AutoCloner

Multiple sequence alignment - TraesCS3B01G291200

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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	TraesCS3B01G291200	chr3B	100.000	2366	0	0	1	2366	466645701	466648066	0.000000e+00	4370
1	TraesCS3B01G291200	chr3B	94.077	1722	97	4	3	1720	687742590	687740870	0.000000e+00	2610
2	TraesCS3B01G291200	chr3B	87.108	1497	175	14	3	1489	775078732	775077244	0.000000e+00	1679
3	TraesCS3B01G291200	chr3B	89.667	600	48	4	1775	2364	386968398	386968993	0.000000e+00	752
4	TraesCS3B01G291200	chr5A	88.979	1724	180	8	3	1720	17705141	17703422	0.000000e+00	2122
5	TraesCS3B01G291200	chr5A	84.286	840	96	19	893	1722	55064756	55065569	0.000000e+00	787
6	TraesCS3B01G291200	chr5B	88.902	1721	184	7	5	1720	485994832	485993114	0.000000e+00	2113
7	TraesCS3B01G291200	chr1B	88.103	1740	193	11	4	1737	300269115	300270846	0.000000e+00	2054
8	TraesCS3B01G291200	chr1B	84.549	466	55	13	1264	1720	646985366	646985823	1.670000e-121	446
9	TraesCS3B01G291200	chr7B	88.088	1721	191	13	3	1718	336807500	336809211	0.000000e+00	2030
10	TraesCS3B01G291200	chr7A	87.486	1726	202	13	5	1720	395547067	395545346	0.000000e+00	1978
11	TraesCS3B01G291200	chr7A	75.887	564	124	9	1806	2365	469972259	469971704	6.440000e-71	278
12	TraesCS3B01G291200	chr1A	87.370	1726	204	12	5	1720	561410355	561408634	0.000000e+00	1967
13	TraesCS3B01G291200	chr2A	87.377	1727	199	16	5	1720	511126985	511128703	0.000000e+00	1964
14	TraesCS3B01G291200	chr2A	86.402	353	36	11	1377	1721	611111533	611111881	2.220000e-100	375
15	TraesCS3B01G291200	chr6B	87.047	579	65	4	1775	2351	158153213	158153783	0.000000e+00	645
16	TraesCS3B01G291200	chr2B	85.294	578	72	7	1775	2351	707517759	707517194	3.390000e-163	584
17	TraesCS3B01G291200	chr2B	79.070	559	94	14	1805	2350	458254661	458255209	1.730000e-96	363
18	TraesCS3B01G291200	chr4B	82.545	550	89	5	1806	2353	613913596	613914140	5.920000e-131	477
19	TraesCS3B01G291200	chr2D	80.071	562	88	20	1805	2355	326450669	326450121	1.700000e-106	396
20	TraesCS3B01G291200	chr3D	81.111	450	77	6	1891	2337	324400587	324401031	1.040000e-93	353
21	TraesCS3B01G291200	chr6D	77.880	434	76	16	1931	2355	89215651	89216073	3.900000e-63	252

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	TraesCS3B01G291200	chr3B	466645701	466648066	2365	False	4370	4370	100.000	1	2366	1	chr3B.!!$F2	2365
1	TraesCS3B01G291200	chr3B	687740870	687742590	1720	True	2610	2610	94.077	3	1720	1	chr3B.!!$R1	1717
2	TraesCS3B01G291200	chr3B	775077244	775078732	1488	True	1679	1679	87.108	3	1489	1	chr3B.!!$R2	1486
3	TraesCS3B01G291200	chr3B	386968398	386968993	595	False	752	752	89.667	1775	2364	1	chr3B.!!$F1	589
4	TraesCS3B01G291200	chr5A	17703422	17705141	1719	True	2122	2122	88.979	3	1720	1	chr5A.!!$R1	1717
