AutoCloner

Multiple sequence alignment - TraesCS1B01G244600

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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	TraesCS1B01G244600	chr1B	100.000	2538	0	0	1	2538	433642918	433640381	0.000000e+00	4687.0
1	TraesCS1B01G244600	chr1A	94.809	1464	73	3	101	1563	402229736	402231197	0.000000e+00	2279.0
2	TraesCS1B01G244600	chr1A	96.176	680	23	3	1861	2538	402232041	402232719	0.000000e+00	1109.0
3	TraesCS1B01G244600	chr1A	91.228	57	3	1	1609	1665	402231314	402231368	2.710000e-10	76.8
4	TraesCS1B01G244600	chr1D	92.726	1361	79	7	2	1360	320729611	320728269	0.000000e+00	1947.0
5	TraesCS1B01G244600	chr1D	96.478	653	23	0	1886	2538	320725734	320725082	0.000000e+00	1079.0
6	TraesCS1B01G244600	chr1D	93.514	185	10	2	1393	1577	320728264	320728082	8.950000e-70	274.0
7	TraesCS1B01G244600	chr1D	93.878	49	1	1	1616	1664	320727969	320727923	3.500000e-09	73.1
8	TraesCS1B01G244600	chr1D	97.143	35	0	1	1575	1608	4310591	4310557	9.810000e-05	58.4
9	TraesCS1B01G244600	chr5B	82.422	1536	251	16	1	1528	695812502	695810978	0.000000e+00	1323.0
10	TraesCS1B01G244600	chr5B	81.741	1539	258	19	1	1528	695694882	695693356	0.000000e+00	1264.0
11	TraesCS1B01G244600	chr5B	80.769	1534	277	13	1	1531	695875370	695873852	0.000000e+00	1182.0
12	TraesCS1B01G244600	chr5B	80.130	1535	281	22	1	1527	571607997	571609515	0.000000e+00	1123.0
13	TraesCS1B01G244600	chr5D	82.085	1535	258	16	1	1528	555637738	555639262	0.000000e+00	1295.0
14	TraesCS1B01G244600	chr5D	81.753	1529	260	15	1	1521	555557414	555558931	0.000000e+00	1260.0
15	TraesCS1B01G244600	chr5D	80.616	1527	267	23	1	1521	555064126	555065629	0.000000e+00	1153.0
16	TraesCS1B01G244600	chr5D	80.052	1524	277	24	3	1516	555908650	555910156	0.000000e+00	1105.0
17	TraesCS1B01G244600	chr5D	79.767	1542	288	22	4	1536	464699295	464697769	0.000000e+00	1098.0
18	TraesCS1B01G244600	chr5D	100.000	32	0	0	1575	1606	497254278	497254247	2.730000e-05	60.2
19	TraesCS1B01G244600	chr6A	80.366	1365	240	26	176	1530	11233972	11232626	0.000000e+00	1011.0
20	TraesCS1B01G244600	chr6A	96.970	33	1	0	1576	1608	587855040	587855072	3.530000e-04	56.5
21	TraesCS1B01G244600	chr7B	93.478	46	2	1	1575	1619	745275380	745275335	1.630000e-07	67.6
22	TraesCS1B01G244600	chr4B	97.297	37	1	0	1572	1608	633949415	633949451	2.110000e-06	63.9
23	TraesCS1B01G244600	chr4B	96.970	33	0	1	1575	1606	298376815	298376847	1.000000e-03	54.7
24	TraesCS1B01G244600	chr2B	100.000	32	0	0	1575	1606	162395080	162395049	2.730000e-05	60.2
25	TraesCS1B01G244600	chr2B	100.000	32	0	0	1575	1606	716978728	716978759	2.730000e-05	60.2
26	TraesCS1B01G244600	chr6B	97.059	34	1	0	1575	1608	12742762	12742795	9.810000e-05	58.4

