AutoCloner

Multiple sequence alignment - TraesCS3D01G488400

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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	TraesCS3D01G488400	chr3D	100.000	3081	0	0	1	3081	583163039	583159959	0.000000e+00	5690.0
1	TraesCS3D01G488400	chr3D	93.614	1331	82	2	632	1960	583179505	583178176	0.000000e+00	1984.0
2	TraesCS3D01G488400	chr3D	90.229	1269	108	7	740	2006	583027130	583025876	0.000000e+00	1642.0
3	TraesCS3D01G488400	chr3D	96.463	311	11	0	632	942	583276245	583275935	5.890000e-142	514.0
4	TraesCS3D01G488400	chr3D	80.000	365	29	12	2403	2725	583025319	583024957	2.390000e-56	230.0
5	TraesCS3D01G488400	chr3B	93.990	1198	56	6	834	2018	780295757	780294563	0.000000e+00	1799.0
6	TraesCS3D01G488400	chr3B	92.148	1057	37	11	2065	3081	780293698	780292648	0.000000e+00	1450.0
7	TraesCS3D01G488400	chr3B	92.636	258	16	3	345	601	67396674	67396419	4.850000e-98	368.0
8	TraesCS3D01G488400	chr3B	90.244	246	8	7	346	575	70310520	70310275	1.070000e-79	307.0
9	TraesCS3D01G488400	chr3B	85.950	121	17	0	632	752	780339251	780339131	2.490000e-26	130.0
10	TraesCS3D01G488400	chr3B	92.727	55	4	0	2018	2072	780293939	780293885	2.550000e-11	80.5
11	TraesCS3D01G488400	chrUn	89.342	1276	111	14	740	2006	41698922	41700181	0.000000e+00	1580.0
12	TraesCS3D01G488400	chrUn	88.497	1191	118	11	820	1998	101984247	101983064	0.000000e+00	1423.0
13	TraesCS3D01G488400	chrUn	84.979	1398	165	28	635	2017	101987758	101986391	0.000000e+00	1376.0
14	TraesCS3D01G488400	chr6B	85.458	1396	167	21	635	2018	62689095	62687724	0.000000e+00	1421.0
15	TraesCS3D01G488400	chr6B	93.607	610	32	5	1	608	177722081	177721477	0.000000e+00	904.0
16	TraesCS3D01G488400	chr6A	87.944	1211	124	11	820	2018	34278153	34276953	0.000000e+00	1408.0
17	TraesCS3D01G488400	chr6A	87.909	1191	120	15	820	1998	34273351	34272173	0.000000e+00	1380.0
18	TraesCS3D01G488400	chr2D	96.682	633	18	3	1	632	296365253	296364623	0.000000e+00	1050.0
19	TraesCS3D01G488400	chr2A	96.203	632	22	2	1	631	258353293	258352663	0.000000e+00	1033.0
20	TraesCS3D01G488400	chr5A	95.419	633	25	4	1	632	225782729	225782100	0.000000e+00	1005.0
21	TraesCS3D01G488400	chr5A	94.581	609	30	3	1	608	155218017	155217411	0.000000e+00	939.0
22	TraesCS3D01G488400	chr5D	94.937	632	27	4	1	631	416031138	416031765	0.000000e+00	985.0
23	TraesCS3D01G488400	chr5D	93.671	632	35	4	1	631	83924011	83923384	0.000000e+00	941.0
24	TraesCS3D01G488400	chr5B	93.691	634	37	3	1	633	693901180	693901811	0.000000e+00	946.0
25	TraesCS3D01G488400	chr5B	93.533	634	37	4	1	633	693889910	693890540	0.000000e+00	941.0
26	TraesCS3D01G488400	chr7A	92.013	601	40	3	2484	3081	54604219	54603624	0.000000e+00	837.0
