AutoCloner

Multiple sequence alignment - TraesCS3D01G154200

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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	TraesCS3D01G154200	chr3D	100.000	2288	0	0	1	2288	121530714	121533001	0.000000e+00	4226.0
1	TraesCS3D01G154200	chr3D	94.833	1703	83	3	1	1700	5431468	5429768	0.000000e+00	2652.0
2	TraesCS3D01G154200	chr3D	91.832	1714	114	12	1	1704	124068685	124066988	0.000000e+00	2366.0
3	TraesCS3D01G154200	chr1D	95.606	1707	69	4	1	1704	423893340	423895043	0.000000e+00	2732.0
4	TraesCS3D01G154200	chr2D	94.918	1712	75	6	1	1704	644388813	644390520	0.000000e+00	2669.0
5	TraesCS3D01G154200	chr5D	94.318	1707	73	5	1	1704	424049049	424047364	0.000000e+00	2593.0
6	TraesCS3D01G154200	chr7D	94.097	1711	85	11	1	1704	621162330	621164031	0.000000e+00	2586.0
7	TraesCS3D01G154200	chr3B	93.466	1714	97	11	1	1704	97752878	97751170	0.000000e+00	2531.0
8	TraesCS3D01G154200	chr3B	94.931	217	8	2	1889	2103	173097414	173097629	1.010000e-88	337.0
9	TraesCS3D01G154200	chr3B	92.893	197	11	2	2092	2288	173098019	173098212	1.340000e-72	283.0
10	TraesCS3D01G154200	chr3B	89.744	78	0	1	1706	1775	173097343	173097420	2.420000e-15	93.5
11	TraesCS3D01G154200	chr7A	93.174	1714	101	11	1	1704	86218350	86216643	0.000000e+00	2503.0
12	TraesCS3D01G154200	chr7A	92.114	596	32	3	1109	1704	514862775	514863355	0.000000e+00	826.0
13	TraesCS3D01G154200	chr7B	92.155	1708	109	17	2	1704	639855954	639857641	0.000000e+00	2388.0
14	TraesCS3D01G154200	chr2A	93.711	1590	84	8	1	1581	706884750	706886332	0.000000e+00	2368.0
15	TraesCS3D01G154200	chr3A	92.039	1231	72	8	475	1704	624176981	624178186	0.000000e+00	1707.0
16	TraesCS3D01G154200	chr3A	82.206	399	29	13	1923	2288	127963275	127963664	2.860000e-79	305.0
17	TraesCS3D01G154200	chr3A	85.484	124	15	3	1706	1829	127962492	127962612	2.390000e-25	126.0
18	TraesCS3D01G154200	chr4D	91.939	459	29	5	1252	1704	398285776	398286232	8.920000e-179	636.0

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	TraesCS3D01G154200	chr3D	121530714	121533001	2287	False	4226.000000	4226	100.000000	1	2288	1	chr3D.!!$F1	2287
1	TraesCS3D01G154200	chr3D	5429768	5431468	1700	True	2652.000000	2652	94.833000	1	1700	1	chr3D.!!$R1	1699
2	TraesCS3D01G154200	chr3D	124066988	124068685	1697	True	2366.000000	2366	91.832000	1	1704	1	chr3D.!!$R2	1703
3	TraesCS3D01G154200	chr1D	423893340	423895043	1703	False	2732.000000	2732	95.606000	1	1704	1	chr1D.!!$F1	1703
4	TraesCS3D01G154200	chr2D	644388813	644390520	1707	False	2669.000000	2669	94.918000	1	1704	1	chr2D.!!$F1	1703
