AutoCloner

Multiple sequence alignment - TraesCS4D01G037400

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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	TraesCS4D01G037400	chr4D	100.000	3099	0	0	1	3099	16333772	16336870	0.000000e+00	5723
1	TraesCS4D01G037400	chr4D	96.409	1643	59	0	1457	3099	16353177	16354819	0.000000e+00	2708
2	TraesCS4D01G037400	chr4D	96.226	1643	62	0	1457	3099	16271025	16272667	0.000000e+00	2691
3	TraesCS4D01G037400	chr4D	96.226	1643	62	0	1457	3099	16312900	16314542	0.000000e+00	2691
4	TraesCS4D01G037400	chr4D	84.981	1618	193	32	723	2310	16345618	16347215	0.000000e+00	1596
5	TraesCS4D01G037400	chr4D	84.920	1618	194	32	723	2310	16264246	16265843	0.000000e+00	1591
6	TraesCS4D01G037400	chr4D	84.920	1618	194	32	723	2310	16305335	16306932	0.000000e+00	1591
7	TraesCS4D01G037400	chr4D	89.019	683	56	8	7	675	16308548	16309225	0.000000e+00	828
8	TraesCS4D01G037400	chr4D	88.873	683	58	7	7	675	16267458	16268136	0.000000e+00	824
9	TraesCS4D01G037400	chr4D	88.580	683	60	8	7	675	16348830	16349508	0.000000e+00	813
10	TraesCS4D01G037400	chr4D	76.092	435	60	19	12	425	16304629	16305040	1.470000e-43	187
11	TraesCS4D01G037400	chr4B	87.838	1628	179	15	675	2291	28185420	28187039	0.000000e+00	1892
12	TraesCS4D01G037400	chr4B	87.714	1636	181	16	675	2298	28174312	28175939	0.000000e+00	1890
13	TraesCS4D01G037400	chr4B	89.174	1247	125	7	675	1912	28179471	28180716	0.000000e+00	1546
14	TraesCS4D01G037400	chr4B	90.173	692	41	12	1	678	28173594	28174272	0.000000e+00	876
15	TraesCS4D01G037400	chr4B	89.260	689	52	10	1	672	28188772	28189455	0.000000e+00	843
16	TraesCS4D01G037400	chr4B	89.244	688	53	10	1	672	28178743	28179425	0.000000e+00	841
17	TraesCS4D01G037400	chr4B	89.115	689	53	10	1	672	28184691	28185374	0.000000e+00	837
18	TraesCS4D01G037400	chr4B	88.410	371	29	5	1	358	28181603	28181972	4.750000e-118	435
19	TraesCS4D01G037400	chr4B	83.333	426	48	8	2677	3099	28191779	28192184	3.770000e-99	372
20	TraesCS4D01G037400	chr4A	89.307	505	22	8	1	493	584070068	584069584	3.420000e-169	604
21	TraesCS4D01G037400	chr4A	82.702	607	83	15	2480	3075	584069588	584068993	1.270000e-143	520

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	TraesCS4D01G037400	chr4D	16333772	16336870	3098	False	5723.000000	5723	100.000000	1	3099	1	chr4D.!!$F1	3098
1	TraesCS4D01G037400	chr4D	16345618	16354819	9201	False	1705.666667	2708	89.990000	7	3099	3	chr4D.!!$F4	3092
2	TraesCS4D01G037400	chr4D	16264246	16272667	8421	False	1702.000000	2691	90.006333	7	3099	3	chr4D.!!$F2	3092
3	TraesCS4D01G037400	chr4D	16304629	16314542	9913	False	1324.250000	2691	86.564250	7	3099	4	chr4D.!!$F3	3092
4	TraesCS4D01G037400	chr4B	28173594	28192184	18590	False	1059.111111	1892	88.251222	1	3099	9	chr4B.!!$F1	3098
