AutoCloner

Multiple sequence alignment - TraesCS2B01G325000

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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	TraesCS2B01G325000	chr2B	100.000	2288	0	0	1	2288	464671494	464673781	0.000000e+00	4226
1	TraesCS2B01G325000	chr1D	94.623	1711	91	1	1	1710	481925575	481927285	0.000000e+00	2649
2	TraesCS2B01G325000	chr5D	94.656	1703	84	3	12	1713	353957345	353959041	0.000000e+00	2634
3	TraesCS2B01G325000	chr5D	93.808	1712	102	2	1	1711	39089844	39091552	0.000000e+00	2571
4	TraesCS2B01G325000	chr5B	94.231	1716	96	2	1	1713	503240482	503238767	0.000000e+00	2617
5	TraesCS2B01G325000	chr3B	94.128	1720	98	2	1	1717	200855008	200856727	0.000000e+00	2614
6	TraesCS2B01G325000	chr3B	93.779	1720	104	2	1	1717	200830099	200831818	0.000000e+00	2580
7	TraesCS2B01G325000	chr3B	93.403	1713	111	2	1	1713	97752876	97751166	0.000000e+00	2536
8	TraesCS2B01G325000	chr4D	93.808	1712	93	5	1	1710	345354855	345356555	0.000000e+00	2562
9	TraesCS2B01G325000	chr7B	93.641	1714	107	2	1	1713	457414301	457416013	0.000000e+00	2560
10	TraesCS2B01G325000	chr2D	94.013	451	14	5	1849	2288	392687142	392687590	0.000000e+00	671
11	TraesCS2B01G325000	chr2D	93.706	143	7	2	1715	1856	392686967	392687108	1.780000e-51	213
12	TraesCS2B01G325000	chr2A	89.362	235	18	4	2060	2288	530744715	530744948	2.880000e-74	289

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	TraesCS2B01G325000	chr2B	464671494	464673781	2287	False	4226	4226	100.0000	1	2288	1	chr2B.!!$F1	2287
1	TraesCS2B01G325000	chr1D	481925575	481927285	1710	False	2649	2649	94.6230	1	1710	1	chr1D.!!$F1	1709
2	TraesCS2B01G325000	chr5D	353957345	353959041	1696	False	2634	2634	94.6560	12	1713	1	chr5D.!!$F2	1701
3	TraesCS2B01G325000	chr5D	39089844	39091552	1708	False	2571	2571	93.8080	1	1711	1	chr5D.!!$F1	1710
4	TraesCS2B01G325000	chr5B	503238767	503240482	1715	True	2617	2617	94.2310	1	1713	1	chr5B.!!$R1	1712
5	TraesCS2B01G325000	chr3B	200855008	200856727	1719	False	2614	2614	94.1280	1	1717	1	chr3B.!!$F2	1716
6	TraesCS2B01G325000	chr3B	200830099	200831818	1719	False	2580	2580	93.7790	1	1717	1	chr3B.!!$F1	1716
7	TraesCS2B01G325000	chr3B	97751166	97752876	1710	True	2536	2536	93.4030	1	1713	1	chr3B.!!$R1	1712
8	TraesCS2B01G325000	chr4D	345354855	345356555	1700	False	2562	2562	93.8080	1	1710	1	chr4D.!!$F1	1709
9	TraesCS2B01G325000	chr7B	457414301	457416013	1712	False	2560	2560	93.6410	1	1713	1	chr7B.!!$F1	1712
10	TraesCS2B01G325000	chr2D	392686967	392687590	623	False	442	671	93.8595	1715	2288	2	chr2D.!!$F1	573

