AutoCloner

Multiple sequence alignment - TraesCS7A01G462700

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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	TraesCS7A01G462700	chr7A	100.000	2384	0	0	1	2384	659368864	659371247	0.000000e+00	4403.0
1	TraesCS7A01G462700	chr7D	92.777	983	43	8	585	1557	570638384	570639348	0.000000e+00	1397.0
2	TraesCS7A01G462700	chr7D	80.200	899	95	36	1059	1921	569703956	569704807	4.390000e-167	597.0
3	TraesCS7A01G462700	chr7D	89.362	423	42	3	1963	2384	570640462	570640882	1.620000e-146	529.0
4	TraesCS7A01G462700	chr7D	83.279	305	27	16	1596	1886	570639344	570639638	2.350000e-65	259.0
5	TraesCS7A01G462700	chr7D	82.162	185	19	10	1350	1529	570639749	570639924	1.910000e-31	147.0
6	TraesCS7A01G462700	chr7D	93.333	45	2	1	1961	2005	569704816	569704859	5.500000e-07	65.8
7	TraesCS7A01G462700	chr7B	87.149	1105	83	28	634	1719	626067245	626068309	0.000000e+00	1199.0
8	TraesCS7A01G462700	chr7B	89.610	616	52	8	1774	2384	626068373	626068981	0.000000e+00	773.0
9	TraesCS7A01G462700	chr3A	95.060	587	22	4	1	585	20188155	20188736	0.000000e+00	917.0
10	TraesCS7A01G462700	chr3A	91.282	585	40	9	1	579	547258280	547257701	0.000000e+00	787.0
11	TraesCS7A01G462700	chr3A	90.909	583	42	6	1	576	691699740	691700318	0.000000e+00	773.0
12	TraesCS7A01G462700	chr3A	90.236	594	45	8	1	585	497204367	497204956	0.000000e+00	763.0
13	TraesCS7A01G462700	chr6A	94.549	587	29	3	1	586	14350157	14350741	0.000000e+00	904.0
14	TraesCS7A01G462700	chr6A	90.444	586	43	8	1	579	40242851	40242272	0.000000e+00	760.0
15	TraesCS7A01G462700	chr4A	90.893	582	44	4	1	576	615412551	615413129	0.000000e+00	773.0
16	TraesCS7A01G462700	chr5A	90.268	596	46	7	1	588	77886133	77885542	0.000000e+00	769.0
17	TraesCS7A01G462700	chr2A	90.566	583	43	7	1	576	770376530	770377107	0.000000e+00	761.0

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	TraesCS7A01G462700	chr7A	659368864	659371247	2383	False	4403.0	4403	100.0000	1	2384	1	chr7A.!!$F1	2383
1	TraesCS7A01G462700	chr7D	570638384	570640882	2498	False	583.0	1397	86.8950	585	2384	4	chr7D.!!$F2	1799
2	TraesCS7A01G462700	chr7D	569703956	569704859	903	False	331.4	597	86.7665	1059	2005	2	chr7D.!!$F1	946
3	TraesCS7A01G462700	chr7B	626067245	626068981	1736	False	986.0	1199	88.3795	634	2384	2	chr7B.!!$F1	1750
