AutoCloner

Multiple sequence alignment - TraesCS2B01G060600

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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	TraesCS2B01G060600	chr2B	100.000	2255	0	0	1	2255	29055527	29057781	0.000000e+00	4165.0
1	TraesCS2B01G060600	chr2B	89.308	1777	165	13	482	2254	28998157	28999912	0.000000e+00	2206.0
2	TraesCS2B01G060600	chr2B	87.784	1629	146	21	1	1606	29980105	29978507	0.000000e+00	1857.0
3	TraesCS2B01G060600	chr2B	84.232	983	99	32	104	1073	29871437	29870498	0.000000e+00	905.0
4	TraesCS2B01G060600	chr2B	82.398	659	102	6	1608	2254	496603132	496603788	1.510000e-156	562.0
5	TraesCS2B01G060600	chr2B	82.114	615	78	16	1604	2188	773994849	773994237	4.330000e-137	497.0
6	TraesCS2B01G060600	chr2A	94.034	1609	76	13	1	1607	18614438	18616028	0.000000e+00	2422.0
7	TraesCS2B01G060600	chr2A	87.752	1788	170	28	1	1777	18647106	18648855	0.000000e+00	2043.0
8	TraesCS2B01G060600	chr2A	88.023	1411	142	15	104	1503	18676053	18677447	0.000000e+00	1644.0
9	TraesCS2B01G060600	chr2D	86.097	1532	142	37	104	1607	17238183	17239671	0.000000e+00	1583.0
10	TraesCS2B01G060600	chr2D	89.400	934	72	16	687	1607	17184009	17184928	0.000000e+00	1151.0
11	TraesCS2B01G060600	chr2D	89.261	866	72	7	753	1606	17336732	17337588	0.000000e+00	1064.0
12	TraesCS2B01G060600	chr2D	89.550	555	45	4	1064	1606	17347191	17347744	0.000000e+00	691.0
13	TraesCS2B01G060600	chr2D	89.550	555	45	4	1064	1606	17356409	17356962	0.000000e+00	691.0
14	TraesCS2B01G060600	chr2D	84.969	652	78	13	1	641	17182995	17183637	0.000000e+00	643.0
15	TraesCS2B01G060600	chr2D	82.586	758	99	18	1	748	17327327	17328061	2.440000e-179	638.0
16	TraesCS2B01G060600	chr2D	80.389	668	89	24	1604	2248	453610620	453611268	9.430000e-129	470.0
17	TraesCS2B01G060600	chr2D	77.361	667	102	25	1606	2255	201280836	201280202	1.280000e-92	350.0
18	TraesCS2B01G060600	chr2D	79.948	384	63	7	1881	2251	95657222	95657604	1.030000e-68	270.0
19	TraesCS2B01G060600	chr2D	79.167	264	47	4	1603	1858	164138786	164138523	2.300000e-40	176.0
20	TraesCS2B01G060600	chr2D	100.000	28	0	0	1598	1625	617399341	617399368	4.000000e-03	52.8
21	TraesCS2B01G060600	chr7D	80.267	674	112	13	1596	2254	104586430	104587097	2.600000e-134	488.0
22	TraesCS2B01G060600	chr6B	80.176	681	103	14	1603	2254	50502208	50502885	4.360000e-132	481.0
23	TraesCS2B01G060600	chr1B	79.370	698	94	20	1606	2254	434337176	434337872	1.590000e-121	446.0
24	TraesCS2B01G060600	chr1B	79.084	655	90	17	1632	2255	666831417	666830779	7.500000e-110	407.0
25	TraesCS2B01G060600	chr6D	81.937	537	67	19	1738	2254	119970459	119969933	5.760000e-116	427.0
26	TraesCS2B01G060600	chr1D	80.096	628	82	20	1602	2215	479390074	479389476	5.760000e-116	427.0
27	TraesCS2B01G060600	chr1D	79.851	268	43	6	1998	2254	42888198	42887931	3.820000e-43	185.0
28	TraesCS2B01G060600	chr7B	78.261	667	113	14	1599	2252	679539513	679540160	1.250000e-107	399.0