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
985	999	0.036388	GGTCATCCTTGCACCGAAGA	60.036	55.0	0.0	0.0	0.0	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1848	1867	0.037605	ACGACGTCCAAATCCCTGTC	60.038	55.0	10.58	0.0	0.0	3.51	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
102	109	1.333177	GTCGATCTGCCAGGTAGGAT	58.667	55.000	4.47	0.00	41.22	3.24
137	144	1.077930	CCTAGCTGGCATGTGCACT	60.078	57.895	19.41	0.15	44.36	4.40
234	241	2.908015	GGCGGTCATTAGGAGCCA	59.092	61.111	0.00	0.00	46.48	4.75
282	289	0.167470	CCTCTGTTTAGCGTCGTCGA	59.833	55.000	6.17	0.00	39.71	4.20
283	290	1.525596	CTCTGTTTAGCGTCGTCGAG	58.474	55.000	6.17	0.00	39.71	4.04
286	293	0.806868	TGTTTAGCGTCGTCGAGGAT	59.193	50.000	18.54	14.66	39.71	3.24
335	342	4.722700	ACTGCCATCGCGCCCTTT	62.723	61.111	0.00	0.00	38.08	3.11
401	408	5.619132	TCATGAGGACTGCATTAGATTCA	57.381	39.130	0.00	0.00	0.00	2.57
485	492	2.123208	TCACCAGTCGACCACCCA	60.123	61.111	13.01	0.00	0.00	4.51
595	602	3.797559	TGACAGTGAGAGAAGAGAGGA	57.202	47.619	0.00	0.00	0.00	3.71
690	702	5.174398	TGTCGTTTTAACTACAAGCTCTTCG	59.826	40.000	0.00	0.00	32.53	3.79
705	717	3.873952	GCTCTTCGATTAGCCATGAACTT	59.126	43.478	8.02	0.00	32.40	2.66
866	879	0.599204	GACAAAGACCCGAAGACGCA	60.599	55.000	0.00	0.00	38.29	5.24
985	999	0.036388	GGTCATCCTTGCACCGAAGA	60.036	55.000	0.00	0.00	0.00	2.87
1030	1044	1.134521	ACTTCACCAAGCACTTCGTCA	60.135	47.619	0.00	0.00	32.09	4.35
1101	1118	2.350522	GTGACGGTCAAGCTGATGAAT	58.649	47.619	13.23	0.00	0.00	2.57
1103	1120	2.028203	TGACGGTCAAGCTGATGAATGA	60.028	45.455	8.68	0.00	0.00	2.57
1105	1122	2.027745	ACGGTCAAGCTGATGAATGACT	60.028	45.455	12.43	0.00	41.42	3.41
1332	1350	5.220303	GCGTACTATCAAGTCTGCTTTGAAG	60.220	44.000	0.00	0.00	37.15	3.02
1387	1405	5.537300	AGTGTGGTACTGCTTATATCTGG	57.463	43.478	0.00	0.00	38.49	3.86
1429	1447	7.412020	GCTCTGTTTATACTCTGTTGTGCTTAC	60.412	40.741	0.00	0.00	0.00	2.34
1500	1518	1.973816	TACCACACACCAGGCGTTGT	61.974	55.000	0.00	0.00	0.00	3.32
1544	1562	2.625790	GGGTTTGTCCACTAACATGCAA	59.374	45.455	0.00	0.00	38.11	4.08
1620	1638	3.305950	GGCAACCAAACAACATGCAGATA	60.306	43.478	0.00	0.00	38.73	1.98
1659	1677	1.294041	TGCATATCCAGGTTGGGTGA	58.706	50.000	0.00	0.00	38.32	4.02
1794	1813	0.100146	GCGTCGGGACCTTGTAGTAG	59.900	60.000	0.00	0.00	0.00	2.57
1811	1830	4.446413	GTGTAGACACGGGGGCGG	62.446	72.222	0.00	0.00	37.10	6.13
1828	1847	4.179579	GCTTCAACGATGGCGGGC	62.180	66.667	0.00	0.00	43.17	6.13
