AutoCloner

Multiple sequence alignment - TraesCS6B01G090700

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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	TraesCS6B01G090700	chr6B	100.000	1480	0	0	749	2228	66746889	66745410	0.000000e+00	2734.0
1	TraesCS6B01G090700	chr6B	95.000	1500	45	10	759	2228	66779465	66777966	0.000000e+00	2327.0
2	TraesCS6B01G090700	chr6B	100.000	428	0	0	1	428	66747637	66747210	0.000000e+00	791.0
3	TraesCS6B01G090700	chr6B	91.600	250	18	2	180	428	66779726	66779479	2.120000e-90	342.0
4	TraesCS6B01G090700	chr6B	94.382	178	7	3	13	187	66780157	66779980	1.010000e-68	270.0
5	TraesCS6B01G090700	chrUn	91.813	342	23	2	979	1316	100515559	100515899	2.590000e-129	472.0
6	TraesCS6B01G090700	chrUn	81.858	452	60	15	1552	1998	100515935	100516369	5.850000e-96	361.0
7	TraesCS6B01G090700	chrUn	91.845	233	18	1	1997	2228	100516407	100516639	7.670000e-85	324.0
8	TraesCS6B01G090700	chrUn	82.913	357	41	12	781	1119	100677425	100677779	1.000000e-78	303.0
9	TraesCS6B01G090700	chrUn	92.857	154	10	1	777	930	100508236	100508388	2.880000e-54	222.0
10	TraesCS6B01G090700	chr6A	79.775	712	87	40	1552	2228	35946309	35945620	4.330000e-127	464.0
11	TraesCS6B01G090700	chr6A	80.634	284	33	16	777	1041	35954659	35954379	1.350000e-47	200.0
12	TraesCS6B01G090700	chr6A	83.186	226	26	6	1337	1550	169514999	169514774	1.750000e-46	196.0
13	TraesCS6B01G090700	chr6A	89.677	155	11	2	1166	1316	35946498	35946345	2.260000e-45	193.0
14	TraesCS6B01G090700	chr6A	97.727	88	2	0	1067	1154	35954384	35954297	3.830000e-33	152.0
15	TraesCS6B01G090700	chr7A	90.000	180	14	4	5	180	20113185	20113006	1.720000e-56	230.0
16	TraesCS6B01G090700	chr7D	89.011	182	17	3	2	180	39652469	39652650	2.880000e-54	222.0
17	TraesCS6B01G090700	chr7D	88.710	124	14	0	1428	1551	509500191	509500068	3.830000e-33	152.0
18	TraesCS6B01G090700	chr1D	87.363	182	20	3	2	180	365788163	365788344	2.900000e-49	206.0
19	TraesCS6B01G090700	chr1D	82.960	223	23	9	1337	1545	397047555	397047776	1.050000e-43	187.0
20	TraesCS6B01G090700	chr1B	87.363	182	18	4	2	179	52827745	52827565	1.040000e-48	204.0
21	TraesCS6B01G090700	chr3B	83.796	216	30	5	1336	1547	697169645	697169859	1.350000e-47	200.0
22	TraesCS6B01G090700	chr3B	79.915	234	33	7	1337	1556	225173399	225173166	2.290000e-35	159.0
23	TraesCS6B01G090700	chr2A	87.222	180	18	5	2	178	44176193	44176016	1.350000e-47	200.0
24	TraesCS6B01G090700	chr1A	87.222	180	18	5	2	178	121464108	121463931	1.350000e-47	200.0
