AutoCloner

Multiple sequence alignment - TraesCS4D01G231900

Loading Multiple Alignment...

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	TraesCS4D01G231900	chr4D	100.000	3041	0	0	1	3041	392218145	392221185	0.000000e+00	5616.0
1	TraesCS4D01G231900	chr4D	78.000	150	29	4	5	152	471229990	471229843	1.160000e-14	91.6
2	TraesCS4D01G231900	chr4A	95.449	3054	107	19	10	3041	73541175	73544218	0.000000e+00	4841.0
3	TraesCS4D01G231900	chr4B	97.239	2354	47	9	702	3041	481801117	481803466	0.000000e+00	3971.0
4	TraesCS4D01G231900	chr4B	94.562	331	15	3	205	535	481800427	481800754	2.700000e-140	508.0
5	TraesCS4D01G231900	chr4B	83.478	115	12	5	1	114	481799890	481799998	1.930000e-17	100.0
6	TraesCS4D01G231900	chr7B	80.508	236	36	8	5	235	162092230	162092460	4.030000e-39	172.0
7	TraesCS4D01G231900	chr7B	82.143	140	21	4	15	152	74484351	74484214	1.920000e-22	117.0
8	TraesCS4D01G231900	chr1D	83.562	146	22	2	14	158	484031519	484031375	5.290000e-28	135.0
9	TraesCS4D01G231900	chr2B	81.169	154	23	5	2	152	84966447	84966597	5.330000e-23	119.0
10	TraesCS4D01G231900	chr2B	100.000	30	0	0	205	234	57691650	57691679	4.240000e-04	56.5
11	TraesCS4D01G231900	chr1B	85.714	112	14	2	2	112	161987815	161987925	1.920000e-22	117.0
12	TraesCS4D01G231900	chr1B	78.571	154	24	9	53	201	622484404	622484255	3.230000e-15	93.5
13	TraesCS4D01G231900	chr3B	83.607	122	18	2	5	125	153997115	153996995	2.480000e-21	113.0
14	TraesCS4D01G231900	chr6D	100.000	31	0	0	205	235	25705427	25705457	1.180000e-04	58.4
15	TraesCS4D01G231900	chr7A	100.000	28	0	0	205	232	112084383	112084410	5.000000e-03	52.8
16	TraesCS4D01G231900	chr6A	100.000	28	0	0	205	232	27779727	27779754	5.000000e-03	52.8

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	TraesCS4D01G231900	chr4D	392218145	392221185	3040	False	5616.000000	5616	100.000000	1	3041	1	chr4D.!!$F1	3040
1	TraesCS4D01G231900	chr4A	73541175	73544218	3043	False	4841.000000	4841	95.449000	10	3041	1	chr4A.!!$F1	3031
2	TraesCS4D01G231900	chr4B	481799890	481803466	3576	False	1526.333333	3971	91.759667	1	3041	3	chr4B.!!$F1	3040

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
544	885	0.037734	TCTCCTAGACTGTGCCACGA	59.962	55.0	0.0	0.00	0.00	4.35	F
1263	1806	0.030638	ACATGGACTTTGTGCGCAAC	59.969	50.0	14.0	7.43	33.82	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1569	2118	0.036388	TTACCAGAGGCTTGCTTCCG	60.036	55.000	1.07	0.00	0.00	4.30	R
