AutoCloner

Multiple sequence alignment - TraesCS5D01G325600

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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	TraesCS5D01G325600	chr5D	100.000	3391	0	0	1	3391	417628569	417625179	0.000000e+00	6263.0
1	TraesCS5D01G325600	chr5D	78.986	138	21	7	1749	1882	322005206	322005339	1.680000e-13	87.9
2	TraesCS5D01G325600	chr5A	94.500	3400	164	14	1	3391	531084639	531081254	0.000000e+00	5221.0
3	TraesCS5D01G325600	chr5A	78.986	138	21	7	1749	1882	417255814	417255947	1.680000e-13	87.9
4	TraesCS5D01G325600	chr5B	91.584	3244	187	49	4	3222	504834728	504831546	0.000000e+00	4399.0
5	TraesCS5D01G325600	chr7B	79.055	487	77	19	1511	1989	672765218	672764749	9.140000e-81	311.0
6	TraesCS5D01G325600	chr7B	78.358	134	23	6	1700	1830	180040926	180040796	7.800000e-12	82.4
7	TraesCS5D01G325600	chr7B	97.297	37	1	0	1970	2006	57633389	57633353	2.820000e-06	63.9
8	TraesCS5D01G325600	chr7D	76.923	130	26	4	1700	1827	219637161	219637288	1.690000e-08	71.3
9	TraesCS5D01G325600	chr4D	100.000	36	0	0	1971	2006	403396616	403396581	2.180000e-07	67.6
10	TraesCS5D01G325600	chr4B	100.000	36	0	0	1971	2006	500254455	500254420	2.180000e-07	67.6
11	TraesCS5D01G325600	chr4A	100.000	36	0	0	1971	2006	60926376	60926341	2.180000e-07	67.6
12	TraesCS5D01G325600	chr4A	97.059	34	1	0	1978	2011	737868597	737868564	1.310000e-04	58.4
13	TraesCS5D01G325600	chrUn	76.119	134	26	6	1700	1830	270733702	270733572	7.850000e-07	65.8
14	TraesCS5D01G325600	chrUn	76.119	134	26	6	1700	1830	282197236	282197366	7.850000e-07	65.8
15	TraesCS5D01G325600	chr3B	100.000	35	0	0	1970	2004	76433062	76433028	7.850000e-07	65.8
16	TraesCS5D01G325600	chr6D	87.273	55	4	3	1972	2026	470961823	470961772	3.650000e-05	60.2

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	TraesCS5D01G325600	chr5D	417625179	417628569	3390	True	6263	6263	100.000	1	3391	1	chr5D.!!$R1	3390
1	TraesCS5D01G325600	chr5A	531081254	531084639	3385	True	5221	5221	94.500	1	3391	1	chr5A.!!$R1	3390
2	TraesCS5D01G325600	chr5B	504831546	504834728	3182	True	4399	4399	91.584	4	3222	1	chr5B.!!$R1	3218

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
817	822	0.534203	GGCAAACACGAGGAGGACAA	60.534	55.0	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2763	2784	2.380084	TTGACTGGACGCATAGAACC	57.62	50.0	0.0	0.0	0.0	3.62	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
57	58	2.173356	CCTTCCAGCAATCCCATCACTA	59.827	50.000	0.00	0.00	0.00	2.74
71	72	2.442272	ACTACCCTCGCAGCCGAT	60.442	61.111	0.00	0.00	43.47	4.18
85	86	1.153107	CCGATGGATGCTGCCAAGA	60.153	57.895	0.00	0.00	42.16	3.02
100	101	1.223187	CAAGAACCCGTAGTTGCGTT	58.777	50.000	0.00	0.00	39.40	4.84
112	113	3.454587	TTGCGTTGTCCGGTGAGCT	62.455	57.895	0.00	0.00	36.94	4.09
