AutoCloner

Multiple sequence alignment - TraesCS1D01G153500

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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	TraesCS1D01G153500	chr1D	100.000	5038	0	0	1	5038	212725466	212720429	0.000000e+00	9304.0
1	TraesCS1D01G153500	chr1D	81.915	188	21	6	4414	4594	212534108	212533927	4.060000e-31	147.0
2	TraesCS1D01G153500	chr1A	94.376	4072	158	31	405	4452	269583377	269579353	0.000000e+00	6185.0
3	TraesCS1D01G153500	chr1A	94.799	596	23	5	4444	5038	269575980	269575392	0.000000e+00	922.0
4	TraesCS1D01G153500	chr1A	92.665	409	26	3	1	408	269584102	269583697	2.020000e-163	586.0
5	TraesCS1D01G153500	chr1A	82.353	187	20	6	4414	4593	268937151	268936971	3.140000e-32	150.0
6	TraesCS1D01G153500	chr1A	89.888	89	2	3	759	840	508639816	508639728	1.920000e-19	108.0
7	TraesCS1D01G153500	chr1A	95.745	47	0	2	4337	4383	268937201	268937157	1.950000e-09	75.0
8	TraesCS1D01G153500	chr1B	97.715	3239	55	7	906	4137	302506800	302510026	0.000000e+00	5553.0
9	TraesCS1D01G153500	chr1B	93.384	922	34	9	4136	5038	302510106	302511019	0.000000e+00	1339.0
10	TraesCS1D01G153500	chr1B	93.821	793	43	4	1	791	302505995	302506783	0.000000e+00	1188.0
11	TraesCS1D01G153500	chr1B	95.706	326	6	1	1501	1826	10976720	10976403	7.480000e-143	518.0
12	TraesCS1D01G153500	chr5B	95.939	591	22	1	1238	1826	94271909	94271319	0.000000e+00	957.0
13	TraesCS1D01G153500	chrUn	100.000	394	0	0	2176	2569	479446559	479446166	0.000000e+00	728.0
14	TraesCS1D01G153500	chr5A	81.818	275	39	6	570	834	454773757	454773484	2.360000e-53	220.0
15	TraesCS1D01G153500	chr5A	91.954	87	2	1	759	840	502580771	502580685	3.190000e-22	117.0
16	TraesCS1D01G153500	chr6D	83.030	165	21	5	4661	4822	336845882	336846042	5.260000e-30	143.0
17	TraesCS1D01G153500	chr6D	88.119	101	5	3	746	840	407474679	407474580	4.120000e-21	113.0
18	TraesCS1D01G153500	chr3B	91.209	91	1	3	756	840	800696276	800696187	3.190000e-22	117.0
19	TraesCS1D01G153500	chr6B	90.000	90	2	3	746	829	611464825	611464737	5.330000e-20	110.0
20	TraesCS1D01G153500	chr4D	89.888	89	3	2	759	842	506899319	506899232	5.330000e-20	110.0
21	TraesCS1D01G153500	chr2B	83.607	122	11	5	726	839	766524081	766524201	6.900000e-19	106.0
22	TraesCS1D01G153500	chr3D	83.516	91	11	4	4685	4772	597211757	597211846	1.160000e-11	82.4

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	TraesCS1D01G153500	chr1D	212720429	212725466	5037	True	9304.000000	9304	100.000000	1	5038	1	chr1D.!!$R2	5037