1848	1867	2.432628	GACGGGTGCTCCTTGTCG	60.433	66.667	12.62	7.17	32.72	4.35
1860	1921	1.003118	TCCTTGTCGACAGGGATTTGG	59.997	52.381	37.38	21.46	45.65	3.28
1873	1934	0.515564	GATTTGGACGTCGTGGTTGG	59.484	55.000	9.92	0.00	0.00	3.77
1876	1937	4.612412	GGACGTCGTGGTTGGGCA	62.612	66.667	9.92	0.00	0.00	5.36
1898	1959	1.376037	GGGACGGCAACTCCTTCAG	60.376	63.158	0.00	0.00	34.96	3.02
1902	1963	2.347490	GGCAACTCCTTCAGGCGA	59.653	61.111	0.00	0.00	34.44	5.54
1973	2034	3.390135	TCAAAGTTAAGAGTGGCAGACG	58.610	45.455	0.00	0.00	0.00	4.18
1994	2055	0.811219	TGCGCGCTAAGATTCATGCT	60.811	50.000	33.29	0.00	0.00	3.79
2044	2115	6.092122	CACCTAAAATGACGTCAGCTGAATAA	59.908	38.462	24.41	3.03	0.00	1.40
2089	2160	2.352960	CGCCTAACAGAAGAAGAATGGC	59.647	50.000	0.00	0.00	35.02	4.40
2109	2180	2.289547	GCAGGCTAAAAACTGACGTCAA	59.710	45.455	20.49	2.14	36.86	3.18
2150	2221	9.573133	CCTTTGTTTTTCAGTTATGCCTAATAG	57.427	33.333	0.00	0.00	0.00	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
137	144	2.334006	AGGAGGAGGAAGAAGAAGCA	57.666	50.000	0.00	0.00	0.00	3.91
201	208	2.357034	CCGTGCCGCAGTGTACTT	60.357	61.111	0.00	0.00	0.00	2.24
234	241	3.389983	TGGTGCAAGTACAAGACCTACTT	59.610	43.478	0.00	0.00	39.70	2.24
282	289	0.178970	GCCATGAATCAGGCCATCCT	60.179	55.000	5.01	0.00	45.18	3.24
283	290	2.348665	GCCATGAATCAGGCCATCC	58.651	57.895	5.01	0.00	45.18	3.51
335	342	0.321564	CGCTGATTCCTGACCCAACA	60.322	55.000	0.00	0.00	0.00	3.33
337	344	0.036388	GACGCTGATTCCTGACCCAA	60.036	55.000	0.00	0.00	0.00	4.12
386	393	5.746307	TGCAGAATGAATCTAATGCAGTC	57.254	39.130	0.00	0.00	39.69	3.51
401	408	4.993307	ATGCCGGACATGCAGAAT	57.007	50.000	5.05	0.00	42.92	2.40
475	482	0.685097	CTTCTTCCTTGGGTGGTCGA	59.315	55.000	0.00	0.00	0.00	4.20
485	492	1.857638	GCTGGAGGGCCTTCTTCCTT	61.858	60.000	14.33	0.00	32.74	3.36
595	602	1.652947	CCACCACTACTTACCCACCT	58.347	55.000	0.00	0.00	0.00	4.00
690	702	4.082571	ACTGCACAAAGTTCATGGCTAATC	60.083	41.667	0.00	0.00	0.00	1.75
705	717	1.887242	GGAGTCACGCACTGCACAA	60.887	57.895	1.11	0.00	42.99	3.33
775	787	1.178534	CCCTTGTTGTCAACGGCCAT	61.179	55.000	11.03	0.00	0.00	4.40
850	863	0.320374	TCATGCGTCTTCGGGTCTTT	59.680	50.000	0.00	0.00	37.56	2.52
866	879	0.606401	CTTGTTGTCGCCACCCTCAT	60.606	55.000	0.00	0.00	0.00	2.90
880	893	1.000396	GCTCCTCCATGCCCTTGTT	60.000	57.895	0.00	0.00	0.00	2.83
985	999	2.816746	GCATGGGGATGCACTCAAT	58.183	52.632	2.14	0.00	46.25	2.57
1030	1044	4.353437	GAACTCCGTCGGCACCGT	62.353	66.667	6.34	0.00	40.74	4.83
1054	1071	3.670377	GCAGCCGGTGTTGTTCCC	61.670	66.667	1.90	0.00	0.00	3.97
