AutoCloner

Multiple sequence alignment - TraesCS7B01G479600

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	TraesCS7B01G479600	chr7B	100.000	2621	0	0	1	2621	733927403	733930023	0.000000e+00	4841
1	TraesCS7B01G479600	chr7B	91.163	2037	157	8	1	2014	733862535	733864571	0.000000e+00	2743
2	TraesCS7B01G479600	chr7B	91.876	1514	122	1	502	2014	733887659	733889172	0.000000e+00	2113
3	TraesCS7B01G479600	chr7B	97.364	607	16	0	2015	2621	733942532	733943138	0.000000e+00	1033
4	TraesCS7B01G479600	chr7B	89.879	494	28	7	1	472	733887173	733887666	1.330000e-172	616
5	TraesCS7B01G479600	chr7A	94.888	2015	99	3	1	2014	727230924	727232935	0.000000e+00	3147
6	TraesCS7B01G479600	chr4B	98.026	608	12	0	2014	2621	138182794	138182187	0.000000e+00	1057
7	TraesCS7B01G479600	chr4B	97.368	608	16	0	2014	2621	786026	785419	0.000000e+00	1035
8	TraesCS7B01G479600	chr4B	97.204	608	17	0	2014	2621	38674285	38673678	0.000000e+00	1029
9	TraesCS7B01G479600	chr4B	97.204	608	17	0	2014	2621	74595077	74595684	0.000000e+00	1029
10	TraesCS7B01G479600	chr4B	97.204	608	16	1	2014	2621	760097	759491	0.000000e+00	1027
11	TraesCS7B01G479600	chr5B	97.533	608	15	0	2014	2621	508338558	508339165	0.000000e+00	1040
12	TraesCS7B01G479600	chr2B	97.209	609	16	1	2014	2621	355895661	355895053	0.000000e+00	1029
13	TraesCS7B01G479600	chr4A	96.895	612	18	1	2010	2621	740724747	740725357	0.000000e+00	1024

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	TraesCS7B01G479600	chr7B	733927403	733930023	2620	False	4841.0	4841	100.0000	1	2621	1	chr7B.!!$F2	2620
1	TraesCS7B01G479600	chr7B	733862535	733864571	2036	False	2743.0	2743	91.1630	1	2014	1	chr7B.!!$F1	2013
2	TraesCS7B01G479600	chr7B	733887173	733889172	1999	False	1364.5	2113	90.8775	1	2014	2	chr7B.!!$F4	2013
3	TraesCS7B01G479600	chr7B	733942532	733943138	606	False	1033.0	1033	97.3640	2015	2621	1	chr7B.!!$F3	606
4	TraesCS7B01G479600	chr7A	727230924	727232935	2011	False	3147.0	3147	94.8880	1	2014	1	chr7A.!!$F1	2013
5	TraesCS7B01G479600	chr4B	138182187	138182794	607	True	1057.0	1057	98.0260	2014	2621	1	chr4B.!!$R4	607
6	TraesCS7B01G479600	chr4B	785419	786026	607	True	1035.0	1035	97.3680	2014	2621	1	chr4B.!!$R2	607
7	TraesCS7B01G479600	chr4B	38673678	38674285	607	True	1029.0	1029	97.2040	2014	2621	1	chr4B.!!$R3	607
8	TraesCS7B01G479600	chr4B	74595077	74595684	607	False	1029.0	1029	97.2040	2014	2621	1	chr4B.!!$F1	607
