AutoCloner

Multiple sequence alignment - TraesCS7B01G361700

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	TraesCS7B01G361700	chr7B	100.000	2643	0	0	1	2643	623934926	623932284	0.000000e+00	4881.0
1	TraesCS7B01G361700	chr7B	79.335	1234	182	42	672	1866	623271265	623270066	0.000000e+00	798.0
2	TraesCS7B01G361700	chr7B	77.729	907	151	32	593	1460	623523326	623522432	2.350000e-140	508.0
3	TraesCS7B01G361700	chr7B	77.520	863	146	28	591	1417	623102501	623101651	2.380000e-130	475.0
4	TraesCS7B01G361700	chr7B	80.871	528	67	14	678	1172	622838241	622837715	4.130000e-103	385.0
5	TraesCS7B01G361700	chr7B	78.346	508	74	13	1175	1677	622832941	622832465	1.990000e-76	296.0
6	TraesCS7B01G361700	chr7B	82.286	175	27	4	1287	1460	623539119	623538948	5.890000e-32	148.0
7	TraesCS7B01G361700	chr7D	93.854	2343	102	16	306	2643	568324515	568322210	0.000000e+00	3491.0
8	TraesCS7B01G361700	chr7D	84.242	1504	191	33	591	2064	568463939	568462452	0.000000e+00	1423.0
9	TraesCS7B01G361700	chr7D	79.497	1629	230	60	299	1866	568236559	568234974	0.000000e+00	1062.0
10	TraesCS7B01G361700	chr7D	80.321	1245	173	37	673	1875	568185804	568184590	0.000000e+00	876.0
11	TraesCS7B01G361700	chr7D	84.661	339	42	9	329	663	568464245	568463913	1.960000e-86	329.0
12	TraesCS7B01G361700	chr7D	87.889	289	10	5	1	282	568324918	568324648	1.530000e-82	316.0
13	TraesCS7B01G361700	chr7A	94.326	1974	99	6	672	2643	656982020	656983982	0.000000e+00	3013.0
14	TraesCS7B01G361700	chr7A	79.906	1060	139	29	673	1694	655452258	655451235	0.000000e+00	710.0
15	TraesCS7B01G361700	chr7A	95.652	299	10	2	316	613	656956948	656957244	6.620000e-131	477.0
16	TraesCS7B01G361700	chr7A	78.273	741	100	28	748	1456	654503678	654502967	1.130000e-113	420.0
17	TraesCS7B01G361700	chr7A	90.047	211	11	5	23	227	656954443	656954649	5.610000e-67	265.0
18	TraesCS7B01G361700	chr7A	94.595	37	2	0	287	323	656955065	656955101	1.020000e-04	58.4

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	TraesCS7B01G361700	chr7B	623932284	623934926	2642	True	4881.0	4881	100.000000	1	2643	1	chr7B.!!$R7	2642
1	TraesCS7B01G361700	chr7B	623270066	623271265	1199	True	798.0	798	79.335000	672	1866	1	chr7B.!!$R4	1194
2	TraesCS7B01G361700	chr7B	623522432	623523326	894	True	508.0	508	77.729000	593	1460	1	chr7B.!!$R5	867
3	TraesCS7B01G361700	chr7B	623101651	623102501	850	True	475.0	475	77.520000	591	1417	1	chr7B.!!$R3	826
4	TraesCS7B01G361700	chr7B	622837715	622838241	526	True	385.0	385	80.871000	678	1172	1	chr7B.!!$R2	494
5	TraesCS7B01G361700	chr7D	568322210	568324918	2708	True	1903.5	3491	90.871500	1	2643	2	chr7D.!!$R3	2642
6	TraesCS7B01G361700	chr7D	568234974	568236559	1585	True	1062.0	1062	79.497000	299	1866	1	chr7D.!!$R2	1567
7	TraesCS7B01G361700	chr7D	568184590	568185804	1214	True	876.0	876	80.321000	673	1875	1	chr7D.!!$R1	1202
