AutoCloner

Multiple sequence alignment - TraesCS1A01G312800

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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	TraesCS1A01G312800	chr1A	100.000	2384	0	0	1	2384	504631416	504633799	0.000000e+00	4403.0
1	TraesCS1A01G312800	chr1A	99.655	579	2	0	1806	2384	252280699	252281277	0.000000e+00	1059.0
2	TraesCS1A01G312800	chr1B	89.517	1698	113	36	1	1663	549890223	549891890	0.000000e+00	2089.0
3	TraesCS1A01G312800	chr1B	98.967	581	6	0	1804	2384	703457	704037	0.000000e+00	1040.0
4	TraesCS1A01G312800	chr1D	90.934	1092	61	15	739	1807	408534569	408535645	0.000000e+00	1434.0
5	TraesCS1A01G312800	chr1D	90.919	925	62	3	519	1424	408556943	408557864	0.000000e+00	1223.0
6	TraesCS1A01G312800	chr1D	90.074	816	55	8	1007	1808	408631294	408632097	0.000000e+00	1035.0
7	TraesCS1A01G312800	chr1D	91.727	689	36	7	1	687	408533892	408534561	0.000000e+00	937.0
8	TraesCS1A01G312800	chr1D	87.370	578	56	7	1804	2375	467450162	467449596	0.000000e+00	647.0
9	TraesCS1A01G312800	chr1D	82.240	625	85	18	895	1512	408711816	408712421	1.260000e-142	516.0
10	TraesCS1A01G312800	chr1D	78.693	765	117	31	482	1233	408769407	408770138	3.590000e-128	468.0
11	TraesCS1A01G312800	chr1D	88.401	319	18	11	1416	1717	408566160	408566476	1.350000e-97	366.0
12	TraesCS1A01G312800	chr1D	82.367	414	32	6	1857	2267	339741635	339742010	2.960000e-84	322.0
13	TraesCS1A01G312800	chr1D	91.549	213	15	3	423	634	408711556	408711766	8.340000e-75	291.0
14	TraesCS1A01G312800	chr1D	81.343	134	17	5	1681	1807	408566498	408566630	4.190000e-18	102.0
15	TraesCS1A01G312800	chr1D	96.226	53	1	1	1810	1862	339741467	339741518	4.220000e-13	86.1
16	TraesCS1A01G312800	chr1D	100.000	30	0	0	1541	1570	408570950	408570979	3.310000e-04	56.5
17	TraesCS1A01G312800	chr6A	99.487	585	2	1	1800	2384	520358712	520358129	0.000000e+00	1062.0
18	TraesCS1A01G312800	chr5A	99.655	579	2	0	1806	2384	445248977	445248399	0.000000e+00	1059.0
19	TraesCS1A01G312800	chr5A	98.976	586	5	1	1800	2384	521282662	521283247	0.000000e+00	1048.0
20	TraesCS1A01G312800	chrUn	98.964	579	6	0	1806	2384	366195652	366195074	0.000000e+00	1037.0
21	TraesCS1A01G312800	chr3A	98.964	579	6	0	1806	2384	738083280	738083858	0.000000e+00	1037.0
22	TraesCS1A01G312800	chr6B	82.609	161	22	4	2136	2290	33462680	33462840	1.150000e-28	137.0

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	TraesCS1A01G312800	chr1A	504631416	504633799	2383	False	4403.00	4403	100.0000	1	2384	1	chr1A.!!$F2	2383
1	TraesCS1A01G312800	chr1A	252280699	252281277	578	False	1059.00	1059	99.6550	1806	2384	1	chr1A.!!$F1	578
2	TraesCS1A01G312800	chr1B	549890223	549891890	1667	False	2089.00	2089	89.5170	1	1663	1	chr1B.!!$F2	1662
3	TraesCS1A01G312800	chr1B	703457	704037	580	False	1040.00	1040	98.9670	1804	2384	1	chr1B.!!$F1	580
4	TraesCS1A01G312800	chr1D	408556943	408557864	921	False	1223.00	1223	90.9190	519	1424	1	chr1D.!!$F1	905
