AutoCloner

Multiple sequence alignment - TraesCS1D01G201500

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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	TraesCS1D01G201500	chr1D	100.000	3350	0	0	1	3350	284247831	284244482	0.000000e+00	6187
1	TraesCS1D01G201500	chr1B	94.450	2054	55	16	667	2680	386199205	386197171	0.000000e+00	3107
2	TraesCS1D01G201500	chr1B	92.119	571	36	7	1	563	408617766	408618335	0.000000e+00	797
3	TraesCS1D01G201500	chr1B	86.797	409	23	6	2754	3152	386197156	386196769	8.590000e-116	427
4	TraesCS1D01G201500	chr1B	96.460	113	4	0	564	676	386200501	386200389	1.590000e-43	187
5	TraesCS1D01G201500	chr1A	96.712	1612	30	7	1156	2747	355722148	355720540	0.000000e+00	2662
6	TraesCS1D01G201500	chr1A	93.853	667	22	7	564	1215	355722790	355722128	0.000000e+00	987
7	TraesCS1D01G201500	chr1A	89.517	601	24	8	2775	3350	355720545	355719959	0.000000e+00	725
8	TraesCS1D01G201500	chr3B	93.229	576	28	9	1	566	23784913	23785487	0.000000e+00	837
9	TraesCS1D01G201500	chr6B	93.170	571	30	7	1	563	547005400	547004831	0.000000e+00	830
10	TraesCS1D01G201500	chr6B	92.267	569	37	5	1	563	437481841	437481274	0.000000e+00	800
11	TraesCS1D01G201500	chr6B	90.411	584	47	5	1	576	83140493	83139911	0.000000e+00	760
12	TraesCS1D01G201500	chr4B	92.644	571	33	7	1	563	660663427	660663996	0.000000e+00	813
13	TraesCS1D01G201500	chr4B	92.105	570	37	6	1	563	74673877	74674445	0.000000e+00	797
14	TraesCS1D01G201500	chr2A	92.430	568	36	5	1	563	772692006	772692571	0.000000e+00	804
15	TraesCS1D01G201500	chr4A	92.281	570	36	6	1	563	659018711	659019279	0.000000e+00	802

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	TraesCS1D01G201500	chr1D	284244482	284247831	3349	True	6187.000000	6187	100.000000	1	3350	1	chr1D.!!$R1	3349
1	TraesCS1D01G201500	chr1B	386196769	386200501	3732	True	1240.333333	3107	92.569000	564	3152	3	chr1B.!!$R1	2588
2	TraesCS1D01G201500	chr1B	408617766	408618335	569	False	797.000000	797	92.119000	1	563	1	chr1B.!!$F1	562
3	TraesCS1D01G201500	chr1A	355719959	355722790	2831	True	1458.000000	2662	93.360667	564	3350	3	chr1A.!!$R1	2786
4	TraesCS1D01G201500	chr3B	23784913	23785487	574	False	837.000000	837	93.229000	1	566	1	chr3B.!!$F1	565
5	TraesCS1D01G201500	chr6B	547004831	547005400	569	True	830.000000	830	93.170000	1	563	1	chr6B.!!$R3	562
6	TraesCS1D01G201500	chr6B	437481274	437481841	567	True	800.000000	800	92.267000	1	563	1	chr6B.!!$R2	562
