AutoCloner

Multiple sequence alignment - TraesCS1B01G119500

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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	TraesCS1B01G119500	chr1B	100.000	3293	0	0	1	3293	141733238	141729946	0.000000e+00	6082
1	TraesCS1B01G119500	chr1B	94.994	1598	60	8	1712	3292	637633731	637632137	0.000000e+00	2490
2	TraesCS1B01G119500	chr1B	94.239	1597	70	12	1712	3292	591153938	591155528	0.000000e+00	2420
3	TraesCS1B01G119500	chr5B	97.312	2716	66	5	581	3292	14353437	14356149	0.000000e+00	4604
4	TraesCS1B01G119500	chr5B	96.364	1595	45	4	1712	3293	455289744	455288150	0.000000e+00	2612
5	TraesCS1B01G119500	chr5B	96.833	221	7	0	1486	1706	455290129	455289909	1.440000e-98	370
6	TraesCS1B01G119500	chr3B	96.489	1595	43	4	1712	3293	3762215	3760621	0.000000e+00	2623
7	TraesCS1B01G119500	chr3B	96.113	1595	49	4	1712	3293	4662688	4661094	0.000000e+00	2590
8	TraesCS1B01G119500	chr3B	95.928	221	9	0	1486	1706	3762565	3762345	3.120000e-95	359
9	TraesCS1B01G119500	chr3B	95.475	221	10	0	1486	1706	4663038	4662818	1.450000e-93	353
10	TraesCS1B01G119500	chrUn	94.668	1594	47	10	1712	3293	8807557	8805990	0.000000e+00	2438
11	TraesCS1B01G119500	chr7B	94.605	1594	47	10	1712	3293	714530355	714528789	0.000000e+00	2431
12	TraesCS1B01G119500	chr7B	94.354	1594	51	10	1712	3293	714451721	714450155	0.000000e+00	2409
13	TraesCS1B01G119500	chr7B	95.475	221	10	0	1486	1706	714530705	714530485	1.450000e-93	353
14	TraesCS1B01G119500	chr5A	94.605	1594	47	10	1712	3293	44278202	44276636	0.000000e+00	2431
15	TraesCS1B01G119500	chr5A	90.242	1117	91	8	578	1693	633045668	633044569	0.000000e+00	1443
16	TraesCS1B01G119500	chr5A	88.468	1136	95	14	579	1714	562130732	562131831	0.000000e+00	1339
17	TraesCS1B01G119500	chr6A	94.448	1585	49	10	1712	3293	223587258	223585710	0.000000e+00	2403
18	TraesCS1B01G119500	chr6A	89.737	1140	85	11	576	1714	508298177	508299285	0.000000e+00	1428
19	TraesCS1B01G119500	chr7D	93.469	1623	59	16	1712	3292	530866217	530864600	0.000000e+00	2366
20	TraesCS1B01G119500	chr7D	93.403	1622	61	15	1712	3292	70679851	70678235	0.000000e+00	2361
21	TraesCS1B01G119500	chr7D	93.284	1623	64	15	1712	3292	596121850	596120231	0.000000e+00	2351
22	TraesCS1B01G119500	chr7D	90.989	1143	83	10	574	1716	592400966	592402088	0.000000e+00	1522
23	TraesCS1B01G119500	chr7D	90.741	1134	71	11	581	1714	11642234	11643333	0.000000e+00	1482
24	TraesCS1B01G119500	chr6B	92.468	1155	54	10	581	1715	650726693	650727834	0.000000e+00	1620
25	TraesCS1B01G119500	chr6B	91.993	1149	48	18	2179	3290	650755239	650756380	0.000000e+00	1572
26	TraesCS1B01G119500	chr6B	92.644	435	23	2	2868	3293	449459800	449459366	4.670000e-173	617