25	TraesCS6B01G090700	chr1A	86.740	181	19	5	2	178	516065166	516065345	1.750000e-46	196.0
26	TraesCS6B01G090700	chr1A	75.862	203	27	10	1356	1544	409834368	409834562	1.420000e-12	84.2
27	TraesCS6B01G090700	chr7B	86.667	180	22	2	2	179	634062477	634062298	4.850000e-47	198.0
28	TraesCS6B01G090700	chr4A	81.780	236	29	8	1323	1545	522958970	522959204	3.780000e-43	185.0
29	TraesCS6B01G090700	chr4A	80.488	123	19	5	1428	1547	628643052	628643172	3.050000e-14	89.8
30	TraesCS6B01G090700	chr3A	80.258	233	33	4	1337	1556	176148008	176148240	1.770000e-36	163.0
31	TraesCS6B01G090700	chr3D	79.487	234	34	7	1337	1556	153507225	153506992	1.070000e-33	154.0

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	TraesCS6B01G090700	chr6B	66745410	66747637	2227	True	1762.500000	2734	100.000000	1	2228	2	chr6B.!!$R1	2227
1	TraesCS6B01G090700	chr6B	66777966	66780157	2191	True	979.666667	2327	93.660667	13	2228	3	chr6B.!!$R2	2215
2	TraesCS6B01G090700	chrUn	100515559	100516639	1080	False	385.666667	472	88.505333	979	2228	3	chrUn.!!$F3	1249
3	TraesCS6B01G090700	chr6A	35945620	35946498	878	True	328.500000	464	84.726000	1166	2228	2	chr6A.!!$R2	1062

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	End Stability	Orientation
115	117	0.597637	ACCAACTTCGCGTCTCACTG	60.598	55.0	5.77	3.66	F
229	494	0.606401	CCGTCACATCAAAGGCACCT	60.606	55.0	0.00	4.00	F
932	1198	0.673644	AATCCAACGACGCTTCAGGG	60.674	55.0	0.00	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1064	1358	0.465705	GATCTTCCTCATGGCCGTCA	59.534	55.0	0.00	4.35	R
1101	1395	0.899720	GGATAACCTCCACCGTGACA	59.100	55.0	44.26	3.58	R
2050	2417	2.229784	GCTTTGTTGAGGATGGTGAAGG	59.770	50.0	0.00	3.46	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
88	90	4.624364	CAGCCTGTGCCACCACGA	62.624	66.667	0.00	0.00	45.04	4.35
115	117	0.597637	ACCAACTTCGCGTCTCACTG	60.598	55.000	5.77	0.00	0.00	3.66
178	181	1.748879	GCTTAGGGCATCCGCAACA	60.749	57.895	0.00	0.00	41.24	3.33
229	494	0.606401	CCGTCACATCAAAGGCACCT	60.606	55.000	0.00	0.00	0.00	4.00
391	657	1.120530	GGTAGGGAAGAATGGCGAGA	58.879	55.000	0.00	0.00	0.00	4.04
417	683	0.762461	CTGGAGGAGAGGTGGGGATC	60.762	65.000	0.00	0.00	0.00	3.36
775	1041	2.440501	GGTATCATGCGCTTTTTCACG	58.559	47.619	9.73	0.00	0.00	4.35
886	1152	3.248602	AGCAAAGTTCAGCTGACTAAACG	59.751	43.478	18.03	4.89	40.13	3.60
893	1159	1.461127	CAGCTGACTAAACGAGGCAAC	59.539	52.381	8.42	0.00	45.07	4.17
900	1166	3.284617	ACTAAACGAGGCAACCAAAGTT	58.715	40.909	0.00	0.00	36.33	2.66