7	TraesCS1D01G201500	chr6B	83139911	83140493	582	True	760.000000	760	90.411000	1	576	1	chr6B.!!$R1	575
8	TraesCS1D01G201500	chr4B	660663427	660663996	569	False	813.000000	813	92.644000	1	563	1	chr4B.!!$F2	562
9	TraesCS1D01G201500	chr4B	74673877	74674445	568	False	797.000000	797	92.105000	1	563	1	chr4B.!!$F1	562
10	TraesCS1D01G201500	chr2A	772692006	772692571	565	False	804.000000	804	92.430000	1	563	1	chr2A.!!$F1	562
11	TraesCS1D01G201500	chr4A	659018711	659019279	568	False	802.000000	802	92.281000	1	563	1	chr4A.!!$F1	562

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	Hairpin	End Stability	Orientation
267	271	0.101759	GAGTTCATAGCGCCGGTACA	59.898	55.000	2.29	0.00	2.90	F
315	319	0.389025	ACATCGGAGATGCGCACATA	59.611	50.000	14.90	45.12	2.29	F
2255	3536	1.001406	CTCTCGGCCTAATGGTGGATC	59.999	57.143	0.00	35.27	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2255	3536	0.740164	TCTTCCTCGTCTCTCGGTCG	60.740	60.000	0.00	40.32	4.79	R
2266	3547	2.074547	TTACGGTTGCTTCTTCCTCG	57.925	50.000	0.00	0.00	4.63	R
3107	4416	1.404391	CAAGATGACATGGCTTCCTGC	59.596	52.381	10.73	41.94	4.85	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
31	32	1.400888	CGCCACGTTGTGCACAATTAT	60.401	47.619	33.16	19.33	38.24	1.28
58	60	2.632377	CACCTCATGCTTAACGACCAT	58.368	47.619	0.00	0.00	0.00	3.55
267	271	0.101759	GAGTTCATAGCGCCGGTACA	59.898	55.000	2.29	0.00	0.00	2.90
315	319	0.389025	ACATCGGAGATGCGCACATA	59.611	50.000	14.90	0.00	45.12	2.29
403	407	2.762887	TGACTGATAGACTTGGGCTCAG	59.237	50.000	0.00	0.00	39.35	3.35
700	1905	2.833631	TCTGGAGAAGGAAACGGAAC	57.166	50.000	0.00	0.00	0.00	3.62
703	1908	1.491332	TGGAGAAGGAAACGGAACCAA	59.509	47.619	0.00	0.00	0.00	3.67
704	1909	2.092321	TGGAGAAGGAAACGGAACCAAA	60.092	45.455	0.00	0.00	0.00	3.28
705	1910	3.154710	GGAGAAGGAAACGGAACCAAAT	58.845	45.455	0.00	0.00	0.00	2.32
706	1911	3.190744	GGAGAAGGAAACGGAACCAAATC	59.809	47.826	0.00	0.00	0.00	2.17
833	2050	3.119096	GCGGTGGCGAAGGTTCTC	61.119	66.667	0.00	0.00	0.00	2.87
873	2090	5.243954	TCTCCGTGGATTCGATCTATTGATT	59.756	40.000	0.00	0.00	32.19	2.57
874	2091	5.230182	TCCGTGGATTCGATCTATTGATTG	58.770	41.667	0.00	0.00	35.82	2.67
875	2092	5.010617	TCCGTGGATTCGATCTATTGATTGA	59.989	40.000	3.24	3.24	40.37	2.57
876	2093	5.871524	CCGTGGATTCGATCTATTGATTGAT	59.128	40.000	7.77	0.12	41.35	2.57
880	2097	7.542477	GTGGATTCGATCTATTGATTGATACGT	59.458	37.037	7.77	0.00	41.35	3.57
891	2108	2.103538	GATACGTGCTTCCGGCGA	59.896	61.111	9.30	0.00	45.43	5.54
