AutoCloner

Multiple sequence alignment - TraesCS3B01G514600

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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	TraesCS3B01G514600	chr3B	100.000	4258	0	0	1	4258	757287642	757283385	0.000000e+00	7864.0
1	TraesCS3B01G514600	chr3B	84.928	1453	167	31	665	2090	757457744	757456317	0.000000e+00	1423.0
2	TraesCS3B01G514600	chr3B	95.510	735	30	1	2124	2858	50677542	50676811	0.000000e+00	1171.0
3	TraesCS3B01G514600	chr3B	94.701	736	33	4	2124	2859	49114552	49113823	0.000000e+00	1138.0
4	TraesCS3B01G514600	chr3B	81.233	1103	161	27	999	2081	757279736	757280812	0.000000e+00	848.0
5	TraesCS3B01G514600	chr3B	85.567	97	10	3	1574	1668	22130160	22130066	9.740000e-17	99.0
6	TraesCS3B01G514600	chr3A	93.703	1604	83	8	529	2123	703100029	703098435	0.000000e+00	2386.0
7	TraesCS3B01G514600	chr3A	83.586	1517	159	41	650	2108	703135290	703133806	0.000000e+00	1339.0
8	TraesCS3B01G514600	chr3A	88.462	806	58	11	2853	3636	703098447	703097655	0.000000e+00	941.0
9	TraesCS3B01G514600	chr3A	87.903	620	70	3	999	1615	703006523	703007140	0.000000e+00	725.0
10	TraesCS3B01G514600	chr3A	78.867	724	112	26	1121	1819	702570427	702571134	6.490000e-123	451.0
11	TraesCS3B01G514600	chr3A	94.286	140	8	0	3641	3780	703097231	703097092	9.270000e-52	215.0
12	TraesCS3B01G514600	chr3A	77.119	118	17	7	1135	1247	21323962	21324074	4.600000e-05	60.2
13	TraesCS3B01G514600	chr3D	88.385	1498	110	28	671	2123	570278680	570277202	0.000000e+00	1744.0
14	TraesCS3B01G514600	chr3D	83.156	1128	160	22	999	2120	570270923	570272026	0.000000e+00	1003.0
15	TraesCS3B01G514600	chr3D	87.129	808	64	15	2853	3638	570277214	570276425	0.000000e+00	880.0
16	TraesCS3B01G514600	chr3D	83.804	531	51	14	1	519	31744211	31744718	4.980000e-129	472.0
17	TraesCS3B01G514600	chr3D	78.495	744	126	25	1090	1819	569976371	569977094	1.400000e-124	457.0
18	TraesCS3B01G514600	chr3D	95.122	205	8	2	3641	3845	570276251	570276049	5.310000e-84	322.0
19	TraesCS3B01G514600	chr3D	92.727	165	10	2	3843	4006	570275603	570275440	1.980000e-58	237.0
20	TraesCS3B01G514600	chr3D	86.957	115	15	0	3879	3993	570265597	570265711	3.460000e-26	130.0
21	TraesCS3B01G514600	chr3D	82.178	101	14	3	1571	1669	14999176	14999274	2.730000e-12	84.2
22	TraesCS3B01G514600	chr2B	95.418	742	29	3	2120	2859	727724358	727725096	0.000000e+00	1177.0
23	TraesCS3B01G514600	chr2B	93.750	736	43	1	2124	2859	301386411	301387143	0.000000e+00	1101.0
24	TraesCS3B01G514600	chr7B	95.380	736	29	3	2124	2858	32588049	32587318	0.000000e+00	1166.0
25	TraesCS3B01G514600	chr7B	86.415	530	56	8	1	519	558751541	558752065	2.220000e-157	566.0
26	TraesCS3B01G514600	chr6B	93.369	739	45	4	2124	2861	253225824	253226559	0.000000e+00	1090.0