5	TraesCS4D01G037400	chr4A	584068993	584070068	1075	True	562.000000	604	86.004500	1	3075	2	chr4A.!!$R1	3074

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
445	11674	0.981183	AATCGGCAGGTAAGGTGACA	59.019	50.0	0.00	0.0	0.0	3.58	F
1191	12470	0.400213	TCGAGGTGTTCAAGGCCAAT	59.600	50.0	5.01	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1540	19939	2.294233	GCTCAACTTCACAATGCCTTCA	59.706	45.455	0.0	0.0	0.0	3.02	R
2977	21630	0.536460	TTGTTTGGGTCTTCCTCCGC	60.536	55.000	0.0	0.0	36.2	5.54	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
132	8268	7.946207	TGACCATCACTATGTCTAAATCTCTC	58.054	38.462	0.00	0.00	0.00	3.20
171	8307	4.220693	ACTCAACAAGCCACTATGCATA	57.779	40.909	6.20	6.20	0.00	3.14
181	8317	5.749462	AGCCACTATGCATAAGAAAAGACT	58.251	37.500	8.00	0.00	0.00	3.24
186	8327	5.753921	ACTATGCATAAGAAAAGACTACCGC	59.246	40.000	8.00	0.00	0.00	5.68
352	11581	5.955355	TCGAAATAATTGAACCAATCCCCTT	59.045	36.000	0.00	0.00	32.43	3.95
433	11662	4.335315	GGAATTCTTACACATCAATCGGCA	59.665	41.667	5.23	0.00	0.00	5.69
445	11674	0.981183	AATCGGCAGGTAAGGTGACA	59.019	50.000	0.00	0.00	0.00	3.58
510	11742	2.479837	TCGTCGTGCATCTTTGAACTT	58.520	42.857	0.00	0.00	0.00	2.66
547	11783	7.981789	TGCTCTTGTTGGACTGTTCTAATATAG	59.018	37.037	0.00	0.00	0.00	1.31
548	11784	7.982354	GCTCTTGTTGGACTGTTCTAATATAGT	59.018	37.037	0.00	0.00	0.00	2.12
564	11800	9.021807	TCTAATATAGTATGTACTTCTGTGGCC	57.978	37.037	0.00	0.00	37.73	5.36
617	11853	7.397892	TTTCTCATTGTTTTGTGTTCACCTA	57.602	32.000	0.37	0.00	0.00	3.08
641	11877	1.900486	CGAACTAGGGGTCAGTTCCTT	59.100	52.381	9.07	0.00	45.97	3.36
735	12013	2.159156	TGCAACATACTTCCGCTCGTAT	60.159	45.455	0.00	0.00	0.00	3.06
746	12024	5.119743	ACTTCCGCTCGTATTTTTACTGAAC	59.880	40.000	0.00	0.00	0.00	3.18
747	12025	3.609373	TCCGCTCGTATTTTTACTGAACG	59.391	43.478	0.00	0.00	34.99	3.95
853	12131	4.539083	ACCGCCACGCTGTTGTCA	62.539	61.111	0.00	0.00	0.00	3.58
858	12136	2.310233	CCACGCTGTTGTCAGTCGG	61.310	63.158	13.09	2.85	43.05	4.79
936	12215	4.044065	TCCCTTACACCCATTTTGACAGAT	59.956	41.667	0.00	0.00	0.00	2.90
1022	12301	1.610086	CCATCCCCAAGGCTTTGCA	60.610	57.895	2.41	0.00	32.79	4.08
1026	12305	0.998928	TCCCCAAGGCTTTGCATCTA	59.001	50.000	2.41	0.00	32.79	1.98
1136	12415	2.708861	AGTGGATGGTGAAGTACAACCA	59.291	45.455	15.03	15.03	34.92	3.67
1191	12470	0.400213	TCGAGGTGTTCAAGGCCAAT	59.600	50.000	5.01	0.00	0.00	3.16
1235	12514	3.086282	ACGTTGGAAACCACAAGTTCTT	58.914	40.909	0.00	0.00	46.28	2.52
1510	19909	2.602878	CACATCACAATTTCAGGCTGC	58.397	47.619	10.34	0.00	0.00	5.25
1515	19914	1.814394	CACAATTTCAGGCTGCTGCTA	59.186	47.619	15.64	0.00	39.59	3.49
1586	19985	1.135373	GGAAGCTCATCTCGTTGTCGA	60.135	52.381	0.00	0.00	44.12	4.20
