AutoCloner

Multiple sequence alignment - TraesCS2D01G229100

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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	TraesCS2D01G229100	chr2D	100.000	5683	0	0	1	5683	198458521	198464203	0.000000e+00	10495.0
1	TraesCS2D01G229100	chr2D	84.770	348	44	7	2284	2623	614805489	614805143	1.960000e-89	340.0
2	TraesCS2D01G229100	chr2D	94.737	38	2	0	2899	2936	116908939	116908976	6.150000e-05	60.2
3	TraesCS2D01G229100	chr2A	96.043	5712	160	25	1	5683	215747455	215753129	0.000000e+00	9236.0
4	TraesCS2D01G229100	chr2A	89.535	86	8	1	3737	3822	416916411	416916327	2.170000e-19	108.0
5	TraesCS2D01G229100	chr2A	94.737	38	2	0	2899	2936	118444821	118444858	6.150000e-05	60.2
6	TraesCS2D01G229100	chr2B	95.958	5467	132	28	1	5427	255050422	255055839	0.000000e+00	8789.0
7	TraesCS2D01G229100	chr2B	84.593	344	46	4	2284	2621	704119609	704119951	9.120000e-88	335.0
8	TraesCS2D01G229100	chr2B	84.302	344	48	1	2284	2621	46671585	46671928	1.180000e-86	331.0
9	TraesCS2D01G229100	chr3D	78.976	547	98	16	5147	5683	184376352	184375813	1.950000e-94	357.0
10	TraesCS2D01G229100	chr7A	78.821	543	103	11	5147	5683	69217821	69218357	7.000000e-94	355.0
11	TraesCS2D01G229100	chr6B	78.871	549	96	16	5147	5681	422985773	422985231	2.520000e-93	353.0
12	TraesCS2D01G229100	chr6B	78.413	542	99	15	5147	5676	422971696	422972231	2.540000e-88	337.0
13	TraesCS2D01G229100	chr6B	97.143	35	1	0	2902	2936	35701273	35701307	6.150000e-05	60.2
14	TraesCS2D01G229100	chr5B	78.967	542	96	15	5147	5676	270439180	270439715	2.520000e-93	353.0
15	TraesCS2D01G229100	chr5B	97.143	35	1	0	2902	2936	234759829	234759863	6.150000e-05	60.2
16	TraesCS2D01G229100	chr5A	84.840	343	46	1	2284	2620	13422897	13423239	1.960000e-89	340.0
17	TraesCS2D01G229100	chr6A	84.548	343	42	4	2284	2620	489860952	489860615	4.240000e-86	329.0
18	TraesCS2D01G229100	chr6A	90.805	87	8	0	3736	3822	472952665	472952751	3.600000e-22	117.0
19	TraesCS2D01G229100	chr1A	84.058	345	49	1	2284	2622	306146126	306146470	1.530000e-85	327.0
20	TraesCS2D01G229100	chr3A	78.004	541	103	13	5147	5679	121688671	121688139	5.490000e-85	326.0
21	TraesCS2D01G229100	chr4D	77.858	551	97	18	5147	5683	277408952	277409491	9.190000e-83	318.0
22	TraesCS2D01G229100	chr4D	78.030	528	99	15	5140	5658	291745667	291745148	3.300000e-82	316.0
23	TraesCS2D01G229100	chr4D	82.825	361	53	5	2282	2636	298223882	298223525	1.190000e-81	315.0
