AutoCloner

Multiple sequence alignment - TraesCS7B01G016700

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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	TraesCS7B01G016700	chr7B	100.000	2602	0	0	1	2602	14696001	14698602	0.000000e+00	4806.0
1	TraesCS7B01G016700	chr7B	85.660	1569	124	54	763	2271	14866752	14865225	0.000000e+00	1557.0
2	TraesCS7B01G016700	chr7B	92.690	1067	50	15	625	1682	14788932	14787885	0.000000e+00	1513.0
3	TraesCS7B01G016700	chr7B	96.820	629	17	3	1	627	684941626	684942253	0.000000e+00	1048.0
4	TraesCS7B01G016700	chr7B	87.831	756	73	12	737	1483	14980458	14981203	0.000000e+00	869.0
5	TraesCS7B01G016700	chr7B	92.671	423	26	4	2179	2600	14778922	14778504	2.860000e-169	604.0
6	TraesCS7B01G016700	chr7B	88.265	196	18	2	1839	2034	14787888	14787698	2.010000e-56	230.0
7	TraesCS7B01G016700	chr7D	88.478	1137	79	19	625	1723	71812130	71813252	0.000000e+00	1327.0
8	TraesCS7B01G016700	chr7D	82.251	1155	118	43	723	1828	72128148	72129264	0.000000e+00	917.0
9	TraesCS7B01G016700	chr7D	85.194	824	75	20	768	1576	71864787	71863996	0.000000e+00	802.0
10	TraesCS7B01G016700	chr7D	79.229	1194	146	60	1069	2212	72216360	72217501	0.000000e+00	737.0
11	TraesCS7B01G016700	chr7D	84.979	466	49	13	2155	2602	71813607	71814069	1.100000e-123	453.0
12	TraesCS7B01G016700	chr7D	87.460	311	21	4	1878	2178	71813282	71813584	2.480000e-90	342.0
13	TraesCS7B01G016700	chrUn	88.557	970	72	18	625	1576	82565509	82566457	0.000000e+00	1140.0
14	TraesCS7B01G016700	chrUn	91.205	830	52	12	761	1569	84318107	84317278	0.000000e+00	1109.0
15	TraesCS7B01G016700	chrUn	86.501	963	82	16	786	1723	84331365	84330426	0.000000e+00	1014.0
16	TraesCS7B01G016700	chrUn	78.771	1644	221	65	690	2271	82605421	82603844	0.000000e+00	985.0
17	TraesCS7B01G016700	chrUn	82.399	1142	116	42	736	1828	273471198	273470093	0.000000e+00	917.0
18	TraesCS7B01G016700	chrUn	88.022	551	37	14	1794	2319	84330430	84329884	2.200000e-175	625.0
19	TraesCS7B01G016700	chrUn	80.318	503	44	25	1780	2239	82566591	82567081	1.930000e-86	329.0
20	TraesCS7B01G016700	chrUn	87.162	296	26	8	2317	2602	82567139	82567432	2.500000e-85	326.0
21	TraesCS7B01G016700	chrUn	86.395	294	30	8	2312	2602	84329863	84329577	1.940000e-81	313.0
22	TraesCS7B01G016700	chrUn	72.583	569	91	34	1753	2273	84316593	84316042	2.720000e-25	126.0
23	TraesCS7B01G016700	chrUn	95.556	45	1	1	1634	1678	82566542	82566585	1.290000e-08	71.3