27	TraesCS3D01G488400	chr7A	93.860	114	7	0	2371	2484	54626036	54625923	4.080000e-39	172.0

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	TraesCS3D01G488400	chr3D	583159959	583163039	3080	True	5690.000000	5690	100.0000	1	3081	1	chr3D.!!$R1	3080
1	TraesCS3D01G488400	chr3D	583178176	583179505	1329	True	1984.000000	1984	93.6140	632	1960	1	chr3D.!!$R2	1328
2	TraesCS3D01G488400	chr3D	583024957	583027130	2173	True	936.000000	1642	85.1145	740	2725	2	chr3D.!!$R4	1985
3	TraesCS3D01G488400	chr3B	780292648	780295757	3109	True	1109.833333	1799	92.9550	834	3081	3	chr3B.!!$R4	2247
4	TraesCS3D01G488400	chrUn	41698922	41700181	1259	False	1580.000000	1580	89.3420	740	2006	1	chrUn.!!$F1	1266
5	TraesCS3D01G488400	chrUn	101983064	101987758	4694	True	1399.500000	1423	86.7380	635	2017	2	chrUn.!!$R1	1382
6	TraesCS3D01G488400	chr6B	62687724	62689095	1371	True	1421.000000	1421	85.4580	635	2018	1	chr6B.!!$R1	1383
7	TraesCS3D01G488400	chr6B	177721477	177722081	604	True	904.000000	904	93.6070	1	608	1	chr6B.!!$R2	607
8	TraesCS3D01G488400	chr6A	34272173	34278153	5980	True	1394.000000	1408	87.9265	820	2018	2	chr6A.!!$R1	1198
9	TraesCS3D01G488400	chr2D	296364623	296365253	630	True	1050.000000	1050	96.6820	1	632	1	chr2D.!!$R1	631
10	TraesCS3D01G488400	chr2A	258352663	258353293	630	True	1033.000000	1033	96.2030	1	631	1	chr2A.!!$R1	630
11	TraesCS3D01G488400	chr5A	225782100	225782729	629	True	1005.000000	1005	95.4190	1	632	1	chr5A.!!$R2	631
12	TraesCS3D01G488400	chr5A	155217411	155218017	606	True	939.000000	939	94.5810	1	608	1	chr5A.!!$R1	607
13	TraesCS3D01G488400	chr5D	416031138	416031765	627	False	985.000000	985	94.9370	1	631	1	chr5D.!!$F1	630
14	TraesCS3D01G488400	chr5D	83923384	83924011	627	True	941.000000	941	93.6710	1	631	1	chr5D.!!$R1	630
15	TraesCS3D01G488400	chr5B	693901180	693901811	631	False	946.000000	946	93.6910	1	633	1	chr5B.!!$F2	632
16	TraesCS3D01G488400	chr5B	693889910	693890540	630	False	941.000000	941	93.5330	1	633	1	chr5B.!!$F1	632
17	TraesCS3D01G488400	chr7A	54603624	54604219	595	True	837.000000	837	92.0130	2484	3081	1	chr7A.!!$R1	597

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
518	519	0.107508	TGCTGCTAAGATGCCAGTCC	60.108	55.0	0.0	0.0	0.00	3.85	F
1463	6293	0.036294	AGTCCTTTACTCGCTTGGCC	60.036	55.0	0.0	0.0	30.33	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2018	10219	0.035439	ACACAATGTAAGAGCGGGGG	60.035	55.0	0.0	0.0	0.0	5.40	R
2526	11661	0.320771	AATCACACACGAGGACCAGC	60.321	55.0	0.0	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
177	178	1.297689	GACCTGCAGACATGGCTCA	59.702	57.895	17.39	0.00	0.00	4.26
253	254	0.252467	AGTCCAGAGGGAGGAAGGTG	60.252	60.000	0.00	0.00	46.12	4.00
340	341	4.645136	ACAAGATAACGAGGCTCTGATACA	59.355	41.667	13.50	0.00	0.00	2.29
