AutoCloner

Multiple sequence alignment - TraesCS5B01G458200

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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	TraesCS5B01G458200	chr5B	100.000	2462	0	0	1	2462	633170449	633172910	0.000000e+00	4547.0
1	TraesCS5B01G458200	chr5B	88.757	1263	85	31	943	2168	629926350	629925108	0.000000e+00	1493.0
2	TraesCS5B01G458200	chr5B	91.966	946	56	9	916	1843	628724436	628723493	0.000000e+00	1308.0
3	TraesCS5B01G458200	chr5B	85.577	1248	90	48	708	1916	629953399	629952203	0.000000e+00	1225.0
4	TraesCS5B01G458200	chr5B	94.894	705	27	8	12	710	625134702	625134001	0.000000e+00	1094.0
5	TraesCS5B01G458200	chr5B	94.468	705	30	7	12	710	628725356	628724655	0.000000e+00	1077.0
6	TraesCS5B01G458200	chr5B	88.143	894	77	18	940	1815	611677696	611678578	0.000000e+00	1037.0
7	TraesCS5B01G458200	chr5B	85.955	1011	82	30	945	1899	649498496	649499502	0.000000e+00	1026.0
8	TraesCS5B01G458200	chr5B	86.561	759	69	17	723	1458	639671347	639670599	0.000000e+00	806.0
9	TraesCS5B01G458200	chr5B	92.070	227	17	1	485	710	629953675	629953449	3.950000e-83	318.0
10	TraesCS5B01G458200	chr5B	93.642	173	10	1	708	879	625133952	625133780	8.740000e-65	257.0
11	TraesCS5B01G458200	chr5B	93.064	173	10	2	708	879	628724606	628724435	4.060000e-63	252.0
12	TraesCS5B01G458200	chr5B	76.585	568	64	26	1394	1899	649694845	649695405	5.260000e-62	248.0
13	TraesCS5B01G458200	chr5B	93.617	141	7	2	2164	2303	625130293	625130154	2.480000e-50	209.0
14	TraesCS5B01G458200	chr5B	83.197	244	26	11	708	938	649694182	649694423	2.480000e-50	209.0
15	TraesCS5B01G458200	chr5B	92.908	141	7	2	2164	2303	628722667	628722529	4.150000e-48	202.0
16	TraesCS5B01G458200	chr5B	92.199	141	10	1	2164	2303	629925038	629924898	5.370000e-47	198.0
17	TraesCS5B01G458200	chr5B	82.377	244	28	11	708	938	649498300	649498541	5.370000e-47	198.0
18	TraesCS5B01G458200	chr5B	96.774	62	2	0	2293	2354	625130140	625130079	1.200000e-18	104.0
19	TraesCS5B01G458200	chr5B	96.774	62	2	0	2293	2354	628722515	628722454	1.200000e-18	104.0
20	TraesCS5B01G458200	chr5B	96.667	60	1	1	2293	2351	629924855	629924796	5.600000e-17	99.0
21	TraesCS5B01G458200	chr5A	89.964	2212	138	46	12	2168	625714448	625716630	0.000000e+00	2778.0
22	TraesCS5B01G458200	chr5A	84.843	1082	88	44	774	1819	619344064	619345105	0.000000e+00	1020.0
23	TraesCS5B01G458200	chr5A	83.725	1149	111	42	708	1817	644310197	644311308	0.000000e+00	1016.0
24	TraesCS5B01G458200	chr5A	98.305	59	1	0	2164	2222	625716696	625716754	1.200000e-18	104.0
25	TraesCS5B01G458200	chr5D	92.244	851	50	8	943	1777	501450067	501449217	0.000000e+00	1192.0
26	TraesCS5B01G458200	chr5D	86.473	998	80	32	776	1757	495199783	495200741	0.000000e+00	1044.0