4	TraesCS7A01G462700	chr3A	20188155	20188736	581	False	917.0	917	95.0600	1	585	1	chr3A.!!$F1	584
5	TraesCS7A01G462700	chr3A	547257701	547258280	579	True	787.0	787	91.2820	1	579	1	chr3A.!!$R1	578
6	TraesCS7A01G462700	chr3A	691699740	691700318	578	False	773.0	773	90.9090	1	576	1	chr3A.!!$F3	575
7	TraesCS7A01G462700	chr3A	497204367	497204956	589	False	763.0	763	90.2360	1	585	1	chr3A.!!$F2	584
8	TraesCS7A01G462700	chr6A	14350157	14350741	584	False	904.0	904	94.5490	1	586	1	chr6A.!!$F1	585
9	TraesCS7A01G462700	chr6A	40242272	40242851	579	True	760.0	760	90.4440	1	579	1	chr6A.!!$R1	578
10	TraesCS7A01G462700	chr4A	615412551	615413129	578	False	773.0	773	90.8930	1	576	1	chr4A.!!$F1	575
11	TraesCS7A01G462700	chr5A	77885542	77886133	591	True	769.0	769	90.2680	1	588	1	chr5A.!!$R1	587
12	TraesCS7A01G462700	chr2A	770376530	770377107	577	False	761.0	761	90.5660	1	576	1	chr2A.!!$F1	575

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
588	605	0.165295	GCAGTTAACGCGACCCTTTC	59.835	55.0	15.93	0.0	0.0	2.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2151	3003	0.179111	CGCGGACAAGGATAGCTTCA	60.179	55.0	0.0	0.0	0.0	3.02	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
80	82	7.478520	AGACACACAACTTATGTAGTGTTTC	57.521	36.000	13.77	0.00	45.62	2.78
140	142	5.415389	GGTAATTTTGCAATTTTCTGCCCAT	59.585	36.000	0.00	0.00	41.90	4.00
141	143	6.597280	GGTAATTTTGCAATTTTCTGCCCATA	59.403	34.615	0.00	0.00	41.90	2.74
222	225	1.070786	GAGGGCGTTGTTGGAGTGA	59.929	57.895	0.00	0.00	0.00	3.41
231	235	1.207488	TGTTGGAGTGAGGGATGGGG	61.207	60.000	0.00	0.00	0.00	4.96
278	286	2.122167	GTGTGGTTTGCGGTGGGAA	61.122	57.895	0.00	0.00	0.00	3.97
525	542	2.046314	CGGGTTCCCGTTCATGCT	60.046	61.111	20.65	0.00	43.86	3.79
588	605	0.165295	GCAGTTAACGCGACCCTTTC	59.835	55.000	15.93	0.00	0.00	2.62
589	606	1.792006	CAGTTAACGCGACCCTTTCT	58.208	50.000	15.93	0.00	0.00	2.52
590	607	2.140717	CAGTTAACGCGACCCTTTCTT	58.859	47.619	15.93	0.00	0.00	2.52
591	608	2.546789	CAGTTAACGCGACCCTTTCTTT	59.453	45.455	15.93	0.00	0.00	2.52
592	609	3.002965	CAGTTAACGCGACCCTTTCTTTT	59.997	43.478	15.93	0.00	0.00	2.27
593	610	3.628942	AGTTAACGCGACCCTTTCTTTTT	59.371	39.130	15.93	0.00	0.00	1.94
682	700	2.770827	CCTTTCCTTCCCACCCCC	59.229	66.667	0.00	0.00	0.00	5.40
806	835	2.947532	TTCCGCTGCTCAGGTGAGG	61.948	63.158	9.03	0.00	42.29	3.86
936	971	2.124278	GACCGGATTTCAGGGGCC	60.124	66.667	9.46	0.00	35.41	5.80