8	TraesCS7B01G361700	chr7D	568462452	568464245	1793	True	876.0	1423	84.451500	329	2064	2	chr7D.!!$R4	1735
9	TraesCS7B01G361700	chr7A	656982020	656983982	1962	False	3013.0	3013	94.326000	672	2643	1	chr7A.!!$F1	1971
10	TraesCS7B01G361700	chr7A	655451235	655452258	1023	True	710.0	710	79.906000	673	1694	1	chr7A.!!$R2	1021
11	TraesCS7B01G361700	chr7A	654502967	654503678	711	True	420.0	420	78.273000	748	1456	1	chr7A.!!$R1	708
12	TraesCS7B01G361700	chr7A	656954443	656957244	2801	False	266.8	477	93.431333	23	613	3	chr7A.!!$F2	590

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
206	220	1.933853	GCGGTGCGAATCTAAATCTGT	59.066	47.619	0.0	0.0	0.0	3.41	F
1211	3700	0.250513	GATCCAAGACTGCTCGGGTT	59.749	55.000	0.0	0.0	0.0	4.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1273	3762	0.173708	GGATGTCCGTCACACCTCTC	59.826	60.0	0.00	0.0	38.04	3.20	R
2333	4862	0.761187	ACCTATGCGCTCATGGACAT	59.239	50.0	9.73	0.0	33.52	3.06	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
97	106	4.099419	AGGCTGGACCAACAAAAGTAAAAG	59.901	41.667	0.00	0.00	43.14	2.27
144	153	4.681744	AGAAAAGAAAAGCAACGCATGAA	58.318	34.783	0.00	0.00	0.00	2.57
206	220	1.933853	GCGGTGCGAATCTAAATCTGT	59.066	47.619	0.00	0.00	0.00	3.41
236	250	9.690913	AGATTTGAAGTGGAATAGATTCAATGA	57.309	29.630	4.71	0.00	40.32	2.57
314	799	7.826690	AGCAATTTCGATATACAAAACAGGTT	58.173	30.769	0.00	0.00	0.00	3.50
364	2703	4.332819	CGGTCCTGATTTTGAGTATTGGAC	59.667	45.833	0.00	0.00	41.19	4.02
413	2753	4.693566	TGAACGTTGGTTAGATTGGATCAC	59.306	41.667	5.00	0.00	36.24	3.06
482	2823	6.588719	TTGAAACATCCAAGGGATTTACTG	57.411	37.500	0.00	0.00	39.79	2.74
828	3286	8.454106	CAAGTTGGGTATGCATATCTATTAAGC	58.546	37.037	16.41	0.00	0.00	3.09
867	3325	3.568007	TCCATCGCCAACAATTATTAGGC	59.432	43.478	0.00	0.00	41.86	3.93
1079	3568	5.376625	ACACAACATAGAACATGACCAACT	58.623	37.500	0.00	0.00	0.00	3.16
1099	3588	4.632153	ACTGTAAAGTAGCTGGAGTGTTG	58.368	43.478	0.00	0.00	0.00	3.33
1163	3652	3.762779	GCACAAGCAATTCATGGAGTAC	58.237	45.455	0.00	0.00	41.58	2.73
1195	3684	6.573725	GCACCATCGATAAAAATAACGTGATC	59.426	38.462	0.00	0.00	0.00	2.92
1211	3700	0.250513	GATCCAAGACTGCTCGGGTT	59.749	55.000	0.00	0.00	0.00	4.11
1266	3755	0.323629	CCGTGGACCCTATGTTGTGT	59.676	55.000	0.00	0.00	0.00	3.72
1273	3762	5.007034	TGGACCCTATGTTGTGTTACAATG	58.993	41.667	0.00	0.00	40.59	2.82
1355	3844	1.188863	TAGTCTACCCAAGTTCGCCC	58.811	55.000	0.00	0.00	0.00	6.13
1417	3906	6.054941	CACTCATTGTGCAGGTTGGTATATA	58.945	40.000	0.00	0.00	40.06	0.86
1418	3907	6.712095	CACTCATTGTGCAGGTTGGTATATAT	59.288	38.462	0.00	0.00	40.06	0.86
1419	3908	7.877612	CACTCATTGTGCAGGTTGGTATATATA	59.122	37.037	0.00	0.00	40.06	0.86
1420	3909	8.605947	ACTCATTGTGCAGGTTGGTATATATAT	58.394	33.333	0.00	0.00	0.00	0.86
1589	4108	2.363925	GCTACGACCTCCACCCCT	60.364	66.667	0.00	0.00	0.00	4.79
