AutoCloner

Multiple sequence alignment - TraesCS1A01G416300

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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	TraesCS1A01G416300	chr1A	100.000	2567	0	0	1	2567	574683109	574680543	0.000000e+00	4741.0
1	TraesCS1A01G416300	chr1A	97.143	35	1	0	1547	1581	574728453	574728487	2.760000e-05	60.2
2	TraesCS1A01G416300	chr1D	95.310	1386	54	8	255	1631	478432671	478431288	0.000000e+00	2189.0
3	TraesCS1A01G416300	chr1D	81.373	714	88	21	904	1581	478692801	478693505	8.080000e-150	540.0
4	TraesCS1A01G416300	chr1D	81.116	699	89	28	904	1581	478452546	478453222	1.050000e-143	520.0
5	TraesCS1A01G416300	chr1D	80.532	714	91	24	904	1581	478508578	478509279	2.950000e-139	505.0
6	TraesCS1A01G416300	chr1D	87.750	400	48	1	1123	1522	490330617	490330219	1.390000e-127	466.0
7	TraesCS1A01G416300	chr1D	93.627	204	12	1	1711	1914	478431175	478430973	1.150000e-78	303.0
8	TraesCS1A01G416300	chr1D	87.234	94	12	0	763	856	490332125	490332032	9.710000e-20	108.0
9	TraesCS1A01G416300	chr1D	87.234	94	12	0	763	856	490333035	490332942	9.710000e-20	108.0
10	TraesCS1A01G416300	chr1D	87.234	94	12	0	763	856	490333947	490333854	9.710000e-20	108.0
11	TraesCS1A01G416300	chr1D	87.234	94	12	0	763	856	490334857	490334764	9.710000e-20	108.0
12	TraesCS1A01G416300	chr3A	99.081	653	4	2	1915	2567	655861782	655862432	0.000000e+00	1171.0
13	TraesCS1A01G416300	chr3A	85.061	656	81	12	11	655	509011209	509010560	0.000000e+00	652.0
14	TraesCS1A01G416300	chr3A	80.640	656	83	26	1917	2556	722686708	722686081	3.870000e-128	468.0
15	TraesCS1A01G416300	chr3A	80.691	637	81	25	1917	2538	722646513	722645904	8.370000e-125	457.0
16	TraesCS1A01G416300	chr3A	80.183	656	86	27	1917	2556	722727080	722726453	3.890000e-123	451.0
17	TraesCS1A01G416300	chr1B	88.538	951	81	9	763	1698	666572368	666571431	0.000000e+00	1127.0
18	TraesCS1A01G416300	chr1B	95.361	194	8	1	1712	1905	666571447	666571255	8.920000e-80	307.0
19	TraesCS1A01G416300	chr5D	86.890	656	71	11	11	656	536543667	536544317	0.000000e+00	721.0
20	TraesCS1A01G416300	chr4D	86.817	622	64	7	11	625	298111446	298110836	0.000000e+00	678.0
21	TraesCS1A01G416300	chr4B	85.518	656	78	8	11	656	369488376	369487728	0.000000e+00	669.0
22	TraesCS1A01G416300	chr4B	93.605	344	18	3	2224	2567	602778598	602778937	6.340000e-141	510.0
23	TraesCS1A01G416300	chr4B	94.064	219	11	2	1955	2172	602777219	602777436	5.290000e-87	331.0
24	TraesCS1A01G416300	chr3B	84.909	656	84	12	11	655	504083092	504082441	0.000000e+00	649.0
25	TraesCS1A01G416300	chr3B	85.458	502	64	6	11	506	755662196	755661698	4.900000e-142	514.0
26	TraesCS1A01G416300	chr2B	84.900	649	88	8	11	654	791124890	791125533	0.000000e+00	647.0
27	TraesCS1A01G416300	chr4A	82.889	637	87	13	25	657	703793611	703794229	1.040000e-153	553.0