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	TraesCS1B01G244600	chr1B	433640381	433642918	2537	True	4687.000000	4687	100.000	1	2538	1	chr1B.!!$R1	2537
1	TraesCS1B01G244600	chr1A	402229736	402232719	2983	False	1154.933333	2279	94.071	101	2538	3	chr1A.!!$F1	2437
2	TraesCS1B01G244600	chr1D	320725082	320729611	4529	True	843.275000	1947	94.149	2	2538	4	chr1D.!!$R2	2536
3	TraesCS1B01G244600	chr5B	695810978	695812502	1524	True	1323.000000	1323	82.422	1	1528	1	chr5B.!!$R2	1527
4	TraesCS1B01G244600	chr5B	695693356	695694882	1526	True	1264.000000	1264	81.741	1	1528	1	chr5B.!!$R1	1527
5	TraesCS1B01G244600	chr5B	695873852	695875370	1518	True	1182.000000	1182	80.769	1	1531	1	chr5B.!!$R3	1530
6	TraesCS1B01G244600	chr5B	571607997	571609515	1518	False	1123.000000	1123	80.130	1	1527	1	chr5B.!!$F1	1526
7	TraesCS1B01G244600	chr5D	555637738	555639262	1524	False	1295.000000	1295	82.085	1	1528	1	chr5D.!!$F3	1527
8	TraesCS1B01G244600	chr5D	555557414	555558931	1517	False	1260.000000	1260	81.753	1	1521	1	chr5D.!!$F2	1520
9	TraesCS1B01G244600	chr5D	555064126	555065629	1503	False	1153.000000	1153	80.616	1	1521	1	chr5D.!!$F1	1520
10	TraesCS1B01G244600	chr5D	555908650	555910156	1506	False	1105.000000	1105	80.052	3	1516	1	chr5D.!!$F4	1513
11	TraesCS1B01G244600	chr5D	464697769	464699295	1526	True	1098.000000	1098	79.767	4	1536	1	chr5D.!!$R1	1532
12	TraesCS1B01G244600	chr6A	11232626	11233972	1346	True	1011.000000	1011	80.366	176	1530	1	chr6A.!!$R1	1354

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
670	673	1.970917	GCTTTGATGCGGAGTGTCGG	61.971	60.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1589	1604	0.389817	TTGTATGAGCGCTTGCGTCT	60.39	50.0	13.26	13.17	45.69	4.18	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
93	96	4.410099	TCAAAGGCTCAATTCCAGTTCAT	58.590	39.130	0.00	0.00	0.00	2.57
111	114	8.342634	CCAGTTCATCTCGAAAAAGTAAAAAGA	58.657	33.333	0.00	0.00	34.69	2.52
144	147	5.223449	TGGACCTCTCGTTTAACAATCTT	57.777	39.130	0.00	0.00	0.00	2.40
153	156	5.295950	TCGTTTAACAATCTTTCGGGTACA	58.704	37.500	0.00	0.00	0.00	2.90
160	163	4.700213	ACAATCTTTCGGGTACAATTCCAG	59.300	41.667	0.00	0.00	0.00	3.86
204	207	6.417044	CGTACTTGAATACCTTGAACCTATCG	59.583	42.308	0.00	0.00	0.00	2.92
542	545	7.271223	CGTCACCAATAATTTCAGTGATGAAAC	59.729	37.037	5.61	0.00	43.82	2.78
582	585	7.045416	GGAAGCTTTGGAAAAGTTTTTAAGGA	58.955	34.615	0.00	0.00	0.00	3.36
670	673	1.970917	GCTTTGATGCGGAGTGTCGG	61.971	60.000	0.00	0.00	0.00	4.79
677	680	2.030562	CGGAGTGTCGGGTGCTTT	59.969	61.111	0.00	0.00	0.00	3.51
710	713	3.199071	ACACCGCAACCTGATAAGGATAA	59.801	43.478	1.89	0.00	0.00	1.75
