AutoCloner

Multiple sequence alignment - TraesCS4A01G022300

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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	TraesCS4A01G022300	chr4A	100.000	2474	0	0	1	2474	16043578	16041105	0.000000e+00	4569.0
1	TraesCS4A01G022300	chr3D	94.346	1521	79	5	1	1515	597169694	597168175	0.000000e+00	2326.0
2	TraesCS4A01G022300	chr3D	90.518	791	67	6	2	790	376259066	376259850	0.000000e+00	1038.0
3	TraesCS4A01G022300	chr7A	94.145	1520	82	7	1	1515	294428	292911	0.000000e+00	2307.0
4	TraesCS4A01G022300	chr7A	96.075	1223	45	3	19	1238	347150594	347149372	0.000000e+00	1989.0
5	TraesCS4A01G022300	chr7A	88.636	44	3	2	1995	2037	548814111	548814069	4.000000e-03	52.8
6	TraesCS4A01G022300	chr3B	93.742	1518	90	5	1	1515	506981519	506980004	0.000000e+00	2272.0
7	TraesCS4A01G022300	chr3B	86.361	1503	188	11	15	1514	490788093	490789581	0.000000e+00	1624.0
8	TraesCS4A01G022300	chr3B	93.757	897	54	2	621	1515	187877147	187878043	0.000000e+00	1345.0
9	TraesCS4A01G022300	chr3B	95.098	102	5	0	532	633	187823556	187823657	7.080000e-36	161.0
10	TraesCS4A01G022300	chr5B	87.653	1393	156	8	125	1514	683399176	683397797	0.000000e+00	1605.0
11	TraesCS4A01G022300	chr5D	94.160	839	45	4	680	1515	495786297	495785460	0.000000e+00	1275.0
12	TraesCS4A01G022300	chr4D	93.766	770	45	3	754	1521	218122568	218121800	0.000000e+00	1153.0
13	TraesCS4A01G022300	chr4D	93.597	734	44	3	754	1485	218258173	218258905	0.000000e+00	1092.0
14	TraesCS4A01G022300	chr4D	91.523	755	50	10	1719	2470	450705698	450706441	0.000000e+00	1027.0
15	TraesCS4A01G022300	chr4D	83.721	301	34	11	1512	1799	450705364	450705662	1.130000e-68	270.0
16	TraesCS4A01G022300	chr1D	93.254	504	32	2	140	641	206822401	206821898	0.000000e+00	741.0
17	TraesCS4A01G022300	chr4B	92.473	186	13	1	2285	2470	564082143	564082327	5.250000e-67	265.0
18	TraesCS4A01G022300	chr2B	79.913	229	39	6	1718	1941	456010217	456010443	7.080000e-36	161.0
19	TraesCS4A01G022300	chr1A	75.346	361	75	11	2	355	584750768	584750415	7.080000e-36	161.0

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	TraesCS4A01G022300	chr4A	16041105	16043578	2473	True	4569.0	4569	100.000	1	2474	1	chr4A.!!$R1	2473
1	TraesCS4A01G022300	chr3D	597168175	597169694	1519	True	2326.0	2326	94.346	1	1515	1	chr3D.!!$R1	1514
2	TraesCS4A01G022300	chr3D	376259066	376259850	784	False	1038.0	1038	90.518	2	790	1	chr3D.!!$F1	788