966	1001	2.431942	CACCCGTACGTGCAGGTC	60.432	66.667	16.53	7.08	0.00	3.85
1450	1513	4.697352	GTGTAACTTGGATGAATCTGTGCT	59.303	41.667	0.00	0.00	0.00	4.40
1457	1520	3.204526	GGATGAATCTGTGCTTGGAGAG	58.795	50.000	0.00	0.00	0.00	3.20
1458	1521	3.370315	GGATGAATCTGTGCTTGGAGAGT	60.370	47.826	0.00	0.00	0.00	3.24
1459	1522	3.049708	TGAATCTGTGCTTGGAGAGTG	57.950	47.619	0.00	0.00	0.00	3.51
1460	1523	2.289882	TGAATCTGTGCTTGGAGAGTGG	60.290	50.000	0.00	0.00	0.00	4.00
1461	1524	1.649321	ATCTGTGCTTGGAGAGTGGA	58.351	50.000	0.00	0.00	0.00	4.02
1462	1525	0.972134	TCTGTGCTTGGAGAGTGGAG	59.028	55.000	0.00	0.00	0.00	3.86
1463	1526	0.972134	CTGTGCTTGGAGAGTGGAGA	59.028	55.000	0.00	0.00	0.00	3.71
1468	1531	1.349357	GCTTGGAGAGTGGAGACCTTT	59.651	52.381	0.00	0.00	0.00	3.11
1477	1540	2.366916	AGTGGAGACCTTTCTGTGACTG	59.633	50.000	0.00	0.00	29.47	3.51
1490	1553	7.957484	CCTTTCTGTGACTGTTATTTGTAATCG	59.043	37.037	0.00	0.00	0.00	3.34
1507	1570	2.325583	TCGGTTCTGCCATATTGGAC	57.674	50.000	0.00	0.00	40.96	4.02
1577	1663	7.789202	TCATATTTCAGTTCCATGGGAAAAA	57.211	32.000	13.02	5.45	43.86	1.94
1578	1664	7.839907	TCATATTTCAGTTCCATGGGAAAAAG	58.160	34.615	13.02	7.90	43.86	2.27
1580	1666	4.935352	TTCAGTTCCATGGGAAAAAGTG	57.065	40.909	13.02	11.76	43.86	3.16
1582	1668	1.970640	AGTTCCATGGGAAAAAGTGCC	59.029	47.619	13.02	0.00	43.86	5.01
1586	1672	4.286447	TGGGAAAAAGTGCCACCC	57.714	55.556	0.00	0.00	44.08	4.61
1587	1673	1.458588	TGGGAAAAAGTGCCACCCC	60.459	57.895	0.00	0.00	44.08	4.95
1588	1674	1.152333	GGGAAAAAGTGCCACCCCT	60.152	57.895	0.00	0.00	37.76	4.79
1589	1675	0.762842	GGGAAAAAGTGCCACCCCTT	60.763	55.000	0.00	0.00	37.76	3.95
1590	1676	1.481615	GGGAAAAAGTGCCACCCCTTA	60.482	52.381	0.00	0.00	37.76	2.69
1591	1677	2.321719	GGAAAAAGTGCCACCCCTTAA	58.678	47.619	0.00	0.00	0.00	1.85
1592	1678	2.701423	GGAAAAAGTGCCACCCCTTAAA	59.299	45.455	0.00	0.00	0.00	1.52
1593	1679	3.326588	GGAAAAAGTGCCACCCCTTAAAT	59.673	43.478	0.00	0.00	0.00	1.40
1594	1680	4.562757	GGAAAAAGTGCCACCCCTTAAATC	60.563	45.833	0.00	0.00	0.00	2.17
1636	1722	6.166984	TGACTCTGAGTTCTTCAATCAACT	57.833	37.500	12.27	0.00	34.81	3.16
1637	1723	7.014711	ACTGACTCTGAGTTCTTCAATCAACTA	59.985	37.037	12.27	0.00	34.81	2.24
1638	1724	7.148641	TGACTCTGAGTTCTTCAATCAACTAC	58.851	38.462	12.27	0.00	34.81	2.73
1639	1725	7.014711	TGACTCTGAGTTCTTCAATCAACTACT	59.985	37.037	12.27	0.00	34.81	2.57
