AutoCloner

Multiple sequence alignment - TraesCS1B01G221200

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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	TraesCS1B01G221200	chr1B	100.000	3686	0	0	1	3686	398144859	398141174	0.000000e+00	6807
1	TraesCS1B01G221200	chr1B	92.857	336	23	1	12	347	683420809	683420475	1.540000e-133	486
2	TraesCS1B01G221200	chr1A	93.723	1609	85	9	1177	2777	369496250	369494650	0.000000e+00	2398
3	TraesCS1B01G221200	chr1A	90.603	1160	54	23	1	1124	369497401	369496261	0.000000e+00	1487
4	TraesCS1B01G221200	chr1D	91.916	1707	72	25	1	1665	296979362	296977680	0.000000e+00	2327
5	TraesCS1B01G221200	chr1D	94.364	692	36	2	1736	2425	296977549	296976859	0.000000e+00	1059
6	TraesCS1B01G221200	chr1D	85.714	497	57	9	2293	2777	296735365	296734871	2.540000e-141	512
7	TraesCS1B01G221200	chr1D	91.740	339	28	0	9	347	46479665	46480003	4.310000e-129	472
8	TraesCS1B01G221200	chr1D	86.555	357	30	11	2422	2777	296974721	296974382	9.660000e-101	377
9	TraesCS1B01G221200	chr1D	96.429	140	5	0	3443	3582	298551927	298551788	7.960000e-57	231
10	TraesCS1B01G221200	chr2D	92.035	339	27	0	9	347	36503387	36503725	9.260000e-131	477
11	TraesCS1B01G221200	chr5B	92.035	339	26	1	9	347	679584577	679584914	3.330000e-130	475
12	TraesCS1B01G221200	chr5B	97.917	144	3	0	3443	3586	54712454	54712597	2.200000e-62	250
13	TraesCS1B01G221200	chr7D	91.445	339	29	0	9	347	277456313	277456651	2.000000e-127	466
14	TraesCS1B01G221200	chr7D	91.642	335	27	1	14	347	168798070	168798404	2.590000e-126	462
15	TraesCS1B01G221200	chr3D	91.667	336	27	1	12	347	12135094	12134760	7.210000e-127	464
16	TraesCS1B01G221200	chr3D	95.833	144	6	0	3443	3586	299088253	299088396	2.210000e-57	233
17	TraesCS1B01G221200	chr7B	96.575	146	5	0	3437	3582	655740275	655740420	3.680000e-60	243
18	TraesCS1B01G221200	chr3A	96.552	145	5	0	3438	3582	97191960	97192104	1.320000e-59	241
19	TraesCS1B01G221200	chr6B	96.528	144	5	0	3443	3586	650917328	650917185	4.760000e-59	239
20	TraesCS1B01G221200	chr5A	97.122	139	4	0	3443	3581	579851070	579851208	6.150000e-58	235
21	TraesCS1B01G221200	chr2B	95.238	147	7	0	3440	3586	117612501	117612647	2.210000e-57	233
22	TraesCS1B01G221200	chr2A	94.558	147	8	0	3440	3586	76350655	76350801	1.030000e-55	228

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	TraesCS1B01G221200	chr1B	398141174	398144859	3685	True	6807.000000	6807	100.000	1	3686	1	chr1B.!!$R1	3685
1	TraesCS1B01G221200	chr1A	369494650	369497401	2751	True	1942.500000	2398	92.163	1	2777	2	chr1A.!!$R1	2776
2	TraesCS1B01G221200	chr1D	296974382	296979362	4980	True	1254.333333	2327	90.945	1	2777	3	chr1D.!!$R3	2776

