AutoCloner

Multiple sequence alignment - TraesCS6B01G441600

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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	TraesCS6B01G441600	chr6B	100.000	2369	0	0	1	2369	705645026	705647394	0.000000e+00	4375.0
1	TraesCS6B01G441600	chr6B	94.946	1484	66	5	1	1479	705941497	705942976	0.000000e+00	2316.0
2	TraesCS6B01G441600	chr6B	89.019	1794	171	14	1	1775	705552950	705554736	0.000000e+00	2198.0
3	TraesCS6B01G441600	chr6B	87.914	1721	192	11	123	1831	705959853	705961569	0.000000e+00	2012.0
4	TraesCS6B01G441600	chr6B	86.731	1771	218	11	1	1759	705921087	705922852	0.000000e+00	1953.0
5	TraesCS6B01G441600	chr6B	86.655	1761	217	13	1	1750	705803700	705805453	0.000000e+00	1934.0
6	TraesCS6B01G441600	chr6B	89.683	1512	140	8	1	1507	705504895	705506395	0.000000e+00	1914.0
7	TraesCS6B01G441600	chr6B	88.748	1573	146	22	1	1555	705843069	705844628	0.000000e+00	1895.0
8	TraesCS6B01G441600	chr6B	94.910	334	17	0	1869	2202	705961569	705961902	7.500000e-145	523.0
9	TraesCS6B01G441600	chr6B	91.011	178	13	2	1768	1943	705554996	705555172	1.090000e-58	237.0
10	TraesCS6B01G441600	chr6B	92.727	110	4	2	2129	2235	705923435	705923543	3.150000e-34	156.0
11	TraesCS6B01G441600	chr6B	84.286	140	18	3	1993	2132	705555173	705555308	1.480000e-27	134.0
12	TraesCS6B01G441600	chr6B	96.104	77	3	0	2232	2308	705845665	705845741	2.470000e-25	126.0
13	TraesCS6B01G441600	chr6B	83.193	119	15	3	1410	1527	705808999	705809113	1.160000e-18	104.0
14	TraesCS6B01G441600	chr6B	98.077	52	1	0	2318	2369	705657714	705657765	9.020000e-15	91.6
15	TraesCS6B01G441600	chr6B	97.619	42	1	0	1993	2034	705923299	705923340	3.270000e-09	73.1
16	TraesCS6B01G441600	chr6B	95.455	44	2	0	1410	1453	705638151	705638194	1.170000e-08	71.3
17	TraesCS6B01G441600	chr6A	88.282	1775	186	15	1	1759	609722754	609724522	0.000000e+00	2106.0
18	TraesCS6B01G441600	chr6A	95.385	65	3	0	1768	1832	609724810	609724874	1.160000e-18	104.0
19	TraesCS6B01G441600	chr6A	96.296	54	2	0	1993	2046	609724925	609724978	3.240000e-14	89.8
20	TraesCS6B01G441600	chr6D	87.341	1572	186	9	1	1562	462858579	462860147	0.000000e+00	1788.0

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	TraesCS6B01G441600	chr6B	705645026	705647394	2368	False	4375.000000	4375	100.000000	1	2369	1	chr6B.!!$F3	2368
1	TraesCS6B01G441600	chr6B	705941497	705942976	1479	False	2316.000000	2316	94.946000	1	1479	1	chr6B.!!$F5	1478
2	TraesCS6B01G441600	chr6B	705504895	705506395	1500	False	1914.000000	1914	89.683000	1	1507	1	chr6B.!!$F1	1506
3	TraesCS6B01G441600	chr6B	705959853	705961902	2049	False	1267.500000	2012	91.412000	123	2202	2	chr6B.!!$F10	2079
4	TraesCS6B01G441600	chr6B	705803700	705809113	5413	False	1019.000000	1934	84.924000	1	1750	2	chr6B.!!$F7	1749