24	TraesCS7B01G016700	chr3B	97.764	626	13	1	1	625	224283029	224283654	0.000000e+00	1077.0
25	TraesCS7B01G016700	chr3B	97.284	626	16	1	1	625	734989075	734989700	0.000000e+00	1061.0
26	TraesCS7B01G016700	chr3B	96.656	628	20	1	1	627	757975563	757976190	0.000000e+00	1042.0
27	TraesCS7B01G016700	chr5B	96.656	628	20	1	1	627	7028180	7028807	0.000000e+00	1042.0
28	TraesCS7B01G016700	chr5B	96.508	630	21	1	1	629	377342894	377342265	0.000000e+00	1040.0
29	TraesCS7B01G016700	chr5B	96.645	626	20	1	1	625	64726528	64727153	0.000000e+00	1038.0
30	TraesCS7B01G016700	chr5B	96.651	627	18	3	1	625	670799053	670798428	0.000000e+00	1038.0
31	TraesCS7B01G016700	chr1B	96.355	631	21	2	1	629	66281258	66281888	0.000000e+00	1037.0
32	TraesCS7B01G016700	chr1B	84.424	443	41	14	1949	2390	10931469	10931884	6.700000e-111	411.0
33	TraesCS7B01G016700	chr7A	74.395	496	98	26	1747	2229	77195924	77196403	4.420000e-43	185.0
34	TraesCS7B01G016700	chr4D	74.721	269	37	21	1976	2229	348396537	348396285	9.920000e-15	91.6

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	TraesCS7B01G016700	chr7B	14696001	14698602	2601	False	4806.000000	4806	100.000000	1	2602	1	chr7B.!!$F1	2601
1	TraesCS7B01G016700	chr7B	14865225	14866752	1527	True	1557.000000	1557	85.660000	763	2271	1	chr7B.!!$R2	1508
2	TraesCS7B01G016700	chr7B	684941626	684942253	627	False	1048.000000	1048	96.820000	1	627	1	chr7B.!!$F3	626
3	TraesCS7B01G016700	chr7B	14787698	14788932	1234	True	871.500000	1513	90.477500	625	2034	2	chr7B.!!$R3	1409
4	TraesCS7B01G016700	chr7B	14980458	14981203	745	False	869.000000	869	87.831000	737	1483	1	chr7B.!!$F2	746
5	TraesCS7B01G016700	chr7D	72128148	72129264	1116	False	917.000000	917	82.251000	723	1828	1	chr7D.!!$F1	1105
6	TraesCS7B01G016700	chr7D	71863996	71864787	791	True	802.000000	802	85.194000	768	1576	1	chr7D.!!$R1	808
7	TraesCS7B01G016700	chr7D	72216360	72217501	1141	False	737.000000	737	79.229000	1069	2212	1	chr7D.!!$F2	1143
8	TraesCS7B01G016700	chr7D	71812130	71814069	1939	False	707.333333	1327	86.972333	625	2602	3	chr7D.!!$F3	1977
9	TraesCS7B01G016700	chrUn	82603844	82605421	1577	True	985.000000	985	78.771000	690	2271	1	chrUn.!!$R1	1581
10	TraesCS7B01G016700	chrUn	273470093	273471198	1105	True	917.000000	917	82.399000	736	1828	1	chrUn.!!$R2	1092
11	TraesCS7B01G016700	chrUn	84329577	84331365	1788	True	650.666667	1014	86.972667	786	2602	3	chrUn.!!$R4	1816
