AutoCloner

Multiple sequence alignment - TraesCS4A01G051300

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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	TraesCS4A01G051300	chr4A	100.000	5176	0	0	1	5176	42116752	42121927	0.000000e+00	9559.0
1	TraesCS4A01G051300	chr4A	86.538	156	21	0	2173	2328	321899378	321899533	6.890000e-39	172.0
2	TraesCS4A01G051300	chr4B	94.188	2013	108	6	2338	4346	518879204	518877197	0.000000e+00	3061.0
3	TraesCS4A01G051300	chr4B	93.966	812	33	6	732	1532	518880301	518879495	0.000000e+00	1214.0
4	TraesCS4A01G051300	chr4B	95.143	350	11	3	4311	4659	518877197	518876853	9.800000e-152	547.0
5	TraesCS4A01G051300	chr4B	88.204	373	28	7	1721	2077	564390429	564390801	1.030000e-116	431.0
6	TraesCS4A01G051300	chr4B	85.407	418	50	9	4712	5122	168565230	168565643	1.720000e-114	424.0
7	TraesCS4A01G051300	chr4B	81.412	425	53	20	4712	5124	99578188	99577778	1.800000e-84	324.0
8	TraesCS4A01G051300	chr4B	90.517	232	18	3	2104	2333	564390855	564391084	2.340000e-78	303.0
9	TraesCS4A01G051300	chr4B	94.737	190	9	1	1532	1720	518879397	518879208	1.410000e-75	294.0
10	TraesCS4A01G051300	chr4B	91.667	120	10	0	2112	2231	462737175	462737294	3.210000e-37	167.0
11	TraesCS4A01G051300	chr4B	92.000	50	4	0	5127	5176	518876834	518876785	2.590000e-08	71.3
12	TraesCS4A01G051300	chr4D	90.612	2237	156	31	2411	4635	421952460	421950266	0.000000e+00	2918.0
13	TraesCS4A01G051300	chr4D	87.006	1593	155	24	2527	4089	421925658	421924088	0.000000e+00	1748.0
14	TraesCS4A01G051300	chr4D	92.692	780	39	4	760	1524	421953545	421952769	0.000000e+00	1109.0
15	TraesCS4A01G051300	chr4D	92.453	583	32	6	4080	4659	421897875	421897302	0.000000e+00	822.0
16	TraesCS4A01G051300	chr4D	90.979	521	29	10	4671	5176	421897320	421896803	0.000000e+00	686.0
17	TraesCS4A01G051300	chr4D	93.085	188	11	1	1533	1720	421952687	421952502	1.840000e-69	274.0
18	TraesCS4A01G051300	chr4D	97.561	41	1	0	2338	2378	421952498	421952458	2.590000e-08	71.3
19	TraesCS4A01G051300	chr4D	100.000	31	0	0	732	762	421962615	421962585	2.010000e-04	58.4
20	TraesCS4A01G051300	chr7A	96.585	615	18	2	1721	2333	380031491	380032104	0.000000e+00	1016.0
21	TraesCS4A01G051300	chr7A	88.283	734	76	10	1	731	267890007	267890733	0.000000e+00	870.0
22	TraesCS4A01G051300	chr5D	90.822	730	57	10	1	727	409442713	409443435	0.000000e+00	968.0
23	TraesCS4A01G051300	chr5D	88.315	736	76	9	1	731	247566604	247565874	0.000000e+00	874.0
24	TraesCS4A01G051300	chr7B	89.698	728	63	11	1	725	94262019	94261301	0.000000e+00	918.0
25	TraesCS4A01G051300	chr3A	94.127	613	21	1	1721	2333	542926507	542925910	0.000000e+00	918.0
26	TraesCS4A01G051300	chr3A	89.062	64	7	0	1721	1784	589400711	589400774	4.300000e-11	80.5
27	TraesCS4A01G051300	chr6D	89.466	731	69	8	3	730	7153797	7154522	0.000000e+00	917.0
