AutoCloner

Multiple sequence alignment - TraesCS1B01G192100

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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	TraesCS1B01G192100	chr1B	100.000	4248	0	0	1	4248	343665738	343661491	0.000000e+00	7845.0
1	TraesCS1B01G192100	chr1B	100.000	46	0	0	391	436	576029140	576029095	7.570000e-13	86.1
2	TraesCS1B01G192100	chr1D	93.765	2422	112	17	919	3325	270024014	270021617	0.000000e+00	3600.0
3	TraesCS1B01G192100	chr1D	97.401	885	23	0	3364	4248	270021618	270020734	0.000000e+00	1507.0
4	TraesCS1B01G192100	chr1D	86.354	491	46	13	2	482	270024704	270024225	2.260000e-142	516.0
5	TraesCS1B01G192100	chr1D	88.506	261	25	5	47	305	430320475	430320218	1.150000e-80	311.0
6	TraesCS1B01G192100	chr1A	94.395	1784	73	9	819	2584	343621942	343620168	0.000000e+00	2715.0
7	TraesCS1B01G192100	chr1A	96.105	1669	54	7	2581	4248	343619141	343617483	0.000000e+00	2712.0
8	TraesCS1B01G192100	chr1A	90.228	307	20	7	473	775	525024586	525024886	3.980000e-105	392.0
9	TraesCS1B01G192100	chr5D	95.063	790	34	5	2334	3123	325957147	325956363	0.000000e+00	1238.0
10	TraesCS1B01G192100	chr5D	86.447	546	33	9	832	1366	325958850	325959365	1.030000e-155	560.0
11	TraesCS1B01G192100	chr5D	85.821	268	36	2	47	313	520111444	520111710	2.500000e-72	283.0
12	TraesCS1B01G192100	chr7B	93.561	792	40	5	2334	3123	5917895	5917113	0.000000e+00	1170.0
13	TraesCS1B01G192100	chr7B	89.902	307	22	2	475	774	739246388	739246084	1.850000e-103	387.0
14	TraesCS1B01G192100	chr7B	86.590	261	32	3	47	305	104298591	104298332	6.950000e-73	285.0
15	TraesCS1B01G192100	chr7B	91.667	60	3	2	384	442	701637092	701637034	9.790000e-12	82.4
16	TraesCS1B01G192100	chr7B	95.745	47	1	1	389	434	683166851	683166897	1.640000e-09	75.0
17	TraesCS1B01G192100	chr5A	94.861	720	35	2	2404	3123	430641801	430642518	0.000000e+00	1123.0
18	TraesCS1B01G192100	chr5A	95.833	72	3	0	2334	2405	430641463	430641534	2.680000e-22	117.0
19	TraesCS1B01G192100	chr5B	92.484	306	16	2	475	773	124716393	124716698	8.440000e-117	431.0
20	TraesCS1B01G192100	chr5B	85.338	266	37	2	48	312	703850174	703849910	1.500000e-69	274.0
21	TraesCS1B01G192100	chr5B	84.758	269	41	0	41	309	511291327	511291595	1.950000e-68	270.0
22	TraesCS1B01G192100	chr4A	92.459	305	17	1	474	772	10642050	10641746	8.440000e-117	431.0
23	TraesCS1B01G192100	chr4A	90.909	55	4	1	389	442	143238944	143238890	5.890000e-09	73.1
24	TraesCS1B01G192100	chr2B	90.203	296	25	4	478	773	30230368	30230077	2.400000e-102	383.0
25	TraesCS1B01G192100	chr2B	91.071	56	3	2	384	439	30299019	30298966	1.640000e-09	75.0
26	TraesCS1B01G192100	chr6A	89.404	302	27	3	474	772	504938819	504939118	4.010000e-100	375.0
27	TraesCS1B01G192100	chr6A	95.833	48	0	1	390	435	456781875	456781922	4.550000e-10	76.8
28	TraesCS1B01G192100	chrUn	89.527	296	27	2	478	773	178511019	178511310	5.190000e-99	372.0
29	TraesCS1B01G192100	chrUn	88.851	296	29	2	478	773	178494292	178494583	1.120000e-95	361.0
30	TraesCS1B01G192100	chr6B	88.026	309	29	6	476	781	233671702	233671399	4.040000e-95	359.0
31	TraesCS1B01G192100	chr7D	86.364	264	34	2	43	305	515486967	515487229	1.930000e-73	287.0
32	TraesCS1B01G192100	chr7D	100.000	43	0	0	392	434	235530992	235530950	3.520000e-11	80.5
33	TraesCS1B01G192100	chr4D	84.871	271	37	4	49	317	12696149	12695881	1.950000e-68	270.0
34	TraesCS1B01G192100	chr3A	84.871	271	38	3	47	315	134257424	134257693	1.950000e-68	270.0
35	TraesCS1B01G192100	chr2A	97.778	45	0	1	391	434	43462451	43462495	4.550000e-10	76.8
36	TraesCS1B01G192100	chr4B	95.745	47	1	1	391	436	591486555	591486601	1.640000e-09	75.0

