AutoCloner

Multiple sequence alignment - TraesCS4B01G284300

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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	TraesCS4B01G284300	chr4B	100.000	3623	0	0	1	3623	567677983	567681605	0.000000e+00	6691
1	TraesCS4B01G284300	chr4B	94.032	3435	180	15	207	3623	338723259	338719832	0.000000e+00	5184
2	TraesCS4B01G284300	chr4B	92.277	3535	249	18	102	3623	447262775	447259252	0.000000e+00	4994
3	TraesCS4B01G284300	chr1B	92.983	3634	237	8	2	3623	593273430	593269803	0.000000e+00	5282
4	TraesCS4B01G284300	chr7B	91.462	3631	278	21	7	3623	242307482	242303870	0.000000e+00	4959
5	TraesCS4B01G284300	chr7B	91.606	3562	274	19	77	3623	387406984	387410535	0.000000e+00	4898
6	TraesCS4B01G284300	chr7B	91.560	3531	271	20	110	3623	246678694	246675174	0.000000e+00	4844
7	TraesCS4B01G284300	chr7B	87.879	231	26	2	1	229	182942617	182942387	1.660000e-68	270
8	TraesCS4B01G284300	chr3B	91.503	3519	271	21	121	3623	528819598	528816092	0.000000e+00	4817
9	TraesCS4B01G284300	chr3B	91.152	3515	271	27	122	3623	51346890	51350377	0.000000e+00	4732
10	TraesCS4B01G284300	chr2B	91.147	3558	292	17	80	3623	566810057	566806509	0.000000e+00	4804
11	TraesCS4B01G284300	chr2B	85.737	1283	118	34	2355	3623	405162906	405164137	0.000000e+00	1295
12	TraesCS4B01G284300	chr2B	86.409	1192	98	39	2442	3623	749455139	749456276	0.000000e+00	1245
13	TraesCS4B01G284300	chr2B	86.314	1191	99	40	2442	3623	637508454	637507319	0.000000e+00	1238
14	TraesCS4B01G284300	chr2B	90.430	930	65	12	2707	3623	279187925	279187007	0.000000e+00	1203
15	TraesCS4B01G284300	chr2B	95.652	230	10	0	1	230	337504246	337504475	1.590000e-98	370

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	TraesCS4B01G284300	chr4B	567677983	567681605	3622	False	6691	6691	100.000	1	3623	1	chr4B.!!$F1	3622
1	TraesCS4B01G284300	chr4B	338719832	338723259	3427	True	5184	5184	94.032	207	3623	1	chr4B.!!$R1	3416
2	TraesCS4B01G284300	chr4B	447259252	447262775	3523	True	4994	4994	92.277	102	3623	1	chr4B.!!$R2	3521
3	TraesCS4B01G284300	chr1B	593269803	593273430	3627	True	5282	5282	92.983	2	3623	1	chr1B.!!$R1	3621
4	TraesCS4B01G284300	chr7B	242303870	242307482	3612	True	4959	4959	91.462	7	3623	1	chr7B.!!$R2	3616
5	TraesCS4B01G284300	chr7B	387406984	387410535	3551	False	4898	4898	91.606	77	3623	1	chr7B.!!$F1	3546
6	TraesCS4B01G284300	chr7B	246675174	246678694	3520	True	4844	4844	91.560	110	3623	1	chr7B.!!$R3	3513
7	TraesCS4B01G284300	chr3B	528816092	528819598	3506	True	4817	4817	91.503	121	3623	1	chr3B.!!$R1	3502