2615	3166	1.068895	TGCAAACCATTGGTGAGCAAG	59.931	47.619	24.87	8.39	41.16	4.01	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
30	31	2.559668	GGACGAATATATGTGGGGTCGA	59.440	50.000	8.76	0.00	32.98	4.20
41	42	3.728373	GGGTCGAGGTGGGCCAAT	61.728	66.667	8.40	0.00	37.19	3.16
45	46	2.220586	TCGAGGTGGGCCAATGTGA	61.221	57.895	8.40	1.01	37.19	3.58
46	47	2.040544	CGAGGTGGGCCAATGTGAC	61.041	63.158	8.40	0.00	37.19	3.67
91	92	2.930562	GGCCTCCCATATCCGCCT	60.931	66.667	0.00	0.00	36.65	5.52
104	105	1.502690	TCCGCCTTAGAATTGGGCTA	58.497	50.000	0.00	0.00	43.29	3.93
132	133	1.301479	GGTGTCGGTCAACCCAGAC	60.301	63.158	0.00	0.00	37.31	3.51
133	134	1.444250	GTGTCGGTCAACCCAGACA	59.556	57.895	5.98	5.98	41.35	3.41
144	468	1.299648	CCCAGACATTTGAGGCCGA	59.700	57.895	0.00	0.00	0.00	5.54
212	540	0.818040	ACCGTCCAAGTGTTTGAGGC	60.818	55.000	0.00	0.00	36.36	4.70
214	542	1.157870	CGTCCAAGTGTTTGAGGCGT	61.158	55.000	0.00	0.00	36.36	5.68
215	543	0.586802	GTCCAAGTGTTTGAGGCGTC	59.413	55.000	0.00	0.00	36.36	5.19
217	545	0.588252	CCAAGTGTTTGAGGCGTCTG	59.412	55.000	8.06	0.00	36.36	3.51
218	546	0.588252	CAAGTGTTTGAGGCGTCTGG	59.412	55.000	8.06	0.00	36.36	3.86
236	575	5.460419	CGTCTGGTTGTAGATGCTCTAATTC	59.540	44.000	0.00	0.00	29.58	2.17
238	577	4.693283	TGGTTGTAGATGCTCTAATTCCG	58.307	43.478	0.00	0.00	29.58	4.30
239	578	4.404394	TGGTTGTAGATGCTCTAATTCCGA	59.596	41.667	0.00	0.00	29.58	4.55
240	579	4.985409	GGTTGTAGATGCTCTAATTCCGAG	59.015	45.833	1.37	1.37	29.58	4.63
311	650	8.656849	ACTCGATCATACATTTCAACTTTACAC	58.343	33.333	0.00	0.00	0.00	2.90
327	666	6.469410	ACTTTACACATTTCGGTTGGAGATA	58.531	36.000	0.00	0.00	0.00	1.98
380	720	1.290009	GTACCGCTTACACGTGGGT	59.710	57.895	21.57	18.44	38.88	4.51
381	721	0.733909	GTACCGCTTACACGTGGGTC	60.734	60.000	21.57	7.41	38.88	4.46
411	751	1.565305	GCGTGGCATTTGTGTCAAAA	58.435	45.000	0.00	0.00	0.00	2.44
471	812	1.416401	ACCTTGCTTTCGTCTTCCTCA	59.584	47.619	0.00	0.00	0.00	3.86
511	852	1.201424	GACCTAACCAATCCGACCCT	58.799	55.000	0.00	0.00	0.00	4.34
538	879	2.622942	GCTCCATCTCTCCTAGACTGTG	59.377	54.545	0.00	0.00	36.93	3.66
544	885	0.037734	TCTCCTAGACTGTGCCACGA	59.962	55.000	0.00	0.00	0.00	4.35
595	936	3.017581	GCCTCACTCCCACCCCAT	61.018	66.667	0.00	0.00	0.00	4.00
597	938	2.378634	CCTCACTCCCACCCCATCC	61.379	68.421	0.00	0.00	0.00	3.51
600	941	2.008723	CACTCCCACCCCATCCCAT	61.009	63.158	0.00	0.00	0.00	4.00
615	956	2.008723	CCATCCCCCACTCCCACAT	61.009	63.158	0.00	0.00	0.00	3.21
667	1008	3.703127	GCCGTCCCCGTTCTTCCT	61.703	66.667	0.00	0.00	0.00	3.36