27	TraesCS5B01G458200	chr5D	93.520	679	28	8	902	1569	296965032	296965705	0.000000e+00	996.0
28	TraesCS5B01G458200	chr5D	91.832	453	32	4	157	606	296959673	296960123	5.780000e-176	627.0
29	TraesCS5B01G458200	chr5D	90.578	329	20	4	1600	1918	296965702	296966029	2.260000e-115	425.0
30	TraesCS5B01G458200	chr5D	93.130	262	11	5	12	267	501450776	501450516	6.430000e-101	377.0
31	TraesCS5B01G458200	chr5D	92.887	239	6	4	1931	2166	296998070	296998300	1.090000e-88	337.0
32	TraesCS5B01G458200	chr5D	95.000	200	9	1	512	710	501450511	501450312	1.840000e-81	313.0
33	TraesCS5B01G458200	chr5D	93.467	199	12	1	708	905	296963445	296963643	6.660000e-76	294.0
34	TraesCS5B01G458200	chr5D	92.537	201	11	4	708	904	501450263	501450063	4.010000e-73	285.0
35	TraesCS5B01G458200	chr5D	88.312	231	18	4	1935	2163	517307078	517307301	4.040000e-68	268.0
36	TraesCS5B01G458200	chr5D	83.221	149	12	3	1764	1899	517214144	517214292	9.240000e-25	124.0
37	TraesCS5B01G458200	chr5D	96.429	56	1	1	12	66	296959619	296959674	9.380000e-15	91.6
38	TraesCS5B01G458200	chr5D	100.000	32	0	0	1916	1947	296966303	296966334	2.640000e-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	TraesCS5B01G458200	chr5B	633170449	633172910	2461	False	4547.000000	4547	100.000000	1	2462	1	chr5B.!!$F2	2461
1	TraesCS5B01G458200	chr5B	611677696	611678578	882	False	1037.000000	1037	88.143000	940	1815	1	chr5B.!!$F1	875
2	TraesCS5B01G458200	chr5B	639670599	639671347	748	True	806.000000	806	86.561000	723	1458	1	chr5B.!!$R1	735
3	TraesCS5B01G458200	chr5B	629952203	629953675	1472	True	771.500000	1225	88.823500	485	1916	2	chr5B.!!$R5	1431
4	TraesCS5B01G458200	chr5B	649498300	649499502	1202	False	612.000000	1026	84.166000	708	1899	2	chr5B.!!$F3	1191
5	TraesCS5B01G458200	chr5B	629924796	629926350	1554	True	596.666667	1493	92.541000	943	2351	3	chr5B.!!$R4	1408
6	TraesCS5B01G458200	chr5B	628722454	628725356	2902	True	588.600000	1308	93.836000	12	2354	5	chr5B.!!$R3	2342
7	TraesCS5B01G458200	chr5B	625130079	625134702	4623	True	416.000000	1094	94.731750	12	2354	4	chr5B.!!$R2	2342
8	TraesCS5B01G458200	chr5B	649694182	649695405	1223	False	228.500000	248	79.891000	708	1899	2	chr5B.!!$F4	1191
9	TraesCS5B01G458200	chr5A	625714448	625716754	2306	False	1441.000000	2778	94.134500	12	2222	2	chr5A.!!$F3	2210
10	TraesCS5B01G458200	chr5A	619344064	619345105	1041	False	1020.000000	1020	84.843000	774	1819	1	chr5A.!!$F1	1045
11	TraesCS5B01G458200	chr5A	644310197	644311308	1111	False	1016.000000	1016	83.725000	708	1817	1	chr5A.!!$F2	1109
12	TraesCS5B01G458200	chr5D	495199783	495200741	958	False	1044.000000	1044	86.473000	776	1757	1	chr5D.!!$F2	981
13	TraesCS5B01G458200	chr5D	501449217	501450776	1559	True	541.750000	1192	93.227750	12	1777	4	chr5D.!!$R1	1765