8	TraesCS4B01G284300	chr3B	51346890	51350377	3487	False	4732	4732	91.152	122	3623	1	chr3B.!!$F1	3501
9	TraesCS4B01G284300	chr2B	566806509	566810057	3548	True	4804	4804	91.147	80	3623	1	chr2B.!!$R2	3543
10	TraesCS4B01G284300	chr2B	405162906	405164137	1231	False	1295	1295	85.737	2355	3623	1	chr2B.!!$F2	1268
11	TraesCS4B01G284300	chr2B	749455139	749456276	1137	False	1245	1245	86.409	2442	3623	1	chr2B.!!$F3	1181
12	TraesCS4B01G284300	chr2B	637507319	637508454	1135	True	1238	1238	86.314	2442	3623	1	chr2B.!!$R3	1181
13	TraesCS4B01G284300	chr2B	279187007	279187925	918	True	1203	1203	90.430	2707	3623	1	chr2B.!!$R1	916

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
841	846	0.322816	AAGCTGCAATCCGTGACCAT	60.323	50.000	1.02	0.00	3.55	F
1142	1148	0.322975	AGCCTCGTGCAATCAGAAGT	59.677	50.000	0.00	44.83	3.01	F
1965	1971	1.754226	GAAGATCCAGAGGAAGAGCGT	59.246	52.381	0.00	34.34	5.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2012	2018	1.891150	CACTTGGGAATTGCAGCTCTT	59.109	47.619	0.00	2.85	R
2493	2499	2.906389	AGAGACAATGCAAGTGGTAGGA	59.094	45.455	35.33	2.94	R
3445	3490	2.099263	CGAAGTGACATACCACCGATCT	59.901	50.000	37.76	2.75	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
46	47	6.857777	AAGCAAAGATAATCTTCATCTCCG	57.142	37.500	0.00	0.00	35.27	4.63
55	56	2.337583	TCTTCATCTCCGTTTGCTTCG	58.662	47.619	0.00	0.00	0.00	3.79
80	81	6.071728	GGTGTCATTTCCTTTGTTGATGATCT	60.072	38.462	0.00	0.00	0.00	2.75
82	83	8.514594	GTGTCATTTCCTTTGTTGATGATCTTA	58.485	33.333	0.00	0.00	0.00	2.10
89	90	9.436957	TTCCTTTGTTGATGATCTTAGTTAGTC	57.563	33.333	0.00	0.00	0.00	2.59
93	94	9.996554	TTTGTTGATGATCTTAGTTAGTCTTGA	57.003	29.630	0.00	0.00	0.00	3.02
94	95	8.988064	TGTTGATGATCTTAGTTAGTCTTGAC	57.012	34.615	0.00	0.00	0.00	3.18
112	113	8.940952	AGTCTTGACTTAATATTCTGCTTTCAC	58.059	33.333	0.00	0.00	0.00	3.18
174	175	2.363795	TCGCCTAGTCCCTGTGGG	60.364	66.667	0.00	0.00	46.11	4.61
194	195	0.503117	GAACACGACACTCGCAGTTC	59.497	55.000	12.04	12.04	45.12	3.01
229	233	4.109766	CCGCTGTACTTACAATCGATCAA	58.890	43.478	0.00	0.00	35.59	2.57
238	242	1.745087	ACAATCGATCAATTTGGCGCT	59.255	42.857	7.64	0.00	0.00	5.92
243	247	1.401409	CGATCAATTTGGCGCTGTTGT	60.401	47.619	7.64	0.00	0.00	3.32
428	433	5.535030	TGTGAGCGTGTGTAGGATATCTTAT	59.465	40.000	2.05	0.00	0.00	1.73
491	496	5.407387	GCTTTAGTACGTGATCTTTGGTTGA	59.593	40.000	0.00	0.00	0.00	3.18
500	505	5.333339	CGTGATCTTTGGTTGACAAGTAGTG	60.333	44.000	0.00	0.00	40.82	2.74
667	672	5.012148	GGAGTATGCCAATACAGTCCAGTAT	59.988	44.000	0.00	0.00	41.09	2.12