668	1009	2.577593	CCGTCCCCGTTCTTCCTC	59.422	66.667	0.00	0.00	0.00	3.71
871	1410	7.562454	TTCGACTTGTTTTCTGAAATAGGTT	57.438	32.000	3.31	0.00	28.77	3.50
963	1503	3.396260	TCTCGTTCCAATCTCGGTTTT	57.604	42.857	0.00	0.00	0.00	2.43
1251	1794	1.498865	CGCCGGCTATTCACATGGAC	61.499	60.000	26.68	0.00	0.00	4.02
1263	1806	0.030638	ACATGGACTTTGTGCGCAAC	59.969	50.000	14.00	7.43	33.82	4.17
1399	1948	1.377856	GCTGTTCCTCTTGGGCCTC	60.378	63.158	4.53	0.00	34.39	4.70
1448	1997	0.613260	GTGCATCACCACCCTACAGA	59.387	55.000	0.00	0.00	0.00	3.41
1583	2132	2.217038	TGGTCGGAAGCAAGCCTCT	61.217	57.895	0.00	0.00	0.00	3.69
1635	2184	0.534203	AGTTGCCGAAGCCGAAGAAA	60.534	50.000	0.00	0.00	38.69	2.52
1659	2208	0.615850	AGAAGGTTGCTACTCCAGGC	59.384	55.000	0.00	0.00	0.00	4.85
2007	2556	0.850100	TGAAGACCTTCTGGGCCAAA	59.150	50.000	8.04	4.31	44.45	3.28
2059	2608	6.765036	CAGGTAAGAGACATGCTATGTTGATT	59.235	38.462	0.00	2.85	45.03	2.57
2130	2679	2.302733	TGCTCTTGCCAATCTGTAGACA	59.697	45.455	0.00	0.00	38.71	3.41
2550	3101	3.313012	TGTTCCGATCTGGTGTTACTG	57.687	47.619	3.97	0.00	39.52	2.74
2608	3159	9.712305	CTCTACCTTAATACCTTGGACATTATG	57.288	37.037	0.00	0.00	0.00	1.90
2615	3166	7.986085	AATACCTTGGACATTATGATAGCAC	57.014	36.000	0.00	0.00	0.00	4.40
2616	3167	5.636903	ACCTTGGACATTATGATAGCACT	57.363	39.130	0.00	0.00	0.00	4.40
2736	3287	6.814954	TCTCTTAGAATTATGCAAGGGAGT	57.185	37.500	0.00	0.00	0.00	3.85
2737	3288	7.914427	TCTCTTAGAATTATGCAAGGGAGTA	57.086	36.000	0.00	0.00	0.00	2.59
2774	3325	9.623000	AGGTATGTGTAAAAGTCTTACAAGTTT	57.377	29.630	0.00	0.00	36.74	2.66
3008	3559	9.241317	CAAAATAATGAAGCTGTCCATACATTC	57.759	33.333	0.00	0.00	34.37	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	4.091549	GACCCCACATATATTCGTCCCTA	58.908	47.826	0.00	0.00	0.00	3.53
7	8	2.904434	GACCCCACATATATTCGTCCCT	59.096	50.000	0.00	0.00	0.00	4.20
8	9	2.353406	CGACCCCACATATATTCGTCCC	60.353	54.545	0.00	0.00	0.00	4.46
30	31	2.440599	GGTCACATTGGCCCACCT	59.559	61.111	0.00	0.00	35.72	4.00
41	42	3.445687	CGTCGGATCCGGGTCACA	61.446	66.667	32.79	10.77	40.25	3.58
91	92	5.488919	CCCCTCATATCTAGCCCAATTCTAA	59.511	44.000	0.00	0.00	0.00	2.10
104	105	1.063190	TGACCGACACCCCTCATATCT	60.063	52.381	0.00	0.00	0.00	1.98
130	131	2.098117	CCTCAAATCGGCCTCAAATGTC	59.902	50.000	0.00	0.00	0.00	3.06
132	133	2.094675	ACCTCAAATCGGCCTCAAATG	58.905	47.619	0.00	0.00	0.00	2.32
133	134	2.094675	CACCTCAAATCGGCCTCAAAT	58.905	47.619	0.00	0.00	0.00	2.32
