AutoCloner

Multiple sequence alignment - TraesCS7D01G275100

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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	TraesCS7D01G275100	chr7D	100.000	2612	0	0	1	2612	264338298	264340909	0.000000e+00	4824
1	TraesCS7D01G275100	chr7D	95.958	1608	59	4	441	2042	264360798	264362405	0.000000e+00	2604
2	TraesCS7D01G275100	chr7D	96.260	1444	52	2	441	1882	264370671	264372114	0.000000e+00	2366
3	TraesCS7D01G275100	chr7D	92.452	1603	101	17	452	2042	264325972	264327566	0.000000e+00	2272
4	TraesCS7D01G275100	chr7D	94.843	446	17	3	1	443	264370201	264370643	0.000000e+00	691
5	TraesCS7D01G275100	chr7D	91.928	446	28	2	1	443	264360330	264360770	3.690000e-173	617
6	TraesCS7D01G275100	chr7D	88.571	455	42	5	2041	2495	264362445	264362889	6.360000e-151	544
7	TraesCS7D01G275100	chr7D	78.025	405	34	23	1	404	264325425	264325775	1.230000e-48	204
8	TraesCS7D01G275100	chr7A	90.087	2633	155	49	7	2611	287889147	287891701	0.000000e+00	3319
9	TraesCS7D01G275100	chr7A	94.021	853	48	3	1192	2042	287862649	287863500	0.000000e+00	1290
10	TraesCS7D01G275100	chr7B	95.327	1926	85	5	688	2611	244651643	244653565	0.000000e+00	3053
11	TraesCS7D01G275100	chr7B	91.957	2064	126	17	441	2495	244692808	244694840	0.000000e+00	2856
12	TraesCS7D01G275100	chr7B	95.641	1606	65	4	441	2042	244645006	244646610	0.000000e+00	2573
13	TraesCS7D01G275100	chr7B	95.983	1444	55	3	441	1882	244716282	244717724	0.000000e+00	2342
14	TraesCS7D01G275100	chr7B	93.722	446	25	1	1	443	244692335	244692780	0.000000e+00	665
15	TraesCS7D01G275100	chr7B	93.732	351	15	3	14	358	244644257	244644606	1.070000e-143	520
16	TraesCS7D01G275100	chr7B	93.662	284	18	0	160	443	244715971	244716254	2.400000e-115	425
17	TraesCS7D01G275100	chr7B	84.396	455	45	11	2041	2495	244646650	244647078	8.640000e-115	424
18	TraesCS7D01G275100	chr7B	84.010	419	30	7	2	416	244651020	244651405	4.110000e-98	368
19	TraesCS7D01G275100	chr7B	94.030	134	5	1	3	133	244715847	244715980	1.590000e-47	200

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	TraesCS7D01G275100	chr7D	264338298	264340909	2611	False	4824.0	4824	100.000000	1	2612	1	chr7D.!!$F1	2611
1	TraesCS7D01G275100	chr7D	264370201	264372114	1913	False	1528.5	2366	95.551500	1	1882	2	chr7D.!!$F4	1881
2	TraesCS7D01G275100	chr7D	264360330	264362889	2559	False	1255.0	2604	92.152333	1	2495	3	chr7D.!!$F3	2494
3	TraesCS7D01G275100	chr7D	264325425	264327566	2141	False	1238.0	2272	85.238500	1	2042	2	chr7D.!!$F2	2041
4	TraesCS7D01G275100	chr7A	287889147	287891701	2554	False	3319.0	3319	90.087000	7	2611	1	chr7A.!!$F2	2604
5	TraesCS7D01G275100	chr7A	287862649	287863500	851	False	1290.0	1290	94.021000	1192	2042	1	chr7A.!!$F1	850
6	TraesCS7D01G275100	chr7B	244692335	244694840	2505	False	1760.5	2856	92.839500	1	2495	2	chr7B.!!$F2	2494
7	TraesCS7D01G275100	chr7B	244644257	244653565	9308	False	1387.6	3053	90.621200	2	2611	5	chr7B.!!$F1	2609
8	TraesCS7D01G275100	chr7B	244715847	244717724	1877	False	989.0	2342	94.558333	3	1882	3	chr7B.!!$F3	1879

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
395	695	0.041576	CATCGTTGCTGGCGATCATG	60.042	55.0	7.45	0.0	45.80	3.07	F