1640	1726	8.410673	ACTCTGAGTTCTTCAATCAACTACTA	57.589	34.615	4.06	0.00	34.81	1.82
1641	1727	9.030452	ACTCTGAGTTCTTCAATCAACTACTAT	57.970	33.333	4.06	0.00	34.81	2.12
1677	1763	9.778741	ACATAAATTCGATAACTGGTGACATAT	57.221	29.630	0.00	0.00	41.51	1.78
1691	1777	7.125811	ACTGGTGACATATACAAGTTCATACCT	59.874	37.037	0.00	0.00	41.51	3.08
1703	1789	8.706322	ACAAGTTCATACCTTAACTTTGGATT	57.294	30.769	0.00	0.00	41.89	3.01
1869	1972	1.551908	GCCAAAATGCCCATGGTGGA	61.552	55.000	18.54	8.69	40.96	4.02
1911	2379	4.759693	CACACTGGTCAAAATAGTGCCTTA	59.240	41.667	0.00	0.00	44.22	2.69
1913	2381	5.830991	ACACTGGTCAAAATAGTGCCTTAAA	59.169	36.000	0.00	0.00	44.22	1.52
1941	2409	3.253230	AGAACAACTGCAAAACAACAGC	58.747	40.909	0.00	0.00	37.42	4.40
1975	2826	7.896811	ACTTGTGTGATTGTATTAGTCTCTCA	58.103	34.615	0.00	0.00	0.00	3.27
2024	2876	0.543277	TCAGACAATGGCAGCTAGGG	59.457	55.000	0.00	0.00	0.00	3.53
2036	2888	3.181454	GGCAGCTAGGGAAAATAGCAGTA	60.181	47.826	7.62	0.00	46.57	2.74
2042	2894	5.639931	GCTAGGGAAAATAGCAGTATACAGC	59.360	44.000	12.03	12.03	44.14	4.40
2087	2939	1.202582	AGTTCCACTCTCCGATGAACG	59.797	52.381	0.00	0.00	40.08	3.95
2119	2971	3.414700	GTGCCGTCGAGCCACTTG	61.415	66.667	0.00	0.00	0.00	3.16
2138	2990	0.616111	GAGAGAAGGGCTGAGGGTCA	60.616	60.000	0.00	0.00	0.00	4.02
2149	3001	2.420642	CTGAGGGTCATCACAACAGTG	58.579	52.381	0.00	0.00	34.56	3.66
2151	3003	1.072331	GAGGGTCATCACAACAGTGGT	59.928	52.381	0.00	0.00	34.04	4.16
2323	3175	3.932710	GTGAAAACGGAGATGAGCACATA	59.067	43.478	0.00	0.00	36.82	2.29
2332	3184	4.501571	GGAGATGAGCACATATACCGTGTT	60.502	45.833	0.00	0.62	36.82	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	6.772605	TGCACTAGATCTGCCATGTAAATAT	58.227	36.000	5.18	0.00	33.36	1.28
15	16	4.486125	TGCACTAGATCTGCCATGTAAA	57.514	40.909	5.18	0.00	33.36	2.01
80	82	1.043816	AGATCCATCCTACAGCGGTG	58.956	55.000	14.13	14.13	0.00	4.94
140	142	5.129485	CCCTACTGCTTCTCATCCTTCTTTA	59.871	44.000	0.00	0.00	0.00	1.85
141	143	4.080638	CCCTACTGCTTCTCATCCTTCTTT	60.081	45.833	0.00	0.00	0.00	2.52
278	286	2.494918	GGCAGATCCGTAGTGCGT	59.505	61.111	0.00	0.00	38.13	5.24
519	536	3.284336	ACGCCTCGTGTAGCATGA	58.716	55.556	0.00	0.00	39.18	3.07
576	593	2.804527	GTCTAAAAAGAAAGGGTCGCGT	59.195	45.455	5.77	0.00	0.00	6.01
588	605	5.753921	GGAGTCCGGATGTATGTCTAAAAAG	59.246	44.000	7.81	0.00	0.00	2.27
