AutoCloner

Multiple sequence alignment - TraesCS1B01G314400

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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	TraesCS1B01G314400	chr1B	100.000	3071	0	0	1	3071	539447378	539450448	0.000000e+00	5672
1	TraesCS1B01G314400	chr1B	87.270	1139	143	2	970	2108	539135527	539136663	0.000000e+00	1299
2	TraesCS1B01G314400	chr1B	84.100	522	48	19	1	489	539564685	539565204	3.580000e-129	472
3	TraesCS1B01G314400	chr1B	87.500	320	30	7	544	858	539565474	539565788	8.100000e-96	361
4	TraesCS1B01G314400	chr1A	94.824	3091	119	15	1	3071	497281200	497284269	0.000000e+00	4783
5	TraesCS1B01G314400	chr1A	82.099	905	103	31	1	857	497516301	497517194	0.000000e+00	719
6	TraesCS1B01G314400	chr1A	79.064	406	73	3	1718	2119	99908338	99907941	5.050000e-68	268
7	TraesCS1B01G314400	chr1D	96.287	2747	98	4	1	2745	401197192	401199936	0.000000e+00	4505
8	TraesCS1B01G314400	chr1D	92.507	347	19	2	2731	3071	401201747	401202092	9.900000e-135	490
9	TraesCS1B01G314400	chr1D	89.873	237	15	3	1	228	401678995	401679231	2.320000e-76	296
10	TraesCS1B01G314400	chr3D	76.403	695	133	23	1382	2056	579614810	579615493	2.270000e-91	346
11	TraesCS1B01G314400	chr3A	76.211	702	134	24	1379	2057	714738667	714739358	1.050000e-89	340
12	TraesCS1B01G314400	chr3A	77.011	522	114	6	1487	2005	714769009	714769527	8.330000e-76	294
13	TraesCS1B01G314400	chr2D	81.093	439	53	11	2315	2748	104272415	104272828	1.060000e-84	324
14	TraesCS1B01G314400	chr2D	80.303	462	51	20	2306	2756	103474909	103475341	2.300000e-81	313
15	TraesCS1B01G314400	chr3B	74.928	698	133	27	1382	2059	735131236	735130561	6.480000e-72	281
16	TraesCS1B01G314400	chr7D	74.839	465	94	21	1556	2004	504766768	504767225	4.040000e-44	189

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	TraesCS1B01G314400	chr1B	539447378	539450448	3070	False	5672.0	5672	100.000	1	3071	1	chr1B.!!$F2	3070
1	TraesCS1B01G314400	chr1B	539135527	539136663	1136	False	1299.0	1299	87.270	970	2108	1	chr1B.!!$F1	1138
2	TraesCS1B01G314400	chr1B	539564685	539565788	1103	False	416.5	472	85.800	1	858	2	chr1B.!!$F3	857
3	TraesCS1B01G314400	chr1A	497281200	497284269	3069	False	4783.0	4783	94.824	1	3071	1	chr1A.!!$F1	3070
4	TraesCS1B01G314400	chr1A	497516301	497517194	893	False	719.0	719	82.099	1	857	1	chr1A.!!$F2	856
5	TraesCS1B01G314400	chr1D	401197192	401202092	4900	False	2497.5	4505	94.397	1	3071	2	chr1D.!!$F2	3070
6	TraesCS1B01G314400	chr3D	579614810	579615493	683	False	346.0	346	76.403	1382	2056	1	chr3D.!!$F1	674