1713	20112	4.162320	CACTGAGTCCAACTACCCATACAT	59.838	45.833	0.00	0.00	0.00	2.29
2362	20768	1.585895	GGGAGTCCCTCTAGCCTTTT	58.414	55.000	22.04	0.00	41.34	2.27
2367	20773	2.432510	AGTCCCTCTAGCCTTTTCATCG	59.567	50.000	0.00	0.00	0.00	3.84
2379	20785	4.735985	CCTTTTCATCGATCAATGCACAA	58.264	39.130	0.00	0.00	0.00	3.33
2498	21069	3.196254	CCATATGGGCTGAACAAAGCTTT	59.804	43.478	14.52	5.69	43.06	3.51
2534	21105	1.228245	GGCTGCACCAAGAGTCCAA	60.228	57.895	0.50	0.00	38.86	3.53
2598	21170	4.957759	ATCCGGTAAAACGATTGGAAAG	57.042	40.909	0.00	0.00	35.47	2.62
2668	21280	2.364647	GCGTAAGTTGTCTATAGCCCCT	59.635	50.000	0.00	0.00	41.68	4.79
2775	21409	4.341366	AAGGGCATGAAAGAAAACAAGG	57.659	40.909	0.00	0.00	0.00	3.61
2784	21420	9.691362	GCATGAAAGAAAACAAGGTCTTTATTA	57.309	29.630	0.00	0.00	42.67	0.98
2830	21466	6.319141	ACACTTTTAGCTGATTTTCCAGTC	57.681	37.500	0.00	0.00	36.57	3.51
2979	21632	5.348451	TCATATCGACATACATGAATTGGCG	59.652	40.000	13.73	13.73	43.17	5.69
3022	21675	3.906720	GGCTCCACCTAAACACATCTA	57.093	47.619	0.00	0.00	34.51	1.98
3057	21710	9.457436	TCTAGATGTACATATAGGCGAACATTA	57.543	33.333	28.51	10.43	34.35	1.90
3062	21715	6.921307	TGTACATATAGGCGAACATTACACTG	59.079	38.462	0.00	0.00	0.00	3.66
3088	21741	5.030147	TGAGTCCACCATATCTACTTTGGT	58.970	41.667	0.00	0.00	44.49	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
118	8254	5.759273	GCTGAATGCTGAGAGATTTAGACAT	59.241	40.000	0.00	0.00	38.95	3.06
171	8307	3.058224	GCATGTTGCGGTAGTCTTTTCTT	60.058	43.478	0.00	0.00	31.71	2.52
181	8317	2.093181	AGGAACTATGCATGTTGCGGTA	60.093	45.455	10.16	0.00	42.56	4.02
186	8327	4.194640	AGTAGCAGGAACTATGCATGTTG	58.805	43.478	10.16	1.95	46.31	3.33
315	8456	9.757227	TTCAATTATTTCGAGGATGTTTTGTTT	57.243	25.926	0.00	0.00	0.00	2.83
329	11558	5.852282	AGGGGATTGGTTCAATTATTTCG	57.148	39.130	0.00	0.00	33.90	3.46
352	11581	1.548081	TACTACCCTGTGCGTTGCTA	58.452	50.000	0.00	0.00	0.00	3.49
433	11662	2.910977	CCTTAGGGTTGTCACCTTACCT	59.089	50.000	0.00	0.00	43.65	3.08
445	11674	4.354087	ACCATTCAGACTTTCCTTAGGGTT	59.646	41.667	0.00	0.00	0.00	4.11
517	11749	0.588252	CAGTCCAACAAGAGCAACGG	59.412	55.000	0.00	0.00	0.00	4.44
518	11750	1.299541	ACAGTCCAACAAGAGCAACG	58.700	50.000	0.00	0.00	0.00	4.10
519	11751	2.945668	AGAACAGTCCAACAAGAGCAAC	59.054	45.455	0.00	0.00	0.00	4.17
547	11783	1.287425	GCGGCCACAGAAGTACATAC	58.713	55.000	2.24	0.00	0.00	2.39
548	11784	0.899019	TGCGGCCACAGAAGTACATA	59.101	50.000	2.24	0.00	0.00	2.29
549	11785	0.036164	TTGCGGCCACAGAAGTACAT	59.964	50.000	2.24	0.00	0.00	2.29
591	11827	5.519927	GGTGAACACAAAACAATGAGAAAGG	59.480	40.000	7.25	0.00	0.00	3.11
617	11853	0.542232	ACTGACCCCTAGTTCGTGCT	60.542	55.000	0.00	0.00	0.00	4.40
