AutoCloner

Multiple sequence alignment - TraesCS6A01G387200

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	TraesCS6A01G387200	chr6A	100.000	5543	0	0	1	5543	603744688	603739146	0.000000e+00	10237.0
1	TraesCS6A01G387200	chr2D	97.935	5520	92	18	40	5543	647572386	647566873	0.000000e+00	9542.0
2	TraesCS6A01G387200	chr2D	98.735	5219	61	5	327	5543	107007474	107002259	0.000000e+00	9267.0
3	TraesCS6A01G387200	chr2D	96.167	287	11	0	41	327	450392931	450393217	2.340000e-128	470.0
4	TraesCS6A01G387200	chr2D	96.167	287	11	0	41	327	601653716	601654002	2.340000e-128	470.0
5	TraesCS6A01G387200	chr4D	97.898	5519	94	17	40	5543	1633419	1627908	0.000000e+00	9529.0
6	TraesCS6A01G387200	chr4D	98.640	5219	68	3	327	5543	350522873	350517656	0.000000e+00	9241.0
7	TraesCS6A01G387200	chr4D	95.470	287	13	0	41	327	437717877	437717591	5.060000e-125	459.0
8	TraesCS6A01G387200	chr4D	95.470	287	13	0	41	327	437728813	437728527	5.060000e-125	459.0
9	TraesCS6A01G387200	chr5D	97.862	5520	96	18	41	5543	45661549	45656035	0.000000e+00	9520.0
10	TraesCS6A01G387200	chr3D	97.875	5507	97	15	41	5543	442860586	442855096	0.000000e+00	9503.0
11	TraesCS6A01G387200	chr3D	98.659	5219	67	3	327	5543	380104413	380099196	0.000000e+00	9247.0
12	TraesCS6A01G387200	chr6D	98.735	5219	62	4	327	5543	237393862	237388646	0.000000e+00	9269.0
13	TraesCS6A01G387200	chr6D	95.819	287	11	1	41	327	237394189	237393904	3.910000e-126	462.0
14	TraesCS6A01G387200	chr1D	98.716	5219	64	3	327	5543	315624676	315629893	0.000000e+00	9263.0
15	TraesCS6A01G387200	chr1D	96.516	287	10	0	41	327	21806462	21806176	5.020000e-130	475.0
16	TraesCS6A01G387200	chr1D	95.222	293	9	2	40	327	126223253	126222961	5.060000e-125	459.0
17	TraesCS6A01G387200	chr2B	95.819	287	10	1	41	327	118846105	118846389	3.910000e-126	462.0
18	TraesCS6A01G387200	chr7D	95.470	287	13	0	41	327	491277791	491277505	5.060000e-125	459.0
19	TraesCS6A01G387200	chr6B	100.000	42	0	0	1	42	695450549	695450508	1.660000e-10	78.7

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	TraesCS6A01G387200	chr6A	603739146	603744688	5542	True	10237.0	10237	100.000	1	5543	1	chr6A.!!$R1	5542
1	TraesCS6A01G387200	chr2D	647566873	647572386	5513	True	9542.0	9542	97.935	40	5543	1	chr2D.!!$R2	5503
2	TraesCS6A01G387200	chr2D	107002259	107007474	5215	True	9267.0	9267	98.735	327	5543	1	chr2D.!!$R1	5216
3	TraesCS6A01G387200	chr4D	1627908	1633419	5511	True	9529.0	9529	97.898	40	5543	1	chr4D.!!$R1	5503
