AutoCloner

Multiple sequence alignment - TraesCS7A01G296300

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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	TraesCS7A01G296300	chr7A	100.000	3590	0	0	1	3590	394759211	394762800	0.000000e+00	6630.0
1	TraesCS7A01G296300	chr7A	95.424	743	33	1	1	742	394727688	394728430	0.000000e+00	1182.0
2	TraesCS7A01G296300	chr7A	90.909	55	5	0	3500	3554	127450808	127450754	1.380000e-09	75.0
3	TraesCS7A01G296300	chr7D	97.511	2852	62	4	740	3590	363051676	363048833	0.000000e+00	4865.0
4	TraesCS7A01G296300	chr7D	82.979	94	9	7	3499	3590	80739437	80739349	1.070000e-10	78.7
5	TraesCS7A01G296300	chr7B	96.610	2861	77	11	740	3590	322491471	322488621	0.000000e+00	4728.0
6	TraesCS7A01G296300	chr3A	95.020	743	36	1	1	742	68904979	68905721	0.000000e+00	1166.0
7	TraesCS7A01G296300	chr3A	94.324	740	41	1	1	739	68919713	68920452	0.000000e+00	1133.0
8	TraesCS7A01G296300	chr3A	93.519	756	47	2	2	755	125397163	125397918	0.000000e+00	1123.0
9	TraesCS7A01G296300	chr3A	94.070	742	41	3	2	742	548675034	548675773	0.000000e+00	1123.0
10	TraesCS7A01G296300	chr3A	88.000	75	9	0	3512	3586	749277817	749277891	4.940000e-14	89.8
11	TraesCS7A01G296300	chr1A	94.347	743	41	1	1	742	148253036	148253778	0.000000e+00	1138.0
12	TraesCS7A01G296300	chr6A	94.213	743	39	2	1	742	502204098	502204837	0.000000e+00	1131.0
13	TraesCS7A01G296300	chr2A	93.952	744	43	2	1	742	639920580	639919837	0.000000e+00	1123.0
14	TraesCS7A01G296300	chr2A	93.943	743	44	1	1	742	624486958	624486216	0.000000e+00	1122.0
15	TraesCS7A01G296300	chrUn	100.000	420	0	0	2674	3093	476912478	476912897	0.000000e+00	776.0
16	TraesCS7A01G296300	chr1B	88.060	67	7	1	3487	3553	127241269	127241204	1.070000e-10	78.7
17	TraesCS7A01G296300	chr4D	81.053	95	12	6	3499	3590	363683970	363683879	1.790000e-08	71.3
18	TraesCS7A01G296300	chr4A	89.286	56	6	0	3499	3554	101743395	101743450	1.790000e-08	71.3
19	TraesCS7A01G296300	chr5D	100.000	33	0	0	3499	3531	241960245	241960213	1.080000e-05	62.1

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	TraesCS7A01G296300	chr7A	394759211	394762800	3589	False	6630	6630	100.000	1	3590	1	chr7A.!!$F2	3589
1	TraesCS7A01G296300	chr7A	394727688	394728430	742	False	1182	1182	95.424	1	742	1	chr7A.!!$F1	741
2	TraesCS7A01G296300	chr7D	363048833	363051676	2843	True	4865	4865	97.511	740	3590	1	chr7D.!!$R2	2850
3	TraesCS7A01G296300	chr7B	322488621	322491471	2850	True	4728	4728	96.610	740	3590	1	chr7B.!!$R1	2850
4	TraesCS7A01G296300	chr3A	68904979	68905721	742	False	1166	1166	95.020	1	742	1	chr3A.!!$F1	741
5	TraesCS7A01G296300	chr3A	68919713	68920452	739	False	1133	1133	94.324	1	739	1	chr3A.!!$F2	738
6	TraesCS7A01G296300	chr3A	125397163	125397918	755	False	1123	1123	93.519	2	755	1	chr3A.!!$F3	753
7	TraesCS7A01G296300	chr3A	548675034	548675773	739	False	1123	1123	94.070	2	742	1	chr3A.!!$F4	740
8	TraesCS7A01G296300	chr1A	148253036	148253778	742	False	1138	1138	94.347	1	742	1	chr1A.!!$F1	741
