AutoCloner

Multiple sequence alignment - TraesCS7D01G220000

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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	TraesCS7D01G220000	chr7D	100.000	3121	0	0	1	3121	180592068	180595188	0.000000e+00	5764.0
1	TraesCS7D01G220000	chr7D	88.447	1835	171	20	554	2363	585182921	585184739	0.000000e+00	2176.0
2	TraesCS7D01G220000	chr7D	88.283	1835	169	23	554	2363	585191941	585193754	0.000000e+00	2156.0
3	TraesCS7D01G220000	chr7B	89.544	2611	232	20	522	3120	146256126	146258707	0.000000e+00	3271.0
4	TraesCS7D01G220000	chr7B	88.227	1444	155	10	885	2325	653800122	653801553	0.000000e+00	1711.0
5	TraesCS7D01G220000	chr7B	87.402	254	29	1	196	449	146251505	146251755	3.940000e-74	289.0
6	TraesCS7D01G220000	chr7A	96.472	1984	62	5	529	2505	185063450	185065432	0.000000e+00	3269.0
7	TraesCS7D01G220000	chr7A	96.319	1983	65	5	529	2505	185132907	185134887	0.000000e+00	3251.0
8	TraesCS7D01G220000	chr7A	95.269	1987	84	7	522	2505	184971492	184973471	0.000000e+00	3140.0
9	TraesCS7D01G220000	chr7A	96.805	626	17	3	2498	3120	185135328	185135953	0.000000e+00	1042.0
10	TraesCS7D01G220000	chr7A	92.338	509	31	6	1	505	184971001	184971505	0.000000e+00	717.0
11	TraesCS7D01G220000	chr7A	91.379	174	13	2	89	260	185132353	185132526	1.450000e-58	237.0
12	TraesCS7D01G220000	chr7A	90.503	179	13	3	301	477	185132731	185132907	1.870000e-57	233.0
13	TraesCS7D01G220000	chr7A	90.643	171	15	1	89	258	185062898	185063068	3.130000e-55	226.0
14	TraesCS7D01G220000	chr5B	87.850	1819	182	18	554	2351	684386322	684388122	0.000000e+00	2098.0
15	TraesCS7D01G220000	chr5B	100.000	31	0	0	4	34	710179411	710179441	1.210000e-04	58.4
16	TraesCS7D01G220000	chr6A	82.567	1153	180	14	1028	2171	579795197	579796337	0.000000e+00	996.0
17	TraesCS7D01G220000	chr6B	81.185	1148	193	20	998	2137	655053467	655054599	0.000000e+00	902.0
18	TraesCS7D01G220000	chr2D	97.727	44	1	0	3078	3121	460913106	460913063	3.340000e-10	76.8

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	TraesCS7D01G220000	chr7D	180592068	180595188	3120	False	5764.00	5764	100.0000	1	3121	1	chr7D.!!$F1	3120
1	TraesCS7D01G220000	chr7D	585182921	585184739	1818	False	2176.00	2176	88.4470	554	2363	1	chr7D.!!$F2	1809
2	TraesCS7D01G220000	chr7D	585191941	585193754	1813	False	2156.00	2156	88.2830	554	2363	1	chr7D.!!$F3	1809
3	TraesCS7D01G220000	chr7B	146256126	146258707	2581	False	3271.00	3271	89.5440	522	3120	1	chr7B.!!$F2	2598
4	TraesCS7D01G220000	chr7B	653800122	653801553	1431	False	1711.00	1711	88.2270	885	2325	1	chr7B.!!$F3	1440
5	TraesCS7D01G220000	chr7A	184971001	184973471	2470	False	1928.50	3140	93.8035	1	2505	2	chr7A.!!$F1	2504