919	1185	2.044451	ATCGGGCGGCAAATCCAA	60.044	55.556	12.47	0.00	34.01	3.53
930	1196	1.725931	GCAAATCCAACGACGCTTCAG	60.726	52.381	0.00	0.00	0.00	3.02
931	1197	1.135972	CAAATCCAACGACGCTTCAGG	60.136	52.381	0.00	0.00	0.00	3.86
932	1198	0.673644	AATCCAACGACGCTTCAGGG	60.674	55.000	0.00	0.00	0.00	4.45
933	1199	1.541310	ATCCAACGACGCTTCAGGGA	61.541	55.000	0.00	0.00	0.00	4.20
934	1200	1.738099	CCAACGACGCTTCAGGGAG	60.738	63.158	0.00	0.00	0.00	4.30
935	1201	2.048127	AACGACGCTTCAGGGAGC	60.048	61.111	0.00	0.00	39.29	4.70
943	1209	2.821991	GCTTCAGGGAGCGTATGTAT	57.178	50.000	0.00	0.00	32.23	2.29
944	1210	3.936372	GCTTCAGGGAGCGTATGTATA	57.064	47.619	0.00	0.00	32.23	1.47
945	1211	4.457834	GCTTCAGGGAGCGTATGTATAT	57.542	45.455	0.00	0.00	32.23	0.86
946	1212	5.578005	GCTTCAGGGAGCGTATGTATATA	57.422	43.478	0.00	0.00	32.23	0.86
947	1213	6.150396	GCTTCAGGGAGCGTATGTATATAT	57.850	41.667	0.00	0.00	32.23	0.86
948	1214	7.273320	GCTTCAGGGAGCGTATGTATATATA	57.727	40.000	0.00	0.00	32.23	0.86
949	1215	7.364200	GCTTCAGGGAGCGTATGTATATATAG	58.636	42.308	0.00	0.00	32.23	1.31
950	1216	7.522399	GCTTCAGGGAGCGTATGTATATATAGG	60.522	44.444	5.17	5.17	32.23	2.57
969	1245	2.494870	AGGAGTACGTATGTGGGTGAAC	59.505	50.000	0.00	0.00	0.00	3.18
970	1246	2.523015	GAGTACGTATGTGGGTGAACG	58.477	52.381	0.00	0.00	40.99	3.95
971	1247	1.203052	AGTACGTATGTGGGTGAACGG	59.797	52.381	0.00	0.00	39.57	4.44
977	1271	4.296265	GTGGGTGAACGGATCCAC	57.704	61.111	13.41	1.56	42.11	4.02
988	1282	1.134401	ACGGATCCACAGCCATAACTG	60.134	52.381	13.41	0.00	43.59	3.16
1164	1458	0.539438	AGTACAACCCCGACCGTGTA	60.539	55.000	0.00	0.00	0.00	2.90
1382	1702	1.677576	ACGAAGTAACACCGTCTGACA	59.322	47.619	8.73	0.00	41.94	3.58
1437	1757	8.023128	AGAAAATTGAACGTATCATCCAAACAG	58.977	33.333	0.00	0.00	38.03	3.16
1523	1843	1.160137	AGGACAGAATTGCTTCGTGC	58.840	50.000	0.00	0.00	43.25	5.34
1528	1848	1.200716	CAGAATTGCTTCGTGCCACAT	59.799	47.619	0.00	0.00	42.00	3.21
1750	2077	5.473846	CCTTCTGCACTATAGATACGGAAGA	59.526	44.000	26.65	12.20	32.19	2.87
1963	2291	7.219344	AGTTCGTAAATTTGAAAAAGTTCACGG	59.781	33.333	0.00	0.00	43.52	4.94
1992	2320	3.627395	AAAGATGTGATTGACCGCCTA	57.373	42.857	0.00	0.00	0.00	3.93
2050	2417	2.603560	GCAAGTAGCACATTACTCCGAC	59.396	50.000	0.00	0.00	44.79	4.79
2153	2521	5.049680	GGGTGCACGTACTTATATTCATTGG	60.050	44.000	11.45	0.00	0.00	3.16
2155	2523	6.037830	GGTGCACGTACTTATATTCATTGGTT	59.962	38.462	11.45	0.00	0.00	3.67
2190	2558	8.902806	GGGTATCAACAAGTTATCATGAATCAA	58.097	33.333	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.422024	TGTTTGGGTCGGGAGAAATCA	59.578	47.619	0.00	0.00	42.89	2.57
