AutoCloner

Multiple sequence alignment - TraesCS3A01G264400

Loading Multiple Alignment...

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	TraesCS3A01G264400	chr3A	100.000	2670	0	0	1	2670	488281784	488284453	0.000000e+00	4931.0
1	TraesCS3A01G264400	chr5A	93.589	2683	152	12	1	2670	37150460	37153135	0.000000e+00	3984.0
2	TraesCS3A01G264400	chr5A	84.225	355	46	8	2302	2653	431973851	431974198	1.180000e-88	337.0
3	TraesCS3A01G264400	chr5A	100.000	30	0	0	680	709	602960655	602960684	3.710000e-04	56.5
4	TraesCS3A01G264400	chr2A	92.092	2491	158	25	208	2670	761042008	761044487	0.000000e+00	3472.0
5	TraesCS3A01G264400	chr2A	92.019	213	17	0	1	213	761041092	761041304	1.550000e-77	300.0
6	TraesCS3A01G264400	chr6B	94.364	763	41	2	1764	2525	124069488	124070249	0.000000e+00	1170.0
7	TraesCS3A01G264400	chr6B	91.165	532	42	4	335	865	581937614	581937087	0.000000e+00	717.0
8	TraesCS3A01G264400	chr6B	91.245	514	40	2	5	516	124068948	124069458	0.000000e+00	695.0
9	TraesCS3A01G264400	chr6B	91.232	422	28	4	1381	1802	581936416	581936004	1.390000e-157	566.0
10	TraesCS3A01G264400	chr6B	91.262	412	33	3	974	1382	581937085	581936674	2.320000e-155	558.0
11	TraesCS3A01G264400	chr6B	91.080	213	19	0	1	213	581938422	581938210	3.360000e-74	289.0
12	TraesCS3A01G264400	chr6D	91.827	832	62	6	974	1802	388972905	388972077	0.000000e+00	1155.0
13	TraesCS3A01G264400	chr6D	90.207	531	47	3	335	865	388973432	388972907	0.000000e+00	688.0
14	TraesCS3A01G264400	chr6D	82.278	316	33	8	29	321	388974279	388973964	4.410000e-63	252.0
15	TraesCS3A01G264400	chr6A	90.986	832	60	8	974	1802	535428807	535427988	0.000000e+00	1107.0
16	TraesCS3A01G264400	chr6A	90.020	511	46	3	355	865	535429314	535428809	0.000000e+00	656.0
17	TraesCS3A01G264400	chr6A	83.117	154	21	2	1872	2020	558612255	558612408	4.640000e-28	135.0
18	TraesCS3A01G264400	chr1B	85.921	554	41	18	2152	2670	481721868	481722419	8.350000e-155	556.0
19	TraesCS3A01G264400	chrUn	85.740	554	42	17	2152	2670	197236462	197237013	3.880000e-153	551.0
20	TraesCS3A01G264400	chr4B	85.740	554	42	17	2152	2670	278518747	278518196	3.880000e-153	551.0
21	TraesCS3A01G264400	chr7D	85.379	554	44	17	2152	2670	254151717	254151166	8.410000e-150	540.0
22	TraesCS3A01G264400	chr7B	84.821	560	42	19	2152	2670	727597762	727598319	8.470000e-145	523.0
23	TraesCS3A01G264400	chr3D	82.432	74	8	3	638	709	560184141	560184071	2.870000e-05	60.2

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	TraesCS3A01G264400	chr3A	488281784	488284453	2669	False	4931.000000	4931	100.00000	1	2670	1	chr3A.!!$F1	2669
1	TraesCS3A01G264400	chr5A	37150460	37153135	2675	False	3984.000000	3984	93.58900	1	2670	1	chr5A.!!$F1	2669