24	TraesCS2D01G229100	chr4D	93.103	87	6	0	3739	3825	381882681	381882595	1.660000e-25	128.0
25	TraesCS2D01G229100	chr1B	79.237	236	38	6	4901	5132	327247774	327248002	2.740000e-33	154.0
26	TraesCS2D01G229100	chr1B	94.118	85	5	0	3738	3822	688114506	688114422	4.620000e-26	130.0
27	TraesCS2D01G229100	chr3B	95.506	89	4	0	3734	3822	556504590	556504502	5.940000e-30	143.0
28	TraesCS2D01G229100	chr3B	90.588	85	5	1	3738	3822	224314659	224314740	6.020000e-20	110.0
29	TraesCS2D01G229100	chr1D	95.506	89	4	0	3734	3822	348128612	348128524	5.940000e-30	143.0

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	TraesCS2D01G229100	chr2D	198458521	198464203	5682	False	10495	10495	100.000	1	5683	1	chr2D.!!$F2	5682
1	TraesCS2D01G229100	chr2A	215747455	215753129	5674	False	9236	9236	96.043	1	5683	1	chr2A.!!$F2	5682
2	TraesCS2D01G229100	chr2B	255050422	255055839	5417	False	8789	8789	95.958	1	5427	1	chr2B.!!$F2	5426
3	TraesCS2D01G229100	chr3D	184375813	184376352	539	True	357	357	78.976	5147	5683	1	chr3D.!!$R1	536
4	TraesCS2D01G229100	chr7A	69217821	69218357	536	False	355	355	78.821	5147	5683	1	chr7A.!!$F1	536
5	TraesCS2D01G229100	chr6B	422985231	422985773	542	True	353	353	78.871	5147	5681	1	chr6B.!!$R1	534
6	TraesCS2D01G229100	chr6B	422971696	422972231	535	False	337	337	78.413	5147	5676	1	chr6B.!!$F2	529
7	TraesCS2D01G229100	chr5B	270439180	270439715	535	False	353	353	78.967	5147	5676	1	chr5B.!!$F2	529
8	TraesCS2D01G229100	chr3A	121688139	121688671	532	True	326	326	78.004	5147	5679	1	chr3A.!!$R1	532
9	TraesCS2D01G229100	chr4D	277408952	277409491	539	False	318	318	77.858	5147	5683	1	chr4D.!!$F1	536
10	TraesCS2D01G229100	chr4D	291745148	291745667	519	True	316	316	78.030	5140	5658	1	chr4D.!!$R1	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
312	321	1.281899	GTGCTTGCTGACGTATCTCC	58.718	55.000	0.00	0.00	0.00	3.71	F
1494	1524	0.390472	GCAAGCTCGTGAGTAAGGCT	60.390	55.000	0.00	0.00	34.52	4.58	F
1770	1800	0.398318	AGCCGGAGAACTTCTTGCTT	59.602	50.000	5.05	0.00	31.54	3.91	F
2416	2447	1.134098	TCTCATTGGGGATTCCTTCGC	60.134	52.381	2.01	0.00	36.20	4.70	F
3197	3233	0.112995	TTGAAAGTCAGCCATGGCCT	59.887	50.000	33.14	20.19	43.17	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1602	1632	1.079612	TGCACAGAGCTCCATCACG	60.080	57.895	10.93	0.00	45.94	4.35	R
2409	2440	1.215382	CCTCACACATCGCGAAGGA	59.785	57.895	15.24	5.63	0.00	3.36	R
