AutoCloner

Multiple sequence alignment - TraesCS7D01G385700

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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	TraesCS7D01G385700	chr7D	100.000	4235	0	0	1	4235	500097688	500101922	0.000000e+00	7821
1	TraesCS7D01G385700	chr7D	78.605	1921	314	65	490	2351	499971530	499973412	0.000000e+00	1181
2	TraesCS7D01G385700	chr7D	81.903	641	95	15	2672	3304	499973683	499974310	4.850000e-144	521
3	TraesCS7D01G385700	chr7D	94.578	332	18	0	1046	1377	499880148	499879817	8.120000e-142	514
4	TraesCS7D01G385700	chr7D	80.357	224	23	4	3900	4102	500139182	500139405	2.640000e-32	150
5	TraesCS7D01G385700	chr7B	94.566	4288	159	27	1	4235	527978659	527982925	0.000000e+00	6560
6	TraesCS7D01G385700	chr7B	78.229	1920	319	67	490	2351	527961763	527963641	0.000000e+00	1138
7	TraesCS7D01G385700	chr7B	94.622	595	26	4	648	1237	527853178	527852585	0.000000e+00	917
8	TraesCS7D01G385700	chr7B	81.123	641	100	16	2671	3303	527963911	527964538	1.060000e-135	494
9	TraesCS7D01G385700	chr7B	92.617	149	10	1	1230	1377	527851168	527851020	3.320000e-51	213
10	TraesCS7D01G385700	chr7B	94.118	102	6	0	550	651	527853371	527853270	5.670000e-34	156
11	TraesCS7D01G385700	chr7B	76.369	347	41	18	3779	4102	528016270	528016598	9.490000e-32	148
12	TraesCS7D01G385700	chr7A	95.749	3458	97	10	810	4235	566017640	566021079	0.000000e+00	5526
13	TraesCS7D01G385700	chr7A	78.583	1919	317	65	490	2351	566007637	566009518	0.000000e+00	1181
14	TraesCS7D01G385700	chr7A	91.609	727	42	5	3	712	566016916	566017640	0.000000e+00	987
15	TraesCS7D01G385700	chr7A	81.931	642	95	15	2671	3304	566009789	566010417	1.350000e-144	523

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	TraesCS7D01G385700	chr7D	500097688	500101922	4234	False	7821.000000	7821	100.000000	1	4235	1	chr7D.!!$F1	4234
1	TraesCS7D01G385700	chr7D	499971530	499974310	2780	False	851.000000	1181	80.254000	490	3304	2	chr7D.!!$F3	2814
2	TraesCS7D01G385700	chr7B	527978659	527982925	4266	False	6560.000000	6560	94.566000	1	4235	1	chr7B.!!$F1	4234
3	TraesCS7D01G385700	chr7B	527961763	527964538	2775	False	816.000000	1138	79.676000	490	3303	2	chr7B.!!$F3	2813
4	TraesCS7D01G385700	chr7B	527851020	527853371	2351	True	428.666667	917	93.785667	550	1377	3	chr7B.!!$R1	827
5	TraesCS7D01G385700	chr7A	566016916	566021079	4163	False	3256.500000	5526	93.679000	3	4235	2	chr7A.!!$F2	4232
6	TraesCS7D01G385700	chr7A	566007637	566010417	2780	False	852.000000	1181	80.257000	490	3304	2	chr7A.!!$F1	2814

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
782	1011	0.110328	CGCACAAGCAAAGAGAGCAG	60.110	55.0	0.00	0.00	42.27	4.24	F
962	1200	0.802494	TTGCTCTTCCGCGGAAAATC	59.198	50.0	37.62	27.56	33.34	2.17	F
1838	3517	1.327690	TATCGGTCACTCCCTGGTGC	61.328	60.0	0.00	0.00	37.16	5.01	F