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	TraesCS1B01G192100	chr1B	343661491	343665738	4247	True	7845.000000	7845	100.000000	1	4248	1	chr1B.!!$R1	4247
1	TraesCS1B01G192100	chr1D	270020734	270024704	3970	True	1874.333333	3600	92.506667	2	4248	3	chr1D.!!$R2	4246
2	TraesCS1B01G192100	chr1A	343617483	343621942	4459	True	2713.500000	2715	95.250000	819	4248	2	chr1A.!!$R1	3429
3	TraesCS1B01G192100	chr5D	325956363	325957147	784	True	1238.000000	1238	95.063000	2334	3123	1	chr5D.!!$R1	789
4	TraesCS1B01G192100	chr5D	325958850	325959365	515	False	560.000000	560	86.447000	832	1366	1	chr5D.!!$F1	534
5	TraesCS1B01G192100	chr7B	5917113	5917895	782	True	1170.000000	1170	93.561000	2334	3123	1	chr7B.!!$R1	789
6	TraesCS1B01G192100	chr5A	430641463	430642518	1055	False	620.000000	1123	95.347000	2334	3123	2	chr5A.!!$F1	789

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
520	528	0.102300	AGCGCTCATATACACGTGCA	59.898	50.0	17.22	2.06	35.49	4.57	F
551	559	0.179250	CTATGAACGCACACACGCAC	60.179	55.0	0.00	0.00	36.19	5.34	F
1393	1535	0.240945	GTCCGAAACCGAGGTAACGA	59.759	55.0	17.60	1.34	46.39	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1952	2107	0.682209	AGCCATTGTCACCCAGCATC	60.682	55.0	3.91	R
1953	2108	0.968901	CAGCCATTGTCACCCAGCAT	60.969	55.0	3.79	R
3260	4718	0.966920	TCCTTCTCTGACCCGTGTTC	59.033	55.0	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
56	57	6.851222	AAGTATAATGTTGCTCTTCATCGG	57.149	37.500	0.00	0.00	0.00	4.18
60	61	1.447838	GTTGCTCTTCATCGGCGGA	60.448	57.895	7.21	0.00	0.00	5.54
61	62	1.153568	TTGCTCTTCATCGGCGGAG	60.154	57.895	7.21	6.39	0.00	4.63
74	75	1.282875	GCGGAGGTTGTTGTTCTGC	59.717	57.895	0.00	0.00	36.21	4.26
81	82	1.534595	GGTTGTTGTTCTGCTGTGCTG	60.535	52.381	0.00	0.00	0.00	4.41
87	88	0.590195	GTTCTGCTGTGCTGGTTCTG	59.410	55.000	0.00	0.00	0.00	3.02
89	90	1.047801	TCTGCTGTGCTGGTTCTGTA	58.952	50.000	0.00	0.00	0.00	2.74
90	91	1.001293	TCTGCTGTGCTGGTTCTGTAG	59.999	52.381	0.00	0.00	0.00	2.74
93	94	1.941668	GCTGTGCTGGTTCTGTAGGAC	60.942	57.143	0.00	0.00	36.03	3.85
102	103	4.616553	TGGTTCTGTAGGACCTTAGCATA	58.383	43.478	10.60	0.00	0.00	3.14
105	106	5.105064	GGTTCTGTAGGACCTTAGCATAACA	60.105	44.000	0.00	0.00	0.00	2.41
111	112	5.763876	AGGACCTTAGCATAACAACTTCT	57.236	39.130	0.00	0.00	0.00	2.85
126	127	7.507672	AACAACTTCTCGATTGTCTATTACG	57.492	36.000	2.79	0.00	38.08	3.18
148	149	2.488153	ACAAGTTTTGCCCGATTCTAGC	59.512	45.455	0.00	0.00	0.00	3.42
149	150	2.487762	CAAGTTTTGCCCGATTCTAGCA	59.512	45.455	0.00	0.00	33.97	3.49
152	153	1.750193	TTTGCCCGATTCTAGCAAGG	58.250	50.000	9.31	0.00	46.30	3.61
153	154	0.908910	TTGCCCGATTCTAGCAAGGA	59.091	50.000	6.22	0.00	41.35	3.36
157	158	1.202698	CCCGATTCTAGCAAGGAAGGG	60.203	57.143	0.00	0.00	0.00	3.95
159	160	1.811941	CGATTCTAGCAAGGAAGGGGC	60.812	57.143	0.00	0.00	0.00	5.80
227	228	3.191581	CGCTAGGTGGTCTATGTATCTGG	59.808	52.174	0.00	0.00	0.00	3.86
280	281	5.181009	TGTACTGCCAAGATTGAAGATGAG	58.819	41.667	0.00	0.00	0.00	2.90
305	307	5.582550	AGAAGGAAGTTTTCTCGCAAAAAG	58.417	37.500	0.00	0.00	29.05	2.27
308	310	5.582550	AGGAAGTTTTCTCGCAAAAAGAAG	58.417	37.500	0.00	0.00	34.42	2.85
309	311	5.125578	AGGAAGTTTTCTCGCAAAAAGAAGT	59.874	36.000	0.00	0.00	34.42	3.01
310	312	6.317893	AGGAAGTTTTCTCGCAAAAAGAAGTA	59.682	34.615	0.00	0.00	34.42	2.24