27	TraesCS1B01G119500	chr5D	91.901	1136	73	10	581	1716	443521254	443522370	0.000000e+00	1570
28	TraesCS1B01G119500	chr4D	91.813	1136	75	9	581	1716	440465454	440464337	0.000000e+00	1567
29	TraesCS1B01G119500	chr2A	91.093	1134	83	8	581	1714	458970802	458969687	0.000000e+00	1519
30	TraesCS1B01G119500	chr2A	90.761	1104	85	7	587	1690	514763732	514764818	0.000000e+00	1458
31	TraesCS1B01G119500	chr1D	88.034	585	48	11	1	576	87778927	87778356	0.000000e+00	673
32	TraesCS1B01G119500	chr1A	86.147	462	46	10	1	454	84025000	84024549	1.780000e-132	483

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	TraesCS1B01G119500	chr1B	141729946	141733238	3292	True	6082.0	6082	100.0000	1	3293	1	chr1B.!!$R1	3292
1	TraesCS1B01G119500	chr1B	637632137	637633731	1594	True	2490.0	2490	94.9940	1712	3292	1	chr1B.!!$R2	1580
2	TraesCS1B01G119500	chr1B	591153938	591155528	1590	False	2420.0	2420	94.2390	1712	3292	1	chr1B.!!$F1	1580
3	TraesCS1B01G119500	chr5B	14353437	14356149	2712	False	4604.0	4604	97.3120	581	3292	1	chr5B.!!$F1	2711
4	TraesCS1B01G119500	chr5B	455288150	455290129	1979	True	1491.0	2612	96.5985	1486	3293	2	chr5B.!!$R1	1807
5	TraesCS1B01G119500	chr3B	3760621	3762565	1944	True	1491.0	2623	96.2085	1486	3293	2	chr3B.!!$R1	1807
6	TraesCS1B01G119500	chr3B	4661094	4663038	1944	True	1471.5	2590	95.7940	1486	3293	2	chr3B.!!$R2	1807
7	TraesCS1B01G119500	chrUn	8805990	8807557	1567	True	2438.0	2438	94.6680	1712	3293	1	chrUn.!!$R1	1581
8	TraesCS1B01G119500	chr7B	714450155	714451721	1566	True	2409.0	2409	94.3540	1712	3293	1	chr7B.!!$R1	1581
9	TraesCS1B01G119500	chr7B	714528789	714530705	1916	True	1392.0	2431	95.0400	1486	3293	2	chr7B.!!$R2	1807
10	TraesCS1B01G119500	chr5A	44276636	44278202	1566	True	2431.0	2431	94.6050	1712	3293	1	chr5A.!!$R1	1581
11	TraesCS1B01G119500	chr5A	633044569	633045668	1099	True	1443.0	1443	90.2420	578	1693	1	chr5A.!!$R2	1115
12	TraesCS1B01G119500	chr5A	562130732	562131831	1099	False	1339.0	1339	88.4680	579	1714	1	chr5A.!!$F1	1135
13	TraesCS1B01G119500	chr6A	223585710	223587258	1548	True	2403.0	2403	94.4480	1712	3293	1	chr6A.!!$R1	1581
14	TraesCS1B01G119500	chr6A	508298177	508299285	1108	False	1428.0	1428	89.7370	576	1714	1	chr6A.!!$F1	1138
15	TraesCS1B01G119500	chr7D	530864600	530866217	1617	True	2366.0	2366	93.4690	1712	3292	1	chr7D.!!$R2	1580
16	TraesCS1B01G119500	chr7D	70678235	70679851	1616	True	2361.0	2361	93.4030	1712	3292	1	chr7D.!!$R1	1580
17	TraesCS1B01G119500	chr7D	596120231	596121850	1619	True	2351.0	2351	93.2840	1712	3292	1	chr7D.!!$R3	1580
18	TraesCS1B01G119500	chr7D	592400966	592402088	1122	False	1522.0	1522	90.9890	574	1716	1	chr7D.!!$F2	1142