2783	2819	4.039703	CAGCACAAATGAATAGCCATTCG	58.960	43.478	0.37	0.00	43.06	3.34	R
4172	4208	2.158623	TCAACTCAAGCCATGTGGTTCT	60.159	45.455	0.35	0.00	37.57	3.01	R
4898	4934	3.820777	TTTGTTTTTGTTGTTGCTGCC	57.179	38.095	0.00	0.00	0.00	4.85	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
25	26	4.340097	CCCTTTTCTCCGTACCAACTTTTT	59.660	41.667	0.00	0.00	0.00	1.94
26	27	5.506815	CCCTTTTCTCCGTACCAACTTTTTC	60.507	44.000	0.00	0.00	0.00	2.29
27	28	5.503662	TTTTCTCCGTACCAACTTTTTCC	57.496	39.130	0.00	0.00	0.00	3.13
153	162	2.511600	GCCGTGCCGAGCTGTTAT	60.512	61.111	0.00	0.00	0.00	1.89
284	293	4.598257	CGTCTCCGCCATGTTCTT	57.402	55.556	0.00	0.00	0.00	2.52
311	320	1.996292	TGTGCTTGCTGACGTATCTC	58.004	50.000	0.00	0.00	0.00	2.75
312	321	1.281899	GTGCTTGCTGACGTATCTCC	58.718	55.000	0.00	0.00	0.00	3.71
342	352	1.606737	GGGTCGCTCTTCCATCTATGC	60.607	57.143	0.00	0.00	0.00	3.14
352	362	6.519721	GCTCTTCCATCTATGCAAGATTAGGA	60.520	42.308	8.19	9.74	42.62	2.94
358	368	7.679881	TCCATCTATGCAAGATTAGGAATAGGA	59.320	37.037	11.88	9.12	42.62	2.94
414	424	4.728917	GATCGAGAATTTGATCTGGCTG	57.271	45.455	0.00	0.00	39.97	4.85
547	573	3.555547	TCGTGCATATGTTCTTGGATTCG	59.444	43.478	4.29	0.00	0.00	3.34
611	637	4.150897	TCCTGTGTGCTGTAGTTTTCTT	57.849	40.909	0.00	0.00	0.00	2.52
612	638	4.127171	TCCTGTGTGCTGTAGTTTTCTTC	58.873	43.478	0.00	0.00	0.00	2.87
613	639	4.130118	CCTGTGTGCTGTAGTTTTCTTCT	58.870	43.478	0.00	0.00	0.00	2.85
614	640	4.212214	CCTGTGTGCTGTAGTTTTCTTCTC	59.788	45.833	0.00	0.00	0.00	2.87
744	770	2.124901	CCAAAGCGACCGGCCATA	60.125	61.111	0.00	0.00	45.17	2.74
854	882	1.889170	CTTTTCCCCTTCTGCTGTTCC	59.111	52.381	0.00	0.00	0.00	3.62
906	934	7.617533	TTCGGCTTTCTTTTCTTTTTATTCG	57.382	32.000	0.00	0.00	0.00	3.34
1029	1059	5.675684	TTTGTTTGAGAGGGCTTTTCTTT	57.324	34.783	0.00	0.00	0.00	2.52
1099	1129	5.205056	ACTGGGTTGTAAATTTGGAACTGA	58.795	37.500	0.00	0.00	0.00	3.41
1213	1243	1.134729	ACCAGCCAAAACAAGCACAAG	60.135	47.619	0.00	0.00	0.00	3.16
1494	1524	0.390472	GCAAGCTCGTGAGTAAGGCT	60.390	55.000	0.00	0.00	34.52	4.58
1770	1800	0.398318	AGCCGGAGAACTTCTTGCTT	59.602	50.000	5.05	0.00	31.54	3.91
2293	2324	1.699054	ATCAGCGCATAGGGAAGGCA	61.699	55.000	11.47	0.00	0.00	4.75
2387	2418	3.513912	TGGTGGAGTCGATTGTCTACATT	59.486	43.478	9.87	0.00	0.00	2.71
2406	2437	2.584835	TCAAGGTGTTCTCATTGGGG	57.415	50.000	0.00	0.00	0.00	4.96