5	TraesCS1A01G312800	chr1D	408533892	408535645	1753	False	1185.50	1434	91.3305	1	1807	2	chr1D.!!$F6	1806
6	TraesCS1A01G312800	chr1D	408631294	408632097	803	False	1035.00	1035	90.0740	1007	1808	1	chr1D.!!$F3	801
7	TraesCS1A01G312800	chr1D	467449596	467450162	566	True	647.00	647	87.3700	1804	2375	1	chr1D.!!$R1	571
8	TraesCS1A01G312800	chr1D	408769407	408770138	731	False	468.00	468	78.6930	482	1233	1	chr1D.!!$F4	751
9	TraesCS1A01G312800	chr1D	408711556	408712421	865	False	403.50	516	86.8945	423	1512	2	chr1D.!!$F8	1089
10	TraesCS1A01G312800	chr1D	339741467	339742010	543	False	204.05	322	89.2965	1810	2267	2	chr1D.!!$F5	457
11	TraesCS1A01G312800	chr6A	520358129	520358712	583	True	1062.00	1062	99.4870	1800	2384	1	chr6A.!!$R1	584
12	TraesCS1A01G312800	chr5A	445248399	445248977	578	True	1059.00	1059	99.6550	1806	2384	1	chr5A.!!$R1	578
13	TraesCS1A01G312800	chr5A	521282662	521283247	585	False	1048.00	1048	98.9760	1800	2384	1	chr5A.!!$F1	584
14	TraesCS1A01G312800	chrUn	366195074	366195652	578	True	1037.00	1037	98.9640	1806	2384	1	chrUn.!!$R1	578
15	TraesCS1A01G312800	chr3A	738083280	738083858	578	False	1037.00	1037	98.9640	1806	2384	1	chr3A.!!$F1	578

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
683	719	0.03213	TGACTGAACCGAGCAGTGTC	59.968	55.0	9.04	0.0	45.94	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1798	1904	1.303317	CAAGCGGGCCCTAACTTGT	60.303	57.895	28.2	7.53	35.81	3.16	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
79	80	1.671054	CAGTGCCACGTTACCCCTG	60.671	63.158	0.00	0.00	0.00	4.45
124	130	1.306642	ACCCACGAGAGCACTAGACG	61.307	60.000	0.00	0.00	0.00	4.18
183	189	4.217550	TGGATTGCCTCGGTAAAAAGAAAG	59.782	41.667	0.00	0.00	34.31	2.62
184	190	4.380550	GGATTGCCTCGGTAAAAAGAAAGG	60.381	45.833	0.00	0.00	0.00	3.11
185	191	3.495434	TGCCTCGGTAAAAAGAAAGGA	57.505	42.857	0.00	0.00	0.00	3.36
186	192	4.028993	TGCCTCGGTAAAAAGAAAGGAT	57.971	40.909	0.00	0.00	0.00	3.24
187	193	4.403734	TGCCTCGGTAAAAAGAAAGGATT	58.596	39.130	0.00	0.00	0.00	3.01
188	194	4.830600	TGCCTCGGTAAAAAGAAAGGATTT	59.169	37.500	0.00	0.00	43.98	2.17
211	227	4.742201	GCTGCGTGGAAGGAGCGA	62.742	66.667	0.00	0.00	45.08	4.93
284	300	1.447314	CCGGCGGTGAGTTAGGTTC	60.447	63.158	19.97	0.00	0.00	3.62
315	348	5.960113	TCTCTCTCTGCTTGATCTGTTTAC	58.040	41.667	0.00	0.00	0.00	2.01
346	379	2.737252	GGTCTTCTGGTTCTTTGTAGCG	59.263	50.000	0.00	0.00	0.00	4.26
351	384	1.455786	CTGGTTCTTTGTAGCGTCGTG	59.544	52.381	0.00	0.00	0.00	4.35
357	390	2.488937	TCTTTGTAGCGTCGTGTGGATA	59.511	45.455	0.00	0.00	0.00	2.59
358	391	3.057386	TCTTTGTAGCGTCGTGTGGATAA	60.057	43.478	0.00	0.00	0.00	1.75
380	413	6.791887	AAATCCATATGAGTAGCGTTCATG	57.208	37.500	3.65	0.00	36.07	3.07
385	418	7.269316	TCCATATGAGTAGCGTTCATGTAAAA	58.731	34.615	3.65	0.00	36.07	1.52
392	425	7.491372	TGAGTAGCGTTCATGTAAAATTAGGAG	59.509	37.037	0.00	0.00	0.00	3.69
394	427	6.422776	AGCGTTCATGTAAAATTAGGAGTG	57.577	37.500	0.00	0.00	0.00	3.51