518	519	0.107508	TGCTGCTAAGATGCCAGTCC	60.108	55.000	0.00	0.00	0.00	3.85
578	580	5.488341	GAACTCTATCCTAACTGCCACAAA	58.512	41.667	0.00	0.00	0.00	2.83
678	680	5.719563	CCCACCAAGGAAAACACCTTATTAT	59.280	40.000	0.00	0.00	46.94	1.28
704	706	2.954318	AGATATGTCACAGCCAAATGCC	59.046	45.455	0.00	0.00	42.71	4.40
803	825	5.938710	ACATGATAATGTGATGGCTCATCTC	59.061	40.000	0.00	11.46	41.06	2.75
812	834	0.251354	TGGCTCATCTCAAGGACAGC	59.749	55.000	0.00	0.00	34.26	4.40
818	840	2.233186	TCATCTCAAGGACAGCAGACAG	59.767	50.000	0.00	0.00	0.00	3.51
829	851	6.711277	AGGACAGCAGACAGACAAAATTATA	58.289	36.000	0.00	0.00	0.00	0.98
910	934	5.010112	GGCATAGTAAGTAGACAGCATCTGA	59.990	44.000	0.29	0.00	38.49	3.27
1054	5884	8.811378	CAGCTATCATCAACCACAATATATACG	58.189	37.037	0.00	0.00	0.00	3.06
1286	6116	0.555769	ACCAAGTTTGCTCCTCCCAA	59.444	50.000	0.00	0.00	0.00	4.12
1422	6252	5.305644	GTGGCTCTAAGGAAAGGAGATGATA	59.694	44.000	0.00	0.00	0.00	2.15
1429	6259	4.036518	AGGAAAGGAGATGATACAGCTGT	58.963	43.478	25.12	25.12	26.98	4.40
1463	6293	0.036294	AGTCCTTTACTCGCTTGGCC	60.036	55.000	0.00	0.00	30.33	5.36
1492	6322	4.221482	GGCCAGGAAACATTTCAAGAAGAT	59.779	41.667	0.00	0.00	38.92	2.40
1522	6352	1.442526	CCTGCATCCGACAAGATGGC	61.443	60.000	3.89	0.00	43.26	4.40
1555	6385	2.281517	CAAGGCAAGAGAGATCTGCAG	58.718	52.381	7.63	7.63	0.00	4.41
1624	6454	2.368548	TGCCAAAGCAGTCTCTTGTCTA	59.631	45.455	0.00	0.00	46.52	2.59
1650	6483	4.082026	AGGCATTTTACATGAAGAAGGCAC	60.082	41.667	0.00	0.00	31.10	5.01
1664	6497	1.301716	GGCACTTGTCTGCGAGGAA	60.302	57.895	0.00	0.00	38.12	3.36
1688	6521	4.243007	GCAATTGCTGGAGTTAAAGTGT	57.757	40.909	23.21	0.00	38.21	3.55
1690	6523	5.154222	GCAATTGCTGGAGTTAAAGTGTAC	58.846	41.667	23.21	0.00	38.21	2.90
1692	6525	3.412237	TGCTGGAGTTAAAGTGTACCC	57.588	47.619	0.00	0.00	0.00	3.69
1720	6553	3.340814	TCTTCAGAATGGAGCAGGAAC	57.659	47.619	0.00	0.00	43.21	3.62
1848	10026	1.565067	TGAGCTGATCTTGAGGCAGA	58.435	50.000	0.00	0.00	0.00	4.26
1864	10047	7.515004	TGAGGCAGATTTCCCATATGTATAT	57.485	36.000	1.24	0.00	0.00	0.86
1920	10103	6.022163	AGCAAAGTTTTGATCCATCTCAAG	57.978	37.500	8.70	0.00	40.55	3.02
1945	10133	9.254133	AGTTTTGTGATATCGATAACATCTCTG	57.746	33.333	17.12	0.00	0.00	3.35
1979	10180	6.320418	TGTGATGAATATGCATGAGAAAAGCT	59.680	34.615	10.16	0.00	0.00	3.74
2018	10219	9.778741	TTCAATCCATCATGTATTTACTAGGTC	57.221	33.333	0.00	0.00	0.00	3.85
2020	10221	6.681729	TCCATCATGTATTTACTAGGTCCC	57.318	41.667	0.00	0.00	0.00	4.46
2021	10222	5.546499	TCCATCATGTATTTACTAGGTCCCC	59.454	44.000	0.00	0.00	0.00	4.81
2022	10223	5.280521	CCATCATGTATTTACTAGGTCCCCC	60.281	48.000	0.00	0.00	0.00	5.40
2023	10224	3.899360	TCATGTATTTACTAGGTCCCCCG	59.101	47.826	0.00	0.00	35.12	5.73