19	TraesCS1B01G119500	chr7D	11642234	11643333	1099	False	1482.0	1482	90.7410	581	1714	1	chr7D.!!$F1	1133
20	TraesCS1B01G119500	chr6B	650726693	650727834	1141	False	1620.0	1620	92.4680	581	1715	1	chr6B.!!$F1	1134
21	TraesCS1B01G119500	chr6B	650755239	650756380	1141	False	1572.0	1572	91.9930	2179	3290	1	chr6B.!!$F2	1111
22	TraesCS1B01G119500	chr5D	443521254	443522370	1116	False	1570.0	1570	91.9010	581	1716	1	chr5D.!!$F1	1135
23	TraesCS1B01G119500	chr4D	440464337	440465454	1117	True	1567.0	1567	91.8130	581	1716	1	chr4D.!!$R1	1135
24	TraesCS1B01G119500	chr2A	458969687	458970802	1115	True	1519.0	1519	91.0930	581	1714	1	chr2A.!!$R1	1133
25	TraesCS1B01G119500	chr2A	514763732	514764818	1086	False	1458.0	1458	90.7610	587	1690	1	chr2A.!!$F1	1103
26	TraesCS1B01G119500	chr1D	87778356	87778927	571	True	673.0	673	88.0340	1	576	1	chr1D.!!$R1	575

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
551	554	0.109458	ACTAGTCGCACGAATCGCAA	60.109	50.0	1.15	0.0	0.0	4.85	F
558	561	0.660005	GCACGAATCGCAAAGCACAA	60.660	50.0	1.15	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2164	2488	2.204090	GTCCCTGTCCCCCTCCAA	60.204	66.667	0.00	0.0	0.00	3.53	R
2345	2669	3.696051	ACCTAACATGCATGACATTCCAC	59.304	43.478	32.75	0.0	36.64	4.02	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
58	59	1.640428	CTCTTGGCGCGAGTATTTCA	58.360	50.000	12.10	0.00	0.00	2.69
63	64	4.632251	TCTTGGCGCGAGTATTTCAAATAA	59.368	37.500	12.10	0.00	0.00	1.40
67	68	7.197071	TGGCGCGAGTATTTCAAATAAATAT	57.803	32.000	12.10	0.00	0.00	1.28
68	69	7.295201	TGGCGCGAGTATTTCAAATAAATATC	58.705	34.615	12.10	0.00	0.00	1.63
153	155	0.755686	TGCATGGGGTTTGGTTTCAC	59.244	50.000	0.00	0.00	0.00	3.18
156	158	1.269448	CATGGGGTTTGGTTTCACGAG	59.731	52.381	0.00	0.00	0.00	4.18
194	196	2.479566	TGCCACTCTCTCACCATTTC	57.520	50.000	0.00	0.00	0.00	2.17
196	198	2.373169	TGCCACTCTCTCACCATTTCTT	59.627	45.455	0.00	0.00	0.00	2.52
220	222	6.401477	CTTTTGACAAAAAGTACTTACGCG	57.599	37.500	8.92	3.53	44.84	6.01
228	230	6.018016	ACAAAAAGTACTTACGCGTGGTATTT	60.018	34.615	24.59	21.75	0.00	1.40
261	264	7.658525	ACATATGCAAAAGATTTACCCATCA	57.341	32.000	1.58	0.00	0.00	3.07
302	305	9.444600	AAAGAATTGCCTAGTTATTTAACGAGA	57.555	29.630	10.90	0.00	40.08	4.04
303	306	9.444600	AAGAATTGCCTAGTTATTTAACGAGAA	57.555	29.630	10.90	1.42	40.08	2.87
304	307	9.444600	AGAATTGCCTAGTTATTTAACGAGAAA	57.555	29.630	10.90	6.63	40.08	2.52
305	308	9.704098	GAATTGCCTAGTTATTTAACGAGAAAG	57.296	33.333	10.90	0.00	40.08	2.62
306	309	9.444600	AATTGCCTAGTTATTTAACGAGAAAGA	57.555	29.630	10.90	0.00	40.08	2.52
307	310	9.614792	ATTGCCTAGTTATTTAACGAGAAAGAT	57.385	29.630	10.90	0.36	40.08	2.40
344	347	8.704668	ACATATATTTCACATGTGGACTACTCA	58.295	33.333	25.16	0.78	31.83	3.41