9	TraesCS7B01G479600	chr4B	759491	760097	606	True	1027.0	1027	97.2040	2014	2621	1	chr4B.!!$R1	607
10	TraesCS7B01G479600	chr5B	508338558	508339165	607	False	1040.0	1040	97.5330	2014	2621	1	chr5B.!!$F1	607
11	TraesCS7B01G479600	chr2B	355895053	355895661	608	True	1029.0	1029	97.2090	2014	2621	1	chr2B.!!$R1	607
12	TraesCS7B01G479600	chr4A	740724747	740725357	610	False	1024.0	1024	96.8950	2010	2621	1	chr4A.!!$F1	611

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
757	780	0.819582	CCCAAAGTTGCCTATGCCAG	59.180	55.0	0.0	0.0	36.33	4.85	F
773	796	1.162698	CCAGTCATGCCTCACACTTG	58.837	55.0	0.0	0.0	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1615	1638	0.899720	CGTGTTACCTTGGGCTAGGA	59.100	55.000	12.18	0.0	38.73	2.94	R
1636	1659	1.743394	GGGAAATGGTAAGAACAGCCG	59.257	52.381	0.00	0.0	0.00	5.52	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
66	67	3.397955	AGTGAGTTGGGGGATTTAACAGT	59.602	43.478	0.00	0.00	0.00	3.55
200	201	3.152341	GGAGAATTGGATGCATCGGAAT	58.848	45.455	20.15	16.64	0.00	3.01
229	252	6.540083	TGATGGTGCATCAGAATCATCTATT	58.460	36.000	5.59	0.00	44.60	1.73
256	279	5.955961	TGATGGTCCAACAGAATCATCTA	57.044	39.130	0.00	0.00	37.86	1.98
517	540	1.351076	TGTTCAGATCAGACCAGGCA	58.649	50.000	0.00	0.00	0.00	4.75
545	568	4.225717	TGGGGTTACGGCTAGAAGTTTTAT	59.774	41.667	0.00	0.00	0.00	1.40
672	695	8.772250	AGAAAATGTCCCAATCTCTATTCACTA	58.228	33.333	0.00	0.00	0.00	2.74
712	735	2.301870	CCTGCGGGCTCTTATAACCATA	59.698	50.000	0.00	0.00	0.00	2.74
716	739	4.202419	TGCGGGCTCTTATAACCATATGTT	60.202	41.667	1.24	0.00	41.11	2.71
756	779	1.257055	GCCCAAAGTTGCCTATGCCA	61.257	55.000	0.00	0.00	36.33	4.92
757	780	0.819582	CCCAAAGTTGCCTATGCCAG	59.180	55.000	0.00	0.00	36.33	4.85
773	796	1.162698	CCAGTCATGCCTCACACTTG	58.837	55.000	0.00	0.00	0.00	3.16
784	807	3.802329	GCCTCACACTTGCACACTAACTA	60.802	47.826	0.00	0.00	0.00	2.24
816	839	4.023365	GTGTATAGTAGGCGTACTGGGAAG	60.023	50.000	25.46	0.00	39.96	3.46
861	884	5.847111	TGTATTTGACGAGGTATAGCAGT	57.153	39.130	4.48	3.80	0.00	4.40
865	888	1.405463	TGACGAGGTATAGCAGTGCAG	59.595	52.381	19.20	0.50	0.00	4.41
867	890	1.405821	ACGAGGTATAGCAGTGCAGTC	59.594	52.381	19.20	4.54	0.00	3.51
895	918	2.622942	CACAATATGGCCGGCAAAGTAT	59.377	45.455	30.85	16.51	0.00	2.12
915	938	8.737168	AAGTATAGAGCATCACATTTAAAGCA	57.263	30.769	0.00	0.00	37.82	3.91
921	944	4.036027	AGCATCACATTTAAAGCAGGATCG	59.964	41.667	0.00	0.00	0.00	3.69
924	947	4.832248	TCACATTTAAAGCAGGATCGACT	58.168	39.130	0.00	0.00	0.00	4.18