400	700	0.677414	TTGCTGGCGATCATGCAAGA	60.677	50.0	1.46	0.0	38.22	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1407	1885	0.249398	ATGTAACCTTCTTCGCGGCT	59.751	50.0	6.13	0.0	0.0	5.52	R
1997	8870	0.881796	GCCTTGTAGTTTGGACCTGC	59.118	55.0	0.00	0.0	0.0	4.85	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
90	94	4.741676	CACAAGAAAAGACTTCCATGCAAC	59.258	41.667	0.00	0.00	0.00	4.17
152	159	4.130118	CAGTGCTTAGACTTTGTTGAGGT	58.870	43.478	0.00	0.00	0.00	3.85
153	160	4.212214	CAGTGCTTAGACTTTGTTGAGGTC	59.788	45.833	0.00	0.00	0.00	3.85
156	163	4.997395	TGCTTAGACTTTGTTGAGGTCATC	59.003	41.667	0.00	0.00	32.98	2.92
200	207	5.667539	TCTGAATGCTCTAAGCTTGTACT	57.332	39.130	9.86	0.00	42.97	2.73
389	689	1.985447	AATGCTCATCGTTGCTGGCG	61.985	55.000	0.00	0.00	0.00	5.69
395	695	0.041576	CATCGTTGCTGGCGATCATG	60.042	55.000	7.45	0.00	45.80	3.07
400	700	0.677414	TTGCTGGCGATCATGCAAGA	60.677	50.000	1.46	0.00	38.22	3.02
406	706	3.479489	TGGCGATCATGCAAGATAACAT	58.521	40.909	4.06	0.00	36.28	2.71
419	840	7.977904	TGCAAGATAACATCATACTGTTTCAG	58.022	34.615	0.00	0.00	39.88	3.02
471	922	2.624838	ACAACAACAGCCAAAGGATCAG	59.375	45.455	0.00	0.00	0.00	2.90
512	964	2.019249	CATAGCTAAAGCAAGCCAGCA	58.981	47.619	4.54	1.66	43.86	4.41
521	973	1.361271	CAAGCCAGCACCAACACTG	59.639	57.895	0.00	0.00	0.00	3.66
660	1137	5.649395	ACACAATTATGTCAAGATCCACCAG	59.351	40.000	0.00	0.00	37.82	4.00
690	1167	2.039746	ACCATCCGGTTGATTCTTGTCA	59.960	45.455	14.27	0.00	46.31	3.58
700	1177	6.920758	CGGTTGATTCTTGTCACCAATTAAAA	59.079	34.615	0.00	0.00	0.00	1.52
747	1224	5.263968	TGGAAGAATAGCTACTGCACTAC	57.736	43.478	0.00	0.00	42.74	2.73
787	1265	2.491693	GGGCGAAGATTCCAAATGTTGA	59.508	45.455	0.00	0.00	0.00	3.18
992	1470	5.598830	TCAACACAGAGGAAAGAGTCTTAGT	59.401	40.000	5.65	0.00	0.00	2.24
1126	1604	4.297510	CATCGAGACAATCTCTGATGGTC	58.702	47.826	20.72	6.91	43.03	4.02
1216	1694	2.816087	TCTTCACAGCAAAGGAAGATGC	59.184	45.455	0.00	0.00	41.38	3.91
1339	1817	1.923204	CGAGCAGAAAAGGAGATGACG	59.077	52.381	0.00	0.00	0.00	4.35
1341	1819	1.277557	AGCAGAAAAGGAGATGACGCT	59.722	47.619	0.00	0.00	0.00	5.07
1407	1885	5.514274	AGGCGAAGAAACATTTCAAGAAA	57.486	34.783	7.10	0.00	39.61	2.52
1446	1924	0.972134	CTGACAAGGAGGACTGCAGA	59.028	55.000	23.35	0.00	0.00	4.26
1547	2026	1.615392	GCAGTGCCAAAATGGTCTCTT	59.385	47.619	2.85	0.00	40.46	2.85
1592	2071	1.021968	ACTCGGTTGTTTGCAAGGAC	58.978	50.000	0.00	0.00	34.94	3.85
1595	2074	0.378962	CGGTTGTTTGCAAGGACGAA	59.621	50.000	0.00	0.00	34.94	3.85
1613	2092	2.093973	CGAACAGTTGCAGGTCCTAGAT	60.094	50.000	0.00	0.00	0.00	1.98
1882	2364	5.733620	ATTCAACCTTTGCATGTTCTGAT	57.266	34.783	0.00	0.00	0.00	2.90
1997	8870	5.484173	TTTAGCATCTTTCGCTTACATGG	57.516	39.130	0.00	0.00	40.96	3.66
2234	9153	7.481275	CACACACATGATAGTGCATTATGTA	57.519	36.000	6.44	0.00	40.79	2.29
2282	9201	6.264518	ACTGACACCAACCAAATAAGTTAAGG	59.735	38.462	0.00	0.00	0.00	2.69
2348	9267	4.023707	GCGAGAGGATTTGGAATAACATGG	60.024	45.833	0.00	0.00	0.00	3.66
2422	9341	1.995484	CGTCATCACAGGCAGTACAAG	59.005	52.381	0.00	0.00	0.00	3.16
2448	9367	1.604593	GGTCACAAGGCATGGCAGT	60.605	57.895	22.64	16.22	0.00	4.40
2597	9521	6.276091	GCTGTTTCATTTTCTCCAACTTTCT	58.724	36.000	0.00	0.00	0.00	2.52