27	TraesCS3B01G514600	chr6B	91.892	740	50	4	2124	2862	13239966	13239236	0.000000e+00	1026.0
28	TraesCS3B01G514600	chr6B	91.622	740	52	5	2124	2862	13307094	13306364	0.000000e+00	1014.0
29	TraesCS3B01G514600	chr6B	91.351	740	54	5	2124	2862	13262275	13261545	0.000000e+00	1003.0
30	TraesCS3B01G514600	chr4D	88.577	534	44	9	1	522	417804627	417805155	2.160000e-177	632.0
31	TraesCS3B01G514600	chr4D	88.506	522	42	12	12	520	401352175	401351659	2.180000e-172	616.0
32	TraesCS3B01G514600	chr4A	87.170	530	51	12	1	515	692423434	692423961	1.710000e-163	586.0
33	TraesCS3B01G514600	chr4A	86.604	530	54	12	1	515	692451547	692452074	1.720000e-158	569.0
34	TraesCS3B01G514600	chr4A	82.066	513	57	18	1	500	674463803	674464293	5.130000e-109	405.0
35	TraesCS3B01G514600	chrUn	86.713	429	40	12	102	515	442890318	442889892	1.080000e-125	460.0
36	TraesCS3B01G514600	chr2D	88.987	227	25	0	1	227	539014935	539015161	9.010000e-72	281.0
37	TraesCS3B01G514600	chr7D	86.235	247	29	3	1	245	62928345	62928588	3.270000e-66	263.0
38	TraesCS3B01G514600	chr6A	100.000	30	0	0	494	523	457071788	457071817	5.950000e-04	56.5

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	TraesCS3B01G514600	chr3B	757283385	757287642	4257	True	7864.000000	7864	100.000000	1	4258	1	chr3B.!!$R4	4257
1	TraesCS3B01G514600	chr3B	757456317	757457744	1427	True	1423.000000	1423	84.928000	665	2090	1	chr3B.!!$R5	1425
2	TraesCS3B01G514600	chr3B	50676811	50677542	731	True	1171.000000	1171	95.510000	2124	2858	1	chr3B.!!$R3	734
3	TraesCS3B01G514600	chr3B	49113823	49114552	729	True	1138.000000	1138	94.701000	2124	2859	1	chr3B.!!$R2	735
4	TraesCS3B01G514600	chr3B	757279736	757280812	1076	False	848.000000	848	81.233000	999	2081	1	chr3B.!!$F1	1082
5	TraesCS3B01G514600	chr3A	703133806	703135290	1484	True	1339.000000	1339	83.586000	650	2108	1	chr3A.!!$R1	1458
6	TraesCS3B01G514600	chr3A	703097092	703100029	2937	True	1180.666667	2386	92.150333	529	3780	3	chr3A.!!$R2	3251
7	TraesCS3B01G514600	chr3A	703006523	703007140	617	False	725.000000	725	87.903000	999	1615	1	chr3A.!!$F3	616
8	TraesCS3B01G514600	chr3A	702570427	702571134	707	False	451.000000	451	78.867000	1121	1819	1	chr3A.!!$F2	698
9	TraesCS3B01G514600	chr3D	570270923	570272026	1103	False	1003.000000	1003	83.156000	999	2120	1	chr3D.!!$F5	1121
10	TraesCS3B01G514600	chr3D	570275440	570278680	3240	True	795.750000	1744	90.840750	671	4006	4	chr3D.!!$R1	3335
11	TraesCS3B01G514600	chr3D	31744211	31744718	507	False	472.000000	472	83.804000	1	519	1	chr3D.!!$F2	518
12	TraesCS3B01G514600	chr3D	569976371	569977094	723	False	457.000000	457	78.495000	1090	1819	1	chr3D.!!$F3	729
13	TraesCS3B01G514600	chr2B	727724358	727725096	738	False	1177.000000	1177	95.418000	2120	2859	1	chr2B.!!$F2	739
14	TraesCS3B01G514600	chr2B	301386411	301387143	732	False	1101.000000	1101	93.750000	2124	2859	1	chr2B.!!$F1	735
