AutoCloner

Multiple sequence alignment - TraesCS3B01G111100

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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	TraesCS3B01G111100	chr3B	100.000	2636	0	0	1	2636	77314304	77316939	0.000000e+00	4868.0
1	TraesCS3B01G111100	chr3B	90.343	1605	112	21	229	1826	77349152	77350720	0.000000e+00	2065.0
2	TraesCS3B01G111100	chr3B	93.836	795	42	6	708	1495	77413602	77414396	0.000000e+00	1190.0
3	TraesCS3B01G111100	chr3B	90.162	803	62	4	1834	2636	77418464	77419249	0.000000e+00	1029.0
4	TraesCS3B01G111100	chr3B	93.103	348	18	2	1484	1831	77416727	77417068	3.030000e-139	505.0
5	TraesCS3B01G111100	chr3B	83.224	459	57	12	2187	2634	592529383	592528934	1.140000e-108	403.0
6	TraesCS3B01G111100	chr3B	86.486	296	26	6	275	567	77413269	77413553	1.970000e-81	313.0
7	TraesCS3B01G111100	chr3B	85.915	71	7	3	175	244	792345062	792345130	3.640000e-09	73.1
8	TraesCS3B01G111100	chr3D	90.261	2567	187	35	8	2525	48542199	48544751	0.000000e+00	3297.0
9	TraesCS3B01G111100	chr3D	91.411	2375	160	18	2	2360	48733607	48731261	0.000000e+00	3216.0
10	TraesCS3B01G111100	chr3D	83.037	507	73	9	2135	2630	180245860	180246364	5.180000e-122	448.0
11	TraesCS3B01G111100	chr3D	85.915	71	7	3	175	244	591120101	591120169	3.640000e-09	73.1
12	TraesCS3B01G111100	chr3A	90.220	1728	117	20	2	1712	60841316	60843008	0.000000e+00	2207.0
13	TraesCS3B01G111100	chr3A	82.846	513	75	5	2135	2636	374321594	374322104	5.180000e-122	448.0
14	TraesCS3B01G111100	chr1D	83.041	513	70	13	2133	2630	467784120	467784630	1.440000e-122	449.0
15	TraesCS3B01G111100	chr6D	82.846	513	74	10	2135	2636	55409171	55408662	5.180000e-122	448.0
16	TraesCS3B01G111100	chr5B	82.806	506	74	9	2137	2631	616729113	616729616	8.660000e-120	440.0
17	TraesCS3B01G111100	chr7A	82.387	511	71	10	2135	2631	21175929	21175424	6.740000e-116	427.0
18	TraesCS3B01G111100	chr7D	81.818	517	73	14	2135	2636	39790995	39791505	5.250000e-112	414.0
19	TraesCS3B01G111100	chr6B	73.439	817	141	36	692	1498	5282601	5283351	1.220000e-58	237.0
20	TraesCS3B01G111100	chrUn	85.915	71	7	3	175	244	155032296	155032228	3.640000e-09	73.1
21	TraesCS3B01G111100	chrUn	85.915	71	7	3	175	244	352277630	352277698	3.640000e-09	73.1

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	TraesCS3B01G111100	chr3B	77314304	77316939	2635	False	4868.00	4868	100.00000	1	2636	1	chr3B.!!$F1	2635