682	11960	9.819267	GGAAGTGCTAACTCTGTACTAAAATAT	57.181	33.333	0.00	0.00	34.77	1.28
690	11968	3.572604	ACGGAAGTGCTAACTCTGTAC	57.427	47.619	0.00	0.00	46.97	2.90
735	12013	5.250235	TCAATGGTTGCGTTCAGTAAAAA	57.750	34.783	0.00	0.00	0.00	1.94
746	12024	1.133025	GTCCTGGAATCAATGGTTGCG	59.867	52.381	0.00	0.00	0.00	4.85
747	12025	1.478105	GGTCCTGGAATCAATGGTTGC	59.522	52.381	0.00	0.00	0.00	4.17
858	12136	1.589196	GCAGATACGGCGTGGAGAC	60.589	63.158	24.86	9.04	0.00	3.36
936	12215	1.953686	GTAGCTTTGGTGGTGCTTTGA	59.046	47.619	0.00	0.00	38.15	2.69
1022	12301	2.694397	TGCAACCTAGGATGGCTAGAT	58.306	47.619	17.98	0.00	0.00	1.98
1026	12305	1.142465	CAGATGCAACCTAGGATGGCT	59.858	52.381	17.98	5.87	0.00	4.75
1136	12415	1.435577	GGCGTCGTCCTTGTAAACAT	58.564	50.000	0.00	0.00	0.00	2.71
1191	12470	2.254546	ACGACTCAATGAAGGCAACA	57.745	45.000	0.00	0.00	41.41	3.33
1217	12496	3.096092	AGCAAGAACTTGTGGTTTCCAA	58.904	40.909	14.62	0.00	42.31	3.53
1540	19939	2.294233	GCTCAACTTCACAATGCCTTCA	59.706	45.455	0.00	0.00	0.00	3.02
1693	20092	3.454447	CCATGTATGGGTAGTTGGACTCA	59.546	47.826	2.87	0.00	44.31	3.41
1713	20112	3.259314	ACTGCCCATCCTGTGCCA	61.259	61.111	0.00	0.00	0.00	4.92
2008	20407	5.011090	TCATTCTGAGGTAACCATTCTCG	57.989	43.478	0.00	0.00	37.17	4.04
2030	20429	7.108847	CCACTCTTGTCAGAAATATCCTTCTT	58.891	38.462	0.00	0.00	33.25	2.52
2044	20443	2.549992	GCCACACATACCACTCTTGTCA	60.550	50.000	0.00	0.00	0.00	3.58
2362	20768	3.188254	ACGTTTTGTGCATTGATCGATGA	59.812	39.130	24.63	8.67	0.00	2.92
2367	20773	5.888412	AAAGAACGTTTTGTGCATTGATC	57.112	34.783	0.46	0.00	0.00	2.92
2498	21069	2.434336	AGCCGATTGATGTTGGTAGCTA	59.566	45.455	0.00	0.00	0.00	3.32
2503	21074	0.608856	TGCAGCCGATTGATGTTGGT	60.609	50.000	0.00	0.00	0.00	3.67
2534	21105	2.601266	GCACATGCAAACGAACGTACTT	60.601	45.455	0.00	0.00	41.59	2.24
2632	21204	4.542735	ACTTACGCCAATTTGTGCTTTAC	58.457	39.130	7.82	0.00	0.00	2.01
2668	21280	9.693739	TTCTGATATGTTTGGGAAATAGCTTTA	57.306	29.630	0.00	0.00	0.00	1.85
2784	21420	5.957842	TGCCATTACAACGAAGAAGAAAT	57.042	34.783	0.00	0.00	0.00	2.17
2918	21571	6.597672	AGTCAATTGGCGTGAAACATATCTAA	59.402	34.615	4.02	0.00	35.74	2.10
2963	21616	2.172505	TCCTCCGCCAATTCATGTATGT	59.827	45.455	0.00	0.00	0.00	2.29
2977	21630	0.536460	TTGTTTGGGTCTTCCTCCGC	60.536	55.000	0.00	0.00	36.20	5.54
2979	21632	2.230660	CACTTGTTTGGGTCTTCCTCC	58.769	52.381	0.00	0.00	36.20	4.30
3022	21675	9.303116	CCTATATGTACATCTAGACCAAGAACT	57.697	37.037	23.15	0.00	0.00	3.01
3041	21694	6.144563	CAGTCAGTGTAATGTTCGCCTATATG	59.855	42.308	0.00	0.00	0.00	1.78
3057	21710	1.722034	ATGGTGGACTCAGTCAGTGT	58.278	50.000	7.24	0.00	34.41	3.55
3062	21715	6.276847	CAAAGTAGATATGGTGGACTCAGTC	58.723	44.000	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.