200	528	0.180406	ACCAGACGCCTCAAACACTT	59.820	50.000	0.00	0.00	0.00	3.16
201	529	0.180406	AACCAGACGCCTCAAACACT	59.820	50.000	0.00	0.00	0.00	3.55
236	575	8.293867	CAGTTAGATTTCCTATCTTCTACTCGG	58.706	40.741	0.00	0.00	0.00	4.63
240	579	9.036671	GCAACAGTTAGATTTCCTATCTTCTAC	57.963	37.037	0.00	0.00	0.00	2.59
311	650	3.123804	CCGAGTATCTCCAACCGAAATG	58.876	50.000	0.00	0.00	0.00	2.32
327	666	0.465460	TCAAAGCCAAACTGCCGAGT	60.465	50.000	0.00	0.00	0.00	4.18
411	751	7.562135	AGAAAATGGCATATTTCTTTCTGCAT	58.438	30.769	18.48	1.04	41.79	3.96
511	852	1.531840	GGAGAGATGGAGCCGCCTA	60.532	63.158	0.00	0.00	37.63	3.93
585	926	2.369568	GGATGGGATGGGGTGGGA	60.370	66.667	0.00	0.00	0.00	4.37
594	935	2.038330	GGGAGTGGGGGATGGGAT	60.038	66.667	0.00	0.00	0.00	3.85
595	936	3.632049	TGGGAGTGGGGGATGGGA	61.632	66.667	0.00	0.00	0.00	4.37
597	938	1.999634	GATGTGGGAGTGGGGGATGG	62.000	65.000	0.00	0.00	0.00	3.51
600	941	2.286121	GGATGTGGGAGTGGGGGA	60.286	66.667	0.00	0.00	0.00	4.81
849	1387	6.017440	TGGAACCTATTTCAGAAAACAAGTCG	60.017	38.462	0.00	0.00	35.70	4.18
850	1388	7.272037	TGGAACCTATTTCAGAAAACAAGTC	57.728	36.000	0.00	0.00	35.70	3.01
883	1422	1.548081	CCACCATTGCATTCCAGACA	58.452	50.000	0.00	0.00	0.00	3.41
963	1503	5.237561	TGAACAAACGAATCGAAATCCAAGA	59.762	36.000	10.55	0.00	0.00	3.02
1251	1794	2.427410	GCCTCGTTGCGCACAAAG	60.427	61.111	11.12	7.41	37.58	2.77
1263	1806	4.864334	GGGTGCATCCAGGCCTCG	62.864	72.222	12.38	0.00	38.11	4.63
1399	1948	3.497405	CCAGGATGTCCAATATGTCCAGG	60.497	52.174	1.30	0.00	38.89	4.45
1448	1997	2.367567	GCATCTGGCATCATCCCAAAAT	59.632	45.455	0.00	0.00	43.97	1.82
1569	2118	0.036388	TTACCAGAGGCTTGCTTCCG	60.036	55.000	1.07	0.00	0.00	4.30
1583	2132	2.553028	CCTTGCTGCCTCTTCTTTACCA	60.553	50.000	0.00	0.00	0.00	3.25
2007	2556	3.608316	ACAAACTTGTTTGTGCCATGT	57.392	38.095	25.13	5.27	42.91	3.21
2130	2679	6.546428	TGGCTACAAGCTACTTCTAAAGAT	57.454	37.500	0.00	0.00	41.99	2.40
2550	3101	1.076332	AAATACTCGGTTCAGCGCAC	58.924	50.000	11.47	0.00	0.00	5.34
2608	3159	5.642117	AACCATTGGTGAGCAAGTGCTATC	61.642	45.833	9.62	2.46	43.72	2.08
2615	3166	1.068895	TGCAAACCATTGGTGAGCAAG	59.931	47.619	24.87	8.39	41.16	4.01
2616	3167	1.117994	TGCAAACCATTGGTGAGCAA	58.882	45.000	24.87	13.49	41.16	3.91
2680	3231	6.750148	TCAAACACCACACAAGTTAAAGTTT	58.250	32.000	0.00	0.00	0.00	2.66
3008	3559	4.224818	ACTCCCAGATCTTTCAGAAAGGAG	59.775	45.833	20.70	19.52	39.01	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.