	0.00	41.41	3.67
317	321	5.623824	CGAGCTAGGTAACAGTTGTAACCAT	60.624	44.000	6.51	0.00	41.41	3.55
347	352	1.435925	CACACGCCCTATGCTACGA	59.564	57.895	0.00	0.00	38.05	3.43
413	418	1.478510	TGCTTACTGCCTCACTAGAGC	59.521	52.381	0.00	0.00	40.68	4.09
429	434	9.598517	CTCACTAGAGCTTCTGAGAAAAATTAT	57.401	33.333	0.00	0.00	34.61	1.28
436	441	9.113838	GAGCTTCTGAGAAAAATTATGTGGATA	57.886	33.333	0.00	0.00	0.00	2.59
479	484	0.108709	CAATTGTGGTGGCATTCGGG	60.109	55.000	0.00	0.00	0.00	5.14
563	569	2.668279	CGCATTTGACCACCTTAGTTGC	60.668	50.000	0.00	0.00	0.00	4.17
583	638	1.451387	CCCGCACCTCCACCATTAC	60.451	63.158	0.00	0.00	0.00	1.89
702	757	1.553704	GTCCCCTAAAGTGTCATCGGT	59.446	52.381	0.00	0.00	0.00	4.69
824	881	5.983540	AGTAGGAAAAGATGTGAGGATGAC	58.016	41.667	0.00	0.00	0.00	3.06
986	1092	2.644798	ACCTAGCTCAACCATCACCTTT	59.355	45.455	0.00	0.00	0.00	3.11
1151	1286	2.292267	CCATGACTGACCCTACATTGC	58.708	52.381	0.00	0.00	0.00	3.56
1233	1384	6.203530	CAGATTCTCTGTTGTGTGTATGTGTT	59.796	38.462	0.00	0.00	39.58	3.32
1245	1396	5.810587	GTGTGTATGTGTTCATAGGGTAGTG	59.189	44.000	0.00	0.00	37.23	2.74
1246	1397	5.482526	TGTGTATGTGTTCATAGGGTAGTGT	59.517	40.000	0.00	0.00	37.23	3.55
1247	1398	6.664384	TGTGTATGTGTTCATAGGGTAGTGTA	59.336	38.462	0.00	0.00	37.23	2.90
1248	1399	7.147966	TGTGTATGTGTTCATAGGGTAGTGTAG	60.148	40.741	0.00	0.00	37.23	2.74
1249	1400	5.871396	ATGTGTTCATAGGGTAGTGTAGG	57.129	43.478	0.00	0.00	31.89	3.18
1250	1401	3.449737	TGTGTTCATAGGGTAGTGTAGGC	59.550	47.826	0.00	0.00	0.00	3.93
1268	1446	3.658709	AGGCTTAGATAGATTTCGCTGC	58.341	45.455	0.00	0.00	0.00	5.25
1278	1456	2.093869	AGATTTCGCTGCCGGTTAGTTA	60.094	45.455	1.90	0.00	34.56	2.24
1281	1459	0.966875	TCGCTGCCGGTTAGTTAGGA	60.967	55.000	1.90	0.00	34.56	2.94
1284	1462	2.210961	GCTGCCGGTTAGTTAGGAATC	58.789	52.381	1.90	0.00	0.00	2.52
1354	1534	5.207110	AGGATGTGCATGTAGTATCTGAC	57.793	43.478	0.00	0.00	0.00	3.51
1450	1633	9.154847	AGAAAAAGCAATTATTATGAAAGTGCC	57.845	29.630	4.82	0.00	46.18	5.01
1451	1634	8.845413	AAAAAGCAATTATTATGAAAGTGCCA	57.155	26.923	4.82	0.00	46.18	4.92
1502	1711	8.628630	TCCAATTGTACATAATTGTGACTTGA	57.371	30.769	15.71	5.51	43.28	3.02
1564	1945	6.369065	GGGATGTTCTTATTTCGCTCGATTAT	59.631	38.462	0.00	0.00	0.00	1.28
1619	2030	4.219070	CCATCTCAAAGGAGTGCATTTTCA	59.781	41.667	0.00	0.00	42.05	2.69
1669	2102	7.147742	GGAAATTGGCACCTTAATATTTCAGGA	60.148	37.037	16.70	0.00	35.02	3.86
1687	2120	6.131544	TCAGGAAAAGTTTACTTTGTGAGC	57.868	37.500	8.51	0.00	44.69	4.26
1689	2122	4.953579	AGGAAAAGTTTACTTTGTGAGCCA	59.046	37.500	8.51	0.00	44.69	4.75
1706	2139	2.145536	GCCAAACATTTCAGGGCAAAG	58.854	47.619	0.00	0.00	44.01	2.77
1763	2198	4.271696	TCTGATGGTAACCTCACACTTG	57.728	45.455	0.00	0.00	36.21	3.16
1782	2217	6.016777	ACACTTGGACATTGAAAGACTCATTC	60.017	38.462	0.00	0.00	32.78	2.67
1862	2308	5.023452	TCCCTCTGACTTTCTTGCAGTATA	58.977	41.667	0.00	0.00	0.00	1.47
