AutoCloner

Multiple sequence alignment - TraesCS3B01G203600

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	TraesCS3B01G203600	chr3B	100.000	2910	0	0	1	2910	237604598	237607507	0.000000e+00	5374
1	TraesCS3B01G203600	chr3B	98.941	944	10	0	1967	2910	688316405	688315462	0.000000e+00	1688
2	TraesCS3B01G203600	chr3B	98.522	947	11	1	1967	2910	688267000	688266054	0.000000e+00	1668
3	TraesCS3B01G203600	chr3B	96.186	944	35	1	1967	2910	4423630	4424572	0.000000e+00	1543
4	TraesCS3B01G203600	chr3A	91.015	1970	166	5	1	1967	189341233	189339272	0.000000e+00	2647
5	TraesCS3B01G203600	chr3A	89.946	368	37	0	1	368	187454133	187454500	2.620000e-130	475
6	TraesCS3B01G203600	chr3D	96.035	1362	51	2	608	1967	160882855	160884215	0.000000e+00	2213
7	TraesCS3B01G203600	chr3D	94.714	454	23	1	158	611	160882223	160882675	0.000000e+00	704
8	TraesCS3B01G203600	chr3D	95.783	166	6	1	1	166	160875399	160875563	1.720000e-67	267
9	TraesCS3B01G203600	chr1A	98.840	948	9	2	1965	2910	567503815	567504762	0.000000e+00	1688
10	TraesCS3B01G203600	chr2A	98.835	944	11	0	1967	2910	762461997	762461054	0.000000e+00	1683
11	TraesCS3B01G203600	chr2A	98.835	944	10	1	1967	2910	770935914	770936856	0.000000e+00	1681
12	TraesCS3B01G203600	chr7A	98.729	944	12	0	1967	2910	561698539	561697596	0.000000e+00	1677
13	TraesCS3B01G203600	chr6B	98.726	942	10	2	1969	2910	577976548	577977487	0.000000e+00	1672
14	TraesCS3B01G203600	chr4B	95.228	943	45	0	1967	2909	667849035	667849977	0.000000e+00	1493

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	TraesCS3B01G203600	chr3B	237604598	237607507	2909	False	5374.0	5374	100.0000	1	2910	1	chr3B.!!$F2	2909
1	TraesCS3B01G203600	chr3B	688315462	688316405	943	True	1688.0	1688	98.9410	1967	2910	1	chr3B.!!$R2	943
2	TraesCS3B01G203600	chr3B	688266054	688267000	946	True	1668.0	1668	98.5220	1967	2910	1	chr3B.!!$R1	943
3	TraesCS3B01G203600	chr3B	4423630	4424572	942	False	1543.0	1543	96.1860	1967	2910	1	chr3B.!!$F1	943
4	TraesCS3B01G203600	chr3A	189339272	189341233	1961	True	2647.0	2647	91.0150	1	1967	1	chr3A.!!$R1	1966
5	TraesCS3B01G203600	chr3D	160882223	160884215	1992	False	1458.5	2213	95.3745	158	1967	2	chr3D.!!$F2	1809
6	TraesCS3B01G203600	chr1A	567503815	567504762	947	False	1688.0	1688	98.8400	1965	2910	1	chr1A.!!$F1	945
7	TraesCS3B01G203600	chr2A	762461054	762461997	943	True	1683.0	1683	98.8350	1967	2910	1	chr2A.!!$R1	943
8	TraesCS3B01G203600	chr2A	770935914	770936856	942	False	1681.0	1681	98.8350	1967	2910	1	chr2A.!!$F1	943
9	TraesCS3B01G203600	chr7A	561697596	561698539	943	True	1677.0	1677	98.7290	1967	2910	1	chr7A.!!$R1	943
10	TraesCS3B01G203600	chr6B	577976548	577977487	939	False	1672.0	1672	98.7260	1969	2910	1	chr6B.!!$F1	941
