AutoCloner

Multiple sequence alignment - TraesCS1B01G198500

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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	TraesCS1B01G198500	chr1B	100.000	4105	0	0	1441	5545	356455488	356451384	0.000000e+00	7581
1	TraesCS1B01G198500	chr1B	100.000	1233	0	0	1	1233	356456928	356455696	0.000000e+00	2278
2	TraesCS1B01G198500	chr1B	95.527	626	16	1	1480	2105	229488952	229489565	0.000000e+00	990
3	TraesCS1B01G198500	chr1A	95.475	3050	99	14	1441	4478	330083285	330086307	0.000000e+00	4831
4	TraesCS1B01G198500	chr1A	93.233	532	12	7	725	1233	330082679	330083209	0.000000e+00	761
5	TraesCS1B01G198500	chr1A	94.488	381	17	3	4964	5341	330086569	330086948	8.000000e-163	584
6	TraesCS1B01G198500	chr1A	93.443	305	12	5	5243	5545	330087323	330087621	3.940000e-121	446
7	TraesCS1B01G198500	chr1A	94.595	259	12	2	5243	5500	330087071	330087328	3.110000e-107	399
8	TraesCS1B01G198500	chr1A	92.381	210	10	2	1	205	330081970	330082178	1.510000e-75	294
9	TraesCS1B01G198500	chr1A	97.600	125	3	0	5376	5500	330086952	330087076	1.210000e-51	215
10	TraesCS1B01G198500	chr1D	97.308	2266	57	2	1441	3705	256780080	256782342	0.000000e+00	3843
11	TraesCS1B01G198500	chr1D	90.754	1763	88	38	3756	5500	256782332	256784037	0.000000e+00	2283
12	TraesCS1B01G198500	chr1D	91.032	1037	70	14	205	1233	256778984	256780005	0.000000e+00	1378
13	TraesCS1B01G198500	chr1D	96.393	305	8	3	5243	5545	256784032	256784335	2.980000e-137	499
14	TraesCS1B01G198500	chr1D	92.925	212	10	3	1	207	256778739	256778950	2.510000e-78	303
15	TraesCS1B01G198500	chr6A	96.486	626	22	0	1480	2105	586055283	586055908	0.000000e+00	1035
16	TraesCS1B01G198500	chr4B	78.793	646	122	13	2705	3335	673250963	673251608	2.390000e-113	420
17	TraesCS1B01G198500	chr4B	92.053	151	12	0	1467	1617	673249000	673249150	4.350000e-51	213
18	TraesCS1B01G198500	chr4B	84.393	173	27	0	1706	1878	673249242	673249414	2.660000e-38	171
19	TraesCS1B01G198500	chrUn	79.019	591	101	18	3063	3639	99825439	99824858	3.130000e-102	383
20	TraesCS1B01G198500	chrUn	79.904	418	60	15	1464	1878	99827460	99827064	9.090000e-73	285
21	TraesCS1B01G198500	chr4A	80.759	369	66	5	428	794	29169115	29168750	3.270000e-72	283
22	TraesCS1B01G198500	chr3D	74.281	591	140	12	213	797	600931723	600931139	7.180000e-59	239
23	TraesCS1B01G198500	chr3A	90.385	156	15	0	1466	1621	703425203	703425048	7.280000e-49	206
24	TraesCS1B01G198500	chr3A	85.806	155	22	0	1724	1878	703424882	703424728	1.240000e-36	165
25	TraesCS1B01G198500	chr4D	90.789	152	14	0	1466	1617	491381165	491381014	2.620000e-48	204
26	TraesCS1B01G198500	chr4D	85.443	158	20	1	1721	1878	491380897	491380743	1.600000e-35	161
27	TraesCS1B01G198500	chr3B	73.415	568	139	11	236	797	808141332	808140771	9.420000e-48	202
28	TraesCS1B01G198500	chr6D	76.426	263	58	4	213	473	311242905	311242645	7.490000e-29	139
29	TraesCS1B01G198500	chr2D	77.143	245	52	4	212	454	125275683	125275925	7.490000e-29	139
30	TraesCS1B01G198500	chr5A	81.646	158	23	4	1	152	321879507	321879664	5.830000e-25	126
31	TraesCS1B01G198500	chr7D	80.124	161	26	4	1	155	543555554	543555714	1.260000e-21	115