7	TraesCS1B01G314400	chr3A	714738667	714739358	691	False	340.0	340	76.211	1379	2057	1	chr3A.!!$F1	678
8	TraesCS1B01G314400	chr3A	714769009	714769527	518	False	294.0	294	77.011	1487	2005	1	chr3A.!!$F2	518
9	TraesCS1B01G314400	chr3B	735130561	735131236	675	True	281.0	281	74.928	1382	2059	1	chr3B.!!$R1	677

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
386	626	1.000607	GCGATTAGCCCGTGTCTATCA	60.001	52.381	0.0	0.0	40.81	2.15	F
1036	1362	0.107643	TTGTGTCGGTGAGCCATTGA	59.892	50.000	0.0	0.0	34.09	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1301	1627	0.321564	CCATGACAGTCGCTTCCCAA	60.322	55.0	0.0	0.0	0.00	4.12	R
2529	2883	0.040204	AAGGGAGAAGGCAACATGGG	59.960	55.0	0.0	0.0	41.41	4.00	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
90	92	2.371179	AGCCATCTGTACCATCCATCAG	59.629	50.000	0.00	0.00	0.00	2.90
386	626	1.000607	GCGATTAGCCCGTGTCTATCA	60.001	52.381	0.00	0.00	40.81	2.15
415	655	1.202359	TCGGCAACTCAAAAACCTTGC	60.202	47.619	0.00	0.00	38.64	4.01
441	681	6.312399	TGATTTCATACCACACTGTTGTTC	57.688	37.500	0.00	0.00	31.66	3.18
484	724	1.684869	CCCACAAATACGAGGGCCATT	60.685	52.381	6.18	0.00	33.91	3.16
512	833	2.028748	GGTCCTAGTCTTTGGCGTGTTA	60.029	50.000	0.00	0.00	0.00	2.41
526	847	4.034279	TGGCGTGTTACAAGTTTTAGTCAC	59.966	41.667	0.00	0.00	0.00	3.67
660	982	7.871463	AGTTAGTAACTTGCTTGTAGGTGTAAG	59.129	37.037	9.85	0.00	39.04	2.34
670	992	5.677091	GCTTGTAGGTGTAAGCATGGAAATG	60.677	44.000	0.00	0.00	46.43	2.32
800	1126	6.183360	TGCACACAACCTCATTTGTTTTCTAT	60.183	34.615	0.00	0.00	37.62	1.98
869	1195	2.567615	ACAGTATTTTCTCCAGTCGCCT	59.432	45.455	0.00	0.00	0.00	5.52
890	1216	1.276421	GCTGCTTCTTCCTCCAGTACA	59.724	52.381	0.00	0.00	0.00	2.90
956	1282	1.009829	GCAAGCGGTGATTAGTCTGG	58.990	55.000	0.00	0.00	0.00	3.86
981	1307	1.668826	ATAGCTTCCAACTCCCCACA	58.331	50.000	0.00	0.00	0.00	4.17
1034	1360	1.237285	GCTTGTGTCGGTGAGCCATT	61.237	55.000	0.00	0.00	34.09	3.16
1036	1362	0.107643	TTGTGTCGGTGAGCCATTGA	59.892	50.000	0.00	0.00	34.09	2.57
1102	1428	1.202382	CCCTCAAGATCGACGGTTACC	60.202	57.143	0.00	0.00	0.00	2.85
1149	1475	2.568956	TGAGTTCCTCCAATCCAGTCAG	59.431	50.000	0.00	0.00	0.00	3.51
1214	1540	0.250338	GGCAAGGACTCCGAAACAGT	60.250	55.000	0.00	0.00	0.00	3.55
1253	1579	7.504924	TTTACCTCAAACTCGATGAAATTGT	57.495	32.000	0.00	0.00	0.00	2.71
1272	1598	2.894765	TGTAACCGAGGATGTGAAGACA	59.105	45.455	0.00	0.00	36.22	3.41
1301	1627	4.096382	CACTATTAATTTCGCCAAGGTGCT	59.904	41.667	0.00	0.00	0.00	4.40
1325	1651	3.188786	GCGACTGTCATGGCCGTC	61.189	66.667	11.45	11.45	0.00	4.79
1371	1697	1.549037	GGTGGTAAGCAAATGTGGGGA	60.549	52.381	0.00	0.00	0.00	4.81