1624	4143	3.440522	GGCCTTCAGTGTAAGAACATTCC	59.559	47.826	0.00	0.00	38.08	3.01
1785	4306	8.756486	ATCATTGGTTCTCATTGATTCACATA	57.244	30.769	0.00	0.00	41.17	2.29
1795	4317	8.620416	TCTCATTGATTCACATAATTTAACGGG	58.380	33.333	0.00	0.00	0.00	5.28
1868	4393	7.595130	TCATCGGTCTTATATGATCAGAAAACG	59.405	37.037	0.09	0.00	0.00	3.60
2005	4534	5.304686	TGGTTTGGAGACAGTTCTAACAT	57.695	39.130	0.00	0.00	44.54	2.71
2101	4630	7.940137	AGTGGACATGTTTAATAAGTACAACCA	59.060	33.333	0.00	0.00	0.00	3.67
2118	4647	5.144100	ACAACCACACAAGATCCCAATAAA	58.856	37.500	0.00	0.00	0.00	1.40
2170	4699	1.265905	GCCCTTAGTTTGAACGGTGTG	59.734	52.381	0.00	0.00	0.00	3.82
2211	4740	5.696270	GTGGAAATCATACGCATCTGATGTA	59.304	40.000	18.19	5.13	32.56	2.29
2221	4750	3.648009	GCATCTGATGTAGGCTGTAGAC	58.352	50.000	18.19	0.00	0.00	2.59
2243	4772	1.220529	TTGCTCAGTTGTCGCTTCTG	58.779	50.000	0.00	0.00	0.00	3.02
2400	4929	1.995626	CTGGTGGGGTTCGAGGGAT	60.996	63.158	0.00	0.00	0.00	3.85
2419	4948	3.547413	GGATCATGTCGTCGTCGTATTCA	60.547	47.826	1.33	0.00	38.33	2.57
2505	5034	3.869912	GCCAGTGTTGCAATCTTCTCCTA	60.870	47.826	0.59	0.00	0.00	2.94
2512	5041	5.045942	TGTTGCAATCTTCTCCTATGTGGTA	60.046	40.000	0.59	0.00	37.07	3.25
2519	5048	7.973048	ATCTTCTCCTATGTGGTAAGTGTTA	57.027	36.000	0.00	0.00	37.07	2.41
2529	5058	4.657039	TGTGGTAAGTGTTAGTTCTCCCTT	59.343	41.667	0.00	0.00	0.00	3.95
2540	5069	2.040412	AGTTCTCCCTTGATTGGTCCAC	59.960	50.000	0.00	0.00	0.00	4.02
2594	5123	5.290400	GGTTTGGCGATCTTACAAGTACTAC	59.710	44.000	0.00	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	58	0.826062	GCATGGGCCAGCTGTATTTT	59.174	50.000	13.78	0.00	0.00	1.82
50	59	0.324552	TGCATGGGCCAGCTGTATTT	60.325	50.000	22.57	0.00	40.13	1.40
51	60	1.039233	GTGCATGGGCCAGCTGTATT	61.039	55.000	22.57	0.00	40.13	1.89
52	61	1.454479	GTGCATGGGCCAGCTGTAT	60.454	57.895	22.57	0.00	40.13	2.29
59	68	2.036098	CCTCTTGTGCATGGGCCA	59.964	61.111	9.61	9.61	40.13	5.36
123	132	4.603825	CGTTCATGCGTTGCTTTTCTTTTC	60.604	41.667	0.00	0.00	0.00	2.29
128	137	1.052287	CCGTTCATGCGTTGCTTTTC	58.948	50.000	0.00	0.00	0.00	2.29
206	220	8.474831	TGAATCTATTCCACTTCAAATCTCGTA	58.525	33.333	0.41	0.00	35.97	3.43
279	352	8.857098	TGTATATCGAAATTGCTAAGTAGGAGT	58.143	33.333	0.00	0.00	0.00	3.85
280	353	9.692749	TTGTATATCGAAATTGCTAAGTAGGAG	57.307	33.333	0.00	0.00	0.00	3.69
314	799	4.669700	TCTCTGTTACTAACCTAGCCACA	58.330	43.478	0.00	0.00	0.00	4.17
364	2703	5.506686	TCCACAAGATAGATGAGAAGTCG	57.493	43.478	0.00	0.00	0.00	4.18
413	2753	3.808728	TCGGCCAGAAAAGGAATAGATG	58.191	45.455	2.24	0.00	0.00	2.90
666	3113	9.798994	GACGATAAAGGATACGTGGATATATTT	57.201	33.333	0.00	0.00	46.39	1.40
667	3114	8.963725	TGACGATAAAGGATACGTGGATATATT	58.036	33.333	0.00	0.00	46.39	1.28
668	3115	8.515695	TGACGATAAAGGATACGTGGATATAT	57.484	34.615	0.00	0.00	46.39	0.86
669	3116	7.926674	TGACGATAAAGGATACGTGGATATA	57.073	36.000	0.00	0.00	46.39	0.86