5	TraesCS6B01G441600	chr6B	705843069	705845741	2672	False	1010.500000	1895	92.426000	1	2308	2	chr6B.!!$F8	2307
6	TraesCS6B01G441600	chr6B	705552950	705555308	2358	False	856.333333	2198	88.105333	1	2132	3	chr6B.!!$F6	2131
7	TraesCS6B01G441600	chr6B	705921087	705923543	2456	False	727.366667	1953	92.359000	1	2235	3	chr6B.!!$F9	2234
8	TraesCS6B01G441600	chr6A	609722754	609724978	2224	False	766.600000	2106	93.321000	1	2046	3	chr6A.!!$F1	2045
9	TraesCS6B01G441600	chr6D	462858579	462860147	1568	False	1788.000000	1788	87.341000	1	1562	1	chr6D.!!$F1	1561

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
899	907	0.609131	ACAGGAGCAATCCCAAACCG	60.609	55.0	0.0	0.0	0.0	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2325	3988	0.843309	TGCCCTCTGTTCTGTTCCAA	59.157	50.0	0.0	0.0	0.0	3.53	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
167	172	6.402550	CGACAATTGGACCTATCTTCAAACTG	60.403	42.308	10.83	0.00	0.00	3.16
264	269	2.092212	AGGCAACATCCCCTTGTCTATG	60.092	50.000	0.00	0.00	31.69	2.23
423	428	6.469782	AACAACAATCTGACTGGTCAATTT	57.530	33.333	4.94	0.00	39.39	1.82
497	505	8.352942	CAATAGGTTATTTGGAGAATTACCAGC	58.647	37.037	8.94	0.00	38.70	4.85
720	728	8.749026	ATGATTACTTTCATGAAGAGAGCATT	57.251	30.769	18.50	0.69	38.77	3.56
735	743	6.656902	AGAGAGCATTCCAGTAATCATGAAA	58.343	36.000	0.00	0.00	0.00	2.69
899	907	0.609131	ACAGGAGCAATCCCAAACCG	60.609	55.000	0.00	0.00	0.00	4.44
1050	1058	2.088423	GCAATACCATCCGGACAACAA	58.912	47.619	6.12	0.00	35.59	2.83
1051	1059	2.687935	GCAATACCATCCGGACAACAAT	59.312	45.455	6.12	0.00	35.59	2.71
1257	1265	3.119708	GCACCATGTTGATGAAGAGAACC	60.120	47.826	0.00	0.00	0.00	3.62
1265	1273	2.225624	TGATGAAGAGAACCTGGAGGGA	60.226	50.000	0.00	0.00	40.27	4.20
1383	1391	2.650116	ATGAAGCGCCCGACTCTGT	61.650	57.895	2.29	0.00	0.00	3.41
1457	1468	8.855804	ATCTCTATTTGTAACTCTAAAGGGGA	57.144	34.615	0.00	0.00	0.00	4.81
1508	1519	8.726068	TGATGTACTGGTATTTGTATGTTTGTG	58.274	33.333	0.00	0.00	0.00	3.33
1536	1547	7.967854	TGTAGCAAATGAAGTGTATATGTTTGC	59.032	33.333	10.84	10.84	46.02	3.68
1557	1574	5.428253	TGCGGATTATTTAAGCTGAAGTCT	58.572	37.500	0.00	0.00	29.81	3.24
1585	1602	1.444383	CGCTCTTCGCTGTGCACTA	60.444	57.895	19.41	3.54	36.13	2.74
1600	1617	6.239217	TGTGCACTACATGGAGAAAGATAT	57.761	37.500	19.41	0.00	33.42	1.63
1601	1618	6.051074	TGTGCACTACATGGAGAAAGATATG	58.949	40.000	19.41	0.00	33.42	1.78
1623	1642	0.764890	GCCCCATATGTACTCTGCCA	59.235	55.000	1.24	0.00	0.00	4.92
1637	1656	5.796424	ACTCTGCCATTTTCATGTTCTTT	57.204	34.783	0.00	0.00	0.00	2.52
1650	1669	5.885881	TCATGTTCTTTAGTTTGCGTTGTT	58.114	33.333	0.00	0.00	0.00	2.83
1653	1672	5.328691	TGTTCTTTAGTTTGCGTTGTTCAG	58.671	37.500	0.00	0.00	0.00	3.02
1911	3437	9.342308	GATGGACATGTATATCAAGGAAAAGAA	57.658	33.333	13.96	0.00	0.00	2.52