2411	4112	2.232452	CCAAGAGTCACCACTTCGAGAT	59.768	50.0	0.00	0.00	30.63	2.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2313	4009	0.453390	GCTTAAGCATGTGCACCTCC	59.547	55.000	22.59	1.76	45.16	4.30	R
2444	4145	3.908103	ACCCAAGAGTACCAGTACACAAT	59.092	43.478	10.41	0.00	38.48	2.71	R
3051	4770	0.173481	CATCGCCGAGGAAGTCTTGA	59.827	55.000	0.00	0.00	0.00	3.02	R
3516	5235	1.135083	ACGCTGATGTAGTAGGTGCAC	60.135	52.381	8.80	8.80	0.00	4.57	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
59	67	8.635983	CGCCAAGTTTTAAAATTAGTTCTTAGC	58.364	33.333	3.52	5.68	0.00	3.09
71	79	1.066787	GTTCTTAGCAGCTCCGGTTCT	60.067	52.381	0.00	0.00	0.00	3.01
92	102	3.210227	TCAAAAACCGCTCTCACAATCA	58.790	40.909	0.00	0.00	0.00	2.57
96	106	0.320771	ACCGCTCTCACAATCACACC	60.321	55.000	0.00	0.00	0.00	4.16
126	136	1.377725	AGGCTCGTTCATTGCAGGG	60.378	57.895	0.00	0.00	0.00	4.45
202	218	1.371389	GTCGTCCACACTGTCGGAC	60.371	63.158	13.53	13.53	46.88	4.79
633	659	2.809696	TGGCTTTACCTTTTACGTCAGC	59.190	45.455	0.00	0.00	40.22	4.26
705	827	7.979444	TCTACACTTTTTGACAGAATAAGGG	57.021	36.000	0.00	0.00	0.00	3.95
764	993	2.159599	GCCTCTGTCAAGCTTGATTTCG	60.160	50.000	30.65	18.82	39.73	3.46
782	1011	0.110328	CGCACAAGCAAAGAGAGCAG	60.110	55.000	0.00	0.00	42.27	4.24
803	1032	5.638234	GCAGTCTAACACTCTTTTCGGTAAT	59.362	40.000	0.00	0.00	30.26	1.89
818	1047	9.437045	CTTTTCGGTAATTTTGTTAAGTTACGT	57.563	29.630	0.00	0.00	37.34	3.57
830	1059	2.159327	AGTTACGTTTCAAGACGGGG	57.841	50.000	0.00	0.00	46.77	5.73
886	1123	2.928801	TATGCCAATACACCAGCGAT	57.071	45.000	0.00	0.00	0.00	4.58
955	1193	1.590238	CACTATTCTTGCTCTTCCGCG	59.410	52.381	0.00	0.00	0.00	6.46
962	1200	0.802494	TTGCTCTTCCGCGGAAAATC	59.198	50.000	37.62	27.56	33.34	2.17
1027	1265	1.970114	CATCATCTGATGGCCCGGC	60.970	63.158	17.06	0.00	46.09	6.13
1271	2934	6.720112	AACTGCAATGTTATGCTTCCATAT	57.280	33.333	0.67	0.00	46.54	1.78
1284	2947	3.887716	GCTTCCATATGACAATTCTGGCT	59.112	43.478	3.65	0.00	0.00	4.75
1377	3041	5.749462	AGGATTCCTCATGGTGTTTCTAAG	58.251	41.667	0.00	0.00	34.23	2.18
1378	3042	5.488919	AGGATTCCTCATGGTGTTTCTAAGA	59.511	40.000	0.00	0.00	34.23	2.10
1381	3045	5.152623	TCCTCATGGTGTTTCTAAGACTG	57.847	43.478	0.00	0.00	34.23	3.51
1401	3077	4.036498	ACTGAGAATACAACGAGGATACCG	59.964	45.833	0.00	0.00	36.50	4.02
1494	3171	6.035843	CCATACCTAAATGAAATGTGTGTGC	58.964	40.000	0.00	0.00	0.00	4.57
1838	3517	1.327690	TATCGGTCACTCCCTGGTGC	61.328	60.000	0.00	0.00	37.16	5.01
2157	3842	9.883142	TGATTTATTTTCTTTGGTTTGTCTTGT	57.117	25.926	0.00	0.00	0.00	3.16
2170	3855	5.278957	GGTTTGTCTTGTACAGGCATTTCAT	60.279	40.000	0.00	0.00	36.83	2.57
2313	4009	3.059120	CGGCAGCTTATTGATCATGAGTG	60.059	47.826	0.09	0.00	0.00	3.51
2353	4049	5.362263	AGCTTTTCTACAAGGTTGTCGTTA	58.638	37.500	0.00	0.00	42.35	3.18
2411	4112	2.232452	CCAAGAGTCACCACTTCGAGAT	59.768	50.000	0.00	0.00	30.63	2.75
2420	4121	3.057315	CACCACTTCGAGATTTGCCATTT	60.057	43.478	0.00	0.00	0.00	2.32