345	348	8.982685	CATATATTTCACATGTGGACTACTCAC	58.017	37.037	25.16	0.00	35.82	3.51
347	350	4.681074	TTCACATGTGGACTACTCACAA	57.319	40.909	25.16	5.64	46.41	3.33
348	351	4.681074	TCACATGTGGACTACTCACAAA	57.319	40.909	25.16	0.00	46.41	2.83
349	352	4.631131	TCACATGTGGACTACTCACAAAG	58.369	43.478	25.16	0.00	46.41	2.77
350	353	3.187227	CACATGTGGACTACTCACAAAGC	59.813	47.826	18.51	0.00	46.41	3.51
351	354	3.181455	ACATGTGGACTACTCACAAAGCA	60.181	43.478	0.00	0.00	46.41	3.91
352	355	3.769739	TGTGGACTACTCACAAAGCAT	57.230	42.857	0.00	0.00	41.50	3.79

Showing 1 to 25 of 201 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
118	120	6.171921	CCCCATGCATTTTATTTTCTTGTGA	58.828	36.000	0.00	0.00	0.00	3.58
153	155	5.515982	GCATGCATACTCATAGATTCTCTCG	59.484	44.000	14.21	0.00	0.00	4.04
156	158	5.350914	GTGGCATGCATACTCATAGATTCTC	59.649	44.000	21.36	0.00	0.00	2.87
164	166	2.704596	AGAGAGTGGCATGCATACTCAT	59.295	45.455	35.54	26.94	42.44	2.90
194	196	7.097570	CGCGTAAGTACTTTTTGTCAAAAGAAG	60.098	37.037	14.49	9.02	45.12	2.85
196	198	6.183360	ACGCGTAAGTACTTTTTGTCAAAAGA	60.183	34.615	11.67	2.72	45.12	2.52
228	230	8.600449	AAATCTTTTGCATATGTTTCGGAAAA	57.400	26.923	4.46	0.00	0.00	2.29
233	235	7.032580	TGGGTAAATCTTTTGCATATGTTTCG	58.967	34.615	4.29	0.00	0.00	3.46
277	280	9.444600	TTCTCGTTAAATAACTAGGCAATTCTT	57.555	29.630	0.00	0.00	34.12	2.52
278	281	9.444600	TTTCTCGTTAAATAACTAGGCAATTCT	57.555	29.630	0.00	0.00	34.12	2.40
318	321	8.704668	TGAGTAGTCCACATGTGAAATATATGT	58.295	33.333	27.46	3.02	41.20	2.29
319	322	8.982685	GTGAGTAGTCCACATGTGAAATATATG	58.017	37.037	27.46	7.74	34.81	1.78
320	323	8.704668	TGTGAGTAGTCCACATGTGAAATATAT	58.295	33.333	27.46	3.65	39.36	0.86
321	324	8.073467	TGTGAGTAGTCCACATGTGAAATATA	57.927	34.615	27.46	9.35	39.36	0.86
322	325	6.946340	TGTGAGTAGTCCACATGTGAAATAT	58.054	36.000	27.46	10.30	39.36	1.28
323	326	6.353404	TGTGAGTAGTCCACATGTGAAATA	57.647	37.500	27.46	7.95	39.36	1.40
324	327	5.227569	TGTGAGTAGTCCACATGTGAAAT	57.772	39.130	27.46	9.19	39.36	2.17
325	328	4.681074	TGTGAGTAGTCCACATGTGAAA	57.319	40.909	27.46	11.91	39.36	2.69
326	329	4.681074	TTGTGAGTAGTCCACATGTGAA	57.319	40.909	27.46	3.21	43.17	3.18
327	330	4.631131	CTTTGTGAGTAGTCCACATGTGA	58.369	43.478	27.46	10.46	43.17	3.58
328	331	3.187227	GCTTTGTGAGTAGTCCACATGTG	59.813	47.826	19.31	19.31	43.17	3.21
329	332	3.181455	TGCTTTGTGAGTAGTCCACATGT	60.181	43.478	0.00	0.00	43.17	3.21
330	333	3.402110	TGCTTTGTGAGTAGTCCACATG	58.598	45.455	0.00	0.00	43.17	3.21
331	334	3.769739	TGCTTTGTGAGTAGTCCACAT	57.230	42.857	0.00	0.00	43.17	3.21
332	335	3.769739	ATGCTTTGTGAGTAGTCCACA	57.230	42.857	0.00	0.00	42.16	4.17

Showing 1 to 25 of 229 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.