15	TraesCS3B01G514600	chr7B	32587318	32588049	731	True	1166.000000	1166	95.380000	2124	2858	1	chr7B.!!$R1	734
16	TraesCS3B01G514600	chr7B	558751541	558752065	524	False	566.000000	566	86.415000	1	519	1	chr7B.!!$F1	518
17	TraesCS3B01G514600	chr6B	253225824	253226559	735	False	1090.000000	1090	93.369000	2124	2861	1	chr6B.!!$F1	737
18	TraesCS3B01G514600	chr6B	13239236	13239966	730	True	1026.000000	1026	91.892000	2124	2862	1	chr6B.!!$R1	738
19	TraesCS3B01G514600	chr6B	13306364	13307094	730	True	1014.000000	1014	91.622000	2124	2862	1	chr6B.!!$R3	738
20	TraesCS3B01G514600	chr6B	13261545	13262275	730	True	1003.000000	1003	91.351000	2124	2862	1	chr6B.!!$R2	738
21	TraesCS3B01G514600	chr4D	417804627	417805155	528	False	632.000000	632	88.577000	1	522	1	chr4D.!!$F1	521
22	TraesCS3B01G514600	chr4D	401351659	401352175	516	True	616.000000	616	88.506000	12	520	1	chr4D.!!$R1	508
23	TraesCS3B01G514600	chr4A	692423434	692423961	527	False	586.000000	586	87.170000	1	515	1	chr4A.!!$F2	514
24	TraesCS3B01G514600	chr4A	692451547	692452074	527	False	569.000000	569	86.604000	1	515	1	chr4A.!!$F3	514

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
975	1059	0.102300	TCATCTCATGTACGCCACCG	59.898	55.0	0.00	0.0	41.14	4.94	F
2885	3053	0.040058	AAGGCATCAACTCCATGGCA	59.960	50.0	6.96	0.0	46.70	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2917	3085	0.103208	CCCTCCTCCATCGACGAAAG	59.897	60.0	0.00	0.0	0.00	2.62	R
4056	5118	0.250901	ACACAACTGGGCCAGATCAC	60.251	55.0	38.99	0.0	35.18	3.06	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
124	125	3.985877	CGCAGTGCAATCTGGGAA	58.014	55.556	16.83	0.00	46.57	3.97
154	155	4.976224	TTCTTCTCCGACAACGATGATA	57.024	40.909	0.00	0.00	42.66	2.15
155	156	5.515797	TTCTTCTCCGACAACGATGATAT	57.484	39.130	0.00	0.00	42.66	1.63
259	262	4.013728	TCTAGTTTGTGCTGTTTGGTTGT	58.986	39.130	0.00	0.00	0.00	3.32
291	294	8.717821	GTTATTTGTATCTGACTAGTTTGTGCA	58.282	33.333	0.00	0.00	0.00	4.57
320	326	3.884169	TGAACTTTGCTTGTATCGTTGC	58.116	40.909	0.00	0.00	0.00	4.17
343	351	7.930217	TGCATTATCTATTTGGTTGAACTAGC	58.070	34.615	0.00	0.00	0.00	3.42
350	358	7.446769	TCTATTTGGTTGAACTAGCTTGTGTA	58.553	34.615	0.36	0.00	0.00	2.90
363	371	0.179070	TTGTGTACTGGTTGCTCGCA	60.179	50.000	0.00	0.00	0.00	5.10
435	445	4.154347	GCCGCTGCTAGAGCCAGT	62.154	66.667	0.00	0.00	46.01	4.00
443	453	2.607442	TAGAGCCAGTGCCCTGCA	60.607	61.111	0.00	0.00	37.38	4.41
520	536	5.196809	CGTCTGTTGAAGATGCTCTAAAC	57.803	43.478	0.00	0.00	37.23	2.01
522	538	4.997395	GTCTGTTGAAGATGCTCTAAACCA	59.003	41.667	0.00	0.00	37.23	3.67
523	539	5.645497	GTCTGTTGAAGATGCTCTAAACCAT	59.355	40.000	0.00	0.00	37.23	3.55
524	540	6.150140	GTCTGTTGAAGATGCTCTAAACCATT	59.850	38.462	0.00	0.00	37.23	3.16
