AutoCloner

Multiple sequence alignment - TraesCS4A01G488500

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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	TraesCS4A01G488500	chr4A	100.000	2852	0	0	1	2852	740064767	740067618	0.000000e+00	5267.0
1	TraesCS4A01G488500	chr4A	87.727	1100	102	12	759	1850	733931161	733932235	0.000000e+00	1253.0
2	TraesCS4A01G488500	chr4A	88.254	928	95	7	924	1850	739828888	739827974	0.000000e+00	1098.0
3	TraesCS4A01G488500	chr4A	84.567	1121	140	14	759	1865	742273777	742274878	0.000000e+00	1081.0
4	TraesCS4A01G488500	chr4A	90.039	773	36	18	1	764	739829844	739829104	0.000000e+00	963.0
5	TraesCS4A01G488500	chr4A	82.932	1037	140	22	985	2004	740872978	740873994	0.000000e+00	900.0
6	TraesCS4A01G488500	chr4A	83.867	781	69	19	1	761	742272991	742273734	0.000000e+00	691.0
7	TraesCS4A01G488500	chr4A	83.877	521	46	19	1	521	733930482	733930964	2.000000e-126	462.0
8	TraesCS4A01G488500	chr4A	89.773	88	6	3	582	667	733930963	733931049	3.000000e-20	110.0
9	TraesCS4A01G488500	chr7A	89.306	879	92	1	989	1865	2570634	2571512	0.000000e+00	1101.0
10	TraesCS4A01G488500	chr7A	84.375	1024	127	20	989	2004	2859953	2860951	0.000000e+00	974.0
11	TraesCS4A01G488500	chr7A	81.363	939	110	36	945	1847	3007832	3008741	0.000000e+00	704.0
12	TraesCS4A01G488500	chr7A	81.385	881	134	12	985	1856	3324663	3323804	0.000000e+00	691.0
13	TraesCS4A01G488500	chr7A	92.308	65	3	1	2	66	2569626	2569688	1.090000e-14	91.6
14	TraesCS4A01G488500	chr7A	89.062	64	4	2	4	67	2856708	2856768	3.050000e-10	76.8
15	TraesCS4A01G488500	chr7D	89.294	878	93	1	989	1865	3740582	3741459	0.000000e+00	1099.0
16	TraesCS4A01G488500	chr7D	80.470	1234	173	37	819	2032	3435229	3434044	0.000000e+00	881.0
17	TraesCS4A01G488500	chr7D	83.333	186	28	3	1584	1767	28884302	28884118	4.890000e-38	169.0
18	TraesCS4A01G488500	chr7D	89.394	66	4	2	2	67	3739662	3739724	2.360000e-11	80.5
19	TraesCS4A01G488500	chr5B	86.853	251	30	3	2337	2585	485664653	485664902	7.780000e-71	278.0
20	TraesCS4A01G488500	chr5B	89.552	67	7	0	2347	2413	485664897	485664831	5.060000e-13	86.1
21	TraesCS4A01G488500	chrUn	83.243	185	30	1	1584	1767	90469202	90469386	4.890000e-38	169.0
22	TraesCS4A01G488500	chr2D	82.353	136	23	1	2423	2557	615472362	615472497	1.800000e-22	117.0
23	TraesCS4A01G488500	chr6D	96.875	32	1	0	2368	2399	94779696	94779665	1.000000e-03	54.7

