AutoCloner

Multiple sequence alignment - TraesCS4D01G196000

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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	TraesCS4D01G196000	chr4D	100.000	2469	0	0	1	2469	340303022	340300554	0.000000e+00	4560.0
1	TraesCS4D01G196000	chr4D	100.000	39	0	0	2730	2768	340300293	340300255	3.820000e-09	73.1
2	TraesCS4D01G196000	chr4B	96.689	1812	31	11	661	2462	421742343	421740551	0.000000e+00	2987.0
3	TraesCS4D01G196000	chr4B	100.000	39	0	0	2730	2768	421740209	421740171	3.820000e-09	73.1
4	TraesCS4D01G196000	chr4A	96.905	1163	22	10	661	1819	127806573	127807725	0.000000e+00	1936.0
5	TraesCS4D01G196000	chr4A	91.000	600	22	13	1853	2428	127807722	127808313	0.000000e+00	780.0
6	TraesCS4D01G196000	chr4A	85.973	663	93	0	1	663	640035142	640034480	0.000000e+00	710.0
7	TraesCS4D01G196000	chr5D	86.336	666	91	0	2	667	374009372	374008707	0.000000e+00	726.0
8	TraesCS4D01G196000	chr6D	86.425	663	88	2	2	663	87998033	87998694	0.000000e+00	725.0
9	TraesCS4D01G196000	chr3A	86.036	666	89	3	1	663	657063506	657064170	0.000000e+00	712.0
10	TraesCS4D01G196000	chr6A	84.812	665	99	2	4	667	377896080	377895417	0.000000e+00	667.0
11	TraesCS4D01G196000	chr2B	83.333	666	111	0	2	667	422275481	422274816	1.410000e-172	616.0
12	TraesCS4D01G196000	chr2B	83.107	663	112	0	1	663	648873340	648874002	3.050000e-169	604.0
13	TraesCS4D01G196000	chr2B	82.477	662	115	1	2	663	3465877	3466537	1.850000e-161	579.0
14	TraesCS4D01G196000	chr7B	83.107	663	112	0	1	663	254543095	254543757	3.050000e-169	604.0

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	TraesCS4D01G196000	chr4D	340300255	340303022	2767	True	2316.55	4560	100.0000	1	2768	2	chr4D.!!$R1	2767
1	TraesCS4D01G196000	chr4B	421740171	421742343	2172	True	1530.05	2987	98.3445	661	2768	2	chr4B.!!$R1	2107
2	TraesCS4D01G196000	chr4A	127806573	127808313	1740	False	1358.00	1936	93.9525	661	2428	2	chr4A.!!$F1	1767
3	TraesCS4D01G196000	chr4A	640034480	640035142	662	True	710.00	710	85.9730	1	663	1	chr4A.!!$R1	662
4	TraesCS4D01G196000	chr5D	374008707	374009372	665	True	726.00	726	86.3360	2	667	1	chr5D.!!$R1	665
5	TraesCS4D01G196000	chr6D	87998033	87998694	661	False	725.00	725	86.4250	2	663	1	chr6D.!!$F1	661
6	TraesCS4D01G196000	chr3A	657063506	657064170	664	False	712.00	712	86.0360	1	663	1	chr3A.!!$F1	662