525	541	6.372659	TCTGTTGAAGATGCTCTAAACCATTC	59.627	38.462	0.00	0.00	0.00	2.67
526	542	5.415701	TGTTGAAGATGCTCTAAACCATTCC	59.584	40.000	0.00	0.00	0.00	3.01
527	543	5.178096	TGAAGATGCTCTAAACCATTCCA	57.822	39.130	0.00	0.00	0.00	3.53
711	729	2.654987	CGAGAGCTTCTTTTTGTTGCC	58.345	47.619	0.00	0.00	0.00	4.52
712	730	2.033299	CGAGAGCTTCTTTTTGTTGCCA	59.967	45.455	0.00	0.00	0.00	4.92
809	847	1.211449	CAGCTAGCTAGATCCGCCG	59.789	63.158	25.15	1.66	0.00	6.46
893	951	3.190849	CGTCGTGAGGCTGCCATG	61.191	66.667	22.65	6.67	0.00	3.66
935	1016	2.237392	CCTCTTCCTCTTCCACCGAATT	59.763	50.000	0.00	0.00	0.00	2.17
975	1059	0.102300	TCATCTCATGTACGCCACCG	59.898	55.000	0.00	0.00	41.14	4.94
1051	1155	1.035923	ATCTCGATCGACCACAGCAT	58.964	50.000	15.15	0.00	0.00	3.79

Showing 1 to 25 of 204 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	3.721706	CCGCCTTGCCCTCCTCTT	61.722	66.667	0.00	0.00	0.00	2.85
124	125	3.877559	TGTCGGAGAAGAATGATGCATT	58.122	40.909	0.00	0.00	39.69	3.56
154	155	2.878406	CAAGAAACACGTCTTCCCACAT	59.122	45.455	3.78	0.00	35.63	3.21
155	156	2.093394	TCAAGAAACACGTCTTCCCACA	60.093	45.455	3.78	0.00	35.63	4.17
277	280	3.616219	ACCAAACTGCACAAACTAGTCA	58.384	40.909	0.00	0.00	0.00	3.41
291	294	4.535526	ACAAGCAAAGTTCAACCAAACT	57.464	36.364	0.00	0.00	41.20	2.66
320	326	9.941664	CAAGCTAGTTCAACCAAATAGATAATG	57.058	33.333	0.00	0.00	35.06	1.90
343	351	0.512952	GCGAGCAACCAGTACACAAG	59.487	55.000	0.00	0.00	0.00	3.16
377	386	2.721231	GCTCCAACAACGCTGCAA	59.279	55.556	0.00	0.00	0.00	4.08
378	387	3.648982	CGCTCCAACAACGCTGCA	61.649	61.111	0.00	0.00	0.00	4.41
379	388	4.389576	CCGCTCCAACAACGCTGC	62.390	66.667	0.00	0.00	0.00	5.25
380	389	3.726517	CCCGCTCCAACAACGCTG	61.727	66.667	0.00	0.00	0.00	5.18
381	390	4.250305	ACCCGCTCCAACAACGCT	62.250	61.111	0.00	0.00	0.00	5.07
383	392	3.411351	CGACCCGCTCCAACAACG	61.411	66.667	0.00	0.00	0.00	4.10
466	478	2.189342	GCACGCTAAAACAGTTTTGCA	58.811	42.857	19.77	1.66	43.14	4.08
491	507	0.249280	TCTTCAACAGACGCGCAAGA	60.249	50.000	5.73	3.01	43.02	3.02
492	508	0.792640	ATCTTCAACAGACGCGCAAG	59.207	50.000	5.73	0.15	32.83	4.01
623	639	2.092374	ATGCTCGTAGCGTCACGTA	58.908	52.632	0.00	0.00	46.26	3.57
711	729	2.284754	TCCAGATCTCTCCTCGGATG	57.715	55.000	0.00	0.00	0.00	3.51
712	730	2.291540	GGATCCAGATCTCTCCTCGGAT	60.292	54.545	6.95	9.23	37.92	4.18
809	847	1.298859	CTGCTCTGGGTGGCGTAAAC	61.299	60.000	0.00	0.00	0.00	2.01
893	951	2.165301	CGTGCCGGGATTCTCGTTC	61.165	63.158	2.18	0.00	0.00	3.95
935	1016	7.665559	AGATGATGTTTGCTGGTTTTCTAAGTA	59.334	33.333	0.00	0.00	0.00	2.24
975	1059	2.158638	ACGGGAGACTAGATGGGTAGAC	60.159	54.545	0.00	0.00	0.00	2.59
1103	1207	0.733150	CAGGATACACAGCGAGACGA	59.267	55.000	0.00	0.00	41.41	4.20

Showing 1 to 25 of 190 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.