5	TraesCS3B01G291200	chr5A	55064756	55065569	813	False	787	787	84.286	893	1722	1	chr5A.!!$F1	829
6	TraesCS3B01G291200	chr5B	485993114	485994832	1718	True	2113	2113	88.902	5	1720	1	chr5B.!!$R1	1715
7	TraesCS3B01G291200	chr1B	300269115	300270846	1731	False	2054	2054	88.103	4	1737	1	chr1B.!!$F1	1733
8	TraesCS3B01G291200	chr7B	336807500	336809211	1711	False	2030	2030	88.088	3	1718	1	chr7B.!!$F1	1715
9	TraesCS3B01G291200	chr7A	395545346	395547067	1721	True	1978	1978	87.486	5	1720	1	chr7A.!!$R1	1715
10	TraesCS3B01G291200	chr7A	469971704	469972259	555	True	278	278	75.887	1806	2365	1	chr7A.!!$R2	559
11	TraesCS3B01G291200	chr1A	561408634	561410355	1721	True	1967	1967	87.370	5	1720	1	chr1A.!!$R1	1715
12	TraesCS3B01G291200	chr2A	511126985	511128703	1718	False	1964	1964	87.377	5	1720	1	chr2A.!!$F1	1715
13	TraesCS3B01G291200	chr6B	158153213	158153783	570	False	645	645	87.047	1775	2351	1	chr6B.!!$F1	576
14	TraesCS3B01G291200	chr2B	707517194	707517759	565	True	584	584	85.294	1775	2351	1	chr2B.!!$R1	576
15	TraesCS3B01G291200	chr2B	458254661	458255209	548	False	363	363	79.070	1805	2350	1	chr2B.!!$F1	545
16	TraesCS3B01G291200	chr4B	613913596	613914140	544	False	477	477	82.545	1806	2353	1	chr4B.!!$F1	547
17	TraesCS3B01G291200	chr2D	326450121	326450669	548	True	396	396	80.071	1805	2355	1	chr2D.!!$R1	550

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
895	897	0.482446	TGGCAAACCTTCCAGGATGT	59.518	50.0	0.0	0.0	37.67	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2286	2317	0.384669	GGACGACCGAAATCTCCGAT	59.615	55.0	0.0	0.0	0.0	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
210	211	2.288458	CACCGTAAACGCTTCTTTTGGA	59.712	45.455	0.00	0.00	38.18	3.53
359	360	2.362077	GTGGAAACTGGAAACACAGCAT	59.638	45.455	0.00	0.00	42.21	3.79
427	428	4.829064	TGGTAACATCAGTCAAAAGCAC	57.171	40.909	0.00	0.00	46.17	4.40
459	460	4.482398	ACTCCCCTATTTGGAAGGCTATTT	59.518	41.667	0.00	0.00	38.35	1.40
495	496	6.713450	AGAATATTATTTGGCCGGTCGTAAAT	59.287	34.615	0.00	5.52	0.00	1.40
612	613	2.826428	GCAATAAGCAGGAGATCACGA	58.174	47.619	0.00	0.00	44.79	4.35
669	670	4.466370	TCTTCCGGAGACAACTTCATACAT	59.534	41.667	3.34	0.00	0.00	2.29
673	674	3.865745	CGGAGACAACTTCATACATCACC	59.134	47.826	0.00	0.00	0.00	4.02
817	819	6.132658	ACTATCTGGAGAGAAACATAGCAGA	58.867	40.000	0.00	0.00	0.00	4.26
895	897	0.482446	TGGCAAACCTTCCAGGATGT	59.518	50.000	0.00	0.00	37.67	3.06
950	954	1.266178	GGGCTGGCACCTAAATGTTT	58.734	50.000	2.88	0.00	0.00	2.83
1014	1018	1.230149	TCCTATGGCCAGGGTGGTT	60.230	57.895	22.11	2.90	40.46	3.67
1122	1126	4.320935	CCTGATGGGGAAAAGTTTTACACG	60.321	45.833	12.62	0.00	0.00	4.49
1157	1161	5.877012	CAGTCATATGTTGGGCTATATGGAC	59.123	44.000	1.90	0.00	37.68	4.02