670	3117	6.829229	TGACGATAAAGGATACGTGGATAT	57.171	37.500	0.00	0.00	46.39	1.63
690	3137	7.760794	TGCATCCAATTCTTGTATCAAATTGAC	59.239	33.333	0.00	0.00	40.97	3.18
708	3155	8.588290	AATTAAATGTAGTTAGGTGCATCCAA	57.412	30.769	0.00	0.00	39.02	3.53
828	3286	5.550981	CGATGGAGTAGTTGATTTCAAACG	58.449	41.667	0.00	0.00	37.63	3.60
867	3325	1.265095	GCAATGGATACGTGGATGCAG	59.735	52.381	0.00	0.00	42.51	4.41
1079	3568	4.377021	CACAACACTCCAGCTACTTTACA	58.623	43.478	0.00	0.00	0.00	2.41
1099	3588	1.813178	GCCAAAAAGACTAGGAGGCAC	59.187	52.381	0.00	0.00	40.29	5.01
1153	3642	2.093500	GGTGCAGTGATGTACTCCATGA	60.093	50.000	0.00	0.00	37.60	3.07
1163	3652	4.880886	TTTTATCGATGGTGCAGTGATG	57.119	40.909	8.54	0.00	0.00	3.07
1195	3684	0.250295	TGAAACCCGAGCAGTCTTGG	60.250	55.000	0.00	0.00	42.55	3.61
1211	3700	6.712998	TGGTTACCAAGATTCTTTTCGATGAA	59.287	34.615	0.00	0.00	0.00	2.57
1266	3755	2.894765	TCCGTCACACCTCTCATTGTAA	59.105	45.455	0.00	0.00	0.00	2.41
1273	3762	0.173708	GGATGTCCGTCACACCTCTC	59.826	60.000	0.00	0.00	38.04	3.20
1355	3844	1.192312	GCCGCATACATGTGTCATACG	59.808	52.381	9.11	0.45	36.60	3.06
1419	3908	9.278978	TGTGTCTGTGTGTACAAATATAACAAT	57.721	29.630	0.00	0.00	36.14	2.71
1420	3909	8.552865	GTGTGTCTGTGTGTACAAATATAACAA	58.447	33.333	0.00	0.00	36.14	2.83
1433	3922	1.270571	TGTGTGTGTGTGTCTGTGTGT	60.271	47.619	0.00	0.00	0.00	3.72
1435	3924	1.270571	TGTGTGTGTGTGTGTCTGTGT	60.271	47.619	0.00	0.00	0.00	3.72
1437	3926	1.270571	TGTGTGTGTGTGTGTGTCTGT	60.271	47.619	0.00	0.00	0.00	3.41
1440	3935	1.152510	TGTGTGTGTGTGTGTGTGTC	58.847	50.000	0.00	0.00	0.00	3.67
2005	4534	3.542648	TGTTGTGTCGTGGTCCAATTTA	58.457	40.909	0.00	0.00	0.00	1.40
2049	4578	5.010282	GGAAACCTGTGTTATGGAAGTGAT	58.990	41.667	0.00	0.00	33.30	3.06
2088	4617	5.944007	GGGATCTTGTGTGGTTGTACTTATT	59.056	40.000	0.00	0.00	0.00	1.40
2149	4678	1.134037	ACACCGTTCAAACTAAGGGCA	60.134	47.619	0.00	0.00	37.82	5.36
2170	4699	6.894339	TTTCCACTAACAAAGAAGATTCCC	57.106	37.500	0.00	0.00	0.00	3.97
2211	4740	1.209019	CTGAGCAATGGTCTACAGCCT	59.791	52.381	13.84	0.00	0.00	4.58
2221	4750	0.877071	AAGCGACAACTGAGCAATGG	59.123	50.000	0.00	0.00	0.00	3.16
2333	4862	0.761187	ACCTATGCGCTCATGGACAT	59.239	50.000	9.73	0.00	33.52	3.06
2400	4929	2.417586	ACTGAATACGACGACGACATGA	59.582	45.455	15.32	0.00	42.66	3.07
2419	4948	2.490991	GTGAAAGCGGTGAAGGTTACT	58.509	47.619	0.00	0.00	0.00	2.24
2505	5034	4.844655	AGGGAGAACTAACACTTACCACAT	59.155	41.667	0.00	0.00	0.00	3.21
2512	5041	5.163088	ACCAATCAAGGGAGAACTAACACTT	60.163	40.000	0.00	0.00	0.00	3.16
2519	5048	2.040412	GTGGACCAATCAAGGGAGAACT	59.960	50.000	0.00	0.00	0.00	3.01
2555	5084	9.313118	GATCGCCAAACCAATATAAAAAGATTT	57.687	29.630	0.00	0.00	0.00	2.17
2594	5123	9.771534	TGTTTACCAAATTATTTCTCAAAAGGG	57.228	29.630	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.