AutoCloner

Multiple sequence alignment - TraesCS2D01G039200

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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	TraesCS2D01G039200	chr2D	100.000	2588	0	0	1	2588	14376709	14374122	0.000000e+00	4780.0
1	TraesCS2D01G039200	chr4B	93.848	959	56	3	3	961	333446092	333447047	0.000000e+00	1441.0
2	TraesCS2D01G039200	chr4B	90.810	457	28	4	1197	1642	333447246	333447699	1.330000e-167	599.0
3	TraesCS2D01G039200	chr4B	97.386	153	4	0	961	1113	333447090	333447242	7.100000e-66	261.0
4	TraesCS2D01G039200	chr4B	94.937	79	2	2	1571	1648	22819175	22819252	3.500000e-24	122.0
5	TraesCS2D01G039200	chr2A	93.568	964	57	3	1	961	167101511	167100550	0.000000e+00	1432.0
6	TraesCS2D01G039200	chr2A	90.570	965	58	11	1642	2588	16615838	16616787	0.000000e+00	1247.0
7	TraesCS2D01G039200	chr2A	90.043	934	55	12	1672	2588	16628732	16629644	0.000000e+00	1175.0
8	TraesCS2D01G039200	chr2A	93.247	696	32	2	961	1645	167100507	167099816	0.000000e+00	1011.0
9	TraesCS2D01G039200	chr2A	80.544	478	69	12	1984	2452	733658233	733657771	1.910000e-91	346.0
10	TraesCS2D01G039200	chr2A	100.000	28	0	0	197	224	689633848	689633821	5.000000e-03	52.8
11	TraesCS2D01G039200	chr6A	83.829	538	68	13	2054	2586	484408745	484409268	6.430000e-136	494.0
12	TraesCS2D01G039200	chr6D	83.616	531	74	10	2058	2586	344057674	344058193	1.080000e-133	486.0
13	TraesCS2D01G039200	chr6B	81.614	533	81	11	2058	2586	519323294	519323813	2.380000e-115	425.0
14	TraesCS2D01G039200	chr3B	89.668	271	13	5	1384	1642	667163495	667163762	5.340000e-87	331.0
15	TraesCS2D01G039200	chr5A	85.714	259	22	3	1396	1643	649864015	649863761	2.550000e-65	259.0
16	TraesCS2D01G039200	chr5A	76.445	467	88	15	1193	1644	134576850	134576391	1.550000e-57	233.0
17	TraesCS2D01G039200	chr2B	100.000	33	0	0	1673	1705	726046098	726046130	7.730000e-06	62.1
18	TraesCS2D01G039200	chr1D	96.774	31	1	0	1678	1708	271837169	271837139	5.000000e-03	52.8

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	TraesCS2D01G039200	chr2D	14374122	14376709	2587	True	4780.0	4780	100.000000	1	2588	1	chr2D.!!$R1	2587
1	TraesCS2D01G039200	chr4B	333446092	333447699	1607	False	767.0	1441	94.014667	3	1642	3	chr4B.!!$F2	1639
2	TraesCS2D01G039200	chr2A	16615838	16616787	949	False	1247.0	1247	90.570000	1642	2588	1	chr2A.!!$F1	946
3	TraesCS2D01G039200	chr2A	167099816	167101511	1695	True	1221.5	1432	93.407500	1	1645	2	chr2A.!!$R3	1644
4	TraesCS2D01G039200	chr2A	16628732	16629644	912	False	1175.0	1175	90.043000	1672	2588	1	chr2A.!!$F2	916
5	TraesCS2D01G039200	chr6A	484408745	484409268	523	False	494.0	494	83.829000	2054	2586	1	chr6A.!!$F1	532
6	TraesCS2D01G039200	chr6D	344057674	344058193	519	False	486.0	486	83.616000	2058	2586	1	chr6D.!!$F1	528
