AutoCloner

Multiple sequence alignment - TraesCS7A01G221000

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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	TraesCS7A01G221000	chr7A	100.000	2453	0	0	1	2453	189348075	189350527	0.000000e+00	4530
1	TraesCS7A01G221000	chr7A	85.846	1519	209	5	938	2453	29988971	29987456	0.000000e+00	1609
2	TraesCS7A01G221000	chrUn	95.712	1516	63	1	938	2453	298401804	298403317	0.000000e+00	2438
3	TraesCS7A01G221000	chrUn	94.982	817	20	5	138	942	357191027	357191834	0.000000e+00	1262
4	TraesCS7A01G221000	chrUn	97.054	679	17	2	264	942	396175567	396176242	0.000000e+00	1140
5	TraesCS7A01G221000	chr7D	90.257	1519	142	6	937	2453	139750257	139748743	0.000000e+00	1980
6	TraesCS7A01G221000	chr3B	89.776	1516	148	5	938	2451	808034615	808036125	0.000000e+00	1934
7	TraesCS7A01G221000	chr3B	86.128	1521	201	8	938	2452	571017753	571019269	0.000000e+00	1631
8	TraesCS7A01G221000	chr3B	94.136	972	24	10	2	947	147870777	147869813	0.000000e+00	1448
9	TraesCS7A01G221000	chr3B	93.568	964	29	9	2	942	808366396	808367349	0.000000e+00	1406
10	TraesCS7A01G221000	chr3B	93.568	964	29	10	2	942	808403331	808404284	0.000000e+00	1406
11	TraesCS7A01G221000	chr3B	93.568	964	29	9	2	942	808439025	808439978	0.000000e+00	1406
12	TraesCS7A01G221000	chr2A	91.516	1379	117	0	938	2316	729213642	729215020	0.000000e+00	1899
13	TraesCS7A01G221000	chr4D	89.822	1346	127	5	1110	2453	482767882	482769219	0.000000e+00	1718
14	TraesCS7A01G221000	chr1B	86.816	1517	198	2	938	2453	41707017	41705502	0.000000e+00	1692
15	TraesCS7A01G221000	chr1B	93.672	964	30	8	2	942	413907876	413908831	0.000000e+00	1413
16	TraesCS7A01G221000	chr1B	92.614	704	20	8	3	683	612904899	612904205	0.000000e+00	983
17	TraesCS7A01G221000	chr1B	90.842	273	10	4	2	263	4103231	4103499	3.880000e-93	351
18	TraesCS7A01G221000	chr6B	85.535	1514	210	4	941	2453	12073650	12072145	0.000000e+00	1574
19	TraesCS7A01G221000	chr6B	95.911	856	17	6	102	942	337731967	337732819	0.000000e+00	1371
20	TraesCS7A01G221000	chr5D	96.025	956	19	5	1	941	163815086	163814135	0.000000e+00	1537
21	TraesCS7A01G221000	chr2D	95.397	956	18	6	2	942	370055824	370056768	0.000000e+00	1498
22	TraesCS7A01G221000	chr2D	95.173	953	23	7	2	942	623755528	623756469	0.000000e+00	1483
23	TraesCS7A01G221000	chr5A	94.682	959	26	5	1	942	590977728	590978678	0.000000e+00	1465
24	TraesCS7A01G221000	chr5B	93.465	964	29	10	2	942	166691779	166692731	0.000000e+00	1400
25	TraesCS7A01G221000	chr7B	89.764	127	5	2	2	120	713434711	713434837	3.270000e-34	156

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	TraesCS7A01G221000	chr7A	189348075	189350527	2452	False	4530	4530	100.000	1	2453	1	chr7A.!!$F1	2452
1	TraesCS7A01G221000	chr7A	29987456	29988971	1515	True	1609	1609	85.846	938	2453	1	chr7A.!!$R1	1515
