AutoCloner

Multiple sequence alignment - TraesCS5A01G419100

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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	TraesCS5A01G419100	chr5A	100.000	1656	0	0	654	2309	606688455	606690110	0.000000e+00	3059
1	TraesCS5A01G419100	chr5A	96.933	1467	31	2	654	2116	288268500	288267044	0.000000e+00	2447
2	TraesCS5A01G419100	chr5A	100.000	431	0	0	1	431	606687802	606688232	0.000000e+00	797
3	TraesCS5A01G419100	chr5A	96.110	437	10	4	1	430	288268819	288268383	0.000000e+00	706
4	TraesCS5A01G419100	chr7A	96.212	1663	55	4	654	2309	38737884	38739545	0.000000e+00	2715
5	TraesCS5A01G419100	chr7A	95.102	1613	46	14	654	2265	134596550	134598130	0.000000e+00	2510
6	TraesCS5A01G419100	chr7A	91.232	1688	100	21	654	2309	699322317	699320646	0.000000e+00	2254
7	TraesCS5A01G419100	chr7A	97.538	1178	24	3	654	1831	124061485	124060313	0.000000e+00	2010
8	TraesCS5A01G419100	chr7A	96.736	1195	33	3	654	1844	192625282	192626474	0.000000e+00	1986
9	TraesCS5A01G419100	chr7A	96.714	1126	37	0	654	1779	643609850	643610975	0.000000e+00	1875
10	TraesCS5A01G419100	chr7A	96.339	437	9	4	1	430	134596231	134596667	0.000000e+00	712
11	TraesCS5A01G419100	chr7A	95.881	437	11	4	1	430	643609531	643609967	0.000000e+00	701
12	TraesCS5A01G419100	chr7A	95.434	438	13	6	1	431	16877952	16877515	0.000000e+00	691
13	TraesCS5A01G419100	chr7A	95.423	437	13	4	1	430	192624963	192625399	0.000000e+00	689
14	TraesCS5A01G419100	chr7A	94.670	394	21	0	1916	2309	192627323	192627716	1.520000e-171	612
15	TraesCS5A01G419100	chr7A	97.193	285	8	0	2025	2309	124060303	124060019	1.240000e-132	483
16	TraesCS5A01G419100	chr7A	82.832	565	36	22	1776	2309	643611003	643611537	1.260000e-122	449
17	TraesCS5A01G419100	chr7A	91.441	222	9	4	2085	2305	134597840	134598052	1.730000e-76	296
18	TraesCS5A01G419100	chr7A	94.149	188	11	0	2122	2309	643611211	643611398	1.040000e-73	287
19	TraesCS5A01G419100	chr7A	94.382	178	10	0	1965	2142	192626470	192626647	8.130000e-70	274
20	TraesCS5A01G419100	chr7A	83.012	259	31	4	1934	2191	124060136	124059890	2.990000e-54	222
21	TraesCS5A01G419100	chr3A	95.843	1660	59	4	654	2309	635312715	635314368	0.000000e+00	2675
22	TraesCS5A01G419100	chr3A	96.119	438	10	4	1	431	635312426	635312863	0.000000e+00	708
23	TraesCS5A01G419100	chr6A	90.283	1698	83	37	654	2309	516297507	516295850	0.000000e+00	2146
24	TraesCS5A01G419100	chr2A	96.714	1126	37	0	654	1779	677898795	677897670	0.000000e+00	1875
25	TraesCS5A01G419100	chr2A	96.065	432	10	2	1	431	778395859	778396284	0.000000e+00	697
26	TraesCS5A01G419100	chr2A	85.401	548	32	19	1776	2309	677897567	677897054	2.030000e-145	525
27	TraesCS5A01G419100	chr2A	93.548	186	12	0	2122	2307	677897359	677897174	6.280000e-71	278