938	961	4.991153	GATCGACTATCCCATGCATAGA	57.009	45.455	14.01	0.00	0.00	1.98
961	984	3.335579	CTCCAAAGTTTAACCTCCCTCG	58.664	50.000	0.00	0.00	0.00	4.63
982	1005	6.150140	CCTCGAGAAACTTGAAATTGAAGGAT	59.850	38.462	15.71	0.00	0.00	3.24
1005	1028	1.302752	AAGCAAGCAGTCGATGGCA	60.303	52.632	12.85	0.00	0.00	4.92
1016	1039	2.013483	CGATGGCATCGCTCTCGTC	61.013	63.158	33.67	2.78	46.55	4.20
1020	1043	2.496817	GCATCGCTCTCGTCCCTT	59.503	61.111	0.00	0.00	36.96	3.95
1033	1056	1.836802	GTCCCTTACGTCTCTCACCT	58.163	55.000	0.00	0.00	0.00	4.00
1041	1064	5.049267	CCTTACGTCTCTCACCTATCTAAGC	60.049	48.000	0.00	0.00	0.00	3.09
1070	1093	8.912988	ACAAGATTGTAAGAATTTCAAAGTGGA	58.087	29.630	0.00	0.00	38.83	4.02
1077	1100	6.499106	AAGAATTTCAAAGTGGATGGGTTT	57.501	33.333	0.00	0.00	0.00	3.27
1100	1123	1.704628	TCTTCTCATGGCTTCCAACCA	59.295	47.619	0.00	0.00	42.61	3.67
1132	1155	3.057174	GGCGGTCCACAACATAATTGAAA	60.057	43.478	0.00	0.00	0.00	2.69
1246	1269	6.055588	TCTTTACTCCAGTTGGAAAGACTTG	58.944	40.000	8.88	0.00	44.91	3.16
1263	1286	4.652881	AGACTTGATGTGGATAGCATCTCA	59.347	41.667	6.80	0.00	42.21	3.27
1265	1288	4.408270	ACTTGATGTGGATAGCATCTCAGT	59.592	41.667	6.80	6.07	42.21	3.41
1299	1322	1.337821	CAGTTTGTCGACTACTCGCC	58.662	55.000	17.92	0.00	39.96	5.54
1308	1331	2.061182	GACTACTCGCCGCTACCCTG	62.061	65.000	0.00	0.00	0.00	4.45
1474	1497	3.699038	CCTTCCTTCTCTCAGGACACTAG	59.301	52.174	0.00	0.00	43.12	2.57
1595	1618	6.306356	CACAATCAAGCCAAGAAACTAAATCG	59.694	38.462	0.00	0.00	0.00	3.34
1615	1638	7.440523	AATCGAAGAAATTTGTCTGTAAGCT	57.559	32.000	0.00	0.00	43.58	3.74
1636	1659	0.743345	CTAGCCCAAGGTAACACGCC	60.743	60.000	0.00	0.00	41.41	5.68
1648	1671	1.226030	AACACGCCGGCTGTTCTTAC	61.226	55.000	27.78	0.00	0.00	2.34
1656	1679	1.743394	CGGCTGTTCTTACCATTTCCC	59.257	52.381	0.00	0.00	0.00	3.97
1666	1689	7.236847	TGTTCTTACCATTTCCCTTCTTCTCTA	59.763	37.037	0.00	0.00	0.00	2.43
1771	1794	0.108567	TAGCTCGGCGCAATGTGTAA	60.109	50.000	10.83	0.00	42.61	2.41
1801	1824	4.721776	TGTGAATCCTTTCAGCCTAGGTAT	59.278	41.667	11.31	0.00	42.41	2.73
1812	1835	5.626142	TCAGCCTAGGTATCTACTCTTCTG	58.374	45.833	11.31	4.55	0.00	3.02
1829	1852	5.344566	TCTTCTGGAGATGGCCATATATCA	58.655	41.667	20.84	16.04	37.30	2.15
1853	1876	4.626042	CAGCTGGATGAGTTATGTCCTAC	58.374	47.826	5.57	0.00	33.15	3.18
1889	1913	6.567891	GCAACAAGTTAGGTTCTCCAATACAC	60.568	42.308	0.00	0.00	35.89	2.90