2	TraesCS7A01G221000	chrUn	298401804	298403317	1513	False	2438	2438	95.712	938	2453	1	chrUn.!!$F1	1515
3	TraesCS7A01G221000	chrUn	357191027	357191834	807	False	1262	1262	94.982	138	942	1	chrUn.!!$F2	804
4	TraesCS7A01G221000	chrUn	396175567	396176242	675	False	1140	1140	97.054	264	942	1	chrUn.!!$F3	678
5	TraesCS7A01G221000	chr7D	139748743	139750257	1514	True	1980	1980	90.257	937	2453	1	chr7D.!!$R1	1516
6	TraesCS7A01G221000	chr3B	808034615	808036125	1510	False	1934	1934	89.776	938	2451	1	chr3B.!!$F2	1513
7	TraesCS7A01G221000	chr3B	571017753	571019269	1516	False	1631	1631	86.128	938	2452	1	chr3B.!!$F1	1514
8	TraesCS7A01G221000	chr3B	147869813	147870777	964	True	1448	1448	94.136	2	947	1	chr3B.!!$R1	945
9	TraesCS7A01G221000	chr3B	808366396	808367349	953	False	1406	1406	93.568	2	942	1	chr3B.!!$F3	940
10	TraesCS7A01G221000	chr3B	808403331	808404284	953	False	1406	1406	93.568	2	942	1	chr3B.!!$F4	940
11	TraesCS7A01G221000	chr3B	808439025	808439978	953	False	1406	1406	93.568	2	942	1	chr3B.!!$F5	940
12	TraesCS7A01G221000	chr2A	729213642	729215020	1378	False	1899	1899	91.516	938	2316	1	chr2A.!!$F1	1378
13	TraesCS7A01G221000	chr4D	482767882	482769219	1337	False	1718	1718	89.822	1110	2453	1	chr4D.!!$F1	1343
14	TraesCS7A01G221000	chr1B	41705502	41707017	1515	True	1692	1692	86.816	938	2453	1	chr1B.!!$R1	1515
15	TraesCS7A01G221000	chr1B	413907876	413908831	955	False	1413	1413	93.672	2	942	1	chr1B.!!$F2	940
16	TraesCS7A01G221000	chr1B	612904205	612904899	694	True	983	983	92.614	3	683	1	chr1B.!!$R2	680
17	TraesCS7A01G221000	chr6B	12072145	12073650	1505	True	1574	1574	85.535	941	2453	1	chr6B.!!$R1	1512
18	TraesCS7A01G221000	chr6B	337731967	337732819	852	False	1371	1371	95.911	102	942	1	chr6B.!!$F1	840
19	TraesCS7A01G221000	chr5D	163814135	163815086	951	True	1537	1537	96.025	1	941	1	chr5D.!!$R1	940
20	TraesCS7A01G221000	chr2D	370055824	370056768	944	False	1498	1498	95.397	2	942	1	chr2D.!!$F1	940
21	TraesCS7A01G221000	chr2D	623755528	623756469	941	False	1483	1483	95.173	2	942	1	chr2D.!!$F2	940
22	TraesCS7A01G221000	chr5A	590977728	590978678	950	False	1465	1465	94.682	1	942	1	chr5A.!!$F1	941
23	TraesCS7A01G221000	chr5B	166691779	166692731	952	False	1400	1400	93.465	2	942	1	chr5B.!!$F1	940

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
922	959	0.324645	GGCCACCCAATCACAATCCT	60.325	55.0	0.0	0.0	0.0	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2043	2083	0.322456	TCCTTAGCTGCCAAATGCGT	60.322	50.0	0.0	0.0	45.6	5.24	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
87	104	4.142071	TGAGCCTGGAGATATAATGATCGC	60.142	45.833	0.00	0.00	0.00	4.58
119	139	2.369394	GTGGTGATAGGGAGGCTTTTG	58.631	52.381	0.00	0.00	0.00	2.44
