AutoCloner

Multiple sequence alignment - TraesCS1B01G141800

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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	bitscore
0	TraesCS1B01G141800	chr1B	100.000	2639	0	0	1	2639	189587240	189589878	4874
1	TraesCS1B01G141800	chr7B	90.841	2653	217	19	1	2639	151132760	151130120	3530
2	TraesCS1B01G141800	chr7B	89.444	2662	228	22	1	2639	396280760	396278129	3310
3	TraesCS1B01G141800	chr7B	87.851	1745	194	14	904	2639	506241333	506239598	2032
4	TraesCS1B01G141800	chr7B	83.271	1327	197	24	649	1964	361254992	361256304	1197
5	TraesCS1B01G141800	chr1D	90.762	2652	218	26	1	2639	307650904	307648267	3515
6	TraesCS1B01G141800	chr1D	82.850	2105	313	38	1	2079	69098931	69101013	1844
7	TraesCS1B01G141800	chr1D	82.938	2110	295	53	1	2079	397992003	397994078	1842
8	TraesCS1B01G141800	chr6D	88.075	2675	270	35	1	2639	333794254	333791593	3127
9	TraesCS1B01G141800	chr6D	91.085	1346	98	11	147	1488	364247743	364246416	1801
10	TraesCS1B01G141800	chr6D	82.312	2024	313	32	1	2003	321241398	321239399	1712
11	TraesCS1B01G141800	chr2B	86.882	2668	288	31	1	2639	263700354	263702988	2931
12	TraesCS1B01G141800	chr4D	89.228	2358	220	26	301	2639	393474112	393471770	2916
13	TraesCS1B01G141800	chr4A	85.732	2432	298	35	165	2579	48884550	48882151	2523
14	TraesCS1B01G141800	chr2D	91.338	1293	89	19	1	1274	162338479	162337191	1746
15	TraesCS1B01G141800	chr2D	85.142	1622	204	31	1	1606	260490827	260489227	1626
16	TraesCS1B01G141800	chr2D	87.993	1166	119	15	1488	2639	162321159	162320001	1358

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	TraesCS1B01G141800	chr1B	189587240	189589878	2638	False	4874	4874	100.000	1	2639	1	chr1B.!!$F1	2638
1	TraesCS1B01G141800	chr7B	151130120	151132760	2640	True	3530	3530	90.841	1	2639	1	chr7B.!!$R1	2638
2	TraesCS1B01G141800	chr7B	396278129	396280760	2631	True	3310	3310	89.444	1	2639	1	chr7B.!!$R2	2638
3	TraesCS1B01G141800	chr7B	506239598	506241333	1735	True	2032	2032	87.851	904	2639	1	chr7B.!!$R3	1735
4	TraesCS1B01G141800	chr7B	361254992	361256304	1312	False	1197	1197	83.271	649	1964	1	chr7B.!!$F1	1315
5	TraesCS1B01G141800	chr1D	307648267	307650904	2637	True	3515	3515	90.762	1	2639	1	chr1D.!!$R1	2638
6	TraesCS1B01G141800	chr1D	69098931	69101013	2082	False	1844	1844	82.850	1	2079	1	chr1D.!!$F1	2078
7	TraesCS1B01G141800	chr1D	397992003	397994078	2075	False	1842	1842	82.938	1	2079	1	chr1D.!!$F2	2078
8	TraesCS1B01G141800	chr6D	333791593	333794254	2661	True	3127	3127	88.075	1	2639	1	chr6D.!!$R2	2638
9	TraesCS1B01G141800	chr6D	364246416	364247743	1327	True	1801	1801	91.085	147	1488	1	chr6D.!!$R3	1341
10	TraesCS1B01G141800	chr6D	321239399	321241398	1999	True	1712	1712	82.312	1	2003	1	chr6D.!!$R1	2002
11	TraesCS1B01G141800	chr2B	263700354	263702988	2634	False	2931	2931	86.882	1	2639	1	chr2B.!!$F1	2638
12	TraesCS1B01G141800	chr4D	393471770	393474112	2342	True	2916	2916	89.228	301	2639	1	chr4D.!!$R1	2338
13	TraesCS1B01G141800	chr4A	48882151	48884550	2399	True	2523	2523	85.732	165	2579	1	chr4A.!!$R1	2414
14	TraesCS1B01G141800	chr2D	162337191	162338479	1288	True	1746	1746	91.338	1	1274	1	chr2D.!!$R2	1273
15	TraesCS1B01G141800	chr2D	260489227	260490827	1600	True	1626	1626	85.142	1	1606	1	chr2D.!!$R3	1605
16	TraesCS1B01G141800	chr2D	162320001	162321159	1158	True	1358	1358	87.993	1488	2639	1	chr2D.!!$R1	1151