29	TraesCS2B01G060600	chr7B	100.000	28	0	0	1604	1631	228799229	228799202	4.000000e-03	52.8
30	TraesCS2B01G060600	chr6A	84.545	330	41	2	1888	2207	548116464	548116793	3.610000e-83	318.0
31	TraesCS2B01G060600	chr6A	78.780	410	71	6	1857	2254	150962528	150962933	6.180000e-66	261.0
32	TraesCS2B01G060600	chr7A	81.685	273	38	9	1604	1866	165945063	165945333	1.360000e-52	217.0
33	TraesCS2B01G060600	chr3B	90.196	102	5	3	1765	1861	741573991	741574092	6.540000e-26	128.0

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	TraesCS2B01G060600	chr2B	29055527	29057781	2254	False	4165	4165	100.0000	1	2255	1	chr2B.!!$F2	2254
1	TraesCS2B01G060600	chr2B	28998157	28999912	1755	False	2206	2206	89.3080	482	2254	1	chr2B.!!$F1	1772
2	TraesCS2B01G060600	chr2B	29978507	29980105	1598	True	1857	1857	87.7840	1	1606	1	chr2B.!!$R2	1605
3	TraesCS2B01G060600	chr2B	29870498	29871437	939	True	905	905	84.2320	104	1073	1	chr2B.!!$R1	969
4	TraesCS2B01G060600	chr2B	496603132	496603788	656	False	562	562	82.3980	1608	2254	1	chr2B.!!$F3	646
5	TraesCS2B01G060600	chr2B	773994237	773994849	612	True	497	497	82.1140	1604	2188	1	chr2B.!!$R3	584
6	TraesCS2B01G060600	chr2A	18614438	18616028	1590	False	2422	2422	94.0340	1	1607	1	chr2A.!!$F1	1606
7	TraesCS2B01G060600	chr2A	18647106	18648855	1749	False	2043	2043	87.7520	1	1777	1	chr2A.!!$F2	1776
8	TraesCS2B01G060600	chr2A	18676053	18677447	1394	False	1644	1644	88.0230	104	1503	1	chr2A.!!$F3	1399
9	TraesCS2B01G060600	chr2D	17238183	17239671	1488	False	1583	1583	86.0970	104	1607	1	chr2D.!!$F1	1503
10	TraesCS2B01G060600	chr2D	17336732	17337588	856	False	1064	1064	89.2610	753	1606	1	chr2D.!!$F3	853
11	TraesCS2B01G060600	chr2D	17182995	17184928	1933	False	897	1151	87.1845	1	1607	2	chr2D.!!$F9	1606
12	TraesCS2B01G060600	chr2D	17347191	17347744	553	False	691	691	89.5500	1064	1606	1	chr2D.!!$F4	542
13	TraesCS2B01G060600	chr2D	17356409	17356962	553	False	691	691	89.5500	1064	1606	1	chr2D.!!$F5	542
14	TraesCS2B01G060600	chr2D	17327327	17328061	734	False	638	638	82.5860	1	748	1	chr2D.!!$F2	747
15	TraesCS2B01G060600	chr2D	453610620	453611268	648	False	470	470	80.3890	1604	2248	1	chr2D.!!$F7	644
16	TraesCS2B01G060600	chr2D	201280202	201280836	634	True	350	350	77.3610	1606	2255	1	chr2D.!!$R2	649
17	TraesCS2B01G060600	chr7D	104586430	104587097	667	False	488	488	80.2670	1596	2254	1	chr7D.!!$F1	658
18	TraesCS2B01G060600	chr6B	50502208	50502885	677	False	481	481	80.1760	1603	2254	1	chr6B.!!$F1	651
19	TraesCS2B01G060600	chr1B	434337176	434337872	696	False	446	446	79.3700	1606	2254	1	chr1B.!!$F1	648
20	TraesCS2B01G060600	chr1B	666830779	666831417	638	True	407	407	79.0840	1632	2255	1	chr1B.!!$R1	623
21	TraesCS2B01G060600	chr6D	119969933	119970459	526	True	427	427	81.9370	1738	2254	1	chr6D.!!$R1	516