1416	2694	1.906333	ACCCAATGCCAACGAACCC	60.906	57.895	0.00	0.00	0.00	4.11
2148	3426	2.343387	GTTGGCATGGTGTTGGGC	59.657	61.111	0.00	0.00	0.00	5.36
2198	3476	1.693083	GCATCTTACCGTGACACCGC	61.693	60.000	0.00	0.00	0.00	5.68
2216	3497	1.604947	CGCTGCTGGTCCTCATCATAG	60.605	57.143	0.00	0.00	0.00	2.23
2219	3500	3.553922	GCTGCTGGTCCTCATCATAGTAC	60.554	52.174	0.00	0.00	0.00	2.73
2255	3536	1.001406	CTCTCGGCCTAATGGTGGATC	59.999	57.143	0.00	0.00	35.27	3.36
2266	3547	1.030488	TGGTGGATCGACCGAGAGAC	61.030	60.000	20.47	0.00	42.61	3.36
2316	3597	0.321653	GTGGTGGAAGAGGAACGCAT	60.322	55.000	0.00	0.00	0.00	4.73
2491	3772	6.314917	ACTATTGGGGTGAATGTTTCTTCTT	58.685	36.000	0.00	0.00	0.00	2.52
2721	4016	6.439636	AGGACTATATAGCAAGATGGCAAA	57.560	37.500	9.78	0.00	35.83	3.68
2747	4042	2.457366	ACAAGAACTCGGCCTAGTTG	57.543	50.000	26.07	15.51	39.78	3.16
2748	4043	1.002087	ACAAGAACTCGGCCTAGTTGG	59.998	52.381	26.07	16.81	39.78	3.77
2749	4044	0.613777	AAGAACTCGGCCTAGTTGGG	59.386	55.000	26.07	0.00	39.78	4.12
2751	4046	0.611714	GAACTCGGCCTAGTTGGGAA	59.388	55.000	26.07	0.00	39.78	3.97
2752	4047	0.323957	AACTCGGCCTAGTTGGGAAC	59.676	55.000	21.08	0.00	38.28	3.62
2769	4064	4.534500	TGGGAACTTAGGATAGAGCAAACA	59.466	41.667	0.00	0.00	0.00	2.83
2775	4070	5.955355	ACTTAGGATAGAGCAAACAGACTCT	59.045	40.000	0.00	0.00	45.15	3.24
2776	4071	7.120051	ACTTAGGATAGAGCAAACAGACTCTA	58.880	38.462	2.49	2.49	46.57	2.43
2793	4088	4.718961	ACTCTAGCTCCAACAAAACACAT	58.281	39.130	0.00	0.00	0.00	3.21
2800	4095	4.270808	GCTCCAACAAAACACATTCAAAGG	59.729	41.667	0.00	0.00	0.00	3.11
2916	4213	2.424956	GGAGCGCCAGATTTCTGAAAAT	59.575	45.455	2.29	0.00	46.59	1.82
2917	4214	3.119352	GGAGCGCCAGATTTCTGAAAATT	60.119	43.478	2.29	0.00	46.59	1.82
2924	4221	4.020839	CCAGATTTCTGAAAATTGGGCACT	60.021	41.667	20.16	0.00	46.59	4.40
2945	4242	1.153429	GCCGTTTCCATACGCTCCT	60.153	57.895	0.00	0.00	40.10	3.69
2962	4259	5.751243	GCTCCTGGCGATTAAAGATAAAA	57.249	39.130	0.00	0.00	0.00	1.52
3002	4303	0.322816	GCTGCACTTGGGAATCAGGA	60.323	55.000	0.00	0.00	0.00	3.86
3026	4327	4.954970	CGTGCAGCCACTGGGGTT	62.955	66.667	0.00	0.00	44.14	4.11
3050	4351	2.938354	CTGTCAACAGGGCTTGGAG	58.062	57.895	0.44	0.00	40.20	3.86
3051	4352	1.228245	TGTCAACAGGGCTTGGAGC	60.228	57.895	0.44	0.00	41.46	4.70
3052	4353	2.032528	TCAACAGGGCTTGGAGCG	59.967	61.111	0.44	0.00	43.62	5.03
3107	4416	5.771153	TGAGATCTTGCAGACAGAGATAG	57.229	43.478	0.00	0.00	30.64	2.08
3180	4489	4.335315	CCTATACTGAATGCCAAGCGAAAA	59.665	41.667	0.00	0.00	0.00	2.29