2606	9530	9.249457	CATTTTCTCCAACTTTCTAACCTTTTC	57.751	33.333	0.00	0.00	0.00	2.29
2610	9534	8.589701	TCTCCAACTTTCTAACCTTTTCTTTT	57.410	30.769	0.00	0.00	0.00	2.27
2611	9535	9.689501	TCTCCAACTTTCTAACCTTTTCTTTTA	57.310	29.630	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
90	94	3.997021	ACTCCAGTTTCAGTAATTGCTCG	59.003	43.478	0.00	0.00	0.00	5.03
120	124	2.093235	GTCTAAGCACTGCCCTCAAGAT	60.093	50.000	0.00	0.00	0.00	2.40
152	159	2.064434	ACTCTGCTCTGGATCGATGA	57.936	50.000	0.54	0.00	0.00	2.92
153	160	2.886862	AACTCTGCTCTGGATCGATG	57.113	50.000	0.54	0.00	0.00	3.84
156	163	2.957491	AGAAACTCTGCTCTGGATCG	57.043	50.000	0.00	0.00	0.00	3.69
200	207	3.738982	CCGTAGGCAATGTATCATCCAA	58.261	45.455	0.00	0.00	46.14	3.53
325	332	4.966965	TCTGAAGATCCGTCTGAGTTAC	57.033	45.455	0.00	0.00	34.13	2.50
389	689	8.320396	ACAGTATGATGTTATCTTGCATGATC	57.680	34.615	17.60	6.38	39.69	2.92
395	695	8.201554	TCTGAAACAGTATGATGTTATCTTGC	57.798	34.615	0.00	0.00	42.49	4.01
406	706	9.076781	TCCAAATTTTGATCTGAAACAGTATGA	57.923	29.630	10.72	0.00	39.69	2.15
419	840	7.439056	ACAAGTGACACATTCCAAATTTTGATC	59.561	33.333	10.72	0.00	0.00	2.92
521	973	4.347453	CCTGCGTGGCCAACTTGC	62.347	66.667	7.24	10.54	0.00	4.01
660	1137	4.857251	CCGGATGGTTGGCTCTAC	57.143	61.111	0.00	0.00	0.00	2.59
690	1167	8.420222	TCACATTGTCATGTTCTTTTAATTGGT	58.580	29.630	0.00	0.00	41.16	3.67
700	1177	8.837389	CAATGAGATATCACATTGTCATGTTCT	58.163	33.333	31.58	8.55	44.39	3.01
747	1224	4.672542	CGCCCATGTGTAGTTCAAATTCTG	60.673	45.833	0.00	0.00	0.00	3.02
787	1265	8.321353	TGTATATCAAGTTTGTGAGATCTGGTT	58.679	33.333	0.00	0.00	31.99	3.67
876	1354	6.385759	TGAGGCCTATTTATACAGAGGAACAA	59.614	38.462	4.42	0.00	0.00	2.83
877	1355	5.903010	TGAGGCCTATTTATACAGAGGAACA	59.097	40.000	4.42	0.00	0.00	3.18
1126	1604	1.138661	GATGTCTCCAAGCCTCCTCAG	59.861	57.143	0.00	0.00	0.00	3.35
1216	1694	1.512926	CACTCGGTTTCACCTTCCAG	58.487	55.000	0.00	0.00	35.66	3.86
1339	1817	3.192001	TGGATCTTGATTTGAACAGCAGC	59.808	43.478	0.00	0.00	0.00	5.25
1341	1819	4.401022	ACTGGATCTTGATTTGAACAGCA	58.599	39.130	0.00	0.00	0.00	4.41
1407	1885	0.249398	ATGTAACCTTCTTCGCGGCT	59.751	50.000	6.13	0.00	0.00	5.52
1446	1924	0.957395	CGCTCAACAGCCTGACCATT	60.957	55.000	0.00	0.00	43.56	3.16
1547	2026	1.361204	TCTGGAATGCCTTGGAGACA	58.639	50.000	0.00	0.00	39.83	3.41
1592	2071	1.272490	TCTAGGACCTGCAACTGTTCG	59.728	52.381	3.53	0.00	0.00	3.95
1595	2074	2.616510	GCAATCTAGGACCTGCAACTGT	60.617	50.000	3.53	0.00	34.87	3.55
1613	2092	3.405831	CTCAAGATCTCCAACACTGCAA	58.594	45.455	0.00	0.00	0.00	4.08
1766	2245	2.632377	ACACACTGGGAAATATCAGCG	58.368	47.619	0.00	0.00	34.57	5.18
1809	2290	8.561738	TTTGTTTCCTTTCTGTATGGAGTATC	57.438	34.615	0.00	0.00	32.16	2.24
1882	2364	2.769663	AGTTATGGACCAGTGCGGAATA	59.230	45.455	0.00	0.00	38.63	1.75
1997	8870	0.881796	GCCTTGTAGTTTGGACCTGC	59.118	55.000	0.00	0.00	0.00	4.85
2282	9201	4.346129	CTTTGCATGTAATTTCTCGCTCC	58.654	43.478	0.00	0.00	0.00	4.70
2348	9267	6.775088	TGAGTCATCAAAATTCGCATCTTAC	58.225	36.000	0.00	0.00	30.61	2.34
2422	9341	1.746991	GCCTTGTGACCTAGCTGGC	60.747	63.158	0.00	0.00	40.22	4.85
2448	9367	6.713276	AGCTCTTAGTTCTCTGTAGTGTCTA	58.287	40.000	0.00	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.