3	TraesCS4A01G022300	chr7A	292911	294428	1517	True	2307.0	2307	94.145	1	1515	1	chr7A.!!$R1	1514
4	TraesCS4A01G022300	chr7A	347149372	347150594	1222	True	1989.0	1989	96.075	19	1238	1	chr7A.!!$R2	1219
5	TraesCS4A01G022300	chr3B	506980004	506981519	1515	True	2272.0	2272	93.742	1	1515	1	chr3B.!!$R1	1514
6	TraesCS4A01G022300	chr3B	490788093	490789581	1488	False	1624.0	1624	86.361	15	1514	1	chr3B.!!$F3	1499
7	TraesCS4A01G022300	chr3B	187877147	187878043	896	False	1345.0	1345	93.757	621	1515	1	chr3B.!!$F2	894
8	TraesCS4A01G022300	chr5B	683397797	683399176	1379	True	1605.0	1605	87.653	125	1514	1	chr5B.!!$R1	1389
9	TraesCS4A01G022300	chr5D	495785460	495786297	837	True	1275.0	1275	94.160	680	1515	1	chr5D.!!$R1	835
10	TraesCS4A01G022300	chr4D	218121800	218122568	768	True	1153.0	1153	93.766	754	1521	1	chr4D.!!$R1	767
11	TraesCS4A01G022300	chr4D	218258173	218258905	732	False	1092.0	1092	93.597	754	1485	1	chr4D.!!$F1	731
12	TraesCS4A01G022300	chr4D	450705364	450706441	1077	False	648.5	1027	87.622	1512	2470	2	chr4D.!!$F2	958
13	TraesCS4A01G022300	chr1D	206821898	206822401	503	True	741.0	741	93.254	140	641	1	chr1D.!!$R1	501

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
387	392	0.179086	TACATCGCGTGGCACATCAT	60.179	50.0	19.09	2.32	44.52	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2182	2326	0.037303	TTCGTACTCCCGACCACTCT	59.963	55.0	0.0	0.0	36.42	3.24	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
44	45	4.878968	TGAGATCAAGGTACTATCCCACA	58.121	43.478	0.00	0.00	38.49	4.17
73	74	9.773328	TGATATTCTAAATTGCGAGTTGAAAAG	57.227	29.630	0.00	0.00	0.00	2.27
141	143	8.388656	ACTTTCAAGAAGGGTAGTATATGGAA	57.611	34.615	0.00	0.00	0.00	3.53
174	176	8.212995	AGATGGAGCAAAAATAAATATTTGGGG	58.787	33.333	11.05	0.00	37.09	4.96
350	355	6.352394	CCACATTCTTCAAATCCCAATCCATT	60.352	38.462	0.00	0.00	0.00	3.16
365	370	5.513788	CCAATCCATTATCAGGAGACGGAAT	60.514	44.000	0.00	0.00	38.83	3.01
387	392	0.179086	TACATCGCGTGGCACATCAT	60.179	50.000	19.09	2.32	44.52	2.45
430	440	9.669887	ACGGTAAGGTCAACATATTATAAACAA	57.330	29.630	0.00	0.00	0.00	2.83
678	689	0.988063	GCCCTTTTTAAATGCCCCCA	59.012	50.000	0.00	0.00	0.00	4.96
820	832	5.772393	TGTATATGGACCCAGTTGAACTT	57.228	39.130	0.00	0.00	0.00	2.66
865	877	1.279558	TGGTACATATGGTGGCAACGT	59.720	47.619	7.80	1.43	42.51	3.99
951	963	7.326063	CGCTTTAACCTTGAATTTTGTTAGAGG	59.674	37.037	0.00	0.00	30.37	3.69