5	TraesCS3D01G154200	chr5D	424047364	424049049	1685	True	2593.000000	2593	94.318000	1	1704	1	chr5D.!!$R1	1703
6	TraesCS3D01G154200	chr7D	621162330	621164031	1701	False	2586.000000	2586	94.097000	1	1704	1	chr7D.!!$F1	1703
7	TraesCS3D01G154200	chr3B	97751170	97752878	1708	True	2531.000000	2531	93.466000	1	1704	1	chr3B.!!$R1	1703
8	TraesCS3D01G154200	chr3B	173097343	173098212	869	False	237.833333	337	92.522667	1706	2288	3	chr3B.!!$F1	582
9	TraesCS3D01G154200	chr7A	86216643	86218350	1707	True	2503.000000	2503	93.174000	1	1704	1	chr7A.!!$R1	1703
10	TraesCS3D01G154200	chr7A	514862775	514863355	580	False	826.000000	826	92.114000	1109	1704	1	chr7A.!!$F1	595
11	TraesCS3D01G154200	chr7B	639855954	639857641	1687	False	2388.000000	2388	92.155000	2	1704	1	chr7B.!!$F1	1702
12	TraesCS3D01G154200	chr2A	706884750	706886332	1582	False	2368.000000	2368	93.711000	1	1581	1	chr2A.!!$F1	1580
13	TraesCS3D01G154200	chr3A	624176981	624178186	1205	False	1707.000000	1707	92.039000	475	1704	1	chr3A.!!$F1	1229
14	TraesCS3D01G154200	chr3A	127962492	127963664	1172	False	215.500000	305	83.845000	1706	2288	2	chr3A.!!$F2	582

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
799	804	0.030638	CGTTGACAACAAGGGCAAGG	59.969	55.0	18.09	0.0	37.97	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1839	1881	0.17691	TTGTCAGGACAGTCGTTGCA	59.823	50.0	2.01	0.0	42.94	4.08	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
181	185	4.457496	CCGCCGATGACTGCTGGT	62.457	66.667	0.00	0.00	0.00	4.00
399	403	3.544684	TCATGAGCACGGCATTAGATTT	58.455	40.909	0.00	0.00	0.00	2.17
465	469	1.202604	GGTGTTCTCGAACTTGGTCCA	60.203	52.381	10.75	0.00	41.67	4.02
588	593	3.711704	AGGAAGGTTGACAGTGAGAGAAA	59.288	43.478	0.00	0.00	0.00	2.52
610	615	0.924090	AGGGGGTGGGTAAATAGTGC	59.076	55.000	0.00	0.00	0.00	4.40
612	617	1.133884	GGGGGTGGGTAAATAGTGCTC	60.134	57.143	0.00	0.00	0.00	4.26
749	754	2.871182	TGTGTGCAGATCGAGGATAC	57.129	50.000	0.00	3.56	0.00	2.24
799	804	0.030638	CGTTGACAACAAGGGCAAGG	59.969	55.000	18.09	0.00	37.97	3.61
822	827	1.748879	CGTTCACCCAATGCCCGAT	60.749	57.895	0.00	0.00	0.00	4.18
838	843	2.360350	ATGAGGTTGTGCTGCCGG	60.360	61.111	0.00	0.00	0.00	6.13
897	903	2.721167	CGACGAGGGCATGGAGGAA	61.721	63.158	0.00	0.00	0.00	3.36
925	933	1.890041	AACAAGCGCCGCAACTACA	60.890	52.632	13.36	0.00	0.00	2.74
1064	1076	3.817647	GAGTTCAAGCTCAGGAACAACAT	59.182	43.478	20.96	6.78	44.46	2.71
1165	1177	2.805099	GTTCATCAGATCAAGATCGGCC	59.195	50.000	5.48	0.00	42.48	6.13
1194	1206	0.605589	CGTTCAAGCTCCTCACTCCT	59.394	55.000	0.00	0.00	0.00	3.69