7	TraesCS4D01G196000	chr6A	377895417	377896080	663	True	667.00	667	84.8120	4	667	1	chr6A.!!$R1	663
8	TraesCS4D01G196000	chr2B	422274816	422275481	665	True	616.00	616	83.3330	2	667	1	chr2B.!!$R1	665
9	TraesCS4D01G196000	chr2B	648873340	648874002	662	False	604.00	604	83.1070	1	663	1	chr2B.!!$F2	662
10	TraesCS4D01G196000	chr2B	3465877	3466537	660	False	579.00	579	82.4770	2	663	1	chr2B.!!$F1	661
11	TraesCS4D01G196000	chr7B	254543095	254543757	662	False	604.00	604	83.1070	1	663	1	chr7B.!!$F1	662

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
447	451	0.884704	GCCTGTTCCACGCTTGAGAA	60.885	55.000	0.0	0.0	0.0	2.87	F
654	659	1.134220	TGTTCGAGCAGAGGGTTTTGT	60.134	47.619	0.0	0.0	0.0	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1575	1587	1.374947	CAGGAAGAGGGAAACGGCA	59.625	57.895	0.0	0.0	0.0	5.69	R
1905	1921	5.163258	TGTGTTGGCAAAGGGTTTATCATTT	60.163	36.000	0.0	0.0	0.0	2.32	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
38	39	5.482175	CGAAGAGTATAGATTCCTTCCCCAT	59.518	44.000	0.00	0.00	32.01	4.00
48	49	6.037290	AGATTCCTTCCCCATATGATCATCT	58.963	40.000	12.53	0.00	0.00	2.90
65	66	7.384477	TGATCATCTACCACAGAATCATCATC	58.616	38.462	0.00	0.00	36.67	2.92
69	70	3.185246	ACCACAGAATCATCATCCGTC	57.815	47.619	0.00	0.00	0.00	4.79
70	71	2.158900	ACCACAGAATCATCATCCGTCC	60.159	50.000	0.00	0.00	0.00	4.79
104	105	8.610035	GGAGATAAAATTCTTTCGGTATCGTTT	58.390	33.333	0.00	0.00	37.69	3.60
114	115	1.533731	CGGTATCGTTTTGTTGCCACT	59.466	47.619	0.00	0.00	0.00	4.00
156	157	3.260475	TCGTCACCGAATTTGATCCAT	57.740	42.857	0.00	0.00	40.86	3.41
162	163	6.017934	CGTCACCGAATTTGATCCATCTAATT	60.018	38.462	8.22	8.22	42.16	1.40
210	211	9.283768	TCTTTCTGATGTTGTAGCAATCTTAAA	57.716	29.630	0.00	0.00	0.00	1.52
255	256	4.546829	AAAGTTATTCTCTGGCACCGTA	57.453	40.909	0.00	0.00	0.00	4.02
296	297	2.225091	TGTGATCCAATTCAAGCAGGGT	60.225	45.455	0.00	0.00	0.00	4.34
324	325	7.653647	TGTTGGTATTCTCTAACGCAATTTTT	58.346	30.769	0.00	0.00	0.00	1.94
408	412	3.651803	AGACTAGTCGCAGCATTATCC	57.348	47.619	17.07	0.00	34.09	2.59
419	423	3.571571	CAGCATTATCCGATTTGCCATG	58.428	45.455	10.72	0.00	35.71	3.66
423	427	5.301551	AGCATTATCCGATTTGCCATGTTTA	59.698	36.000	10.72	0.00	35.71	2.01
438	442	1.254026	GTTTAAGGGGCCTGTTCCAC	58.746	55.000	0.84	0.00	0.00	4.02
447	451	0.884704	GCCTGTTCCACGCTTGAGAA	60.885	55.000	0.00	0.00	0.00	2.87
483	488	2.180086	TCCAGGGTGAGCTATCCAGTAT	59.820	50.000	8.60	0.00	28.98	2.12