1380	1706	3.706086	AGCAAATGTGGGGATATCCAAAC	59.294	43.478	23.27	19.03	38.72	2.93
1396	1722	3.909995	TCCAAACTTCATCAAGAGGGAGA	59.090	43.478	0.00	0.00	33.34	3.71
1425	1751	1.786937	AGTCGGAGCATCTCAAGGAT	58.213	50.000	0.00	0.00	33.73	3.24
1489	1824	1.077140	TGCACCAAACAGACCAGCA	60.077	52.632	0.00	0.00	0.00	4.41
1518	1853	2.983592	GTCTTTGTGCCCCCACCG	60.984	66.667	0.00	0.00	41.35	4.94
1595	1930	1.207329	GTTTGAGGTAGGCGGTGAGAT	59.793	52.381	0.00	0.00	0.00	2.75
1600	1935	1.689273	AGGTAGGCGGTGAGATGATTC	59.311	52.381	0.00	0.00	0.00	2.52
1738	2088	2.731976	GTGTTCAAGGAGTTGCTCTACG	59.268	50.000	0.00	0.00	33.23	3.51
2027	2378	3.225104	AGAATTTGTGCAAGAGCTTCCA	58.775	40.909	0.00	0.00	42.74	3.53
2401	2755	3.256383	CCCTGATTTGATGTTTGCTGACA	59.744	43.478	0.00	0.00	0.00	3.58
2454	2808	2.561733	TACTCTGTCATTTCTCGCGG	57.438	50.000	6.13	0.00	0.00	6.46
2529	2883	9.833182	GATCTCTTGAGAAACCAAAAATACTTC	57.167	33.333	4.33	0.00	0.00	3.01
2540	2894	4.020307	CCAAAAATACTTCCCATGTTGCCT	60.020	41.667	0.00	0.00	0.00	4.75
2613	2971	8.236586	TCATGATCACTATGTTTTTGTGTTAGC	58.763	33.333	0.00	0.00	33.82	3.09
2614	2972	6.598525	TGATCACTATGTTTTTGTGTTAGCG	58.401	36.000	0.00	0.00	33.82	4.26
2617	2975	5.297278	TCACTATGTTTTTGTGTTAGCGGTT	59.703	36.000	0.00	0.00	33.82	4.44
2643	3001	1.486726	CCTTTCTGTAGGGCCTACCAG	59.513	57.143	34.70	29.21	43.89	4.00
2837	5027	6.782082	TGGTTGGCAAATGCATTATACTTA	57.218	33.333	13.39	0.00	44.36	2.24
2868	5058	7.362920	CCTGTTATTCCAAGAATTACCTTGTGG	60.363	40.741	6.24	0.00	41.34	4.17
2935	5126	5.570205	TTACTCACACCCCATGTAAGAAA	57.430	39.130	0.00	0.00	40.64	2.52
2954	5145	6.625873	AGAAATCAAACTCAGGTTCTTCAC	57.374	37.500	0.00	0.00	34.14	3.18
2999	5196	9.125026	GAACATAATCACCCTTCAGATTTATGT	57.875	33.333	0.00	0.00	36.07	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
90	92	4.443621	GGCAGTTACCACTCTTCTATTCC	58.556	47.826	0.00	0.00	0.00	3.01
386	626	3.678056	TTGAGTTGCCGACTAATCACT	57.322	42.857	0.00	0.00	39.19	3.41
415	655	6.680810	ACAACAGTGTGGTATGAAATCAATG	58.319	36.000	0.00	0.00	36.31	2.82
441	681	7.038729	TGGGCCTCTAATAAATCTAGACATGAG	60.039	40.741	4.53	0.00	0.00	2.90
484	724	1.275291	CAAAGACTAGGACCGCCTCAA	59.725	52.381	0.00	0.00	45.54	3.02
491	731	0.320697	ACACGCCAAAGACTAGGACC	59.679	55.000	0.00	0.00	0.00	4.46
512	833	3.275999	ACAAGGCGTGACTAAAACTTGT	58.724	40.909	7.60	0.00	42.40	3.16
670	992	7.750229	TTGATACCAAGGATAAAGCATGATC	57.250	36.000	0.00	0.00	0.00	2.92
869	1195	1.276421	GTACTGGAGGAAGAAGCAGCA	59.724	52.381	0.00	0.00	0.00	4.41