674	679	4.444733	CCAATACAGTCCAGTATCATGGCA	60.445	45.833	0.00	0.00	40.41	4.92
748	753	4.501743	GCTGCTAAGGACTGGTACTATTCC	60.502	50.000	7.46	7.46	0.00	3.01
801	806	4.503741	TTTCACAAGCTTTCCTGCATAC	57.496	40.909	0.00	0.00	34.99	2.39
841	846	0.322816	AAGCTGCAATCCGTGACCAT	60.323	50.000	1.02	0.00	0.00	3.55
865	870	1.267806	CTCAGTTTTGCGCAAGATGGT	59.732	47.619	23.68	5.17	43.02	3.55
1032	1038	4.520492	GGTGGAACAATCATGAACAAGACT	59.480	41.667	0.00	0.00	44.16	3.24
1035	1041	5.239306	TGGAACAATCATGAACAAGACTGTC	59.761	40.000	0.00	0.00	30.42	3.51
1142	1148	0.322975	AGCCTCGTGCAATCAGAAGT	59.677	50.000	0.00	0.00	44.83	3.01
1342	1348	5.013079	ACTGTAGATCAGATGGAAACCACAA	59.987	40.000	0.00	0.00	46.27	3.33
1355	1361	4.142381	GGAAACCACAATAGCAGATCCAAC	60.142	45.833	0.00	0.00	0.00	3.77
1535	1541	2.660572	TGCCCACACTTGTGTTACAAT	58.339	42.857	8.52	0.00	44.21	2.71
1536	1542	2.360483	TGCCCACACTTGTGTTACAATG	59.640	45.455	8.52	0.00	44.21	2.82
1794	1800	3.258372	GGTGGAAGTCATCAGTGTCACTA	59.742	47.826	4.85	0.00	0.00	2.74
1894	1900	8.899427	ACCAGATCATGTTAGTGAATATTCAG	57.101	34.615	18.47	5.43	37.98	3.02
1904	1910	7.293299	TGTTAGTGAATATTCAGAGATGGGGAT	59.707	37.037	18.47	0.00	37.98	3.85
1963	1969	4.021192	CCATAGAAGATCCAGAGGAAGAGC	60.021	50.000	0.00	0.00	34.34	4.09
1965	1971	1.754226	GAAGATCCAGAGGAAGAGCGT	59.246	52.381	0.00	0.00	34.34	5.07
1983	1989	3.007398	AGCGTCCTCAACTTGAAGAAGAT	59.993	43.478	0.00	0.00	32.98	2.40
1984	1990	3.748568	GCGTCCTCAACTTGAAGAAGATT	59.251	43.478	0.00	0.00	32.98	2.40
1988	1994	6.423905	CGTCCTCAACTTGAAGAAGATTTACA	59.576	38.462	0.00	0.00	32.98	2.41
1989	1995	7.042051	CGTCCTCAACTTGAAGAAGATTTACAA	60.042	37.037	0.00	0.00	32.98	2.41
2012	2018	6.119240	AGAAGACAAGGAACAAGATGATCA	57.881	37.500	0.00	0.00	0.00	2.92
2019	2025	4.515361	AGGAACAAGATGATCAAGAGCTG	58.485	43.478	0.00	0.00	0.00	4.24
2020	2026	3.065095	GGAACAAGATGATCAAGAGCTGC	59.935	47.826	0.00	0.00	0.00	5.25
2023	2029	4.270834	ACAAGATGATCAAGAGCTGCAAT	58.729	39.130	0.00	0.00	0.00	3.56
2024	2030	4.705507	ACAAGATGATCAAGAGCTGCAATT	59.294	37.500	0.00	0.00	0.00	2.32
2025	2031	5.163642	ACAAGATGATCAAGAGCTGCAATTC	60.164	40.000	0.00	0.00	0.00	2.17
2063	2069	7.284489	AGTTGAAGACTCATCATCTACTACTCC	59.716	40.741	0.00	0.00	37.03	3.85
2085	2091	3.403038	TGAAGAAGTACAAGAAGCTGCC	58.597	45.455	0.00	0.00	0.00	4.85
2105	2111	4.081697	TGCCGTAGATGAAGATGAAGAACA	60.082	41.667	0.00	0.00	0.00	3.18
2177	2183	3.284617	CCAATCCTCTTGATGACATGCA	58.715	45.455	0.00	0.00	32.68	3.96
2321	2327	5.410924	TGATGATCACAGTTACTTTCCTCG	58.589	41.667	0.00	0.00	0.00	4.63