28	TraesCS5A01G419100	chr4A	96.575	438	8	4	1	431	637836942	637836505	0.000000e+00	719
29	TraesCS5A01G419100	chr4A	96.356	247	8	1	2063	2309	637835444	637835199	2.760000e-109	405
30	TraesCS5A01G419100	chr1A	95.662	438	11	5	1	431	559589732	559590168	0.000000e+00	697
31	TraesCS5A01G419100	chr4B	91.892	148	6	2	654	801	664037090	664036949	3.890000e-48	202

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	TraesCS5A01G419100	chr5A	606687802	606690110	2308	False	1928.000000	3059	100.000000	1	2309	2	chr5A.!!$F1	2308
1	TraesCS5A01G419100	chr5A	288267044	288268819	1775	True	1576.500000	2447	96.521500	1	2116	2	chr5A.!!$R1	2115
2	TraesCS5A01G419100	chr7A	38737884	38739545	1661	False	2715.000000	2715	96.212000	654	2309	1	chr7A.!!$F1	1655
3	TraesCS5A01G419100	chr7A	699320646	699322317	1671	True	2254.000000	2254	91.232000	654	2309	1	chr7A.!!$R2	1655
4	TraesCS5A01G419100	chr7A	134596231	134598130	1899	False	1172.666667	2510	94.294000	1	2305	3	chr7A.!!$F2	2304
5	TraesCS5A01G419100	chr7A	124059890	124061485	1595	True	905.000000	2010	92.581000	654	2309	3	chr7A.!!$R3	1655
6	TraesCS5A01G419100	chr7A	192624963	192627716	2753	False	890.250000	1986	95.302750	1	2309	4	chr7A.!!$F3	2308
7	TraesCS5A01G419100	chr7A	643609531	643611537	2006	False	828.000000	1875	92.394000	1	2309	4	chr7A.!!$F4	2308
8	TraesCS5A01G419100	chr3A	635312426	635314368	1942	False	1691.500000	2675	95.981000	1	2309	2	chr3A.!!$F1	2308
9	TraesCS5A01G419100	chr6A	516295850	516297507	1657	True	2146.000000	2146	90.283000	654	2309	1	chr6A.!!$R1	1655
10	TraesCS5A01G419100	chr2A	677897054	677898795	1741	True	892.666667	1875	91.887667	654	2309	3	chr2A.!!$R1	1655
11	TraesCS5A01G419100	chr4A	637835199	637836942	1743	True	562.000000	719	96.465500	1	2309	2	chr4A.!!$R1	2308

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
428	431	0.033504	GTGGTCGAAGAGGAAGCACA	59.966	55.0	0.0	0.0	40.26	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2016	3037	0.527565	GCGTGACCAAAATGAGCCAT	59.472	50.0	0.0	0.0	0.0	4.4	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
322	325	1.215647	GTGCTAGAGGTGGTGGTCG	59.784	63.158	0.00	0.00	0.00	4.79
323	326	1.076014	TGCTAGAGGTGGTGGTCGA	59.924	57.895	0.00	0.00	0.00	4.20
324	327	0.965866	TGCTAGAGGTGGTGGTCGAG	60.966	60.000	0.00	0.00	0.00	4.04
325	328	1.810532	CTAGAGGTGGTGGTCGAGC	59.189	63.158	7.89	7.89	0.00	5.03
326	329	0.965866	CTAGAGGTGGTGGTCGAGCA	60.966	60.000	14.39	14.39	0.00	4.26
327	330	0.965866	TAGAGGTGGTGGTCGAGCAG	60.966	60.000	19.24	0.00	30.97	4.24
328	331	3.302347	GAGGTGGTGGTCGAGCAGG	62.302	68.421	19.24	0.00	30.97	4.85
330	333	4.314440	GTGGTGGTCGAGCAGGCA	62.314	66.667	19.24	0.00	30.97	4.75