1	TraesCS1D01G153500	chr1A	269575392	269584102	8710	True	2564.333333	6185	93.946667	1	5038	3	chr1A.!!$R3	5037
2	TraesCS1D01G153500	chr1B	302505995	302511019	5024	False	2693.333333	5553	94.973333	1	5038	3	chr1B.!!$F1	5037
3	TraesCS1D01G153500	chr5B	94271319	94271909	590	True	957.000000	957	95.939000	1238	1826	1	chr5B.!!$R1	588

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
641	988	0.179936	GGGAGAGCCATGAACTCTGG	59.820	60.000	19.29	0.00	44.50	3.86	F
998	1358	0.958382	TTTGGAAATGCCGGACCGAG	60.958	55.000	17.49	6.74	40.66	4.63	F
999	1359	1.832719	TTGGAAATGCCGGACCGAGA	61.833	55.000	17.49	0.57	40.66	4.04	F
1966	2328	2.086869	TGCAGAGAGTTTGCTTATGCC	58.913	47.619	0.00	0.00	42.02	4.40	F
3873	4244	1.270550	GCAACCCATGAAACTGTCAGG	59.729	52.381	4.53	0.00	40.43	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2569	2931	1.609061	GCTGCTAGCAGACTGTTCCAA	60.609	52.381	41.87	5.85	46.30	3.53	R
2822	3184	1.484240	AGCCAGTCTAGCATCCTCAAC	59.516	52.381	0.00	0.00	0.00	3.18	R
3370	3732	0.250467	ACTGGCTCTCAACGTGCAAT	60.250	50.000	0.00	0.00	33.89	3.56	R
3880	4251	1.288037	GGGAGGGGTTAAAGATGGCTT	59.712	52.381	0.00	0.00	35.37	4.35	R
4740	8594	0.618981	TGTCCGTCTCTAGCTCCTGA	59.381	55.000	0.00	0.00	0.00	3.86	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
266	268	6.453943	CATTGTCTATATGCTCTGTAGTGCT	58.546	40.000	7.36	0.00	35.73	4.40
267	269	7.597386	CATTGTCTATATGCTCTGTAGTGCTA	58.403	38.462	7.36	0.00	35.73	3.49
329	331	3.717913	ACTCCTTAGGGTGTGTTTGGTTA	59.282	43.478	0.00	0.00	37.85	2.85
330	332	4.166531	ACTCCTTAGGGTGTGTTTGGTTAA	59.833	41.667	0.00	0.00	37.85	2.01
331	333	5.163023	ACTCCTTAGGGTGTGTTTGGTTAAT	60.163	40.000	0.00	0.00	37.85	1.40
402	404	6.088541	TGGAAGTACTAACCAGGAGATACT	57.911	41.667	15.03	0.00	0.00	2.12
445	770	6.559810	TCGAAGAAAACAACAATGACATGTT	58.440	32.000	0.00	0.00	44.08	2.71
468	793	2.238646	GTGGGAGTCCAACCATGATGTA	59.761	50.000	12.30	0.00	46.04	2.29
480	806	9.527157	TCCAACCATGATGTAAATCTAAGAAAA	57.473	29.630	0.00	0.00	0.00	2.29
641	988	0.179936	GGGAGAGCCATGAACTCTGG	59.820	60.000	19.29	0.00	44.50	3.86
653	1000	2.306847	GAACTCTGGAAAAAGCCACCA	58.693	47.619	0.00	0.00	33.52	4.17
662	1009	3.244044	GGAAAAAGCCACCACATTGCTTA	60.244	43.478	0.00	0.00	44.11	3.09
691	1038	5.794687	TGTCGTTAATGCTGAATGGTAAG	57.205	39.130	0.00	0.00	0.00	2.34