2484	4185	3.831715	GGTAACCAGTGTCAATTCTGC	57.168	47.619	0.00	0.00	0.00	4.26
3141	4860	3.430374	GCGACAACATGGAGGTACTGTAT	60.430	47.826	0.00	0.00	41.55	2.29
3144	4863	5.163591	CGACAACATGGAGGTACTGTATGTA	60.164	44.000	0.00	0.00	41.55	2.29
3244	4963	2.965783	GCCACTGAGAGAGTCGCA	59.034	61.111	0.00	0.00	38.59	5.10
3327	5046	6.765512	CCAACCAAAACTTCAACCACATATTT	59.234	34.615	0.00	0.00	0.00	1.40
3336	5055	4.900684	TCAACCACATATTTCTTGTCCGA	58.099	39.130	0.00	0.00	0.00	4.55
3481	5200	4.085261	CGTTATGTCGAATCCCACGTTATG	60.085	45.833	0.00	0.00	0.00	1.90
3516	5235	1.486310	TCTCGGATTCTGGACCCATTG	59.514	52.381	0.00	0.00	0.00	2.82
3555	5274	2.106418	GTGTTTTCTTTTGTCGACCGC	58.894	47.619	14.12	0.00	0.00	5.68
3583	5302	4.346709	TCTTCATGGTTCACTGTGGTCTAA	59.653	41.667	8.11	0.00	0.00	2.10
3654	5397	3.186702	TGCCGCAGCACTTTATATGTA	57.813	42.857	0.00	0.00	46.52	2.29
3669	5412	9.990868	ACTTTATATGTACTTCTTTTGGGGAAT	57.009	29.630	0.00	0.00	0.00	3.01
3694	5437	0.250513	AGCTCCTCGGTCATTCAACC	59.749	55.000	0.00	0.00	35.86	3.77
3781	5524	4.681744	TCTTGCTGTTGAAACCATGAAAC	58.318	39.130	0.00	0.00	0.00	2.78
3833	5576	3.947834	CCTCTTTTCCGTATTGCCAAGAT	59.052	43.478	0.00	0.00	0.00	2.40
3846	5589	1.164411	CCAAGATGCGCAACCAACTA	58.836	50.000	17.11	0.00	0.00	2.24
3880	5623	4.650588	TGAGCCATTTTGCTTTATGCCTAT	59.349	37.500	0.00	0.00	42.95	2.57
4005	5767	4.202245	TGCTCTAACTAAACGCCTGATT	57.798	40.909	0.00	0.00	0.00	2.57
4111	5873	2.431954	AGCCATTCCTGGATCAACAG	57.568	50.000	0.00	0.00	46.37	3.16
4113	5875	2.019984	GCCATTCCTGGATCAACAGAC	58.980	52.381	0.00	0.00	46.37	3.51
4117	5879	4.097437	CCATTCCTGGATCAACAGACATTG	59.903	45.833	0.00	0.00	46.37	2.82
4119	5881	5.497464	TTCCTGGATCAACAGACATTGTA	57.503	39.130	0.00	0.00	39.73	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	6.554419	ACCGTAAAGTTTTACCAAAAGTGTC	58.446	36.000	8.69	0.00	39.81	3.67
59	67	1.266989	GGTTTTTGAGAACCGGAGCTG	59.733	52.381	9.46	0.00	39.68	4.24
71	79	3.003275	GTGATTGTGAGAGCGGTTTTTGA	59.997	43.478	0.00	0.00	0.00	2.69
96	106	0.314935	ACGAGCCTGCAACCAAAATG	59.685	50.000	0.00	0.00	0.00	2.32
185	201	3.036577	GTCCGACAGTGTGGACGA	58.963	61.111	21.38	5.03	44.68	4.20
368	384	2.764572	ACCTCAAACCGTTCCGAGATAT	59.235	45.455	10.75	0.00	0.00	1.63
422	441	4.024556	GGATTCAGATACAACGGCATTCAG	60.025	45.833	0.00	0.00	0.00	3.02
633	659	6.527372	GCTAAGTAAGTAGAACAGAAGAACGG	59.473	42.308	0.00	0.00	0.00	4.44
718	947	2.359850	GGCCACACGATTGCAGGA	60.360	61.111	0.00	0.00	0.00	3.86
721	950	1.965930	GACAGGCCACACGATTGCA	60.966	57.895	5.01	0.00	0.00	4.08
748	977	1.946081	TGTGCGAAATCAAGCTTGACA	59.054	42.857	30.66	20.21	40.49	3.58
764	993	0.950116	ACTGCTCTCTTTGCTTGTGC	59.050	50.000	0.00	0.00	40.20	4.57
782	1011	8.340443	ACAAAATTACCGAAAAGAGTGTTAGAC	58.660	33.333	0.00	0.00	0.00	2.59
803	1032	6.960431	CCGTCTTGAAACGTAACTTAACAAAA	59.040	34.615	0.00	0.00	41.01	2.44