28	TraesCS1A01G416300	chr4A	81.504	665	90	16	11	663	661684549	661685192	1.360000e-142	516.0
29	TraesCS1A01G416300	chrUn	80.534	637	82	25	1917	2538	372030786	372031395	3.890000e-123	451.0
30	TraesCS1A01G416300	chrUn	79.940	663	81	29	1913	2538	165318741	165318094	8.430000e-120	440.0
31	TraesCS1A01G416300	chrUn	87.234	94	12	0	763	856	392125173	392125266	9.710000e-20	108.0
32	TraesCS1A01G416300	chrUn	87.234	94	12	0	763	856	392126086	392126179	9.710000e-20	108.0
33	TraesCS1A01G416300	chr6B	79.732	671	82	30	1905	2538	240333358	240334011	1.090000e-118	436.0
34	TraesCS1A01G416300	chr7D	79.589	632	65	35	1914	2495	520852524	520853141	6.660000e-106	394.0
35	TraesCS1A01G416300	chr5A	77.486	533	93	18	133	656	30764570	30764056	6.950000e-76	294.0
36	TraesCS1A01G416300	chr6D	86.640	247	20	7	1915	2157	131633416	131633179	7.040000e-66	261.0
37	TraesCS1A01G416300	chr6D	84.387	269	32	7	2274	2538	131633004	131632742	3.280000e-64	255.0
38	TraesCS1A01G416300	chr7B	80.377	265	28	10	1913	2175	707836019	707835777	2.030000e-41	180.0

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	TraesCS1A01G416300	chr1A	574680543	574683109	2566	True	4741.0	4741	100.0000	1	2567	1	chr1A.!!$R1	2566
1	TraesCS1A01G416300	chr1D	478430973	478432671	1698	True	1246.0	2189	94.4685	255	1914	2	chr1D.!!$R1	1659
2	TraesCS1A01G416300	chr1D	478692801	478693505	704	False	540.0	540	81.3730	904	1581	1	chr1D.!!$F3	677
3	TraesCS1A01G416300	chr1D	478452546	478453222	676	False	520.0	520	81.1160	904	1581	1	chr1D.!!$F1	677
4	TraesCS1A01G416300	chr1D	478508578	478509279	701	False	505.0	505	80.5320	904	1581	1	chr1D.!!$F2	677
5	TraesCS1A01G416300	chr3A	655861782	655862432	650	False	1171.0	1171	99.0810	1915	2567	1	chr3A.!!$F1	652
6	TraesCS1A01G416300	chr3A	509010560	509011209	649	True	652.0	652	85.0610	11	655	1	chr3A.!!$R1	644
7	TraesCS1A01G416300	chr3A	722686081	722686708	627	True	468.0	468	80.6400	1917	2556	1	chr3A.!!$R3	639
8	TraesCS1A01G416300	chr3A	722645904	722646513	609	True	457.0	457	80.6910	1917	2538	1	chr3A.!!$R2	621
9	TraesCS1A01G416300	chr3A	722726453	722727080	627	True	451.0	451	80.1830	1917	2556	1	chr3A.!!$R4	639
10	TraesCS1A01G416300	chr1B	666571255	666572368	1113	True	717.0	1127	91.9495	763	1905	2	chr1B.!!$R1	1142
11	TraesCS1A01G416300	chr5D	536543667	536544317	650	False	721.0	721	86.8900	11	656	1	chr5D.!!$F1	645
12	TraesCS1A01G416300	chr4D	298110836	298111446	610	True	678.0	678	86.8170	11	625	1	chr4D.!!$R1	614
13	TraesCS1A01G416300	chr4B	369487728	369488376	648	True	669.0	669	85.5180	11	656	1	chr4B.!!$R1	645
14	TraesCS1A01G416300	chr4B	602777219	602778937	1718	False	420.5	510	93.8345	1955	2567	2	chr4B.!!$F1	612
15	TraesCS1A01G416300	chr3B	504082441	504083092	651	True	649.0	649	84.9090	11	655	1	chr3B.!!$R1	644