22	TraesCS2B01G060600	chr1D	479389476	479390074	598	True	427	427	80.0960	1602	2215	1	chr1D.!!$R2	613
23	TraesCS2B01G060600	chr7B	679539513	679540160	647	False	399	399	78.2610	1599	2252	1	chr7B.!!$F1	653

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
726	1087	1.275856	CCACCATTTCCCCACACAATG	59.724	52.381	0.0	0.0	0.0	2.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2105	2636	0.673333	CGAACCAGTACCTGCATGCA	60.673	55.0	21.29	21.29	0.0	3.96	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
44	45	3.864583	TGAAAGTTTCATGTTGTTGCTGC	59.135	39.130	14.35	0.00	34.08	5.25
65	68	3.917985	GCGCGGAACAAAAATATTGACTT	59.082	39.130	8.83	0.00	0.00	3.01
250	265	7.293073	ACCAAGATATGCAGATGGTAATCTTT	58.707	34.615	3.28	0.00	41.43	2.52
251	266	8.439971	ACCAAGATATGCAGATGGTAATCTTTA	58.560	33.333	3.28	0.00	41.43	1.85
294	309	5.613358	AGCTAAAACTGTGTACTGAATGC	57.387	39.130	0.00	0.00	0.00	3.56
296	311	4.215399	GCTAAAACTGTGTACTGAATGCCA	59.785	41.667	0.00	0.00	0.00	4.92
346	362	3.930336	TGTGGCACTCTTTCATGTAGAG	58.070	45.455	19.83	19.35	43.78	2.43
406	424	6.714278	ACTTCGTGTAGGTACCCATATTTTT	58.286	36.000	8.74	0.00	0.00	1.94
508	532	4.080356	TGGAGAAACCTAATCCACCATCTG	60.080	45.833	0.00	0.00	38.19	2.90
685	1037	6.770785	TGTTTACCTTAGCTTTGAAGTCATGT	59.229	34.615	0.00	0.00	0.00	3.21
726	1087	1.275856	CCACCATTTCCCCACACAATG	59.724	52.381	0.00	0.00	0.00	2.82
786	1147	9.248291	GTAGATTGTCAAATGTGAACAAACAAT	57.752	29.630	12.61	12.61	34.87	2.71
797	1159	4.032786	GTGAACAAACAATGAGGCAAACAC	59.967	41.667	0.00	0.00	0.00	3.32
852	1214	8.799091	CACATCACACTAAGTTTATTCTCTACG	58.201	37.037	0.00	0.00	0.00	3.51
881	1243	7.876068	AGAGAATTGTACGAAACCATTCAGTTA	59.124	33.333	16.00	0.00	40.87	2.24
887	1249	6.487331	TGTACGAAACCATTCAGTTAAACCAT	59.513	34.615	0.00	0.00	35.15	3.55
963	1325	8.325787	TCTTCCTGCAGTTATCCTAATTAACAA	58.674	33.333	13.81	0.00	0.00	2.83
1134	1496	1.079543	GCGCAGTCTGATGTCTGGT	60.080	57.895	0.30	0.00	31.60	4.00
1296	1663	7.684317	TGAGTATGGAATGAATACCCTAACA	57.316	36.000	0.00	0.00	31.98	2.41
1350	1717	6.091849	GTCATGTGGCATGAGATATGTATCAC	59.908	42.308	11.54	0.00	35.17	3.06
1456	1841	3.134985	TGCTACTGGTGTACTGGTTGAAA	59.865	43.478	0.00	0.00	0.00	2.69
1457	1842	3.497262	GCTACTGGTGTACTGGTTGAAAC	59.503	47.826	0.00	0.00	0.00	2.78
1477	1863	5.502153	AACTACGGACTCTCATATGTGTC	57.498	43.478	1.90	9.54	0.00	3.67
1655	2056	2.085532	CGATCCGCAAAATAACCGTG	57.914	50.000	0.00	0.00	0.00	4.94
1722	2124	0.664166	TGCGTCCGACCGTAAAAGTC	60.664	55.000	0.00	0.00	0.00	3.01
1729	2131	1.523934	CGACCGTAAAAGTCTTTGCGT	59.476	47.619	16.33	8.48	45.69	5.24
1756	2158	1.680735	GCATAATTCGCATCCCAACCA	59.319	47.619	0.00	0.00	0.00	3.67
1807	2211	0.391263	GGTGCCCTGTATATAGCGGC	60.391	60.000	16.81	16.81	40.16	6.53
1878	2340	4.974438	ACTCTCCCCAACGCCCCA	62.974	66.667	0.00	0.00	0.00	4.96
1964	2469	4.479993	CCCGAGCTTGCCCTCAGG	62.480	72.222	0.00	0.00	0.00	3.86
2024	2530	3.335534	GGCTGTTCGTCGCGTTGT	61.336	61.111	5.77	0.00	0.00	3.32