7	TraesCS2D01G039200	chr6B	519323294	519323813	519	False	425.0	425	81.614000	2058	2586	1	chr6B.!!$F1	528

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
472	473	0.24746	TGGACTCATTCTCTGTGGCG	59.753	55.0	0.0	0.0	0.0	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1915	1990	0.457337	CGGGCAATTTCAGCTTGCTC	60.457	55.0	7.24	2.25	46.41	4.26	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
34	35	4.870991	CAGATGACAGCTATGATATGCAGG	59.129	45.833	0.00	0.00	0.00	4.85
62	63	4.987408	TGGGCACAACAAGATAATGATG	57.013	40.909	0.00	0.00	0.00	3.07
108	109	6.683974	TGAGAAGTTGACTCTTTCCAAAAG	57.316	37.500	0.00	0.00	35.66	2.27
131	132	3.397955	AGAAGGTGGTTTGGGATACAAGT	59.602	43.478	0.00	0.00	40.82	3.16
163	164	2.116533	CAATCTGGCCATGCTCGCA	61.117	57.895	5.51	0.00	0.00	5.10
243	244	3.127030	GCGAAGTATTTCCCTGAAACTGG	59.873	47.826	0.00	0.00	34.23	4.00
267	268	2.315176	ACTGCATGCTACACCCAAAAA	58.685	42.857	20.33	0.00	0.00	1.94
282	283	2.539476	CAAAAAGGGAATGCCGTATGC	58.461	47.619	0.00	0.00	41.77	3.14
315	316	3.686016	TCTTACAGGGAATTGAAGTGGC	58.314	45.455	0.00	0.00	0.00	5.01
372	373	2.560542	CGATAGTGAAGATCTGGGAGGG	59.439	54.545	0.00	0.00	0.00	4.30
415	416	0.603569	ACAGGAGACGGATGACACAC	59.396	55.000	0.00	0.00	0.00	3.82
449	450	0.319383	CGTCTCAACTGCTGCTGAGT	60.319	55.000	19.56	0.00	40.06	3.41
458	459	0.689055	TGCTGCTGAGTTGATGGACT	59.311	50.000	0.00	0.00	0.00	3.85
472	473	0.247460	TGGACTCATTCTCTGTGGCG	59.753	55.000	0.00	0.00	0.00	5.69
668	669	2.554344	GGTGAGGTTGGTCAGGCAAATA	60.554	50.000	0.00	0.00	0.00	1.40
740	744	4.996758	GCCCAAATAAAGTGCAACAATTCT	59.003	37.500	0.00	0.00	41.43	2.40
778	782	2.530151	AGCCTTCCCCTCTGTGCA	60.530	61.111	0.00	0.00	0.00	4.57
854	858	6.080682	AGAAGAGATGAAGATGGTAGCCATA	58.919	40.000	0.04	0.00	45.26	2.74
1104	1151	0.681733	AGAAGAAACCAGCTGAGCGA	59.318	50.000	17.39	0.00	0.00	4.93
1167	1214	6.874288	AAGATTAATACTGATGGCAGCTTC	57.126	37.500	3.69	0.00	46.26	3.86
1184	1231	1.083806	TTCTGTGCGGCGTCATCATC	61.084	55.000	9.37	0.00	0.00	2.92
1263	1310	1.802960	GGAAGGATATCGCATGCACAG	59.197	52.381	19.57	0.99	0.00	3.66
1276	1323	2.949106	CACAGGACGCCTTGCAAG	59.051	61.111	19.93	19.93	0.00	4.01
1457	1504	8.507524	ACTTTTGCTAGTCTGAACTTTAGTTT	57.492	30.769	0.00	0.00	38.56	2.66
1458	1505	8.957466	ACTTTTGCTAGTCTGAACTTTAGTTTT	58.043	29.630	0.00	0.00	38.56	2.43
1459	1506	9.788960	CTTTTGCTAGTCTGAACTTTAGTTTTT	57.211	29.630	0.00	0.00	38.56	1.94
1504	1551	3.761752	GAGGGCTTGTAATAAGGTTGCAA	59.238	43.478	0.00	0.00	0.00	4.08
1569	1627	0.965866	GGTCTTGCCCCTACCTTTGC	60.966	60.000	0.00	0.00	0.00	3.68
1662	1720	3.409026	AAAGGTGTGGTCAGATCTCAC	57.591	47.619	7.27	7.27	0.00	3.51