14	TraesCS5B01G458200	chr5D	296959619	296966334	6715	False	415.633333	996	94.304333	12	1947	6	chr5D.!!$F5	1935

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
386	400	0.034896	CAGGCGTGTTCCTGTTACCT	59.965	55.0	0.0	0.0	46.59	3.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1741	8920	0.178953	ACTGCAGGTTTGGGATGCTT	60.179	50.0	19.93	0.0	40.62	3.91	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
108	115	5.719173	ACTACACTCAAAAGCAAAAGCAAA	58.281	33.333	0.00	0.00	0.00	3.68
112	119	5.063817	ACACTCAAAAGCAAAAGCAAACATC	59.936	36.000	0.00	0.00	0.00	3.06
198	209	3.689347	TGTGCATGAAGGTGCTTATTCT	58.311	40.909	0.00	0.00	45.27	2.40
386	400	0.034896	CAGGCGTGTTCCTGTTACCT	59.965	55.000	0.00	0.00	46.59	3.08
394	408	5.616204	GCGTGTTCCTGTTACCTGTTATTTC	60.616	44.000	0.00	0.00	0.00	2.17
492	507	4.725359	ACTGTTTCACACGGTTTTTACAC	58.275	39.130	0.00	0.00	43.05	2.90
635	3824	2.962421	GTGGTTTCATTCCTTGACCCAA	59.038	45.455	0.00	0.00	37.36	4.12
687	3877	9.921637	GTGAAAAACCTTGTATCCAAATAATGA	57.078	29.630	0.00	0.00	0.00	2.57
694	3884	6.660949	CCTTGTATCCAAATAATGATCCCCTC	59.339	42.308	0.00	0.00	0.00	4.30
833	4079	4.129737	CCTGTGGTCGCGGATCGT	62.130	66.667	6.13	0.00	39.67	3.73
938	5578	0.531532	ATCGCCAAATCTCTCCGCAG	60.532	55.000	0.00	0.00	0.00	5.18
988	5656	1.447945	TCGCGCCAAATCTCAAATCA	58.552	45.000	0.00	0.00	0.00	2.57
1092	5770	1.612442	TAGGAAGAAGGCGGTGGCT	60.612	57.895	0.00	0.00	41.24	4.75
1095	5773	3.296709	GAAGAAGGCGGTGGCTCGA	62.297	63.158	5.12	0.00	37.50	4.04
1387	8448	1.228429	CCCAACATCAACCCCGTGT	60.228	57.895	0.00	0.00	0.00	4.49
1472	8599	6.406624	CCCAAGAAGGCTTAGTCGATTACTAA	60.407	42.308	0.00	0.00	41.10	2.24
1540	8673	9.703892	GTTGATATAGTATGATCTGTTCTGCTT	57.296	33.333	0.00	0.00	0.00	3.91
1542	8675	9.702494	TGATATAGTATGATCTGTTCTGCTTTG	57.298	33.333	0.00	0.00	0.00	2.77
1716	8882	8.218488	ACTTGGTCTGGTTATTAGAAAAACTCT	58.782	33.333	0.00	0.00	38.28	3.24
1741	8920	1.202639	TGCAAGCTGAAGAAACCGAGA	60.203	47.619	0.00	0.00	0.00	4.04
1757	8960	0.813821	GAGAAGCATCCCAAACCTGC	59.186	55.000	0.00	0.00	36.15	4.85
1761	8964	0.896940	AGCATCCCAAACCTGCAGTG	60.897	55.000	13.81	6.81	38.37	3.66
1819	9026	1.754226	ACCAAATGCCAACGTTTCACT	59.246	42.857	0.00	0.00	32.57	3.41
1982	9500	5.278463	GCAAGATTAACAAGTCAAGGAGCAA	60.278	40.000	0.00	0.00	0.00	3.91
1988	9506	1.351017	CAAGTCAAGGAGCAACCCCTA	59.649	52.381	0.00	0.00	40.05	3.53
1993	9511	0.038310	AAGGAGCAACCCCTAACTGC	59.962	55.000	0.00	0.00	40.05	4.40
2007	9525	4.375272	CCTAACTGCAGTCATGTATGAGG	58.625	47.826	21.95	12.18	37.51	3.86
2012	9530	3.099141	TGCAGTCATGTATGAGGTCAGA	58.901	45.455	4.42	0.00	37.51	3.27
2013	9531	3.515104	TGCAGTCATGTATGAGGTCAGAA	59.485	43.478	4.42	0.00	37.51	3.02
2014	9532	4.162888	TGCAGTCATGTATGAGGTCAGAAT	59.837	41.667	4.42	0.00	37.51	2.40