16	TraesCS1A01G416300	chr2B	791124890	791125533	643	False	647.0	647	84.9000	11	654	1	chr2B.!!$F1	643
17	TraesCS1A01G416300	chr4A	703793611	703794229	618	False	553.0	553	82.8890	25	657	1	chr4A.!!$F2	632
18	TraesCS1A01G416300	chr4A	661684549	661685192	643	False	516.0	516	81.5040	11	663	1	chr4A.!!$F1	652
19	TraesCS1A01G416300	chrUn	372030786	372031395	609	False	451.0	451	80.5340	1917	2538	1	chrUn.!!$F1	621
20	TraesCS1A01G416300	chrUn	165318094	165318741	647	True	440.0	440	79.9400	1913	2538	1	chrUn.!!$R1	625
21	TraesCS1A01G416300	chr6B	240333358	240334011	653	False	436.0	436	79.7320	1905	2538	1	chr6B.!!$F1	633
22	TraesCS1A01G416300	chr7D	520852524	520853141	617	False	394.0	394	79.5890	1914	2495	1	chr7D.!!$F1	581
23	TraesCS1A01G416300	chr5A	30764056	30764570	514	True	294.0	294	77.4860	133	656	1	chr5A.!!$R1	523
24	TraesCS1A01G416300	chr6D	131632742	131633416	674	True	258.0	261	85.5135	1915	2538	2	chr6D.!!$R1	623

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
761	787	0.458669	CTCATGTCAATGGGCAAGCC	59.541	55.0	1.52	1.52	34.3	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1865	2015	0.609957	ACTCGACCGTGTCCATACCA	60.61	55.0	0.0	0.0	0.0	3.25	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
85	98	4.684484	AGGAACGAGAACTAAAGTTGGT	57.316	40.909	0.00	0.00	38.56	3.67
119	132	6.378564	AGAAAGAAGAAGATGAGGTGTCGATA	59.621	38.462	0.00	0.00	0.00	2.92
145	158	5.842327	CGAACAAACTAATGTTAACGTGGTC	59.158	40.000	0.00	0.00	43.31	4.02
166	179	1.112315	TGGTTGGCGCCAATGAAACT	61.112	50.000	41.80	0.00	38.28	2.66
170	183	2.192664	TGGCGCCAATGAAACTTCTA	57.807	45.000	30.74	0.00	0.00	2.10
209	222	2.389715	AGAAGATGTAGGGAAGGACGG	58.610	52.381	0.00	0.00	0.00	4.79
632	656	3.560636	AACATGGTGGATAGCCTGTAC	57.439	47.619	0.00	0.00	34.31	2.90
637	661	1.557832	GGTGGATAGCCTGTACCAACA	59.442	52.381	0.00	0.00	39.58	3.33
694	718	5.335348	CCCTTCGAACGGTATTGACAAATTT	60.335	40.000	5.13	0.00	0.00	1.82
714	738	2.507407	TTTGGAGAGGATTTTCCCGG	57.493	50.000	0.00	0.00	37.19	5.73
761	787	0.458669	CTCATGTCAATGGGCAAGCC	59.541	55.000	1.52	1.52	34.30	4.35
968	1002	5.197549	CGTTTATGCAGGATTGTATTCGTG	58.802	41.667	0.00	0.00	35.22	4.35
1040	1088	2.334946	GCTTGGAACGATGCAGCCA	61.335	57.895	0.00	0.00	0.00	4.75
1054	1119	2.231964	TGCAGCCATTGAATTGAACCTC	59.768	45.455	0.00	0.00	0.00	3.85
1189	1264	2.125106	GCCGCCTCCTCAAACGAT	60.125	61.111	0.00	0.00	0.00	3.73
1313	1390	0.526954	GTACTACACGACCATGGCCG	60.527	60.000	19.73	19.73	0.00	6.13
1378	1455	0.108992	TCAACGCGACCGATAAGCTT	60.109	50.000	15.93	3.48	38.29	3.74
1471	1548	2.767394	TCGTAATCCCATTCGGAAGGAA	59.233	45.455	3.61	0.00	46.47	3.36
1477	1554	0.808755	CCATTCGGAAGGAAAACGGG	59.191	55.000	3.61	0.00	38.36	5.28