1665	1723	1.135257	GGTGTGGTCAGATCTCACTCG	60.135	57.143	14.17	0.00	33.04	4.18
1667	1725	1.813178	TGTGGTCAGATCTCACTCGAC	59.187	52.381	12.69	7.81	33.04	4.20
1669	1727	3.271729	GTGGTCAGATCTCACTCGACTA	58.728	50.000	0.00	0.00	0.00	2.59
1670	1728	3.690139	GTGGTCAGATCTCACTCGACTAA	59.310	47.826	0.00	0.00	0.00	2.24
1674	1732	4.873827	GTCAGATCTCACTCGACTAAGACT	59.126	45.833	0.00	0.00	0.00	3.24
1686	1744	8.074972	CACTCGACTAAGACTTAACAAGTACTT	58.925	37.037	1.12	1.12	43.03	2.24
1690	1748	7.750014	CGACTAAGACTTAACAAGTACTTCCTC	59.250	40.741	4.77	0.00	43.03	3.71
1691	1749	7.894708	ACTAAGACTTAACAAGTACTTCCTCC	58.105	38.462	4.77	0.00	43.03	4.30
1705	1763	2.953466	TCCTCCGTCCGAAAATACTG	57.047	50.000	0.00	0.00	0.00	2.74
1708	1766	2.354403	CCTCCGTCCGAAAATACTGGTT	60.354	50.000	0.00	0.00	0.00	3.67
1769	1831	8.954950	AGACACATTCATTTCTATCGATTTCT	57.045	30.769	1.71	0.00	0.00	2.52
1772	1834	9.599866	ACACATTCATTTCTATCGATTTCTACA	57.400	29.630	1.71	0.00	0.00	2.74
1788	1850	8.388103	CGATTTCTACAACAAGTAATTTCGGAT	58.612	33.333	0.00	0.00	30.92	4.18
1806	1869	9.987272	ATTTCGGATGAAAAGAGAAAGAAAAAT	57.013	25.926	0.00	0.00	46.53	1.82
1830	1893	7.692908	TTTTAAAGAGAAAAATTGCACGGAG	57.307	32.000	0.00	0.00	0.00	4.63
1833	1896	2.887152	AGAGAAAAATTGCACGGAGCTT	59.113	40.909	3.79	0.00	45.94	3.74
1834	1897	4.072131	AGAGAAAAATTGCACGGAGCTTA	58.928	39.130	3.79	0.00	45.94	3.09
1836	1899	4.546570	AGAAAAATTGCACGGAGCTTAAC	58.453	39.130	3.79	0.00	45.94	2.01
1840	1903	2.373540	TTGCACGGAGCTTAACGTAT	57.626	45.000	10.91	0.00	45.94	3.06
1841	1904	3.507103	TTGCACGGAGCTTAACGTATA	57.493	42.857	10.91	2.46	45.94	1.47
1842	1905	3.074504	TGCACGGAGCTTAACGTATAG	57.925	47.619	10.91	0.00	45.94	1.31
1843	1906	2.223641	TGCACGGAGCTTAACGTATAGG	60.224	50.000	10.91	2.19	45.94	2.57
1850	1913	5.124138	CGGAGCTTAACGTATAGGATCTCAT	59.876	44.000	0.00	0.00	0.00	2.90
1866	1929	7.566569	AGGATCTCATGAATATAGCATCCAAG	58.433	38.462	0.00	0.00	32.43	3.61
1875	1938	6.324770	TGAATATAGCATCCAAGTCTCAGTCA	59.675	38.462	0.00	0.00	0.00	3.41
1909	1984	9.765795	AATATAAAAACGGATTCAACCAAAACA	57.234	25.926	0.00	0.00	0.00	2.83
1915	1990	3.796178	CGGATTCAACCAAAACACACAAG	59.204	43.478	0.00	0.00	0.00	3.16
1942	2017	3.141398	GCTGAAATTGCCCGATAGATCA	58.859	45.455	0.00	0.00	39.76	2.92
1943	2018	3.755378	GCTGAAATTGCCCGATAGATCAT	59.245	43.478	0.00	0.00	39.76	2.45
1944	2019	4.937620	GCTGAAATTGCCCGATAGATCATA	59.062	41.667	0.00	0.00	39.76	2.15
1945	2020	5.064452	GCTGAAATTGCCCGATAGATCATAG	59.936	44.000	0.00	0.00	39.76	2.23
1946	2021	5.491070	TGAAATTGCCCGATAGATCATAGG	58.509	41.667	0.00	0.00	39.76	2.57
1947	2022	5.013079	TGAAATTGCCCGATAGATCATAGGT	59.987	40.000	0.00	0.00	39.76	3.08
1948	2023	3.961480	TTGCCCGATAGATCATAGGTG	57.039	47.619	0.00	0.00	39.76	4.00