2407	2438	2.061848	TCAAGGTGTTCTCATTGGGGA	58.938	47.619	0.00	0.00	0.00	4.81
2409	2440	3.075882	TCAAGGTGTTCTCATTGGGGATT	59.924	43.478	0.00	0.00	0.00	3.01
2411	2442	2.024941	AGGTGTTCTCATTGGGGATTCC	60.025	50.000	0.00	0.00	0.00	3.01
2413	2444	3.564352	GGTGTTCTCATTGGGGATTCCTT	60.564	47.826	2.01	0.00	36.20	3.36
2414	2445	3.696548	GTGTTCTCATTGGGGATTCCTTC	59.303	47.826	2.01	0.00	36.20	3.46
2415	2446	2.945668	GTTCTCATTGGGGATTCCTTCG	59.054	50.000	2.01	0.00	36.20	3.79
2416	2447	1.134098	TCTCATTGGGGATTCCTTCGC	60.134	52.381	2.01	0.00	36.20	4.70
2482	2518	2.823758	TTGGCGGTGTGGTCATGGA	61.824	57.895	0.00	0.00	0.00	3.41
2563	2599	5.575157	TCTCCATTAATTAACTGGGCAACA	58.425	37.500	18.59	6.14	39.74	3.33
2566	2602	5.184864	TCCATTAATTAACTGGGCAACACTG	59.815	40.000	18.59	4.38	39.74	3.66
2610	2646	2.731451	GCAAATCTTTTGCCTCCGTTTC	59.269	45.455	12.74	0.00	39.38	2.78
2706	2742	5.632764	CGATATTGAGGTAGTCATGCTTCAG	59.367	44.000	0.00	0.00	34.17	3.02
2783	2819	4.864704	TTGGGTTGCAAAGATTAAGACC	57.135	40.909	0.00	0.00	0.00	3.85
3197	3233	0.112995	TTGAAAGTCAGCCATGGCCT	59.887	50.000	33.14	20.19	43.17	5.19
3347	3383	8.506168	AGTTCTTTTCGCCAAAATCTGATATA	57.494	30.769	0.00	0.00	30.91	0.86
3745	3781	3.617775	GCAACTCTTCTGAACTACTCCCC	60.618	52.174	0.00	0.00	0.00	4.81
4059	4095	6.109359	ACTGTCAATTCCTACAACTGATAGC	58.891	40.000	0.00	0.00	30.80	2.97
4100	4136	6.412362	ACCTTACCAGTGAGACATGATATC	57.588	41.667	0.00	0.00	0.00	1.63
4189	4225	2.746362	GAGAAGAACCACATGGCTTGAG	59.254	50.000	7.45	0.00	39.32	3.02
4360	4396	7.039293	TGGCAGTATTTTCTCTGACTACAACTA	60.039	37.037	0.00	0.00	40.08	2.24
4361	4397	7.982354	GGCAGTATTTTCTCTGACTACAACTAT	59.018	37.037	0.00	0.00	36.82	2.12
4521	4557	5.230323	TGGTGTACCATTAGCAACTGTTA	57.770	39.130	0.00	0.00	42.01	2.41
4638	4674	5.690865	TGTTGTTCCTCTAGTGTTTTGGAT	58.309	37.500	0.00	0.00	0.00	3.41
4898	4934	0.679505	TGGGAGGACAAGAAGACACG	59.320	55.000	0.00	0.00	0.00	4.49
4980	5017	8.713271	GCTAGAATTGAAACCGATAAGATAAGG	58.287	37.037	0.00	0.00	0.00	2.69
5043	5080	4.314440	ACGCACGCCTGTCCATGT	62.314	61.111	0.00	0.00	0.00	3.21
5055	5092	4.804261	GCCTGTCCATGTCTAGTTCTTTGT	60.804	45.833	0.00	0.00	0.00	2.83
5085	5124	7.773224	TGTTTCTGTCCTTGATTTCTCTTAACA	59.227	33.333	0.00	0.00	0.00	2.41
5119	5158	3.009033	TGTCAAAGATTGGTCTACCCTGG	59.991	47.826	0.00	0.00	33.30	4.45
5209	5251	0.391661	AGCACGCTTCATTCGTCCAT	60.392	50.000	0.00	0.00	38.19	3.41