1496	1573	1.000955	GGGAGAACGAGAAGCTTGTCA	59.999	52.381	22.08	0.00	0.00	3.58
1526	1603	2.332654	AACATCTTGAACCCGCCGC	61.333	57.895	0.00	0.00	0.00	6.53
1606	1684	6.514541	CGGGTCTGTAACATATGTAATCGACT	60.515	42.308	9.21	0.00	0.00	4.18
1607	1685	6.641314	GGGTCTGTAACATATGTAATCGACTG	59.359	42.308	9.21	6.96	0.00	3.51
1609	1687	8.082852	GGTCTGTAACATATGTAATCGACTGAT	58.917	37.037	9.21	0.00	35.98	2.90
1631	1715	8.737168	TGATATTTTTGGTGGTTCTGATCTAG	57.263	34.615	0.00	0.00	0.00	2.43
1632	1716	8.328758	TGATATTTTTGGTGGTTCTGATCTAGT	58.671	33.333	0.00	0.00	0.00	2.57
1633	1717	9.832445	GATATTTTTGGTGGTTCTGATCTAGTA	57.168	33.333	0.00	0.00	0.00	1.82
1688	1838	9.113838	GGAGAATTGTGATGCTTAGAAATTCTA	57.886	33.333	13.51	0.00	41.82	2.10
1798	1948	7.875554	TCTTTTTCCAAGTTATATGGCAAAACC	59.124	33.333	0.00	0.00	37.87	3.27
1842	1992	2.284405	ACAGTAGGTGACCCGGGG	60.284	66.667	27.92	12.73	35.12	5.73
1865	2015	3.039988	CCGTCTGGCCGATCGTAT	58.960	61.111	15.09	0.00	0.00	3.06
1877	2027	2.581637	CGATCGTATGGTATGGACACG	58.418	52.381	7.03	0.00	0.00	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.508526	ACACTCTTTCTCCAATGCCAC	58.491	47.619	0.00	0.00	0.00	5.01
1	2	2.957402	ACACTCTTTCTCCAATGCCA	57.043	45.000	0.00	0.00	0.00	4.92
2	3	2.489722	GGAACACTCTTTCTCCAATGCC	59.510	50.000	0.00	0.00	0.00	4.40
3	4	3.149196	TGGAACACTCTTTCTCCAATGC	58.851	45.455	0.00	0.00	35.02	3.56
4	5	5.772825	TTTGGAACACTCTTTCTCCAATG	57.227	39.130	3.38	0.00	45.10	2.82
85	98	7.250032	TCATCTTCTTCTTTCTCATTCCTCA	57.750	36.000	0.00	0.00	0.00	3.86
119	132	6.183360	ACCACGTTAACATTAGTTTGTTCGTT	60.183	34.615	6.39	0.00	37.71	3.85
127	140	4.202388	ACCAGGACCACGTTAACATTAGTT	60.202	41.667	6.39	0.00	41.74	2.24
145	158	1.814772	TTTCATTGGCGCCAACCAGG	61.815	55.000	42.32	29.48	41.82	4.45
166	179	2.952978	CTCTTAGCCTCTTCGCCTAGAA	59.047	50.000	0.00	0.00	37.31	2.10
170	183	2.092321	TCTACTCTTAGCCTCTTCGCCT	60.092	50.000	0.00	0.00	0.00	5.52
209	222	3.388345	ACTTGTCGTTCTTCTCTTCCC	57.612	47.619	0.00	0.00	0.00	3.97
475	497	1.905637	AGCCACCTCCTTAAAAACCG	58.094	50.000	0.00	0.00	0.00	4.44
482	504	0.902984	TCGCTGAAGCCACCTCCTTA	60.903	55.000	0.00	0.00	37.91	2.69
534	556	7.346471	TCTTTTTCTATAGGAACCTCCCATTG	58.654	38.462	0.00	0.00	37.19	2.82
587	611	4.832823	TCTCTAACATCTGAGTCCAACACA	59.167	41.667	0.00	0.00	0.00	3.72
632	656	2.224606	AGCAGAACATCTGTGTGTTGG	58.775	47.619	8.97	1.41	45.94	3.77
637	661	8.067751	TCTATTAACTAGCAGAACATCTGTGT	57.932	34.615	8.97	3.84	45.94	3.72
694	718	2.377193	TCCGGGAAAATCCTCTCCAAAA	59.623	45.455	0.00	0.00	36.57	2.44
735	759	2.945668	GCCCATTGACATGAGGTTAGTC	59.054	50.000	0.00	0.00	31.07	2.59
736	760	2.308570	TGCCCATTGACATGAGGTTAGT	59.691	45.455	0.00	0.00	31.07	2.24
737	761	3.003394	TGCCCATTGACATGAGGTTAG	57.997	47.619	0.00	0.00	31.07	2.34
761	787	6.198778	TGCATGATTTTGTGAACTTCGAAAAG	59.801	34.615	0.00	0.00	38.54	2.27