1252	1264	0.176910	TGAGGTCGTCAACAAGTGCA	59.823	50.000	0.00	0.00	29.64	4.57
1352	1370	5.703592	AGTTGATGGTTTATGCGTTGAACTA	59.296	36.000	0.00	0.67	0.00	2.24
1405	1424	8.814038	AATTATGCTAGTTGATCCTCTGTTTT	57.186	30.769	0.00	0.00	0.00	2.43
1406	1425	9.905713	AATTATGCTAGTTGATCCTCTGTTTTA	57.094	29.630	0.00	0.00	0.00	1.52
1409	1428	8.894768	ATGCTAGTTGATCCTCTGTTTTATAC	57.105	34.615	0.00	0.00	0.00	1.47
1432	1462	4.640364	TCTGTTGTGCTTATGATGTGTGA	58.360	39.130	0.00	0.00	0.00	3.58
1495	1525	2.693762	CCACACATCAGGCCTTGCG	61.694	63.158	0.00	0.00	0.00	4.85
1608	1638	2.034878	TGCAGGCAACCAAACAACATA	58.965	42.857	0.00	0.00	37.17	2.29
1609	1639	2.632028	TGCAGGCAACCAAACAACATAT	59.368	40.909	0.00	0.00	37.17	1.78
1650	1680	1.752498	CATTTGCATAGCCAGGCTGAA	59.248	47.619	25.59	5.05	40.10	3.02
1672	1702	2.544685	AGAGAAGTGTATGCGATGCAC	58.455	47.619	0.00	8.54	43.04	4.57
1799	1841	1.104630	TGTGTGTACTGTGTGGACGA	58.895	50.000	0.00	0.00	0.00	4.20
1806	1848	4.293648	TGTGTGGACGACCGCTGG	62.294	66.667	17.96	0.00	45.89	4.85
1834	1876	1.915228	ACTGACCAGTGCCAAGTGT	59.085	52.632	1.31	0.00	40.75	3.55
1835	1877	0.179045	ACTGACCAGTGCCAAGTGTC	60.179	55.000	1.31	0.00	40.75	3.67
1836	1878	1.224069	CTGACCAGTGCCAAGTGTCG	61.224	60.000	0.00	0.00	0.00	4.35
1839	1881	2.967076	CAGTGCCAAGTGTCGCGT	60.967	61.111	5.77	0.00	0.00	6.01
1840	1882	2.967076	AGTGCCAAGTGTCGCGTG	60.967	61.111	5.77	0.00	0.00	5.34
1860	2064	0.861837	CAACGACTGTCCTGACAAGC	59.138	55.000	1.55	0.00	41.33	4.01
1868	2072	2.023673	TGTCCTGACAAGCCAAAACAG	58.976	47.619	0.00	0.00	38.56	3.16
1880	2085	1.480205	CAAAACAGCTTGCTTCGGTG	58.520	50.000	0.00	0.00	36.06	4.94
1881	2086	1.102978	AAAACAGCTTGCTTCGGTGT	58.897	45.000	0.00	0.00	44.14	4.16
1882	2087	0.663153	AAACAGCTTGCTTCGGTGTC	59.337	50.000	5.93	0.00	41.72	3.67
1883	2088	1.166531	AACAGCTTGCTTCGGTGTCC	61.167	55.000	5.93	0.00	41.72	4.02
1884	2089	1.302033	CAGCTTGCTTCGGTGTCCT	60.302	57.895	0.00	0.00	0.00	3.85
1885	2090	1.302033	AGCTTGCTTCGGTGTCCTG	60.302	57.895	0.00	0.00	0.00	3.86
1886	2091	2.328099	GCTTGCTTCGGTGTCCTGG	61.328	63.158	0.00	0.00	0.00	4.45
1887	2092	2.281484	TTGCTTCGGTGTCCTGGC	60.281	61.111	0.00	0.00	0.00	4.85
1888	2093	2.738213	CTTGCTTCGGTGTCCTGGCT	62.738	60.000	0.00	0.00	0.00	4.75
1889	2094	1.476845	TTGCTTCGGTGTCCTGGCTA	61.477	55.000	0.00	0.00	0.00	3.93
1890	2095	1.264749	TGCTTCGGTGTCCTGGCTAT	61.265	55.000	0.00	0.00	0.00	2.97
1891	2096	0.750850	GCTTCGGTGTCCTGGCTATA	59.249	55.000	0.00	0.00	0.00	1.31
1892	2097	1.269831	GCTTCGGTGTCCTGGCTATAG	60.270	57.143	0.00	0.00	0.00	1.31
1893	2098	2.032620	CTTCGGTGTCCTGGCTATAGT	58.967	52.381	0.84	0.00	0.00	2.12
