AutoCloner

Multiple sequence alignment - TraesCS4B01G064700

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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	TraesCS4B01G064700	chr4B	100.000	2495	0	0	1	2495	57750839	57748345	0.000000	4608.0
1	TraesCS4B01G064700	chr4D	94.818	1679	66	6	827	2495	39361496	39363163	0.000000	2599.0
2	TraesCS4B01G064700	chr4D	95.497	755	30	2	1	755	39360742	39361492	0.000000	1203.0
3	TraesCS4B01G064700	chr4A	94.892	1018	51	1	818	1835	560994458	560995474	0.000000	1591.0
4	TraesCS4B01G064700	chr4A	85.769	787	73	23	1	757	560993684	560994461	0.000000	797.0
5	TraesCS4B01G064700	chr4A	88.226	654	53	6	1833	2473	560995577	560996219	0.000000	760.0
6	TraesCS4B01G064700	chr4A	94.737	38	1	1	754	790	559487111	559487148	0.000096	58.4
7	TraesCS4B01G064700	chr7D	91.489	47	2	2	757	802	423706991	423706946	0.000002	63.9
8	TraesCS4B01G064700	chr5D	92.857	42	2	1	761	802	264635038	264634998	0.000027	60.2
9	TraesCS4B01G064700	chr5A	92.857	42	2	1	761	802	622203859	622203899	0.000027	60.2
10	TraesCS4B01G064700	chr1A	91.304	46	1	3	758	802	473042202	473042159	0.000027	60.2
11	TraesCS4B01G064700	chr1A	89.362	47	3	2	757	802	560251676	560251631	0.000096	58.4
12	TraesCS4B01G064700	chr6A	94.737	38	1	1	751	787	460621956	460621919	0.000096	58.4
13	TraesCS4B01G064700	chr2D	90.476	42	4	0	747	788	2450905	2450864	0.000347	56.5
14	TraesCS4B01G064700	chr7B	92.105	38	3	0	752	789	682354660	682354697	0.001000	54.7

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	TraesCS4B01G064700	chr4B	57748345	57750839	2494	True	4608.000000	4608	100.0000	1	2495	1	chr4B.!!$R1	2494
1	TraesCS4B01G064700	chr4D	39360742	39363163	2421	False	1901.000000	2599	95.1575	1	2495	2	chr4D.!!$F1	2494
2	TraesCS4B01G064700	chr4A	560993684	560996219	2535	False	1049.333333	1591	89.6290	1	2473	3	chr4A.!!$F2	2472

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
872	909	0.105039	CCTTCACATACGCCCTCTCC	59.895	60.0	0.0	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1704	1742	1.345741	TCTCCCTTGCTCACACTCAAG	59.654	52.381	0.0	0.0	39.38	3.02	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
66	67	1.855978	CAACGTCGAACAAGTGTAGCA	59.144	47.619	0.00	0.00	0.00	3.49
91	92	9.918630	CAGAAAAGAAACATGATTGACCTAAAT	57.081	29.630	0.00	0.00	0.00	1.40
131	132	5.479724	TGTCTTTTGATGATGGTTTATGCCA	59.520	36.000	0.00	0.00	43.48	4.92
288	289	3.694072	CGCTATCAAGGGGAAACATTTCA	59.306	43.478	6.68	0.00	38.92	2.69
362	363	5.478332	GCCCTTGAAGAATCCCATAATTAGG	59.522	44.000	0.00	0.00	0.00	2.69
559	566	8.149647	CCTCTCTAAAGCAATACTGAAGATCAT	58.850	37.037	0.00	0.00	0.00	2.45
560	567	9.195411	CTCTCTAAAGCAATACTGAAGATCATC	57.805	37.037	0.00	0.00	0.00	2.92
561	568	8.699130	TCTCTAAAGCAATACTGAAGATCATCA	58.301	33.333	0.01	0.01	0.00	3.07
572	579	7.621428	ACTGAAGATCATCAACATTACCAAG	57.379	36.000	1.81	0.00	0.00	3.61
634	667	5.092781	TCACGTTTGAAAAGAAGTTCAAGC	58.907	37.500	5.50	4.90	45.62	4.01
672	705	4.037858	ACCTAGCTTTATTGACGTACGG	57.962	45.455	21.06	1.43	0.00	4.02
730	763	7.335422	AGTTGTCTTCTTCAGATAAATCGCAAT	59.665	33.333	0.00	0.00	34.62	3.56
758	795	9.050601	CCAATTGTCTTTCTTCAGATATAGTCC	57.949	37.037	4.43	0.00	0.00	3.85
759	796	9.829507	CAATTGTCTTTCTTCAGATATAGTCCT	57.170	33.333	0.00	0.00	0.00	3.85
762	799	8.830915	TGTCTTTCTTCAGATATAGTCCTTCT	57.169	34.615	0.00	0.00	0.00	2.85
763	800	8.690884	TGTCTTTCTTCAGATATAGTCCTTCTG	58.309	37.037	0.00	0.00	38.56	3.02
764	801	8.691797	GTCTTTCTTCAGATATAGTCCTTCTGT	58.308	37.037	0.00	0.00	38.39	3.41
765	802	9.922477	TCTTTCTTCAGATATAGTCCTTCTGTA	57.078	33.333	0.00	0.00	38.39	2.74
766	803	9.959749	CTTTCTTCAGATATAGTCCTTCTGTAC	57.040	37.037	0.00	0.00	38.39	2.90
767	804	8.466617	TTCTTCAGATATAGTCCTTCTGTACC	57.533	38.462	0.00	0.00	38.39	3.34
768	805	6.711194	TCTTCAGATATAGTCCTTCTGTACCG	59.289	42.308	0.00	0.00	38.39	4.02
769	806	6.183810	TCAGATATAGTCCTTCTGTACCGA	57.816	41.667	0.00	0.00	38.39	4.69
770	807	6.598503	TCAGATATAGTCCTTCTGTACCGAA	58.401	40.000	0.00	0.00	38.39	4.30
771	808	7.058525	TCAGATATAGTCCTTCTGTACCGAAA	58.941	38.462	1.23	0.00	38.39	3.46
772	809	7.724506	TCAGATATAGTCCTTCTGTACCGAAAT	59.275	37.037	1.23	0.00	38.39	2.17