2454	2532	1.739196	GACCCCGTTGCCGAAGTAC	60.739	63.158	0.00	0.00	35.63	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	5.064452	CAGCAGACAACCAATGTATCTTCTC	59.936	44.000	0.00	0.00	44.12	2.87
108	109	3.713826	TGTATCCCAAACCACCTTCTC	57.286	47.619	0.00	0.00	0.00	2.87
131	132	4.454678	GCCAGATTGAACACATGGAGATA	58.545	43.478	0.00	0.00	32.55	1.98
163	164	4.819630	TCTAACAATCTCCACGCTTGTTTT	59.180	37.500	5.35	0.00	41.77	2.43
282	283	2.138320	CCTGTAAGATACTGCGCCATG	58.862	52.381	4.18	0.00	34.07	3.66
283	284	1.070758	CCCTGTAAGATACTGCGCCAT	59.929	52.381	4.18	0.00	34.07	4.40
288	289	6.037610	CACTTCAATTCCCTGTAAGATACTGC	59.962	42.308	0.00	0.00	34.07	4.40
289	290	6.540189	CCACTTCAATTCCCTGTAAGATACTG	59.460	42.308	0.00	0.00	34.07	2.74
315	316	3.118956	ACGCTTGATGACTCCCTTCTTAG	60.119	47.826	0.00	0.00	0.00	2.18
354	355	1.692762	GGCCCTCCCAGATCTTCACTA	60.693	57.143	0.00	0.00	0.00	2.74
405	406	3.599285	TTCCGGCGGTGTGTCATCC	62.599	63.158	27.32	0.00	0.00	3.51
449	450	3.620719	GCCACAGAGAATGAGTCCATCAA	60.621	47.826	0.00	0.00	42.53	2.57
458	459	1.191489	TCCCACGCCACAGAGAATGA	61.191	55.000	0.00	0.00	0.00	2.57
472	473	1.014564	GCACTAGCTGTTCGTCCCAC	61.015	60.000	0.00	0.00	37.91	4.61
594	595	1.269723	TGTACGCTGACTTCACAGAGG	59.730	52.381	0.00	0.00	40.85	3.69
668	669	2.024414	GAAACTGTTGTTGCTGTCCCT	58.976	47.619	0.00	0.00	36.39	4.20
740	744	3.809905	TGTTGTATGCCATACGCCATAA	58.190	40.909	10.12	0.00	38.59	1.90
755	759	0.984230	CAGAGGGGAAGGCTGTTGTA	59.016	55.000	0.00	0.00	0.00	2.41
778	782	6.498651	TGTCTACTCCTTTCCTCTTCAGATTT	59.501	38.462	0.00	0.00	0.00	2.17
818	822	3.750130	TCATCTCTTCTTTTGCAGACTGC	59.250	43.478	20.86	20.86	45.29	4.40
854	858	5.650266	TGACCTGTTTACACTGAAACAACAT	59.350	36.000	3.58	0.00	45.98	2.71
1104	1151	4.202253	GGCTTGGTCCAAACTTCAGATTTT	60.202	41.667	5.64	0.00	0.00	1.82
1167	1214	1.759293	CTGATGATGACGCCGCACAG	61.759	60.000	0.00	0.00	0.00	3.66
1184	1231	1.694169	ACATAGCCCCACCCTCCTG	60.694	63.158	0.00	0.00	0.00	3.86
1276	1323	0.815734	ATGCATGCTTCAGCTTCACC	59.184	50.000	20.33	0.00	42.66	4.02
1277	1324	3.984508	ATATGCATGCTTCAGCTTCAC	57.015	42.857	20.33	0.00	42.66	3.18
1471	1518	1.004745	ACAAGCCCTCGGACAATGAAT	59.995	47.619	0.00	0.00	0.00	2.57
1569	1627	0.521735	GCTAGCAACAAAAGACCGGG	59.478	55.000	10.63	0.00	0.00	5.73
1642	1700	2.975489	AGTGAGATCTGACCACACCTTT	59.025	45.455	8.86	0.00	33.53	3.11
1645	1703	1.135257	CGAGTGAGATCTGACCACACC	60.135	57.143	8.86	2.82	33.53	4.16
1652	1710	5.092554	AGTCTTAGTCGAGTGAGATCTGA	57.907	43.478	16.80	0.00	0.00	3.27
1653	1711	5.811399	AAGTCTTAGTCGAGTGAGATCTG	57.189	43.478	16.80	0.00	0.00	2.90
1660	1718	7.583230	AGTACTTGTTAAGTCTTAGTCGAGTG	58.417	38.462	19.34	0.00	41.77	3.51