1894	2099	1.399714	TCGGTGTCCTGGCTATAGTG	58.600	55.000	0.84	0.00	0.00	2.74
1910	2115	7.619302	TGGCTATAGTGAAAAATGAAAAGGGAT	59.381	33.333	0.84	0.00	0.00	3.85
1972	2595	1.214589	CCAAGCCAGCACATTCAGC	59.785	57.895	0.00	0.00	0.00	4.26
1987	2624	6.458206	GCACATTCAGCGGAACTTCATTATTA	60.458	38.462	0.00	0.00	35.46	0.98
1997	2634	5.353123	GGAACTTCATTATTAGCGTGACCAA	59.647	40.000	0.00	0.00	0.00	3.67
2175	3214	5.118664	TCTGAAAATCGTCGACTTCACAATC	59.881	40.000	14.70	4.12	0.00	2.67
2238	3277	5.971763	AGTTTTATCCTAGTCAGCACTCAG	58.028	41.667	0.00	0.00	33.62	3.35
2255	3294	4.308526	GCAGTGCCACATGCTAGT	57.691	55.556	2.85	0.00	42.00	2.57
2256	3295	2.559785	GCAGTGCCACATGCTAGTT	58.440	52.632	2.85	0.00	42.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	52	4.996434	ACGACGAGGACGACCCGT	62.996	66.667	16.94	16.94	45.10	5.28
222	226	2.795960	AGGACCTACTGGGCTCCTAATA	59.204	50.000	0.00	0.00	42.43	0.98
242	246	2.808543	GGAAGAAGTGGTGCAAGTACAG	59.191	50.000	0.00	0.00	0.00	2.74
399	403	1.002257	ATGCCGGACATGCAGAACA	60.002	52.632	5.05	0.00	42.92	3.18
419	423	1.069090	TGTGCTCGAACTTCGGCTT	59.931	52.632	19.00	0.00	40.88	4.35
465	469	3.626924	GGTGGACGGCTGGTGACT	61.627	66.667	0.00	0.00	0.00	3.41
588	593	2.850568	CACTATTTACCCACCCCCTCTT	59.149	50.000	0.00	0.00	0.00	2.85
610	615	3.753294	ATATTTACTCACCCTGCCGAG	57.247	47.619	0.00	0.00	35.30	4.63
612	617	3.306780	CCCTATATTTACTCACCCTGCCG	60.307	52.174	0.00	0.00	0.00	5.69
749	754	0.816825	CTCCGTGCCCATCTCATTGG	60.817	60.000	0.00	0.00	36.46	3.16
799	804	2.700773	GCATTGGGTGAACGGGCTC	61.701	63.158	0.00	0.00	0.00	4.70
805	810	0.679640	TCATCGGGCATTGGGTGAAC	60.680	55.000	0.00	0.00	0.00	3.18
838	843	2.126031	GTCTTCCTCGACGGTGGC	60.126	66.667	0.00	0.00	0.00	5.01
845	851	1.303799	CGTCTTCGGGTCTTCCTCGA	61.304	60.000	0.00	0.00	35.68	4.04
925	933	0.324368	TCCTCGTGATGGTAGTGGCT	60.324	55.000	0.00	0.00	0.00	4.75
1064	1076	3.393970	CCTTCCAGGAGCAGCCGA	61.394	66.667	0.00	0.00	43.43	5.54
1165	1177	1.195448	GAGCTTGAACGTCACCATGTG	59.805	52.381	0.00	0.00	34.45	3.21
1252	1264	4.719369	GGCGTCGTCGTGCTTCCT	62.719	66.667	3.66	0.00	39.49	3.36
1396	1415	5.934625	AGCACAACAGAGTATAAAACAGAGG	59.065	40.000	0.00	0.00	0.00	3.69
1399	1418	8.935844	TCATAAGCACAACAGAGTATAAAACAG	58.064	33.333	0.00	0.00	0.00	3.16
1405	1424	7.492344	CACACATCATAAGCACAACAGAGTATA	59.508	37.037	0.00	0.00	0.00	1.47
1406	1425	6.314648	CACACATCATAAGCACAACAGAGTAT	59.685	38.462	0.00	0.00	0.00	2.12
1407	1426	5.639082	CACACATCATAAGCACAACAGAGTA	59.361	40.000	0.00	0.00	0.00	2.59
1408	1427	4.453478	CACACATCATAAGCACAACAGAGT	59.547	41.667	0.00	0.00	0.00	3.24