193	194	3.400054	GGTGCCCCGCTACCTTCT	61.400	66.667	0.00	0.00	34.11	2.85
271	272	1.956869	TGGCTTGAATCCTCCTCTGA	58.043	50.000	0.00	0.00	0.00	3.27
354	355	2.542020	TCGTTTTGCTGATGGACTCA	57.458	45.000	0.00	0.00	0.00	3.41
383	384	9.740239	ATGACTATGTGTTTATCATTTTCATGC	57.260	29.630	0.00	0.00	31.00	4.06
384	385	8.959548	TGACTATGTGTTTATCATTTTCATGCT	58.040	29.630	0.00	0.00	0.00	3.79
391	392	9.423061	GTGTTTATCATTTTCATGCTACCTTTT	57.577	29.630	0.00	0.00	0.00	2.27
392	393	9.421806	TGTTTATCATTTTCATGCTACCTTTTG	57.578	29.630	0.00	0.00	0.00	2.44
393	394	9.423061	GTTTATCATTTTCATGCTACCTTTTGT	57.577	29.630	0.00	0.00	0.00	2.83
399	400	7.817418	TTTTCATGCTACCTTTTGTAAGTCT	57.183	32.000	0.00	0.00	0.00	3.24
402	403	7.435068	TCATGCTACCTTTTGTAAGTCTTTC	57.565	36.000	0.00	0.00	0.00	2.62
411	412	8.638873	ACCTTTTGTAAGTCTTTCTATTTTGGG	58.361	33.333	0.00	0.00	0.00	4.12
426	427	4.871871	TTTTGGGACCAGGCAATATAGA	57.128	40.909	0.00	0.00	0.00	1.98
466	467	7.361286	GCAGAGACATAGACGATCATACATACA	60.361	40.741	0.00	0.00	0.00	2.29
475	476	6.422100	AGACGATCATACATACAACATTGAGC	59.578	38.462	0.00	0.00	0.00	4.26
476	477	6.048509	ACGATCATACATACAACATTGAGCA	58.951	36.000	0.00	0.00	0.00	4.26
477	478	6.538381	ACGATCATACATACAACATTGAGCAA	59.462	34.615	0.00	0.00	0.00	3.91
508	510	7.750229	ATAGTTATGGTGGTATGCATTCAAG	57.250	36.000	3.54	0.00	0.00	3.02
546	549	6.772716	GGGAGGCATGTCATTATTTCTCTAAA	59.227	38.462	0.00	0.00	0.00	1.85
547	550	7.285401	GGGAGGCATGTCATTATTTCTCTAAAA	59.715	37.037	0.00	0.00	0.00	1.52
548	551	8.686334	GGAGGCATGTCATTATTTCTCTAAAAA	58.314	33.333	0.00	0.00	0.00	1.94
633	638	9.894783	TCAGTTATTTAGCAACTACTATCGATC	57.105	33.333	0.00	0.00	34.50	3.69
661	666	1.001974	TGTTCCGTTGACCATCTGGAG	59.998	52.381	2.55	0.00	38.94	3.86
734	739	3.742433	CCCTTCTAGAGGCACATGTAG	57.258	52.381	0.00	0.00	44.85	2.74
817	822	0.534203	GGCAAACACGAGGAGGACAA	60.534	55.000	0.00	0.00	0.00	3.18
877	882	2.224646	GCCCTTGGAACATCCCTATCTC	60.225	54.545	0.00	0.00	39.30	2.75
1137	1145	5.972107	AGTTCTTGATTCATTTGGTGAGG	57.028	39.130	0.00	0.00	38.29	3.86
1162	1170	0.605050	TTGGCTGAGTTGCATGCGTA	60.605	50.000	14.09	0.00	34.04	4.42
1166	1174	1.131126	GCTGAGTTGCATGCGTATTGT	59.869	47.619	14.09	0.00	0.00	2.71
1188	1198	1.288752	GCGGTGTTGATGTTTGGGG	59.711	57.895	0.00	0.00	0.00	4.96
1199	1209	2.536633	TTTGGGGGCAGGGATCCA	60.537	61.111	15.23	0.00	0.00	3.41
1304	1314	3.003689	CCAACAACTTCAACGAGAGCAAT	59.996	43.478	0.00	0.00	0.00	3.56
1387	1397	3.078594	ACGCCGGAAAATCAATTATGC	57.921	42.857	5.05	0.00	0.00	3.14
1388	1398	2.223711	ACGCCGGAAAATCAATTATGCC	60.224	45.455	5.05	0.00	0.00	4.40
1389	1399	2.393764	GCCGGAAAATCAATTATGCCG	58.606	47.619	5.05	0.00	37.20	5.69
1396	1406	5.220892	GGAAAATCAATTATGCCGTCCGTTA	60.221	40.000	0.00	0.00	0.00	3.18
1403	1413	2.582728	ATGCCGTCCGTTATTCGTTA	57.417	45.000	0.00	0.00	37.94	3.18