396	429	7.101054	AGCGTTCATGTAAAATTAGGAGTGTA	58.899	34.615	0.00	0.00	0.00	2.90
441	474	0.988832	TGTAGTTGCTCCGGGGAATT	59.011	50.000	4.80	1.03	0.00	2.17
501	534	3.382546	AGCAGTTGATTTGTGCTCTGTTT	59.617	39.130	0.00	0.00	44.28	2.83
544	578	6.992715	AGTCAAATTAATCTTGGCGCTAGTAT	59.007	34.615	7.64	0.00	33.56	2.12
577	612	7.610580	AGTTTTGGTGAAAGATTTAATGGGA	57.389	32.000	0.00	0.00	0.00	4.37
626	662	6.466308	TCGTGATGTTTGATAGTTTCTGTG	57.534	37.500	0.00	0.00	0.00	3.66
683	719	0.032130	TGACTGAACCGAGCAGTGTC	59.968	55.000	9.04	0.00	45.94	3.67
700	736	1.939934	TGTCGCTTTGGAACTTCTGTG	59.060	47.619	0.00	0.00	0.00	3.66
733	777	6.806751	TGTAAGGCACAGCTAGAGTAATTAG	58.193	40.000	0.00	0.00	31.89	1.73
735	779	3.706594	AGGCACAGCTAGAGTAATTAGCA	59.293	43.478	6.98	0.00	44.65	3.49
736	780	4.162320	AGGCACAGCTAGAGTAATTAGCAA	59.838	41.667	6.98	0.00	44.65	3.91
737	781	5.059833	GGCACAGCTAGAGTAATTAGCAAT	58.940	41.667	6.98	0.00	44.65	3.56
738	782	5.529060	GGCACAGCTAGAGTAATTAGCAATT	59.471	40.000	6.98	0.00	44.65	2.32
739	783	6.038714	GGCACAGCTAGAGTAATTAGCAATTT	59.961	38.462	6.98	0.00	44.65	1.82
740	784	7.226720	GGCACAGCTAGAGTAATTAGCAATTTA	59.773	37.037	6.98	0.00	44.65	1.40
744	788	9.922305	CAGCTAGAGTAATTAGCAATTTAACAC	57.078	33.333	6.98	0.00	44.65	3.32
827	878	1.480205	CTGCAGTTTCCTTTGTTGCG	58.520	50.000	5.25	0.00	37.58	4.85
936	1014	7.941795	AATAGAAAGCATTTTAGCATGATGC	57.058	32.000	9.89	9.89	44.89	3.91
965	1043	4.881273	TGTATAATGTGGTGTCTTGGCATC	59.119	41.667	0.00	0.00	0.00	3.91
1075	1157	0.176680	CTTGACAGACGATCAGGGGG	59.823	60.000	0.00	0.00	0.00	5.40
1076	1158	1.899437	TTGACAGACGATCAGGGGGC	61.899	60.000	0.00	0.00	0.00	5.80
1077	1159	2.284625	ACAGACGATCAGGGGGCA	60.285	61.111	0.00	0.00	0.00	5.36
1116	1198	2.571653	AGATTCTCACACCGGAAATCCA	59.428	45.455	9.46	0.00	35.14	3.41
1194	1280	2.202932	GATGTCATGCGAGCCGGT	60.203	61.111	1.90	0.00	0.00	5.28
1257	1343	0.246635	CGATGGACTCCACCGACTTT	59.753	55.000	5.85	0.00	44.65	2.66
1368	1454	1.521681	GGGAATCAAGCCGTCGGAG	60.522	63.158	17.49	3.78	0.00	4.63
1733	1836	4.092968	GCAAATATTTTCGAGAGACCACGT	59.907	41.667	0.00	0.00	41.84	4.49
1738	1841	4.410492	TTTTCGAGAGACCACGTAGTAC	57.590	45.455	0.00	0.00	38.73	2.73
1739	1842	2.015736	TCGAGAGACCACGTAGTACC	57.984	55.000	0.00	0.00	33.87	3.34
1775	1881	4.170468	AGATCAGTGTTCTTGGGTGTTT	57.830	40.909	0.00	0.00	0.00	2.83
1798	1904	1.002430	CTCTTGGCTCTGGCTAACACA	59.998	52.381	0.00	0.00	35.19	3.72
1860	2087	4.694760	ACACCGGTAAAATATACCTCCC	57.305	45.455	6.87	0.00	35.49	4.30
1965	2192	8.860780	TTACACCTGTAATTAACCGGTATTTT	57.139	30.769	8.00	4.12	43.25	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
124	130	1.216710	CTCGGCCAGTTCACTCCTC	59.783	63.158	2.24	0.00	0.00	3.71
183	189	1.508088	CACGCAGCCAAGGAAATCC	59.492	57.895	0.00	0.00	0.00	3.01
184	190	0.960364	TCCACGCAGCCAAGGAAATC	60.960	55.000	0.00	0.00	0.00	2.17
185	191	0.539438	TTCCACGCAGCCAAGGAAAT	60.539	50.000	5.59	0.00	37.22	2.17