6	TraesCS7D01G220000	chr7A	185062898	185065432	2534	False	1747.50	3269	93.5575	89	2505	2	chr7A.!!$F2	2416
7	TraesCS7D01G220000	chr7A	185132353	185135953	3600	False	1190.75	3251	93.7515	89	3120	4	chr7A.!!$F3	3031
8	TraesCS7D01G220000	chr5B	684386322	684388122	1800	False	2098.00	2098	87.8500	554	2351	1	chr5B.!!$F1	1797
9	TraesCS7D01G220000	chr6A	579795197	579796337	1140	False	996.00	996	82.5670	1028	2171	1	chr6A.!!$F1	1143
10	TraesCS7D01G220000	chr6B	655053467	655054599	1132	False	902.00	902	81.1850	998	2137	1	chr6B.!!$F1	1139

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
70	71	1.287815	CGGCAGGACTTGACACGTA	59.712	57.895	0.00	0.00	32.77	3.57	F
1326	1529	0.394565	ACAAAGCGAGCTTGGAGAGT	59.605	50.000	18.17	6.73	36.26	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1780	1996	0.175760	GTAGCTCTTGATGGTGGCGA	59.824	55.000	0.00	0.0	0.00	5.54	R
2446	2664	2.164422	TGAATTCGTTGTTTGCCACACA	59.836	40.909	0.04	0.0	33.98	3.72	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
44	45	3.317603	AAGCTTATTGTGCCGCAAATT	57.682	38.095	0.00	0.00	40.91	1.82
70	71	1.287815	CGGCAGGACTTGACACGTA	59.712	57.895	0.00	0.00	32.77	3.57
230	233	6.821031	TTGTACCTTCTCAGAGACTAAGAC	57.179	41.667	0.00	0.00	0.00	3.01
234	237	4.204012	CCTTCTCAGAGACTAAGACCGAT	58.796	47.826	0.00	0.00	0.00	4.18
251	254	1.857217	CGATCTCGGAAGCAATGACAG	59.143	52.381	0.00	0.00	35.37	3.51
262	265	4.825546	AGCAATGACAGTTGTTCTTGAG	57.174	40.909	10.21	0.00	0.00	3.02
280	283	6.105333	TCTTGAGAAGCAATAAGAGAAGAGC	58.895	40.000	0.00	0.00	35.59	4.09
286	289	4.512484	AGCAATAAGAGAAGAGCTGTTCC	58.488	43.478	19.26	11.21	31.72	3.62
338	505	2.476619	CCAGAGCGAAGTTGTAACTGTG	59.523	50.000	0.00	0.00	39.66	3.66
491	662	1.985895	AGGAAATTCCCGTGTTCCTCT	59.014	47.619	8.66	0.00	46.61	3.69
492	663	3.178865	AGGAAATTCCCGTGTTCCTCTA	58.821	45.455	8.66	0.00	46.61	2.43
493	664	3.780850	AGGAAATTCCCGTGTTCCTCTAT	59.219	43.478	8.66	0.00	46.61	1.98
494	665	4.127907	GGAAATTCCCGTGTTCCTCTATC	58.872	47.826	0.00	0.00	38.24	2.08
495	666	4.141688	GGAAATTCCCGTGTTCCTCTATCT	60.142	45.833	0.00	0.00	38.24	1.98
496	667	5.070047	GGAAATTCCCGTGTTCCTCTATCTA	59.930	44.000	0.00	0.00	38.24	1.98
497	668	6.239629	GGAAATTCCCGTGTTCCTCTATCTAT	60.240	42.308	0.00	0.00	38.24	1.98
498	669	7.039223	GGAAATTCCCGTGTTCCTCTATCTATA	60.039	40.741	0.00	0.00	38.24	1.31
499	670	6.837471	ATTCCCGTGTTCCTCTATCTATAC	57.163	41.667	0.00	0.00	0.00	1.47
500	671	5.314718	TCCCGTGTTCCTCTATCTATACA	57.685	43.478	0.00	0.00	0.00	2.29
501	672	5.698104	TCCCGTGTTCCTCTATCTATACAA	58.302	41.667	0.00	0.00	0.00	2.41
502	673	5.768662	TCCCGTGTTCCTCTATCTATACAAG	59.231	44.000	0.00	0.00	0.00	3.16
503	674	5.768662	CCCGTGTTCCTCTATCTATACAAGA	59.231	44.000	0.00	0.00	39.02	3.02
504	675	6.294065	CCCGTGTTCCTCTATCTATACAAGAC	60.294	46.154	0.00	0.00	36.93	3.01