1959	3487	5.189736	AGGAGCACCAGTGAATTTCATACTA	59.810	40.000	2.07	0.00	38.94	1.82
2037	3576	3.576550	GGCATTAAACTTGTTTCCAGGGA	59.423	43.478	1.72	0.00	0.00	4.20
2106	3645	3.447586	CGAGGGAAACTCTGGATGAACTA	59.552	47.826	0.00	0.00	44.33	2.24
2143	3726	3.795877	TCTTTGGCCTGCAAAAGAAAAG	58.204	40.909	17.24	6.77	41.47	2.27
2154	3737	6.036408	CCTGCAAAAGAAAAGGAACTGAAAAG	59.964	38.462	0.00	0.00	40.86	2.27
2175	3780	8.546597	AAAAGTGTAAAACAATGCTGAAAGTT	57.453	26.923	0.00	0.00	35.30	2.66
2215	3820	3.533547	TGCAAACAAGCAAAAGCAGATT	58.466	36.364	0.00	0.00	42.46	2.40
2251	3914	0.813184	CTGGTGACATTGACATGGCC	59.187	55.000	0.00	0.00	37.69	5.36
2273	3936	2.526304	TGGACAGAAGTCAAGAACCG	57.474	50.000	0.00	0.00	46.80	4.44
2308	3971	6.455113	CCCAAAGTGTATAGATTGAACGAACG	60.455	42.308	0.00	0.00	0.00	3.95
2309	3972	6.309494	CCAAAGTGTATAGATTGAACGAACGA	59.691	38.462	0.14	0.00	0.00	3.85
2310	3973	7.148705	CCAAAGTGTATAGATTGAACGAACGAA	60.149	37.037	0.14	0.00	0.00	3.85
2311	3974	6.866179	AGTGTATAGATTGAACGAACGAAC	57.134	37.500	0.14	0.00	0.00	3.95
2313	3976	6.307318	AGTGTATAGATTGAACGAACGAACAC	59.693	38.462	0.14	0.00	34.13	3.32
2314	3977	6.088483	GTGTATAGATTGAACGAACGAACACA	59.912	38.462	0.14	0.00	34.12	3.72
2316	3979	3.191669	AGATTGAACGAACGAACACACA	58.808	40.909	0.14	0.00	0.00	3.72
2317	3980	3.619483	AGATTGAACGAACGAACACACAA	59.381	39.130	0.14	0.00	0.00	3.33
2318	3981	3.377434	TTGAACGAACGAACACACAAG	57.623	42.857	0.14	0.00	0.00	3.16
2319	3982	2.608268	TGAACGAACGAACACACAAGA	58.392	42.857	0.14	0.00	0.00	3.02
2320	3983	2.601314	TGAACGAACGAACACACAAGAG	59.399	45.455	0.14	0.00	0.00	2.85
2321	3984	2.288961	ACGAACGAACACACAAGAGT	57.711	45.000	0.14	0.00	0.00	3.24
2322	3985	3.425577	ACGAACGAACACACAAGAGTA	57.574	42.857	0.14	0.00	0.00	2.59
2323	3986	3.973657	ACGAACGAACACACAAGAGTAT	58.026	40.909	0.14	0.00	0.00	2.12
2324	3987	3.734231	ACGAACGAACACACAAGAGTATG	59.266	43.478	0.14	0.00	0.00	2.39
2325	3988	3.734231	CGAACGAACACACAAGAGTATGT	59.266	43.478	0.00	0.00	36.85	2.29
2327	3990	5.403897	AACGAACACACAAGAGTATGTTG	57.596	39.130	0.00	0.00	44.84	3.33
2328	3991	3.807622	ACGAACACACAAGAGTATGTTGG	59.192	43.478	0.00	0.00	44.84	3.77
2330	3993	4.509970	CGAACACACAAGAGTATGTTGGAA	59.490	41.667	0.00	0.00	44.84	3.53
2335	3998	5.527214	CACACAAGAGTATGTTGGAACAGAA	59.473	40.000	0.00	0.00	44.74	3.02
2336	3999	5.527582	ACACAAGAGTATGTTGGAACAGAAC	59.472	40.000	0.00	0.00	44.74	3.01
2337	4000	5.527214	CACAAGAGTATGTTGGAACAGAACA	59.473	40.000	9.31	0.00	44.74	3.18
2343	4559	1.239347	GTTGGAACAGAACAGAGGGC	58.761	55.000	0.00	0.00	42.39	5.19
2349	4565	1.972872	ACAGAACAGAGGGCAAACAG	58.027	50.000	0.00	0.00	0.00	3.16
2350	4566	1.490490	ACAGAACAGAGGGCAAACAGA	59.510	47.619	0.00	0.00	0.00	3.41
2351	4567	2.149578	CAGAACAGAGGGCAAACAGAG	58.850	52.381	0.00	0.00	0.00	3.35
