AutoCloner

Multiple sequence alignment - TraesCS6B01G101500

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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	TraesCS6B01G101500	chr6B	100.000	2936	0	0	1	2936	79721002	79718067	0.000000e+00	5422.0
1	TraesCS6B01G101500	chr6B	93.532	1979	113	8	463	2432	78452574	78454546	0.000000e+00	2931.0
2	TraesCS6B01G101500	chr6B	85.212	1366	153	34	512	1862	59870796	59872127	0.000000e+00	1358.0
3	TraesCS6B01G101500	chr6B	84.462	502	52	15	1941	2432	59872734	59873219	3.430000e-129	472.0
4	TraesCS6B01G101500	chr6B	84.140	372	33	10	159	515	59870329	59870689	1.300000e-88	337.0
5	TraesCS6B01G101500	chr6B	97.484	159	3	1	297	455	78388892	78389049	1.340000e-68	270.0
6	TraesCS6B01G101500	chr6A	93.092	2345	142	14	101	2432	45651939	45654276	0.000000e+00	3415.0
7	TraesCS6B01G101500	chr6A	83.703	1804	206	42	162	1938	33018761	33020503	0.000000e+00	1622.0
8	TraesCS6B01G101500	chr6A	85.294	374	37	7	2064	2432	33020586	33020946	1.290000e-98	370.0
9	TraesCS6B01G101500	chr6A	98.246	57	1	0	1	57	45651885	45651941	1.860000e-17	100.0
10	TraesCS6B01G101500	chrUn	94.724	1668	81	5	770	2432	27714333	27715998	0.000000e+00	2586.0
11	TraesCS6B01G101500	chrUn	89.736	643	47	13	64	694	27713533	27714168	0.000000e+00	804.0
12	TraesCS6B01G101500	chrUn	97.895	380	7	1	2436	2814	65754167	65754546	0.000000e+00	656.0
13	TraesCS6B01G101500	chrUn	99.138	116	0	1	2821	2936	65754622	65754736	1.070000e-49	207.0
14	TraesCS6B01G101500	chrUn	96.875	64	2	0	1	64	27713432	27713495	1.110000e-19	108.0
15	TraesCS6B01G101500	chrUn	100.000	38	0	0	2755	2792	65754583	65754620	1.460000e-08	71.3
16	TraesCS6B01G101500	chr6D	82.725	2275	255	75	207	2432	29377447	29375262	0.000000e+00	1897.0
17	TraesCS6B01G101500	chr3D	98.603	501	7	0	2436	2936	579076086	579075586	0.000000e+00	887.0
18	TraesCS6B01G101500	chr4D	98.488	463	7	0	2474	2936	438110272	438110734	0.000000e+00	817.0
19	TraesCS6B01G101500	chr7B	97.015	335	10	0	2436	2770	130742992	130742658	5.490000e-157	564.0
20	TraesCS6B01G101500	chr7B	97.024	168	5	0	2769	2936	130740969	130740802	1.720000e-72	283.0
21	TraesCS6B01G101500	chr4A	88.095	210	17	3	2727	2936	713519012	713518811	2.920000e-60	243.0

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	TraesCS6B01G101500	chr6B	79718067	79721002	2935	True	5422.000000	5422	100.000000	1	2936	1	chr6B.!!$R1	2935
1	TraesCS6B01G101500	chr6B	78452574	78454546	1972	False	2931.000000	2931	93.532000	463	2432	1	chr6B.!!$F2	1969
2	TraesCS6B01G101500	chr6B	59870329	59873219	2890	False	722.333333	1358	84.604667	159	2432	3	chr6B.!!$F3	2273
3	TraesCS6B01G101500	chr6A	45651885	45654276	2391	False	1757.500000	3415	95.669000	1	2432	2	chr6A.!!$F2	2431
4	TraesCS6B01G101500	chr6A	33018761	33020946	2185	False	996.000000	1622	84.498500	162	2432	2	chr6A.!!$F1	2270
5	TraesCS6B01G101500	chrUn	27713432	27715998	2566	False	1166.000000	2586	93.778333	1	2432	3	chrUn.!!$F1	2431
6	TraesCS6B01G101500	chrUn	65754167	65754736	569	False	311.433333	656	99.011000	2436	2936	3	chrUn.!!$F2	500
