AutoCloner

Multiple sequence alignment - TraesCS3A01G481100

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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	TraesCS3A01G481100	chr3A	100.000	2185	0	0	1	2185	712308948	712311132	0.000000e+00	4036.0
1	TraesCS3A01G481100	chr3A	96.347	219	8	0	1230	1448	412693765	412693547	5.730000e-96	361.0
2	TraesCS3A01G481100	chr3A	95.000	220	11	0	1229	1448	684741811	684741592	1.610000e-91	346.0
3	TraesCS3A01G481100	chr3A	85.156	128	19	0	1633	1760	714629034	714629161	4.890000e-27	132.0
4	TraesCS3A01G481100	chr3A	87.129	101	9	3	1985	2082	727378211	727378310	6.380000e-21	111.0
5	TraesCS3A01G481100	chr3D	88.121	1187	96	21	57	1231	577153033	577151880	0.000000e+00	1369.0
6	TraesCS3A01G481100	chr3D	94.149	188	10	1	1447	1633	577151879	577151692	3.550000e-73	285.0
7	TraesCS3A01G481100	chr3B	89.861	1006	85	14	57	1052	766832586	766831588	0.000000e+00	1277.0
8	TraesCS3A01G481100	chr3B	86.719	768	65	22	57	810	768513251	768513995	0.000000e+00	819.0
9	TraesCS3A01G481100	chr3B	90.355	197	9	6	1447	1633	766831450	766831254	1.300000e-62	250.0
10	TraesCS3A01G481100	chr5D	91.971	274	15	4	922	1188	512411144	512411417	5.690000e-101	377.0
11	TraesCS3A01G481100	chr5D	91.971	274	15	4	922	1188	512418081	512418354	5.690000e-101	377.0
12	TraesCS3A01G481100	chr5D	91.941	273	15	4	922	1187	503292829	503293101	2.050000e-100	375.0
13	TraesCS3A01G481100	chr5D	91.513	271	15	5	925	1188	6175955	6175686	1.230000e-97	366.0
14	TraesCS3A01G481100	chr2D	91.971	274	15	4	922	1188	638425463	638425736	5.690000e-101	377.0
15	TraesCS3A01G481100	chr2D	78.109	201	31	10	323	513	640025656	640025853	4.930000e-22	115.0
16	TraesCS3A01G481100	chr1B	91.209	273	18	3	922	1188	633708651	633708923	1.230000e-97	366.0
17	TraesCS3A01G481100	chr1D	91.481	270	16	4	926	1188	254435995	254436264	4.430000e-97	364.0
18	TraesCS3A01G481100	chr1D	92.308	91	5	2	1985	2073	473673000	473673090	6.330000e-26	128.0
19	TraesCS3A01G481100	chr5A	90.647	278	19	4	917	1187	657452548	657452825	1.590000e-96	363.0
20	TraesCS3A01G481100	chr4A	94.783	230	12	0	1220	1449	572504790	572504561	2.060000e-95	359.0
21	TraesCS3A01G481100	chr4A	95.434	219	10	0	1230	1448	640236064	640235846	1.240000e-92	350.0
22	TraesCS3A01G481100	chr7A	95.516	223	8	1	1228	1448	50272272	50272050	2.670000e-94	355.0
23	TraesCS3A01G481100	chr7A	95.023	221	11	0	1229	1449	401405380	401405160	4.460000e-92	348.0
24	TraesCS3A01G481100	chr7A	94.196	224	12	1	1225	1448	641431636	641431414	7.470000e-90	340.0
25	TraesCS3A01G481100	chr6A	95.000	220	11	0	1229	1448	606612050	606611831	1.610000e-91	346.0
26	TraesCS3A01G481100	chr6A	84.138	145	22	1	1623	1766	586991194	586991050	2.920000e-29	139.0
27	TraesCS3A01G481100	chr6A	82.836	134	23	0	1633	1766	50190770	50190637	1.060000e-23	121.0
28	TraesCS3A01G481100	chr2A	94.570	221	12	0	1230	1450	417360448	417360228	2.080000e-90	342.0
29	TraesCS3A01G481100	chr2A	93.421	76	5	0	1985	2060	3261960	3261885	1.770000e-21	113.0
30	TraesCS3A01G481100	chr7B	96.059	203	7	1	1726	1928	60457608	60457407	1.620000e-86	329.0
31	TraesCS3A01G481100	chr7B	96.923	65	2	0	1960	2024	60457407	60457343	2.290000e-20	110.0
32	TraesCS3A01G481100	chr7B	93.548	62	4	0	2027	2088	60457318	60457257	2.310000e-15	93.5
33	TraesCS3A01G481100	chr7B	93.220	59	4	0	1632	1690	741954889	741954947	1.070000e-13	87.9
34	TraesCS3A01G481100	chr7B	93.220	59	4	0	1632	1690	741957905	741957963	1.070000e-13	87.9
35	TraesCS3A01G481100	chr7B	90.769	65	6	0	1632	1696	742899482	742899418	1.070000e-13	87.9
36	TraesCS3A01G481100	chr7B	90.769	65	6	0	1632	1696	742902756	742902692	1.070000e-13	87.9
37	TraesCS3A01G481100	chr4D	83.704	135	22	0	1632	1766	312585740	312585606	6.330000e-26	128.0
38	TraesCS3A01G481100	chr4D	92.308	65	5	0	1985	2049	469583074	469583010	2.310000e-15	93.5
39	TraesCS3A01G481100	chr7D	91.209	91	6	2	1985	2073	529483689	529483599	2.950000e-24	122.0
40	TraesCS3A01G481100	chr6B	90.000	90	7	2	1985	2072	7787	7876	4.930000e-22	115.0
41	TraesCS3A01G481100	chr5B	85.849	106	13	2	1985	2088	687395519	687395414	6.380000e-21	111.0
42	TraesCS3A01G481100	chrUn	93.220	59	4	0	1632	1690	344285179	344285237	1.070000e-13	87.9