1649	1664	2.036256	ATGCCCAACCACAGCCTC	59.964	61.111	0.00	0.00	0.00	4.70
2428	2443	0.670162	CCACCATTTCGATCCATGCC	59.330	55.000	0.00	0.00	0.00	4.40
2435	2450	0.881600	TTCGATCCATGCCTGCATCG	60.882	55.000	8.81	8.81	33.90	3.84
2464	2479	1.331756	CACTGCCTTACGATCCAATGC	59.668	52.381	0.00	0.00	0.00	3.56
2495	2510	7.765307	AGATGCAAATTCATGATTAGTCGTTT	58.235	30.769	0.00	0.00	0.00	3.60
2496	2511	7.912250	AGATGCAAATTCATGATTAGTCGTTTC	59.088	33.333	0.00	0.00	0.00	2.78
2498	2513	7.366513	TGCAAATTCATGATTAGTCGTTTCAA	58.633	30.769	0.00	0.00	0.00	2.69
2922	2949	6.151817	AGTCAATGAAAGCTTCCATTTCCTAC	59.848	38.462	8.36	5.24	36.11	3.18
2966	2994	2.219458	TGACGCGGTAATGTCCAAAAA	58.781	42.857	12.47	0.00	34.18	1.94
3193	3227	3.500680	GGCGTTAAGGAAGATTGTCAACA	59.499	43.478	0.00	0.00	0.00	3.33
3305	3339	0.174845	TCAAACCGGTGAGCCTATCG	59.825	55.000	8.52	0.00	0.00	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	0.398522	TGCGAGGGTAGTGATGGGAT	60.399	55.000	0.00	0.00	0.00	3.85
71	72	1.304381	GGGTTCTTGGCAGCATCCA	60.304	57.895	0.00	0.00	0.00	3.41
85	86	0.881600	GGACAACGCAACTACGGGTT	60.882	55.000	0.00	0.00	42.19	4.11
100	101	4.357947	GCGTCAGCTCACCGGACA	62.358	66.667	9.46	0.00	38.38	4.02
112	113	3.911698	CCGGGGATGATCGCGTCA	61.912	66.667	5.77	10.02	42.06	4.35
242	243	0.251341	ATTCAAGCCAACCTCGCCTT	60.251	50.000	0.00	0.00	0.00	4.35
271	272	2.590092	GCATCCAACCCTAGCCGT	59.410	61.111	0.00	0.00	0.00	5.68
302	303	4.758251	TCATGTGCCACCGCTCCG	62.758	66.667	0.00	0.00	35.36	4.63
334	335	3.057969	TGAGTCCATCAGCAAAACGAT	57.942	42.857	0.00	0.00	32.77	3.73
354	355	9.685276	TGAAAATGATAAACACATAGTCATCCT	57.315	29.630	0.00	0.00	0.00	3.24
363	364	8.297470	AGGTAGCATGAAAATGATAAACACAT	57.703	30.769	0.00	0.00	0.00	3.21
391	392	6.843752	TGGTCCCAAAATAGAAAGACTTACA	58.156	36.000	0.00	0.00	0.00	2.41
392	393	6.374613	CCTGGTCCCAAAATAGAAAGACTTAC	59.625	42.308	0.00	0.00	0.00	2.34
393	394	6.481643	CCTGGTCCCAAAATAGAAAGACTTA	58.518	40.000	0.00	0.00	0.00	2.24
395	396	4.811063	GCCTGGTCCCAAAATAGAAAGACT	60.811	45.833	0.00	0.00	0.00	3.24
396	397	3.444034	GCCTGGTCCCAAAATAGAAAGAC	59.556	47.826	0.00	0.00	0.00	3.01
399	400	3.534357	TGCCTGGTCCCAAAATAGAAA	57.466	42.857	0.00	0.00	0.00	2.52
402	403	6.542821	TCTATATTGCCTGGTCCCAAAATAG	58.457	40.000	0.00	0.00	0.00	1.73
438	439	6.231211	TGTATGATCGTCTATGTCTCTGCTA	58.769	40.000	0.00	0.00	0.00	3.49
443	444	8.290325	TGTTGTATGTATGATCGTCTATGTCTC	58.710	37.037	0.00	0.00	0.00	3.36
448	449	9.631452	CTCAATGTTGTATGTATGATCGTCTAT	57.369	33.333	0.00	0.00	0.00	1.98
475	476	8.721478	GCATACCACCATAACTATATTGTCTTG	58.279	37.037	0.00	0.00	0.00	3.02
476	477	8.436778	TGCATACCACCATAACTATATTGTCTT	58.563	33.333	0.00	0.00	0.00	3.01
477	478	7.973402	TGCATACCACCATAACTATATTGTCT	58.027	34.615	0.00	0.00	0.00	3.41