968	1002	6.770303	AGAGGCCTCTATTTTAGAAAGAATGC	59.230	38.462	34.40	0.00	38.35	3.56
1040	1088	1.468520	CGTGCGGAGGTTCAATTCAAT	59.531	47.619	0.00	0.00	0.00	2.57
1054	1119	1.327460	CTCATGGTGATTTACGTGCGG	59.673	52.381	0.00	0.00	0.00	5.69
1094	1160	4.828925	GGCTGCTGCGAGGAGGAC	62.829	72.222	9.65	0.00	40.82	3.85
1471	1548	0.320508	GCTTCTCGTTCTCCCCGTTT	60.321	55.000	0.00	0.00	0.00	3.60
1477	1554	2.440539	TGACAAGCTTCTCGTTCTCC	57.559	50.000	0.00	0.00	0.00	3.71
1496	1573	5.183904	GGTTCAAGATGTTGATGGCTAACTT	59.816	40.000	6.07	0.00	42.41	2.66
1526	1603	2.219458	TCCGTATGTCCTCTAGCTTCG	58.781	52.381	0.00	0.00	0.00	3.79
1606	1684	8.328758	ACTAGATCAGAACCACCAAAAATATCA	58.671	33.333	0.00	0.00	0.00	2.15
1607	1685	8.738645	ACTAGATCAGAACCACCAAAAATATC	57.261	34.615	0.00	0.00	0.00	1.63
1609	1687	8.598916	TGTACTAGATCAGAACCACCAAAAATA	58.401	33.333	0.00	0.00	0.00	1.40
1610	1688	7.458397	TGTACTAGATCAGAACCACCAAAAAT	58.542	34.615	0.00	0.00	0.00	1.82
1700	1850	8.103935	ACCAAACTAAGAATTTTCCCACAAAAA	58.896	29.630	0.00	0.00	32.99	1.94
1701	1851	7.625469	ACCAAACTAAGAATTTTCCCACAAAA	58.375	30.769	0.00	0.00	0.00	2.44
1702	1852	7.189079	ACCAAACTAAGAATTTTCCCACAAA	57.811	32.000	0.00	0.00	0.00	2.83
1703	1853	6.800072	ACCAAACTAAGAATTTTCCCACAA	57.200	33.333	0.00	0.00	0.00	3.33
1704	1854	6.578023	CAACCAAACTAAGAATTTTCCCACA	58.422	36.000	0.00	0.00	0.00	4.17
1705	1855	5.465390	GCAACCAAACTAAGAATTTTCCCAC	59.535	40.000	0.00	0.00	0.00	4.61
1706	1856	5.365314	AGCAACCAAACTAAGAATTTTCCCA	59.635	36.000	0.00	0.00	0.00	4.37
1707	1857	5.853936	AGCAACCAAACTAAGAATTTTCCC	58.146	37.500	0.00	0.00	0.00	3.97
1708	1858	6.292865	GCAAGCAACCAAACTAAGAATTTTCC	60.293	38.462	0.00	0.00	0.00	3.13
1709	1859	6.479990	AGCAAGCAACCAAACTAAGAATTTTC	59.520	34.615	0.00	0.00	0.00	2.29
1710	1860	6.258507	CAGCAAGCAACCAAACTAAGAATTTT	59.741	34.615	0.00	0.00	0.00	1.82
1711	1861	5.754890	CAGCAAGCAACCAAACTAAGAATTT	59.245	36.000	0.00	0.00	0.00	1.82
1712	1862	5.291971	CAGCAAGCAACCAAACTAAGAATT	58.708	37.500	0.00	0.00	0.00	2.17
1713	1863	4.797275	GCAGCAAGCAACCAAACTAAGAAT	60.797	41.667	0.00	0.00	44.79	2.40
1714	1864	3.490761	GCAGCAAGCAACCAAACTAAGAA	60.491	43.478	0.00	0.00	44.79	2.52
1715	1865	2.034558	GCAGCAAGCAACCAAACTAAGA	59.965	45.455	0.00	0.00	44.79	2.10
1716	1866	2.397549	GCAGCAAGCAACCAAACTAAG	58.602	47.619	0.00	0.00	44.79	2.18
1717	1867	2.507339	GCAGCAAGCAACCAAACTAA	57.493	45.000	0.00	0.00	44.79	2.24
1798	1948	1.522355	CGGCAGTGCTGTCCCTATG	60.522	63.158	16.21	0.00	0.00	2.23
1865	2015	0.609957	ACTCGACCGTGTCCATACCA	60.610	55.000	0.00	0.00	0.00	3.25
1877	2027	2.187946	CTCCCCATGCACTCGACC	59.812	66.667	0.00	0.00	0.00	4.79
2310	3684	4.202284	ACTTTTAGTCTTCCACGGCTTGTA	60.202	41.667	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.