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	TraesCS4A01G488500	chr4A	740064767	740067618	2851	False	5267.000000	5267	100.000000	1	2852	1	chr4A.!!$F1	2851
1	TraesCS4A01G488500	chr4A	739827974	739829844	1870	True	1030.500000	1098	89.146500	1	1850	2	chr4A.!!$R1	1849
2	TraesCS4A01G488500	chr4A	740872978	740873994	1016	False	900.000000	900	82.932000	985	2004	1	chr4A.!!$F2	1019
3	TraesCS4A01G488500	chr4A	742272991	742274878	1887	False	886.000000	1081	84.217000	1	1865	2	chr4A.!!$F4	1864
4	TraesCS4A01G488500	chr4A	733930482	733932235	1753	False	608.333333	1253	87.125667	1	1850	3	chr4A.!!$F3	1849
5	TraesCS4A01G488500	chr7A	3007832	3008741	909	False	704.000000	704	81.363000	945	1847	1	chr7A.!!$F1	902
6	TraesCS4A01G488500	chr7A	3323804	3324663	859	True	691.000000	691	81.385000	985	1856	1	chr7A.!!$R1	871
7	TraesCS4A01G488500	chr7A	2569626	2571512	1886	False	596.300000	1101	90.807000	2	1865	2	chr7A.!!$F2	1863
8	TraesCS4A01G488500	chr7A	2856708	2860951	4243	False	525.400000	974	86.718500	4	2004	2	chr7A.!!$F3	2000
9	TraesCS4A01G488500	chr7D	3434044	3435229	1185	True	881.000000	881	80.470000	819	2032	1	chr7D.!!$R1	1213
10	TraesCS4A01G488500	chr7D	3739662	3741459	1797	False	589.750000	1099	89.344000	2	1865	2	chr7D.!!$F1	1863

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
563	3237	0.392193	AAGGCGAGCATCCTGTTCTG	60.392	55.0	0.0	0.0	33.43	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2561	5416	0.032267	GTATCTGGTGCTACCGAGGC	59.968	60.0	0.0	0.0	42.58	4.7	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
50	51	3.243401	GGACACAAGTAAAGTTGGCAAGG	60.243	47.826	0.00	0.00	0.00	3.61
107	108	4.499019	GCATGCATGATTGACATCACATCA	60.499	41.667	30.64	8.30	42.46	3.07
108	109	5.772521	CATGCATGATTGACATCACATCAT	58.227	37.500	22.59	10.93	42.46	2.45
110	111	4.037446	TGCATGATTGACATCACATCATGG	59.963	41.667	26.71	17.92	42.46	3.66
111	112	4.546570	CATGATTGACATCACATCATGGC	58.453	43.478	22.89	0.00	42.46	4.40
112	113	2.953648	TGATTGACATCACATCATGGCC	59.046	45.455	0.00	0.00	34.22	5.36
143	162	3.648339	TGCATGAACTTTGCTCCTTTC	57.352	42.857	0.00	0.00	40.77	2.62
242	297	1.712056	TCGAGGAAAGGTGTGGAAGA	58.288	50.000	0.00	0.00	0.00	2.87
390	599	2.738846	ACATCAGTACGCTCAAAGCAAG	59.261	45.455	0.00	0.00	42.58	4.01
434	701	9.612620	GATAGTGTTCCACAATAACAAAGAAAG	57.387	33.333	0.00	0.00	38.50	2.62
450	717	4.374689	AGAAAGAGAAAAGGGAAGGGTC	57.625	45.455	0.00	0.00	0.00	4.46
458	725	4.835056	AGAAAAGGGAAGGGTCATTCTTTG	59.165	41.667	0.00	0.00	0.00	2.77
467	734	4.411013	AGGGTCATTCTTTGGGAAAAGAG	58.589	43.478	1.59	0.00	39.65	2.85
468	735	4.106341	AGGGTCATTCTTTGGGAAAAGAGA	59.894	41.667	1.59	0.00	39.65	3.10
469	736	4.832823	GGGTCATTCTTTGGGAAAAGAGAA	59.167	41.667	1.59	0.00	39.65	2.87
470	737	5.047731	GGGTCATTCTTTGGGAAAAGAGAAG	60.048	44.000	1.59	0.00	39.65	2.85
471	738	5.465051	GTCATTCTTTGGGAAAAGAGAAGC	58.535	41.667	1.59	0.00	39.65	3.86
548	3217	7.655521	ATTCTTGGGGTAAGTAAATTAAGGC	57.344	36.000	0.00	0.00	37.65	4.35
562	3236	1.195115	TAAGGCGAGCATCCTGTTCT	58.805	50.000	0.00	0.00	33.43	3.01
563	3237	0.392193	AAGGCGAGCATCCTGTTCTG	60.392	55.000	0.00	0.00	33.43	3.02
564	3238	1.078848	GGCGAGCATCCTGTTCTGT	60.079	57.895	0.00	0.00	0.00	3.41
565	3239	0.674895	GGCGAGCATCCTGTTCTGTT	60.675	55.000	0.00	0.00	0.00	3.16
566	3240	0.723981	GCGAGCATCCTGTTCTGTTC	59.276	55.000	0.00	0.00	0.00	3.18
589	3263	3.328382	TGCTTCGCTAGTACAAATGGT	57.672	42.857	0.00	0.00	0.00	3.55
603	3277	2.138596	AATGGTGCACTGCTTTTTCG	57.861	45.000	17.98	0.00	0.00	3.46