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	TraesCS3A01G481100	chr3A	712308948	712311132	2184	False	4036.0	4036	100.000	1	2185	1	chr3A.!!$F1	2184
1	TraesCS3A01G481100	chr3D	577151692	577153033	1341	True	827.0	1369	91.135	57	1633	2	chr3D.!!$R1	1576
2	TraesCS3A01G481100	chr3B	768513251	768513995	744	False	819.0	819	86.719	57	810	1	chr3B.!!$F1	753
3	TraesCS3A01G481100	chr3B	766831254	766832586	1332	True	763.5	1277	90.108	57	1633	2	chr3B.!!$R1	1576

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
55	56	0.449388	GATTAGTGGTGTGCTGCTGC	59.551	55.0	8.89	8.89	40.2	5.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1261	1292	0.035439	ATTGACAACCTAGGGGCACG	60.035	55.0	14.81	0.0	35.63	5.34	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability
20	21	2.595750	TGTGATGTTGGGTTTAGGGG	57.404	50.000	4.79
21	22	1.076350	TGTGATGTTGGGTTTAGGGGG	59.924	52.381	5.40
22	23	1.076513	GTGATGTTGGGTTTAGGGGGT	59.923	52.381	4.95
23	24	1.356398	TGATGTTGGGTTTAGGGGGTC	59.644	52.381	4.46
24	25	1.639108	GATGTTGGGTTTAGGGGGTCT	59.361	52.381	3.85
25	26	1.536644	TGTTGGGTTTAGGGGGTCTT	58.463	50.000	3.01
26	27	1.860906	TGTTGGGTTTAGGGGGTCTTT	59.139	47.619	2.52
27	28	2.244695	GTTGGGTTTAGGGGGTCTTTG	58.755	52.381	2.77
28	29	1.835895	TGGGTTTAGGGGGTCTTTGA	58.164	50.000	2.69
29	30	2.364190	TGGGTTTAGGGGGTCTTTGAT	58.636	47.619	2.57
30	31	3.543661	TGGGTTTAGGGGGTCTTTGATA	58.456	45.455	2.15
31	32	4.123745	TGGGTTTAGGGGGTCTTTGATAT	58.876	43.478	1.63
32	33	4.079443	TGGGTTTAGGGGGTCTTTGATATG	60.079	45.833	1.78
33	34	3.889538	GGTTTAGGGGGTCTTTGATATGC	59.110	47.826	3.14
34	35	4.386424	GGTTTAGGGGGTCTTTGATATGCT	60.386	45.833	3.79
35	36	4.437682	TTAGGGGGTCTTTGATATGCTG	57.562	45.455	4.41
36	37	1.496429	AGGGGGTCTTTGATATGCTGG	59.504	52.381	4.85
37	38	1.494721	GGGGGTCTTTGATATGCTGGA	59.505	52.381	3.86
38	39	2.108952	GGGGGTCTTTGATATGCTGGAT	59.891	50.000	3.41
39	40	3.437052	GGGGGTCTTTGATATGCTGGATT	60.437	47.826	3.01
40	41	4.202567	GGGGGTCTTTGATATGCTGGATTA	60.203	45.833	1.75
41	42	5.006386	GGGGTCTTTGATATGCTGGATTAG	58.994	45.833	1.73
42	43	5.456763	GGGGTCTTTGATATGCTGGATTAGT	60.457	44.000	2.24
43	44	5.471456	GGGTCTTTGATATGCTGGATTAGTG	59.529	44.000	2.74
44	45	5.471456	GGTCTTTGATATGCTGGATTAGTGG	59.529	44.000	4.00