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	TraesCS1B01G198500	chr1B	356451384	356456928	5544	True	4929.500000	7581	100.000000	1	5545	2	chr1B.!!$R1	5544
1	TraesCS1B01G198500	chr1B	229488952	229489565	613	False	990.000000	990	95.527000	1480	2105	1	chr1B.!!$F1	625
2	TraesCS1B01G198500	chr1A	330081970	330087621	5651	False	1075.714286	4831	94.459286	1	5545	7	chr1A.!!$F1	5544
3	TraesCS1B01G198500	chr1D	256778739	256784335	5596	False	1661.200000	3843	93.682400	1	5545	5	chr1D.!!$F1	5544
4	TraesCS1B01G198500	chr6A	586055283	586055908	625	False	1035.000000	1035	96.486000	1480	2105	1	chr6A.!!$F1	625
5	TraesCS1B01G198500	chr4B	673249000	673251608	2608	False	268.000000	420	85.079667	1467	3335	3	chr4B.!!$F1	1868
6	TraesCS1B01G198500	chrUn	99824858	99827460	2602	True	334.000000	383	79.461500	1464	3639	2	chrUn.!!$R1	2175
7	TraesCS1B01G198500	chr3D	600931139	600931723	584	True	239.000000	239	74.281000	213	797	1	chr3D.!!$R1	584
8	TraesCS1B01G198500	chr3B	808140771	808141332	561	True	202.000000	202	73.415000	236	797	1	chr3B.!!$R1	561

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
661	840	0.107703	TGCACCAGAAATAGCCTCCG	60.108	55.000	0.00	0.00	0.00	4.63	F
665	844	0.109342	CCAGAAATAGCCTCCGCCAT	59.891	55.000	0.00	0.00	34.57	4.40	F
666	845	1.477558	CCAGAAATAGCCTCCGCCATT	60.478	52.381	0.00	0.00	34.57	3.16	F
2227	2931	1.229336	CCCCGCCCTCTGGATCTAT	60.229	63.158	0.00	0.00	0.00	1.98	F
3098	4583	1.477700	GCATTGCTTGGAGCCATACAA	59.522	47.619	0.16	7.04	41.51	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2227	2931	0.388778	CTGTGCATTGCATTTCGGCA	60.389	50.000	15.49	5.93	41.91	5.69	R
2228	2932	0.388907	ACTGTGCATTGCATTTCGGC	60.389	50.000	15.49	1.01	41.91	5.54	R
2393	3097	0.472471	ACGTGGGAACAGTGGAACAT	59.528	50.000	0.00	0.00	44.46	2.71	R
3983	5480	3.452627	AGTCCGCATCTAATTCCAAGAGT	59.547	43.478	0.00	0.00	0.00	3.24	R
4769	6318	0.026803	GCAGAAAGTTAGATGCGGCG	59.973	55.000	0.51	0.51	0.00	6.46	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	Hairpin	End Stability
104	110	2.251818	TCCCTCTCCTTGACTGAACTG	58.748	52.381	0.00	0.00	3.16
123	129	0.545171	GGTTGGGCTAGAAGGTACCC	59.455	60.000	8.74	43.14	3.69
227	302	7.809806	CCAAATGTTTCCATCAGAAAAGTACTC	59.190	37.037	0.00	45.93	2.59
306	381	4.114794	GCTTGGCTAACATGGCTAAATTG	58.885	43.478	0.00	30.37	2.32
335	410	1.777272	GAGATCCCTAAACCCCATGCT	59.223	52.381	0.00	0.00	3.79
406	482	3.367646	TCTTCTACTCATCCGTGTCCT	57.632	47.619	0.00	0.00	3.85
426	502	3.192212	CCTCTCACCAAAAAGCTTCCATC	59.808	47.826	0.00	0.00	3.51
544	635	2.101582	CTCCCTCCTAAGGACATCAACG	59.898	54.545	0.00	46.67	4.10
576	667	3.314553	ACCTACAAGTCGATTCACAACG	58.685	45.455	0.00	0.00	4.10
588	679	3.840890	TTCACAACGCTTTCAACAAGT	57.159	38.095	0.00	0.00	3.16
606	697	7.653713	TCAACAAGTTGAGAGAAACTATCACTC	59.346	37.037	10.54	43.90	3.51
642	821	9.383519	CGCACCATAGATAAAATACCAAGATAT	57.616	33.333	0.00	0.00	1.63
649	828	8.627208	AGATAAAATACCAAGATATGCACCAG	57.373	34.615	0.00	0.00	4.00
650	829	8.439971	AGATAAAATACCAAGATATGCACCAGA	58.560	33.333	0.00	0.00	3.86
651	830	8.995027	ATAAAATACCAAGATATGCACCAGAA	57.005	30.769	0.00	0.00	3.02
652	831	7.716799	AAAATACCAAGATATGCACCAGAAA	57.283	32.000	0.00	0.00	2.52
653	832	7.902920	AAATACCAAGATATGCACCAGAAAT	57.097	32.000	0.00	0.00	2.17
654	833	8.995027	AAATACCAAGATATGCACCAGAAATA	57.005	30.769	0.00	0.00	1.40
655	834	8.627208	AATACCAAGATATGCACCAGAAATAG	57.373	34.615	0.00	0.00	1.73
656	835	4.823989	ACCAAGATATGCACCAGAAATAGC	59.176	41.667	0.00	0.00	2.97
657	836	4.217118	CCAAGATATGCACCAGAAATAGCC	59.783	45.833	0.00	0.00	3.93
658	837	4.989875	AGATATGCACCAGAAATAGCCT	57.010	40.909	0.00	0.00	4.58
659	838	4.904241	AGATATGCACCAGAAATAGCCTC	58.096	43.478	0.00	0.00	4.70
660	839	2.355010	ATGCACCAGAAATAGCCTCC	57.645	50.000	0.00	0.00	4.30
661	840	0.107703	TGCACCAGAAATAGCCTCCG	60.108	55.000	0.00	0.00	4.63