Showing 1 to 25 of 670 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	0.939419	CAAAAGCAAAAGCCCAGCAC	59.061	50.000	0.00	0.00	0.00	4.40
107	108	2.438975	CATGCACGGTCAGGCCAT	60.439	61.111	5.01	0.00	36.97	4.40
110	111	3.136123	ATGCATGCACGGTCAGGC	61.136	61.111	25.37	8.52	43.30	4.85
111	112	1.307355	TTCATGCATGCACGGTCAGG	61.307	55.000	25.37	0.00	0.00	3.86
112	113	0.179181	GTTCATGCATGCACGGTCAG	60.179	55.000	25.37	9.01	0.00	3.51
143	162	2.950309	CAGGAATGATGCTTCCCTTCTG	59.050	50.000	0.00	0.00	44.93	3.02
242	297	4.401925	CTTGTTCCTTTGATCAAGTCCCT	58.598	43.478	8.41	0.00	40.82	4.20
377	582	0.890542	TGCCATCTTGCTTTGAGCGT	60.891	50.000	0.00	0.00	46.26	5.07
390	599	5.747197	CACTATCATTTCAAGCTTTGCCATC	59.253	40.000	0.00	0.00	0.00	3.51
434	701	4.308526	AGAATGACCCTTCCCTTTTCTC	57.691	45.455	0.00	0.00	0.00	2.87
450	717	5.225642	GTGCTTCTCTTTTCCCAAAGAATG	58.774	41.667	0.00	0.00	46.35	2.67
458	725	1.270893	ACTCGGTGCTTCTCTTTTCCC	60.271	52.381	0.00	0.00	0.00	3.97
469	736	0.671781	CAGCAAAGCTACTCGGTGCT	60.672	55.000	0.00	0.00	46.16	4.40
470	737	1.639298	CCAGCAAAGCTACTCGGTGC	61.639	60.000	0.00	0.00	36.40	5.01
471	738	0.320771	ACCAGCAAAGCTACTCGGTG	60.321	55.000	0.00	0.00	36.40	4.94
548	3217	1.066573	AGGAACAGAACAGGATGCTCG	60.067	52.381	0.00	0.00	42.53	5.03
668	3352	1.468520	CTGATAACCCAACACAAGCCG	59.531	52.381	0.00	0.00	0.00	5.52
706	3398	1.651240	CCCACAAGGCAAGCGATCTG	61.651	60.000	0.00	0.00	0.00	2.90
780	3517	1.615392	GTTGCAGCAAACCCAGATTCT	59.385	47.619	10.11	0.00	0.00	2.40
814	3551	8.954950	ATCATAACAGAGGTGAGATTAAGTTG	57.045	34.615	0.00	0.00	0.00	3.16
827	3564	5.282055	TCAGCTGGTTATCATAACAGAGG	57.718	43.478	15.13	2.38	32.86	3.69
883	3620	4.418392	CTTGCAAATTGTGTCTATCTGGC	58.582	43.478	0.00	0.00	0.00	4.85
915	3654	0.810031	GTGTGTGTGTGTCGAAGCCT	60.810	55.000	0.00	0.00	0.00	4.58
1110	3900	4.828939	AGCTTGGATTTGATGAACTTGACA	59.171	37.500	0.00	0.00	0.00	3.58
1351	4144	0.606401	CACCGGCCTGACACTTCATT	60.606	55.000	0.00	0.00	0.00	2.57

Showing 1 to 25 of 672 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.