589	606	5.667466	GGAGTCCGGATGTATGTCTAAAAA	58.333	41.667	7.81	0.00	0.00	1.94
590	607	4.202080	CGGAGTCCGGATGTATGTCTAAAA	60.202	45.833	24.39	0.00	44.15	1.52
591	608	3.317149	CGGAGTCCGGATGTATGTCTAAA	59.683	47.826	24.39	0.00	44.15	1.85
592	609	2.882761	CGGAGTCCGGATGTATGTCTAA	59.117	50.000	24.39	0.00	44.15	2.10
593	610	2.501261	CGGAGTCCGGATGTATGTCTA	58.499	52.381	24.39	0.00	44.15	2.59
682	700	0.394565	GGTTGATGGAGATCGGAGGG	59.605	60.000	0.00	0.00	0.00	4.30
806	835	4.785453	CCTTGGACTGGCGAGGGC	62.785	72.222	0.00	0.00	38.90	5.19
816	851	1.155424	TGTGACGCGAAACCTTGGAC	61.155	55.000	15.93	0.00	0.00	4.02
936	971	1.146930	CGGGTGGTCATCAGATGGG	59.853	63.158	10.67	0.00	0.00	4.00
1016	1058	1.407437	GGATCACTTGGCCGTCAGAAT	60.407	52.381	0.00	0.00	0.00	2.40
1323	1386	1.812922	GCAGTCGACATGGCAGGAG	60.813	63.158	19.50	0.00	0.00	3.69
1450	1513	2.634940	CAGAAAGGTCTCCACTCTCCAA	59.365	50.000	0.00	0.00	28.78	3.53
1457	1520	2.103263	ACAGTCACAGAAAGGTCTCCAC	59.897	50.000	0.00	0.00	28.78	4.02
1458	1521	2.398588	ACAGTCACAGAAAGGTCTCCA	58.601	47.619	0.00	0.00	28.78	3.86
1459	1522	3.477210	AACAGTCACAGAAAGGTCTCC	57.523	47.619	0.00	0.00	28.78	3.71
1460	1523	6.483640	ACAAATAACAGTCACAGAAAGGTCTC	59.516	38.462	0.00	0.00	28.78	3.36
1461	1524	6.357367	ACAAATAACAGTCACAGAAAGGTCT	58.643	36.000	0.00	0.00	32.85	3.85
1462	1525	6.619801	ACAAATAACAGTCACAGAAAGGTC	57.380	37.500	0.00	0.00	0.00	3.85
1463	1526	8.691661	ATTACAAATAACAGTCACAGAAAGGT	57.308	30.769	0.00	0.00	0.00	3.50
1468	1531	6.460781	ACCGATTACAAATAACAGTCACAGA	58.539	36.000	0.00	0.00	0.00	3.41
1477	1540	5.554822	TGGCAGAACCGATTACAAATAAC	57.445	39.130	0.00	0.00	43.94	1.89
1490	1553	2.099756	GCAAGTCCAATATGGCAGAACC	59.900	50.000	0.00	0.00	37.47	3.62
1548	1615	7.581814	TCCCATGGAACTGAAATATGAATACA	58.418	34.615	15.22	0.00	0.00	2.29
1577	1663	2.378547	TGAAGATTTAAGGGGTGGCACT	59.621	45.455	18.45	0.00	0.00	4.40
1578	1664	2.802719	TGAAGATTTAAGGGGTGGCAC	58.197	47.619	9.70	9.70	0.00	5.01
1580	1666	3.631250	TGATGAAGATTTAAGGGGTGGC	58.369	45.455	0.00	0.00	0.00	5.01
1582	1668	6.604795	ACTGATTGATGAAGATTTAAGGGGTG	59.395	38.462	0.00	0.00	0.00	4.61
1583	1669	6.604795	CACTGATTGATGAAGATTTAAGGGGT	59.395	38.462	0.00	0.00	0.00	4.95
1584	1670	6.604795	ACACTGATTGATGAAGATTTAAGGGG	59.395	38.462	0.00	0.00	0.00	4.79
1585	1671	7.337689	TGACACTGATTGATGAAGATTTAAGGG	59.662	37.037	0.00	0.00	0.00	3.95