1863	2309	5.663106	TCCCTCTGACTTTCTTGCAGTATAT	59.337	40.000	0.00	0.00	0.00	0.86
1864	2310	5.988561	CCCTCTGACTTTCTTGCAGTATATC	59.011	44.000	0.00	0.00	0.00	1.63
1865	2311	6.407412	CCCTCTGACTTTCTTGCAGTATATCA	60.407	42.308	0.00	0.00	0.00	2.15
1866	2312	7.215789	CCTCTGACTTTCTTGCAGTATATCAT	58.784	38.462	0.00	0.00	0.00	2.45
1867	2313	8.363390	CCTCTGACTTTCTTGCAGTATATCATA	58.637	37.037	0.00	0.00	0.00	2.15
1870	2316	8.877808	TGACTTTCTTGCAGTATATCATACAG	57.122	34.615	0.00	0.00	0.00	2.74
1871	2317	8.478066	TGACTTTCTTGCAGTATATCATACAGT	58.522	33.333	0.00	0.00	0.00	3.55
1872	2318	9.967346	GACTTTCTTGCAGTATATCATACAGTA	57.033	33.333	0.00	0.00	0.00	2.74
1994	2442	5.404366	ACGTACAGTACTTGCAGTATTGTTG	59.596	40.000	20.73	17.25	45.49	3.33
1996	2444	3.502211	ACAGTACTTGCAGTATTGTTGGC	59.498	43.478	14.33	0.00	45.49	4.52
2009	2457	1.241165	TGTTGGCTGAGATGTTGCTG	58.759	50.000	0.00	0.00	0.00	4.41
2012	2460	0.614812	TGGCTGAGATGTTGCTGCTA	59.385	50.000	0.00	0.00	0.00	3.49
2013	2461	1.003464	TGGCTGAGATGTTGCTGCTAA	59.997	47.619	0.00	0.00	0.00	3.09
2014	2462	1.399791	GGCTGAGATGTTGCTGCTAAC	59.600	52.381	0.00	4.71	0.00	2.34
2015	2463	2.079158	GCTGAGATGTTGCTGCTAACA	58.921	47.619	16.07	16.07	43.93	2.41
2050	2538	1.827969	CAACCTGAATCTCGAGGAGGT	59.172	52.381	13.56	15.17	33.16	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	2.421739	GGTGACTCTGGCACGTGT	59.578	61.111	18.38	0.00	37.13	4.49
55	56	2.887360	GATGCATGCAAAGGCGGT	59.113	55.556	26.68	5.83	45.35	5.68
81	82	0.249741	CTTCCCTCGACAACCACGTT	60.250	55.000	0.00	0.00	0.00	3.99
142	145	1.285078	GGACCACTGGCTAGGGAAATT	59.715	52.381	0.00	0.00	0.00	1.82
169	172	1.280142	CGGCAGGACTCTATCGACG	59.720	63.158	0.00	0.00	0.00	5.12
176	179	1.381872	ATGGTAGCGGCAGGACTCT	60.382	57.895	1.45	0.00	0.00	3.24
183	186	3.430565	CTCAGCGATGGTAGCGGCA	62.431	63.158	0.00	0.00	40.04	5.69
198	201	2.601666	AGCCCACTCTCACGCTCA	60.602	61.111	0.00	0.00	0.00	4.26
204	207	1.997311	CATCCCCAGCCCACTCTCA	60.997	63.158	0.00	0.00	0.00	3.27
235	238	4.081531	CCTCATCTCTGTCTTGCTTTCTCT	60.082	45.833	0.00	0.00	0.00	3.10
253	256	0.039764	TCACTCGTCTCCCACCTCAT	59.960	55.000	0.00	0.00	0.00	2.90
290	293	6.183360	GGTTACAACTGTTACCTAGCTCGATA	60.183	42.308	10.13	0.00	42.61	2.92
347	352	2.032528	CCCCACGTGTCATGCTGT	59.967	61.111	15.65	0.00	0.00	4.40
359	364	2.125106	CTAGCCAGTTCGCCCCAC	60.125	66.667	0.00	0.00	0.00	4.61
413	418	8.338259	CGGTATCCACATAATTTTTCTCAGAAG	58.662	37.037	0.00	0.00	0.00	2.85
429	434	4.829872	ACAGAAATAACCGGTATCCACA	57.170	40.909	8.00	0.00	0.00	4.17
436	441	4.999311	GGTTTCACTACAGAAATAACCGGT	59.001	41.667	0.00	0.00	39.46	5.28
479	484	3.429960	CGCTAGTGAGGGTTTAGGGTTAC	60.430	52.174	0.00	0.00	0.00	2.50
583	638	9.787532	ACATTTTATGAAAATAATCCACACGAG	57.212	29.630	0.00	0.00	38.97	4.18
702	757	2.016393	CTCTCAAGGTGCGGCGGATA	62.016	60.000	9.78	0.00	0.00	2.59
824	881	3.560068	ACAAAAGACAAACTACTCTGGCG	59.440	43.478	0.00	0.00	0.00	5.69