9	TraesCS7A01G296300	chr6A	502204098	502204837	739	False	1131	1131	94.213	1	742	1	chr6A.!!$F1	741
10	TraesCS7A01G296300	chr2A	639919837	639920580	743	True	1123	1123	93.952	1	742	1	chr2A.!!$R2	741
11	TraesCS7A01G296300	chr2A	624486216	624486958	742	True	1122	1122	93.943	1	742	1	chr2A.!!$R1	741

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	End Stability	Orientation
823	829	0.105709	TCGGTGGAGATGGCCTGATA	60.106	55.000	3.32	2.15	F
824	830	0.758734	CGGTGGAGATGGCCTGATAA	59.241	55.000	3.32	1.75	F
825	831	1.349026	CGGTGGAGATGGCCTGATAAT	59.651	52.381	3.32	1.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
1655	1662	0.976641	GGCATACCCGGAGATCATCA	59.023	55.000	0.73	3.07	R
2274	2281	1.417890	CGCCCAAGGAGATCTACCATT	59.582	52.381	0.00	3.16	R
3157	3173	1.021390	AAGCCTCGCACAAGATTCCG	61.021	55.000	0.00	4.30	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
74	75	4.462133	TCAATTCACGTCCAAAACCCTAA	58.538	39.130	0.00	0.00	0.00	2.69
83	84	4.461081	CGTCCAAAACCCTAATCCAATTCA	59.539	41.667	0.00	0.00	0.00	2.57
182	183	1.137086	CGACCTCGGATGGAAATGAGT	59.863	52.381	0.00	0.00	35.37	3.41
322	325	5.687166	TCAAAATCCGGACTAACATACCT	57.313	39.130	6.12	0.00	0.00	3.08
438	442	2.858745	ACTTTTGCATACAACCTCGGT	58.141	42.857	0.00	0.00	34.87	4.69
447	451	1.043022	ACAACCTCGGTTTAGGACGT	58.957	50.000	0.00	0.00	39.15	4.34
481	485	0.876399	TCATCCGTTTCGACGAGACA	59.124	50.000	17.47	0.58	34.64	3.41
753	759	2.744202	GTCAACACATTCTTCCGCATCT	59.256	45.455	0.00	0.00	0.00	2.90
761	767	5.569059	CACATTCTTCCGCATCTTTGTTTAC	59.431	40.000	0.00	0.00	0.00	2.01
765	771	2.070783	TCCGCATCTTTGTTTACGGAC	58.929	47.619	0.00	0.00	44.14	4.79
767	773	3.056678	TCCGCATCTTTGTTTACGGACTA	60.057	43.478	0.00	0.00	44.14	2.59
778	784	6.252599	TGTTTACGGACTAGTCCCTCTATA	57.747	41.667	31.78	15.80	46.96	1.31
779	785	6.845908	TGTTTACGGACTAGTCCCTCTATAT	58.154	40.000	31.78	13.61	46.96	0.86
804	810	1.684450	ACGGAGAAAATTTGCGGGTTT	59.316	42.857	0.00	0.00	33.42	3.27
807	813	2.324860	GAGAAAATTTGCGGGTTTCGG	58.675	47.619	0.00	0.00	39.69	4.30
820	826	1.026718	GTTTCGGTGGAGATGGCCTG	61.027	60.000	3.32	0.00	0.00	4.85
822	828	0.982852	TTCGGTGGAGATGGCCTGAT	60.983	55.000	3.32	0.00	0.00	2.90
823	829	0.105709	TCGGTGGAGATGGCCTGATA	60.106	55.000	3.32	0.00	0.00	2.15
824	830	0.758734	CGGTGGAGATGGCCTGATAA	59.241	55.000	3.32	0.00	0.00	1.75
825	831	1.349026	CGGTGGAGATGGCCTGATAAT	59.651	52.381	3.32	0.00	0.00	1.28
826	832	2.787994	GGTGGAGATGGCCTGATAATG	58.212	52.381	3.32	0.00	0.00	1.90
1400	1406	1.377366	CTCGCCTCACTTCTCCGCTA	61.377	60.000	0.00	0.00	0.00	4.26
1655	1662	3.488778	GAGCAACATCTCCTGGATCAT	57.511	47.619	0.00	0.00	31.27	2.45
1715	1722	1.737355	GCTGCTGGCCTGTTTGAACA	61.737	55.000	11.69	0.00	37.37	3.18
1780	1787	2.206750	CATGCTATGCACAAAATGGCC	58.793	47.619	0.00	0.00	43.04	5.36
1872	1879	6.589523	AGAAAACTTTCTCATCTGTCATCTCG	59.410	38.462	0.00	0.00	43.72	4.04