1586	1672	8.180267	GTGACACTGATTGATGAAGATTTAAGG	58.820	37.037	0.00	0.00	0.00	2.69
1587	1673	8.944029	AGTGACACTGATTGATGAAGATTTAAG	58.056	33.333	7.47	0.00	0.00	1.85
1588	1674	8.853077	AGTGACACTGATTGATGAAGATTTAA	57.147	30.769	7.47	0.00	0.00	1.52
1615	1701	7.296628	AGTAGTTGATTGAAGAACTCAGAGT	57.703	36.000	0.00	0.00	34.81	3.24
1646	1732	9.607988	TCACCAGTTATCGAATTTATGTACAAT	57.392	29.630	0.00	0.00	0.00	2.71
1661	1747	8.942338	TGAACTTGTATATGTCACCAGTTATC	57.058	34.615	0.00	0.00	33.43	1.75
1677	1763	9.802039	AATCCAAAGTTAAGGTATGAACTTGTA	57.198	29.630	1.07	0.00	43.41	2.41
1678	1764	8.706322	AATCCAAAGTTAAGGTATGAACTTGT	57.294	30.769	1.07	0.00	43.41	3.16
1691	1777	9.567776	TCACTTGATCACTTAATCCAAAGTTAA	57.432	29.630	0.00	0.00	37.61	2.01
1703	1789	7.334421	GCCAGAGTAATTTCACTTGATCACTTA	59.666	37.037	0.00	0.00	0.00	2.24
1752	1847	3.248363	TCTTTCTGTCTGTTGTGCAATCG	59.752	43.478	0.00	0.00	0.00	3.34
1812	1913	4.122776	TCACAGCAGAAGACTGAAAAGAC	58.877	43.478	0.00	0.00	46.03	3.01
1814	1915	4.024218	CCTTCACAGCAGAAGACTGAAAAG	60.024	45.833	13.20	1.40	46.18	2.27
1869	1972	7.921214	CCAGTGTGATTACTGTTAGAATCGTAT	59.079	37.037	0.00	0.00	45.12	3.06
1927	2395	3.988379	TCCTTAGCTGTTGTTTTGCAG	57.012	42.857	0.00	0.00	35.93	4.41
1930	2398	7.379529	CACAAGTATTCCTTAGCTGTTGTTTTG	59.620	37.037	0.00	0.00	0.00	2.44
1975	2826	9.838339	ATGTATTATTACAGTTAAGCAGCTCTT	57.162	29.630	0.00	4.26	41.49	2.85
2024	2876	8.128016	AGTAAACGCTGTATACTGCTATTTTC	57.872	34.615	26.12	21.79	38.46	2.29
2036	2888	3.706600	TGGGGAAAGTAAACGCTGTAT	57.293	42.857	0.00	0.00	0.00	2.29
2042	2894	5.878116	TGTGATAGAATGGGGAAAGTAAACG	59.122	40.000	0.00	0.00	0.00	3.60
2087	2939	1.806542	CGGCACATGTATCCATTAGCC	59.193	52.381	14.45	11.88	41.64	3.93
2119	2971	0.616111	TGACCCTCAGCCCTTCTCTC	60.616	60.000	0.00	0.00	0.00	3.20
2138	2990	2.645838	AGCTTCACCACTGTTGTGAT	57.354	45.000	14.51	0.00	46.55	3.06
2149	3001	1.941325	CGGACAAGGATAGCTTCACC	58.059	55.000	0.00	0.00	0.00	4.02
2151	3003	0.179111	CGCGGACAAGGATAGCTTCA	60.179	55.000	0.00	0.00	0.00	3.02
2284	3136	0.315869	CACACAAAGTCGAACGGTGC	60.316	55.000	7.44	0.00	32.89	5.01
2323	3175	1.468565	CCGATCGACACAACACGGTAT	60.469	52.381	18.66	0.00	36.38	2.73
2332	3184	1.934220	GAGCTCACCCGATCGACACA	61.934	60.000	18.66	0.00	0.00	3.72
2353	3205	6.744537	CGTTGGATTTGTCTTTCAATGAGATC	59.255	38.462	0.00	0.00	35.84	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.