1662	1720	7.750014	GGAAGTACTTGTTAAGTCTTAGTCGAG	59.250	40.741	14.14	10.24	41.77	4.04
1665	1723	8.028354	GGAGGAAGTACTTGTTAAGTCTTAGTC	58.972	40.741	14.14	0.00	41.77	2.59
1667	1725	7.028361	CGGAGGAAGTACTTGTTAAGTCTTAG	58.972	42.308	14.14	0.00	41.77	2.18
1669	1727	5.303845	ACGGAGGAAGTACTTGTTAAGTCTT	59.696	40.000	14.14	0.00	41.77	3.01
1670	1728	4.831710	ACGGAGGAAGTACTTGTTAAGTCT	59.168	41.667	14.14	0.00	41.77	3.24
1674	1732	3.057315	CGGACGGAGGAAGTACTTGTTAA	60.057	47.826	14.14	0.00	0.00	2.01
1686	1744	1.479323	CCAGTATTTTCGGACGGAGGA	59.521	52.381	0.00	0.00	0.00	3.71
1690	1748	2.690786	TCAACCAGTATTTTCGGACGG	58.309	47.619	0.00	0.00	0.00	4.79
1691	1749	3.991773	TCTTCAACCAGTATTTTCGGACG	59.008	43.478	0.00	0.00	0.00	4.79
1763	1825	9.490663	CATCCGAAATTACTTGTTGTAGAAATC	57.509	33.333	0.00	0.00	32.08	2.17
1766	1828	8.610248	TTCATCCGAAATTACTTGTTGTAGAA	57.390	30.769	0.00	0.00	32.08	2.10
1769	1831	9.058174	TCTTTTCATCCGAAATTACTTGTTGTA	57.942	29.630	0.00	0.00	40.75	2.41
1770	1832	7.936584	TCTTTTCATCCGAAATTACTTGTTGT	58.063	30.769	0.00	0.00	40.75	3.32
1771	1833	8.289618	TCTCTTTTCATCCGAAATTACTTGTTG	58.710	33.333	0.00	0.00	40.75	3.33
1772	1834	8.391075	TCTCTTTTCATCCGAAATTACTTGTT	57.609	30.769	0.00	0.00	40.75	2.83
1806	1869	6.200097	GCTCCGTGCAATTTTTCTCTTTAAAA	59.800	34.615	0.00	0.00	42.31	1.52
1834	1897	9.190317	TGCTATATTCATGAGATCCTATACGTT	57.810	33.333	0.00	0.00	0.00	3.99
1836	1899	9.838975	GATGCTATATTCATGAGATCCTATACG	57.161	37.037	0.00	0.00	0.00	3.06
1840	1903	8.613922	TTGGATGCTATATTCATGAGATCCTA	57.386	34.615	0.00	0.00	31.22	2.94
1841	1904	7.182387	ACTTGGATGCTATATTCATGAGATCCT	59.818	37.037	0.00	0.00	31.22	3.24
1842	1905	7.337167	ACTTGGATGCTATATTCATGAGATCC	58.663	38.462	0.00	0.00	0.00	3.36
1843	1906	8.259411	AGACTTGGATGCTATATTCATGAGATC	58.741	37.037	0.00	0.00	0.00	2.75
1850	1913	6.324770	TGACTGAGACTTGGATGCTATATTCA	59.675	38.462	0.00	0.00	0.00	2.57
1858	1921	2.740981	CAGTTGACTGAGACTTGGATGC	59.259	50.000	5.19	0.00	46.59	3.91
1909	1984	3.797865	GCAATTTCAGCTTGCTCTTGTGT	60.798	43.478	0.00	0.00	44.36	3.72
1915	1990	0.457337	CGGGCAATTTCAGCTTGCTC	60.457	55.000	7.24	2.25	46.41	4.26
1943	2018	8.800332	GGATTAATTTCGTAGACCTATCACCTA	58.200	37.037	0.00	0.00	34.32	3.08
1944	2019	7.289317	TGGATTAATTTCGTAGACCTATCACCT	59.711	37.037	0.00	0.00	34.32	4.00
1945	2020	7.384387	GTGGATTAATTTCGTAGACCTATCACC	59.616	40.741	0.00	0.00	34.32	4.02
1946	2021	7.924412	TGTGGATTAATTTCGTAGACCTATCAC	59.076	37.037	0.00	0.00	34.32	3.06
1947	2022	7.924412	GTGTGGATTAATTTCGTAGACCTATCA	59.076	37.037	0.00	0.00	34.32	2.15
1948	2023	7.924412	TGTGTGGATTAATTTCGTAGACCTATC	59.076	37.037	0.00	0.00	34.32	2.08
2301	2376	1.171308	CGGTGGACTACTTCGAGGAA	58.829	55.000	0.00	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.