980	993	4.457949	GGATTTTGACCAAGTTCCACGTAT	59.542	41.667	0.00	0.00	0.00	3.06
1112	1125	1.489649	AGGCTTCATCTGTGCAGCTAT	59.510	47.619	0.00	0.00	43.07	2.97
1242	1255	2.552155	GGACAACCTGATAGTGGTGCAA	60.552	50.000	0.00	0.00	37.93	4.08
1273	1287	7.726216	ACATAATAATGAAGGACACTCGATGA	58.274	34.615	0.00	0.00	36.54	2.92
1347	1361	5.950544	AGGCTGTGGTAGAACATTGTATA	57.049	39.130	0.00	0.00	0.00	1.47
1371	1385	3.458189	AGAGTCTAATATGGTTGCGCAC	58.542	45.455	11.12	5.37	0.00	5.34
1437	1451	2.124695	GCTCCGCCGGATTTCCTT	60.125	61.111	6.16	0.00	0.00	3.36
1476	1490	7.601073	TGATGATGTAACTGTCATTTGAGTC	57.399	36.000	0.00	0.00	35.33	3.36
1495	1509	6.291377	TGAGTCTTAATAAAGCTAGCCATGG	58.709	40.000	12.13	7.63	32.36	3.66
1545	1559	3.515502	AGTCGGGAGTGAATCATTCAAGA	59.484	43.478	0.29	3.67	42.15	3.02
1587	1601	2.350522	AGACACGCTTTCTATTGCAGG	58.649	47.619	0.00	0.00	0.00	4.85
1608	1622	4.578928	AGGCTGATTTGTAGAAAAACGTGT	59.421	37.500	0.00	0.00	0.00	4.49
1653	1674	9.252962	CACTTAAAAGCTCACAGATTTGAAAAT	57.747	29.630	0.00	0.00	33.65	1.82
1660	1681	9.768662	AAGCTCACAGATTTGAAAATAAAACAT	57.231	25.926	0.00	0.00	0.00	2.71
1771	1915	7.134815	AGTTCATCAGTTCTGAAAAATGTTCG	58.865	34.615	6.60	0.00	34.59	3.95
1775	1919	5.830912	TCAGTTCTGAAAAATGTTCGCAAT	58.169	33.333	0.00	0.00	0.00	3.56
1825	1969	7.134163	GCCAAAAATCAATGGTTTGAAAAGAG	58.866	34.615	0.00	0.00	44.70	2.85
1830	1974	8.424274	AAATCAATGGTTTGAAAAGAGTTCAC	57.576	30.769	0.00	0.00	44.70	3.18
1843	1987	7.978975	TGAAAAGAGTTCACGGATTTTGAAAAT	59.021	29.630	2.27	2.27	34.78	1.82
1844	1988	8.716646	AAAAGAGTTCACGGATTTTGAAAATT	57.283	26.923	4.46	0.00	34.78	1.82
1940	2084	7.225784	TGAAAGGAATTCATCGATTTTGGAA	57.774	32.000	7.93	0.00	43.08	3.53
1943	2087	9.801873	GAAAGGAATTCATCGATTTTGGAATTA	57.198	29.630	16.87	0.00	39.37	1.40
1978	2122	4.399004	TTGAACAAAAGTTCATGGTGGG	57.601	40.909	11.34	0.00	42.14	4.61
2034	2178	7.754475	TGTTCATGAATTTGTGAATAATCCACG	59.246	33.333	12.12	0.00	36.79	4.94
2038	2182	6.264832	TGAATTTGTGAATAATCCACGCATC	58.735	36.000	0.00	0.00	37.34	3.91
2147	2291	7.796958	AAAGAGTGAAAAAGAAAGTGTTTCG	57.203	32.000	0.00	0.00	44.29	3.46
2150	2294	5.465935	AGTGAAAAAGAAAGTGTTTCGCAA	58.534	33.333	10.48	0.00	44.29	4.85
2151	2295	6.099341	AGTGAAAAAGAAAGTGTTTCGCAAT	58.901	32.000	10.48	0.00	44.29	3.56
2154	2298	5.949233	AAAAGAAAGTGTTTCGCAATGAC	57.051	34.783	0.00	0.00	44.29	3.06