1	TraesCS3B01G111100	chr3B	77349152	77350720	1568	False	2065.00	2065	90.34300	229	1826	1	chr3B.!!$F2	1597
2	TraesCS3B01G111100	chr3B	77413269	77419249	5980	False	759.25	1190	90.89675	275	2636	4	chr3B.!!$F4	2361
3	TraesCS3B01G111100	chr3D	48542199	48544751	2552	False	3297.00	3297	90.26100	8	2525	1	chr3D.!!$F1	2517
4	TraesCS3B01G111100	chr3D	48731261	48733607	2346	True	3216.00	3216	91.41100	2	2360	1	chr3D.!!$R1	2358
5	TraesCS3B01G111100	chr3D	180245860	180246364	504	False	448.00	448	83.03700	2135	2630	1	chr3D.!!$F2	495
6	TraesCS3B01G111100	chr3A	60841316	60843008	1692	False	2207.00	2207	90.22000	2	1712	1	chr3A.!!$F1	1710
7	TraesCS3B01G111100	chr3A	374321594	374322104	510	False	448.00	448	82.84600	2135	2636	1	chr3A.!!$F2	501
8	TraesCS3B01G111100	chr1D	467784120	467784630	510	False	449.00	449	83.04100	2133	2630	1	chr1D.!!$F1	497
9	TraesCS3B01G111100	chr6D	55408662	55409171	509	True	448.00	448	82.84600	2135	2636	1	chr6D.!!$R1	501
10	TraesCS3B01G111100	chr5B	616729113	616729616	503	False	440.00	440	82.80600	2137	2631	1	chr5B.!!$F1	494
11	TraesCS3B01G111100	chr7A	21175424	21175929	505	True	427.00	427	82.38700	2135	2631	1	chr7A.!!$R1	496
12	TraesCS3B01G111100	chr7D	39790995	39791505	510	False	414.00	414	81.81800	2135	2636	1	chr7D.!!$F1	501
13	TraesCS3B01G111100	chr6B	5282601	5283351	750	False	237.00	237	73.43900	692	1498	1	chr6B.!!$F1	806

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
741	812	1.135888	GGTTTTATGTCCGTTCCGTGC	60.136	52.381	0.0	0.0	0.0	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2590	6453	0.03759	TGCCGGCTATGGTTCTTGTT	59.962	50.0	29.7	0.0	0.0	2.83	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	6.661377	TGCCACATGTACCTATTGTATTTGTT	59.339	34.615	0.00	0.00	29.81	2.83
34	35	4.698304	CCTATTGTATTTGTTGTGTCCGGT	59.302	41.667	0.00	0.00	0.00	5.28
64	65	5.239744	ACAACGCCACTACAAAATATGACAA	59.760	36.000	0.00	0.00	0.00	3.18
104	105	7.218228	AGTTGTGTTGCATATGAAATCTTGA	57.782	32.000	6.97	0.00	0.00	3.02
105	106	7.310664	AGTTGTGTTGCATATGAAATCTTGAG	58.689	34.615	6.97	0.00	0.00	3.02
111	112	9.176460	TGTTGCATATGAAATCTTGAGACATTA	57.824	29.630	6.97	0.00	0.00	1.90
316	369	4.925054	CGTTCAAATCCGGTAGTGAACTTA	59.075	41.667	27.87	7.00	44.90	2.24
364	417	6.139169	CGTCTTTTGAAAGAGAAAACATCACG	59.861	38.462	6.43	0.75	45.01	4.35
379	432	5.633830	ACATCACGCATGATTTCTTTTCT	57.366	34.783	0.00	0.00	43.40	2.52
447	503	4.109766	CAATCTTGTGTATGCATTGGCTG	58.890	43.478	3.54	0.00	41.91	4.85