1891	1915	5.072600	ACAAGTTAGGTTCTCCAATACACCA	59.927	40.000	0.00	0.00	35.89	4.17
2001	2025	5.166398	GCCTCCAAAGATTCACTTCATTTG	58.834	41.667	0.00	0.00	37.93	2.32
2061	2085	7.651808	AGTGATTTTGGTGTATTGAAGACTTG	58.348	34.615	0.00	0.00	0.00	3.16
2074	2098	6.697641	TTGAAGACTTGTAGGTTAAGGGAT	57.302	37.500	0.00	0.00	0.00	3.85
2114	2138	7.502895	AGTGTACACAGGTCTATAAGTCTATGG	59.497	40.741	27.06	0.00	0.00	2.74
2124	2148	7.435305	GTCTATAAGTCTATGGGGAGTTTGAC	58.565	42.308	0.00	0.00	32.06	3.18
2147	2171	1.252904	TACAGGGAAAGTCGACCCCG	61.253	60.000	19.04	16.29	46.64	5.73
2227	2251	6.813152	ACTTTGAAAGTGAAGAAATTGGTGTG	59.187	34.615	10.18	0.00	41.01	3.82
2279	2303	3.820777	ATGAAGCTTGAAGACTTTCGC	57.179	42.857	2.10	0.00	36.04	4.70
2441	2466	6.096001	GCCTTTGGAAATCTCATACAGTTCAT	59.904	38.462	0.00	0.00	0.00	2.57
2495	2520	2.554032	CTGGTCGCTGAGGAATTTGTTT	59.446	45.455	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	1.722034	ACTGAGTTCTCCTCCAAGCA	58.278	50.000	0.00	0.00	39.65	3.91
229	252	1.741028	TCTGTTGGACCATCAAGGGA	58.259	50.000	6.70	0.00	43.89	4.20
256	279	0.035056	GCTGTACCATCAAGGGCACT	60.035	55.000	0.00	0.00	43.89	4.40
517	540	1.910671	TCTAGCCGTAACCCCAACAAT	59.089	47.619	0.00	0.00	0.00	2.71
545	568	4.090761	AGAACAATCTCCTTCAACTGCA	57.909	40.909	0.00	0.00	0.00	4.41
712	735	7.224557	GCAACCAGTAATTTCAAGTTTCAACAT	59.775	33.333	0.00	0.00	0.00	2.71
716	739	5.596845	GGCAACCAGTAATTTCAAGTTTCA	58.403	37.500	0.00	0.00	0.00	2.69
756	779	0.109153	TGCAAGTGTGAGGCATGACT	59.891	50.000	0.00	0.00	31.58	3.41
757	780	0.239347	GTGCAAGTGTGAGGCATGAC	59.761	55.000	0.00	0.00	40.05	3.06
784	807	6.521151	ACGCCTACTATACACAGTAACTTT	57.479	37.500	0.00	0.00	30.77	2.66
800	823	1.068741	CCATCTTCCCAGTACGCCTAC	59.931	57.143	0.00	0.00	0.00	3.18
816	839	2.319136	TATGGTTGGCGTACACCATC	57.681	50.000	16.56	10.07	40.13	3.51
865	888	2.024918	CCATATTGTGCCAGGCGAC	58.975	57.895	7.03	7.00	0.00	5.19
867	890	2.723746	GCCATATTGTGCCAGGCG	59.276	61.111	7.03	0.00	35.42	5.52
895	918	5.744171	TCCTGCTTTAAATGTGATGCTCTA	58.256	37.500	0.00	0.00	0.00	2.43
921	944	3.196685	GGAGGTCTATGCATGGGATAGTC	59.803	52.174	10.16	5.97	0.00	2.59
924	947	3.274281	TGGAGGTCTATGCATGGGATA	57.726	47.619	10.16	0.00	0.00	2.59
933	956	5.880887	GGAGGTTAAACTTTGGAGGTCTATG	59.119	44.000	0.00	0.00	0.00	2.23
938	961	3.061369	AGGGAGGTTAAACTTTGGAGGT	58.939	45.455	0.00	0.00	0.00	3.85
961	984	9.003658	TGAGTATCCTTCAATTTCAAGTTTCTC	57.996	33.333	0.00	0.00	0.00	2.87