331	334	4.314440	TGGTGGTCGAGCAGGCAC	62.314	66.667	19.24	5.94	0.00	5.01
332	335	4.314440	GGTGGTCGAGCAGGCACA	62.314	66.667	19.24	0.00	0.00	4.57
333	336	2.280797	GTGGTCGAGCAGGCACAA	60.281	61.111	19.24	0.00	0.00	3.33
334	337	2.031012	TGGTCGAGCAGGCACAAG	59.969	61.111	14.39	0.00	0.00	3.16
335	338	2.031163	GGTCGAGCAGGCACAAGT	59.969	61.111	10.30	0.00	0.00	3.16
336	339	2.320587	GGTCGAGCAGGCACAAGTG	61.321	63.158	10.30	0.00	0.00	3.16
347	350	2.846371	CACAAGTGCTAGAGGTGGC	58.154	57.895	0.00	0.00	0.00	5.01
348	351	1.016130	CACAAGTGCTAGAGGTGGCG	61.016	60.000	0.00	0.00	31.29	5.69
349	352	1.448540	CAAGTGCTAGAGGTGGCGG	60.449	63.158	0.00	0.00	31.29	6.13
350	353	1.913762	AAGTGCTAGAGGTGGCGGT	60.914	57.895	0.00	0.00	31.29	5.68
351	354	1.889530	AAGTGCTAGAGGTGGCGGTC	61.890	60.000	0.00	0.00	31.29	4.79
392	395	2.280797	GGTGGTCGAGCAAGCACA	60.281	61.111	20.46	0.00	46.81	4.57
393	396	1.891919	GGTGGTCGAGCAAGCACAA	60.892	57.895	20.46	0.00	46.81	3.33
394	397	1.571460	GTGGTCGAGCAAGCACAAG	59.429	57.895	20.46	0.00	44.90	3.16
395	398	1.146041	TGGTCGAGCAAGCACAAGT	59.854	52.632	16.20	0.00	0.00	3.16
396	399	1.159713	TGGTCGAGCAAGCACAAGTG	61.160	55.000	16.20	0.00	0.00	3.16
408	411	1.800805	CACAAGTGCTAGAGGTGGTG	58.199	55.000	0.00	0.00	0.00	4.17
409	412	0.687354	ACAAGTGCTAGAGGTGGTGG	59.313	55.000	0.00	0.00	0.00	4.61
410	413	0.687354	CAAGTGCTAGAGGTGGTGGT	59.313	55.000	0.00	0.00	0.00	4.16
411	414	0.687354	AAGTGCTAGAGGTGGTGGTG	59.313	55.000	0.00	0.00	0.00	4.17
412	415	1.194781	AGTGCTAGAGGTGGTGGTGG	61.195	60.000	0.00	0.00	0.00	4.61
413	416	1.152118	TGCTAGAGGTGGTGGTGGT	60.152	57.895	0.00	0.00	0.00	4.16
414	417	1.192146	TGCTAGAGGTGGTGGTGGTC	61.192	60.000	0.00	0.00	0.00	4.02
415	418	1.890894	CTAGAGGTGGTGGTGGTCG	59.109	63.158	0.00	0.00	0.00	4.79
416	419	0.611062	CTAGAGGTGGTGGTGGTCGA	60.611	60.000	0.00	0.00	0.00	4.20
417	420	0.178955	TAGAGGTGGTGGTGGTCGAA	60.179	55.000	0.00	0.00	0.00	3.71
418	421	1.004918	GAGGTGGTGGTGGTCGAAG	60.005	63.158	0.00	0.00	0.00	3.79
419	422	1.458777	AGGTGGTGGTGGTCGAAGA	60.459	57.895	0.00	0.00	0.00	2.87
420	423	1.004918	GGTGGTGGTGGTCGAAGAG	60.005	63.158	0.00	0.00	36.95	2.85
421	424	1.004918	GTGGTGGTGGTCGAAGAGG	60.005	63.158	0.00	0.00	36.95	3.69
422	425	1.152419	TGGTGGTGGTCGAAGAGGA	60.152	57.895	0.00	0.00	36.95	3.71
423	426	0.761323	TGGTGGTGGTCGAAGAGGAA	60.761	55.000	0.00	0.00	36.95	3.36
424	427	0.037232	GGTGGTGGTCGAAGAGGAAG	60.037	60.000	0.00	0.00	36.95	3.46
425	428	0.670854	GTGGTGGTCGAAGAGGAAGC	60.671	60.000	0.00	0.00	36.95	3.86
426	429	1.118965	TGGTGGTCGAAGAGGAAGCA	61.119	55.000	0.00	0.00	36.95	3.91
427	430	0.670854	GGTGGTCGAAGAGGAAGCAC	60.671	60.000	0.00	0.00	36.95	4.40
428	431	0.033504	GTGGTCGAAGAGGAAGCACA	59.966	55.000	0.00	0.00	40.26	4.57