7	TraesCS6B01G101500	chr6D	29375262	29377447	2185	True	1897.000000	1897	82.725000	207	2432	1	chr6D.!!$R1	2225
8	TraesCS6B01G101500	chr3D	579075586	579076086	500	True	887.000000	887	98.603000	2436	2936	1	chr3D.!!$R1	500
9	TraesCS6B01G101500	chr7B	130740802	130742992	2190	True	423.500000	564	97.019500	2436	2936	2	chr7B.!!$R1	500

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
59	60	1.968540	GCGGCAGGAAAAGAGCTGT	60.969	57.895	0.0	0.0	37.0	4.4	F
624	817	2.158475	TCAGTGCCAGAAATCCAAAGGT	60.158	45.455	0.0	0.0	0.0	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1207	1505	0.904865	ATGCTCAGAACCTCCACCGA	60.905	55.0	0.00	0.0	0.00	4.69	R
2500	3397	0.815213	GGTGCAACAGCTGACAGTGA	60.815	55.0	23.35	0.0	39.98	3.41	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
59	60	1.968540	GCGGCAGGAAAAGAGCTGT	60.969	57.895	0.00	0.00	37.00	4.40
76	115	5.766670	AGAGCTGTCTATCTCTTCTCATCAG	59.233	44.000	0.00	0.00	36.33	2.90
155	194	2.948979	ACACTCGCTTCCAATTCACAAA	59.051	40.909	0.00	0.00	0.00	2.83
166	206	4.523943	TCCAATTCACAAATGGTCAGGAAG	59.476	41.667	0.00	0.00	0.00	3.46
175	215	2.615986	TGGTCAGGAAGTAGGTAGCA	57.384	50.000	0.00	0.00	0.00	3.49
202	246	3.947834	GCAGTCACAGCCCAGTTAATAAT	59.052	43.478	0.00	0.00	0.00	1.28
228	273	2.630580	AGTCTTCCAGTCCTGTTGAGAC	59.369	50.000	11.11	11.11	34.74	3.36
484	552	3.493176	GCCTGGACAGCAACAAAATCTTT	60.493	43.478	0.00	0.00	0.00	2.52
487	555	3.629855	TGGACAGCAACAAAATCTTTCGA	59.370	39.130	0.00	0.00	0.00	3.71
556	738	6.483640	ACTTTGCAAACAACCAAAAACTTACA	59.516	30.769	8.05	0.00	34.87	2.41
558	740	6.473397	TGCAAACAACCAAAAACTTACAAG	57.527	33.333	0.00	0.00	0.00	3.16
559	741	5.106908	TGCAAACAACCAAAAACTTACAAGC	60.107	36.000	0.00	0.00	0.00	4.01
624	817	2.158475	TCAGTGCCAGAAATCCAAAGGT	60.158	45.455	0.00	0.00	0.00	3.50
662	856	8.843262	TCTTGCATAATTCAAATCTAGACATGG	58.157	33.333	0.00	0.00	0.00	3.66
827	1115	6.855836	TGTTAAAATTCTTCAGCCATGCTAG	58.144	36.000	0.00	0.00	36.40	3.42
935	1223	7.063426	GGCCATTAGTTTGCTCACTAATTTTTC	59.937	37.037	14.84	7.45	44.30	2.29
954	1246	2.986050	TCCCCTCTTTTCCTGTAGTGT	58.014	47.619	0.00	0.00	0.00	3.55
1153	1451	5.391629	GGTTGTGCTATTAAAGGTTTCGAGG	60.392	44.000	0.00	0.00	0.00	4.63
1207	1505	2.297701	AGCCGTTCATGTTTGTTGAGT	58.702	42.857	0.00	0.00	0.00	3.41
1555	1853	7.388638	AGGGGCTATAGCTTCAGTTTTTATA	57.611	36.000	23.53	0.00	41.70	0.98
1721	2020	0.323629	GACTGGGTGGTCGGAAATGA	59.676	55.000	0.00	0.00	0.00	2.57
1739	2038	1.341482	TGAAACTTGTGAAGTGGCCCA	60.341	47.619	0.00	0.00	41.91	5.36
1906	2708	3.887716	GCTTGATCCCTGTGCATCTTTAT	59.112	43.478	0.00	0.00	0.00	1.40
1917	2719	6.308371	TGTGCATCTTTATATCATGTGCAG	57.692	37.500	2.47	0.00	41.18	4.41
2308	3202	3.181468	GCCACAACACTATAGGAGGGTAC	60.181	52.174	4.43	0.00	42.82	3.34
2422	3319	9.691362	GATGTTTTTAGCATTTCCTTTCTTGTA	57.309	29.630	0.00	0.00	0.00	2.41
2463	3360	1.130054	AAGAGCTGAGGAACCTGGCA	61.130	55.000	14.34	0.00	0.00	4.92
2500	3397	0.676782	CGGGGACAAAAGGATCGCTT	60.677	55.000	0.00	0.00	0.00	4.68
2646	3543	0.610232	GAGCTGTTGCAAGGGACCAT	60.610	55.000	0.00	0.00	42.74	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	3.894427	GTGGGCTGATGAGAAGAGATAGA	59.106	47.826	0.00	0.00	0.00	1.98