2	TraesCS3A01G264400	chr2A	761041092	761044487	3395	False	1886.000000	3472	92.05550	1	2670	2	chr2A.!!$F1	2669
3	TraesCS3A01G264400	chr6B	124068948	124070249	1301	False	932.500000	1170	92.80450	5	2525	2	chr6B.!!$F1	2520
4	TraesCS3A01G264400	chr6B	581936004	581938422	2418	True	532.500000	717	91.18475	1	1802	4	chr6B.!!$R1	1801
5	TraesCS3A01G264400	chr6D	388972077	388974279	2202	True	698.333333	1155	88.10400	29	1802	3	chr6D.!!$R1	1773
6	TraesCS3A01G264400	chr6A	535427988	535429314	1326	True	881.500000	1107	90.50300	355	1802	2	chr6A.!!$R1	1447
7	TraesCS3A01G264400	chr1B	481721868	481722419	551	False	556.000000	556	85.92100	2152	2670	1	chr1B.!!$F1	518
8	TraesCS3A01G264400	chrUn	197236462	197237013	551	False	551.000000	551	85.74000	2152	2670	1	chrUn.!!$F1	518
9	TraesCS3A01G264400	chr4B	278518196	278518747	551	True	551.000000	551	85.74000	2152	2670	1	chr4B.!!$R1	518
10	TraesCS3A01G264400	chr7D	254151166	254151717	551	True	540.000000	540	85.37900	2152	2670	1	chr7D.!!$R1	518
11	TraesCS3A01G264400	chr7B	727597762	727598319	557	False	523.000000	523	84.82100	2152	2670	1	chr7B.!!$F1	518

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
623	2344	0.755686	GGATCAGGAGCGGATGAACT	59.244	55.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1787	3789	1.527311	GTCGTCTGTCTGCAAGTTTCC	59.473	52.381	0.0	0.0	33.76	3.13	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
24	25	2.192443	CGAGGAGGAGGCGGACTA	59.808	66.667	0.00	0.00	0.00	2.59
313	1061	3.994392	CGCCACTTCTTTTACTCTTGCTA	59.006	43.478	0.00	0.00	0.00	3.49
333	2044	3.855689	ATGCTTTGTTTCGGAAGGATG	57.144	42.857	0.00	0.00	33.46	3.51
374	2085	4.838986	ACACTAACTCTGTTACCTGGTGAT	59.161	41.667	10.23	0.00	0.00	3.06
378	2089	3.511477	ACTCTGTTACCTGGTGATCAGT	58.489	45.455	10.23	2.16	41.83	3.41
516	2227	4.141551	CCTTTATTCGCCTAGGTAACCCTT	60.142	45.833	11.31	0.00	42.66	3.95
522	2240	2.737679	CGCCTAGGTAACCCTTTTCTCG	60.738	54.545	11.31	0.00	42.66	4.04
553	2271	3.848272	ATTTGTAACACGCCTTGATGG	57.152	42.857	0.00	0.00	39.35	3.51
623	2344	0.755686	GGATCAGGAGCGGATGAACT	59.244	55.000	0.00	0.00	0.00	3.01
634	2355	5.758296	GGAGCGGATGAACTTGTTCATATTA	59.242	40.000	23.64	1.72	41.38	0.98
647	2368	8.294577	ACTTGTTCATATTATCGCATACTACGA	58.705	33.333	0.00	0.00	44.75	3.43
742	2466	3.181451	TGCCAAGGAGATGCTATCGAAAT	60.181	43.478	0.00	0.00	0.00	2.17
785	2509	7.301054	CCATTGAACTTTGAAGATGTGTCTAC	58.699	38.462	0.00	0.00	33.30	2.59
853	2577	3.117550	TGCCATGGTTGTAGCTGGATATT	60.118	43.478	14.67	0.00	0.00	1.28
888	2613	0.988832	TAAGCCCAGAACCGTGGAAT	59.011	50.000	0.00	0.00	40.44	3.01