823	1175	3.560534	GAGGTTCAAGCCCTCCTTC	57.439	57.895	0.00	0.00	42.29	3.46
829	1181	1.144936	CAAGCCCTCCTTCTAGCGG	59.855	63.158	0.00	0.00	0.00	5.52
830	1182	1.306226	AAGCCCTCCTTCTAGCGGT	60.306	57.895	0.00	0.00	0.00	5.68
846	1198	6.235664	TCTAGCGGTTTTCTTTTTATCACCT	58.764	36.000	0.00	0.00	0.00	4.00
853	1205	3.085952	TCTTTTTATCACCTGGCCCAG	57.914	47.619	2.91	2.91	0.00	4.45
875	1228	9.747293	CCCAGCATTTTGTTTTTGATAATTTTT	57.253	25.926	0.00	0.00	0.00	1.94
896	1249	1.975680	ACCGGGCCCAGTAATACATAG	59.024	52.381	24.92	0.00	0.00	2.23
897	1250	2.253610	CCGGGCCCAGTAATACATAGA	58.746	52.381	24.92	0.00	0.00	1.98
900	1253	4.099573	CCGGGCCCAGTAATACATAGATAG	59.900	50.000	24.92	0.00	0.00	2.08
903	1256	6.183360	CGGGCCCAGTAATACATAGATAGTAC	60.183	46.154	24.92	0.00	0.00	2.73
904	1257	6.666546	GGGCCCAGTAATACATAGATAGTACA	59.333	42.308	19.95	0.00	29.90	2.90
954	1307	1.765314	CCAAAACCCATGGTCCACAAA	59.235	47.619	11.73	0.00	33.12	2.83
998	1358	0.958382	TTTGGAAATGCCGGACCGAG	60.958	55.000	17.49	6.74	40.66	4.63
999	1359	1.832719	TTGGAAATGCCGGACCGAGA	61.833	55.000	17.49	0.57	40.66	4.04
1003	1363	3.665675	AATGCCGGACCGAGAGCAC	62.666	63.158	17.49	0.00	38.21	4.40
1415	1775	2.713967	GCCGTGGTAGGGAACGCTA	61.714	63.158	0.00	0.00	38.46	4.26
1966	2328	2.086869	TGCAGAGAGTTTGCTTATGCC	58.913	47.619	0.00	0.00	42.02	4.40
2569	2931	9.167311	GGAATCAGTAATAAGAATGTTGTCACT	57.833	33.333	0.00	0.00	0.00	3.41
2596	2958	3.244215	ACAGTCTGCTAGCAGCTTACAAA	60.244	43.478	35.21	16.87	42.97	2.83
2822	3184	7.461749	AGATATGTATGGGAAATGTGGTAAGG	58.538	38.462	0.00	0.00	0.00	2.69
2924	3286	5.583932	TGCTTCATAGGATGCCTAGAGATA	58.416	41.667	12.08	0.00	39.70	1.98
3370	3732	1.902765	ATGCCATGACAGAGCACGGA	61.903	55.000	4.43	0.00	39.77	4.69
3873	4244	1.270550	GCAACCCATGAAACTGTCAGG	59.729	52.381	4.53	0.00	40.43	3.86
3880	4251	4.144297	CCATGAAACTGTCAGGAAAAGGA	58.856	43.478	4.53	0.00	40.61	3.36
3915	4286	0.753111	CTCCCCTGGGCTGCAAATAC	60.753	60.000	7.39	0.00	34.68	1.89
4100	4474	2.198827	TACTGCTGATGGGTTGTTGG	57.801	50.000	0.00	0.00	0.00	3.77
4101	4475	0.185901	ACTGCTGATGGGTTGTTGGT	59.814	50.000	0.00	0.00	0.00	3.67
4102	4476	0.599558	CTGCTGATGGGTTGTTGGTG	59.400	55.000	0.00	0.00	0.00	4.17
4194	4649	2.682856	TGAATCGAAATGTTAGGCTGCC	59.317	45.455	11.65	11.65	0.00	4.85
4313	4770	0.456221	CAGGTCGGAGCTAATCGTGT	59.544	55.000	9.71	0.00	0.00	4.49
4399	4856	6.636705	TCGGTGTTATTTGCTAGTAGTTGAT	58.363	36.000	0.00	0.00	0.00	2.57