2352	4568	2.050144	AGAACAGAGGGCAAACAGAGA	58.950	47.619	0.00	0.00	0.00	3.10
2353	4569	2.038295	AGAACAGAGGGCAAACAGAGAG	59.962	50.000	0.00	0.00	0.00	3.20
2354	4570	1.428869	ACAGAGGGCAAACAGAGAGT	58.571	50.000	0.00	0.00	0.00	3.24
2358	4574	3.196469	CAGAGGGCAAACAGAGAGTATGA	59.804	47.826	0.00	0.00	0.00	2.15
2360	4576	4.100808	AGAGGGCAAACAGAGAGTATGATC	59.899	45.833	0.00	0.00	0.00	2.92
2364	4580	4.937620	GGCAAACAGAGAGTATGATCAACA	59.062	41.667	0.00	0.00	0.00	3.33
2367	4583	6.314648	GCAAACAGAGAGTATGATCAACATGA	59.685	38.462	0.00	0.00	39.77	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
264	269	5.872070	CCTAGACAGAGAAGTCAATTGGAAC	59.128	44.000	5.42	0.00	40.98	3.62
339	344	4.290711	TCTGGAGTTTGCATCAGATTCA	57.709	40.909	0.00	0.00	32.10	2.57
378	383	6.889722	TGTTATTTAGGGCTAAGCTGAACATT	59.110	34.615	0.00	0.00	0.00	2.71
423	428	7.265599	TCTATGTGACCCAAGAAATTTAGGA	57.734	36.000	5.59	0.00	0.00	2.94
497	505	2.167075	GGGATCTTTTCTGGCAACCATG	59.833	50.000	0.00	0.00	30.82	3.66
513	521	9.178758	ACTCTTAATATTTTCAACTGTGGGATC	57.821	33.333	0.00	0.00	0.00	3.36
720	728	7.414429	CGCTTTTGATCTTTCATGATTACTGGA	60.414	37.037	0.00	0.00	0.00	3.86
735	743	5.599999	AGGTATAGTCACGCTTTTGATCT	57.400	39.130	0.00	0.00	0.00	2.75
845	853	4.973168	TGACAAGTTCAGATTGGTAAGCT	58.027	39.130	0.00	0.00	31.76	3.74
899	907	5.047377	TCCAACTGCCTTAAATCACCAATTC	60.047	40.000	0.00	0.00	0.00	2.17
926	934	7.825331	AACTCATTGAAGGATAGATCGAGTA	57.175	36.000	0.00	0.00	31.31	2.59
1050	1058	7.341805	ACATCTGGTTATCAAGAGCTTGTAAT	58.658	34.615	9.79	0.80	41.16	1.89
1051	1059	6.711277	ACATCTGGTTATCAAGAGCTTGTAA	58.289	36.000	9.79	5.87	41.16	2.41
1177	1185	4.577693	GCTCATGGCAAGATAAACAGATGA	59.422	41.667	0.00	0.00	41.35	2.92
1257	1265	0.182299	GGAAGAAGGCATCCCTCCAG	59.818	60.000	4.15	0.00	41.90	3.86
1265	1273	9.370930	TCATATCAATAAATTGGAAGAAGGCAT	57.629	29.630	3.00	0.00	38.30	4.40
1376	1384	1.298859	AATTCGCCCGCAACAGAGTC	61.299	55.000	0.00	0.00	0.00	3.36
1383	1391	1.237954	TACAAGCAATTCGCCCGCAA	61.238	50.000	0.00	0.00	44.04	4.85
1457	1468	3.055385	ACAATACATACGTCCAGCCAAGT	60.055	43.478	0.00	0.00	0.00	3.16
1508	1519	7.251704	ACATATACACTTCATTTGCTACAGC	57.748	36.000	0.00	0.00	42.50	4.40
1536	1547	5.277538	GGCAGACTTCAGCTTAAATAATCCG	60.278	44.000	0.00	0.00	0.00	4.18
1557	1574	1.911293	GCGAAGAGCGAACAATGGCA	61.911	55.000	0.00	0.00	44.57	4.92
1585	1602	3.484407	GGCTGCATATCTTTCTCCATGT	58.516	45.455	0.50	0.00	0.00	3.21
1600	1617	1.417517	CAGAGTACATATGGGGCTGCA	59.582	52.381	7.80	0.00	0.00	4.41
1601	1618	1.879796	GCAGAGTACATATGGGGCTGC	60.880	57.143	19.18	19.18	40.15	5.25
1623	1642	7.491048	ACAACGCAAACTAAAGAACATGAAAAT	59.509	29.630	0.00	0.00	0.00	1.82
1637	1656	2.215196	GGGACTGAACAACGCAAACTA	58.785	47.619	0.00	0.00	0.00	2.24
