AutoCloner

Multiple sequence alignment - TraesCS4B01G297300

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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	TraesCS4B01G297300	chr4B	100.000	3650	0	0	1	3650	582828335	582824686	0.000000e+00	6741
1	TraesCS4B01G297300	chr4B	80.987	547	50	25	2670	3166	595269381	595269923	5.720000e-103	385
2	TraesCS4B01G297300	chr4D	87.513	1866	135	55	2	1837	465761856	465760059	0.000000e+00	2065
3	TraesCS4B01G297300	chr4D	93.054	1123	47	11	1853	2971	465760011	465758916	0.000000e+00	1613
4	TraesCS4B01G297300	chr4D	89.137	313	19	5	2670	2971	472923434	472923742	3.440000e-100	375
5	TraesCS4B01G297300	chr4A	88.502	1635	94	36	1609	3191	4820376	4821968	0.000000e+00	1892
6	TraesCS4B01G297300	chr4A	91.759	813	24	15	1	798	4797074	4797858	0.000000e+00	1090
7	TraesCS4B01G297300	chr4A	89.711	865	40	24	789	1620	4817855	4818703	0.000000e+00	1059
8	TraesCS4B01G297300	chr1D	87.855	387	45	2	3265	3650	340670077	340669692	1.550000e-123	453
9	TraesCS4B01G297300	chr1D	86.780	295	34	4	1017	1306	204024059	204024353	1.260000e-84	324
10	TraesCS4B01G297300	chr3D	86.632	389	49	1	3265	3650	283307024	283306636	9.370000e-116	427
11	TraesCS4B01G297300	chr3B	85.677	384	50	3	3265	3645	377404077	377403696	2.040000e-107	399
12	TraesCS4B01G297300	chr3A	84.833	389	54	3	3265	3649	370215583	370215196	1.590000e-103	387
13	TraesCS4B01G297300	chr7D	85.879	347	45	2	3307	3650	107676926	107676581	2.070000e-97	366
14	TraesCS4B01G297300	chr6D	84.511	368	46	7	3291	3650	27322058	27322422	1.610000e-93	353
15	TraesCS4B01G297300	chr6B	84.153	366	54	4	3281	3644	719907275	719907638	5.800000e-93	351
16	TraesCS4B01G297300	chr6B	83.465	381	57	4	3268	3645	193825	193448	2.090000e-92	350
17	TraesCS4B01G297300	chr5B	83.641	379	56	6	3275	3650	372087659	372087284	5.800000e-93	351
18	TraesCS4B01G297300	chr1A	86.780	295	34	4	1017	1306	259049416	259049710	1.260000e-84	324
19	TraesCS4B01G297300	chr1B	85.763	295	37	4	1017	1306	299438023	299438317	1.270000e-79	307

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	TraesCS4B01G297300	chr4B	582824686	582828335	3649	True	6741.0	6741	100.0000	1	3650	1	chr4B.!!$R1	3649
1	TraesCS4B01G297300	chr4B	595269381	595269923	542	False	385.0	385	80.9870	2670	3166	1	chr4B.!!$F1	496
2	TraesCS4B01G297300	chr4D	465758916	465761856	2940	True	1839.0	2065	90.2835	2	2971	2	chr4D.!!$R1	2969
3	TraesCS4B01G297300	chr4A	4817855	4821968	4113	False	1475.5	1892	89.1065	789	3191	2	chr4A.!!$F2	2402
4	TraesCS4B01G297300	chr4A	4797074	4797858	784	False	1090.0	1090	91.7590	1	798	1	chr4A.!!$F1	797