4447	4904	3.439476	CGGTTAAGAGACGGAGAGAGAAA	59.561	47.826	0.00	0.00	0.00	2.52
4456	8294	3.436243	ACGGAGAGAGAAAGGACAGAAT	58.564	45.455	0.00	0.00	0.00	2.40
4512	8364	4.894784	TCTTTAGTAGTTTGAGGCCACTG	58.105	43.478	5.01	0.00	0.00	3.66
4545	8397	5.357742	AACCTCATTTCCCCAAAATATGC	57.642	39.130	0.00	0.00	35.77	3.14
4725	8579	2.359850	GCTCCATCACGTTGGGCA	60.360	61.111	6.44	0.00	37.37	5.36
4740	8594	1.355381	TGGGCATCAATGAGACTGGTT	59.645	47.619	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	8.344098	CAATGGTTGTTGACTTTATTTTGCAAT	58.656	29.630	0.00	0.00	0.00	3.56
266	268	7.873910	CATATGAAACCATATGTGCACATGTA	58.126	34.615	36.72	21.97	44.28	2.29
267	269	6.741109	CATATGAAACCATATGTGCACATGT	58.259	36.000	36.72	29.69	44.28	3.21
300	302	2.165845	CACACCCTAAGGAGTAAGGACG	59.834	54.545	0.00	0.00	34.30	4.79
329	331	8.306038	TGCTTTGTTATGACTAATTTCAGCATT	58.694	29.630	0.00	0.00	0.00	3.56
330	332	7.829725	TGCTTTGTTATGACTAATTTCAGCAT	58.170	30.769	0.00	0.00	0.00	3.79
331	333	7.213216	TGCTTTGTTATGACTAATTTCAGCA	57.787	32.000	0.00	0.00	0.00	4.41
402	404	7.833786	TCTTCGAGGCACTAGTAAATTAAGAA	58.166	34.615	0.00	0.00	41.55	2.52
410	735	5.204409	TGTTTTCTTCGAGGCACTAGTAA	57.796	39.130	0.00	0.00	41.55	2.24
445	770	1.144691	TCATGGTTGGACTCCCACAA	58.855	50.000	1.87	0.00	43.41	3.33
480	806	9.347240	AGCTTGCTTACATTATGTCATCTTATT	57.653	29.630	0.00	0.00	0.00	1.40
494	820	2.584835	TGGTTGGAGCTTGCTTACAT	57.415	45.000	0.00	0.00	0.00	2.29
641	988	2.531522	AGCAATGTGGTGGCTTTTTC	57.468	45.000	0.00	0.00	33.21	2.29
662	1009	6.203530	CCATTCAGCATTAACGACATAGACAT	59.796	38.462	0.00	0.00	0.00	3.06
691	1038	3.578688	AGTTTCGCATCATTTCCAAAGC	58.421	40.909	0.00	0.00	0.00	3.51
820	1172	7.021790	GGTGATAAAAAGAAAACCGCTAGAAG	58.978	38.462	0.00	0.00	0.00	2.85
823	1175	6.314784	CAGGTGATAAAAAGAAAACCGCTAG	58.685	40.000	0.00	0.00	32.83	3.42
829	1181	4.039852	TGGGCCAGGTGATAAAAAGAAAAC	59.960	41.667	0.00	0.00	0.00	2.43
830	1182	4.227197	TGGGCCAGGTGATAAAAAGAAAA	58.773	39.130	0.00	0.00	0.00	2.29
846	1198	2.092753	TCAAAAACAAAATGCTGGGCCA	60.093	40.909	5.85	5.85	0.00	5.36
875	1228	2.106187	ATGTATTACTGGGCCCGGTA	57.894	50.000	35.66	35.66	36.80	4.02
880	1233	7.713734	TGTACTATCTATGTATTACTGGGCC	57.286	40.000	0.00	0.00	0.00	5.80
998	1358	0.809385	TGGCGTCAGTAGTAGTGCTC	59.191	55.000	0.00	0.00	0.00	4.26
999	1359	1.475403	ATGGCGTCAGTAGTAGTGCT	58.525	50.000	0.00	0.00	0.00	4.40