1161	1165	4.796110	ATGTTGGGCTATATGGACTTGT	57.204	40.909	0.00	0.00	0.00	3.16
1162	1166	4.584638	TGTTGGGCTATATGGACTTGTT	57.415	40.909	0.00	0.00	0.00	2.83
1269	1274	2.175202	GGGATGATGACTAGAGCGGAT	58.825	52.381	0.00	0.00	0.00	4.18
1306	1311	4.723789	AGAGAGGATCCAAAATGCTAAGGA	59.276	41.667	15.82	0.00	33.66	3.36
1385	1395	1.332195	AGGAGGGAAACTTTGCTTGC	58.668	50.000	0.00	0.00	0.00	4.01
1450	1460	8.144478	GGTCTTAGTATTTGATCATACTGCTCA	58.856	37.037	16.09	0.00	39.79	4.26
1504	1516	5.086621	AGCCCTTTTGATGTCATAAACCTT	58.913	37.500	0.00	0.00	0.00	3.50
1518	1530	1.792757	AACCTTGCTGGATGCTCCCA	61.793	55.000	3.40	0.00	43.37	4.37
1597	1611	0.389948	GACGAGTGCTTGTAGTGGGG	60.390	60.000	0.00	0.00	0.00	4.96
1747	1762	7.765695	AGCTTCATAAAATTTGACTTGAGGA	57.234	32.000	0.00	0.00	0.00	3.71
1748	1763	7.824672	AGCTTCATAAAATTTGACTTGAGGAG	58.175	34.615	0.00	0.00	0.00	3.69
1749	1764	7.449704	AGCTTCATAAAATTTGACTTGAGGAGT	59.550	33.333	0.00	0.00	42.70	3.85
1750	1765	8.730680	GCTTCATAAAATTTGACTTGAGGAGTA	58.269	33.333	0.00	0.00	39.19	2.59
1759	1774	9.883142	AATTTGACTTGAGGAGTAAGATAAGAG	57.117	33.333	0.00	0.00	39.19	2.85
1760	1775	6.458232	TGACTTGAGGAGTAAGATAAGAGC	57.542	41.667	0.00	0.00	39.19	4.09
1761	1776	5.952347	TGACTTGAGGAGTAAGATAAGAGCA	59.048	40.000	0.00	0.00	39.19	4.26
1762	1777	6.127591	TGACTTGAGGAGTAAGATAAGAGCAC	60.128	42.308	0.00	0.00	39.19	4.40
1763	1778	5.717178	ACTTGAGGAGTAAGATAAGAGCACA	59.283	40.000	0.00	0.00	36.65	4.57
1764	1779	6.382570	ACTTGAGGAGTAAGATAAGAGCACAT	59.617	38.462	0.00	0.00	36.65	3.21
1765	1780	7.561722	ACTTGAGGAGTAAGATAAGAGCACATA	59.438	37.037	0.00	0.00	36.65	2.29
1766	1781	8.484214	TTGAGGAGTAAGATAAGAGCACATAT	57.516	34.615	0.00	0.00	0.00	1.78
1767	1782	7.890515	TGAGGAGTAAGATAAGAGCACATATG	58.109	38.462	0.00	0.00	0.00	1.78
1768	1783	7.725844	TGAGGAGTAAGATAAGAGCACATATGA	59.274	37.037	10.38	0.00	0.00	2.15
1769	1784	7.891561	AGGAGTAAGATAAGAGCACATATGAC	58.108	38.462	10.38	0.79	0.00	3.06
1770	1785	7.039363	AGGAGTAAGATAAGAGCACATATGACC	60.039	40.741	10.38	0.00	0.00	4.02
1771	1786	6.998802	AGTAAGATAAGAGCACATATGACCC	58.001	40.000	10.38	0.00	0.00	4.46
1772	1787	6.784969	AGTAAGATAAGAGCACATATGACCCT	59.215	38.462	10.38	2.01	0.00	4.34
1773	1788	5.736951	AGATAAGAGCACATATGACCCTC	57.263	43.478	10.38	11.07	0.00	4.30
1846	1869	4.084147	CCCCCGTCCCCTACCTCA	62.084	72.222	0.00	0.00	0.00	3.86
1934	1957	4.671590	TCGTCTGGGCGGACCTCA	62.672	66.667	0.00	0.00	41.11	3.86
1985	2008	4.380781	TCGTTTGCCGGGATCGCA	62.381	61.111	14.18	0.00	37.11	5.10
2011	2034	2.528127	TCCCAAAGCTCCGGTCCA	60.528	61.111	0.00	0.00	0.00	4.02
2124	2151	4.444838	CGTCGTTGCCGATGGGGA	62.445	66.667	0.00	0.00	46.30	4.81
2300	2331	4.420143	CGCATCGGAGATTTCGGT	57.580	55.556	0.00	0.00	45.12	4.69