972	2712	8.623903	ACAGTATCTGCATAAATTGGTAACATG	58.376	33.333	0.00	0.00	40.37	3.21
1095	2836	6.333416	CAGCAGATGCAGAGTAGTTAGTTTA	58.667	40.000	7.68	0.00	45.16	2.01
1168	2910	5.997746	GGGAATCTGTTGTGCAGCTAATATA	59.002	40.000	0.00	0.00	44.66	0.86
1171	2913	8.660373	GGAATCTGTTGTGCAGCTAATATATAC	58.340	37.037	0.00	0.00	44.66	1.47
1173	2915	8.768957	ATCTGTTGTGCAGCTAATATATACAG	57.231	34.615	0.00	0.00	44.66	2.74
1220	2963	2.025793	TCCGTGGGCATTGAAAATCCTA	60.026	45.455	0.00	0.00	0.00	2.94
1295	3038	5.509716	TCGAAGCGATGGAAAACTATCTA	57.490	39.130	0.00	0.00	0.00	1.98
1303	3046	8.589338	AGCGATGGAAAACTATCTAGTATGAAT	58.411	33.333	0.00	0.00	34.99	2.57
1304	3047	8.651588	GCGATGGAAAACTATCTAGTATGAATG	58.348	37.037	0.00	0.00	34.99	2.67
1466	3468	9.129209	GGAATTAACTGCTGAATTTGTCTAAAC	57.871	33.333	0.00	0.00	0.00	2.01
1621	3623	2.819608	TGAGGTAGCTCAACCAATTTGC	59.180	45.455	21.91	0.00	42.40	3.68
1787	3789	1.383248	AGATTGAGGTCCTCCGGGG	60.383	63.158	16.60	0.00	39.05	5.73
1904	3906	1.001406	AGCAACTACAGGCACTCAGTC	59.999	52.381	0.00	0.00	34.60	3.51
1910	3912	0.533755	ACAGGCACTCAGTCAAGCAC	60.534	55.000	0.00	0.00	34.60	4.40
1918	3920	3.256879	CACTCAGTCAAGCACTAGGAAGA	59.743	47.826	0.00	0.00	32.21	2.87
1922	3924	2.569404	AGTCAAGCACTAGGAAGAAGGG	59.431	50.000	0.00	0.00	31.37	3.95
2030	4040	3.423539	TTGAGAGGCATGCTACAGTTT	57.576	42.857	18.92	0.00	0.00	2.66
2150	4160	5.221561	TGGAACTGAAGTTTCCTGTTCGATA	60.222	40.000	15.19	7.31	38.92	2.92
2317	4334	3.947834	GTGCCCAAGCTTCAAGTATGTAT	59.052	43.478	0.00	0.00	40.80	2.29
2323	4340	5.050769	CCAAGCTTCAAGTATGTATAGTGCG	60.051	44.000	0.00	0.00	0.00	5.34
2348	4366	7.270365	CGCACACTTTGTTCGACAAATTATAAT	59.730	33.333	11.71	0.00	45.79	1.28
2370	4388	4.599041	TCCCAATCAAGGTCAAAATCGAT	58.401	39.130	0.00	0.00	0.00	3.59
2406	4450	4.289410	TCACAAATCTCCTCCAAGGAATGA	59.711	41.667	0.00	0.00	45.28	2.57
2656	4707	9.632638	AAAATTGACATACTAATCCTACATGCT	57.367	29.630	0.00	0.00	0.00	3.79
2660	4711	7.238710	TGACATACTAATCCTACATGCTCCTA	58.761	38.462	0.00	0.00	0.00	2.94
2661	4712	7.394641	TGACATACTAATCCTACATGCTCCTAG	59.605	40.741	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
136	137	1.677633	GCTTACCCCATTGCGGTGT	60.678	57.895	3.16	0.00	34.66	4.16
213	220	1.813513	ACTGAAGAACATTGGAGCCG	58.186	50.000	0.00	0.00	0.00	5.52
313	1061	3.420893	TCATCCTTCCGAAACAAAGCAT	58.579	40.909	0.00	0.00	0.00	3.79
333	2044	1.809619	TGCGAACGTGCTAGGCATC	60.810	57.895	0.00	0.00	41.91	3.91
374	2085	1.618837	GAGCACCTTCACCTGTACTGA	59.381	52.381	0.60	0.00	0.00	3.41
378	2089	1.292223	GCGAGCACCTTCACCTGTA	59.708	57.895	0.00	0.00	0.00	2.74
440	2151	3.660501	GGAAAATTCCTTTGCCGACTT	57.339	42.857	4.91	0.00	44.11	3.01