131	151	3.812097	GCTTTTGCAGCTTGTTTGC	57.188	47.368	0.00	0.00	46.27	3.68
226	246	1.354031	TGTGGTGGGCAATCAGTACAT	59.646	47.619	0.00	0.00	0.00	2.29
339	371	5.565592	TGCTTTGGTTAATGCATACTCAG	57.434	39.130	0.00	0.00	40.67	3.35
340	372	4.142403	TGCTTTGGTTAATGCATACTCAGC	60.142	41.667	0.00	5.59	40.67	4.26
495	527	4.059773	ACCTCCCAAAAATGGCAATCTA	57.940	40.909	0.00	0.00	0.00	1.98
922	959	0.324645	GGCCACCCAATCACAATCCT	60.325	55.000	0.00	0.00	0.00	3.24
992	1029	1.406069	CGTGGCTCAAGCTATTCCTGT	60.406	52.381	1.46	0.00	41.70	4.00
999	1036	5.008118	GGCTCAAGCTATTCCTGTTTATGTC	59.992	44.000	1.46	0.00	41.70	3.06
1260	1297	4.196193	TCATGAAGGCAAAGTATTACCCG	58.804	43.478	0.00	0.00	0.00	5.28
1452	1489	2.121506	ACCCCCAAAGGCTCCTGA	60.122	61.111	0.00	0.00	0.00	3.86
1509	1546	4.087892	GCTTGGAGGGCAGAGCGA	62.088	66.667	0.00	0.00	0.00	4.93
1547	1586	3.181451	TGGGAGATGGATGTTCAGCATAC	60.181	47.826	0.00	0.00	38.06	2.39
1559	1598	7.148188	GGATGTTCAGCATACTCTCAAAATTCA	60.148	37.037	0.00	0.00	38.06	2.57
1638	1677	7.173390	GGTGTTTTCTCAGTTAGAAGTGCTTAT	59.827	37.037	0.00	0.00	44.95	1.73
1639	1678	9.204570	GTGTTTTCTCAGTTAGAAGTGCTTATA	57.795	33.333	0.00	0.00	44.95	0.98
1682	1722	1.812571	CACGACATTTTCTGAAGGGGG	59.187	52.381	0.00	0.00	0.00	5.40
1697	1737	2.280592	GGGAACAAGTGCGTCGGT	60.281	61.111	0.00	0.00	0.00	4.69
1705	1745	2.421877	AAGTGCGTCGGTGAGTGGAG	62.422	60.000	0.00	0.00	0.00	3.86
1720	1760	2.111251	GAGCCCGTTCCCTATGGC	59.889	66.667	0.00	0.00	44.35	4.40
1749	1789	2.112198	GCAATCATCGGTCCCGCAA	61.112	57.895	0.00	0.00	39.59	4.85
1765	1805	4.081142	TCCCGCAAAAGATGAAGATCACTA	60.081	41.667	0.00	0.00	0.00	2.74
1767	1807	4.872691	CCGCAAAAGATGAAGATCACTACT	59.127	41.667	0.00	0.00	0.00	2.57
1784	1824	5.047164	TCACTACTTGGCAAGTTATAACGGA	60.047	40.000	35.13	19.95	42.81	4.69
1806	1846	2.356069	GGCTTTACCTATGCAGAAGTGC	59.644	50.000	0.00	0.00	42.56	4.40
1818	1858	1.531149	CAGAAGTGCAAGGTGTTACGG	59.469	52.381	0.00	0.00	0.00	4.02
1867	1907	2.104792	CTGTGTGGACTTGAGGAGGAAA	59.895	50.000	0.00	0.00	0.00	3.13
1992	2032	2.135189	AGGGAATGGCTTATGCACCTA	58.865	47.619	2.72	0.00	41.91	3.08
2121	2161	2.097825	GCTACGGTGGACTTCCTAGAA	58.902	52.381	0.00	0.00	36.82	2.10
2152	2192	2.097825	GATCCATCAAGCTTGCTGGTT	58.902	47.619	36.06	30.99	43.21	3.67
2166	2207	1.737793	GCTGGTTGTTATTCGGTGGAG	59.262	52.381	0.00	0.00	0.00	3.86
2213	2254	1.491668	TTGGCGGTTCCTATAGCTCA	58.508	50.000	0.00	0.00	35.26	4.26
2216	2257	1.618837	GGCGGTTCCTATAGCTCATCA	59.381	52.381	0.00	0.00	0.00	3.07
2295	2336	2.993937	ACTGTTGACGGTTCTTTCCAA	58.006	42.857	0.00	0.00	29.59	3.53
2307	2348	5.561679	GGTTCTTTCCAAGGAACAGATAGT	58.438	41.667	14.24	0.00	42.29	2.12
2360	2401	5.191426	CCATCAAGGACAGATCATCTTTGT	58.809	41.667	16.44	3.58	41.22	2.83