Showing 1 to 25 of 93 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.510360	AGTTTCACTATAGTCCTGCGTGT	59.490	43.478	1.26	0.00	0.00	4.49
8	9	4.499357	GGGTAGTTTCACTATAGTCCTGCG	60.499	50.000	1.26	0.00	32.65	5.18
91	92	6.831353	TCAAAAGACAAAGGAACCATTCACTA	59.169	34.615	0.00	0.00	0.00	2.74
172	173	2.043526	AGTGAAGCCCCAATCTCCAATT	59.956	45.455	0.00	0.00	0.00	2.32
288	289	1.619669	GAGACCCCTCACCCCCAAT	60.620	63.158	0.00	0.00	39.24	3.16
559	566	5.616270	TGTTAGCAGTCTTGGTAATGTTGA	58.384	37.500	2.97	0.00	45.77	3.18
560	567	5.940192	TGTTAGCAGTCTTGGTAATGTTG	57.060	39.130	2.97	0.00	45.77	3.33
561	568	6.062095	ACTTGTTAGCAGTCTTGGTAATGTT	58.938	36.000	2.97	0.00	45.77	2.71
572	579	5.636837	TGTGACAAAAACTTGTTAGCAGTC	58.363	37.500	0.00	0.00	34.90	3.51
619	652	6.507023	TCAAAGATGGCTTGAACTTCTTTTC	58.493	36.000	0.00	0.00	39.09	2.29
634	667	4.754114	GCTAGGTAGCTGATTCAAAGATGG	59.246	45.833	4.27	0.00	45.62	3.51
672	705	0.942252	ACGGTCCTTGAAGAAAACGC	59.058	50.000	5.17	0.00	0.00	4.84
682	715	3.004862	GGTTTGTATACCACGGTCCTTG	58.995	50.000	0.00	0.00	38.12	3.61
705	738	6.408858	TGCGATTTATCTGAAGAAGACAAC	57.591	37.500	0.00	0.00	37.88	3.32
755	792	5.476614	ACAAGTATTTCGGTACAGAAGGAC	58.523	41.667	8.46	10.29	0.00	3.85
756	793	5.733620	ACAAGTATTTCGGTACAGAAGGA	57.266	39.130	8.46	0.00	0.00	3.36
758	795	7.063074	CCAACTACAAGTATTTCGGTACAGAAG	59.937	40.741	8.46	0.00	0.00	2.85
759	796	6.869913	CCAACTACAAGTATTTCGGTACAGAA	59.130	38.462	4.18	4.18	0.00	3.02
760	797	6.392354	CCAACTACAAGTATTTCGGTACAGA	58.608	40.000	0.00	0.00	0.00	3.41
761	798	5.579511	CCCAACTACAAGTATTTCGGTACAG	59.420	44.000	0.00	0.00	0.00	2.74
762	799	5.481105	CCCAACTACAAGTATTTCGGTACA	58.519	41.667	0.00	0.00	0.00	2.90
763	800	4.872124	CCCCAACTACAAGTATTTCGGTAC	59.128	45.833	0.00	0.00	0.00	3.34
764	801	4.776837	TCCCCAACTACAAGTATTTCGGTA	59.223	41.667	0.00	0.00	0.00	4.02
765	802	3.583966	TCCCCAACTACAAGTATTTCGGT	59.416	43.478	0.00	0.00	0.00	4.69
766	803	4.210724	TCCCCAACTACAAGTATTTCGG	57.789	45.455	0.00	0.00	0.00	4.30

Showing 1 to 25 of 101 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.