982	1005	2.610433	CATCGACTGCTTGCTTGAGTA	58.390	47.619	0.00	0.00	0.00	2.59
1014	1037	1.836802	AGGTGAGAGACGTAAGGGAC	58.163	55.000	0.00	0.00	46.39	4.46
1016	1039	3.822940	AGATAGGTGAGAGACGTAAGGG	58.177	50.000	0.00	0.00	46.39	3.95
1020	1043	5.032327	TGCTTAGATAGGTGAGAGACGTA	57.968	43.478	0.00	0.00	0.00	3.57
1070	1093	5.134725	AGCCATGAGAAGATTAAACCCAT	57.865	39.130	0.00	0.00	0.00	4.00
1077	1100	4.018506	TGGTTGGAAGCCATGAGAAGATTA	60.019	41.667	0.00	0.00	31.53	1.75
1100	1123	1.076632	TGGACCGCCAAAACCTTGT	60.077	52.632	0.00	0.00	42.49	3.16
1132	1155	2.892784	GCTACAGAGCGAGGGTAATT	57.107	50.000	0.00	0.00	39.39	1.40
1246	1269	4.510711	CACAACTGAGATGCTATCCACATC	59.489	45.833	0.00	0.00	43.49	3.06
1299	1322	2.100989	ACTAACTCCTTCAGGGTAGCG	58.899	52.381	0.00	0.00	36.25	4.26
1308	1331	3.921021	CACACGTGATCACTAACTCCTTC	59.079	47.826	25.01	0.00	0.00	3.46
1353	1376	4.153117	TGAAGCGCTTTCTCTTCATCTTTC	59.847	41.667	25.84	6.56	42.43	2.62
1595	1618	6.809630	AGGAGCTTACAGACAAATTTCTTC	57.190	37.500	0.00	0.00	0.00	2.87
1615	1638	0.899720	CGTGTTACCTTGGGCTAGGA	59.100	55.000	12.18	0.00	38.73	2.94
1636	1659	1.743394	GGGAAATGGTAAGAACAGCCG	59.257	52.381	0.00	0.00	0.00	5.52
1771	1794	9.512588	CTAGGCTGAAAGGATTCACAATATATT	57.487	33.333	0.00	0.00	40.59	1.28
1801	1824	2.023984	TGGCCATCTCCAGAAGAGTAGA	60.024	50.000	0.00	0.00	43.71	2.59
1812	1835	3.806380	CTGCTGATATATGGCCATCTCC	58.194	50.000	24.80	10.78	0.00	3.71
1829	1852	2.158842	GGACATAACTCATCCAGCTGCT	60.159	50.000	8.66	0.00	32.35	4.24
1889	1913	7.970614	GCCTGATCTTTAATTTTACTTCTGTGG	59.029	37.037	0.00	0.00	0.00	4.17
1891	1915	8.870075	AGCCTGATCTTTAATTTTACTTCTGT	57.130	30.769	0.00	0.00	0.00	3.41
1907	1931	4.843516	CCTCCTAATTTCCTAGCCTGATCT	59.156	45.833	0.00	0.00	0.00	2.75
2001	2025	9.708222	CTAGATGCACTTACACATGAAAATAAC	57.292	33.333	0.00	0.00	0.00	1.89
2061	2085	6.094464	ACAAACGCATTAATCCCTTAACCTAC	59.906	38.462	0.00	0.00	29.85	3.18
2074	2098	4.571176	TGTGTACACTCACAAACGCATTAA	59.429	37.500	25.60	0.00	43.92	1.40
2114	2138	4.028993	TCCCTGTAAATGTCAAACTCCC	57.971	45.455	0.00	0.00	0.00	4.30
2124	2148	3.007635	GGGTCGACTTTCCCTGTAAATG	58.992	50.000	16.46	0.00	40.48	2.32
2227	2251	5.277058	GCATGAATATCAAGTCTTCACGGAC	60.277	44.000	0.00	0.00	32.16	4.79
2441	2466	5.923114	CGTCTCTCTCACTGAAGAAATTGAA	59.077	40.000	0.00	0.00	0.00	2.69
2495	2520	4.620803	GCGAATTCCTAACTCCTCAGTCAA	60.621	45.833	0.00	0.00	29.93	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.