76	115	1.682344	GGGAATGGTTCAGGTGGGC	60.682	63.158	0.00	0.00	0.00	5.36
86	125	2.440599	GGCTGTGGTGGGAATGGT	59.559	61.111	0.00	0.00	0.00	3.55
155	194	3.116096	TGCTACCTACTTCCTGACCAT	57.884	47.619	0.00	0.00	0.00	3.55
166	206	2.737252	GTGACTGCAACTTGCTACCTAC	59.263	50.000	14.78	4.61	45.31	3.18
175	215	0.820891	CTGGGCTGTGACTGCAACTT	60.821	55.000	16.18	0.00	0.00	2.66
188	228	4.475016	AGACTGGTGATTATTAACTGGGCT	59.525	41.667	0.00	0.00	0.00	5.19
189	229	4.781934	AGACTGGTGATTATTAACTGGGC	58.218	43.478	0.00	0.00	0.00	5.36
202	246	1.342074	CAGGACTGGAAGACTGGTGA	58.658	55.000	0.00	0.00	38.28	4.02
228	273	3.093278	GCCATGGAAAGAGCGACG	58.907	61.111	18.40	0.00	0.00	5.12
256	301	1.639722	TGTGCTTGACTAGGCTACCA	58.360	50.000	0.00	0.00	0.00	3.25
484	552	7.942894	TCTTAGATACAGATAATCCTTGGTCGA	59.057	37.037	0.00	0.00	0.00	4.20
487	555	9.440761	ACTTCTTAGATACAGATAATCCTTGGT	57.559	33.333	0.00	0.00	0.00	3.67
662	856	6.851222	TTTCATCTTTTGTCTGACTGTCTC	57.149	37.500	9.51	0.91	0.00	3.36
672	866	5.459536	AGAAGGCCTTTTCATCTTTTGTC	57.540	39.130	21.54	1.23	0.00	3.18
935	1223	3.181443	ACAACACTACAGGAAAAGAGGGG	60.181	47.826	0.00	0.00	0.00	4.79
1153	1451	1.648467	GCAGTCCTCCGGCAAATGAC	61.648	60.000	0.00	0.00	0.00	3.06
1179	1477	1.227999	ACATGAACGGCTTGTCGGTG	61.228	55.000	0.00	0.00	29.69	4.94
1207	1505	0.904865	ATGCTCAGAACCTCCACCGA	60.905	55.000	0.00	0.00	0.00	4.69
1555	1853	8.819974	CGTACTATTGGAATTATGGTAAACGTT	58.180	33.333	0.00	0.00	0.00	3.99
1721	2020	1.756538	CTTGGGCCACTTCACAAGTTT	59.243	47.619	5.23	0.00	40.46	2.66
1739	2038	1.337823	ACGCGTAAGAAGGCATGTCTT	60.338	47.619	13.52	13.52	38.80	3.01
1823	2122	1.411612	GGTTCCCTTCATATCCGTCGT	59.588	52.381	0.00	0.00	0.00	4.34
1906	2708	5.523552	CCTCATAAAACGACTGCACATGATA	59.476	40.000	0.00	0.00	0.00	2.15
1948	2783	5.864474	CGGGATAGACAGCAAGTAATGATAC	59.136	44.000	0.00	0.00	0.00	2.24
1967	2802	1.215173	TCCAGGCATCAAAATCGGGAT	59.785	47.619	0.00	0.00	0.00	3.85
2099	2984	2.036089	TGTAACGTTTGGCATTTTCCCC	59.964	45.455	5.91	0.00	0.00	4.81
2102	2987	4.602995	TGAGTGTAACGTTTGGCATTTTC	58.397	39.130	5.91	4.72	45.86	2.29
2104	2989	4.846779	ATGAGTGTAACGTTTGGCATTT	57.153	36.364	5.91	0.00	45.86	2.32
2109	2994	4.155099	TGGCATAATGAGTGTAACGTTTGG	59.845	41.667	5.91	0.00	45.86	3.28
2191	3085	6.933514	ATTATTTGGGGTCAAGTGTGATTT	57.066	33.333	0.00	0.00	35.80	2.17
2308	3202	4.264253	TGCCTGGAGAACATGAACAATAG	58.736	43.478	0.00	0.00	0.00	1.73
2422	3319	9.703892	CTCTTCCTCATAATCGATGTTTTCTAT	57.296	33.333	0.00	0.00	36.84	1.98
2432	3329	3.571828	CCTCAGCTCTTCCTCATAATCGA	59.428	47.826	0.00	0.00	0.00	3.59
2433	3330	3.571828	TCCTCAGCTCTTCCTCATAATCG	59.428	47.826	0.00	0.00	0.00	3.34
2434	3331	5.296748	GTTCCTCAGCTCTTCCTCATAATC	58.703	45.833	0.00	0.00	0.00	1.75
2463	3360	3.606886	GACACCATCGGTTGACAGT	57.393	52.632	0.00	0.00	31.02	3.55
2500	3397	0.815213	GGTGCAACAGCTGACAGTGA	60.815	55.000	23.35	0.00	39.98	3.41
2646	3543	3.640498	CAGACATGAGAGCCAATCCTCTA	59.360	47.826	0.00	0.00	42.06	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.