AutoCloner

Multiple sequence alignment - TraesCS2A01G441400

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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	TraesCS2A01G441400	chr2A	100.000	2552	0	0	1	2552	691392986	691390435	0.000000e+00	4713
1	TraesCS2A01G441400	chr2A	82.077	915	110	19	802	1678	690747285	690748183	0.000000e+00	732
2	TraesCS2A01G441400	chr2A	82.821	780	109	15	909	1675	690805346	690806113	0.000000e+00	675
3	TraesCS2A01G441400	chr2A	87.042	355	46	0	2190	2544	690808525	690808879	3.950000e-108	401
4	TraesCS2A01G441400	chr2A	85.714	364	44	5	2190	2545	690781441	690781804	6.660000e-101	377
5	TraesCS2A01G441400	chr2A	78.621	435	83	10	1123	1552	632390817	632391246	1.930000e-71	279
6	TraesCS2A01G441400	chr2A	94.444	144	8	0	802	945	690805072	690805215	3.300000e-54	222
7	TraesCS2A01G441400	chr2D	91.808	1770	108	10	802	2548	547559293	547561048	0.000000e+00	2431
8	TraesCS2A01G441400	chr2D	89.591	1662	115	19	909	2548	547574530	547576155	0.000000e+00	2058
9	TraesCS2A01G441400	chr2D	91.583	796	59	5	6	800	547487817	547488605	0.000000e+00	1092
10	TraesCS2A01G441400	chr2D	85.379	896	102	19	802	1678	547489063	547489948	0.000000e+00	902
11	TraesCS2A01G441400	chr2D	84.512	891	111	16	802	1678	547450614	547451491	0.000000e+00	856
12	TraesCS2A01G441400	chr2D	82.394	869	110	24	802	1644	547426984	547427835	0.000000e+00	717
13	TraesCS2A01G441400	chr2D	92.632	475	33	2	3	476	547425768	547426241	0.000000e+00	682
14	TraesCS2A01G441400	chr2D	87.606	355	44	0	2190	2544	547452704	547453058	1.830000e-111	412
15	TraesCS2A01G441400	chr2D	87.143	350	45	0	2190	2539	547289047	547289396	5.120000e-107	398
16	TraesCS2A01G441400	chr2D	91.743	218	18	0	561	778	547426239	547426456	1.150000e-78	303
17	TraesCS2A01G441400	chr2B	91.678	1418	79	13	906	2307	653808259	653809653	0.000000e+00	1929
18	TraesCS2A01G441400	chr2B	84.802	908	111	17	802	1696	653796088	653796981	0.000000e+00	887
19	TraesCS2A01G441400	chr2B	83.630	843	120	11	1724	2552	653800485	653801323	0.000000e+00	776
20	TraesCS2A01G441400	chr2B	82.353	867	119	21	852	1702	653788261	653789109	0.000000e+00	723
21	TraesCS2A01G441400	chr2B	88.051	544	61	2	2009	2548	653809684	653810227	2.140000e-180	641
22	TraesCS2A01G441400	chr2B	85.440	364	45	5	2190	2545	653792893	653793256	3.100000e-99	372
23	TraesCS2A01G441400	chr2B	78.622	421	80	10	1137	1552	572079908	572080323	1.160000e-68	270
24	TraesCS2A01G441400	chr2B	81.395	301	46	10	102	399	781263062	781263355	1.180000e-58	237
25	TraesCS2A01G441400	chr7D	86.025	322	38	5	79	399	104618142	104617827	3.150000e-89	339
26	TraesCS2A01G441400	chr1B	86.458	288	35	4	114	399	437607343	437607058	1.910000e-81	313
27	TraesCS2A01G441400	chr3B	86.159	289	36	4	114	400	763493319	763493605	2.470000e-80	309
28	TraesCS2A01G441400	chr3B	84.483	290	41	4	114	401	412509881	412510168	1.490000e-72	283