851	854	2.440627	AGACTGGGCATCATGCTTGATA	59.559	45.455	14.19	0.00	44.28	2.15
1021	1025	0.864455	GATAAGTGCGAGCATGCCTC	59.136	55.000	15.66	10.41	37.22	4.70
1042	1046	2.446435	GAACAGTTGGGTACATGGCAT	58.554	47.619	0.00	0.00	0.00	4.40
1214	1228	0.955428	AAAAGCATCGCGGAAGAGCA	60.955	50.000	6.13	0.00	36.85	4.26
1541	1556	2.222213	CGGACAGCAAAAACATGACGTA	59.778	45.455	0.00	0.00	0.00	3.57
1548	1563	3.980775	GCAAAAACATGACGTAGCACAAT	59.019	39.130	0.00	0.00	0.00	2.71
1563	1578	6.238103	CGTAGCACAATGGAATTATCGTTCTT	60.238	38.462	0.00	0.00	32.46	2.52
1565	1580	5.882557	AGCACAATGGAATTATCGTTCTTCT	59.117	36.000	0.00	0.00	32.46	2.85
1570	1585	5.560966	TGGAATTATCGTTCTTCTTTGCC	57.439	39.130	0.00	0.00	0.00	4.52
1571	1586	5.253330	TGGAATTATCGTTCTTCTTTGCCT	58.747	37.500	0.00	0.00	0.00	4.75
1573	1588	6.030228	GGAATTATCGTTCTTCTTTGCCTTG	58.970	40.000	0.00	0.00	0.00	3.61
1575	1590	6.575162	ATTATCGTTCTTCTTTGCCTTGTT	57.425	33.333	0.00	0.00	0.00	2.83
1576	1591	4.918810	ATCGTTCTTCTTTGCCTTGTTT	57.081	36.364	0.00	0.00	0.00	2.83
1578	1593	5.066968	TCGTTCTTCTTTGCCTTGTTTTT	57.933	34.783	0.00	0.00	0.00	1.94
1579	1594	6.197364	TCGTTCTTCTTTGCCTTGTTTTTA	57.803	33.333	0.00	0.00	0.00	1.52
1581	1596	6.528774	TCGTTCTTCTTTGCCTTGTTTTTAAC	59.471	34.615	0.00	0.00	0.00	2.01
1582	1597	6.309251	CGTTCTTCTTTGCCTTGTTTTTAACA	59.691	34.615	0.00	0.00	40.21	2.41
1595	1610	6.179504	TGTTTTTAACAAAGTACAGACGCA	57.820	33.333	0.00	0.00	38.72	5.24
1597	1612	6.743627	TGTTTTTAACAAAGTACAGACGCAAG	59.256	34.615	0.00	0.00	38.72	4.01
1599	1614	0.859232	ACAAAGTACAGACGCAAGCG	59.141	50.000	13.50	13.50	46.03	4.68
1600	1615	0.451135	CAAAGTACAGACGCAAGCGC	60.451	55.000	15.09	0.00	44.19	5.92
1602	1617	1.009389	AAGTACAGACGCAAGCGCTC	61.009	55.000	12.06	11.06	44.19	5.03
1603	1618	1.733041	GTACAGACGCAAGCGCTCA	60.733	57.895	12.06	0.83	44.19	4.26
1605	1620	0.454196	TACAGACGCAAGCGCTCATA	59.546	50.000	12.06	5.16	44.19	2.15
1606	1621	1.078759	ACAGACGCAAGCGCTCATAC	61.079	55.000	12.06	1.58	44.19	2.39
1607	1622	1.078201	CAGACGCAAGCGCTCATACA	61.078	55.000	12.06	0.00	44.19	2.29
1619	1706	7.360017	GCAAGCGCTCATACAATATGTATACAA	60.360	37.037	12.06	0.00	36.98	2.41
1777	1986	4.547406	TCGATAGTGTCCGTTATGTCTG	57.453	45.455	0.00	0.00	37.40	3.51
1792	2002	3.790437	CTGGCTCTCCACCCGCAT	61.790	66.667	0.00	0.00	37.47	4.73
1797	2007	0.811616	GCTCTCCACCCGCATACTTG	60.812	60.000	0.00	0.00	0.00	3.16
1826	2038	3.366052	AAAGGTCCACTTGAGTGTTGT	57.634	42.857	10.03	0.00	44.21	3.32
1894	4034	9.962783	ACATACTTTCGAGACATTATAACCTAC	57.037	33.333	0.00	0.00	0.00	3.18
1937	4077	5.225642	ACAAAACGACTTACTAGCACTACC	58.774	41.667	0.00	0.00	0.00	3.18
1945	4085	4.406003	ACTTACTAGCACTACCTTCATGGG	59.594	45.833	0.00	0.00	41.11	4.00