11	TraesCS3B01G203600	chr4B	667849035	667849977	942	False	1493.0	1493	95.2280	1967	2909	1	chr4B.!!$F1	942

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
80	81	0.390124	AACACGAGGCCACGAAACTA	59.610	50.0	29.67	0.0	37.03	2.24	F
1296	1483	0.546988	AACCACCTCCCACTCCTACC	60.547	60.0	0.00	0.0	0.00	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1352	1539	0.034896	GATACGGGGAATGCATCGGT	59.965	55.000	0.0	0.77	0.0	4.69	R
2884	3075	2.505405	TCAGTTCAGACGAGTGCTAGT	58.495	47.619	0.0	0.00	0.0	2.57	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
56	57	8.910944	TCATATAAGAGGGAGTAGTGTTGTTAC	58.089	37.037	0.00	0.00	0.00	2.50
80	81	0.390124	AACACGAGGCCACGAAACTA	59.610	50.000	29.67	0.00	37.03	2.24
95	96	5.627780	CACGAAACTAGGTAAAATTTGTGCC	59.372	40.000	0.00	0.00	0.00	5.01
96	97	5.158494	CGAAACTAGGTAAAATTTGTGCCC	58.842	41.667	0.00	0.00	0.00	5.36
132	133	6.946340	AGTAATGTGAGGTGACATGTTATCA	58.054	36.000	0.00	0.00	36.66	2.15
134	135	7.882791	AGTAATGTGAGGTGACATGTTATCAAA	59.117	33.333	0.00	0.00	36.66	2.69
135	136	7.523293	AATGTGAGGTGACATGTTATCAAAA	57.477	32.000	0.00	0.00	36.66	2.44
136	137	7.707624	ATGTGAGGTGACATGTTATCAAAAT	57.292	32.000	0.00	0.00	35.17	1.82
137	138	7.144722	TGTGAGGTGACATGTTATCAAAATC	57.855	36.000	0.00	0.00	0.00	2.17
138	139	6.150976	TGTGAGGTGACATGTTATCAAAATCC	59.849	38.462	0.00	0.00	0.00	3.01
139	140	6.150976	GTGAGGTGACATGTTATCAAAATCCA	59.849	38.462	0.00	0.00	0.00	3.41
140	141	6.891361	TGAGGTGACATGTTATCAAAATCCAT	59.109	34.615	0.00	0.00	0.00	3.41
172	173	6.759356	TCACCATATTGTTGTTAGGTACATCG	59.241	38.462	0.00	0.00	36.44	3.84
290	291	4.404394	TCACCTTCTTGGCGTAATCATCTA	59.596	41.667	0.00	0.00	40.22	1.98
367	369	7.588497	ACATCCTCCTTTTTATTAGGCATTC	57.412	36.000	0.00	0.00	32.59	2.67
378	380	8.551682	TTTTATTAGGCATTCCATCCATCTTT	57.448	30.769	0.00	0.00	33.74	2.52
391	393	5.066893	CCATCCATCTTTTCGACAATGTCAT	59.933	40.000	14.24	0.00	32.09	3.06
427	429	6.153851	TCTCCACTTCTACCGAAATATTGACA	59.846	38.462	0.00	0.00	0.00	3.58
517	519	5.486735	TGACCCGTCCAAAAGAGTAAATA	57.513	39.130	0.00	0.00	0.00	1.40
584	586	4.652421	AGTCAACACTTCCTGTACTGGTTA	59.348	41.667	17.42	7.29	30.51	2.85
601	603	2.287915	GGTTATGCATGCACCGACTAAG	59.712	50.000	25.37	0.00	0.00	2.18
606	608	1.532505	GCATGCACCGACTAAGCAATG	60.533	52.381	14.21	0.00	42.15	2.82
686	871	2.033801	GCTTTCTTCGGTATGCATGCAT	59.966	45.455	33.92	33.92	40.19	3.96
691	876	0.936600	TCGGTATGCATGCATCAACG	59.063	50.000	35.35	32.03	37.82	4.10
698	883	0.804364	GCATGCATCAACGTCTTGGA	59.196	50.000	14.21	0.00	0.00	3.53
707	892	6.428465	TGCATCAACGTCTTGGACTAATTAAA	59.572	34.615	0.00	0.00	0.00	1.52
714	899	5.469084	CGTCTTGGACTAATTAAATAGGGGC	59.531	44.000	2.71	0.00	0.00	5.80
743	928	6.397272	TCGGTAACAATAATCGTACTTTGGT	58.603	36.000	0.00	0.00	0.00	3.67