1650	1669	8.548025	TGATGAATTATTACTCTTTGGGACTGA	58.452	33.333	0.00	0.00	0.00	3.41
1653	1672	7.283127	TGCTGATGAATTATTACTCTTTGGGAC	59.717	37.037	0.00	0.00	0.00	4.46
1693	1720	5.703978	TTCACATATTGAACAACAGGTGG	57.296	39.130	9.94	0.00	39.45	4.61
1867	3391	5.126707	GTCCATCATGAGAGCCAGAAAATTT	59.873	40.000	0.09	0.00	0.00	1.82
1899	3425	3.884895	TGCTCACAGTTCTTTTCCTTGA	58.115	40.909	0.00	0.00	0.00	3.02
1911	3437	2.436417	ACAACACAGTTTGCTCACAGT	58.564	42.857	0.00	0.00	0.00	3.55
2106	3645	3.126831	CAAAGAGCTGAACGTCTTCTGT	58.873	45.455	0.00	0.00	31.61	3.41
2143	3726	6.756542	AGCATTGTTTTACACTTTTCAGTTCC	59.243	34.615	0.00	0.00	0.00	3.62
2154	3737	5.276820	GCCAACTTTCAGCATTGTTTTACAC	60.277	40.000	0.00	0.00	0.00	2.90
2175	3780	2.281484	GTGAAACAGGGAGCGCCA	60.281	61.111	9.31	0.00	36.32	5.69
2215	3820	7.532199	TGTCACCAGAGACCCTTATATATACA	58.468	38.462	0.00	0.00	37.73	2.29
2251	3914	3.077359	GGTTCTTGACTTCTGTCCATGG	58.923	50.000	4.97	4.97	42.28	3.66
2263	3926	2.617274	GCACCTGGCGGTTCTTGAC	61.617	63.158	0.00	0.00	42.13	3.18
2273	3936	2.116125	ACTTTGGGAGCACCTGGC	59.884	61.111	0.00	0.00	45.30	4.85
2311	3974	5.056480	TCTGTTCCAACATACTCTTGTGTG	58.944	41.667	0.00	0.00	40.48	3.82
2313	3976	5.527214	TGTTCTGTTCCAACATACTCTTGTG	59.473	40.000	0.00	0.00	38.41	3.33
2314	3977	5.680619	TGTTCTGTTCCAACATACTCTTGT	58.319	37.500	0.00	0.00	38.41	3.16
2316	3979	6.174720	TCTGTTCTGTTCCAACATACTCTT	57.825	37.500	0.00	0.00	38.41	2.85
2317	3980	5.279708	CCTCTGTTCTGTTCCAACATACTCT	60.280	44.000	0.00	0.00	38.41	3.24
2318	3981	4.932200	CCTCTGTTCTGTTCCAACATACTC	59.068	45.833	0.00	0.00	38.41	2.59
2319	3982	4.263068	CCCTCTGTTCTGTTCCAACATACT	60.263	45.833	0.00	0.00	38.41	2.12
2320	3983	4.003648	CCCTCTGTTCTGTTCCAACATAC	58.996	47.826	0.00	0.00	38.41	2.39
2321	3984	3.559171	GCCCTCTGTTCTGTTCCAACATA	60.559	47.826	0.00	0.00	38.41	2.29
2322	3985	2.815589	GCCCTCTGTTCTGTTCCAACAT	60.816	50.000	0.00	0.00	38.41	2.71
2323	3986	1.476833	GCCCTCTGTTCTGTTCCAACA	60.477	52.381	0.00	0.00	37.37	3.33
2324	3987	1.239347	GCCCTCTGTTCTGTTCCAAC	58.761	55.000	0.00	0.00	0.00	3.77
2325	3988	0.843309	TGCCCTCTGTTCTGTTCCAA	59.157	50.000	0.00	0.00	0.00	3.53
2326	3989	0.843309	TTGCCCTCTGTTCTGTTCCA	59.157	50.000	0.00	0.00	0.00	3.53
2327	3990	1.609072	GTTTGCCCTCTGTTCTGTTCC	59.391	52.381	0.00	0.00	0.00	3.62
2328	3991	2.291741	CTGTTTGCCCTCTGTTCTGTTC	59.708	50.000	0.00	0.00	0.00	3.18
2330	3993	1.490490	TCTGTTTGCCCTCTGTTCTGT	59.510	47.619	0.00	0.00	0.00	3.41
2335	3998	1.428869	ACTCTCTGTTTGCCCTCTGT	58.571	50.000	0.00	0.00	0.00	3.41
2336	3999	3.196469	TCATACTCTCTGTTTGCCCTCTG	59.804	47.826	0.00	0.00	0.00	3.35
2337	4000	3.445008	TCATACTCTCTGTTTGCCCTCT	58.555	45.455	0.00	0.00	0.00	3.69
2343	4559	7.838771	TCATGTTGATCATACTCTCTGTTTG	57.161	36.000	0.00	0.00	34.67	2.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.