1966	4106	3.425758	GGCCAAACGAGTTTGCAGTATAC	60.426	47.826	19.88	0.00	46.25	1.47
2010	4150	4.713553	TCATATTTGCTTGCCGAATCCTA	58.286	39.130	0.00	0.00	0.00	2.94
2054	4194	5.047448	ACATGGCTTTACATACATTTGCACA	60.047	36.000	0.00	0.00	0.00	4.57
2098	4238	7.732996	ACTTGTATTATGCCGGACTATACTTT	58.267	34.615	5.05	0.00	0.00	2.66
2135	4275	7.895759	ACTTTATACAATGCAGGTTTCACAAT	58.104	30.769	0.00	0.00	0.00	2.71
2437	4577	5.400485	CGAAAACAGGCTTTTCATTCTTCAG	59.600	40.000	11.17	0.00	38.07	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	96	8.603242	ATGCTAGTCTTTTTACTTTTTCGAGA	57.397	30.769	0.00	0.00	0.00	4.04
111	114	2.363680	CGAGAGGTCCAATGATGCTAGT	59.636	50.000	0.00	0.00	0.00	2.57
144	147	3.404899	GAACACTGGAATTGTACCCGAA	58.595	45.455	0.00	0.00	0.00	4.30
153	156	4.729868	AGTTAGCAAGGAACACTGGAATT	58.270	39.130	0.00	0.00	0.00	2.17
160	163	5.693555	AGTACGTAAAGTTAGCAAGGAACAC	59.306	40.000	0.00	0.00	0.00	3.32
204	207	7.226918	GGTATTTGTCCTTCTAGCCTATTGAAC	59.773	40.741	0.00	0.00	0.00	3.18
303	306	4.019174	CAAGGCATGGTGGAAATCTTAGT	58.981	43.478	0.00	0.00	0.00	2.24
574	577	4.280677	CCATTGCTCAGTTGGTCCTTAAAA	59.719	41.667	0.00	0.00	0.00	1.52
582	585	1.688197	CCAAACCATTGCTCAGTTGGT	59.312	47.619	0.00	0.00	45.54	3.67
670	673	2.100216	CGCGCCATACAAAGCACC	59.900	61.111	0.00	0.00	0.00	5.01
710	713	5.833131	AGTCAAGGTTGGAACATGTGTTAAT	59.167	36.000	0.00	0.00	39.30	1.40
779	782	2.040145	TCTGTGATCCATGAAGGTGCAA	59.960	45.455	0.00	0.00	39.02	4.08
783	786	1.911357	TGCTCTGTGATCCATGAAGGT	59.089	47.619	0.00	0.00	39.02	3.50
851	854	4.510038	GATAAGCCATTGCCATCGAAAT	57.490	40.909	0.00	0.00	38.69	2.17
873	876	1.914634	CTCGTAGTGCTCATGGTGTC	58.085	55.000	0.00	0.00	0.00	3.67
1021	1025	0.802494	GCCATGTACCCAACTGTTCG	59.198	55.000	0.00	0.00	0.00	3.95
1042	1046	9.073475	ACAACAACAAGCTAATTAAATACCTGA	57.927	29.630	0.00	0.00	0.00	3.86
1184	1198	2.095059	GCGATGCTTTTCCAAGTGACAT	60.095	45.455	0.00	0.00	31.86	3.06
1185	1199	1.266718	GCGATGCTTTTCCAAGTGACA	59.733	47.619	0.00	0.00	31.86	3.58
1214	1228	2.766263	TGATCCCATAGCTGAAGACGTT	59.234	45.455	0.00	0.00	0.00	3.99
1541	1556	5.882557	AGAAGAACGATAATTCCATTGTGCT	59.117	36.000	0.00	0.00	30.36	4.40
1548	1563	5.253330	AGGCAAAGAAGAACGATAATTCCA	58.747	37.500	0.00	0.00	0.00	3.53
1573	1588	6.290904	GCTTGCGTCTGTACTTTGTTAAAAAC	60.291	38.462	0.00	0.00	0.00	2.43
1575	1590	5.267776	GCTTGCGTCTGTACTTTGTTAAAA	58.732	37.500	0.00	0.00	0.00	1.52
1576	1591	4.551217	CGCTTGCGTCTGTACTTTGTTAAA	60.551	41.667	6.86	0.00	0.00	1.52
1578	1593	2.473609	CGCTTGCGTCTGTACTTTGTTA	59.526	45.455	6.86	0.00	0.00	2.41
1579	1594	1.260561	CGCTTGCGTCTGTACTTTGTT	59.739	47.619	6.86	0.00	0.00	2.83
1581	1596	0.451135	GCGCTTGCGTCTGTACTTTG	60.451	55.000	16.38	0.00	0.00	2.77