Showing 1 to 25 of 209 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
145	151	4.415596	AGTGGGCATATTTGGTGAGAAAA	58.584	39.130	0.00	0.00	0.00	2.29
306	381	3.823304	GGTTTAGGGATCTCCATGCATTC	59.177	47.826	0.00	0.00	38.24	2.67
356	431	0.179034	GCTAGCTTGGTGGAGGATGG	60.179	60.000	7.70	0.00	0.00	3.51
406	482	2.813754	CGATGGAAGCTTTTTGGTGAGA	59.186	45.455	0.00	0.00	0.00	3.27
426	502	4.475028	TGTGCAAAGAAATTACAGATGCG	58.525	39.130	0.00	0.00	35.18	4.73
462	552	8.918202	TGGTGTATGTTCTAACTCTTTTCAAT	57.082	30.769	0.00	0.00	0.00	2.57
470	560	8.688151	AGTCTATTCTGGTGTATGTTCTAACTC	58.312	37.037	0.00	0.00	0.00	3.01
473	563	7.782049	CCAGTCTATTCTGGTGTATGTTCTAA	58.218	38.462	4.75	0.00	46.92	2.10
474	564	7.348080	CCAGTCTATTCTGGTGTATGTTCTA	57.652	40.000	4.75	0.00	46.92	2.10
523	613	2.101582	CGTTGATGTCCTTAGGAGGGAG	59.898	54.545	0.00	0.00	43.72	4.30
528	618	3.006110	ACGAAACGTTGATGTCCTTAGGA	59.994	43.478	0.00	0.00	36.35	2.94
544	635	3.060070	CGACTTGTAGGTTGGAACGAAAC	60.060	47.826	0.00	0.00	0.00	2.78
559	650	1.865865	AGCGTTGTGAATCGACTTGT	58.134	45.000	0.00	0.00	0.00	3.16
576	667	5.884771	AGTTTCTCTCAACTTGTTGAAAGC	58.115	37.500	15.70	10.13	32.81	3.51
588	679	4.087182	ACCGGAGTGATAGTTTCTCTCAA	58.913	43.478	9.46	0.00	43.65	3.02
642	821	0.107703	CGGAGGCTATTTCTGGTGCA	60.108	55.000	0.00	0.00	0.00	4.57
643	822	1.440145	GCGGAGGCTATTTCTGGTGC	61.440	60.000	0.00	0.00	35.83	5.01
644	823	2.695314	GCGGAGGCTATTTCTGGTG	58.305	57.895	0.00	0.00	35.83	4.17
656	835	4.157656	TGAAACTGAAAATAATGGCGGAGG	59.842	41.667	0.00	0.00	0.00	4.30
657	836	5.095490	GTGAAACTGAAAATAATGGCGGAG	58.905	41.667	0.00	0.00	0.00	4.63
658	837	4.378978	CGTGAAACTGAAAATAATGGCGGA	60.379	41.667	0.00	0.00	31.75	5.54
659	838	3.851403	CGTGAAACTGAAAATAATGGCGG	59.149	43.478	0.00	0.00	31.75	6.13
660	839	3.300590	GCGTGAAACTGAAAATAATGGCG	59.699	43.478	0.00	0.00	31.75	5.69
661	840	4.233789	TGCGTGAAACTGAAAATAATGGC	58.766	39.130	0.00	0.00	31.75	4.40
662	841	6.346518	GGTTTGCGTGAAACTGAAAATAATGG	60.347	38.462	10.69	0.00	43.20	3.16

Showing 1 to 25 of 211 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.