2365	2397	4.443266	GCGTCGCTGCTTCCCTCT	62.443	66.667	10.68	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.295423	GCAGGCTACGAAGGGTCAA	59.705	57.895	0.00	0.00	0.00	3.18
1	2	1.264749	ATGCAGGCTACGAAGGGTCA	61.265	55.000	0.00	0.00	0.00	4.02
86	87	3.338110	AGAAGGATAAGTCTCCCTCCC	57.662	52.381	0.00	0.00	35.79	4.30
210	211	2.154462	CTTGCGACCCTCATGTTCTTT	58.846	47.619	0.00	0.00	0.00	2.52
359	360	1.152777	CACCTCTTGCCACAACCCA	60.153	57.895	0.00	0.00	0.00	4.51
363	364	0.321564	CGGATCACCTCTTGCCACAA	60.322	55.000	0.00	0.00	0.00	3.33
406	407	4.203226	TGTGCTTTTGACTGATGTTACCA	58.797	39.130	0.00	0.00	0.00	3.25
416	417	5.239525	GGAGTCACTAAATGTGCTTTTGACT	59.760	40.000	1.08	1.08	43.08	3.41
427	428	6.001449	TCCAAATAGGGGAGTCACTAAATG	57.999	41.667	0.00	0.00	38.24	2.32
495	496	4.277476	AGATTGCCCGAATTCATAACCAA	58.723	39.130	6.22	1.92	0.00	3.67
612	613	6.239572	CCCACACCATTTCTAAACTTTTCCAT	60.240	38.462	0.00	0.00	0.00	3.41
669	670	5.351948	TCATTCCATTGATCTAACGGTGA	57.648	39.130	0.00	0.00	0.00	4.02
673	674	5.998454	AAGCTCATTCCATTGATCTAACG	57.002	39.130	0.00	0.00	0.00	3.18
785	787	8.367660	TGTTTCTCTCCAGATAGTCATAAACT	57.632	34.615	0.00	0.00	42.33	2.66
817	819	6.668645	TGCCAAATCCACCTATAGTTACATT	58.331	36.000	0.00	0.00	0.00	2.71
1014	1018	2.073716	ACAACCCACCGTCCTCCAA	61.074	57.895	0.00	0.00	0.00	3.53
1122	1126	5.327091	CAACATATGACTGCTAGCACAAAC	58.673	41.667	14.93	6.07	0.00	2.93
1136	1140	6.044287	ACAAGTCCATATAGCCCAACATATGA	59.956	38.462	10.38	0.00	37.32	2.15
1157	1161	1.956477	AGGTAGCTTGGTTGCAACAAG	59.044	47.619	29.55	26.81	46.15	3.16
1161	1165	2.622942	CTCAAAGGTAGCTTGGTTGCAA	59.377	45.455	8.16	0.00	34.99	4.08
1162	1166	2.229792	CTCAAAGGTAGCTTGGTTGCA	58.770	47.619	8.16	0.00	34.99	4.08
1269	1274	0.106469	CTCTCTCCATCACCTCCCGA	60.106	60.000	0.00	0.00	0.00	5.14
1306	1311	1.466856	ATCATGTTTGATGCGCTGGT	58.533	45.000	9.73	0.00	41.12	4.00
1350	1355	1.377725	CCTTCAGTCCTGCGCCATT	60.378	57.895	4.18	0.00	0.00	3.16
1385	1395	3.454375	ACGAAGTTAATATGACCCAGCG	58.546	45.455	0.00	0.00	37.78	5.18
1518	1530	5.221783	ACCCAAACACGAACTAGTCCTAAAT	60.222	40.000	0.00	0.00	0.00	1.40
1723	1738	7.449704	ACTCCTCAAGTCAAATTTTATGAAGCT	59.550	33.333	0.00	0.00	30.02	3.74
1735	1750	7.039011	TGCTCTTATCTTACTCCTCAAGTCAAA	60.039	37.037	0.00	0.00	39.55	2.69
1738	1753	6.127591	TGTGCTCTTATCTTACTCCTCAAGTC	60.128	42.308	0.00	0.00	39.55	3.01
1739	1754	5.717178	TGTGCTCTTATCTTACTCCTCAAGT	59.283	40.000	0.00	0.00	42.33	3.16
1740	1755	6.214191	TGTGCTCTTATCTTACTCCTCAAG	57.786	41.667	0.00	0.00	0.00	3.02
1741	1756	6.798427	ATGTGCTCTTATCTTACTCCTCAA	57.202	37.500	0.00	0.00	0.00	3.02
1742	1757	7.725844	TCATATGTGCTCTTATCTTACTCCTCA	59.274	37.037	1.90	0.00	0.00	3.86