2493	2499	6.936900	CGATTGATGACTTGGAGGGTATTATT	59.063	38.462	0.00	0.00	0.00	1.40
2846	2862	7.718753	TGCTGAAATCAAATGTTATTTGGGTTT	59.281	29.630	12.72	13.04	0.00	3.27
3050	3069	9.077885	ACTTAATCATTTTCTGCTTTTACCTCA	57.922	29.630	0.00	0.00	0.00	3.86
3199	3219	5.248640	TGGAGAAGTGATGATTCCTGTTTC	58.751	41.667	0.00	0.00	0.00	2.78
3399	3421	2.041216	GTGGTATGTTCCTTTGGGGAGT	59.959	50.000	0.00	0.00	46.01	3.85
3460	3505	2.219458	TCTCGAGATCGGTGGTATGTC	58.781	52.381	12.08	0.00	40.29	3.06
3461	3506	1.947456	CTCGAGATCGGTGGTATGTCA	59.053	52.381	6.58	0.00	40.29	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	6.909357	GCAAACGGAGATGAAGATTATCTTTG	59.091	38.462	8.99	0.91	36.73	2.77
46	47	2.293399	AGGAAATGACACCGAAGCAAAC	59.707	45.455	0.00	0.00	0.00	2.93
55	56	5.452078	TCATCAACAAAGGAAATGACACC	57.548	39.130	0.00	0.00	0.00	4.16
89	90	8.044060	TGGTGAAAGCAGAATATTAAGTCAAG	57.956	34.615	0.00	0.00	40.88	3.02
112	113	5.996644	TCTAGGTAACACAATATTGGGTGG	58.003	41.667	23.69	10.06	45.74	4.61
174	175	0.874607	AACTGCGAGTGTCGTGTTCC	60.875	55.000	0.00	0.00	42.81	3.62
198	199	5.601583	TGTAAGTACAGCGGGATATTTCA	57.398	39.130	0.00	0.00	0.00	2.69
199	200	6.128902	CGATTGTAAGTACAGCGGGATATTTC	60.129	42.308	0.00	0.00	37.52	2.17
229	233	2.625823	CCCGACAACAGCGCCAAAT	61.626	57.895	2.29	0.00	0.00	2.32
238	242	1.870055	GACGCTAGTCCCCGACAACA	61.870	60.000	0.00	0.00	41.41	3.33
243	247	2.513204	CTCGACGCTAGTCCCCGA	60.513	66.667	0.00	0.00	44.28	5.14
269	273	7.852971	ATACTAAGCCTAGTCTATAGCTTCG	57.147	40.000	16.56	13.94	44.13	3.79
392	397	3.066621	ACACGCTCACAAACATCAAACAT	59.933	39.130	0.00	0.00	0.00	2.71
491	496	2.626266	TCATCGTGTCCACACTACTTGT	59.374	45.455	8.19	0.00	44.34	3.16
500	505	1.741770	GCCCTGTCATCGTGTCCAC	60.742	63.158	0.00	0.00	0.00	4.02
667	672	1.758280	GCATCTTGGGAAATGCCATGA	59.242	47.619	11.08	11.08	41.92	3.07
674	679	5.513233	ACACTTGATAGCATCTTGGGAAAT	58.487	37.500	0.00	0.00	0.00	2.17
832	837	3.543680	AAACTGAGGATATGGTCACGG	57.456	47.619	0.00	0.00	0.00	4.94
841	846	3.052455	TCTTGCGCAAAACTGAGGATA	57.948	42.857	25.01	0.00	0.00	2.59
865	870	2.762887	AGCTGCATACAAGCTCTCACTA	59.237	45.455	1.02	0.00	32.98	2.74
1032	1038	3.055458	TGAGAATAATTGCACCCTCGACA	60.055	43.478	0.00	0.00	0.00	4.35
1035	1041	4.576053	TCAATGAGAATAATTGCACCCTCG	59.424	41.667	0.00	0.00	0.00	4.63
1127	1133	2.287644	CACACAACTTCTGATTGCACGA	59.712	45.455	0.00	0.00	0.00	4.35
1128	1134	2.032054	ACACACAACTTCTGATTGCACG	59.968	45.455	0.00	0.00	0.00	5.34
1142	1148	5.432645	TCTGTTCACTTATGGAACACACAA	58.567	37.500	4.02	0.00	46.95	3.33