892	978	2.356125	GGATTGGTCTGCCTCTGCTTTA	60.356	50.000	0.00	0.00	38.71	1.85
1151	1286	3.433615	GGATCAAACGAAGAACAGGACAG	59.566	47.826	0.00	0.00	0.00	3.51
1233	1384	5.658198	TCTAAGCCTACACTACCCTATGA	57.342	43.478	0.00	0.00	0.00	2.15
1245	1396	4.623595	GCAGCGAAATCTATCTAAGCCTAC	59.376	45.833	0.00	0.00	0.00	3.18
1246	1397	4.322049	GGCAGCGAAATCTATCTAAGCCTA	60.322	45.833	0.00	0.00	35.63	3.93
1247	1398	3.556004	GGCAGCGAAATCTATCTAAGCCT	60.556	47.826	0.00	0.00	35.63	4.58
1248	1399	2.739379	GGCAGCGAAATCTATCTAAGCC	59.261	50.000	0.00	0.00	0.00	4.35
1249	1400	2.410053	CGGCAGCGAAATCTATCTAAGC	59.590	50.000	0.00	0.00	0.00	3.09
1250	1401	2.989840	CCGGCAGCGAAATCTATCTAAG	59.010	50.000	0.00	0.00	0.00	2.18
1268	1446	5.731591	ACTTCAAGATTCCTAACTAACCGG	58.268	41.667	0.00	0.00	0.00	5.28
1278	1456	4.956075	ACCACACAAAACTTCAAGATTCCT	59.044	37.500	0.00	0.00	0.00	3.36
1281	1459	5.913137	TCACCACACAAAACTTCAAGATT	57.087	34.783	0.00	0.00	0.00	2.40
1284	1462	6.151691	CCATATCACCACACAAAACTTCAAG	58.848	40.000	0.00	0.00	0.00	3.02
1431	1614	5.811613	TGCTTGGCACTTTCATAATAATTGC	59.188	36.000	0.00	0.00	31.71	3.56
1450	1633	5.051816	TGCCAAGAGAAAATCTTTTGCTTG	58.948	37.500	14.55	14.55	46.49	4.01
1451	1634	5.280654	TGCCAAGAGAAAATCTTTTGCTT	57.719	34.783	5.39	0.00	46.49	3.91
1502	1711	3.157932	GCGTTAGCAATCAGAGACTCT	57.842	47.619	0.00	0.00	44.35	3.24
1542	1923	7.438160	TGACATAATCGAGCGAAATAAGAACAT	59.562	33.333	0.00	0.00	0.00	2.71
1564	1945	2.631160	AATCGTCCCAACAACTGACA	57.369	45.000	0.00	0.00	0.00	3.58
1619	2030	7.231317	TCCTGAGTAACTTTGCAAATTCATTCT	59.769	33.333	13.23	6.86	0.00	2.40
1687	2120	3.473923	ACTTTGCCCTGAAATGTTTGG	57.526	42.857	0.00	0.00	0.00	3.28
1689	2122	4.751767	TGAACTTTGCCCTGAAATGTTT	57.248	36.364	0.00	0.00	0.00	2.83
1763	2198	8.729805	AAGATAGAATGAGTCTTTCAATGTCC	57.270	34.615	18.11	4.42	39.77	4.02
1807	2242	3.756963	TGTGTGTAGATAGTCGCTCAGTT	59.243	43.478	0.00	0.00	0.00	3.16
1841	2276	6.577103	TGATATACTGCAAGAAAGTCAGAGG	58.423	40.000	0.00	0.00	37.43	3.69
1844	2279	8.877808	TGTATGATATACTGCAAGAAAGTCAG	57.122	34.615	0.00	0.00	37.43	3.51
1867	2313	9.702494	GACAAACTGGTTTATAAGTACTACTGT	57.298	33.333	0.00	0.00	0.00	3.55
1872	2318	9.317827	TCCTAGACAAACTGGTTTATAAGTACT	57.682	33.333	0.00	0.00	0.00	2.73
1994	2442	1.399791	GTTAGCAGCAACATCTCAGCC	59.600	52.381	0.00	0.00	0.00	4.85
1996	2444	2.676839	CCTGTTAGCAGCAACATCTCAG	59.323	50.000	0.17	2.28	41.26	3.35
2009	2457	1.962100	AGGCGAGTATACCCTGTTAGC	59.038	52.381	0.00	0.00	0.00	3.09
2012	2460	2.154567	TGAGGCGAGTATACCCTGTT	57.845	50.000	4.10	0.00	0.00	3.16
2013	2461	1.755380	GTTGAGGCGAGTATACCCTGT	59.245	52.381	4.10	0.00	0.00	4.00
2014	2462	1.068741	GGTTGAGGCGAGTATACCCTG	59.931	57.143	4.10	0.00	0.00	4.45
2015	2463	1.063114	AGGTTGAGGCGAGTATACCCT	60.063	52.381	0.00	0.00	0.00	4.34
2050	2538	4.764823	CCATCTTGCACTAAACCCAAAGTA	59.235	41.667	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.