505	676	6.262496	CCGTGTTCCTCTATCTATACAAGACA	59.738	42.308	0.00	0.00	36.93	3.41
506	677	7.040340	CCGTGTTCCTCTATCTATACAAGACAT	60.040	40.741	0.00	0.00	36.93	3.06
507	678	8.353684	CGTGTTCCTCTATCTATACAAGACATT	58.646	37.037	0.00	0.00	36.93	2.71
568	739	7.653713	CAGTCAGAGCTAAGAAGTTGTAAGAAA	59.346	37.037	0.00	0.00	0.00	2.52
569	740	8.371699	AGTCAGAGCTAAGAAGTTGTAAGAAAT	58.628	33.333	0.00	0.00	0.00	2.17
570	741	8.652463	GTCAGAGCTAAGAAGTTGTAAGAAATC	58.348	37.037	0.00	0.00	0.00	2.17
572	743	8.655092	CAGAGCTAAGAAGTTGTAAGAAATCTG	58.345	37.037	0.00	0.00	0.00	2.90
576	747	7.118390	GCTAAGAAGTTGTAAGAAATCTGCTGA	59.882	37.037	0.00	0.00	0.00	4.26
577	748	6.793492	AGAAGTTGTAAGAAATCTGCTGAC	57.207	37.500	0.00	0.00	0.00	3.51
578	749	6.529220	AGAAGTTGTAAGAAATCTGCTGACT	58.471	36.000	0.00	0.00	0.00	3.41
580	751	7.816995	AGAAGTTGTAAGAAATCTGCTGACTAG	59.183	37.037	0.00	0.00	0.00	2.57
613	791	9.836076	GAAGTTGTAATCGTTAAAGGCTAATTT	57.164	29.630	0.00	0.00	0.00	1.82
685	863	2.736670	ATGGACCAGAAGTAATGGCC	57.263	50.000	0.00	0.00	41.87	5.36
938	1139	5.047188	AGTTCCATTTGTTAAACCAAAGCG	58.953	37.500	0.00	0.00	37.71	4.68
1274	1477	0.817634	TTTGCTGACCTCACCAACGG	60.818	55.000	0.00	0.00	0.00	4.44
1326	1529	0.394565	ACAAAGCGAGCTTGGAGAGT	59.605	50.000	18.17	6.73	36.26	3.24
1780	1996	3.245016	TGCAAGAGTGGATCCAAAGATGT	60.245	43.478	18.20	0.00	30.90	3.06
2351	2569	7.877097	TGGTTTTATGCTGCTACATTTGATTTT	59.123	29.630	0.00	0.00	0.00	1.82
2446	2664	6.980416	AGTTTACTGTCCTACAAGTTCTCT	57.020	37.500	0.00	0.00	0.00	3.10
2469	2687	2.425312	TGTGGCAAACAACGAATTCAGT	59.575	40.909	6.22	1.76	35.24	3.41
2470	2688	2.788786	GTGGCAAACAACGAATTCAGTG	59.211	45.455	6.22	5.10	0.00	3.66
2487	2705	3.824443	TCAGTGTGTTCGTCTTCTCCATA	59.176	43.478	0.00	0.00	0.00	2.74
2587	3254	8.863049	CAGATAAATATTTGAACAAAGTGGTGC	58.137	33.333	11.05	0.00	33.32	5.01
2714	3381	3.128349	AGTAGCGATTTTCACACAACGT	58.872	40.909	0.00	0.00	0.00	3.99
2750	3417	4.634004	CCCACGTATTACTTGCAGAATGAA	59.366	41.667	0.00	0.00	39.69	2.57
3120	3789	1.198759	AGCGGCCTCTTAAGGTTGGA	61.199	55.000	0.00	0.00	45.34	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	7.410728	CGGCACAATAAGCTTTAAGTTTCAATG	60.411	37.037	3.20	0.00	0.00	2.82
31	32	4.651585	GCTCAATTTGCGGCACAA	57.348	50.000	0.05	0.82	36.13	3.33
57	58	1.145803	GGCACTTACGTGTCAAGTCC	58.854	55.000	0.00	0.80	45.01	3.85
93	94	1.745087	TCCATTGCGGAAATTCTCAGC	59.255	47.619	0.00	6.05	42.52	4.26
234	237	2.224281	ACAACTGTCATTGCTTCCGAGA	60.224	45.455	0.00	0.00	32.47	4.04
247	250	4.882671	TTGCTTCTCAAGAACAACTGTC	57.117	40.909	0.00	0.00	0.00	3.51
251	254	7.426929	TCTCTTATTGCTTCTCAAGAACAAC	57.573	36.000	8.77	0.00	38.22	3.32
262	265	5.064579	GGAACAGCTCTTCTCTTATTGCTTC	59.935	44.000	1.57	0.00	0.00	3.86