2243	2250	5.511234	GCTTCCATGTCAAGCAAATATCT	57.489	39.130	17.65	0.00	44.87	1.98
3107	3123	6.728200	TGTACGGTTAAGATTATAGGTCACG	58.272	40.000	0.00	0.00	0.00	4.35
3471	3487	4.095483	GGCATTTTCTTGATCGACTCATGT	59.905	41.667	0.00	0.00	32.72	3.21
3576	3592	9.092876	CTTTAAATGCTTTCCACAAGTTTGTAA	57.907	29.630	0.00	0.00	39.91	2.41
3580	3596	8.504812	AATGCTTTCCACAAGTTTGTAAAAAT	57.495	26.923	0.00	0.00	39.91	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	75	5.336690	CGGACCAAACAAATCTGAATTGGAT	60.337	40.000	13.04	0.00	41.52	3.41
83	84	4.037565	GGAAAGTTCGGACCAAACAAATCT	59.962	41.667	0.00	0.00	0.00	2.40
182	183	2.582052	ACGGTCAAGATTGCTTTTGGA	58.418	42.857	0.00	0.00	30.14	3.53
322	325	1.229051	TGGATGACCGGACACTCCA	60.229	57.895	23.36	23.36	35.91	3.86
370	373	4.101448	ATGGCCGGACACTCCAGC	62.101	66.667	15.41	0.00	39.21	4.85
372	375	3.399181	GGATGGCCGGACACTCCA	61.399	66.667	25.42	15.33	35.91	3.86
403	407	4.399618	TGCAAAAGTTACAGCCAGTACAAA	59.600	37.500	0.00	0.00	30.91	2.83
513	517	7.051000	GCTTGAAACCCTATTAAGATGACTCT	58.949	38.462	0.00	0.00	0.00	3.24
527	531	7.147672	CCAGATTAAATAATGGCTTGAAACCCT	60.148	37.037	0.00	0.00	0.00	4.34
566	570	8.721478	GCAAAAGTTATGACAAGTTCAGAGATA	58.279	33.333	0.00	0.00	37.77	1.98
702	708	3.630312	AGTGGCACAATCGTAAAAGTTGT	59.370	39.130	21.41	0.00	44.16	3.32
765	771	4.011023	CCGTCCACATATAGAGGGACTAG	58.989	52.174	14.14	0.00	45.98	2.57
767	773	2.445905	TCCGTCCACATATAGAGGGACT	59.554	50.000	14.14	0.00	45.98	3.85
778	784	2.095263	CGCAAATTTTCTCCGTCCACAT	60.095	45.455	0.00	0.00	0.00	3.21
779	785	1.265635	CGCAAATTTTCTCCGTCCACA	59.734	47.619	0.00	0.00	0.00	4.17
804	810	0.105709	TATCAGGCCATCTCCACCGA	60.106	55.000	5.01	0.00	0.00	4.69
807	813	2.157738	GCATTATCAGGCCATCTCCAC	58.842	52.381	5.01	0.00	0.00	4.02
851	857	3.608073	GGAAATTTTTGGTCGATCGCAAG	59.392	43.478	11.09	0.00	0.00	4.01
956	962	1.870055	GACTCACGTTCCCGGTAGCA	61.870	60.000	0.00	0.00	38.78	3.49
1276	1282	1.067582	GGTCGCGGGAATAGAGGTG	59.932	63.158	6.13	0.00	0.00	4.00
1348	1354	1.067354	GGAAACGAGTAGGGAAAGCGA	60.067	52.381	0.00	0.00	0.00	4.93
1655	1662	0.976641	GGCATACCCGGAGATCATCA	59.023	55.000	0.73	0.00	0.00	3.07
1715	1722	9.339850	CATAAAGATCATTCTTGTTCTCCATCT	57.660	33.333	0.00	0.00	41.42	2.90
1780	1787	4.514577	AATCGCCTCCCTCGCACG	62.515	66.667	0.00	0.00	0.00	5.34
1872	1879	2.191641	CCTAGCTGGGAGCAAGCC	59.808	66.667	11.42	0.00	45.56	4.35
2242	2249	6.176183	AGTGTTCCATTGAAGGTCTAATCAG	58.824	40.000	0.00	0.00	0.00	2.90
2243	2250	6.126863	AGTGTTCCATTGAAGGTCTAATCA	57.873	37.500	0.00	0.00	0.00	2.57
2274	2281	1.417890	CGCCCAAGGAGATCTACCATT	59.582	52.381	0.00	0.00	0.00	3.16
3157	3173	1.021390	AAGCCTCGCACAAGATTCCG	61.021	55.000	0.00	0.00	0.00	4.30
3444	3460	2.421424	GTCGATCAAGAAAATGCCAGCT	59.579	45.455	0.00	0.00	0.00	4.24
3471	3487	4.144297	ACTCAGTGCCTGAAAATAAAGCA	58.856	39.130	6.39	0.00	40.18	3.91
3498	3514	5.872963	AGTAAACAAAAACGGAGGGAGTAT	58.127	37.500	0.00	0.00	0.00	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.