489	545	5.595952	AGCACTCCCATTTAATGATTTCCTC	59.404	40.000	6.50	0.00	0.00	3.71
490	546	5.360714	GCACTCCCATTTAATGATTTCCTCA	59.639	40.000	6.50	0.00	38.53	3.86
491	547	6.681368	GCACTCCCATTTAATGATTTCCTCAC	60.681	42.308	6.50	0.00	36.48	3.51
492	548	5.590259	ACTCCCATTTAATGATTTCCTCACG	59.410	40.000	6.50	0.00	36.48	4.35
541	601	7.833183	AGATGAATCTTGCATTCCTAGTTTTCT	59.167	33.333	0.00	0.00	31.97	2.52
619	681	5.229423	TGGAAAGCTGACAATTATGCAAAC	58.771	37.500	0.00	0.00	0.00	2.93
697	768	1.999634	AAGCCCACAAGCCACTCACT	62.000	55.000	0.00	0.00	0.00	3.41
741	812	1.135888	GGTTTTATGTCCGTTCCGTGC	60.136	52.381	0.00	0.00	0.00	5.34
970	1054	6.476706	CGCAGATCATGAACAACTTATGTCTA	59.523	38.462	0.00	0.00	42.99	2.59
978	1062	7.377766	TGAACAACTTATGTCTATTGCCTTC	57.622	36.000	0.00	0.00	42.99	3.46
1051	1135	8.421784	AGTGTAGTTATCCATATACACAACTGG	58.578	37.037	14.62	0.00	46.64	4.00
1225	1315	2.135189	TGCTATCCAGGGTATGCCTTT	58.865	47.619	0.00	0.00	34.45	3.11
1234	1324	1.341581	GGGTATGCCTTTAAGGTGCCA	60.342	52.381	13.03	2.59	37.80	4.92
1309	1399	1.395826	CCGAGGCTGTCCTAAGGGAG	61.396	65.000	0.00	0.00	44.46	4.30
1513	3948	1.575244	CCATCGTCATTGATGCGTCT	58.425	50.000	7.58	0.00	43.52	4.18
1539	3974	0.811616	GGAGCGTATGTCTGCAAGGG	60.812	60.000	0.00	0.00	0.00	3.95
1746	4185	5.874810	TGCAAAAGAATAAGTAGACGCATCT	59.125	36.000	0.00	0.00	39.15	2.90
1753	4192	1.107114	AGTAGACGCATCTCCTGTGG	58.893	55.000	0.00	0.00	39.79	4.17
1787	4226	0.179045	CCTTTGGCTATACCGCAGCT	60.179	55.000	0.00	0.00	43.94	4.24
1812	4251	5.357032	AGGTGTTGTTTTTGTAAGAGTGGAG	59.643	40.000	0.00	0.00	0.00	3.86
1829	5665	3.792736	GGCATCCGGGTGCTGGTA	61.793	66.667	37.00	0.00	44.45	3.25
1830	5666	2.203070	GCATCCGGGTGCTGGTAG	60.203	66.667	32.57	0.00	41.82	3.18
1831	5667	3.031417	GCATCCGGGTGCTGGTAGT	62.031	63.158	32.57	0.00	41.82	2.73
1832	5668	1.144057	CATCCGGGTGCTGGTAGTC	59.856	63.158	0.00	0.00	0.00	2.59
1841	5677	2.496817	CTGGTAGTCAGAGGGCGC	59.503	66.667	0.00	0.00	46.18	6.53
1849	5685	2.437180	CAGAGGGCGCTGCATCAA	60.437	61.111	8.56	0.00	0.00	2.57
1917	5753	4.570369	CGGTGCAGTATGATGTGACAATTA	59.430	41.667	0.00	0.00	39.69	1.40
2035	5871	6.074516	CCATCTTTGCATCTGATTTAAATGCG	60.075	38.462	5.17	0.00	46.86	4.73
2152	5988	4.134563	TGTCTTTTTAGAGAAAAGGCGCT	58.865	39.130	7.64	0.00	42.88	5.92
2198	6034	8.852135	TCGAACTTAACCCAACTTTGAATTAAT	58.148	29.630	0.00	0.00	0.00	1.40
2199	6035	9.471084	CGAACTTAACCCAACTTTGAATTAATT	57.529	29.630	0.00	0.00	0.00	1.40