186	192	1.152860	TTCCACGCAGCCAAGGAAA	60.153	52.632	5.59	0.00	37.22	3.13
187	193	1.600636	CTTCCACGCAGCCAAGGAA	60.601	57.895	7.44	7.44	37.79	3.36
188	194	2.032528	CTTCCACGCAGCCAAGGA	59.967	61.111	0.00	0.00	0.00	3.36
189	195	3.058160	CCTTCCACGCAGCCAAGG	61.058	66.667	0.00	0.00	0.00	3.61
190	196	2.032528	TCCTTCCACGCAGCCAAG	59.967	61.111	0.00	0.00	0.00	3.61
191	197	2.032528	CTCCTTCCACGCAGCCAA	59.967	61.111	0.00	0.00	0.00	4.52
192	198	4.704833	GCTCCTTCCACGCAGCCA	62.705	66.667	0.00	0.00	0.00	4.75
284	300	1.037030	AGCAGAGAGAGAGCGGAAGG	61.037	60.000	0.00	0.00	0.00	3.46
357	390	6.291377	ACATGAACGCTACTCATATGGATTT	58.709	36.000	0.00	0.00	32.20	2.17
358	391	5.858381	ACATGAACGCTACTCATATGGATT	58.142	37.500	0.00	0.00	32.20	3.01
364	397	9.256477	CCTAATTTTACATGAACGCTACTCATA	57.744	33.333	0.00	0.00	32.20	2.15
366	399	7.324935	TCCTAATTTTACATGAACGCTACTCA	58.675	34.615	0.00	0.00	0.00	3.41
380	413	8.947115	ACTGCAGAAATACACTCCTAATTTTAC	58.053	33.333	23.35	0.00	0.00	2.01
385	418	6.070538	ACTGACTGCAGAAATACACTCCTAAT	60.071	38.462	23.35	0.00	45.17	1.73
392	425	4.058124	TCACACTGACTGCAGAAATACAC	58.942	43.478	23.35	3.20	45.17	2.90
394	427	5.869753	AATCACACTGACTGCAGAAATAC	57.130	39.130	23.35	6.69	45.17	1.89
396	429	4.022589	CCAAATCACACTGACTGCAGAAAT	60.023	41.667	23.35	0.00	45.17	2.17
441	474	2.168521	CCTACTTTCCCTTGCTCGATCA	59.831	50.000	0.00	0.00	0.00	2.92
501	534	8.940397	ATTTGACTCCCTTTTCTTCATCTAAA	57.060	30.769	0.00	0.00	0.00	1.85
544	578	7.817418	ATCTTTCACCAAAACTTGCTACTTA	57.183	32.000	0.00	0.00	0.00	2.24
577	612	9.790344	ATGCTACAGATCTCAGCTTATAATTTT	57.210	29.630	20.99	0.00	36.26	1.82
588	624	3.978718	TCACGATGCTACAGATCTCAG	57.021	47.619	0.00	0.00	0.00	3.35
683	719	0.040067	GCCACAGAAGTTCCAAAGCG	60.040	55.000	0.00	0.00	0.00	4.68
700	736	1.172180	TGTGCCTTACAGTTGCAGCC	61.172	55.000	0.00	0.00	35.33	4.85
733	777	5.613142	GCACAAAGCATCAGTGTTAAATTGC	60.613	40.000	0.00	0.00	44.79	3.56
936	1014	6.535150	CCAAGACACCACATTATACACAGTAG	59.465	42.308	0.00	0.00	0.00	2.57
965	1043	7.008719	CGATATGCCACTAGATATGAAAACTCG	59.991	40.741	0.00	0.00	0.00	4.18
1075	1157	2.282040	AGTGTGCTTCAGGGCTGC	60.282	61.111	0.00	0.00	0.00	5.25
1076	1158	2.623915	GCAGTGTGCTTCAGGGCTG	61.624	63.158	0.00	0.00	40.96	4.85
1077	1159	2.282040	GCAGTGTGCTTCAGGGCT	60.282	61.111	0.00	0.00	40.96	5.19
1275	1361	2.668212	CCTTCAAAGTCGCGGGCA	60.668	61.111	6.13	0.00	0.00	5.36
1623	1715	3.655777	AGTATCCCCTGTTCCTGAAAACA	59.344	43.478	0.00	0.00	37.56	2.83
1733	1836	6.370186	TCTTGTGAGAGTAGAGTGGTACTA	57.630	41.667	0.00	0.00	33.18	1.82
1738	1841	4.704540	ACTGATCTTGTGAGAGTAGAGTGG	59.295	45.833	0.00	0.00	34.85	4.00
1739	1842	5.182950	ACACTGATCTTGTGAGAGTAGAGTG	59.817	44.000	20.57	11.34	38.65	3.51
1798	1904	1.303317	CAAGCGGGCCCTAACTTGT	60.303	57.895	28.20	7.53	35.81	3.16
1860	2087	3.545703	AGCCGGTCTGAATTTTCCATAG	58.454	45.455	1.90	0.00	0.00	2.23
1965	2192	3.066190	CGGGCCGAGGTCTGTACA	61.066	66.667	24.41	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.