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
195	198	0.690762	AGTACTGCGGGTTGTGGATT	59.309	50.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1715	1815	0.598065	ATTCCACCAAGAAAGTGCGC	59.402	50.0	0.0	0.0	33.75	6.09	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
34	35	5.078411	TGAGATTGGAGAGCTCTTGTTAC	57.922	43.478	19.36	10.02	41.40	2.50
67	68	4.154737	CGTGATTCCTTGAGAAATTGCTCA	59.845	41.667	12.45	12.45	42.81	4.26
83	84	3.888583	TGCTCATAATTCATGCTCCACA	58.111	40.909	0.00	0.00	34.35	4.17
180	182	1.606224	CGTGGTTGTGTGGGGTAGTAC	60.606	57.143	0.00	0.00	0.00	2.73
195	198	0.690762	AGTACTGCGGGTTGTGGATT	59.309	50.000	0.00	0.00	0.00	3.01
221	224	3.921119	ATGTTCGAATTGCAAGCTTCA	57.079	38.095	4.94	0.00	0.00	3.02
355	362	3.165087	TGTACTCCCTCTTCTCCGAAA	57.835	47.619	0.00	0.00	0.00	3.46
381	388	3.466836	GGTCGCATCATCTGGTATTCAA	58.533	45.455	0.00	0.00	0.00	2.69
544	567	3.256879	TCTTTGTGTTTGCACCAAGTTCA	59.743	39.130	10.09	0.00	44.19	3.18
567	596	1.065401	CCGAAGCTGCTGTTGTTTTCA	59.935	47.619	1.35	0.00	0.00	2.69
744	811	1.094785	AGTGTTGCAGCTCAAACGTT	58.905	45.000	1.17	0.00	36.26	3.99
847	929	1.139058	CCAGATCCACCTAGAAACCGG	59.861	57.143	0.00	0.00	0.00	5.28
880	962	1.541310	TTCATTCGCCCGTCCACTCT	61.541	55.000	0.00	0.00	0.00	3.24
929	1012	7.684428	GCCAAGGAATCATTAGAATTTGGGTAC	60.684	40.741	0.00	0.00	35.52	3.34
997	1091	6.147864	TGTCCACTTTCTTCCAAAAGATTG	57.852	37.500	3.56	0.00	41.12	2.67
1019	1113	1.841302	ATGGCAGGCTCCAACTCGAA	61.841	55.000	9.27	0.00	39.96	3.71
1072	1166	2.048222	CCAAGACTCGAGCCGCAA	60.048	61.111	13.61	0.00	0.00	4.85
1146	1240	1.874345	GACGTCTTCCTCTTGCGGGA	61.874	60.000	8.70	0.00	0.00	5.14
1157	1251	0.106519	CTTGCGGGAAATGGGGATCT	60.107	55.000	0.00	0.00	0.00	2.75
1457	1552	5.047847	CCCAAATCATAACGATGAGTACGT	58.952	41.667	0.00	0.00	45.29	3.57
1496	1595	2.093658	AGTCATATTCCACGCCTCGTTT	60.094	45.455	0.00	0.00	38.32	3.60
1583	1682	0.948678	GCAAGGGTGAAGTTACGCAA	59.051	50.000	0.00	0.00	36.11	4.85
1635	1735	4.591321	TGCTTATTTTGAGTGGGAGGAT	57.409	40.909	0.00	0.00	0.00	3.24
1636	1736	4.934356	TGCTTATTTTGAGTGGGAGGATT	58.066	39.130	0.00	0.00	0.00	3.01
1715	1815	8.091449	ACTCACTCTTAATAAGTTCTCTGGTTG	58.909	37.037	0.00	0.00	0.00	3.77