2300	6139	4.278419	GGAACTAGGCAGAACAACACAAAT	59.722	41.667	0.00	0.00	0.00	2.32
2314	6153	0.968405	ACAAATGCAACAGCGGGAAT	59.032	45.000	0.00	0.00	0.00	3.01
2353	6196	1.246056	ACTACGCCTGCACCGACTAA	61.246	55.000	8.82	0.00	0.00	2.24
2368	6211	4.021981	ACCGACTAACCAACTAAGTACACC	60.022	45.833	0.00	0.00	0.00	4.16
2449	6292	2.550978	CAACACTTGAGTTGTCTCCGT	58.449	47.619	0.00	0.00	42.93	4.69
2545	6408	1.050988	AGGTGTCCGAGCTGCCATAT	61.051	55.000	0.00	0.00	0.00	1.78
2556	6419	3.563223	AGCTGCCATATGAGAAGCAAAT	58.437	40.909	20.14	5.24	36.32	2.32
2569	6432	0.905357	AGCAAATAGAGCTGACCCGT	59.095	50.000	0.00	0.00	41.61	5.28
2590	6453	0.923358	AACCACAGGAGACCAACCAA	59.077	50.000	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.184068	ACAAATACAATAGGTACATGTGGCA	58.816	36.000	9.11	0.00	34.56	4.92
12	13	5.873179	ACCGGACACAACAAATACAATAG	57.127	39.130	9.46	0.00	0.00	1.73
81	82	7.272084	GTCTCAAGATTTCATATGCAACACAAC	59.728	37.037	0.00	0.00	0.00	3.32
102	103	7.908827	ATGCAATGCAATTTTTAATGTCTCA	57.091	28.000	13.45	0.00	43.62	3.27
104	105	7.758980	TCGTATGCAATGCAATTTTTAATGTCT	59.241	29.630	13.45	0.00	43.62	3.41
105	106	7.893824	TCGTATGCAATGCAATTTTTAATGTC	58.106	30.769	13.45	0.00	43.62	3.06
111	112	7.331440	TCTGATTTCGTATGCAATGCAATTTTT	59.669	29.630	13.45	0.00	43.62	1.94
165	166	8.865978	CATATGCAATGCAATATGGTTTCATAC	58.134	33.333	13.45	0.00	43.62	2.39
167	168	7.672240	TCATATGCAATGCAATATGGTTTCAT	58.328	30.769	23.84	6.38	43.62	2.57
227	280	8.455598	TTCATATGCAATGCAATATGATTTCG	57.544	30.769	25.67	10.18	43.62	3.46
285	338	1.794222	GGATTTGAACGTCTGCCGG	59.206	57.895	0.00	0.00	42.24	6.13
316	369	5.351465	CGCAGTCCAAATATACAACAAGACT	59.649	40.000	0.00	0.00	33.78	3.24
364	417	6.808704	GGAGTTTGGTAGAAAAGAAATCATGC	59.191	38.462	0.00	0.00	0.00	4.06
379	432	1.339631	CGAGGCCAATGGAGTTTGGTA	60.340	52.381	5.01	0.00	46.54	3.25
489	545	1.327460	CGATATGTCCACCTTTGCGTG	59.673	52.381	0.00	0.00	0.00	5.34
490	546	1.066430	ACGATATGTCCACCTTTGCGT	60.066	47.619	0.00	0.00	0.00	5.24
491	547	1.327460	CACGATATGTCCACCTTTGCG	59.673	52.381	0.00	0.00	0.00	4.85
492	548	1.064060	GCACGATATGTCCACCTTTGC	59.936	52.381	0.00	0.00	0.00	3.68
541	601	9.485206	GAGGATCCTATATTAGTTTACGCAAAA	57.515	33.333	16.16	0.00	0.00	2.44
619	681	2.330231	ACAATGTCGTGCGGATTTTG	57.670	45.000	0.00	0.00	0.00	2.44
655	718	6.263615	TGTATTATGTTGACGCATCGTAAC	57.736	37.500	0.00	0.00	41.37	2.50
659	722	4.203828	GCTTGTATTATGTTGACGCATCG	58.796	43.478	0.00	0.00	0.00	3.84