4	TraesCS6A01G387200	chr4D	350517656	350522873	5217	True	9241.0	9241	98.640	327	5543	1	chr4D.!!$R2	5216
5	TraesCS6A01G387200	chr5D	45656035	45661549	5514	True	9520.0	9520	97.862	41	5543	1	chr5D.!!$R1	5502
6	TraesCS6A01G387200	chr3D	442855096	442860586	5490	True	9503.0	9503	97.875	41	5543	1	chr3D.!!$R2	5502
7	TraesCS6A01G387200	chr3D	380099196	380104413	5217	True	9247.0	9247	98.659	327	5543	1	chr3D.!!$R1	5216
8	TraesCS6A01G387200	chr6D	237388646	237394189	5543	True	4865.5	9269	97.277	41	5543	2	chr6D.!!$R1	5502
9	TraesCS6A01G387200	chr1D	315624676	315629893	5217	False	9263.0	9263	98.716	327	5543	1	chr1D.!!$F1	5216

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
624	674	1.153349	GCACCGGGAGAGGATGAAC	60.153	63.158	6.32	34.73	3.18	F
1140	1191	1.418334	CTCCAGAGGGAATGACCGAT	58.582	55.000	0.00	44.38	4.18	F
1905	1956	0.679640	GGTGGATTGATTCGGGTGCA	60.680	55.000	0.00	0.00	4.57	F
3671	3725	1.289160	TCCTTGGCTGCCTCTTATGT	58.711	50.000	21.03	0.00	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1780	1831	1.609208	GAGCTTGTTTTCCCTCTGCA	58.391	50.000	0.00	4.41	R
2323	2375	4.740235	GCTGGATAGCCGAGACAC	57.260	61.111	44.33	3.67	R
3866	3920	4.437390	CCTCGTTAATGACAAATCCTGCAC	60.437	45.833	0.00	4.57	R
5062	5117	4.151883	AGAACCACATTAAGGCATGTTGT	58.848	39.130	35.03	3.32	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
26	27	7.578310	GGTATACCCCTTATTTTTCTTGACC	57.422	40.000	11.17	0.00	0.00	4.02
27	28	7.120716	GGTATACCCCTTATTTTTCTTGACCA	58.879	38.462	11.17	0.00	0.00	4.02
28	29	7.616542	GGTATACCCCTTATTTTTCTTGACCAA	59.383	37.037	11.17	0.00	0.00	3.67
29	30	9.197306	GTATACCCCTTATTTTTCTTGACCAAT	57.803	33.333	0.00	0.00	0.00	3.16
30	31	8.679344	ATACCCCTTATTTTTCTTGACCAATT	57.321	30.769	0.00	0.00	0.00	2.32
31	32	9.777008	ATACCCCTTATTTTTCTTGACCAATTA	57.223	29.630	0.00	0.00	0.00	1.40
32	33	8.499288	ACCCCTTATTTTTCTTGACCAATTAA	57.501	30.769	0.00	0.00	0.00	1.40
33	34	9.111519	ACCCCTTATTTTTCTTGACCAATTAAT	57.888	29.630	0.00	0.00	0.00	1.40
34	35	9.599866	CCCCTTATTTTTCTTGACCAATTAATC	57.400	33.333	0.00	0.00	0.00	1.75
35	36	9.301153	CCCTTATTTTTCTTGACCAATTAATCG	57.699	33.333	0.00	0.00	0.00	3.34
36	37	9.301153	CCTTATTTTTCTTGACCAATTAATCGG	57.699	33.333	0.00	0.00	0.00	4.18
37	38	9.301153	CTTATTTTTCTTGACCAATTAATCGGG	57.699	33.333	0.00	1.15	0.00	5.14
38	39	4.712122	TTTCTTGACCAATTAATCGGGC	57.288	40.909	0.00	0.00	0.00	6.13
218	220	5.505780	TGTGTGAGAAGAGAAAGGGAAAAA	58.494	37.500	0.00	0.00	0.00	1.94