1020	1205	3.075882	TGATGGGGGAGATGTTGTTTCTT	59.924	43.478	0.00	0.00	0.00	2.52
1104	1289	2.375345	CGTTGCCCACCTATCCCCT	61.375	63.158	0.00	0.00	0.00	4.79
1121	1308	1.204062	CTGCGCACTAACAACCACG	59.796	57.895	5.66	0.00	0.00	4.94
1159	1346	2.939103	GCATCCACTCTTTCGCATACTT	59.061	45.455	0.00	0.00	0.00	2.24
1220	1407	2.128507	CCCACCTCTCGCCTACTCC	61.129	68.421	0.00	0.00	0.00	3.85
1296	1483	0.546988	AACCACCTCCCACTCCTACC	60.547	60.000	0.00	0.00	0.00	3.18
1352	1539	4.373116	GCGCCGTGGGTCTTCTCA	62.373	66.667	0.00	0.00	0.00	3.27
1399	1586	2.304180	CCAGGTTCACACTCTCTCCATT	59.696	50.000	0.00	0.00	0.00	3.16
1478	1665	1.152756	AGAACCACCCACCACTTGC	60.153	57.895	0.00	0.00	0.00	4.01
1540	1727	0.768221	TCTGGGCTCTCCAAAGTGGT	60.768	55.000	0.00	0.00	46.51	4.16
1553	1740	4.080243	TCCAAAGTGGTCTCAACCTTTACA	60.080	41.667	0.00	0.00	46.60	2.41
1757	1944	1.931705	GGGGTTGATGGTGGGGGTA	60.932	63.158	0.00	0.00	0.00	3.69
1763	1950	4.106663	GGGTTGATGGTGGGGGTATTAATA	59.893	45.833	0.00	0.00	0.00	0.98
1844	2031	1.002624	GTGCCTTTGTCATCGGGGA	60.003	57.895	0.00	0.00	0.00	4.81
1870	2057	0.694771	AGGAGACAGAGCATTTGCCA	59.305	50.000	0.00	0.00	43.38	4.92
1913	2100	3.019564	GCTGTGGCACAGGAATAAGAAT	58.980	45.455	39.74	0.00	46.01	2.40
2319	2510	1.251527	ACCACGAACGGATCAGAGCT	61.252	55.000	0.00	0.00	0.00	4.09
2590	2781	5.305386	TGTTGAATAGTCTCATCCCGATCAT	59.695	40.000	0.00	0.00	0.00	2.45
2884	3075	0.468214	TTGTTCCCAACGATTGCCCA	60.468	50.000	0.00	0.00	0.00	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	75	5.475719	GGGGCACAAATTTTACCTAGTTTC	58.524	41.667	0.00	0.00	0.00	2.78
80	81	1.616374	CACGGGGCACAAATTTTACCT	59.384	47.619	0.00	0.00	0.00	3.08
95	96	3.383505	TCACATTACTAGATGGTCACGGG	59.616	47.826	0.00	0.00	0.00	5.28
96	97	4.499865	CCTCACATTACTAGATGGTCACGG	60.500	50.000	0.00	0.00	0.00	4.94
132	133	8.980596	ACAATATGGTGAATGTACATGGATTTT	58.019	29.630	9.63	0.00	0.00	1.82
134	135	8.415553	CAACAATATGGTGAATGTACATGGATT	58.584	33.333	9.63	0.00	37.20	3.01
135	136	7.560991	ACAACAATATGGTGAATGTACATGGAT	59.439	33.333	9.63	0.00	37.20	3.41
136	137	6.889177	ACAACAATATGGTGAATGTACATGGA	59.111	34.615	9.63	0.00	37.20	3.41
137	138	7.099266	ACAACAATATGGTGAATGTACATGG	57.901	36.000	9.63	0.00	37.20	3.66
138	139	9.720667	CTAACAACAATATGGTGAATGTACATG	57.279	33.333	9.63	0.00	37.20	3.21
139	140	8.902806	CCTAACAACAATATGGTGAATGTACAT	58.097	33.333	1.41	1.41	37.20	2.29
140	141	7.885922	ACCTAACAACAATATGGTGAATGTACA	59.114	33.333	0.00	0.00	37.20	2.90
172	173	3.694734	CCAAATATCGATGGTGTTGCAC	58.305	45.455	8.54	0.00	31.84	4.57
214	215	2.226912	AGCAGATCCGATCTACTAACGC	59.773	50.000	10.65	8.94	37.58	4.84
367	369	4.395854	TGACATTGTCGAAAAGATGGATGG	59.604	41.667	11.97	0.00	34.95	3.51