28	TraesCS4A01G051300	chr5B	89.148	728	73	6	1	726	655140842	655140119	0.000000e+00	902.0
29	TraesCS4A01G051300	chr5B	88.528	462	42	5	1881	2333	605630309	605629850	2.720000e-152	549.0
30	TraesCS4A01G051300	chr5B	79.469	414	73	11	4712	5116	61649897	61650307	3.050000e-72	283.0
31	TraesCS4A01G051300	chr3D	88.950	733	71	7	1	728	357731135	357731862	0.000000e+00	896.0
32	TraesCS4A01G051300	chr3D	84.670	424	49	12	4712	5126	570566281	570565865	4.820000e-110	409.0
33	TraesCS4A01G051300	chr5A	88.587	736	74	8	1	732	456611214	456610485	0.000000e+00	885.0
34	TraesCS4A01G051300	chr2A	88.602	737	70	12	1	731	674497112	674497840	0.000000e+00	883.0
35	TraesCS4A01G051300	chr2A	79.854	412	68	9	4711	5115	70662815	70662412	2.360000e-73	287.0
36	TraesCS4A01G051300	chr2B	88.204	373	28	7	1721	2077	382733953	382733581	1.030000e-116	431.0
37	TraesCS4A01G051300	chr2B	90.435	230	22	0	2104	2333	382733527	382733298	2.340000e-78	303.0
38	TraesCS4A01G051300	chr7D	84.382	429	49	12	4712	5124	45814823	45815249	6.240000e-109	405.0
39	TraesCS4A01G051300	chr6B	82.904	427	46	14	4711	5125	658193612	658194023	4.930000e-95	359.0
40	TraesCS4A01G051300	chr6B	88.312	231	25	2	2104	2333	533282263	533282034	5.110000e-70	276.0
41	TraesCS4A01G051300	chr6B	91.667	120	10	0	2112	2231	622014828	622014947	3.210000e-37	167.0
42	TraesCS4A01G051300	chr6B	91.379	116	10	0	2112	2227	621582347	621582232	5.360000e-35	159.0
43	TraesCS4A01G051300	chr1D	81.295	417	56	17	4709	5115	62690855	62690451	8.360000e-83	318.0
44	TraesCS4A01G051300	chr2D	86.538	156	21	0	2173	2328	81159689	81159534	6.890000e-39	172.0

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	TraesCS4A01G051300	chr4A	42116752	42121927	5175	False	9559.000	9559	100.0000	1	5176	1	chr4A.!!$F1	5175
1	TraesCS4A01G051300	chr4B	518876785	518880301	3516	True	1037.460	3061	94.0068	732	5176	5	chr4B.!!$R2	4444
2	TraesCS4A01G051300	chr4B	564390429	564391084	655	False	367.000	431	89.3605	1721	2333	2	chr4B.!!$F3	612
3	TraesCS4A01G051300	chr4D	421924088	421925658	1570	True	1748.000	1748	87.0060	2527	4089	1	chr4D.!!$R1	1562
4	TraesCS4A01G051300	chr4D	421950266	421953545	3279	True	1093.075	2918	93.4875	760	4635	4	chr4D.!!$R4	3875
5	TraesCS4A01G051300	chr4D	421896803	421897875	1072	True	754.000	822	91.7160	4080	5176	2	chr4D.!!$R3	1096
6	TraesCS4A01G051300	chr7A	380031491	380032104	613	False	1016.000	1016	96.5850	1721	2333	1	chr7A.!!$F2	612
7	TraesCS4A01G051300	chr7A	267890007	267890733	726	False	870.000	870	88.2830	1	731	1	chr7A.!!$F1	730
8	TraesCS4A01G051300	chr5D	409442713	409443435	722	False	968.000	968	90.8220	1	727	1	chr5D.!!$F1	726
9	TraesCS4A01G051300	chr5D	247565874	247566604	730	True	874.000	874	88.3150	1	731	1	chr5D.!!$R1	730
10	TraesCS4A01G051300	chr7B	94261301	94262019	718	True	918.000	918	89.6980	1	725	1	chr7B.!!$R1	724