1409	1428	4.692155	TCACACATCATAAGCACAACAGAG	59.308	41.667	0.00	0.00	0.00	3.35
1432	1462	0.398696	TTACCACCACACTTCGGCAT	59.601	50.000	0.00	0.00	0.00	4.40
1455	1485	4.019950	GGTAACCTCTTTGGCTAGTTGGTA	60.020	45.833	0.00	0.00	40.22	3.25
1495	1525	4.499019	CCAAGACATGGTGTTTGGTTGTAC	60.499	45.833	0.00	0.00	44.85	2.90
1608	1638	5.014202	TGCAGCCTCAAATGCATCATATAT	58.986	37.500	0.00	0.00	46.97	0.86
1609	1639	4.400120	TGCAGCCTCAAATGCATCATATA	58.600	39.130	0.00	0.00	46.97	0.86
1650	1680	4.302455	GTGCATCGCATACACTTCTCTAT	58.698	43.478	0.00	0.00	41.91	1.98
1829	1871	2.583868	TCGTTGCACGCGACACTT	60.584	55.556	15.93	0.00	42.21	3.16
1834	1876	3.028019	GACAGTCGTTGCACGCGA	61.028	61.111	15.93	8.28	42.21	5.87
1835	1877	4.059459	GGACAGTCGTTGCACGCG	62.059	66.667	3.53	3.53	42.21	6.01
1836	1878	2.661866	AGGACAGTCGTTGCACGC	60.662	61.111	4.15	0.00	42.21	5.34
1839	1881	0.176910	TTGTCAGGACAGTCGTTGCA	59.823	50.000	2.01	0.00	42.94	4.08
1840	1882	0.861837	CTTGTCAGGACAGTCGTTGC	59.138	55.000	2.01	0.00	42.94	4.17
1860	2064	0.385390	ACCGAAGCAAGCTGTTTTGG	59.615	50.000	13.67	13.67	44.72	3.28
1868	2072	2.328099	CCAGGACACCGAAGCAAGC	61.328	63.158	0.00	0.00	0.00	4.01
1880	2085	7.391148	TTTCATTTTTCACTATAGCCAGGAC	57.609	36.000	0.00	0.00	0.00	3.85
1881	2086	7.122650	CCTTTTCATTTTTCACTATAGCCAGGA	59.877	37.037	0.00	0.00	0.00	3.86
1882	2087	7.260603	CCTTTTCATTTTTCACTATAGCCAGG	58.739	38.462	0.00	0.00	0.00	4.45
1883	2088	7.122650	TCCCTTTTCATTTTTCACTATAGCCAG	59.877	37.037	0.00	0.00	0.00	4.85
1884	2089	6.951198	TCCCTTTTCATTTTTCACTATAGCCA	59.049	34.615	0.00	0.00	0.00	4.75
1885	2090	7.404671	TCCCTTTTCATTTTTCACTATAGCC	57.595	36.000	0.00	0.00	0.00	3.93
1886	2091	8.470002	ACATCCCTTTTCATTTTTCACTATAGC	58.530	33.333	0.00	0.00	0.00	2.97
1889	2094	9.492973	CAAACATCCCTTTTCATTTTTCACTAT	57.507	29.630	0.00	0.00	0.00	2.12
1890	2095	8.700051	TCAAACATCCCTTTTCATTTTTCACTA	58.300	29.630	0.00	0.00	0.00	2.74
1891	2096	7.563906	TCAAACATCCCTTTTCATTTTTCACT	58.436	30.769	0.00	0.00	0.00	3.41
1892	2097	7.784633	TCAAACATCCCTTTTCATTTTTCAC	57.215	32.000	0.00	0.00	0.00	3.18
1893	2098	7.826252	TGTTCAAACATCCCTTTTCATTTTTCA	59.174	29.630	0.00	0.00	33.17	2.69
1894	2099	8.207521	TGTTCAAACATCCCTTTTCATTTTTC	57.792	30.769	0.00	0.00	33.17	2.29
1910	2115	2.224018	GCTCATTTGGCCTGTTCAAACA	60.224	45.455	3.32	0.00	37.00	2.83
1972	2595	4.025979	GGTCACGCTAATAATGAAGTTCCG	60.026	45.833	0.00	0.00	0.00	4.30
1987	2624	2.503331	TCATTCACATTTGGTCACGCT	58.497	42.857	0.00	0.00	0.00	5.07
2175	3214	6.803154	AAGACGGGTTAATTGAGAAAGAAG	57.197	37.500	0.00	0.00	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.