2026	10880	1.421480	ATTTACTAGGTCCCCCGCTC	58.579	55.000	0.00	0.00	35.12	5.03
2036	10890	0.251916	TCCCCCGCTCTTACATTGTG	59.748	55.000	0.00	0.00	0.00	3.33
2180	11247	0.396435	ACCTTGTCACTCAATGGCGA	59.604	50.000	0.00	0.00	34.72	5.54
2278	11355	3.813443	CAGTACTCAATGGATCTTGGGG	58.187	50.000	0.00	0.00	30.50	4.96
2351	11428	2.224744	TGGCATGAGCTTGGTTGTAAGA	60.225	45.455	0.00	0.00	41.70	2.10
2428	11530	3.897122	GCACCAACCACCCCCTCA	61.897	66.667	0.00	0.00	0.00	3.86
2479	11581	2.039746	ACAAGGCTGTACAATACCAGCA	59.960	45.455	13.02	0.00	42.00	4.41
2544	11679	1.188219	AGCTGGTCCTCGTGTGTGAT	61.188	55.000	0.00	0.00	0.00	3.06
2710	11853	4.714308	AGGCTCTTCTACTTCTGCACTATT	59.286	41.667	0.00	0.00	0.00	1.73
2777	11920	3.244735	GCAAAGTTCCTCCTCTCTTCCTT	60.245	47.826	0.00	0.00	0.00	3.36
2785	11928	3.134442	CCTCCTCTCTTCCTTTCCATCTG	59.866	52.174	0.00	0.00	0.00	2.90
2854	12000	2.993853	CCTTCCAGCCCTCACTCC	59.006	66.667	0.00	0.00	0.00	3.85
2928	12074	3.678056	TGGTATGCGAAACAGAGAACT	57.322	42.857	0.00	0.00	0.00	3.01
3028	12174	4.097361	GGGGAGAACTCGGGCCAC	62.097	72.222	4.39	0.00	0.00	5.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	2.743928	CAAGGGTGTCGAGGCTGC	60.744	66.667	0.00	0.00	0.00	5.25
253	254	2.888863	CTCCGTCTGCCTCTGGTC	59.111	66.667	0.00	0.00	0.00	4.02
340	341	5.751586	TCAGGTTCAAAGGTCTAACAAGTT	58.248	37.500	0.00	0.00	0.00	2.66
518	519	4.953667	TGGCATCTTAGACTAGCATCTTG	58.046	43.478	5.71	0.00	0.00	3.02
578	580	2.360852	GCTGCAGCACATGGTCCT	60.361	61.111	33.36	0.00	41.59	3.85
601	603	3.369242	AGTCTGTGTACTAGGGTCCTC	57.631	52.381	0.00	0.00	0.00	3.71
678	680	6.427853	GCATTTGGCTGTGACATATCTGTATA	59.572	38.462	0.00	0.00	40.25	1.47
685	687	2.691526	CTGGCATTTGGCTGTGACATAT	59.308	45.455	5.67	0.00	44.01	1.78
730	732	2.198266	GCATAATTGCGCGCTCAAC	58.802	52.632	33.29	11.26	39.49	3.18
803	825	2.245159	TTGTCTGTCTGCTGTCCTTG	57.755	50.000	0.00	0.00	0.00	3.61
829	851	6.405953	CCCTAAAGTCGTCTCATGTTCAGTAT	60.406	42.308	0.00	0.00	0.00	2.12
910	934	4.708576	AGAATCATGCCATCACATCTCT	57.291	40.909	0.00	0.00	0.00	3.10
1286	6116	3.184628	TCCATCCAACATCTTCCTCTGT	58.815	45.455	0.00	0.00	0.00	3.41
1323	6153	4.750021	TGCAGAGATCTAACAGCTCAAT	57.250	40.909	0.00	0.00	0.00	2.57
1429	6259	1.988107	AGGACTGGATCTTGGCTTGAA	59.012	47.619	0.00	0.00	0.00	2.69
1463	6293	3.321682	TGAAATGTTTCCTGGCCTTCTTG	59.678	43.478	3.32	0.00	36.36	3.02
1492	6322	1.252904	GGATGCAGGCTTCTTGGCAA	61.253	55.000	0.00	0.00	44.55	4.52
1522	6352	1.667236	TGCCTTGGTCAATAGCATCG	58.333	50.000	4.97	0.00	32.06	3.84
1523	6353	3.282021	TCTTGCCTTGGTCAATAGCATC	58.718	45.455	8.64	0.00	32.11	3.91
1555	6385	0.681733	TGTGGACTCCAACAGAGAGC	59.318	55.000	0.00	0.00	46.50	4.09
1624	6454	5.567423	GCCTTCTTCATGTAAAATGCCTTGT	60.567	40.000	0.00	0.00	0.00	3.16