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
947	967	0.977395	CACTCCCTTCCTTCGTCCTT	59.023	55.0	0.0	0.0	0.0	3.36	F
1405	1435	0.032813	AGATTGTGGCTGGATTGGGG	60.033	55.0	0.0	0.0	0.0	4.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1921	3691	1.196127	GCCCCTTTAACTTTGTCGACG	59.804	52.381	11.62	0.0	0.0	5.12	R
3341	5177	0.394625	AGTAGTCGACAGAGGGGAGC	60.395	60.000	19.50	0.0	0.0	4.70	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
383	384	1.371512	CAGGCATTTGCGCGAACAA	60.372	52.632	13.41	1.72	43.26	2.83
385	386	2.719774	GGCATTTGCGCGAACAAGC	61.720	57.895	13.41	16.39	43.26	4.01
420	421	2.322830	GGTGCCGACGGAAAAGACC	61.323	63.158	20.50	10.60	0.00	3.85
448	449	4.777463	AGGGTTAAAACGATGGTATGAGG	58.223	43.478	0.00	0.00	0.00	3.86
575	585	4.521062	GCCGCGGAGATGAGTGCT	62.521	66.667	33.48	0.00	0.00	4.40
576	586	2.279120	CCGCGGAGATGAGTGCTC	60.279	66.667	24.07	0.00	0.00	4.26
586	596	1.908340	ATGAGTGCTCCAGTCCCAGC	61.908	60.000	0.00	0.00	33.27	4.85
587	597	3.322318	GAGTGCTCCAGTCCCAGCC	62.322	68.421	0.00	0.00	34.47	4.85
588	598	3.640407	GTGCTCCAGTCCCAGCCA	61.640	66.667	0.00	0.00	34.47	4.75
589	599	3.640407	TGCTCCAGTCCCAGCCAC	61.640	66.667	0.00	0.00	34.47	5.01
590	600	3.640407	GCTCCAGTCCCAGCCACA	61.640	66.667	0.00	0.00	0.00	4.17
591	601	2.667418	CTCCAGTCCCAGCCACAG	59.333	66.667	0.00	0.00	0.00	3.66
675	686	2.232298	GAGAACTCAGCTGGACCGGG	62.232	65.000	15.13	0.00	0.00	5.73
929	945	1.685224	GGCCAGTTCACTCCCATCA	59.315	57.895	0.00	0.00	0.00	3.07
947	967	0.977395	CACTCCCTTCCTTCGTCCTT	59.023	55.000	0.00	0.00	0.00	3.36
972	992	1.987855	CCCACTCCTACGCTTCCCA	60.988	63.158	0.00	0.00	0.00	4.37
973	993	1.550130	CCCACTCCTACGCTTCCCAA	61.550	60.000	0.00	0.00	0.00	4.12
1226	1250	1.176619	TCACCGAAGAGCTCGTGGAA	61.177	55.000	23.22	11.39	46.65	3.53
1262	1286	1.590147	CTTCCGCTCGTACAACCCT	59.410	57.895	0.00	0.00	0.00	4.34
1339	1365	5.761165	TTTTCAGTACAACTTTAGCCCAC	57.239	39.130	0.00	0.00	0.00	4.61
1382	1412	0.958091	CTTGTTGGCGTCAAATGGGA	59.042	50.000	2.85	0.00	34.28	4.37
1403	1433	2.431954	AGAGATTGTGGCTGGATTGG	57.568	50.000	0.00	0.00	0.00	3.16
1405	1435	0.032813	AGATTGTGGCTGGATTGGGG	60.033	55.000	0.00	0.00	0.00	4.96
1408	1438	2.042639	GTGGCTGGATTGGGGCAT	60.043	61.111	0.00	0.00	40.00	4.40
1409	1439	2.042741	TGGCTGGATTGGGGCATG	60.043	61.111	0.00	0.00	33.16	4.06

Showing 1 to 25 of 350 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	2.995872	GCTCTTCGAGGTCTGCCGT	61.996	63.158	0.00	0.00	40.50	5.68
83	84	2.671619	GCCAAGCCGCACAAGGTA	60.672	61.111	0.00	0.00	0.00	3.08
239	240	3.479370	CGGAGCAAGAAGAAGCGG	58.521	61.111	0.00	0.00	35.48	5.52
420	421	2.277084	CATCGTTTTAACCCTCTCCGG	58.723	52.381	0.00	0.00	0.00	5.14
430	431	5.180271	GGTGACCTCATACCATCGTTTTAA	58.820	41.667	0.00	0.00	36.94	1.52
564	574	0.463620	GGGACTGGAGCACTCATCTC	59.536	60.000	0.00	0.00	0.00	2.75
568	578	2.587247	GCTGGGACTGGAGCACTCA	61.587	63.158	0.00	0.00	35.15	3.41
572	582	3.640407	GTGGCTGGGACTGGAGCA	61.640	66.667	0.00	0.00	36.90	4.26
574	584	2.667418	CTGTGGCTGGGACTGGAG	59.333	66.667	0.00	0.00	0.00	3.86
575	585	3.640407	GCTGTGGCTGGGACTGGA	61.640	66.667	0.00	0.00	35.22	3.86
576	586	4.729918	GGCTGTGGCTGGGACTGG	62.730	72.222	0.00	0.00	38.73	4.00
578	588	3.644606	CTGGCTGTGGCTGGGACT	61.645	66.667	0.00	0.00	38.73	3.85
579	589	4.729918	CCTGGCTGTGGCTGGGAC	62.730	72.222	8.73	0.00	41.97	4.46
586	596	4.463879	CTCTCGCCCTGGCTGTGG	62.464	72.222	6.60	0.00	39.32	4.17
587	597	3.368190	CTCTCTCGCCCTGGCTGTG	62.368	68.421	6.60	1.76	39.32	3.66
588	598	3.073735	CTCTCTCGCCCTGGCTGT	61.074	66.667	6.60	0.00	39.32	4.40
589	599	3.073735	ACTCTCTCGCCCTGGCTG	61.074	66.667	6.60	0.24	39.32	4.85
590	600	3.073735	CACTCTCTCGCCCTGGCT	61.074	66.667	6.60	0.00	39.32	4.75
591	601	3.071206	TCACTCTCTCGCCCTGGC	61.071	66.667	0.00	0.00	37.85	4.85
656	667	1.216710	CCGGTCCAGCTGAGTTCTC	59.783	63.158	17.39	0.00	0.00	2.87
675	686	3.179048	GGCGAATAAGTGTTTCATTGGC	58.821	45.455	0.00	0.00	34.00	4.52
871	886	2.436646	CCGCCCGGATATGCCATC	60.437	66.667	0.73	0.00	37.50	3.51
929	945	1.348036	CAAAGGACGAAGGAAGGGAGT	59.652	52.381	0.00	0.00	0.00	3.85
947	967	1.972198	CGTAGGAGTGGGAGTGCAA	59.028	57.895	0.00	0.00	0.00	4.08
972	992	2.125673	CGACGGAATGGCGAGGTT	60.126	61.111	0.00	0.00	0.00	3.50

Showing 1 to 25 of 362 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.