11	TraesCS4A01G051300	chr3A	542925910	542926507	597	True	918.000	918	94.1270	1721	2333	1	chr3A.!!$R1	612
12	TraesCS4A01G051300	chr6D	7153797	7154522	725	False	917.000	917	89.4660	3	730	1	chr6D.!!$F1	727
13	TraesCS4A01G051300	chr5B	655140119	655140842	723	True	902.000	902	89.1480	1	726	1	chr5B.!!$R2	725
14	TraesCS4A01G051300	chr3D	357731135	357731862	727	False	896.000	896	88.9500	1	728	1	chr3D.!!$F1	727
15	TraesCS4A01G051300	chr5A	456610485	456611214	729	True	885.000	885	88.5870	1	732	1	chr5A.!!$R1	731
16	TraesCS4A01G051300	chr2A	674497112	674497840	728	False	883.000	883	88.6020	1	731	1	chr2A.!!$F1	730
17	TraesCS4A01G051300	chr2B	382733298	382733953	655	True	367.000	431	89.3195	1721	2333	2	chr2B.!!$R1	612

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	Hairpin	End Stability	Orientation
866	886	0.743345	CGTCTTCCCGCCCCTTAAAG	60.743	60.0	0.00	0.00	1.85	F
1350	1370	0.393402	GGGGTCGGGTTTACATGGTC	60.393	60.0	0.00	0.00	4.02	F
2903	3094	0.318869	TACTGGCAACACGTACACCG	60.319	55.0	0.00	46.17	4.94	F
3756	3975	0.108396	TCAGTTGTTGCTGCTGCCTA	59.892	50.0	13.47	38.71	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2709	2897	2.553602	CACACCAAGTAATTGCAGCTCA	59.446	45.455	0.00	0.00	0.00	4.26	R
2945	3138	1.829222	AGCATTCAAGCCCTGGAAATG	59.171	47.619	0.00	0.00	34.23	2.32	R
4096	4317	1.070758	ACACACCCTCAAGCTGTACAG	59.929	52.381	18.93	18.93	0.00	2.74	R
5081	5355	0.107643	GCTCCATGGAGGCCTCTAAC	59.892	60.000	36.92	17.91	42.19	2.34	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	Self any TH	Self end TH	Hairpin	End Stability
116	121	6.770076	GTGCAAACACTTTTTGAAGCATAAA	58.230	32.000	0.91	0.00	43.85	1.40
239	245	5.959527	CAGAATATACGTGACATGTGTTTGC	59.040	40.000	1.15	0.00	0.00	3.68
600	620	3.013921	GACCCAATTCAGCAAATACCGA	58.986	45.455	0.00	0.00	0.00	4.69
632	652	5.761205	TCCCAAGATTTAAAATGGATCGGA	58.239	37.500	15.75	5.59	34.82	4.55
648	668	7.762588	TGGATCGGAATTAAAAAGTTTGGTA	57.237	32.000	0.00	0.00	0.00	3.25
660	680	7.713764	AAAAAGTTTGGTATGCTGATTTCAC	57.286	32.000	0.00	0.00	0.00	3.18
666	686	6.993786	TTGGTATGCTGATTTCACGAATTA	57.006	33.333	0.00	0.00	0.00	1.40
674	694	6.650807	TGCTGATTTCACGAATTAAGAGTTCT	59.349	34.615	0.00	0.00	0.00	3.01
677	697	7.158697	TGATTTCACGAATTAAGAGTTCTGGA	58.841	34.615	0.00	0.00	0.00	3.86
693	713	6.071320	AGTTCTGGATTTGGTTTAGCTTTCT	58.929	36.000	0.00	0.00	0.00	2.52
700	720	9.920946	TGGATTTGGTTTAGCTTTCTTCTATAT	57.079	29.630	0.00	0.00	0.00	0.86
744	764	6.712998	ACTTTTTCCTTTAGCTTTCCTCTCTC	59.287	38.462	0.00	0.00	0.00	3.20
745	765	4.828072	TTCCTTTAGCTTTCCTCTCTCC	57.172	45.455	0.00	0.00	0.00	3.71
755	775	2.018086	CCTCTCTCCCTCTCCCCCT	61.018	68.421	0.00	0.00	0.00	4.79
756	776	1.541672	CTCTCTCCCTCTCCCCCTC	59.458	68.421	0.00	0.00	0.00	4.30
758	778	2.204624	TCTCCCTCTCCCCCTCCA	60.205	66.667	0.00	0.00	0.00	3.86