664	731	3.687212	TGTGGGCTTGTATTATGTTGACG	59.313	43.478	0.00	0.00	0.00	4.35
697	768	3.311990	AGCTGTCCATCATACCATCTGA	58.688	45.455	0.00	0.00	0.00	3.27
741	812	2.611224	GCAAGGGAAATGCAAAGAGGTG	60.611	50.000	0.00	0.00	43.29	4.00
791	862	5.611374	AGGATGGTTACCATATCGACAAAG	58.389	41.667	17.75	0.00	45.26	2.77
970	1054	3.510459	AGCTAAAAAGGTGGAAGGCAAT	58.490	40.909	0.00	0.00	0.00	3.56
973	1057	5.419155	AGATAAAGCTAAAAAGGTGGAAGGC	59.581	40.000	0.00	0.00	0.00	4.35
1513	3948	1.683385	CAGACATACGCTCCATCTCCA	59.317	52.381	0.00	0.00	0.00	3.86
1632	4070	4.400884	AGGCGCATACACCATTTTATTCAA	59.599	37.500	10.83	0.00	0.00	2.69
1670	4108	8.190784	CAGGGAACTTCGCTTTTATTCATTAAT	58.809	33.333	5.63	0.00	37.59	1.40
1746	4185	0.608130	CCACAAGATCGACCACAGGA	59.392	55.000	0.00	0.00	0.00	3.86
1753	4192	1.734465	CAAAGGCTCCACAAGATCGAC	59.266	52.381	0.00	0.00	0.00	4.20
1787	4226	6.416415	TCCACTCTTACAAAAACAACACCTA	58.584	36.000	0.00	0.00	0.00	3.08
1829	5665	3.382803	GATGCAGCGCCCTCTGACT	62.383	63.158	2.29	0.00	36.19	3.41
1830	5666	2.894387	GATGCAGCGCCCTCTGAC	60.894	66.667	2.29	0.00	36.19	3.51
1831	5667	2.958281	TTGATGCAGCGCCCTCTGA	61.958	57.895	2.29	0.00	36.19	3.27
1832	5668	2.437180	TTGATGCAGCGCCCTCTG	60.437	61.111	2.29	0.00	37.15	3.35
1849	5685	6.096423	TCCGTGAGTTTCTGCATATTACTAGT	59.904	38.462	0.00	0.00	0.00	2.57
1863	5699	4.324936	CGAATTTCTCTCTCCGTGAGTTTC	59.675	45.833	3.20	0.00	43.13	2.78
2077	5913	6.265196	GGGGTGCATATATCACAAAGAAATCA	59.735	38.462	13.68	0.00	36.22	2.57
2152	5988	2.602267	TCTTCTCGGGTTCGGCCA	60.602	61.111	2.24	0.00	39.65	5.36
2178	6014	9.713713	GGCTTAATTAATTCAAAGTTGGGTTAA	57.286	29.630	3.39	0.00	0.00	2.01
2181	6017	7.309770	TGGCTTAATTAATTCAAAGTTGGGT	57.690	32.000	3.39	0.00	0.00	4.51
2300	6139	3.372730	GGCATTCCCGCTGTTGCA	61.373	61.111	0.00	0.00	39.64	4.08
2323	6166	1.202582	CAGGCGTAGTGCTAGTTGTCT	59.797	52.381	0.00	0.00	45.43	3.41
2330	6173	2.577059	GGTGCAGGCGTAGTGCTA	59.423	61.111	7.20	0.00	45.43	3.49
2353	6196	4.262335	CCTTCTTCGGTGTACTTAGTTGGT	60.262	45.833	0.00	0.00	0.00	3.67
2368	6211	2.742372	CGGTGTGGCCCTTCTTCG	60.742	66.667	0.00	0.00	0.00	3.79
2545	6408	3.369892	GGGTCAGCTCTATTTGCTTCTCA	60.370	47.826	0.00	0.00	38.92	3.27
2556	6419	0.541063	TGGTTCACGGGTCAGCTCTA	60.541	55.000	0.00	0.00	0.00	2.43
2569	6432	0.472471	GGTTGGTCTCCTGTGGTTCA	59.528	55.000	0.00	0.00	0.00	3.18
2590	6453	0.037590	TGCCGGCTATGGTTCTTGTT	59.962	50.000	29.70	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.