2015	9533	5.121811	GCAGTCATGTATGAGGTCAGAATT	58.878	41.667	4.42	0.00	37.51	2.17
2016	9534	5.236047	GCAGTCATGTATGAGGTCAGAATTC	59.764	44.000	0.00	0.00	37.51	2.17
2017	9535	6.343703	CAGTCATGTATGAGGTCAGAATTCA	58.656	40.000	8.44	0.00	37.51	2.57
2031	9549	6.481644	GGTCAGAATTCAGATACACTGGAATC	59.518	42.308	8.44	0.00	45.76	2.52
2092	9610	3.316308	GCTTATGCAGGAGTAATGGGTTG	59.684	47.826	0.00	0.00	39.41	3.77
2124	9644	7.334844	AGATCACTACATTCGAGAACATGTA	57.665	36.000	0.00	7.31	35.24	2.29
2125	9645	7.772166	AGATCACTACATTCGAGAACATGTAA	58.228	34.615	0.00	0.00	35.84	2.41
2153	9673	6.712095	TGTTGCTTGATGACTGAATAAGTTCT	59.288	34.615	0.00	0.00	40.07	3.01
2437	10719	9.631257	TTGGCTCAAAATAGATTATCAAGATGA	57.369	29.630	0.00	0.00	0.00	2.92
2438	10720	9.803507	TGGCTCAAAATAGATTATCAAGATGAT	57.196	29.630	0.00	0.00	40.72	2.45
2458	10740	9.698309	AGATGATATATAACATAATAGGCGCAC	57.302	33.333	10.83	0.00	0.00	5.34
2459	10741	9.476202	GATGATATATAACATAATAGGCGCACA	57.524	33.333	10.83	0.00	0.00	4.57
2460	10742	8.642908	TGATATATAACATAATAGGCGCACAC	57.357	34.615	10.83	0.00	0.00	3.82
2461	10743	7.709182	TGATATATAACATAATAGGCGCACACC	59.291	37.037	10.83	0.00	0.00	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.798776	AGGCATCGTCTTTCGCTTTG	59.201	50.000	0.00	0.00	39.67	2.77
1	2	1.523758	AAGGCATCGTCTTTCGCTTT	58.476	45.000	0.00	0.00	39.67	3.51
2	3	2.380084	TAAGGCATCGTCTTTCGCTT	57.620	45.000	0.00	0.00	39.67	4.68
3	4	2.101582	AGATAAGGCATCGTCTTTCGCT	59.898	45.455	0.00	0.00	38.81	4.93
4	5	2.474816	AGATAAGGCATCGTCTTTCGC	58.525	47.619	0.00	0.00	38.81	4.70
5	6	5.692204	ACATAAGATAAGGCATCGTCTTTCG	59.308	40.000	3.96	0.19	38.81	3.46
6	7	8.764524	ATACATAAGATAAGGCATCGTCTTTC	57.235	34.615	3.96	0.00	38.81	2.62
7	8	9.561069	AAATACATAAGATAAGGCATCGTCTTT	57.439	29.630	3.96	0.00	38.81	2.52
8	9	8.993121	CAAATACATAAGATAAGGCATCGTCTT	58.007	33.333	4.08	4.08	38.81	3.01
9	10	7.604164	CCAAATACATAAGATAAGGCATCGTCT	59.396	37.037	0.00	0.00	38.81	4.18
10	11	7.602644	TCCAAATACATAAGATAAGGCATCGTC	59.397	37.037	0.00	0.00	38.81	4.20
42	47	8.772250	TCTATCTTTGTGATCCATTTCTTACCT	58.228	33.333	0.00	0.00	36.65	3.08
108	115	3.771577	AACAAGAAAGAGTCGGGATGT	57.228	42.857	0.00	0.00	0.00	3.06
112	119	2.221055	CGTCAAACAAGAAAGAGTCGGG	59.779	50.000	0.00	0.00	0.00	5.14
198	209	7.974501	TGAACACTAAACGAAAATAAAAAGGCA	59.025	29.630	0.00	0.00	0.00	4.75
246	257	5.642063	TCCGTACTTTAGGCTTGAATTTCTG	59.358	40.000	0.00	0.00	0.00	3.02
394	408	7.542025	AGCCTTTTGTATCTCAAATAGCTTTG	58.458	34.615	0.00	0.00	44.64	2.77
687	3877	1.222567	AACCCATAAAGCGAGGGGAT	58.777	50.000	12.22	0.00	43.55	3.85
694	3884	2.442413	TGGAAGGAAACCCATAAAGCG	58.558	47.619	0.00	0.00	0.00	4.68
954	5596	0.882042	CGCGATGGGGGATTTCAGAG	60.882	60.000	0.00	0.00	0.00	3.35