516	2227	3.892588	ACAAATTTTAGGGTGGCGAGAAA	59.107	39.130	0.00	0.00	0.00	2.52
522	2240	4.231439	CGTGTTACAAATTTTAGGGTGGC	58.769	43.478	0.00	0.00	0.00	5.01
647	2368	0.853586	TTTCCCAGGGCCCCAACTAT	60.854	55.000	21.43	0.00	0.00	2.12
648	2369	0.853586	ATTTCCCAGGGCCCCAACTA	60.854	55.000	21.43	0.00	0.00	2.24
649	2370	2.168272	GATTTCCCAGGGCCCCAACT	62.168	60.000	21.43	0.00	0.00	3.16
676	2400	7.094377	CCTGATGCTAGATAGAACCTTCTCTAC	60.094	44.444	0.00	0.00	38.70	2.59
742	2466	0.393808	GGCATGCCGAGGTTCCTAAA	60.394	55.000	23.48	0.00	0.00	1.85
785	2509	2.289945	GCCACTCCATTCCCTGCTATAG	60.290	54.545	0.00	0.00	0.00	1.31
1037	2777	5.581479	GCAAAAACATGCATGACCATGATTA	59.419	36.000	32.75	0.29	44.12	1.75
1095	2836	6.942005	TGAACAACAGAAATCCACATCAGTAT	59.058	34.615	0.00	0.00	0.00	2.12
1114	2855	4.203226	TCACTGCCACTACAAATGAACAA	58.797	39.130	0.00	0.00	0.00	2.83
1142	2883	1.272313	AGCTGCACAACAGATTCCCAT	60.272	47.619	1.02	0.00	44.43	4.00
1168	2910	0.769776	AGCTATGCCCCCAGCTGTAT	60.770	55.000	13.81	1.79	46.21	2.29
1173	2915	0.972471	AAAACAGCTATGCCCCCAGC	60.972	55.000	0.00	0.00	44.14	4.85
1245	2988	3.881089	CTCAATAGCATGCAGACCATCAA	59.119	43.478	21.98	0.00	29.71	2.57
1295	3038	8.014070	TGAAAAATGATCATGCCATTCATACT	57.986	30.769	9.46	0.00	33.51	2.12
1303	3046	5.925506	ATGACTGAAAAATGATCATGCCA	57.074	34.783	9.46	4.43	0.00	4.92
1304	3047	7.259882	TGTTATGACTGAAAAATGATCATGCC	58.740	34.615	9.46	0.00	32.42	4.40
1402	3404	9.907576	GATACATTAGACATTTTCTTCTCAACG	57.092	33.333	0.00	0.00	35.55	4.10
1564	3566	1.734465	GCCAAGACTGGAAGATCAACG	59.266	52.381	0.00	0.00	46.92	4.10
1621	3623	7.461107	CAAAAATTTCCTTGATAGCATTGCAG	58.539	34.615	11.91	0.00	0.00	4.41
1727	3729	2.155279	GTTCTGGAGAAGAAAGGCACC	58.845	52.381	0.00	0.00	46.51	5.01
1760	3762	4.442753	GGAGGACCTCAATCTCAGAATCAC	60.443	50.000	23.06	0.00	31.08	3.06
1787	3789	1.527311	GTCGTCTGTCTGCAAGTTTCC	59.473	52.381	0.00	0.00	33.76	3.13
1904	3906	2.569404	ACTCCCTTCTTCCTAGTGCTTG	59.431	50.000	0.00	0.00	0.00	4.01
1910	3912	3.173965	TGACCAACTCCCTTCTTCCTAG	58.826	50.000	0.00	0.00	0.00	3.02
1918	3920	1.645710	ATCGTCTGACCAACTCCCTT	58.354	50.000	1.55	0.00	0.00	3.95
2030	4040	4.343231	TGAGCAATTCTCAGGGCAAAATA	58.657	39.130	4.18	0.00	46.34	1.40
2150	4160	7.672239	TGGCCTAGACAAAAGGTATGTAAAAAT	59.328	33.333	3.32	0.00	36.43	1.82
2348	4366	4.027674	TCGATTTTGACCTTGATTGGGA	57.972	40.909	0.00	0.00	0.00	4.37
2370	4388	7.455891	AGGAGATTTGTGATGTCATATATGCA	58.544	34.615	7.92	9.62	0.00	3.96
2433	4477	7.149192	GGAAAACAACATACTTCGAACGAATTG	60.149	37.037	9.97	12.60	33.28	2.32
2630	4681	9.632638	AGCATGTAGGATTAGTATGTCAATTTT	57.367	29.630	0.00	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.