12	TraesCS7B01G016700	chrUn	84316042	84318107	2065	True	617.500000	1109	81.894000	761	2273	2	chrUn.!!$R3	1512
13	TraesCS7B01G016700	chrUn	82565509	82567432	1923	False	466.575000	1140	87.898250	625	2602	4	chrUn.!!$F1	1977
14	TraesCS7B01G016700	chr3B	224283029	224283654	625	False	1077.000000	1077	97.764000	1	625	1	chr3B.!!$F1	624
15	TraesCS7B01G016700	chr3B	734989075	734989700	625	False	1061.000000	1061	97.284000	1	625	1	chr3B.!!$F2	624
16	TraesCS7B01G016700	chr3B	757975563	757976190	627	False	1042.000000	1042	96.656000	1	627	1	chr3B.!!$F3	626
17	TraesCS7B01G016700	chr5B	7028180	7028807	627	False	1042.000000	1042	96.656000	1	627	1	chr5B.!!$F1	626
18	TraesCS7B01G016700	chr5B	377342265	377342894	629	True	1040.000000	1040	96.508000	1	629	1	chr5B.!!$R1	628
19	TraesCS7B01G016700	chr5B	64726528	64727153	625	False	1038.000000	1038	96.645000	1	625	1	chr5B.!!$F2	624
20	TraesCS7B01G016700	chr5B	670798428	670799053	625	True	1038.000000	1038	96.651000	1	625	1	chr5B.!!$R2	624
21	TraesCS7B01G016700	chr1B	66281258	66281888	630	False	1037.000000	1037	96.355000	1	629	1	chr1B.!!$F2	628

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
498	500	1.550976	AGTGCTAGGAGTAGTGTTGCC	59.449	52.381	0.0	0.0	0.0	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1889	2018	0.106268	TGCCCAGCCAAGTTCAGAAA	60.106	50.0	0.0	0.0	0.0	2.52	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
237	239	1.894756	GTTGCTGGGTTGTGGCGTA	60.895	57.895	0.00	0.00	0.00	4.42
498	500	1.550976	AGTGCTAGGAGTAGTGTTGCC	59.449	52.381	0.00	0.00	0.00	4.52
546	548	2.815647	TGTGTGCGTGTGTTGCGA	60.816	55.556	0.00	0.00	34.24	5.10
634	637	6.250344	AGCCTTTTTCGGTATAAAGTGTTC	57.750	37.500	0.00	0.00	31.07	3.18
734	741	4.099419	GCCAGAAAAGAAAAGGGAAACTCA	59.901	41.667	0.00	0.00	0.00	3.41
1520	1574	3.700038	GGCTAGTAGCTGTTCTTGTCCTA	59.300	47.826	21.20	0.00	41.99	2.94
1528	1582	4.713814	AGCTGTTCTTGTCCTATGATCTGA	59.286	41.667	0.00	0.00	0.00	3.27
1535	1597	6.950842	TCTTGTCCTATGATCTGAATGTGTT	58.049	36.000	0.00	0.00	0.00	3.32
1536	1598	7.044181	TCTTGTCCTATGATCTGAATGTGTTC	58.956	38.462	0.00	0.00	34.85	3.18
1537	1599	6.298441	TGTCCTATGATCTGAATGTGTTCA	57.702	37.500	0.00	0.00	41.89	3.18
1598	1679	6.401688	CGTGATGCTTGAATGAAATTGCAATT	60.402	34.615	18.99	18.99	36.52	2.32
1599	1680	7.201453	CGTGATGCTTGAATGAAATTGCAATTA	60.201	33.333	24.35	10.96	36.52	1.40
1628	1721	8.430801	AGTTCAGTTATCATGCTTATTCTGTC	57.569	34.615	0.00	0.00	0.00	3.51