429	432	0.756294	TGGTCGAAGAGGAAGCACAA	59.244	50.000	0.00	0.00	36.95	3.33
430	433	1.270305	TGGTCGAAGAGGAAGCACAAG	60.270	52.381	0.00	0.00	36.95	3.16
695	698	3.050275	GTGGTGGTCGAGCAAGCC	61.050	66.667	20.46	17.49	32.64	4.35
1143	1186	2.293122	GTGTGGTGATGTTTGCAAGCTA	59.707	45.455	14.67	1.64	0.00	3.32
1253	1296	5.531122	ACTAACGCATATGACATACCACT	57.469	39.130	6.97	0.00	0.00	4.00
1425	1469	2.928334	TCGAGATTACTTACGGAGGCT	58.072	47.619	0.00	0.00	0.00	4.58
1583	1627	2.898840	CAAGGGCTCGCGATGCAT	60.899	61.111	24.72	0.00	0.00	3.96
1593	1637	1.301558	GCGATGCATGAGAGGAGGG	60.302	63.158	2.46	0.00	0.00	4.30
1930	2941	4.025040	ACATGACCAGAGAGCATTTTGA	57.975	40.909	0.00	0.00	0.00	2.69
1949	2960	2.243478	TGACTATCCAGAGAGCCAGACT	59.757	50.000	0.00	0.00	0.00	3.24
1969	2980	1.967535	CAGGAACTCTGGCGTCTGA	59.032	57.895	0.00	0.00	39.76	3.27
2016	3037	3.712907	GCCAAGGTCCCTGGCGTA	61.713	66.667	15.91	0.00	39.06	4.42
2023	3044	2.364973	TCCCTGGCGTATGGCTCA	60.365	61.111	10.19	0.00	42.94	4.26
2049	3070	1.112916	TCACGCAGGAGACCAGACAA	61.113	55.000	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
197	200	1.602377	CCACCTCCACGACTTGTTTTC	59.398	52.381	0.00	0.00	0.00	2.29
322	325	0.036952	TCTAGCACTTGTGCCTGCTC	60.037	55.000	20.39	0.00	42.86	4.26
323	326	0.036577	CTCTAGCACTTGTGCCTGCT	60.037	55.000	20.39	6.33	45.76	4.24
324	327	1.023513	CCTCTAGCACTTGTGCCTGC	61.024	60.000	20.39	0.00	34.90	4.85
325	328	0.322975	ACCTCTAGCACTTGTGCCTG	59.677	55.000	20.39	13.89	34.90	4.85
326	329	0.322975	CACCTCTAGCACTTGTGCCT	59.677	55.000	20.39	11.33	34.90	4.75
327	330	0.674895	CCACCTCTAGCACTTGTGCC	60.675	60.000	20.39	4.86	34.90	5.01
328	331	1.301677	GCCACCTCTAGCACTTGTGC	61.302	60.000	16.98	16.98	0.00	4.57
329	332	1.016130	CGCCACCTCTAGCACTTGTG	61.016	60.000	0.00	0.00	0.00	3.33
330	333	1.293498	CGCCACCTCTAGCACTTGT	59.707	57.895	0.00	0.00	0.00	3.16
331	334	1.448540	CCGCCACCTCTAGCACTTG	60.449	63.158	0.00	0.00	0.00	3.16
332	335	1.889530	GACCGCCACCTCTAGCACTT	61.890	60.000	0.00	0.00	0.00	3.16
333	336	2.283966	ACCGCCACCTCTAGCACT	60.284	61.111	0.00	0.00	0.00	4.40
334	337	2.184579	GACCGCCACCTCTAGCAC	59.815	66.667	0.00	0.00	0.00	4.40
335	338	3.449227	CGACCGCCACCTCTAGCA	61.449	66.667	0.00	0.00	0.00	3.49
336	339	3.127352	CTCGACCGCCACCTCTAGC	62.127	68.421	0.00	0.00	0.00	3.42
337	340	3.111939	CTCGACCGCCACCTCTAG	58.888	66.667	0.00	0.00	0.00	2.43
338	341	3.138798	GCTCGACCGCCACCTCTA	61.139	66.667	0.00	0.00	0.00	2.43
340	343	4.373116	TTGCTCGACCGCCACCTC	62.373	66.667	0.00	0.00	0.00	3.85
341	344	4.379243	CTTGCTCGACCGCCACCT	62.379	66.667	0.00	0.00	0.00	4.00
346	349	3.300667	CTTGTGCTTGCTCGACCGC	62.301	63.158	0.00	0.00	0.00	5.68