785	805	2.032030	CCAGCACGAAGAAACGAAATGT	60.032	45.455	0.00	0.00	37.03	2.71
787	807	4.386230	CAGCACGAAGAAACGAAATGTAG	58.614	43.478	0.00	0.00	37.03	2.74
815	835	2.604686	AGCGGCAACAGAGGAGGA	60.605	61.111	1.45	0.00	0.00	3.71
866	886	0.743345	CGTCTTCCCGCCCCTTAAAG	60.743	60.000	0.00	0.00	0.00	1.85
1029	1049	2.392181	CGACGAGGAGAGCGTGACT	61.392	63.158	0.00	0.00	42.77	3.41
1323	1343	0.966920	AGTTCGTTCTCCATGTCGGT	59.033	50.000	0.00	0.00	35.57	4.69
1350	1370	0.393402	GGGGTCGGGTTTACATGGTC	60.393	60.000	0.00	0.00	0.00	4.02
1370	1390	3.022914	GCGGTCGGATTAGTCGCG	61.023	66.667	0.00	0.00	37.12	5.87
1454	1485	3.701542	GAGTTTCTGGAATTTGGGGGATC	59.298	47.826	0.00	0.00	0.00	3.36

Showing 1 to 25 of 84 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
270	277	3.250040	ACACGAACACTCTTTTACATGGC	59.750	43.478	0.00	0.00	0.00	4.40
534	552	2.974536	GCACGCGCACTAATTTGTTTTA	59.025	40.909	5.73	0.00	38.36	1.52
600	620	4.903045	TTAAATCTTGGGAGGACTTCGT	57.097	40.909	0.00	0.00	0.00	3.85
639	659	4.759693	TCGTGAAATCAGCATACCAAACTT	59.240	37.500	0.00	0.00	0.00	2.66
648	668	6.992063	ACTCTTAATTCGTGAAATCAGCAT	57.008	33.333	0.00	0.00	0.00	3.79
660	680	6.743575	ACCAAATCCAGAACTCTTAATTCG	57.256	37.500	0.00	0.00	0.00	3.34
666	686	5.635120	AGCTAAACCAAATCCAGAACTCTT	58.365	37.500	0.00	0.00	0.00	2.85
674	694	9.920946	ATATAGAAGAAAGCTAAACCAAATCCA	57.079	29.630	0.00	0.00	0.00	3.41
700	720	9.157104	GAAAAAGTCCAAAACAAACCTTGAATA	57.843	29.630	0.00	0.00	0.00	1.75
744	764	0.039764	GTTTTTGGAGGGGGAGAGGG	59.960	60.000	0.00	0.00	0.00	4.30
745	765	0.039764	GGTTTTTGGAGGGGGAGAGG	59.960	60.000	0.00	0.00	0.00	3.69
755	775	1.028905	CTTCGTGCTGGGTTTTTGGA	58.971	50.000	0.00	0.00	0.00	3.53
756	776	1.028905	TCTTCGTGCTGGGTTTTTGG	58.971	50.000	0.00	0.00	0.00	3.28
758	778	2.478879	CGTTTCTTCGTGCTGGGTTTTT	60.479	45.455	0.00	0.00	0.00	1.94
981	1001	2.434359	CTCTTCCGGTTGCGGGTC	60.434	66.667	0.00	0.00	0.00	4.46
988	1008	0.252742	ACCTCCATCCTCTTCCGGTT	60.253	55.000	0.00	0.00	0.00	4.44
1113	1133	3.122250	CTCGTCGTCGATGTCCCCC	62.122	68.421	13.91	0.00	45.21	5.40
1317	1337	1.540797	CGACCCCTAACAAAACCGACA	60.541	52.381	0.00	0.00	0.00	4.35
1323	1343	2.752075	AAACCCGACCCCTAACAAAA	57.248	45.000	0.00	0.00	0.00	2.44
1350	1370	1.480219	GCGACTAATCCGACCGCAAG	61.480	60.000	0.00	0.00	44.55	4.01
1370	1390	1.823610	ACCTCGCCTTAACTACCAGAC	59.176	52.381	0.00	0.00	0.00	3.51
1454	1485	5.469373	AGATGTATGCACAACACAATACG	57.531	39.130	5.89	0.00	38.42	3.06
1468	1499	6.846350	TCACTGCAGTATATCGAGATGTATG	58.154	40.000	21.20	0.94	0.00	2.39
1529	1564	9.189723	CACAAGTAACTAAACAACTACTCCTAC	57.810	37.037	0.00	0.00	0.00	3.18
1640	1774	9.742144	TGTAACCTGCTTCTGGTTTATTAATAA	57.258	29.630	12.23	3.71	41.70	1.40

Showing 1 to 25 of 91 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.