282	288	3.733960	CGTGGCGAGGTGAGACGA	61.734	66.667	0.00	0.00	31.71	4.20
283	289	2.179517	GTGGCGAGGTGAGACGAG	59.820	66.667	0.00	0.00	0.00	4.18
620	670	2.611964	ATCCTGCACCGGGAGAGGAT	62.612	60.000	19.57	19.57	42.74	3.24
624	674	1.153349	GCACCGGGAGAGGATGAAC	60.153	63.158	6.32	0.00	34.73	3.18
807	858	3.959293	TCAGTACGTCCAACATCCTCTA	58.041	45.455	0.00	0.00	0.00	2.43
1140	1191	1.418334	CTCCAGAGGGAATGACCGAT	58.582	55.000	0.00	0.00	44.38	4.18
1192	1243	7.267128	CAATACTATGTTTGTGGGATGCATTT	58.733	34.615	0.00	0.00	0.00	2.32
1254	1305	6.073167	TGCACATAAACGACGGAAAAATTCTA	60.073	34.615	0.00	0.00	0.00	2.10
1780	1831	2.031163	GCCCTGAACGTGCAGACT	59.969	61.111	25.81	0.00	38.14	3.24
1905	1956	0.679640	GGTGGATTGATTCGGGTGCA	60.680	55.000	0.00	0.00	0.00	4.57
2237	2289	6.345565	CGCTTTTCTCTTTCAGATTTTTGCAG	60.346	38.462	0.00	0.00	0.00	4.41
2297	2349	3.138884	TGCAAGTATTTGGCACTCTCA	57.861	42.857	0.00	0.00	34.79	3.27
2569	2622	9.438291	CGACTAGATTTTGCTATGTTTATTTGG	57.562	33.333	0.00	0.00	0.00	3.28
3210	3264	8.998377	GCTAGATTTTCTTCTGAGATAATTCCC	58.002	37.037	0.00	0.00	34.85	3.97
3671	3725	1.289160	TCCTTGGCTGCCTCTTATGT	58.711	50.000	21.03	0.00	0.00	2.29
3866	3920	8.023128	TGAGAAGTTTGAAAGAACTTTGACTTG	58.977	33.333	16.98	0.00	46.73	3.16
3954	4008	9.851686	AGTGTCATATTATGTTTGTATGTGGAT	57.148	29.630	3.67	0.00	0.00	3.41
4089	4143	6.823689	TCAAACTTATTAAGGATGAGAGTGGC	59.176	38.462	8.26	0.00	0.00	5.01
4294	4348	7.187824	ACAAGACCAGATATCTCTTTTGCTA	57.812	36.000	1.03	0.00	0.00	3.49
4470	4525	6.275494	TCTCCGATGTTGATGTACTTTACA	57.725	37.500	0.00	0.00	43.80	2.41
4885	4940	3.102972	CATCGAGGGAGATGGGTATGAT	58.897	50.000	0.00	0.00	43.07	2.45
5138	5193	3.060003	CAGAGCAGTCTTGAAAGAACACG	60.060	47.826	0.00	0.00	36.68	4.49
5326	5381	5.102953	ACTAGCAATTCAAGGCATAGTCA	57.897	39.130	0.00	0.00	0.00	3.41
5356	5411	7.066284	GTCAAGTTGTGAATGGATGTAGCTTAT	59.934	37.037	2.11	0.00	38.23	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	7.120716	TGGTCAAGAAAAATAAGGGGTATACC	58.879	38.462	13.99	13.99	39.11	2.73
3	4	8.584063	TTGGTCAAGAAAAATAAGGGGTATAC	57.416	34.615	0.00	0.00	0.00	1.47
4	5	9.777008	AATTGGTCAAGAAAAATAAGGGGTATA	57.223	29.630	0.00	0.00	0.00	1.47
5	6	8.679344	AATTGGTCAAGAAAAATAAGGGGTAT	57.321	30.769	0.00	0.00	0.00	2.73
6	7	9.603189	TTAATTGGTCAAGAAAAATAAGGGGTA	57.397	29.630	0.00	0.00	0.00	3.69
7	8	8.499288	TTAATTGGTCAAGAAAAATAAGGGGT	57.501	30.769	0.00	0.00	0.00	4.95