2182	2326	0.393132	TGTGGTGGTTCGTTTGAGCA	60.393	50.000	0.00	0.00	0.00	4.26
2197	2341	0.680280	GAGCAGAGTGGTCGGGAGTA	60.680	60.000	0.00	0.00	35.04	2.59
2203	2347	0.251077	AGTGGTCGGGAGTACGAAGT	60.251	55.000	0.00	0.00	45.38	3.01
2359	2503	2.353011	CGTTTTACCTAAGCTGGGTCGA	60.353	50.000	13.95	3.64	38.19	4.20
2371	2515	3.815401	AGCTGGGTCGACATTTAATATGC	59.185	43.478	18.91	7.73	0.00	3.14
2434	2578	6.216801	TCGTTATAGTCTTACTTGGTGCAT	57.783	37.500	0.00	0.00	0.00	3.96
2436	2580	5.810587	CGTTATAGTCTTACTTGGTGCATGT	59.189	40.000	0.00	0.00	0.00	3.21
2465	2609	4.151867	GTCTTCGTGGTGAATAAAGGTGTC	59.848	45.833	0.00	0.00	35.63	3.67
2470	2614	2.289819	TGGTGAATAAAGGTGTCGGGTC	60.290	50.000	0.00	0.00	0.00	4.46
2471	2615	2.289819	GGTGAATAAAGGTGTCGGGTCA	60.290	50.000	0.00	0.00	0.00	4.02
2472	2616	3.606687	GTGAATAAAGGTGTCGGGTCAT	58.393	45.455	0.00	0.00	0.00	3.06
2473	2617	3.374058	GTGAATAAAGGTGTCGGGTCATG	59.626	47.826	0.00	0.00	0.00	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	7.047891	TCAACTCGCAATTTAGAATATCACCT	58.952	34.615	0.00	0.00	0.00	4.00
73	74	2.639065	TGCCATACGAAAGATGAACCC	58.361	47.619	0.00	0.00	0.00	4.11
141	143	6.916360	TTATTTTTGCTCCATCTCCAACTT	57.084	33.333	0.00	0.00	0.00	2.66
174	176	3.433615	GCTATTCGGTATCCAGCAATCAC	59.566	47.826	0.00	0.00	32.46	3.06
350	355	5.642491	CGATGTAGTATTCCGTCTCCTGATA	59.358	44.000	0.00	0.00	0.00	2.15
365	370	0.458260	ATGTGCCACGCGATGTAGTA	59.542	50.000	15.93	0.00	0.00	1.82
387	392	1.868498	CCGTAAAAACGCCACTCTTCA	59.132	47.619	0.00	0.00	0.00	3.02
430	440	1.750193	CCGCATAACACACTTCCCAT	58.250	50.000	0.00	0.00	0.00	4.00
678	689	5.246883	AGAGCTTCCCAAATTTGCATTACTT	59.753	36.000	12.92	0.00	0.00	2.24
865	877	1.926489	ACCCCGGACCAATTGCCTA	60.926	57.895	0.73	0.00	0.00	3.93
951	963	5.163353	TGGAACTTGGTCAAAATCCCTTTTC	60.163	40.000	10.17	0.00	32.21	2.29
980	993	2.265367	TGCCAGGAGACCATCTGTTTA	58.735	47.619	0.00	0.00	0.00	2.01
1112	1125	2.338620	CGTGGTCAAGTCTCGCCA	59.661	61.111	0.00	0.00	0.00	5.69
1197	1210	7.064134	TCCATACGTACTAAAAGATTGTTGCAG	59.936	37.037	0.00	0.00	0.00	4.41
1242	1255	5.696724	GTGTCCTTCATTATTATGTAGCGCT	59.303	40.000	17.26	17.26	33.34	5.92
1273	1287	0.395586	TGCAAAATAGGAGCCGCCAT	60.396	50.000	0.00	0.00	40.02	4.40
1347	1361	4.141937	TGCGCAACCATATTAGACTCTCTT	60.142	41.667	8.16	0.00	0.00	2.85
1371	1385	2.811101	CCCCACTGAGCTAGCTCG	59.189	66.667	33.55	28.91	45.48	5.03