988	5656	2.786495	CGTCCATGGCGGCTAGAGT	61.786	63.158	17.50	0.00	33.14	3.24
1074	5752	1.612442	AGCCACCGCCTTCTTCCTA	60.612	57.895	0.00	0.00	34.57	2.94
1387	8448	1.374947	CCGTCTTCTTGGGGAGCAA	59.625	57.895	0.00	0.00	0.00	3.91
1472	8599	8.009974	GCGAACATTAATTCTATTACGAAGCAT	58.990	33.333	0.00	0.00	0.00	3.79
1491	8618	5.472137	ACACCATTACTTAAACAGCGAACAT	59.528	36.000	0.00	0.00	0.00	2.71
1588	8722	1.662629	CATGAACAGACGGATGACAGC	59.337	52.381	0.00	0.00	0.00	4.40
1716	8882	2.358898	GGTTTCTTCAGCTTGCAACTCA	59.641	45.455	0.00	0.00	0.00	3.41
1741	8920	0.178953	ACTGCAGGTTTGGGATGCTT	60.179	50.000	19.93	0.00	40.62	3.91
1757	8960	1.143305	CTGAACCTGAACTCGCACTG	58.857	55.000	0.00	0.00	0.00	3.66
1761	8964	2.086054	ATGTCTGAACCTGAACTCGC	57.914	50.000	0.00	0.00	0.00	5.03
1819	9026	2.221169	CAGCAGCTGGACAAAGTACAA	58.779	47.619	17.12	0.00	0.00	2.41
1982	9500	1.362224	ACATGACTGCAGTTAGGGGT	58.638	50.000	24.49	15.55	0.00	4.95
1988	9506	3.261643	TGACCTCATACATGACTGCAGTT	59.738	43.478	22.65	7.48	32.50	3.16
1993	9511	6.343703	TGAATTCTGACCTCATACATGACTG	58.656	40.000	7.05	0.00	32.50	3.51
2007	9525	7.271511	AGATTCCAGTGTATCTGAATTCTGAC	58.728	38.462	16.26	7.11	46.27	3.51
2012	9530	7.682787	ACCTAGATTCCAGTGTATCTGAATT	57.317	36.000	12.79	0.00	46.27	2.17
2013	9531	7.345653	TGAACCTAGATTCCAGTGTATCTGAAT	59.654	37.037	12.79	3.90	46.27	2.57
2014	9532	6.667848	TGAACCTAGATTCCAGTGTATCTGAA	59.332	38.462	12.79	0.00	46.27	3.02
2015	9533	6.194967	TGAACCTAGATTCCAGTGTATCTGA	58.805	40.000	12.79	0.00	46.27	3.27
2016	9534	6.322456	TCTGAACCTAGATTCCAGTGTATCTG	59.678	42.308	12.79	3.18	43.27	2.90
2017	9535	6.322712	GTCTGAACCTAGATTCCAGTGTATCT	59.677	42.308	0.00	9.26	33.68	1.98
2092	9610	5.161358	TCGAATGTAGTGATCTTGTGACAC	58.839	41.667	0.00	0.00	35.15	3.67
2124	9644	5.717078	ATTCAGTCATCAAGCAACATGTT	57.283	34.783	4.92	4.92	0.00	2.71
2125	9645	6.432162	ACTTATTCAGTCATCAAGCAACATGT	59.568	34.615	0.00	0.00	0.00	3.21
2153	9673	3.313249	CACTGAAACAGAGATGTGCAACA	59.687	43.478	5.76	0.00	42.99	3.33
2223	10450	4.595986	TCAAAAGTTATACCCCTTCCTGC	58.404	43.478	0.00	0.00	0.00	4.85
2411	10693	9.631257	TCATCTTGATAATCTATTTTGAGCCAA	57.369	29.630	0.00	0.00	0.00	4.52
2412	10694	9.803507	ATCATCTTGATAATCTATTTTGAGCCA	57.196	29.630	0.00	0.00	34.88	4.75
2432	10714	9.698309	GTGCGCCTATTATGTTATATATCATCT	57.302	33.333	4.18	3.00	0.00	2.90
2433	10715	9.476202	TGTGCGCCTATTATGTTATATATCATC	57.524	33.333	4.18	0.00	0.00	2.92
2434	10716	9.261180	GTGTGCGCCTATTATGTTATATATCAT	57.739	33.333	4.18	10.42	0.00	2.45
2435	10717	7.709182	GGTGTGCGCCTATTATGTTATATATCA	59.291	37.037	4.18	0.00	0.00	2.15
2436	10718	8.073355	GGTGTGCGCCTATTATGTTATATATC	57.927	38.462	4.18	0.00	0.00	1.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.