1582	1597	0.600255	AGCGCTTGCGTCTGTACTTT	60.600	50.000	16.38	0.00	45.69	2.66
1583	1598	1.006102	AGCGCTTGCGTCTGTACTT	60.006	52.632	16.38	0.00	45.69	2.24
1585	1600	1.078759	ATGAGCGCTTGCGTCTGTAC	61.079	55.000	13.26	0.00	45.69	2.90
1586	1601	0.454196	TATGAGCGCTTGCGTCTGTA	59.546	50.000	13.26	6.26	45.69	2.74
1587	1602	1.078759	GTATGAGCGCTTGCGTCTGT	61.079	55.000	13.26	7.66	45.69	3.41
1588	1603	1.078201	TGTATGAGCGCTTGCGTCTG	61.078	55.000	13.26	0.00	45.69	3.51
1589	1604	0.389817	TTGTATGAGCGCTTGCGTCT	60.390	50.000	13.26	13.17	45.69	4.18
1590	1605	0.652592	ATTGTATGAGCGCTTGCGTC	59.347	50.000	13.26	12.36	45.69	5.19
1591	1606	1.934589	TATTGTATGAGCGCTTGCGT	58.065	45.000	13.26	3.24	45.69	5.24
1592	1607	2.221749	ACATATTGTATGAGCGCTTGCG	59.778	45.455	13.26	10.90	45.69	4.85
1593	1608	3.885484	ACATATTGTATGAGCGCTTGC	57.115	42.857	13.26	0.00	39.58	4.01
1594	1609	7.581011	TGTATACATATTGTATGAGCGCTTG	57.419	36.000	13.26	4.64	42.93	4.01
1595	1610	8.088365	TCTTGTATACATATTGTATGAGCGCTT	58.912	33.333	13.26	0.00	42.93	4.68
1597	1612	7.812309	TCTTGTATACATATTGTATGAGCGC	57.188	36.000	6.36	0.00	42.93	5.92
1670	1757	6.427974	TGTATGTACATCGTTTTCGCAAAAA	58.572	32.000	12.68	0.00	43.73	1.94
1671	1758	5.986936	TGTATGTACATCGTTTTCGCAAAA	58.013	33.333	12.68	0.00	43.73	2.44
1672	1759	5.593183	TGTATGTACATCGTTTTCGCAAA	57.407	34.783	12.68	0.00	43.73	3.68
1673	1760	5.788055	ATGTATGTACATCGTTTTCGCAA	57.212	34.783	12.68	0.00	42.96	4.85
1674	1761	7.648510	TGTATATGTATGTACATCGTTTTCGCA	59.351	33.333	12.68	1.86	45.11	5.10
1675	1762	7.999213	TGTATATGTATGTACATCGTTTTCGC	58.001	34.615	12.68	0.00	45.11	4.70
1676	1763	9.937577	CATGTATATGTATGTACATCGTTTTCG	57.062	33.333	12.68	0.00	45.11	3.46
1756	1965	3.314357	CCAGACATAACGGACACTATCGA	59.686	47.826	0.00	0.00	0.00	3.59
1777	1986	1.972660	AAGTATGCGGGTGGAGAGCC	61.973	60.000	0.00	0.00	36.28	4.70
1792	2002	7.504926	AGTGGACCTTTATTATGGACAAGTA	57.495	36.000	0.00	0.00	0.00	2.24
1797	2007	6.316390	CACTCAAGTGGACCTTTATTATGGAC	59.684	42.308	2.08	0.00	42.10	4.02
1826	2038	0.689412	TGTCACCGGGAGCCATATCA	60.689	55.000	6.32	0.00	0.00	2.15
1920	4060	4.959596	TGAAGGTAGTGCTAGTAAGTCG	57.040	45.455	0.00	0.00	0.00	4.18
1937	4077	1.247567	AACTCGTTTGGCCCATGAAG	58.752	50.000	0.00	0.00	0.00	3.02
1966	4106	7.381766	TGAAGTCCATGAACTAAATGTCATG	57.618	36.000	6.66	6.66	39.52	3.07
2054	4194	2.687935	AGTTGTTTCGTCATTGCCAGTT	59.312	40.909	0.00	0.00	0.00	3.16
2135	4275	2.042464	TGGGTTGCCTGCAAATTGTTA	58.958	42.857	6.07	0.00	37.70	2.41
2347	4487	3.314541	AGTACGGAAGCGATTGAGTTT	57.685	42.857	0.00	0.00	0.00	2.66
2437	4577	5.180868	AGAACTGTGAAAGATCTGCACAATC	59.819	40.000	23.82	22.68	41.45	2.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.