942	1268	4.920640	ATACTGTCCAGACTAATCACCG	57.079	45.455	0.40	0.00	0.00	4.94
956	1282	3.181464	GGGGAGTTGGAAGCTATACTGTC	60.181	52.174	0.00	0.00	0.00	3.51
1034	1360	1.752358	GATGGCAGAGGCGGATCTCA	61.752	60.000	0.00	0.00	42.47	3.27
1036	1362	2.865598	CGATGGCAGAGGCGGATCT	61.866	63.158	0.00	0.00	42.47	2.75
1239	1565	4.081862	TCCTCGGTTACAATTTCATCGAGT	60.082	41.667	0.00	0.00	40.36	4.18
1253	1579	4.020573	ACATTGTCTTCACATCCTCGGTTA	60.021	41.667	0.00	0.00	30.55	2.85
1272	1598	7.093945	ACCTTGGCGAAATTAATAGTGAACATT	60.094	33.333	0.00	0.00	0.00	2.71
1301	1627	0.321564	CCATGACAGTCGCTTCCCAA	60.322	55.000	0.00	0.00	0.00	4.12
1304	1630	2.109126	GGCCATGACAGTCGCTTCC	61.109	63.158	0.00	0.00	0.00	3.46
1371	1697	6.388100	TCTCCCTCTTGATGAAGTTTGGATAT	59.612	38.462	0.00	0.00	0.00	1.63
1380	1706	5.503927	TCCAAATTCTCCCTCTTGATGAAG	58.496	41.667	0.00	0.00	0.00	3.02
1396	1722	2.859165	TGCTCCGACTTCTCCAAATT	57.141	45.000	0.00	0.00	0.00	1.82
1595	1930	1.302431	CACCGGTGTGCAGGAATCA	60.302	57.895	26.95	0.00	35.31	2.57
1738	2088	2.160417	GCAATGAGTCAGTGTAGGCAAC	59.840	50.000	20.69	0.00	31.72	4.17
1807	2157	0.466543	TTATACCTGTCCGCCGCAAT	59.533	50.000	0.00	0.00	0.00	3.56
2027	2378	4.774660	ATCAGCTCCATCACAAGAGAAT	57.225	40.909	0.00	0.00	31.43	2.40
2374	2728	5.634859	CAGCAAACATCAAATCAGGGTTAAC	59.365	40.000	0.00	0.00	0.00	2.01
2401	2755	2.694628	CAGGCAGAGAAGTAGAGATGCT	59.305	50.000	0.00	0.00	34.19	3.79
2454	2808	8.443937	ACTAGCAAACGATATCTGTTCTTTTTC	58.556	33.333	11.54	0.00	0.00	2.29
2529	2883	0.040204	AAGGGAGAAGGCAACATGGG	59.960	55.000	0.00	0.00	41.41	4.00
2540	2894	5.860941	TTTGTTTTGTGCATAAGGGAGAA	57.139	34.783	0.00	0.00	0.00	2.87
2614	2972	9.946140	GTAGGCCCTACAGAAAGGTAATGAACC	62.946	48.148	16.19	0.00	41.30	3.62
2617	2975	3.460825	AGGCCCTACAGAAAGGTAATGA	58.539	45.455	0.00	0.00	34.56	2.57
2643	3001	4.677673	ATAAAAGCCATTCCTGATTGCC	57.322	40.909	0.00	0.00	0.00	4.52
2663	3021	9.686683	AGTTTAATCAGTAAGCAACCTGATTAT	57.313	29.630	22.05	11.93	43.69	1.28
2792	4982	5.587844	CCATCAAACCAGAGATCGATTTTCT	59.412	40.000	0.00	3.36	0.00	2.52
2793	4983	5.355350	ACCATCAAACCAGAGATCGATTTTC	59.645	40.000	0.00	0.76	0.00	2.29
2837	5027	6.547510	GGTAATTCTTGGAATAACAGGCAGAT	59.452	38.462	0.00	0.00	0.00	2.90
2868	5058	6.619801	AACTACATCTGTTTTTGGTGAGAC	57.380	37.500	0.00	0.00	0.00	3.36
2917	5108	4.649267	TGATTTCTTACATGGGGTGTGA	57.351	40.909	0.00	0.00	42.24	3.58
2954	5145	9.825109	TTATGTTCCCTTTAAAGTTTGAAAAGG	57.175	29.630	17.72	17.72	45.83	3.11
2973	5164	9.125026	ACATAAATCTGAAGGGTGATTATGTTC	57.875	33.333	0.00	0.00	33.17	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.