1743	1758	8.026607	GTCATATGTGCTCTTATCTTACTCCTC	58.973	40.741	1.90	0.00	0.00	3.71
1744	1759	7.039363	GGTCATATGTGCTCTTATCTTACTCCT	60.039	40.741	1.90	0.00	0.00	3.69
1745	1760	7.093992	GGTCATATGTGCTCTTATCTTACTCC	58.906	42.308	1.90	0.00	0.00	3.85
1746	1761	7.039363	AGGGTCATATGTGCTCTTATCTTACTC	60.039	40.741	1.90	0.00	0.00	2.59
1747	1762	6.784969	AGGGTCATATGTGCTCTTATCTTACT	59.215	38.462	1.90	0.00	0.00	2.24
1748	1763	6.998802	AGGGTCATATGTGCTCTTATCTTAC	58.001	40.000	1.90	0.00	0.00	2.34
1749	1764	6.782494	TGAGGGTCATATGTGCTCTTATCTTA	59.218	38.462	1.90	0.00	0.00	2.10
1750	1765	5.604231	TGAGGGTCATATGTGCTCTTATCTT	59.396	40.000	1.90	0.00	0.00	2.40
1751	1766	5.150715	TGAGGGTCATATGTGCTCTTATCT	58.849	41.667	1.90	0.00	0.00	1.98
1752	1767	5.474578	TGAGGGTCATATGTGCTCTTATC	57.525	43.478	1.90	0.00	0.00	1.75
1753	1768	5.280368	CCATGAGGGTCATATGTGCTCTTAT	60.280	44.000	1.90	2.54	34.28	1.73
1754	1769	4.040829	CCATGAGGGTCATATGTGCTCTTA	59.959	45.833	1.90	0.22	34.28	2.10
1755	1770	3.181447	CCATGAGGGTCATATGTGCTCTT	60.181	47.826	1.90	0.00	34.28	2.85
1756	1771	2.371179	CCATGAGGGTCATATGTGCTCT	59.629	50.000	1.90	2.45	34.28	4.09
1757	1772	2.369860	TCCATGAGGGTCATATGTGCTC	59.630	50.000	1.90	0.00	34.28	4.26
1758	1773	2.371179	CTCCATGAGGGTCATATGTGCT	59.629	50.000	1.90	0.00	34.28	4.40
1759	1774	2.369860	TCTCCATGAGGGTCATATGTGC	59.630	50.000	1.90	0.00	34.28	4.57
1760	1775	3.553715	CGTCTCCATGAGGGTCATATGTG	60.554	52.174	1.90	0.00	34.28	3.21
1761	1776	2.630098	CGTCTCCATGAGGGTCATATGT	59.370	50.000	1.90	0.00	34.28	2.29
1762	1777	2.611473	GCGTCTCCATGAGGGTCATATG	60.611	54.545	0.00	0.00	34.28	1.78
1763	1778	1.620819	GCGTCTCCATGAGGGTCATAT	59.379	52.381	0.00	0.00	34.28	1.78
1764	1779	1.040646	GCGTCTCCATGAGGGTCATA	58.959	55.000	0.00	0.00	34.28	2.15
1765	1780	1.690219	GGCGTCTCCATGAGGGTCAT	61.690	60.000	0.00	0.00	37.65	3.06
1766	1781	2.359169	GGCGTCTCCATGAGGGTCA	61.359	63.158	0.00	0.00	38.11	4.02
1767	1782	2.501610	GGCGTCTCCATGAGGGTC	59.498	66.667	0.00	0.00	38.11	4.46
1768	1783	3.083997	GGGCGTCTCCATGAGGGT	61.084	66.667	0.00	0.00	38.11	4.34
1769	1784	4.227134	CGGGCGTCTCCATGAGGG	62.227	72.222	0.00	0.00	36.21	4.30
1770	1785	2.076622	CTACGGGCGTCTCCATGAGG	62.077	65.000	0.00	0.00	36.21	3.86
1771	1786	1.360551	CTACGGGCGTCTCCATGAG	59.639	63.158	0.00	0.00	36.21	2.90
1772	1787	2.125326	CCTACGGGCGTCTCCATGA	61.125	63.158	0.00	0.00	36.21	3.07
1773	1788	2.417516	CCTACGGGCGTCTCCATG	59.582	66.667	0.00	0.00	36.21	3.66
1989	2012	4.115199	CGGAGCTTTGGGAGGGGG	62.115	72.222	0.00	0.00	0.00	5.40
1990	2013	4.115199	CCGGAGCTTTGGGAGGGG	62.115	72.222	0.00	0.00	0.00	4.79
2216	2246	2.959484	CGGGCTTCCAGGAAGAGCA	61.959	63.158	30.67	0.00	41.71	4.26
2286	2317	0.384669	GGACGACCGAAATCTCCGAT	59.615	55.000	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.