608	611	9.678941	TGATCGATAGTAGTTGCTAAATAACTG	57.321	33.333	0.00	0.00	38.70	3.16
630	635	4.378459	GGTCAACGGAACAAAGTCATGATC	60.378	45.833	0.00	0.00	0.00	2.92
631	636	3.502211	GGTCAACGGAACAAAGTCATGAT	59.498	43.478	0.00	0.00	0.00	2.45
632	637	2.875933	GGTCAACGGAACAAAGTCATGA	59.124	45.455	0.00	0.00	0.00	3.07
633	638	2.616376	TGGTCAACGGAACAAAGTCATG	59.384	45.455	0.00	0.00	37.93	3.07
661	666	2.554032	AGTGTGAAGCAAATGTGTAGCC	59.446	45.455	0.00	0.00	0.00	3.93
817	822	4.070009	GTTTGTTTCTCCGGGTACAAGAT	58.930	43.478	0.00	0.00	32.67	2.40
969	975	0.243907	ATGGACGACGTGAGGAACAG	59.756	55.000	4.58	0.00	0.00	3.16
976	982	0.952010	TCAGACGATGGACGACGTGA	60.952	55.000	4.58	0.00	45.77	4.35
1137	1145	0.961019	TGCAACTCAGCCAAATCCAC	59.039	50.000	0.00	0.00	0.00	4.02
1162	1170	1.680735	ACATCAACACCGCACAACAAT	59.319	42.857	0.00	0.00	0.00	2.71
1166	1174	1.202348	CCAAACATCAACACCGCACAA	60.202	47.619	0.00	0.00	0.00	3.33
1188	1198	1.825281	CTCCTCGATGGATCCCTGCC	61.825	65.000	9.90	0.00	45.16	4.85
1199	1209	1.383248	CTTGGACCCCCTCCTCGAT	60.383	63.158	0.00	0.00	40.26	3.59
1374	1384	4.712122	AACGGACGGCATAATTGATTTT	57.288	36.364	0.00	0.00	0.00	1.82
1434	1444	0.460311	ATGAGACCTTCCTAACCGCG	59.540	55.000	0.00	0.00	0.00	6.46
1438	1448	3.637229	TCGATCCATGAGACCTTCCTAAC	59.363	47.826	0.00	0.00	0.00	2.34
1439	1449	3.637229	GTCGATCCATGAGACCTTCCTAA	59.363	47.826	0.00	0.00	0.00	2.69
1440	1450	3.223435	GTCGATCCATGAGACCTTCCTA	58.777	50.000	0.00	0.00	0.00	2.94
1441	1451	2.035632	GTCGATCCATGAGACCTTCCT	58.964	52.381	0.00	0.00	0.00	3.36
1535	1550	1.690633	GCCCAGGATCTCCACCTCA	60.691	63.158	0.00	0.00	38.89	3.86
1649	1664	2.650116	CGGGTGGAGGTGAGTGAGG	61.650	68.421	0.00	0.00	0.00	3.86
2435	2450	4.265436	TCGTAAGGCAGTGCAATGTTGC	62.265	50.000	18.61	10.66	46.84	4.17
2464	2479	9.888878	ACTAATCATGAATTTGCATCTTAATCG	57.111	29.630	0.00	0.00	0.00	3.34
2491	2506	5.988092	ACAAAATGCAATCCAATTGAAACG	58.012	33.333	7.12	0.00	42.83	3.60
2495	2510	7.747155	AATCAACAAAATGCAATCCAATTGA	57.253	28.000	7.12	0.00	42.83	2.57
2498	2513	9.233649	ACATTAATCAACAAAATGCAATCCAAT	57.766	25.926	0.00	0.00	34.63	3.16
2501	2516	8.254178	TGACATTAATCAACAAAATGCAATCC	57.746	30.769	0.00	0.00	34.63	3.01
2747	2768	9.950680	CGCATAGAACCAACATCTTTATTTATT	57.049	29.630	0.00	0.00	0.00	1.40
2763	2784	2.380084	TTGACTGGACGCATAGAACC	57.620	50.000	0.00	0.00	0.00	3.62
2885	2912	6.541641	AGCTTTCATTGACTCTGATGATAACC	59.458	38.462	0.00	0.00	32.73	2.85
3114	3142	6.683715	TGTCATCTGTTCGTCAACTGTTATA	58.316	36.000	0.00	0.00	34.06	0.98
3121	3153	8.015087	TGAATTAAATGTCATCTGTTCGTCAAC	58.985	33.333	0.00	0.00	0.00	3.18
3305	3339	5.409520	AGTTCGACGGGTAAAAATTAGAACC	59.590	40.000	0.00	0.00	36.94	3.62
3340	3374	8.251750	TGTCTAATAAAACAGAGATTGAACCG	57.748	34.615	0.00	0.00	0.00	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.