2395	2436	0.942410	GTTCCACTGCAACGACGCTA	60.942	55.000	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	9.448438	TGTAATTCAGCATACATAAACAAGAGT	57.552	29.630	0.00	0.00	0.00	3.24
87	104	4.443457	CCCTATCACCACCACTTGTATCAG	60.443	50.000	0.00	0.00	0.00	2.90
119	139	1.559831	AACGAAAGCAAACAAGCTGC	58.440	45.000	0.00	0.00	45.89	5.25
130	150	7.429340	CAGTATCCATGTATCAAAAACGAAAGC	59.571	37.037	0.00	0.00	0.00	3.51
131	151	7.910162	CCAGTATCCATGTATCAAAAACGAAAG	59.090	37.037	0.00	0.00	0.00	2.62
226	246	2.700371	ACATCGATCAGACTTATGGCCA	59.300	45.455	8.56	8.56	0.00	5.36
339	371	4.890088	TCAATAATAGACCATACCCGTGC	58.110	43.478	0.00	0.00	0.00	5.34
340	372	6.464222	ACATCAATAATAGACCATACCCGTG	58.536	40.000	0.00	0.00	0.00	4.94
922	959	3.500448	TGACATGCCCAGACAAAGTAA	57.500	42.857	0.00	0.00	0.00	2.24
992	1029	5.764686	AGCTTGAACACACTCATGACATAAA	59.235	36.000	0.00	0.00	0.00	1.40
999	1036	2.880268	TGGAAGCTTGAACACACTCATG	59.120	45.455	2.10	0.00	0.00	3.07
1260	1297	0.606401	TGTCTAGCAACTGGCCTTGC	60.606	55.000	19.39	19.39	46.50	4.01
1452	1489	1.792949	GCTGAAACACGATTGAGACGT	59.207	47.619	0.00	0.00	44.83	4.34
1547	1586	7.144000	CCTTGGAGAAGTTTGAATTTTGAGAG	58.856	38.462	0.00	0.00	0.00	3.20
1559	1598	0.179018	ACGCTGCCTTGGAGAAGTTT	60.179	50.000	0.00	0.00	0.00	2.66
1638	1677	8.664798	GTGTTGTGATCACATGTAGCTAATTTA	58.335	33.333	28.32	6.65	41.52	1.40
1639	1678	7.530010	GTGTTGTGATCACATGTAGCTAATTT	58.470	34.615	28.32	0.00	41.52	1.82
1682	1722	0.874607	ACTCACCGACGCACTTGTTC	60.875	55.000	0.00	0.00	0.00	3.18
1697	1737	2.449967	TAGGGAACGGGCTCCACTCA	62.450	60.000	3.28	0.00	37.20	3.41
1705	1745	2.516225	GTGCCATAGGGAACGGGC	60.516	66.667	0.00	0.00	44.05	6.13
1749	1789	5.809001	TGCCAAGTAGTGATCTTCATCTTT	58.191	37.500	0.00	0.00	0.00	2.52
1765	1805	3.606687	CCTCCGTTATAACTTGCCAAGT	58.393	45.455	13.56	3.74	45.46	3.16
1767	1807	2.026636	AGCCTCCGTTATAACTTGCCAA	60.027	45.455	13.56	0.00	0.00	4.52
1784	1824	3.933061	GCACTTCTGCATAGGTAAAGCCT	60.933	47.826	0.00	0.00	46.15	4.58
1806	1846	1.735571	GGTATGTGCCGTAACACCTTG	59.264	52.381	0.00	0.00	39.93	3.61
1818	1858	1.472480	GTGGATGTTGTGGGTATGTGC	59.528	52.381	0.00	0.00	0.00	4.57
1867	1907	4.428845	CAAGGCATGGAAGGTGCT	57.571	55.556	0.00	0.00	42.16	4.40
2043	2083	0.322456	TCCTTAGCTGCCAAATGCGT	60.322	50.000	0.00	0.00	45.60	5.24
2121	2161	6.552445	AGCTTGATGGATCTGTAGTAACTT	57.448	37.500	0.00	0.00	0.00	2.66
2152	2192	4.941263	CAGAATTTCCTCCACCGAATAACA	59.059	41.667	0.00	0.00	0.00	2.41
2166	2207	5.997129	TGGCATTTTTCCTTTCAGAATTTCC	59.003	36.000	0.00	0.00	0.00	3.13
2213	2254	5.251700	AGTGGTATGTTTTCCTTCTCCTGAT	59.748	40.000	0.00	0.00	0.00	2.90
2216	2257	5.045797	GGTAGTGGTATGTTTTCCTTCTCCT	60.046	44.000	0.00	0.00	0.00	3.69
2395	2436	0.674895	GCGTGAAGTTCAGCCTCCAT	60.675	55.000	5.62	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.