1673	1766	2.927553	AATTGCTCCGTGATTCTTGC	57.072	45.000	0.00	0.00	0.00	4.01
1723	1822	6.422333	TGATTATGCAAGTGATAGGTTTGGA	58.578	36.000	0.00	0.00	0.00	3.53
1725	1824	7.395772	TGATTATGCAAGTGATAGGTTTGGAAA	59.604	33.333	0.00	0.00	0.00	3.13
1727	1826	4.469657	TGCAAGTGATAGGTTTGGAAAGT	58.530	39.130	0.00	0.00	0.00	2.66
1728	1827	5.626142	TGCAAGTGATAGGTTTGGAAAGTA	58.374	37.500	0.00	0.00	0.00	2.24
1729	1828	6.245408	TGCAAGTGATAGGTTTGGAAAGTAT	58.755	36.000	0.00	0.00	0.00	2.12
1730	1829	6.150976	TGCAAGTGATAGGTTTGGAAAGTATG	59.849	38.462	0.00	0.00	0.00	2.39
1732	1831	5.815581	AGTGATAGGTTTGGAAAGTATGCA	58.184	37.500	0.00	0.00	0.00	3.96
1733	1832	6.245408	AGTGATAGGTTTGGAAAGTATGCAA	58.755	36.000	0.00	0.00	37.61	4.08
1735	1834	6.151144	GTGATAGGTTTGGAAAGTATGCAAGT	59.849	38.462	0.00	0.00	40.70	3.16
1736	1835	4.853924	AGGTTTGGAAAGTATGCAAGTG	57.146	40.909	0.00	0.00	40.70	3.16
1737	1836	4.469657	AGGTTTGGAAAGTATGCAAGTGA	58.530	39.130	0.00	0.00	40.70	3.41
1738	1837	5.079643	AGGTTTGGAAAGTATGCAAGTGAT	58.920	37.500	0.00	0.00	40.70	3.06
1739	1838	5.539955	AGGTTTGGAAAGTATGCAAGTGATT	59.460	36.000	0.00	0.00	40.70	2.57
1740	1839	6.719370	AGGTTTGGAAAGTATGCAAGTGATTA	59.281	34.615	0.00	0.00	40.70	1.75
1741	1840	7.397192	AGGTTTGGAAAGTATGCAAGTGATTAT	59.603	33.333	0.00	0.00	40.70	1.28
1742	1841	7.489113	GGTTTGGAAAGTATGCAAGTGATTATG	59.511	37.037	0.00	0.00	40.70	1.90
1743	1842	6.135290	TGGAAAGTATGCAAGTGATTATGC	57.865	37.500	0.00	0.00	42.86	3.14
1763	1862	3.721370	ATGTCCCCATGGGCTTCGC	62.721	63.158	26.87	12.60	43.94	4.70
1772	1871	2.202610	GGGCTTCGCGATTTTGCC	60.203	61.111	24.77	24.77	42.56	4.52
1790	1891	0.841289	CCGGGGCCCTCTGTTATTTA	59.159	55.000	24.38	0.00	0.00	1.40
1800	1901	5.009110	GCCCTCTGTTATTTATCTTTGCTCC	59.991	44.000	0.00	0.00	0.00	4.70
1826	1953	5.105797	TGTGTGATTCAGTTTCTTGCACTTT	60.106	36.000	0.00	0.00	0.00	2.66
1829	1956	6.127647	TGTGATTCAGTTTCTTGCACTTTTCT	60.128	34.615	0.00	0.00	0.00	2.52
1830	1957	6.753744	GTGATTCAGTTTCTTGCACTTTTCTT	59.246	34.615	0.00	0.00	0.00	2.52
1861	1990	1.539388	TGCAGGCGTTAGGTGAATTTG	59.461	47.619	0.00	0.00	0.00	2.32
1889	2018	0.035317	TTCGGCTCTGCTTGATGTGT	59.965	50.000	0.00	0.00	0.00	3.72
1908	2045	0.106268	TTTCTGAACTTGGCTGGGCA	60.106	50.000	0.00	0.00	0.00	5.36
1970	2119	0.180406	ACAAGTCGCCACTTCACCTT	59.820	50.000	0.00	0.00	41.24	3.50
1993	2163	5.012239	TCTCAGCTAGTTGGAAATTTGCAT	58.988	37.500	13.51	2.12	36.81	3.96
1999	2169	5.521372	GCTAGTTGGAAATTTGCATTGGATC	59.479	40.000	13.51	0.00	34.73	3.36