5357	5411	7.062322	TGATCCTTTCATGTTAGCCACATATT	58.938	34.615	0.00	0.00	45.06	1.28
5547	5608	2.041485	TCACCCATCCAGCTTTGATTCA	59.959	45.455	0.00	0.00	0.00	2.57
5604	5667	3.149196	CCAGGATTGACCCAAATATCGG	58.851	50.000	0.00	0.00	40.05	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	2.853235	AGTTGGTACGGAGAAAAGGG	57.147	50.000	0.00	0.00	0.00	3.95
152	161	4.284490	TGGAGTAGTTGAAGACAGAGCAAT	59.716	41.667	0.00	0.00	0.00	3.56
153	162	3.641436	TGGAGTAGTTGAAGACAGAGCAA	59.359	43.478	0.00	0.00	0.00	3.91
284	293	0.250252	TCAGCAAGCACATCGAACCA	60.250	50.000	0.00	0.00	0.00	3.67
311	320	2.511600	GCGACCCAATCCACGAGG	60.512	66.667	0.00	0.00	0.00	4.63
312	321	1.519455	GAGCGACCCAATCCACGAG	60.519	63.158	0.00	0.00	0.00	4.18
358	368	3.305064	CGAACCCAAAACACGGAATGATT	60.305	43.478	0.00	0.00	0.00	2.57
411	421	2.653115	GGGCAAGCTTTCCACAGC	59.347	61.111	17.24	6.56	40.44	4.40
413	423	0.899717	GATGGGGCAAGCTTTCCACA	60.900	55.000	22.68	22.68	40.53	4.17
414	424	0.613012	AGATGGGGCAAGCTTTCCAC	60.613	55.000	17.24	14.24	31.48	4.02
547	573	2.290323	ACACCAGCACCAGAAATCTACC	60.290	50.000	0.00	0.00	0.00	3.18
611	637	1.073923	GCACCCAGGGAAAAAGAGAGA	59.926	52.381	14.54	0.00	0.00	3.10
612	638	1.539157	GCACCCAGGGAAAAAGAGAG	58.461	55.000	14.54	0.00	0.00	3.20
613	639	0.112412	GGCACCCAGGGAAAAAGAGA	59.888	55.000	14.54	0.00	0.00	3.10
614	640	1.244019	CGGCACCCAGGGAAAAAGAG	61.244	60.000	14.54	0.00	0.00	2.85
854	882	5.580297	GGATCTAGAAGCAGAACTCAAACAG	59.420	44.000	0.00	0.00	0.00	3.16
1005	1033	5.876651	AGAAAAGCCCTCTCAAACAAATT	57.123	34.783	0.00	0.00	0.00	1.82
1008	1036	4.141959	CCAAAGAAAAGCCCTCTCAAACAA	60.142	41.667	0.00	0.00	0.00	2.83
1010	1038	3.384789	ACCAAAGAAAAGCCCTCTCAAAC	59.615	43.478	0.00	0.00	0.00	2.93
1029	1059	3.788227	ACCTGAATCTGTAAGCAACCA	57.212	42.857	0.00	0.00	0.00	3.67
1099	1129	5.047519	CCATCTGTGCTCAAATTCTTCCTTT	60.048	40.000	0.00	0.00	0.00	3.11
1213	1243	3.127030	GCATTGTTGTAACTAGGAGGTGC	59.873	47.826	0.00	0.00	0.00	5.01
1494	1524	1.688735	CTGCGGATATCCTCCTTGTCA	59.311	52.381	19.61	5.62	42.47	3.58
1602	1632	1.079612	TGCACAGAGCTCCATCACG	60.080	57.895	10.93	0.00	45.94	4.35
1770	1800	2.013563	GCATTCTCATCCTTGGTCGCA	61.014	52.381	0.00	0.00	0.00	5.10
2293	2324	2.426024	CAACCATTAAGCAGCTGCAGAT	59.574	45.455	38.24	25.68	45.16	2.90
2387	2418	2.061848	TCCCCAATGAGAACACCTTGA	58.938	47.619	0.00	0.00	0.00	3.02
2406	2437	1.590238	CTCACACATCGCGAAGGAATC	59.410	52.381	15.24	0.00	0.00	2.52