Showing 1 to 25 of 103 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	4.630644	AACAAGAGCTCTCCAATCTCAA	57.369	40.909	18.55	0.00	0.00	3.02
34	35	5.023533	TCAAGGAATCACGAGAATAAGGG	57.976	43.478	0.00	0.00	0.00	3.95
67	68	6.648310	CGATCTAGTTGTGGAGCATGAATTAT	59.352	38.462	0.00	0.00	0.00	1.28
83	84	4.537135	ATCCACACAACACGATCTAGTT	57.463	40.909	0.00	0.00	0.00	2.24
180	182	2.993471	GCCAATCCACAACCCGCAG	61.993	63.158	0.00	0.00	0.00	5.18
221	224	1.379309	GACGAGGAGGAGGCTCACT	60.379	63.158	17.69	10.95	0.00	3.41
355	362	0.107508	CCAGATGATGCGACCCTGTT	60.108	55.000	0.00	0.00	0.00	3.16
381	388	2.369532	TCCTACCGTGTAAACCTTGCTT	59.630	45.455	0.00	0.00	0.00	3.91
544	567	1.609208	AACAACAGCAGCTTCGGATT	58.391	45.000	0.00	0.00	0.00	3.01
567	596	6.966534	AAAGATCCAACAACAAGACTCAAT	57.033	33.333	0.00	0.00	0.00	2.57
847	929	2.159462	CGAATGAAAGGAAGGAAGCTGC	60.159	50.000	0.00	0.00	0.00	5.25
880	962	4.713553	TGTTGTGAGGAAGTAGCAATCAA	58.286	39.130	0.00	0.00	0.00	2.57
929	1012	2.029828	ACACTCAGCTCACCTTCTTACG	60.030	50.000	0.00	0.00	0.00	3.18
997	1091	1.001641	AGTTGGAGCCTGCCATGTC	60.002	57.895	0.00	0.00	37.86	3.06
1019	1113	6.554784	TCCATAATATTTCCTCCATGTGCAT	58.445	36.000	0.00	0.00	0.00	3.96
1072	1166	6.906157	ACTTTCTTCAATCACATCACCAAT	57.094	33.333	0.00	0.00	0.00	3.16
1146	1240	3.075283	TGTGTTGGTGTAGATCCCCATTT	59.925	43.478	0.00	0.00	0.00	2.32
1157	1251	2.428187	CGGGGCTGTGTTGGTGTA	59.572	61.111	0.00	0.00	0.00	2.90
1391	1486	1.968017	CCACCATGTGCAGCTCGTT	60.968	57.895	0.00	0.00	31.34	3.85
1457	1552	3.776417	TGACTCATCATCCACCATCTCAA	59.224	43.478	0.00	0.00	0.00	3.02
1561	1660	1.607148	GCGTAACTTCACCCTTGCTTT	59.393	47.619	0.00	0.00	0.00	3.51
1583	1682	6.267471	GTCCTCTTCTCTAGTGAATGATGGAT	59.733	42.308	7.65	0.00	0.00	3.41
1635	1735	9.452287	TGAGTATTGAAGATTTGATCACATCAA	57.548	29.630	20.98	12.98	46.77	2.57
1636	1736	9.623000	ATGAGTATTGAAGATTTGATCACATCA	57.377	29.630	20.98	5.32	37.55	3.07
1715	1815	0.598065	ATTCCACCAAGAAAGTGCGC	59.402	50.000	0.00	0.00	33.75	6.09

Showing 1 to 25 of 118 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.