2015	2187	8.435187	TGCATTGGATCTGATCTACTTTATCTT	58.565	33.333	16.61	0.00	0.00	2.40
2072	2249	6.403866	TTGGATGTTAAGTTTGCTGAATGT	57.596	33.333	0.00	0.00	0.00	2.71
2086	2263	3.372025	GCTGAATGTTATCCTTCTGGGGT	60.372	47.826	0.00	0.00	35.33	4.95
2108	2285	5.460091	GGTTGATTCTTGTGCTGAGTTTTTC	59.540	40.000	0.00	0.00	0.00	2.29
2125	2302	5.422012	AGTTTTTCCTGGTTGTGATTGTTCT	59.578	36.000	0.00	0.00	0.00	3.01
2145	2329	8.037382	TGTTCTTGTCTTCATGATGATTCTTC	57.963	34.615	13.82	2.58	0.00	2.87
2253	2511	6.260936	ACCATGCAGTTGTACATTATAAGAGC	59.739	38.462	0.00	0.00	0.00	4.09
2380	2668	0.717224	CAGAATGCGCAATTTGGTGC	59.283	50.000	17.11	0.00	44.35	5.01
2413	2701	1.324736	CTCCGAATAAACTCGTGCTGC	59.675	52.381	0.00	0.00	37.11	5.25
2448	2742	5.215160	GTGGCTATGTCTCACAAAGTTTTG	58.785	41.667	3.17	3.17	43.62	2.44
2464	2758	8.195617	CAAAGTTTTGTTGAAAGATTAAGGCA	57.804	30.769	0.00	0.00	33.59	4.75
2484	2779	4.039245	GGCAGATATGAGTACAAGCCACTA	59.961	45.833	0.00	0.00	40.50	2.74
2506	2984	5.998454	AATCACTGCAGTTGCTATGATAC	57.002	39.130	18.94	0.00	41.81	2.24
2541	3019	2.109774	GTGGCATGAATTCCATCCCAA	58.890	47.619	2.27	0.00	44.35	4.12
2552	3030	3.090210	TCCATCCCAACTCACGTAGTA	57.910	47.619	0.00	0.00	41.61	1.82
2555	3033	3.194968	CCATCCCAACTCACGTAGTACTT	59.805	47.826	0.00	0.00	41.61	2.24
2556	3034	3.928727	TCCCAACTCACGTAGTACTTG	57.071	47.619	0.00	0.37	41.61	3.16
2564	3042	2.490903	TCACGTAGTACTTGGCTTCTCC	59.509	50.000	0.00	0.00	41.61	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	98	1.524863	AAGACCTCGACACCACCTCG	61.525	60.000	0.00	0.00	0.00	4.63
161	163	3.972276	GCGCGGGCTTTGTCCAAA	61.972	61.111	18.33	0.00	35.83	3.28
224	226	3.548484	ACCGTACGCCACAACCCA	61.548	61.111	10.49	0.00	0.00	4.51
237	239	2.112297	AACATTCACCGCCACCGT	59.888	55.556	0.00	0.00	0.00	4.83
443	445	9.411801	GAAGATATGAAGCTACATATGACGAAA	57.588	33.333	10.38	0.00	41.60	3.46
546	548	2.032634	CAACCACACGCTACGCCAT	61.033	57.895	0.00	0.00	0.00	4.40
1528	1582	0.250901	AGAAGCGCCCTGAACACATT	60.251	50.000	2.29	0.00	0.00	2.71
1535	1597	0.465460	AACAAACAGAAGCGCCCTGA	60.465	50.000	27.41	0.00	35.69	3.86
1536	1598	0.318107	CAACAAACAGAAGCGCCCTG	60.318	55.000	21.38	21.38	37.64	4.45
1537	1599	1.455383	CCAACAAACAGAAGCGCCCT	61.455	55.000	2.29	0.00	0.00	5.19
1541	1603	2.159448	TCAACACCAACAAACAGAAGCG	60.159	45.455	0.00	0.00	0.00	4.68
1673	1766	4.862350	TGCTTCATGTCACAAGAACATTG	58.138	39.130	0.00	0.00	0.00	2.82