378	380	4.941263	CCCTTTTCCTATGACATTGTCGAA	59.059	41.667	11.97	6.55	34.95	3.71
391	393	3.870559	AGAAGTGGAGACCCTTTTCCTA	58.129	45.455	0.00	0.00	34.48	2.94
427	429	0.322456	TTTAGCTGCAAGGCGGACAT	60.322	50.000	1.02	0.00	37.02	3.06
517	519	2.521708	GTGCCCCTTTGCCACACT	60.522	61.111	0.00	0.00	0.00	3.55
584	586	0.392863	TGCTTAGTCGGTGCATGCAT	60.393	50.000	25.64	10.06	0.00	3.96
601	603	0.381089	GCATCTGAGCCTCACATTGC	59.619	55.000	0.00	0.00	0.00	3.56
606	608	1.202615	TGCATAGCATCTGAGCCTCAC	60.203	52.381	0.00	0.00	31.71	3.51
631	816	9.743057	CCCGCTTTATAAATAAATCAACATTGA	57.257	29.630	0.00	0.00	42.14	2.57
686	871	7.767198	CCCTATTTAATTAGTCCAAGACGTTGA	59.233	37.037	0.00	0.00	37.67	3.18
691	876	6.362248	TGCCCCTATTTAATTAGTCCAAGAC	58.638	40.000	4.22	0.00	0.00	3.01
698	883	6.183361	ACCGATCTTGCCCCTATTTAATTAGT	60.183	38.462	4.22	0.00	0.00	2.24
707	892	2.404559	TGTTACCGATCTTGCCCCTAT	58.595	47.619	0.00	0.00	0.00	2.57
714	899	7.925703	AGTACGATTATTGTTACCGATCTTG	57.074	36.000	0.00	0.00	0.00	3.02
743	928	0.537188	GGCTCGTGGATGAAGGAGAA	59.463	55.000	0.00	0.00	34.67	2.87
928	1113	1.639722	TGAGAGAAACGATGGGTGGA	58.360	50.000	0.00	0.00	0.00	4.02
1020	1205	3.240134	GAGGAGAAGGTGGCACGCA	62.240	63.158	12.17	0.00	43.02	5.24
1104	1289	2.248135	CCGTGGTTGTTAGTGCGCA	61.248	57.895	5.66	5.66	0.00	6.09
1220	1407	1.132500	GGAGGTAGGAGGGTGAATGG	58.868	60.000	0.00	0.00	0.00	3.16
1296	1483	4.252010	AGGGAGGGATAAGAATAAAGGGG	58.748	47.826	0.00	0.00	0.00	4.79
1352	1539	0.034896	GATACGGGGAATGCATCGGT	59.965	55.000	0.00	0.77	0.00	4.69
1399	1586	1.690633	GATGAGGAGGAGGGTGGCA	60.691	63.158	0.00	0.00	0.00	4.92
1478	1665	2.094854	AGGTAAACAACGTCTCCGCTAG	60.095	50.000	0.00	0.00	37.70	3.42
1540	1727	4.082190	CAGGAGTCGATGTAAAGGTTGAGA	60.082	45.833	0.00	0.00	0.00	3.27
1553	1740	3.148279	GGGGACGCAGGAGTCGAT	61.148	66.667	0.00	0.00	41.81	3.59
1575	1762	0.965363	GTCCATCAACCGGTGGCAAT	60.965	55.000	8.52	0.00	35.43	3.56
1586	1773	1.069978	TGCGAGAGTTGTGTCCATCAA	59.930	47.619	0.00	0.00	0.00	2.57
1675	1862	1.079875	CCGCAATCAAGCAATGCACC	61.080	55.000	8.35	0.00	40.04	5.01
1757	1944	6.521770	CGACCTGTCCCCATACCAATATTAAT	60.522	42.308	0.00	0.00	0.00	1.40
1763	1950	0.837272	CGACCTGTCCCCATACCAAT	59.163	55.000	0.00	0.00	0.00	3.16
1844	2031	1.649321	TGCTCTGTCTCCTCAATGGT	58.351	50.000	0.00	0.00	37.07	3.55
1870	2057	1.675641	GCCAATGACGCCCTTCACT	60.676	57.895	0.00	0.00	0.00	3.41
1883	2070	2.203669	TGCCACAGCCTTGCCAAT	60.204	55.556	0.00	0.00	38.69	3.16
2158	2349	6.680540	TCTAGTATTCCTACCTACTTTGCCT	58.319	40.000	0.00	0.00	30.98	4.75
2319	2510	3.008157	TGCAGGTTTTATTCCGGACTACA	59.992	43.478	1.83	0.00	0.00	2.74
2884	3075	2.505405	TCAGTTCAGACGAGTGCTAGT	58.495	47.619	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.