1313	1319	7.038302	TGGTTTCCATCTGATCTACAGTAGTTT	60.038	37.037	7.50	0.00	45.86	2.66
1317	1323	5.719563	TGTGGTTTCCATCTGATCTACAGTA	59.280	40.000	0.00	0.00	45.86	2.74
1342	1348	3.181447	CCATGAGGTGTTGGATCTGCTAT	60.181	47.826	0.00	0.00	34.81	2.97
1355	1361	2.559668	ACAGTTTCATTGCCATGAGGTG	59.440	45.455	0.24	3.23	40.66	4.00
1535	1541	4.473196	TCTTGACAAATAGCCCAGATACCA	59.527	41.667	0.00	0.00	0.00	3.25
1536	1542	5.036117	TCTTGACAAATAGCCCAGATACC	57.964	43.478	0.00	0.00	0.00	2.73
1794	1800	5.316167	TCACCATCACTGCTAAGTTTCAAT	58.684	37.500	0.00	0.00	32.98	2.57
1894	1900	4.219115	TGAGTCTGAAGTATCCCCATCTC	58.781	47.826	0.00	0.00	0.00	2.75
1904	1910	7.171508	CAGCAACACTTAATTGAGTCTGAAGTA	59.828	37.037	9.82	0.00	0.00	2.24
1963	1969	5.931441	AAATCTTCTTCAAGTTGAGGACG	57.069	39.130	16.57	14.86	31.94	4.79
1965	1971	8.210946	TCTTGTAAATCTTCTTCAAGTTGAGGA	58.789	33.333	13.28	13.28	37.39	3.71
1983	1989	7.773224	TCATCTTGTTCCTTGTCTTCTTGTAAA	59.227	33.333	0.00	0.00	0.00	2.01
1984	1990	7.279615	TCATCTTGTTCCTTGTCTTCTTGTAA	58.720	34.615	0.00	0.00	0.00	2.41
1988	1994	6.537355	TGATCATCTTGTTCCTTGTCTTCTT	58.463	36.000	0.00	0.00	0.00	2.52
1989	1995	6.119240	TGATCATCTTGTTCCTTGTCTTCT	57.881	37.500	0.00	0.00	0.00	2.85
2012	2018	1.891150	CACTTGGGAATTGCAGCTCTT	59.109	47.619	0.00	0.00	0.00	2.85
2019	2025	4.022068	TCAACTTGATCACTTGGGAATTGC	60.022	41.667	10.92	0.00	0.00	3.56
2020	2026	5.710513	TCAACTTGATCACTTGGGAATTG	57.289	39.130	10.92	0.00	0.00	2.32
2023	2029	4.821805	GTCTTCAACTTGATCACTTGGGAA	59.178	41.667	10.92	4.79	0.00	3.97
2024	2030	4.103153	AGTCTTCAACTTGATCACTTGGGA	59.897	41.667	10.92	7.93	33.03	4.37
2025	2031	4.392940	AGTCTTCAACTTGATCACTTGGG	58.607	43.478	10.92	6.31	33.03	4.12
2063	2069	3.434984	GGCAGCTTCTTGTACTTCTTCAG	59.565	47.826	0.00	0.00	0.00	3.02
2085	2091	7.199078	TCTCATGTTCTTCATCTTCATCTACG	58.801	38.462	0.00	0.00	34.09	3.51
2105	2111	7.834881	ATGACAATAGGCAAATGAATCTCAT	57.165	32.000	0.00	0.00	39.09	2.90
2177	2183	7.001073	GGTAGAAGCAAAGGAATCATAAGGAT	58.999	38.462	0.00	0.00	38.05	3.24
2321	2327	6.538742	TGTTTCATTAAGCATAGGTCTAGCAC	59.461	38.462	0.00	0.00	0.00	4.40
2493	2499	2.906389	AGAGACAATGCAAGTGGTAGGA	59.094	45.455	0.00	0.00	35.33	2.94
2846	2862	6.350110	GGCAACATTTAAGACATGGCTTAAGA	60.350	38.462	28.14	20.64	40.35	2.10
3050	3069	5.416271	AAACGTGGTGATCTAGGTGTATT	57.584	39.130	0.00	0.00	0.00	1.89
3199	3219	8.015087	TCTTAAATGAACAACGCATAAGAACAG	58.985	33.333	0.00	0.00	0.00	3.16
3445	3490	2.099263	CGAAGTGACATACCACCGATCT	59.901	50.000	0.00	0.00	37.76	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.