8	9	9.599866	GATTAATTGGTCAAGAAAAATAAGGGG	57.400	33.333	0.00	0.00	0.00	4.79
9	10	9.301153	CGATTAATTGGTCAAGAAAAATAAGGG	57.699	33.333	0.00	0.00	0.00	3.95
10	11	9.301153	CCGATTAATTGGTCAAGAAAAATAAGG	57.699	33.333	13.07	0.00	0.00	2.69
11	12	9.301153	CCCGATTAATTGGTCAAGAAAAATAAG	57.699	33.333	18.74	0.00	0.00	1.73
12	13	7.762159	GCCCGATTAATTGGTCAAGAAAAATAA	59.238	33.333	18.74	0.00	0.00	1.40
13	14	7.262048	GCCCGATTAATTGGTCAAGAAAAATA	58.738	34.615	18.74	0.00	0.00	1.40
14	15	6.106003	GCCCGATTAATTGGTCAAGAAAAAT	58.894	36.000	18.74	0.00	0.00	1.82
15	16	5.474825	GCCCGATTAATTGGTCAAGAAAAA	58.525	37.500	18.74	0.00	0.00	1.94
16	17	4.081917	GGCCCGATTAATTGGTCAAGAAAA	60.082	41.667	18.74	0.00	0.00	2.29
17	18	3.445805	GGCCCGATTAATTGGTCAAGAAA	59.554	43.478	18.74	0.00	0.00	2.52
18	19	3.020984	GGCCCGATTAATTGGTCAAGAA	58.979	45.455	18.74	0.00	0.00	2.52
19	20	2.241176	AGGCCCGATTAATTGGTCAAGA	59.759	45.455	18.74	0.00	0.00	3.02
20	21	2.358898	CAGGCCCGATTAATTGGTCAAG	59.641	50.000	18.74	6.23	0.00	3.02
21	22	2.291282	ACAGGCCCGATTAATTGGTCAA	60.291	45.455	18.74	0.00	0.00	3.18
22	23	1.283613	ACAGGCCCGATTAATTGGTCA	59.716	47.619	18.74	0.00	0.00	4.02
23	24	2.052782	ACAGGCCCGATTAATTGGTC	57.947	50.000	18.74	7.56	0.00	4.02
24	25	2.525105	AACAGGCCCGATTAATTGGT	57.475	45.000	18.74	0.00	0.00	3.67
25	26	3.815809	TCTAACAGGCCCGATTAATTGG	58.184	45.455	14.20	14.20	0.00	3.16
26	27	6.391227	AATTCTAACAGGCCCGATTAATTG	57.609	37.500	0.00	0.00	0.00	2.32
27	28	8.576442	CATTAATTCTAACAGGCCCGATTAATT	58.424	33.333	0.00	1.95	0.00	1.40
28	29	7.176690	CCATTAATTCTAACAGGCCCGATTAAT	59.823	37.037	0.00	0.00	0.00	1.40
29	30	6.488683	CCATTAATTCTAACAGGCCCGATTAA	59.511	38.462	0.00	0.00	0.00	1.40
30	31	6.001460	CCATTAATTCTAACAGGCCCGATTA	58.999	40.000	0.00	0.00	0.00	1.75
31	32	4.827284	CCATTAATTCTAACAGGCCCGATT	59.173	41.667	0.00	0.00	0.00	3.34
32	33	4.398319	CCATTAATTCTAACAGGCCCGAT	58.602	43.478	0.00	0.00	0.00	4.18
33	34	3.434453	CCCATTAATTCTAACAGGCCCGA	60.434	47.826	0.00	0.00	0.00	5.14
34	35	2.884639	CCCATTAATTCTAACAGGCCCG	59.115	50.000	0.00	0.00	0.00	6.13
35	36	2.628178	GCCCATTAATTCTAACAGGCCC	59.372	50.000	0.00	0.00	34.52	5.80
36	37	3.566351	AGCCCATTAATTCTAACAGGCC	58.434	45.455	0.00	0.00	38.49	5.19
37	38	4.762251	CCTAGCCCATTAATTCTAACAGGC	59.238	45.833	0.00	0.00	38.20	4.85
38	39	4.762251	GCCTAGCCCATTAATTCTAACAGG	59.238	45.833	0.00	0.00	0.00	4.00
275	281	3.963687	TACGCCTCGCCTCGTCTCA	62.964	63.158	0.00	0.00	39.79	3.27
279	285	3.138798	ATGTACGCCTCGCCTCGT	61.139	61.111	0.00	0.00	42.09	4.18