1639	6469	1.597742	GCAGACAAGTGCCTTCTTCA	58.402	50.000	0.00	0.00	37.49	3.02
1650	6483	0.037882	TGCTCTTCCTCGCAGACAAG	60.038	55.000	0.00	0.00	0.00	3.16
1675	6508	2.564062	CCGAGGGTACACTTTAACTCCA	59.436	50.000	0.00	0.00	0.00	3.86
1683	6516	2.830651	AGATCTCCGAGGGTACACTT	57.169	50.000	0.00	0.00	0.00	3.16
1688	6521	3.664551	TTCTGAAGATCTCCGAGGGTA	57.335	47.619	0.00	0.00	0.00	3.69
1690	6523	2.036992	CCATTCTGAAGATCTCCGAGGG	59.963	54.545	0.00	0.00	0.00	4.30
1692	6525	3.552684	GCTCCATTCTGAAGATCTCCGAG	60.553	52.174	0.00	0.00	0.00	4.63
1720	6553	6.042638	TCTGGACTAATTTCCTGAACAGAG	57.957	41.667	3.19	0.00	39.84	3.35
1834	10012	2.577563	TGGGAAATCTGCCTCAAGATCA	59.422	45.455	0.00	0.00	35.83	2.92
1920	10103	9.035607	ACAGAGATGTTATCGATATCACAAAAC	57.964	33.333	16.43	7.94	0.00	2.43
1945	10133	3.497640	GCATATTCATCACAGAGCTCCAC	59.502	47.826	10.93	0.00	0.00	4.02
2018	10219	0.035439	ACACAATGTAAGAGCGGGGG	60.035	55.000	0.00	0.00	0.00	5.40
2020	10221	2.967362	TGTACACAATGTAAGAGCGGG	58.033	47.619	0.00	0.00	34.21	6.13
2021	10222	5.323900	CATTTGTACACAATGTAAGAGCGG	58.676	41.667	16.31	0.00	34.21	5.52
2022	10223	4.788100	GCATTTGTACACAATGTAAGAGCG	59.212	41.667	21.34	0.00	34.21	5.03
2023	10224	5.095490	GGCATTTGTACACAATGTAAGAGC	58.905	41.667	21.34	10.98	34.21	4.09
2026	10880	6.012658	ACTGGCATTTGTACACAATGTAAG	57.987	37.500	21.34	20.05	34.21	2.34
2036	10890	7.704899	GGTAATGGATTTTACTGGCATTTGTAC	59.295	37.037	0.00	0.00	33.49	2.90
2081	11130	4.502282	CACGAAGTCTTACAGCATGAGATC	59.498	45.833	0.00	0.00	41.61	2.75
2130	11180	2.176798	ACCTGGAACCATGTTTCTTGGA	59.823	45.455	16.75	0.00	37.69	3.53
2234	11306	2.446435	AGGTGTTCAAGTGCACAAACT	58.554	42.857	21.04	2.04	37.35	2.66
2278	11355	5.600484	TGTATCTTCTCTCTTGGGATCCTTC	59.400	44.000	12.58	0.00	0.00	3.46
2287	11364	5.885352	TCAGAGGTCTGTATCTTCTCTCTTG	59.115	44.000	6.87	0.00	44.12	3.02
2369	11446	1.975660	TGTTCCGCTAACAGCCTTTT	58.024	45.000	0.00	0.00	43.22	2.27
2428	11530	1.816835	CAGTGGCAAACTCATCTGCAT	59.183	47.619	0.00	0.00	40.46	3.96
2526	11661	0.320771	AATCACACACGAGGACCAGC	60.321	55.000	0.00	0.00	0.00	4.85
2544	11679	8.677300	GTCATGTCTAAATTATCAGAGGCAAAA	58.323	33.333	0.00	0.00	0.00	2.44
2603	11738	1.539712	CGCTCTGCTGCCATCTTATCA	60.540	52.381	0.00	0.00	0.00	2.15
2710	11853	4.667573	TGCACATTTTGGTACCCTCATAA	58.332	39.130	10.07	0.00	0.00	1.90
2854	12000	5.008217	CGAAGAGTAGAGACCTAGTCCATTG	59.992	48.000	0.00	0.00	43.29	2.82
2906	12052	3.935203	AGTTCTCTGTTTCGCATACCATG	59.065	43.478	0.00	0.00	0.00	3.66
2915	12061	1.795286	GTCCAGCAGTTCTCTGTTTCG	59.205	52.381	0.00	0.00	43.05	3.46
2928	12074	6.438186	TGATCTATTATGAATGGTCCAGCA	57.562	37.500	0.00	0.00	0.00	4.41
3028	12174	2.674220	GGACAAGGAGCAGGGGAGG	61.674	68.421	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.