1729	1828	3.130869	GGGACATTGCATAATCACTTGCA	59.869	43.478	0.00	0.00	46.51	4.08
1730	1829	3.491447	GGGGACATTGCATAATCACTTGC	60.491	47.826	0.00	0.00	39.33	4.01
1732	1831	3.979911	TGGGGACATTGCATAATCACTT	58.020	40.909	0.00	0.00	33.40	3.16
1733	1832	3.668141	TGGGGACATTGCATAATCACT	57.332	42.857	0.00	0.00	33.40	3.41
1772	1871	2.372172	AGATAAATAACAGAGGGCCCCG	59.628	50.000	21.43	10.47	0.00	5.73
1778	1877	6.261826	CAGGGAGCAAAGATAAATAACAGAGG	59.738	42.308	0.00	0.00	0.00	3.69
1790	1891	3.245016	TGAATCACACAGGGAGCAAAGAT	60.245	43.478	0.00	0.00	0.00	2.40
1800	1901	3.316029	TGCAAGAAACTGAATCACACAGG	59.684	43.478	0.00	0.00	39.38	4.00
1889	2018	0.106268	TGCCCAGCCAAGTTCAGAAA	60.106	50.000	0.00	0.00	0.00	2.52
1908	2045	4.521146	CTTCAGCTAATCCACATCAACCT	58.479	43.478	0.00	0.00	0.00	3.50
1970	2119	4.397420	TGCAAATTTCCAACTAGCTGAGA	58.603	39.130	0.00	0.00	0.00	3.27
2040	2217	6.922957	GCAAACTTAACATCCAATCACAGAAA	59.077	34.615	0.00	0.00	0.00	2.52
2059	2236	5.416952	CCAGAAGGATAACATTCAGCAAACT	59.583	40.000	0.17	0.00	38.97	2.66
2072	2249	5.015178	ACAAGAATCAACCCCAGAAGGATAA	59.985	40.000	0.00	0.00	38.24	1.75
2086	2263	5.360714	AGGAAAAACTCAGCACAAGAATCAA	59.639	36.000	0.00	0.00	0.00	2.57
2108	2285	3.885297	AGACAAGAACAATCACAACCAGG	59.115	43.478	0.00	0.00	0.00	4.45
2125	2302	6.714278	TCCAGAAGAATCATCATGAAGACAA	58.286	36.000	2.13	0.00	0.00	3.18
2229	2474	6.260714	TGCTCTTATAATGTACAACTGCATGG	59.739	38.462	0.00	0.00	0.00	3.66
2262	2520	7.359595	TGATCACAGCACAAGTTTAATTACAC	58.640	34.615	0.00	0.00	0.00	2.90
2380	2668	1.881903	TTCGGAGAGAGTGCTGCTGG	61.882	60.000	0.00	0.00	38.43	4.85
2426	2714	5.437289	CAAAACTTTGTGAGACATAGCCA	57.563	39.130	0.00	0.00	31.57	4.75
2448	2742	8.443953	ACTCATATCTGCCTTAATCTTTCAAC	57.556	34.615	0.00	0.00	0.00	3.18
2461	2755	3.134458	GTGGCTTGTACTCATATCTGCC	58.866	50.000	0.00	0.00	39.53	4.85
2462	2756	4.065321	AGTGGCTTGTACTCATATCTGC	57.935	45.455	0.00	0.00	0.00	4.26
2463	2757	7.383572	GTGATTAGTGGCTTGTACTCATATCTG	59.616	40.741	0.00	0.00	0.00	2.90
2464	2758	7.288852	AGTGATTAGTGGCTTGTACTCATATCT	59.711	37.037	0.00	0.00	0.00	1.98
2484	2779	5.526479	CAGTATCATAGCAACTGCAGTGATT	59.474	40.000	22.49	11.14	41.37	2.57
2541	3019	5.876018	GGAGAAGCCAAGTACTACGTGAGT	61.876	50.000	0.00	0.33	42.25	3.41
2552	3030	2.348998	CCTGCGGAGAAGCCAAGT	59.651	61.111	5.10	0.00	35.94	3.16
2564	3042	4.688419	CAAGTGCAACGGCCTGCG	62.688	66.667	11.96	0.00	45.74	5.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.