Showing 1 to 25 of 488 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability
0	1	2.292192	CCCCCTAAACCCAACATCACAT	60.292	50.000	3.21
1	2	1.076350	CCCCCTAAACCCAACATCACA	59.924	52.381	3.58
2	3	1.076513	ACCCCCTAAACCCAACATCAC	59.923	52.381	3.06
3	4	1.356398	GACCCCCTAAACCCAACATCA	59.644	52.381	3.07
4	5	1.639108	AGACCCCCTAAACCCAACATC	59.361	52.381	3.06
5	6	1.768265	AGACCCCCTAAACCCAACAT	58.232	50.000	2.71
6	7	1.536644	AAGACCCCCTAAACCCAACA	58.463	50.000	3.33
7	8	2.158430	TCAAAGACCCCCTAAACCCAAC	60.158	50.000	3.77
8	9	2.145298	TCAAAGACCCCCTAAACCCAA	58.855	47.619	4.12
9	10	1.835895	TCAAAGACCCCCTAAACCCA	58.164	50.000	4.51
10	11	4.470602	CATATCAAAGACCCCCTAAACCC	58.529	47.826	4.11
11	12	3.889538	GCATATCAAAGACCCCCTAAACC	59.110	47.826	3.27
12	13	4.580580	CAGCATATCAAAGACCCCCTAAAC	59.419	45.833	2.01
13	14	4.386312	CCAGCATATCAAAGACCCCCTAAA	60.386	45.833	1.85
14	15	3.138283	CCAGCATATCAAAGACCCCCTAA	59.862	47.826	2.69
15	16	2.711009	CCAGCATATCAAAGACCCCCTA	59.289	50.000	3.53
16	17	1.496429	CCAGCATATCAAAGACCCCCT	59.504	52.381	4.79
17	18	1.494721	TCCAGCATATCAAAGACCCCC	59.505	52.381	5.40
18	19	3.515602	ATCCAGCATATCAAAGACCCC	57.484	47.619	4.95
19	20	5.471456	CACTAATCCAGCATATCAAAGACCC	59.529	44.000	4.46
20	21	5.471456	CCACTAATCCAGCATATCAAAGACC	59.529	44.000	3.85
21	22	6.017605	CACCACTAATCCAGCATATCAAAGAC	60.018	42.308	3.01
22	23	6.057533	CACCACTAATCCAGCATATCAAAGA	58.942	40.000	2.52
23	24	5.824624	ACACCACTAATCCAGCATATCAAAG	59.175	40.000	2.77
24	25	5.589855	CACACCACTAATCCAGCATATCAAA	59.410	40.000	2.69

Showing 1 to 25 of 486 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.