Showing 1 to 25 of 298 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	8.473796	CACAAAAATAAACTTGGCGTACTAAAC	58.526	33.333	0.00	0.00	2.01
41	42	1.741401	CCGCCGATGAAGAGCAACA	60.741	57.895	0.00	0.00	3.33
43	44	1.153568	CTCCGCCGATGAAGAGCAA	60.154	57.895	0.00	0.00	3.91
45	46	2.279784	CCTCCGCCGATGAAGAGC	60.280	66.667	0.00	0.00	4.09
56	57	1.166531	AGCAGAACAACAACCTCCGC	61.167	55.000	0.00	0.00	5.54
60	61	0.740737	GCACAGCAGAACAACAACCT	59.259	50.000	0.00	0.00	3.50
61	62	0.740737	AGCACAGCAGAACAACAACC	59.259	50.000	0.00	0.00	3.77
74	75	1.338200	GGTCCTACAGAACCAGCACAG	60.338	57.143	0.00	0.00	3.66
81	82	5.105064	TGTTATGCTAAGGTCCTACAGAACC	60.105	44.000	17.61	32.87	3.62
87	88	6.641474	AGAAGTTGTTATGCTAAGGTCCTAC	58.359	40.000	0.00	0.00	3.18
89	90	5.624738	CGAGAAGTTGTTATGCTAAGGTCCT	60.625	44.000	0.00	0.00	3.85
90	91	4.567159	CGAGAAGTTGTTATGCTAAGGTCC	59.433	45.833	0.00	0.00	4.46
93	94	6.313905	ACAATCGAGAAGTTGTTATGCTAAGG	59.686	38.462	0.00	35.13	2.69
102	103	7.272948	GTCGTAATAGACAATCGAGAAGTTGTT	59.727	37.037	3.79	38.57	2.83
105	106	6.849502	TGTCGTAATAGACAATCGAGAAGTT	58.150	36.000	0.00	46.81	2.66
126	127	3.426292	GCTAGAATCGGGCAAAACTTGTC	60.426	47.826	0.00	33.62	3.18
137	138	1.202698	CCCTTCCTTGCTAGAATCGGG	60.203	57.143	0.00	0.00	5.14
148	149	1.815421	CGTCATCGCCCCTTCCTTG	60.815	63.158	0.00	0.00	3.61
149	150	2.584608	CGTCATCGCCCCTTCCTT	59.415	61.111	0.00	0.00	3.36
248	249	1.470098	CTTGGCAGTACAATGAGCACC	59.530	52.381	0.00	0.00	5.01
255	256	6.182627	TCATCTTCAATCTTGGCAGTACAAT	58.817	36.000	0.00	0.00	2.71
280	281	5.668558	TTTGCGAGAAAACTTCCTTCTAC	57.331	39.130	0.00	33.24	2.59
330	338	8.765219	CGTATTATACTTCCCTCAACATGAAAG	58.235	37.037	0.00	0.00	2.62
397	405	8.530311	ACATGTGATAAGCAATCCAAACAATTA	58.470	29.630	0.00	33.22	1.40
398	406	7.332430	CACATGTGATAAGCAATCCAAACAATT	59.668	33.333	21.64	33.22	2.32

Showing 1 to 25 of 340 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.