280	286	2.655364	CATGTACGCCTCGCCTCG	60.655	66.667	0.00	0.00	0.00	4.63
281	287	2.962253	GCATGTACGCCTCGCCTC	60.962	66.667	0.00	0.00	0.00	4.70
282	288	4.873129	CGCATGTACGCCTCGCCT	62.873	66.667	0.00	0.00	0.00	5.52
283	289	4.865761	TCGCATGTACGCCTCGCC	62.866	66.667	0.00	0.00	0.00	5.54
471	520	4.202493	ACCCTAGGTGTTTTTCGGTGTATT	60.202	41.667	8.29	0.00	32.98	1.89
620	670	2.882137	CGCTTCCCAAAAACCTAGTTCA	59.118	45.455	0.00	0.00	0.00	3.18
624	674	1.200020	CAGCGCTTCCCAAAAACCTAG	59.800	52.381	7.50	0.00	0.00	3.02
1140	1191	4.225042	TCCTGGAATTTTCTCCGATCTTCA	59.775	41.667	0.00	0.00	38.44	3.02
1192	1243	1.134521	ACGGTCAGCAAGAACACTCAA	60.135	47.619	0.00	0.00	31.63	3.02
1480	1531	4.284490	TCTCTTATGCTTCAGAGTTGTGGT	59.716	41.667	9.82	0.00	38.20	4.16
1780	1831	1.609208	GAGCTTGTTTTCCCTCTGCA	58.391	50.000	0.00	0.00	0.00	4.41
1905	1956	2.013400	TCAGCACACACATGAACGTTT	58.987	42.857	0.46	0.00	0.00	3.60
2237	2289	8.587952	AGCACAAATTTGGTTTATTGACTTAC	57.412	30.769	21.74	0.00	0.00	2.34
2323	2375	4.740235	GCTGGATAGCCGAGACAC	57.260	61.111	0.00	0.00	44.33	3.67
2569	2622	7.483059	GTCTAATGCTTCATCTTTAGTTTGCAC	59.517	37.037	0.00	0.00	31.92	4.57
3105	3159	9.645059	CGAGATTCCATTATAGTATCAACATGT	57.355	33.333	0.00	0.00	0.00	3.21
3388	3442	5.869649	TCTTTCCAATCATCTACATCCGA	57.130	39.130	0.00	0.00	0.00	4.55
3866	3920	4.437390	CCTCGTTAATGACAAATCCTGCAC	60.437	45.833	0.00	0.00	0.00	4.57
3954	4008	9.733556	ATGTTTGTACCAAAGATTAGTATGTCA	57.266	29.630	0.00	0.00	0.00	3.58
3963	4017	9.723601	ATTGCATTAATGTTTGTACCAAAGATT	57.276	25.926	16.61	14.09	0.00	2.40
4089	4143	8.551205	ACATAGTGAGATTGCGTTAATGTAATG	58.449	33.333	14.74	3.48	0.00	1.90
4149	4203	0.595095	GTGTTGGAGAAGGCTTGCTG	59.405	55.000	3.46	0.00	0.00	4.41
4294	4348	4.623932	TGAACCTACTCAGTTTGCTCAT	57.376	40.909	0.00	0.00	0.00	2.90
4470	4525	7.455058	TGAGTAAATACATACCCACTTGTTGT	58.545	34.615	0.00	0.00	0.00	3.32
4885	4940	8.229605	ACTACTATGGTGTAACATCTATGGGTA	58.770	37.037	0.00	0.00	39.98	3.69
5062	5117	4.151883	AGAACCACATTAAGGCATGTTGT	58.848	39.130	0.00	0.00	35.03	3.32
5138	5193	6.418226	CGTTTACAGTCAGAACTCATATAGGC	59.582	42.308	0.00	0.00	31.71	3.93
5274	5329	5.815740	GTGAACAGGTTTCACTCAAAGTCTA	59.184	40.000	9.41	0.00	43.91	2.59
5326	5381	6.409524	ACATCCATTCACAACTTGACAATT	57.590	33.333	0.00	0.00	32.26	2.32
5356	5411	6.420913	AAGTTGAACTTCTGCCTAGAACTA	57.579	37.500	4.45	0.00	37.99	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.