1	2	1.810755	GTGTTTGGGTCGGGAGAAATC	59.189	52.381	0.00	0.00	42.89	2.17
2	3	1.546998	GGTGTTTGGGTCGGGAGAAAT	60.547	52.381	0.00	0.00	42.89	2.17
3	4	0.179012	GGTGTTTGGGTCGGGAGAAA	60.179	55.000	0.00	0.00	42.89	2.52
4	5	1.452801	GGTGTTTGGGTCGGGAGAA	59.547	57.895	0.00	0.00	42.89	2.87
5	6	2.522367	GGGTGTTTGGGTCGGGAGA	61.522	63.158	0.00	0.00	0.00	3.71
6	7	2.033602	GGGTGTTTGGGTCGGGAG	59.966	66.667	0.00	0.00	0.00	4.30
7	8	2.773053	TGGGTGTTTGGGTCGGGA	60.773	61.111	0.00	0.00	0.00	5.14
8	9	2.596338	GTGGGTGTTTGGGTCGGG	60.596	66.667	0.00	0.00	0.00	5.14
9	10	2.596338	GGTGGGTGTTTGGGTCGG	60.596	66.667	0.00	0.00	0.00	4.79
10	11	2.190841	GTGGTGGGTGTTTGGGTCG	61.191	63.158	0.00	0.00	0.00	4.79
11	12	1.830847	GGTGGTGGGTGTTTGGGTC	60.831	63.158	0.00	0.00	0.00	4.46
35	36	1.084289	GCGGTACACTTGGATTGTCC	58.916	55.000	0.00	0.00	36.96	4.02
39	40	0.402504	TTGGGCGGTACACTTGGATT	59.597	50.000	0.00	0.00	0.00	3.01
115	117	3.371063	TCTCGTGTCGGTGGCCTC	61.371	66.667	3.32	0.00	0.00	4.70
368	634	0.539986	GCCATTCTTCCCTACCGTCA	59.460	55.000	0.00	0.00	0.00	4.35
371	637	0.249489	CTCGCCATTCTTCCCTACCG	60.249	60.000	0.00	0.00	0.00	4.02
372	638	1.120530	TCTCGCCATTCTTCCCTACC	58.879	55.000	0.00	0.00	0.00	3.18
376	642	0.464554	CCCTTCTCGCCATTCTTCCC	60.465	60.000	0.00	0.00	0.00	3.97
382	648	3.017581	AGCCCCCTTCTCGCCATT	61.018	61.111	0.00	0.00	0.00	3.16
391	657	2.041928	CTCTCCTCCAGCCCCCTT	59.958	66.667	0.00	0.00	0.00	3.95
748	1014	2.750350	CGCATGATACCCTCCCCC	59.250	66.667	0.00	0.00	0.00	5.40
749	1015	2.032681	GCGCATGATACCCTCCCC	59.967	66.667	0.30	0.00	0.00	4.81
750	1016	0.179018	AAAGCGCATGATACCCTCCC	60.179	55.000	11.47	0.00	0.00	4.30
751	1017	1.680338	AAAAGCGCATGATACCCTCC	58.320	50.000	11.47	0.00	0.00	4.30
752	1018	2.682856	TGAAAAAGCGCATGATACCCTC	59.317	45.455	11.47	0.00	0.00	4.30
753	1019	2.423538	GTGAAAAAGCGCATGATACCCT	59.576	45.455	11.47	0.00	0.00	4.34
754	1020	2.791158	CGTGAAAAAGCGCATGATACCC	60.791	50.000	11.47	0.00	0.00	3.69
755	1021	2.095213	TCGTGAAAAAGCGCATGATACC	59.905	45.455	11.47	0.00	0.00	2.73
756	1022	3.181520	ACTCGTGAAAAAGCGCATGATAC	60.182	43.478	11.47	0.00	30.39	2.24
757	1023	3.000041	ACTCGTGAAAAAGCGCATGATA	59.000	40.909	11.47	0.00	30.39	2.15
775	1041	3.358775	CATCGACAATCACGAGAGACTC	58.641	50.000	0.00	0.00	42.81	3.36
784	1050	4.100529	CAAATTGAGCCATCGACAATCAC	58.899	43.478	0.00	0.00	33.90	3.06
893	1159	3.051392	GCCGCCCGATCAACTTTGG	62.051	63.158	0.00	0.00	0.00	3.28