29	TraesCS2A01G441400	chr7B	81.848	303	43	9	100	399	709321938	709322231	7.050000e-61	244
30	TraesCS2A01G441400	chr4B	83.721	258	36	6	144	400	343042316	343042064	3.280000e-59	239

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	TraesCS2A01G441400	chr2A	691390435	691392986	2551	True	4713.000000	4713	100.000000	1	2552	1	chr2A.!!$R1	2551
1	TraesCS2A01G441400	chr2A	690747285	690748183	898	False	732.000000	732	82.077000	802	1678	1	chr2A.!!$F2	876
2	TraesCS2A01G441400	chr2A	690805072	690808879	3807	False	432.666667	675	88.102333	802	2544	3	chr2A.!!$F4	1742
3	TraesCS2A01G441400	chr2D	547559293	547561048	1755	False	2431.000000	2431	91.808000	802	2548	1	chr2D.!!$F2	1746
4	TraesCS2A01G441400	chr2D	547574530	547576155	1625	False	2058.000000	2058	89.591000	909	2548	1	chr2D.!!$F3	1639
5	TraesCS2A01G441400	chr2D	547487817	547489948	2131	False	997.000000	1092	88.481000	6	1678	2	chr2D.!!$F6	1672
6	TraesCS2A01G441400	chr2D	547450614	547453058	2444	False	634.000000	856	86.059000	802	2544	2	chr2D.!!$F5	1742
7	TraesCS2A01G441400	chr2D	547425768	547427835	2067	False	567.333333	717	88.923000	3	1644	3	chr2D.!!$F4	1641
8	TraesCS2A01G441400	chr2B	653808259	653810227	1968	False	1285.000000	1929	89.864500	906	2548	2	chr2B.!!$F4	1642
9	TraesCS2A01G441400	chr2B	653788261	653801323	13062	False	689.500000	887	84.056250	802	2552	4	chr2B.!!$F3	1750

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
928	1466	0.165944	CGCTTCTGCAAGTTAACCCG	59.834	55.0	0.88	0.0	39.64	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1786	14314	0.02877	GTGTGCACGTGCTAGCAAAA	59.971	50.0	37.59	16.06	43.2	2.44	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
50	51	2.032681	GTGGGCTTGCCGAAGAGT	59.967	61.111	5.49	0.00	0.00	3.24
107	108	1.067071	CCGGTAGAGGTGGTGAGAAAC	60.067	57.143	0.00	0.00	0.00	2.78
108	109	1.616865	CGGTAGAGGTGGTGAGAAACA	59.383	52.381	0.00	0.00	0.00	2.83
138	139	4.835284	AAGAGGAGAGGAAATTGAGGAC	57.165	45.455	0.00	0.00	0.00	3.85
227	228	3.932710	GACTAATCTTCGCCACATCAACA	59.067	43.478	0.00	0.00	0.00	3.33
235	236	3.457234	TCGCCACATCAACATAGACATC	58.543	45.455	0.00	0.00	0.00	3.06
239	240	4.684214	GCCACATCAACATAGACATCTGGA	60.684	45.833	0.00	0.00	0.00	3.86
327	328	2.742053	GCGCAGAAGTGGTGATCTTTTA	59.258	45.455	0.30	0.00	0.00	1.52
333	334	7.360861	CGCAGAAGTGGTGATCTTTTATGTTTA	60.361	37.037	0.00	0.00	0.00	2.01
337	338	8.986477	AAGTGGTGATCTTTTATGTTTATTGC	57.014	30.769	0.00	0.00	0.00	3.56
355	356	2.461695	TGCCAAAAGAGGTGGTTTTGA	58.538	42.857	9.35	0.00	44.33	2.69
357	358	3.261897	TGCCAAAAGAGGTGGTTTTGAAA	59.738	39.130	9.35	0.00	44.33	2.69
374	375	5.913137	TTGAAATACCCTAGCCACAAATG	57.087	39.130	0.00	0.00	0.00	2.32
403	405	3.426787	TTTGAGCAATTTACTCCCCGA	57.573	42.857	3.39	0.00	32.98	5.14
406	408	2.569853	TGAGCAATTTACTCCCCGAAGA	59.430	45.455	3.39	0.00	32.98	2.87