2039	2401	1.667595	TTGTCCATCCTCCCATCACA	58.332	50.000	0.00	0.00	0.00	3.58
2569	2931	1.609061	GCTGCTAGCAGACTGTTCCAA	60.609	52.381	41.87	5.85	46.30	3.53
2596	2958	6.067217	ACAACTTCTGGCTTCCTATTATGT	57.933	37.500	0.00	0.00	0.00	2.29
2822	3184	1.484240	AGCCAGTCTAGCATCCTCAAC	59.516	52.381	0.00	0.00	0.00	3.18
3370	3732	0.250467	ACTGGCTCTCAACGTGCAAT	60.250	50.000	0.00	0.00	33.89	3.56
3802	4164	1.463831	GCATATGAGCCAGCATTCTCG	59.536	52.381	6.97	0.00	32.20	4.04
3859	4230	5.766222	CTTCCTTTTCCTGACAGTTTCATG	58.234	41.667	0.93	0.00	32.17	3.07
3869	4240	3.814504	AAGATGGCTTCCTTTTCCTGA	57.185	42.857	0.00	0.00	0.00	3.86
3873	4244	4.081642	GGGGTTAAAGATGGCTTCCTTTTC	60.082	45.833	0.00	0.00	34.74	2.29
3880	4251	1.288037	GGGAGGGGTTAAAGATGGCTT	59.712	52.381	0.00	0.00	35.37	4.35
3915	4286	2.046892	CTCCCCTGAAGCACACCG	60.047	66.667	0.00	0.00	0.00	4.94
4022	4393	8.870116	ACTTACTGGATATCTGCACAATACATA	58.130	33.333	2.05	0.00	0.00	2.29
4023	4394	7.739825	ACTTACTGGATATCTGCACAATACAT	58.260	34.615	2.05	0.00	0.00	2.29
4024	4395	7.124573	ACTTACTGGATATCTGCACAATACA	57.875	36.000	2.05	0.00	0.00	2.29
4034	4405	8.924303	TGTACATGCTTTACTTACTGGATATCT	58.076	33.333	2.05	0.00	0.00	1.98
4100	4474	4.092821	TGCTTACATAACAGACGCAATCAC	59.907	41.667	0.00	0.00	0.00	3.06
4101	4475	4.249661	TGCTTACATAACAGACGCAATCA	58.750	39.130	0.00	0.00	0.00	2.57
4102	4476	4.857871	TGCTTACATAACAGACGCAATC	57.142	40.909	0.00	0.00	0.00	2.67
4194	4649	3.318839	TCAACAAAGTTGGCTGATTCCAG	59.681	43.478	9.72	0.00	43.22	3.86
4313	4770	8.882557	AACCATTATTCACCATATCATGCATA	57.117	30.769	0.00	0.00	0.00	3.14
4423	4880	2.352342	CTCTCTCCGTCTCTTAACCGAC	59.648	54.545	0.00	0.00	0.00	4.79
4447	4904	5.762179	TGGTGTTTCAGATATTCTGTCCT	57.238	39.130	4.56	0.00	44.58	3.85
4456	8294	4.513442	CCCGAAGAATGGTGTTTCAGATA	58.487	43.478	0.00	0.00	0.00	1.98
4498	8349	1.062488	AGGGACAGTGGCCTCAAACT	61.062	55.000	16.57	0.00	0.00	2.66
4512	8364	2.808906	AATGAGGTTTAGCCAGGGAC	57.191	50.000	0.00	0.00	40.61	4.46
4682	8534	5.425630	GACCGGAGACACCTGTATTTTTAT	58.574	41.667	9.46	0.00	36.26	1.40
4683	8535	4.322953	GGACCGGAGACACCTGTATTTTTA	60.323	45.833	9.46	0.00	36.26	1.52
4725	8579	3.370315	GCTCCTGAACCAGTCTCATTGAT	60.370	47.826	0.00	0.00	0.00	2.57
4740	8594	0.618981	TGTCCGTCTCTAGCTCCTGA	59.381	55.000	0.00	0.00	0.00	3.86
4898	8752	3.376859	TCGTGTTTGAAGCATGTTTGTCT	59.623	39.130	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.