2105	2636	1.074248	CCGGTAAAGCCCCAACACT	59.926	57.895	0.00	0.00	0.00	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	5.401079	ACAAAGTCAATATTTTTGTTCCGCG	59.599	36.000	9.83	0.00	40.93	6.46
250	265	8.792830	AGCTAGTCATTTGCAAACTAAGAATA	57.207	30.769	15.41	12.14	0.00	1.75
251	266	7.693969	AGCTAGTCATTTGCAAACTAAGAAT	57.306	32.000	15.41	11.67	0.00	2.40
264	279	8.148351	TCAGTACACAGTTTTAGCTAGTCATTT	58.852	33.333	0.00	0.00	0.00	2.32
508	532	8.634475	AATTTTCAGCTGTCTTGTCTTAAAAC	57.366	30.769	14.67	0.00	0.00	2.43
726	1087	2.532843	TGGGTACTCCACTAACTGGAC	58.467	52.381	0.00	0.00	44.99	4.02
743	1104	8.021898	ACAATCTACCATGGAAATTAAATGGG	57.978	34.615	21.47	4.62	44.34	4.00
749	1110	9.253832	ACATTTGACAATCTACCATGGAAATTA	57.746	29.630	21.47	0.00	0.00	1.40
750	1111	8.036575	CACATTTGACAATCTACCATGGAAATT	58.963	33.333	21.47	11.61	0.00	1.82
751	1112	7.396907	TCACATTTGACAATCTACCATGGAAAT	59.603	33.333	21.47	7.58	0.00	2.17
786	1147	1.962807	CAAGAATGGGTGTTTGCCTCA	59.037	47.619	0.00	0.00	0.00	3.86
797	1159	2.447047	ACTTATAGGGGGCAAGAATGGG	59.553	50.000	0.00	0.00	0.00	4.00
852	1214	6.590292	TGAATGGTTTCGTACAATTCTCTCTC	59.410	38.462	16.17	0.00	44.41	3.20
881	1243	9.643693	CTTACATAATTCTGCTCAAAATGGTTT	57.356	29.630	0.00	0.00	0.00	3.27
920	1282	4.154918	AGGAAGACAATGCACTTCGAAATC	59.845	41.667	0.00	0.00	42.06	2.17
1134	1496	0.539986	GCCCGTTCCTTCCATCAGTA	59.460	55.000	0.00	0.00	0.00	2.74
1295	1662	9.646336	GTACGTGGAAGTAAAAGCAATATAATG	57.354	33.333	0.00	0.00	0.00	1.90
1296	1663	9.386010	TGTACGTGGAAGTAAAAGCAATATAAT	57.614	29.630	0.00	0.00	0.00	1.28
1350	1717	0.506932	ACGCAGAAACATTGACGACG	59.493	50.000	0.00	0.00	0.00	5.12
1456	1841	4.576873	CAGACACATATGAGAGTCCGTAGT	59.423	45.833	10.38	0.00	0.00	2.73
1457	1842	4.816925	TCAGACACATATGAGAGTCCGTAG	59.183	45.833	10.38	5.56	0.00	3.51
1624	2022	0.942410	GCGGATCGCGGCTTTATACA	60.942	55.000	6.13	0.00	44.55	2.29
1655	2056	2.032185	CTGCGCCGACCCGTATTTTC	62.032	60.000	4.18	0.00	0.00	2.29
1729	2131	3.947841	GCGAATTATGCCGCGCCA	61.948	61.111	0.00	0.00	43.33	5.69
1821	2252	2.745884	CGCGGGCTGAAATGTCCA	60.746	61.111	0.00	0.00	0.00	4.02
1861	2304	4.974438	TGGGGCGTTGGGGAGAGT	62.974	66.667	0.00	0.00	0.00	3.24
1964	2469	1.817099	CCGATGCAGGAGGAAGTGC	60.817	63.158	0.00	0.00	40.29	4.40
1987	2492	2.998667	CGATCTGCTCGTTTCCGC	59.001	61.111	0.00	0.00	42.56	5.54
2005	2510	4.936823	AACGCGACGAACAGCCGT	62.937	61.111	15.93	0.00	46.43	5.68
2021	2526	1.611491	GGAAACGCCAAATCCAGACAA	59.389	47.619	0.00	0.00	36.34	3.18
2052	2563	2.678934	CCATGGCTTGGCACAGCT	60.679	61.111	17.11	0.00	42.39	4.24
2057	2568	2.036098	CCAGTCCATGGCTTGGCA	59.964	61.111	17.96	0.00	46.01	4.92
2091	2622	1.255882	CATGCAGTGTTGGGGCTTTA	58.744	50.000	0.00	0.00	0.00	1.85
2105	2636	0.673333	CGAACCAGTACCTGCATGCA	60.673	55.000	21.29	21.29	0.00	3.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.