435	437	2.634453	TCACATCCTCTTCTCTTGCACA	59.366	45.455	0.00	0.00	0.00	4.57
440	442	1.271271	CCTCTTCTCTTGCACAGCCTT	60.271	52.381	0.00	0.00	0.00	4.35
447	449	3.071602	TCTCTTGCACAGCCTTAAGAGTT	59.928	43.478	3.36	0.00	43.98	3.01
462	464	4.639135	AAGAGTTTCTGTGGAGTTTTGC	57.361	40.909	0.00	0.00	0.00	3.68
467	469	0.534203	TCTGTGGAGTTTTGCCCGTC	60.534	55.000	0.00	0.00	0.00	4.79
506	508	2.359975	GGCCCTTGAACTGGTCGG	60.360	66.667	0.00	0.00	0.00	4.79
603	605	1.195448	GACTTTGTGGATGACGCACAG	59.805	52.381	0.00	0.00	41.85	3.66
605	607	0.943673	TTTGTGGATGACGCACAGTG	59.056	50.000	0.00	0.00	39.78	3.66
700	702	5.297547	CATTAGCACCCGTTGTATAGACAT	58.702	41.667	0.00	0.00	34.86	3.06
721	723	0.249238	GAGATCGCGATTGCCTGAGT	60.249	55.000	24.55	0.00	38.08	3.41
796	798	2.104622	CCCATGAAACTTTGGCCACTTT	59.895	45.455	3.88	2.98	0.00	2.66
798	800	2.977772	TGAAACTTTGGCCACTTTGG	57.022	45.000	3.88	0.00	41.55	3.28
928	1466	0.165944	CGCTTCTGCAAGTTAACCCG	59.834	55.000	0.88	0.00	39.64	5.28
949	9384	4.498513	CCGTCGTGTTGTCCTATATAAGCA	60.499	45.833	0.00	0.00	0.00	3.91
1047	9486	0.602638	TCTGCGTCGCCATCTTGTTT	60.603	50.000	15.88	0.00	0.00	2.83
1071	9510	4.069232	CTGGTCTCGCCTTCGCCA	62.069	66.667	0.00	0.00	38.35	5.69
1322	9767	3.495729	CTACTGGGGCAGTGGGTT	58.504	61.111	0.00	0.00	45.01	4.11
1564	10024	4.321230	CGCCATACTGAGCACATCTATACA	60.321	45.833	0.00	0.00	0.00	2.29
1565	10025	5.623141	CGCCATACTGAGCACATCTATACAT	60.623	44.000	0.00	0.00	0.00	2.29
1566	10026	5.809562	GCCATACTGAGCACATCTATACATC	59.190	44.000	0.00	0.00	0.00	3.06
1568	10028	7.554211	CCATACTGAGCACATCTATACATCAT	58.446	38.462	0.00	0.00	0.00	2.45
1569	10029	7.491696	CCATACTGAGCACATCTATACATCATG	59.508	40.741	0.00	0.00	0.00	3.07
1571	10031	6.453943	ACTGAGCACATCTATACATCATGTC	58.546	40.000	0.00	0.00	0.00	3.06
1572	10032	6.267242	ACTGAGCACATCTATACATCATGTCT	59.733	38.462	0.00	0.00	0.00	3.41
1603	10080	8.672815	TCAAATAATGTATGATGCGAAACAAGA	58.327	29.630	0.00	0.00	0.00	3.02
1657	10137	5.937975	ATGGGAAATTTGGATTACACTGG	57.062	39.130	0.00	0.00	0.00	4.00
1661	10141	4.159693	GGAAATTTGGATTACACTGGGACC	59.840	45.833	0.00	0.00	0.00	4.46
1717	12256	2.644418	CCACATGTGCACCCAACG	59.356	61.111	20.81	0.00	0.00	4.10
1727	12266	1.507141	GCACCCAACGTGTTCTCCTG	61.507	60.000	0.00	0.00	44.97	3.86
1773	13725	3.058160	CCGAAAGCCCACAGCCTG	61.058	66.667	0.00	0.00	45.47	4.85
1786	14314	4.722700	GCCTGACCCGCATGTGGT	62.723	66.667	23.44	15.91	39.32	4.16
1824	14352	5.507817	GCACACATTCATCTTCAGAAAACCA	60.508	40.000	0.00	0.00	0.00	3.67
1843	14841	2.069273	CAACACCAGGCTAAGAACTCG	58.931	52.381	0.00	0.00	0.00	4.18
1864	14862	6.151144	ACTCGCTAATTTTCTGCTTATTTGGT	59.849	34.615	0.00	0.00	0.00	3.67
1930	14928	2.631160	TCACCGTTGGTTTGATGAGT	57.369	45.000	0.00	0.00	31.02	3.41
2239	15886	1.803334	TGATGGTGTTGTTACTCCGC	58.197	50.000	0.00	0.00	40.13	5.54
2249	15896	2.273179	TTACTCCGCGCAGGACACT	61.273	57.895	15.44	5.57	45.98	3.55