3182	4491	3.221964	ACTGAATGCCAAGCGAAAATC	57.778	42.857	0.00	0.00	0.00	2.17
3216	4525	1.632965	AAAGGGGATAGCCACGACCC	61.633	60.000	0.00	0.00	44.66	4.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	1.851065	TAAGCATGAGGTGGCAGCCA	61.851	55.000	11.22	11.22	0.00	4.75
139	142	1.692519	AGGTTCCTAGTGTCGCAAAGT	59.307	47.619	0.00	0.00	0.00	2.66
235	239	0.250124	TGAACTCCACCGACGCATTT	60.250	50.000	0.00	0.00	0.00	2.32
267	271	1.673767	TTTCCTCCTCTTGCCATCCT	58.326	50.000	0.00	0.00	0.00	3.24
315	319	2.177016	ACCTAAGCAGGAAAAAGGTGGT	59.823	45.455	0.00	0.00	45.91	4.16
700	1905	7.830940	TGGATTGAAATTCGATTTGATTTGG	57.169	32.000	0.00	0.00	31.47	3.28
703	1908	7.254185	CGCATTGGATTGAAATTCGATTTGATT	60.254	33.333	0.00	0.00	31.47	2.57
704	1909	6.199531	CGCATTGGATTGAAATTCGATTTGAT	59.800	34.615	0.00	0.00	31.47	2.57
705	1910	5.515982	CGCATTGGATTGAAATTCGATTTGA	59.484	36.000	0.00	0.00	31.47	2.69
706	1911	5.720239	CGCATTGGATTGAAATTCGATTTG	58.280	37.500	0.00	0.00	31.47	2.32
786	1995	0.770557	TAATAATCCTGGGGCCGGCT	60.771	55.000	28.56	6.02	0.00	5.52
873	2090	2.202690	CGCCGGAAGCACGTATCA	60.203	61.111	5.05	0.00	44.04	2.15
874	2091	2.103538	TCGCCGGAAGCACGTATC	59.896	61.111	5.05	0.00	44.04	2.24
875	2092	2.202703	GTCGCCGGAAGCACGTAT	60.203	61.111	5.05	0.00	44.04	3.06
876	2093	4.424566	GGTCGCCGGAAGCACGTA	62.425	66.667	5.05	0.00	44.04	3.57
1331	2609	3.053291	GTGGACGATTTGGCCGCA	61.053	61.111	4.31	0.00	32.58	5.69
1340	2618	2.982130	GAGGCTGTGGTGGACGAT	59.018	61.111	0.00	0.00	0.00	3.73
2148	3426	2.034053	GTCCTCGATCCTCAAGCTACTG	59.966	54.545	0.00	0.00	0.00	2.74
2198	3476	3.894427	AGTACTATGATGAGGACCAGCAG	59.106	47.826	0.00	0.00	45.18	4.24
2255	3536	0.740164	TCTTCCTCGTCTCTCGGTCG	60.740	60.000	0.00	0.00	40.32	4.79
2266	3547	2.074547	TTACGGTTGCTTCTTCCTCG	57.925	50.000	0.00	0.00	0.00	4.63
2316	3597	1.417890	GCTCCTTGCCTCCTGCTATTA	59.582	52.381	0.00	0.00	42.00	0.98
2370	3651	9.264719	GAATAATTCAAGGCTGGATTTATTTGG	57.735	33.333	23.05	0.00	33.97	3.28
2721	4016	3.816994	AGGCCGAGTTCTTGTAAGTTTT	58.183	40.909	0.00	0.00	0.00	2.43
2747	4042	5.099042	TGTTTGCTCTATCCTAAGTTCCC	57.901	43.478	0.00	0.00	0.00	3.97
2748	4043	5.813157	GTCTGTTTGCTCTATCCTAAGTTCC	59.187	44.000	0.00	0.00	0.00	3.62
2749	4044	6.635755	AGTCTGTTTGCTCTATCCTAAGTTC	58.364	40.000	0.00	0.00	0.00	3.01
2751	4046	5.955355	AGAGTCTGTTTGCTCTATCCTAAGT	59.045	40.000	0.00	0.00	39.99	2.24
2752	4047	6.463995	AGAGTCTGTTTGCTCTATCCTAAG	57.536	41.667	0.00	0.00	39.99	2.18