900	1166	2.515991	GGATTTGCCGCCCGATCA	60.516	61.111	0.00	0.00	0.00	2.92
930	1196	7.117523	CGTACTCCTATATATACATACGCTCCC	59.882	44.444	0.00	0.00	0.00	4.30
931	1197	7.655328	ACGTACTCCTATATATACATACGCTCC	59.345	40.741	14.37	0.00	38.11	4.70
932	1198	8.586570	ACGTACTCCTATATATACATACGCTC	57.413	38.462	14.37	0.00	38.11	5.03
938	1204	9.570468	CCCACATACGTACTCCTATATATACAT	57.430	37.037	0.00	0.00	0.00	2.29
940	1206	8.834465	CACCCACATACGTACTCCTATATATAC	58.166	40.741	0.00	0.00	0.00	1.47
941	1207	8.771286	TCACCCACATACGTACTCCTATATATA	58.229	37.037	0.00	0.00	0.00	0.86
942	1208	7.636579	TCACCCACATACGTACTCCTATATAT	58.363	38.462	0.00	0.00	0.00	0.86
943	1209	7.019656	TCACCCACATACGTACTCCTATATA	57.980	40.000	0.00	0.00	0.00	0.86
944	1210	5.884322	TCACCCACATACGTACTCCTATAT	58.116	41.667	0.00	0.00	0.00	0.86
945	1211	5.308976	TCACCCACATACGTACTCCTATA	57.691	43.478	0.00	0.00	0.00	1.31
946	1212	4.174704	TCACCCACATACGTACTCCTAT	57.825	45.455	0.00	0.00	0.00	2.57
947	1213	3.650281	TCACCCACATACGTACTCCTA	57.350	47.619	0.00	0.00	0.00	2.94
948	1214	2.494870	GTTCACCCACATACGTACTCCT	59.505	50.000	0.00	0.00	0.00	3.69
949	1215	2.733227	CGTTCACCCACATACGTACTCC	60.733	54.545	0.00	0.00	0.00	3.85
950	1216	2.523015	CGTTCACCCACATACGTACTC	58.477	52.381	0.00	0.00	0.00	2.59
969	1245	1.138859	TCAGTTATGGCTGTGGATCCG	59.861	52.381	7.39	0.00	37.70	4.18
970	1246	2.843701	CTCAGTTATGGCTGTGGATCC	58.156	52.381	4.20	4.20	37.70	3.36
971	1247	2.216898	GCTCAGTTATGGCTGTGGATC	58.783	52.381	0.00	0.00	37.70	3.36
977	1271	1.202568	TGATCCGCTCAGTTATGGCTG	60.203	52.381	0.00	0.00	37.81	4.85
988	1282	1.068281	TCTGCTCATCTTGATCCGCTC	59.932	52.381	0.00	0.00	0.00	5.03
1064	1358	0.465705	GATCTTCCTCATGGCCGTCA	59.534	55.000	0.00	0.00	0.00	4.35
1101	1395	0.899720	GGATAACCTCCACCGTGACA	59.100	55.000	0.00	0.00	44.26	3.58
1390	1710	6.539649	TCTTTTCGGATGACAACTTTAGTG	57.460	37.500	0.00	0.00	0.00	2.74
1437	1757	2.796593	GTTGTGAAGCATGGCAACTTTC	59.203	45.455	7.47	4.81	38.41	2.62
1523	1843	3.686241	CCTGATAAGTGTCACACATGTGG	59.314	47.826	28.64	17.57	45.65	4.17
1528	1848	2.301870	GGTCCCTGATAAGTGTCACACA	59.698	50.000	11.40	0.00	36.74	3.72
1606	1926	1.673626	CCACTGCATTTTGATGGCCAC	60.674	52.381	8.16	2.36	0.00	5.01
2050	2417	2.229784	GCTTTGTTGAGGATGGTGAAGG	59.770	50.000	0.00	0.00	0.00	3.46
2153	2521	4.546829	TGTTGATACCCACAGTAGGAAC	57.453	45.455	0.00	0.00	33.42	3.62
2155	2523	4.164981	ACTTGTTGATACCCACAGTAGGA	58.835	43.478	0.00	0.00	33.42	2.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.