2316	16295	7.670364	CATGTCTATGGGTATCAATGACACTA	58.330	38.462	0.00	0.00	41.09	2.74
2331	16310	7.451255	TCAATGACACTAACAAAGGAATTCCAT	59.549	33.333	26.22	12.25	38.89	3.41
2376	16355	6.867519	TGTATGAACCTAAGAATGACTGGA	57.132	37.500	0.00	0.00	0.00	3.86
2417	16396	2.166254	CAGGTGCCCAATATGGTTTGTC	59.834	50.000	0.00	0.00	35.17	3.18
2429	16408	6.959639	ATATGGTTTGTCTGTGAACTGTTT	57.040	33.333	0.00	0.00	0.00	2.83
2463	16442	6.460781	TCTTCTCACGCTTAAATAGGAACAA	58.539	36.000	0.00	0.00	0.00	2.83
2531	16511	2.024080	ACTTCCATAATGGGCACATGGT	60.024	45.455	0.00	0.00	40.18	3.55
2548	16528	4.779987	CATGGTCATTCATGTATTGCTCG	58.220	43.478	0.00	0.00	39.56	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	108	2.024464	TCCTCTCCTCTTTCTCCCTCTG	60.024	54.545	0.00	0.00	0.00	3.35
108	109	2.293246	TCCTCTCCTCTTTCTCCCTCT	58.707	52.381	0.00	0.00	0.00	3.69
138	139	3.004839	TCTGTCTCACACCTTCTTCTTCG	59.995	47.826	0.00	0.00	0.00	3.79
227	228	2.625639	GGGTGGGATCCAGATGTCTAT	58.374	52.381	15.23	0.00	32.34	1.98
235	236	1.553690	AACTGACGGGTGGGATCCAG	61.554	60.000	15.23	1.71	32.34	3.86
239	240	0.893727	GCAAAACTGACGGGTGGGAT	60.894	55.000	0.00	0.00	0.00	3.85
327	328	4.592778	ACCACCTCTTTTGGCAATAAACAT	59.407	37.500	0.00	0.00	37.69	2.71
333	334	3.454082	TCAAAACCACCTCTTTTGGCAAT	59.546	39.130	0.00	0.00	38.57	3.56
337	338	5.989168	GGTATTTCAAAACCACCTCTTTTGG	59.011	40.000	4.30	0.00	38.57	3.28
355	356	4.929479	TCACATTTGTGGCTAGGGTATTT	58.071	39.130	10.60	0.00	45.65	1.40
357	358	4.464008	CATCACATTTGTGGCTAGGGTAT	58.536	43.478	10.60	0.00	45.65	2.73
374	375	6.366061	GGAGTAAATTGCTCAAAAACCATCAC	59.634	38.462	12.84	0.00	34.83	3.06
377	378	5.279960	GGGGAGTAAATTGCTCAAAAACCAT	60.280	40.000	12.84	0.00	34.83	3.55
403	405	2.122768	GAGGATGTGAGTCCCCATCTT	58.877	52.381	15.56	10.54	39.17	2.40
406	408	2.122768	GAAGAGGATGTGAGTCCCCAT	58.877	52.381	0.00	0.00	39.17	4.00
435	437	3.648545	ACTCCACAGAAACTCTTAAGGCT	59.351	43.478	1.85	0.00	0.00	4.58
440	442	4.578928	GGCAAAACTCCACAGAAACTCTTA	59.421	41.667	0.00	0.00	0.00	2.10
447	449	0.106918	ACGGGCAAAACTCCACAGAA	60.107	50.000	0.00	0.00	0.00	3.02
482	484	1.284785	CCAGTTCAAGGGCCTCCAATA	59.715	52.381	6.46	0.00	34.83	1.90
484	486	1.360393	ACCAGTTCAAGGGCCTCCAA	61.360	55.000	6.46	0.00	34.83	3.53
495	497	0.841289	AAAGGAACCCGACCAGTTCA	59.159	50.000	6.04	0.00	44.40	3.18
506	508	4.864704	TGGCATGACTTTTAAAGGAACC	57.135	40.909	9.64	4.07	0.00	3.62
559	561	1.398832	GCTAACGCCGTAAACACCAAC	60.399	52.381	0.00	0.00	0.00	3.77
569	571	2.288640	ACAAAGTCTAAGCTAACGCCGT	60.289	45.455	0.00	0.00	36.60	5.68
603	605	4.130118	GACCCACTCAATCACCATATCAC	58.870	47.826	0.00	0.00	0.00	3.06
605	607	4.636249	GAGACCCACTCAATCACCATATC	58.364	47.826	0.00	0.00	44.36	1.63
700	702	1.299392	CAGGCAATCGCGATCTCGA	60.299	57.895	23.92	10.63	43.02	4.04
721	723	7.015974	AGAGCAGTTATCTCATCCATCATAACA	59.984	37.037	0.00	0.00	35.16	2.41