830	1059	3.119955	GGTCTCCAAATAAGAAACGGTGC	60.120	47.826	0.00	0.00	0.00	5.01
955	1193	3.071479	TCTGCAAGTGGTACGATTTTCC	58.929	45.455	0.00	0.00	33.76	3.13
962	1200	4.242475	TGATAGTTTCTGCAAGTGGTACG	58.758	43.478	0.00	0.00	33.76	3.67
1024	1262	8.635124	CAACAAACTAACTACAAATAAATGCCG	58.365	33.333	0.00	0.00	0.00	5.69
1271	2934	6.872920	ACTTTACAAAAAGCCAGAATTGTCA	58.127	32.000	0.00	0.00	45.06	3.58
1377	3041	5.521544	GGTATCCTCGTTGTATTCTCAGTC	58.478	45.833	0.00	0.00	0.00	3.51
1378	3042	4.036498	CGGTATCCTCGTTGTATTCTCAGT	59.964	45.833	0.00	0.00	0.00	3.41
1381	3045	3.317430	ACCGGTATCCTCGTTGTATTCTC	59.683	47.826	4.49	0.00	0.00	2.87
1401	3077	2.295629	GAGCCCGTGGAATAGTAGTACC	59.704	54.545	0.00	0.00	0.00	3.34
1494	3171	3.535561	AGAAACGCTATCCTGTCCAATG	58.464	45.455	0.00	0.00	0.00	2.82
1716	3395	3.133003	CGTCCAATTCCAGTACTCCTGAT	59.867	47.826	0.00	0.00	44.49	2.90
1838	3517	3.068732	TCTTCAACAGGGATATCTCAGCG	59.931	47.826	5.15	0.00	0.00	5.18
2157	3842	9.507329	GATATCCTAGAAAATGAAATGCCTGTA	57.493	33.333	0.00	0.00	0.00	2.74
2170	3855	7.926555	GGATTGAACTCACGATATCCTAGAAAA	59.073	37.037	0.00	0.00	31.11	2.29
2262	3958	4.202010	TGCAAAACTACAAGCAGGAACTTC	60.202	41.667	0.00	0.00	34.60	3.01
2296	3992	4.514441	CACCTCCACTCATGATCAATAAGC	59.486	45.833	0.00	0.00	0.00	3.09
2313	4009	0.453390	GCTTAAGCATGTGCACCTCC	59.547	55.000	22.59	1.76	45.16	4.30
2353	4049	5.845985	CAACGAGATTCATAGTTGTGTGT	57.154	39.130	0.00	0.00	39.11	3.72
2444	4145	3.908103	ACCCAAGAGTACCAGTACACAAT	59.092	43.478	10.41	0.00	38.48	2.71
2484	4185	6.785488	TTTGTACTTGTCAATAGAGCACAG	57.215	37.500	0.00	0.00	0.00	3.66
3051	4770	0.173481	CATCGCCGAGGAAGTCTTGA	59.827	55.000	0.00	0.00	0.00	3.02
3141	4860	2.035469	TGGGCGTAGTCGGGTACA	59.965	61.111	0.00	0.00	37.56	2.90
3244	4963	2.588464	TCGGAGAGAGACCTGAAGTT	57.412	50.000	0.00	0.00	0.00	2.66
3327	5046	3.704566	ACAAGCCATATACTCGGACAAGA	59.295	43.478	0.00	0.00	0.00	3.02
3336	5055	6.500589	AAGACCATACACAAGCCATATACT	57.499	37.500	0.00	0.00	0.00	2.12
3516	5235	1.135083	ACGCTGATGTAGTAGGTGCAC	60.135	52.381	8.80	8.80	0.00	4.57
3555	5274	5.649395	ACCACAGTGAACCATGAAGATTATG	59.351	40.000	0.62	0.00	0.00	1.90
3654	5397	4.281941	GCTCTGAAATTCCCCAAAAGAAGT	59.718	41.667	0.00	0.00	0.00	3.01
3669	5412	1.561643	ATGACCGAGGAGCTCTGAAA	58.438	50.000	14.64	0.00	0.00	2.69
3753	5496	5.284861	TGGTTTCAACAGCAAGAGTACTA	57.715	39.130	0.00	0.00	0.00	1.82
3781	5524	7.796660	TGAAGAATAATCAAACGTGAAAGTTCG	59.203	33.333	0.00	0.00	37.30	3.95
3791	5534	9.846248	AAAGAGGAAATGAAGAATAATCAAACG	57.154	29.630	0.00	0.00	0.00	3.60
3833	5576	2.419673	CTGATGAATAGTTGGTTGCGCA	59.580	45.455	5.66	5.66	0.00	6.09
3846	5589	5.128827	AGCAAAATGGCTCAATCTGATGAAT	59.871	36.000	0.00	0.00	41.05	2.57
3880	5623	5.011431	CAGATATCCCATGCTTCAGTCTACA	59.989	44.000	0.00	0.00	0.00	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.