1476	1490	5.695851	CCACCATGGCTAGCTTTATTAAG	57.304	43.478	13.04	0.00	34.36	1.85
1571	1585	1.089920	CAGCCTGCAATAGAAAGCGT	58.910	50.000	0.00	0.00	0.00	5.07
1587	1601	6.806120	AAACACGTTTTTCTACAAATCAGC	57.194	33.333	0.00	0.00	0.00	4.26
1624	1645	7.195646	TCAAATCTGTGAGCTTTTAAGTGTTG	58.804	34.615	0.00	0.00	0.00	3.33
1627	1648	8.633075	TTTTCAAATCTGTGAGCTTTTAAGTG	57.367	30.769	0.00	0.00	0.00	3.16
1748	1892	5.914635	GCGAACATTTTTCAGAACTGATGAA	59.085	36.000	5.34	4.54	39.64	2.57
1801	1945	8.212317	ACTCTTTTCAAACCATTGATTTTTGG	57.788	30.769	0.00	0.00	44.70	3.28
1814	1958	6.750039	TCAAAATCCGTGAACTCTTTTCAAAC	59.250	34.615	0.00	0.00	0.00	2.93
1962	2106	5.239087	CCATTTTTCCCACCATGAACTTTTG	59.761	40.000	0.00	0.00	0.00	2.44
2101	2245	5.843019	TTATTCCTTCTTCAGTTCCTGGT	57.157	39.130	0.00	0.00	31.51	4.00
2105	2249	7.661847	TCACTCTTTTATTCCTTCTTCAGTTCC	59.338	37.037	0.00	0.00	0.00	3.62
2150	2294	0.674581	CACCACACCATCGCAGTCAT	60.675	55.000	0.00	0.00	0.00	3.06
2151	2295	1.301637	CACCACACCATCGCAGTCA	60.302	57.895	0.00	0.00	0.00	3.41
2154	2298	1.577328	GAACCACCACACCATCGCAG	61.577	60.000	0.00	0.00	0.00	5.18
2157	2301	0.882927	AACGAACCACCACACCATCG	60.883	55.000	0.00	0.00	36.45	3.84
2163	2307	0.393132	TGCTCAAACGAACCACCACA	60.393	50.000	0.00	0.00	0.00	4.17
2182	2326	0.037303	TTCGTACTCCCGACCACTCT	59.963	55.000	0.00	0.00	36.42	3.24
2197	2341	1.378531	TGTGAAGCAAGCAACTTCGT	58.621	45.000	8.33	0.00	45.29	3.85
2224	2368	1.002087	AGGCAAACAGACTAAGACCCG	59.998	52.381	0.00	0.00	29.36	5.28
2229	2373	3.971245	AGAGGAGGCAAACAGACTAAG	57.029	47.619	0.00	0.00	33.72	2.18
2235	2379	2.157738	CCAAGAAGAGGAGGCAAACAG	58.842	52.381	0.00	0.00	0.00	3.16
2274	2418	6.281405	AGCTAAATTACGACCGAAGAATGAT	58.719	36.000	0.00	0.00	0.00	2.45
2306	2450	3.884693	CCAGCCATAATAGACACATGCAA	59.115	43.478	0.00	0.00	0.00	4.08
2307	2451	3.479489	CCAGCCATAATAGACACATGCA	58.521	45.455	0.00	0.00	0.00	3.96
2359	2503	3.822735	AGCGGCATGAGCATATTAAATGT	59.177	39.130	14.56	0.00	44.61	2.71
2371	2515	1.888215	ACCATAATCAGCGGCATGAG	58.112	50.000	1.45	0.00	31.44	2.90
2414	2558	6.707290	ACACATGCACCAAGTAAGACTATAA	58.293	36.000	0.00	0.00	0.00	0.98
2429	2573	2.094258	CACGAAGACCATACACATGCAC	59.906	50.000	0.00	0.00	0.00	4.57
2434	2578	1.964933	TCACCACGAAGACCATACACA	59.035	47.619	0.00	0.00	0.00	3.72
2436	2580	3.973206	ATTCACCACGAAGACCATACA	57.027	42.857	0.00	0.00	36.95	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.