347	350	1.956170	ACTTGTGCTTGCTCGACCG	60.956	57.895	0.00	0.00	0.00	4.79
348	351	1.571460	CACTTGTGCTTGCTCGACC	59.429	57.895	0.00	0.00	0.00	4.79
349	352	1.082496	GCACTTGTGCTTGCTCGAC	60.082	57.895	17.36	0.00	35.74	4.20
350	353	0.033366	TAGCACTTGTGCTTGCTCGA	59.967	50.000	29.37	10.97	46.31	4.04
351	354	0.441533	CTAGCACTTGTGCTTGCTCG	59.558	55.000	29.37	12.09	46.31	5.03
392	395	0.687354	CACCACCACCTCTAGCACTT	59.313	55.000	0.00	0.00	0.00	3.16
393	396	1.194781	CCACCACCACCTCTAGCACT	61.195	60.000	0.00	0.00	0.00	4.40
394	397	1.296715	CCACCACCACCTCTAGCAC	59.703	63.158	0.00	0.00	0.00	4.40
395	398	1.152118	ACCACCACCACCTCTAGCA	60.152	57.895	0.00	0.00	0.00	3.49
396	399	1.597461	GACCACCACCACCTCTAGC	59.403	63.158	0.00	0.00	0.00	3.42
397	400	0.611062	TCGACCACCACCACCTCTAG	60.611	60.000	0.00	0.00	0.00	2.43
398	401	0.178955	TTCGACCACCACCACCTCTA	60.179	55.000	0.00	0.00	0.00	2.43
399	402	1.458777	TTCGACCACCACCACCTCT	60.459	57.895	0.00	0.00	0.00	3.69
400	403	1.004918	CTTCGACCACCACCACCTC	60.005	63.158	0.00	0.00	0.00	3.85
401	404	1.458777	TCTTCGACCACCACCACCT	60.459	57.895	0.00	0.00	0.00	4.00
402	405	1.004918	CTCTTCGACCACCACCACC	60.005	63.158	0.00	0.00	0.00	4.61
403	406	1.004918	CCTCTTCGACCACCACCAC	60.005	63.158	0.00	0.00	0.00	4.16
404	407	0.761323	TTCCTCTTCGACCACCACCA	60.761	55.000	0.00	0.00	0.00	4.17
405	408	0.037232	CTTCCTCTTCGACCACCACC	60.037	60.000	0.00	0.00	0.00	4.61
406	409	0.670854	GCTTCCTCTTCGACCACCAC	60.671	60.000	0.00	0.00	0.00	4.16
407	410	1.118965	TGCTTCCTCTTCGACCACCA	61.119	55.000	0.00	0.00	0.00	4.17
408	411	0.670854	GTGCTTCCTCTTCGACCACC	60.671	60.000	0.00	0.00	0.00	4.61
409	412	0.033504	TGTGCTTCCTCTTCGACCAC	59.966	55.000	0.00	0.00	0.00	4.16
410	413	0.756294	TTGTGCTTCCTCTTCGACCA	59.244	50.000	0.00	0.00	0.00	4.02
411	414	1.433534	CTTGTGCTTCCTCTTCGACC	58.566	55.000	0.00	0.00	0.00	4.79
695	698	0.036010	CCACCACCTCTAGCACTTGG	60.036	60.000	0.00	0.00	0.00	3.61
1143	1186	2.424302	CGGTCCGTGGACACCTTT	59.576	61.111	20.02	0.00	46.20	3.11
1425	1469	3.282745	GACTCCTCGAACAGGCGCA	62.283	63.158	10.83	0.00	43.08	6.09
1470	1514	4.619394	GCTCATTCTTCTCCTTCTCACGAA	60.619	45.833	0.00	0.00	0.00	3.85
1583	1627	4.382541	TGCCTCGCCCTCCTCTCA	62.383	66.667	0.00	0.00	0.00	3.27
1593	1637	1.891060	CTTCTTGTCACGTGCCTCGC	61.891	60.000	11.67	0.00	44.19	5.03
1930	2941	2.424234	GGAGTCTGGCTCTCTGGATAGT	60.424	54.545	9.42	0.00	43.62	2.12
1969	2980	3.404869	TGTCTGGTCTGGATATGGAGT	57.595	47.619	0.00	0.00	0.00	3.85
2016	3037	0.527565	GCGTGACCAAAATGAGCCAT	59.472	50.000	0.00	0.00	0.00	4.40
2023	3044	1.523758	GTCTCCTGCGTGACCAAAAT	58.476	50.000	0.00	0.00	0.00	1.82
2049	3070	3.370315	GGCTTTCTGGATGATCAGACAGT	60.370	47.826	21.81	0.00	42.74	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.