1152	1169	3.895041	TCACCATGTAGCCGATCTTGATA	59.105	43.478	0.00	0.00	0.00	2.15
1332	1350	7.008266	CAGTTCAACGCATAAACCATAAACATC	59.992	37.037	0.00	0.00	0.00	3.06
1387	1405	6.857777	AACAGAGCATCAACTAGCATAATC	57.142	37.500	0.00	0.00	37.82	1.75
1429	1447	2.029288	ACTTCGGCAGCACACATCG	61.029	57.895	0.00	0.00	0.00	3.84
1455	1473	2.270352	TTGGCTAGTTGGTGAGGTTG	57.730	50.000	0.00	0.00	0.00	3.77
1500	1518	4.040936	AGGCATGGTGTTTGGTTGTATA	57.959	40.909	0.00	0.00	0.00	1.47
1544	1562	1.203050	ACTGCCTGGTATTTGGTTGCT	60.203	47.619	0.00	0.00	0.00	3.91
1646	1664	1.142870	CACTTCTTCACCCAACCTGGA	59.857	52.381	0.00	0.00	40.96	3.86
1659	1677	1.745087	CCCGCATTGCATACACTTCTT	59.255	47.619	9.69	0.00	0.00	2.52
1794	1813	4.446413	CCGCCCCCGTGTCTACAC	62.446	72.222	3.08	3.08	43.15	2.90
1808	1827	4.520846	CGCCATCGTTGAAGCCGC	62.521	66.667	0.00	0.00	0.00	6.53
1809	1828	3.864686	CCGCCATCGTTGAAGCCG	61.865	66.667	0.00	0.00	0.00	5.52
1811	1830	4.179579	GCCCGCCATCGTTGAAGC	62.180	66.667	0.00	0.00	0.00	3.86
1812	1831	2.745884	TGCCCGCCATCGTTGAAG	60.746	61.111	0.00	0.00	0.00	3.02
1814	1833	4.776322	CCTGCCCGCCATCGTTGA	62.776	66.667	0.00	0.00	0.00	3.18
1815	1834	4.776322	TCCTGCCCGCCATCGTTG	62.776	66.667	0.00	0.00	0.00	4.10
1828	1847	2.046892	CAAGGAGCACCCGTCCTG	60.047	66.667	0.00	0.00	44.17	3.86
1848	1867	0.037605	ACGACGTCCAAATCCCTGTC	60.038	55.000	10.58	0.00	0.00	3.51
1856	1875	1.524165	CCCAACCACGACGTCCAAA	60.524	57.895	10.58	0.00	0.00	3.28
1857	1876	2.109387	CCCAACCACGACGTCCAA	59.891	61.111	10.58	0.00	0.00	3.53
1860	1921	2.589442	TTGCCCAACCACGACGTC	60.589	61.111	5.18	5.18	0.00	4.34
1876	1937	4.324991	GGAGTTGCCGTCCCCGTT	62.325	66.667	0.00	0.00	0.00	4.44
1898	1959	1.153549	CAGACTAGCCACCTTCGCC	60.154	63.158	0.00	0.00	0.00	5.54
1902	1963	0.612174	TCGCTCAGACTAGCCACCTT	60.612	55.000	0.00	0.00	39.43	3.50
1973	2034	1.724018	GCATGAATCTTAGCGCGCATC	60.724	52.381	35.10	19.80	0.00	3.91
1982	2043	7.047891	ACTACGGATTTTGAGCATGAATCTTA	58.952	34.615	0.00	0.00	0.00	2.10
1994	2055	3.745799	TCCAGCAAACTACGGATTTTGA	58.254	40.909	14.18	0.00	35.13	2.69
2044	2115	3.562182	ACCGAGAAACAAAGGGAAATGT	58.438	40.909	0.00	0.00	0.00	2.71
2089	2160	3.560068	AGTTGACGTCAGTTTTTAGCCTG	59.440	43.478	19.11	0.00	0.00	4.85
2109	2180	6.670695	AAACAAAGGGAAATGCTATTCAGT	57.329	33.333	4.78	0.00	0.00	3.41
2159	2230	2.818921	TGAAATAACAAGGCCTGCCAT	58.181	42.857	5.69	0.00	38.92	4.40
2265	2336	2.552315	GCTTTCGGATCTTTTGTGGTCA	59.448	45.455	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.