297	300	4.901868	TGGTTAGCGAAACTGTTATCCTT	58.098	39.130	0.00	0.00	38.23	3.36
299	302	4.501071	TCTGGTTAGCGAAACTGTTATCC	58.499	43.478	0.00	0.00	38.23	2.59
338	505	5.752892	GCTAACTGGTTAATTAGCCTTCC	57.247	43.478	18.01	3.62	44.97	3.46
378	546	8.911247	AAAACAGCATACGATTATTTTCCTTC	57.089	30.769	0.00	0.00	0.00	3.46
420	589	6.680874	TTACGATCTGTAGAGAGTTTCCTC	57.319	41.667	0.00	0.00	34.53	3.71
478	649	5.314718	TGTATAGATAGAGGAACACGGGA	57.685	43.478	0.00	0.00	0.00	5.14
511	682	5.521010	CGTCTTGTATAGATACCCGCAAAAA	59.479	40.000	0.00	0.00	34.79	1.94
512	683	5.045215	CGTCTTGTATAGATACCCGCAAAA	58.955	41.667	0.00	0.00	34.79	2.44
513	684	4.098349	ACGTCTTGTATAGATACCCGCAAA	59.902	41.667	0.00	0.00	34.79	3.68
514	685	3.633525	ACGTCTTGTATAGATACCCGCAA	59.366	43.478	0.00	0.00	34.79	4.85
515	686	3.216800	ACGTCTTGTATAGATACCCGCA	58.783	45.455	0.00	0.00	34.79	5.69
516	687	3.911661	ACGTCTTGTATAGATACCCGC	57.088	47.619	0.00	0.00	34.79	6.13
517	688	4.543692	CCAACGTCTTGTATAGATACCCG	58.456	47.826	0.00	0.00	34.79	5.28
518	689	4.304939	GCCAACGTCTTGTATAGATACCC	58.695	47.826	0.00	0.00	34.79	3.69
519	690	3.979495	CGCCAACGTCTTGTATAGATACC	59.021	47.826	0.00	0.00	34.79	2.73
520	691	3.424529	GCGCCAACGTCTTGTATAGATAC	59.575	47.826	0.00	0.00	42.83	2.24
568	739	5.509498	ACTTCTTCTCTCTAGTCAGCAGAT	58.491	41.667	0.00	0.00	0.00	2.90
569	740	4.917385	ACTTCTTCTCTCTAGTCAGCAGA	58.083	43.478	0.00	0.00	0.00	4.26
570	741	5.048083	ACAACTTCTTCTCTCTAGTCAGCAG	60.048	44.000	0.00	0.00	0.00	4.24
572	743	5.385509	ACAACTTCTTCTCTCTAGTCAGC	57.614	43.478	0.00	0.00	0.00	4.26
576	747	7.690952	ACGATTACAACTTCTTCTCTCTAGT	57.309	36.000	0.00	0.00	0.00	2.57
580	751	8.648968	CCTTTAACGATTACAACTTCTTCTCTC	58.351	37.037	0.00	0.00	0.00	3.20
613	791	5.113446	TCTTTGGGCATAACCGGTTAATA	57.887	39.130	29.74	11.17	40.62	0.98
664	842	3.477530	GGCCATTACTTCTGGTCCATAC	58.522	50.000	0.00	0.00	36.10	2.39
722	902	6.399986	GCCAACGTTTGATTATTTTTCTGCTC	60.400	38.462	3.12	0.00	0.00	4.26
938	1139	4.253685	AGTATGCAGTATGTGTGTGGTTC	58.746	43.478	0.00	0.00	39.31	3.62
1274	1477	2.489722	GCCTTTGTCATCTTGAACTCCC	59.510	50.000	0.00	0.00	0.00	4.30
1780	1996	0.175760	GTAGCTCTTGATGGTGGCGA	59.824	55.000	0.00	0.00	0.00	5.54
2446	2664	2.164422	TGAATTCGTTGTTTGCCACACA	59.836	40.909	0.04	0.00	33.98	3.72
2469	2687	6.525578	AATACTATGGAGAAGACGAACACA	57.474	37.500	0.00	0.00	0.00	3.72
2470	2688	7.115095	GCATAATACTATGGAGAAGACGAACAC	59.885	40.741	0.00	0.00	36.22	3.32
2690	3357	5.407387	ACGTTGTGTGAAAATCGCTACTATT	59.593	36.000	0.00	0.00	0.00	1.73
2750	3417	3.942748	TGCCAACTCAAAAACTTAGACGT	59.057	39.130	0.00	0.00	0.00	4.34
2836	3503	7.391554	CCCTCTTTTATGATCTTGAACAGTTGA	59.608	37.037	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.