768	770	1.535204	AAAGTTTCATGGGGCCTGCG	61.535	55.000	0.84	0.00	0.00	5.18
796	798	2.733301	CCGTTTTGCATGTGGCCA	59.267	55.556	0.00	0.00	43.89	5.36
798	800	0.038709	TTAGCCGTTTTGCATGTGGC	60.039	50.000	10.74	10.74	46.07	5.01
799	801	1.668628	GGTTAGCCGTTTTGCATGTGG	60.669	52.381	0.00	0.00	0.00	4.17
800	802	1.269448	AGGTTAGCCGTTTTGCATGTG	59.731	47.619	0.00	0.00	40.50	3.21
928	1466	5.051907	CGTTGCTTATATAGGACAACACGAC	60.052	44.000	20.86	4.98	40.42	4.34
949	9384	6.017357	GGTGAAGTTTTAGAGGAATTGACGTT	60.017	38.462	0.00	0.00	0.00	3.99
1047	9486	1.758440	AAGGCGAGACCAGTGCAAGA	61.758	55.000	0.00	0.00	43.14	3.02
1071	9510	4.018490	TGTTGTTAATGCTGGCTGATGAT	58.982	39.130	0.00	0.00	0.00	2.45
1286	9731	1.755380	AGGTGTTCAGCCCGTAGATAC	59.245	52.381	0.00	0.00	0.00	2.24
1298	9743	0.766674	ACTGCCCCAGTAGGTGTTCA	60.767	55.000	0.00	0.00	43.46	3.18
1364	9809	2.960170	GGTGGTCGTACGACTGCT	59.040	61.111	38.47	0.00	44.04	4.24
1415	9860	2.337170	CCACCTGCGTGTACGACA	59.663	61.111	8.82	5.14	43.02	4.35
1419	9864	1.959226	CCACACCACCTGCGTGTAC	60.959	63.158	0.00	0.00	42.49	2.90
1565	10025	9.447157	TCATACATTATTTGAACACAGACATGA	57.553	29.630	0.00	0.00	0.00	3.07
1568	10028	8.183536	GCATCATACATTATTTGAACACAGACA	58.816	33.333	0.00	0.00	0.00	3.41
1569	10029	7.374228	CGCATCATACATTATTTGAACACAGAC	59.626	37.037	0.00	0.00	0.00	3.51
1571	10031	7.408910	TCGCATCATACATTATTTGAACACAG	58.591	34.615	0.00	0.00	0.00	3.66
1572	10032	7.313951	TCGCATCATACATTATTTGAACACA	57.686	32.000	0.00	0.00	0.00	3.72
1657	10137	1.272769	AGTAACAGACAGCTTCGGTCC	59.727	52.381	0.00	0.00	35.89	4.46
1661	10141	4.162096	AGTACAGTAACAGACAGCTTCG	57.838	45.455	0.00	0.00	0.00	3.79
1717	12256	1.600916	GGGTGGCACAGGAGAACAC	60.601	63.158	20.82	0.00	41.80	3.32
1773	13725	1.372872	GCAAAACCACATGCGGGTC	60.373	57.895	9.86	0.00	37.77	4.46
1786	14314	0.028770	GTGTGCACGTGCTAGCAAAA	59.971	50.000	37.59	16.06	43.20	2.44
1824	14352	1.608283	GCGAGTTCTTAGCCTGGTGTT	60.608	52.381	0.00	0.00	0.00	3.32
1843	14841	7.640240	CGTCTACCAAATAAGCAGAAAATTAGC	59.360	37.037	0.00	0.00	0.00	3.09
1864	14862	2.094390	CCATTCGTTTGGGTCTCGTCTA	60.094	50.000	0.00	0.00	32.80	2.59
1930	14928	2.171870	AGTCAAAAACCCTCAACTCCGA	59.828	45.455	0.00	0.00	0.00	4.55
2239	15886	1.354040	CAAAGCTCTAGTGTCCTGCG	58.646	55.000	0.00	0.00	0.00	5.18
2316	16295	5.163322	TGTGCTCAAATGGAATTCCTTTGTT	60.163	36.000	28.96	17.50	33.67	2.83
2376	16355	2.972713	TGAGCCAACCAAAGAGTAGAGT	59.027	45.455	0.00	0.00	0.00	3.24
2417	16396	5.762218	AGAGAGATGGAAAAACAGTTCACAG	59.238	40.000	0.00	0.00	0.00	3.66
2429	16408	2.828520	AGCGTGAGAAGAGAGATGGAAA	59.171	45.455	0.00	0.00	0.00	3.13
2463	16442	0.814457	ATGGTTGTTGCAACACACGT	59.186	45.000	31.17	23.16	38.92	4.49
2531	16511	2.916640	TGCCGAGCAATACATGAATGA	58.083	42.857	0.00	0.00	34.76	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.