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
593	603	0.110056	GTTCTTGTGATGGCTGTGCG	60.110	55.0	0.00	0.0	0.00	5.34	F
1391	1454	0.107703	TTAGCTCCATGGCTTCCGTG	60.108	55.0	6.96	0.0	42.97	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1721	1817	0.961019	TGCCATTGGAGTCAACAAGC	59.039	50.0	6.95	0.0	35.48	4.01	R
3369	5637	0.037326	GATGTGCCTGTCTCGGAACA	60.037	55.0	0.00	0.0	46.47	3.18	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
271	272	3.379445	GGTTCTCGCTCCCCGTCA	61.379	66.667	0.00	0.00	38.35	4.35
569	579	1.373497	CCTAGATGATGCGCCGTCC	60.373	63.158	4.18	0.00	0.00	4.79
570	580	1.730902	CTAGATGATGCGCCGTCCG	60.731	63.158	4.18	0.00	40.75	4.79
578	588	4.719369	GCGCCGTCCGAGTGTTCT	62.719	66.667	0.00	0.00	40.02	3.01
590	600	2.498167	GAGTGTTCTTGTGATGGCTGT	58.502	47.619	0.00	0.00	0.00	4.40
592	602	0.953727	TGTTCTTGTGATGGCTGTGC	59.046	50.000	0.00	0.00	0.00	4.57
593	603	0.110056	GTTCTTGTGATGGCTGTGCG	60.110	55.000	0.00	0.00	0.00	5.34
594	604	0.534877	TTCTTGTGATGGCTGTGCGT	60.535	50.000	0.00	0.00	0.00	5.24
595	605	0.320050	TCTTGTGATGGCTGTGCGTA	59.680	50.000	0.00	0.00	0.00	4.42
623	636	5.168569	CGTTGCATCTTTTACTCCAGTAGA	58.831	41.667	0.00	0.00	0.00	2.59
634	647	8.911918	TTTTACTCCAGTAGATTGTTGCTTTA	57.088	30.769	0.00	0.00	0.00	1.85
635	648	8.911918	TTTACTCCAGTAGATTGTTGCTTTAA	57.088	30.769	0.00	0.00	0.00	1.52
677	691	6.480763	TGGCCATGTAAAATTTCTCAGTAGA	58.519	36.000	0.00	0.00	0.00	2.59
678	692	7.118723	TGGCCATGTAAAATTTCTCAGTAGAT	58.881	34.615	0.00	0.00	0.00	1.98
679	693	7.067372	TGGCCATGTAAAATTTCTCAGTAGATG	59.933	37.037	0.00	0.00	0.00	2.90
696	712	3.987547	AGATGTAGATGTCAGCGAATGG	58.012	45.455	0.00	0.00	0.00	3.16
724	740	4.574828	GGTACCCTGTATGCACATTTACTG	59.425	45.833	0.00	0.00	33.14	2.74
743	763	1.435966	GCGCACGTACGTTTGTGAC	60.436	57.895	20.23	7.94	38.36	3.67
863	883	1.290134	GGTTGGGGGAATCTCTGTCT	58.710	55.000	0.00	0.00	0.00	3.41
866	886	3.459969	GGTTGGGGGAATCTCTGTCTATT	59.540	47.826	0.00	0.00	0.00	1.73
918	938	2.417933	AGCTCACATGCATTTCGTCTTC	59.582	45.455	0.00	0.00	34.99	2.87
919	939	2.785681	GCTCACATGCATTTCGTCTTCG	60.786	50.000	0.00	0.00	38.55	3.79
920	940	2.667969	CTCACATGCATTTCGTCTTCGA	59.332	45.455	0.00	0.00	44.66	3.71
923	943	3.612423	CACATGCATTTCGTCTTCGAGTA	59.388	43.478	0.00	0.00	46.81	2.59
924	944	4.268644	CACATGCATTTCGTCTTCGAGTAT	59.731	41.667	0.00	0.00	46.81	2.12

Showing 1 to 25 of 788 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
532	542	7.278461	TCTAGGAATCCTTCTTATCTTCGTG	57.722	40.000	7.30	0.00	34.61	4.35
561	571	4.719369	AGAACACTCGGACGGCGC	62.719	66.667	6.90	0.00	0.00	6.53
569	579	1.462283	CAGCCATCACAAGAACACTCG	59.538	52.381	0.00	0.00	0.00	4.18
570	580	2.225019	CACAGCCATCACAAGAACACTC	59.775	50.000	0.00	0.00	0.00	3.51
578	588	1.298157	GCTACGCACAGCCATCACAA	61.298	55.000	0.00	0.00	35.40	3.33
592	602	1.966493	AAAGATGCAACGCGGCTACG	61.966	55.000	12.47	0.00	44.63	3.51
593	603	0.168128	AAAAGATGCAACGCGGCTAC	59.832	50.000	12.47	3.79	34.04	3.58
594	604	1.395608	GTAAAAGATGCAACGCGGCTA	59.604	47.619	12.47	0.00	34.04	3.93
595	605	0.168128	GTAAAAGATGCAACGCGGCT	59.832	50.000	12.47	0.00	34.04	5.52
608	618	7.440523	AAGCAACAATCTACTGGAGTAAAAG	57.559	36.000	0.00	0.00	0.00	2.27
623	636	4.687976	AGGGAAGGGATTAAAGCAACAAT	58.312	39.130	0.00	0.00	0.00	2.71
634	647	5.155161	GGCCAAAATATTAGGGAAGGGATT	58.845	41.667	0.00	0.00	0.00	3.01
635	648	4.171841	TGGCCAAAATATTAGGGAAGGGAT	59.828	41.667	0.61	0.00	0.00	3.85
677	691	4.122776	GTTCCATTCGCTGACATCTACAT	58.877	43.478	0.00	0.00	0.00	2.29
678	692	3.195610	AGTTCCATTCGCTGACATCTACA	59.804	43.478	0.00	0.00	0.00	2.74
679	693	3.553511	CAGTTCCATTCGCTGACATCTAC	59.446	47.826	0.00	0.00	32.39	2.59
724	740	2.127906	CACAAACGTACGTGCGCC	60.128	61.111	26.01	0.00	34.88	6.53
743	763	3.403038	ACATTCAAACTCAAGAGTCCCG	58.597	45.455	2.78	0.00	41.58	5.14
863	883	8.840321	GCCAAGCTCTATTTCTTTATGACAATA	58.160	33.333	0.00	0.00	0.00	1.90
866	886	6.179756	TGCCAAGCTCTATTTCTTTATGACA	58.820	36.000	0.00	0.00	0.00	3.58
918	938	5.842843	CGTTGTAACATACTCCGTATACTCG	59.157	44.000	0.56	0.00	0.00	4.18
919	939	6.719365	ACGTTGTAACATACTCCGTATACTC	58.281	40.000	0.56	0.00	35.25	2.59
920	940	6.510157	CGACGTTGTAACATACTCCGTATACT	60.510	42.308	0.56	0.00	36.42	2.12
923	943	4.496341	CCGACGTTGTAACATACTCCGTAT	60.496	45.833	1.30	0.00	36.42	3.06
924	944	3.181511	CCGACGTTGTAACATACTCCGTA	60.182	47.826	1.30	0.00	36.42	4.02

Showing 1 to 25 of 768 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.