550	555	2.674380	CAGAGCAAGGGGTGTGGC	60.674	66.667	0.00	0.00	32.61	5.01
590	595	4.895889	CAGAGGATTGACCATGGTACTAGA	59.104	45.833	19.80	2.34	42.04	2.43
618	623	6.102663	AGAAGATGTCCAATTTAGAGTCGTG	58.897	40.000	0.00	0.00	0.00	4.35
624	629	7.504924	TGTCCAATTTAGAGTCGTGAAAAAT	57.495	32.000	0.00	0.00	0.00	1.82
636	641	7.280205	AGAGTCGTGAAAAATTAGTCAAGTTGT	59.720	33.333	2.11	0.00	0.00	3.32
654	659	1.134220	TGTTCGAGCAGAGGGTTTTGT	60.134	47.619	0.00	0.00	0.00	2.83
751	760	1.538950	CTGGCAGAAAACTGGAGAAGC	59.461	52.381	9.42	0.00	0.00	3.86
769	779	1.554160	AGCTCAGATCCTTGTCACCTG	59.446	52.381	0.00	0.00	0.00	4.00
781	791	4.069869	CACCTGAGCAACCTGGTG	57.930	61.111	0.00	12.69	45.32	4.17
786	796	1.233019	CTGAGCAACCTGGTGAAGTG	58.767	55.000	0.00	0.00	0.00	3.16
792	802	2.404215	CAACCTGGTGAAGTGAGTACG	58.596	52.381	0.00	0.00	0.00	3.67
795	805	3.225104	ACCTGGTGAAGTGAGTACGTAA	58.775	45.455	0.00	0.00	0.00	3.18
810	821	7.756722	GTGAGTACGTAATTGCTCCTTTACTTA	59.243	37.037	0.00	0.00	0.00	2.24
812	823	8.471361	AGTACGTAATTGCTCCTTTACTTAAC	57.529	34.615	0.00	0.00	0.00	2.01
829	840	2.127758	CCACGAAACGCGCAACTC	60.128	61.111	5.73	0.00	46.04	3.01
841	852	1.260561	GCGCAACTCGAAAACTGAAGA	59.739	47.619	0.30	0.00	41.67	2.87
1575	1587	2.406559	CTCCCCATGGTCATCTTCTCT	58.593	52.381	11.73	0.00	0.00	3.10
1593	1605	0.674895	CTGCCGTTTCCCTCTTCCTG	60.675	60.000	0.00	0.00	0.00	3.86
1812	1825	8.439971	AGGTATGCTTTCATAATTCACCAGATA	58.560	33.333	0.00	0.00	36.96	1.98
2451	2492	2.593468	TAGCTTGGAGATGCACCGGC	62.593	60.000	0.00	0.00	41.68	6.13
2464	2505	4.832608	CCGGCCGGTGGTTAGAGC	62.833	72.222	36.64	0.00	0.00	4.09
2465	2506	3.771160	CGGCCGGTGGTTAGAGCT	61.771	66.667	20.10	0.00	0.00	4.09
2466	2507	2.420568	CGGCCGGTGGTTAGAGCTA	61.421	63.158	20.10	0.00	0.00	3.32
2467	2508	1.442148	GGCCGGTGGTTAGAGCTAG	59.558	63.158	1.90	0.00	0.00	3.42
2468	2509	1.227292	GCCGGTGGTTAGAGCTAGC	60.227	63.158	6.62	6.62	0.00	3.42

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	6.943899	ATGGGGAAGGAATCTATACTCTTC	57.056	41.667	0.00	0.00	34.69	2.87
38	39	8.426569	TGATGATTCTGTGGTAGATGATCATA	57.573	34.615	8.54	0.00	40.75	2.15
48	49	3.069586	GGACGGATGATGATTCTGTGGTA	59.930	47.826	0.00	0.00	32.88	3.25
65	66	1.403814	TATCTCCAGCTTGAGGACGG	58.596	55.000	14.43	0.00	33.04	4.79
69	70	7.401955	AAAGAATTTTATCTCCAGCTTGAGG	57.598	36.000	14.43	0.00	31.62	3.86