2769	4064	4.141711	TGTGTTTTGTTGGAGCTAGAGTCT	60.142	41.667	0.00	0.00	0.00	3.24
2775	4070	5.843673	TTGAATGTGTTTTGTTGGAGCTA	57.156	34.783	0.00	0.00	0.00	3.32
2776	4071	4.734398	TTGAATGTGTTTTGTTGGAGCT	57.266	36.364	0.00	0.00	0.00	4.09
2793	4088	6.354130	AGTTTAGACAGTAGTTGCCTTTGAA	58.646	36.000	0.00	0.00	0.00	2.69
2822	4117	5.595952	GGAAGTTTGCCAAAGAGATGGATAT	59.404	40.000	0.00	0.00	43.54	1.63
2924	4221	1.004320	AGCGTATGGAAACGGCACA	60.004	52.632	0.00	0.00	43.06	4.57
2945	4242	7.389330	TGACACTCTTTTTATCTTTAATCGCCA	59.611	33.333	0.00	0.00	0.00	5.69
2955	4252	5.077564	GGGGGTTTGACACTCTTTTTATCT	58.922	41.667	0.00	0.00	0.00	1.98
2961	4258	2.136026	AGAGGGGGTTTGACACTCTTT	58.864	47.619	0.00	0.00	35.10	2.52
2962	4259	1.821088	AGAGGGGGTTTGACACTCTT	58.179	50.000	0.00	0.00	35.10	2.85
2975	4272	1.975407	CCAAGTGCAGCAAGAGGGG	60.975	63.158	0.00	0.00	0.00	4.79
3002	4303	0.742281	CAGTGGCTGCACGCTAGAAT	60.742	55.000	0.50	0.00	39.13	2.40
3020	4321	2.632996	CTGTTGACAGTCTAGAACCCCA	59.367	50.000	1.31	0.00	39.09	4.96
3021	4322	2.028020	CCTGTTGACAGTCTAGAACCCC	60.028	54.545	10.03	0.00	42.27	4.95
3026	4327	2.300152	CAAGCCCTGTTGACAGTCTAGA	59.700	50.000	10.03	0.00	42.27	2.43
3041	4342	4.803908	CTTCCCCGCTCCAAGCCC	62.804	72.222	0.00	0.00	38.18	5.19
3042	4343	3.268103	TTCTTCCCCGCTCCAAGCC	62.268	63.158	0.00	0.00	38.18	4.35
3043	4344	1.746991	CTTCTTCCCCGCTCCAAGC	60.747	63.158	0.00	0.00	38.02	4.01
3044	4345	0.036875	AACTTCTTCCCCGCTCCAAG	59.963	55.000	0.00	0.00	0.00	3.61
3045	4346	0.036306	GAACTTCTTCCCCGCTCCAA	59.964	55.000	0.00	0.00	0.00	3.53
3046	4347	0.836400	AGAACTTCTTCCCCGCTCCA	60.836	55.000	0.00	0.00	0.00	3.86
3047	4348	0.391793	CAGAACTTCTTCCCCGCTCC	60.392	60.000	0.00	0.00	0.00	4.70
3048	4349	0.321996	ACAGAACTTCTTCCCCGCTC	59.678	55.000	0.00	0.00	0.00	5.03
3049	4350	0.765510	AACAGAACTTCTTCCCCGCT	59.234	50.000	0.00	0.00	0.00	5.52
3050	4351	1.157585	GAACAGAACTTCTTCCCCGC	58.842	55.000	0.00	0.00	0.00	6.13
3051	4352	2.037251	TCAGAACAGAACTTCTTCCCCG	59.963	50.000	0.00	0.00	0.00	5.73
3052	4353	3.771577	TCAGAACAGAACTTCTTCCCC	57.228	47.619	0.00	0.00	0.00	4.81
3107	4416	1.404391	CAAGATGACATGGCTTCCTGC	59.596	52.381	10.73	0.00	41.94	4.85
3160	4469	4.641989	AGATTTTCGCTTGGCATTCAGTAT	59.358	37.500	0.00	0.00	0.00	2.12
3180	4489	3.070015	CCCTTTTCCAACACTTGCAAGAT	59.930	43.478	32.50	16.97	0.00	2.40
3182	4491	2.483538	CCCCTTTTCCAACACTTGCAAG	60.484	50.000	24.84	24.84	0.00	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.