2407	2438	1.645034	CTCACACATCGCGAAGGAAT	58.355	50.000	15.24	0.00	0.00	3.01
2409	2440	1.215382	CCTCACACATCGCGAAGGA	59.785	57.895	15.24	5.63	0.00	3.36
2411	2442	2.456119	GCCCTCACACATCGCGAAG	61.456	63.158	15.24	12.48	0.00	3.79
2413	2444	2.942796	AAGCCCTCACACATCGCGA	61.943	57.895	13.09	13.09	0.00	5.87
2414	2445	2.434884	AAGCCCTCACACATCGCG	60.435	61.111	0.00	0.00	0.00	5.87
2415	2446	2.401766	CCAAGCCCTCACACATCGC	61.402	63.158	0.00	0.00	0.00	4.58
2416	2447	1.746615	CCCAAGCCCTCACACATCG	60.747	63.158	0.00	0.00	0.00	3.84
2482	2518	4.468153	GGACTACTCCCAAATTCTGAGACT	59.532	45.833	6.00	0.00	0.00	3.24
2658	2694	4.265073	AGTCGCAATGCCTCTAGAAAATT	58.735	39.130	0.00	0.00	0.00	1.82
2783	2819	4.039703	CAGCACAAATGAATAGCCATTCG	58.960	43.478	0.37	0.00	43.06	3.34
3108	3144	9.120538	AGTTTCTGCAAAGTAAAACAGAAGATA	57.879	29.630	4.68	0.00	46.52	1.98
3197	3233	5.120830	GTCTTTAGCGCTCTCAGAAATTGAA	59.879	40.000	16.34	0.00	34.81	2.69
3347	3383	5.711506	TGTTCTGATCCAGCATACACAAAAT	59.288	36.000	0.00	0.00	0.00	1.82
3745	3781	4.796038	ACGTTCTATATTATGGGACGGG	57.204	45.455	20.75	0.30	0.00	5.28
3762	3798	7.954786	CAGTTCAATTTAAACTGCAAAAACGTT	59.045	29.630	14.40	0.00	44.94	3.99
4059	4095	6.416750	GGTAAGGTTTGATGAAGAAAACAACG	59.583	38.462	0.00	0.00	37.89	4.10
4100	4136	5.241506	ACATTAATGAAGTGTGAACCTGTGG	59.758	40.000	22.16	0.00	0.00	4.17
4172	4208	2.158623	TCAACTCAAGCCATGTGGTTCT	60.159	45.455	0.35	0.00	37.57	3.01
4360	4396	7.662669	CCATCAAGAAAATGGAAGGAACAAAAT	59.337	33.333	0.00	0.00	45.51	1.82
4361	4397	6.991531	CCATCAAGAAAATGGAAGGAACAAAA	59.008	34.615	0.00	0.00	45.51	2.44
4638	4674	9.457436	AAAAACCAACTTACAGAAGAAAGTAGA	57.543	29.630	0.00	0.00	34.91	2.59
4860	4896	6.040166	CCTCCCAACTATCATTTTCCTTGATG	59.960	42.308	0.00	0.00	35.50	3.07
4898	4934	3.820777	TTTGTTTTTGTTGTTGCTGCC	57.179	38.095	0.00	0.00	0.00	4.85
5043	5080	7.226720	GGACAGAAACATCAACAAAGAACTAGA	59.773	37.037	0.00	0.00	0.00	2.43
5055	5092	7.000472	AGAGAAATCAAGGACAGAAACATCAA	59.000	34.615	0.00	0.00	0.00	2.57
5085	5124	5.709164	CCAATCTTTGACATGGAAGAAGTCT	59.291	40.000	10.99	0.00	35.69	3.24
5209	5251	3.002791	CTCCAAAAGCTCTCGTGCATAA	58.997	45.455	0.00	0.00	34.99	1.90
5357	5411	4.124970	GCAGAGATGCATATGTTGAGACA	58.875	43.478	0.00	0.00	36.00	3.41
5652	5715	5.106157	TGGTTTTAGTACTACTAGGCACGAC	60.106	44.000	0.91	0.00	31.47	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.