70	71	7.185453	CGAAAGAATTTTATCTCCAGCTTGAG	58.815	38.462	8.52	8.52	39.27	3.02
147	148	5.263599	AGGTGCACAATTAGATGGATCAAA	58.736	37.500	20.43	0.00	0.00	2.69
156	157	5.136828	TGGAAAAAGAGGTGCACAATTAGA	58.863	37.500	20.43	0.00	0.00	2.10
162	163	4.469657	AGTATTGGAAAAAGAGGTGCACA	58.530	39.130	20.43	0.00	0.00	4.57
241	242	0.834687	ACCCTTACGGTGCCAGAGAA	60.835	55.000	0.00	0.00	46.09	2.87
255	256	1.895020	TTGCAGATCGCCGTACCCTT	61.895	55.000	7.00	0.00	41.33	3.95
296	297	6.621316	TTGCGTTAGAGAATACCAACAAAA	57.379	33.333	0.00	0.00	0.00	2.44
324	325	5.815581	TGGAGCAAGAAAATTTCTAGGCTA	58.184	37.500	24.87	14.00	45.09	3.93
408	412	2.738321	GCCCCTTAAACATGGCAAATCG	60.738	50.000	0.00	0.00	43.46	3.34
419	423	1.254026	GTGGAACAGGCCCCTTAAAC	58.746	55.000	0.00	0.00	41.80	2.01
438	442	0.878523	TGGACGTGGTTTCTCAAGCG	60.879	55.000	0.00	0.00	32.63	4.68
447	451	2.356741	CCCTGGATTTATGGACGTGGTT	60.357	50.000	0.00	0.00	0.00	3.67
552	557	4.065281	CTGGGTCGACCGGTGTCC	62.065	72.222	27.68	13.52	44.64	4.02
567	572	4.895889	TCTAGTACCATGGTCAATCCTCTG	59.104	45.833	23.76	7.59	37.07	3.35
590	595	8.507249	CGACTCTAAATTGGACATCTTCTTTTT	58.493	33.333	0.00	0.00	0.00	1.94
618	623	6.910433	TGCTCGAACAACTTGACTAATTTTTC	59.090	34.615	0.00	0.00	0.00	2.29
624	629	4.299155	CTCTGCTCGAACAACTTGACTAA	58.701	43.478	0.00	0.00	0.00	2.24
632	637	1.594331	AAACCCTCTGCTCGAACAAC	58.406	50.000	0.00	0.00	0.00	3.32
636	641	1.946768	CAACAAAACCCTCTGCTCGAA	59.053	47.619	0.00	0.00	0.00	3.71
751	760	3.523606	CTCAGGTGACAAGGATCTGAG	57.476	52.381	0.00	0.00	43.29	3.35
769	779	1.202698	ACTCACTTCACCAGGTTGCTC	60.203	52.381	0.00	0.00	0.00	4.26
781	791	4.745649	AGGAGCAATTACGTACTCACTTC	58.254	43.478	11.64	0.49	0.00	3.01
786	796	8.590470	GTTAAGTAAAGGAGCAATTACGTACTC	58.410	37.037	0.00	0.00	37.16	2.59
792	802	6.369615	TCGTGGTTAAGTAAAGGAGCAATTAC	59.630	38.462	0.00	0.00	33.25	1.89
795	805	4.901868	TCGTGGTTAAGTAAAGGAGCAAT	58.098	39.130	0.00	0.00	0.00	3.56
810	821	2.023601	GTTGCGCGTTTCGTGGTT	59.976	55.556	8.43	0.00	41.07	3.67
812	823	2.127758	GAGTTGCGCGTTTCGTGG	60.128	61.111	8.43	0.00	41.07	4.94
829	840	3.483558	GCTGTGCTTTTCTTCAGTTTTCG	59.516	43.478	0.00	0.00	0.00	3.46
841	852	0.100503	GTGACCAACGCTGTGCTTTT	59.899	50.000	0.00	0.00	0.00	2.27
1575	1587	1.374947	CAGGAAGAGGGAAACGGCA	59.625	57.895	0.00	0.00	0.00	5.69
1905	1921	5.163258	TGTGTTGGCAAAGGGTTTATCATTT	60.163	36.000	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.