AutoCloner

Multiple sequence alignment - TraesCS3D01G420200

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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	TraesCS3D01G420200	chr3D	100.000	2389	0	0	1	2389	532584788	532582400	0.000000e+00	4412.0
1	TraesCS3D01G420200	chr3D	89.418	756	48	13	970	1701	532343845	532343098	0.000000e+00	924.0
2	TraesCS3D01G420200	chr3B	94.344	2104	82	14	312	2389	704654784	704652692	0.000000e+00	3192.0
3	TraesCS3D01G420200	chr3B	91.608	715	38	10	970	1666	704577853	704577143	0.000000e+00	968.0
4	TraesCS3D01G420200	chr3A	94.022	920	40	5	759	1667	667705087	667704172	0.000000e+00	1380.0
5	TraesCS3D01G420200	chr3A	90.389	437	29	5	970	1396	667514136	667513703	1.600000e-156	562.0
6	TraesCS3D01G420200	chr3A	93.923	362	13	2	297	658	667705872	667705520	2.700000e-149	538.0
7	TraesCS3D01G420200	chr3A	92.683	287	9	5	1390	1668	667513276	667512994	1.030000e-108	403.0
8	TraesCS3D01G420200	chr3A	86.544	379	36	11	1	365	667706244	667705867	1.030000e-108	403.0
9	TraesCS3D01G420200	chr3A	92.982	114	6	2	654	767	667705383	667705272	5.280000e-37	165.0
10	TraesCS3D01G420200	chr7A	85.649	655	74	12	1740	2389	3355177	3354538	0.000000e+00	671.0
11	TraesCS3D01G420200	chr2B	85.317	647	83	10	1747	2389	54345179	54344541	0.000000e+00	658.0
12	TraesCS3D01G420200	chr4A	84.759	643	86	9	1740	2376	607185206	607184570	3.350000e-178	634.0
13	TraesCS3D01G420200	chr4A	80.808	99	16	2	425	520	498698762	498698664	9.160000e-10	75.0
14	TraesCS3D01G420200	chr2A	85.739	582	68	8	1812	2389	773373790	773374360	3.400000e-168	601.0
15	TraesCS3D01G420200	chr4D	88.699	469	44	7	1926	2389	235508810	235508346	4.460000e-157	564.0
16	TraesCS3D01G420200	chr4D	83.505	97	14	1	426	520	85007356	85007260	3.270000e-14	89.8
17	TraesCS3D01G420200	chr4B	88.462	468	47	5	1926	2389	249059153	249059617	2.070000e-155	558.0
18	TraesCS3D01G420200	chr4B	81.188	101	16	2	422	520	122218294	122218195	7.080000e-11	78.7
19	TraesCS3D01G420200	chr7B	88.337	463	50	3	1929	2389	468729031	468728571	9.650000e-154	553.0
20	TraesCS3D01G420200	chr1A	88.121	463	50	4	1929	2389	117249060	117249519	1.610000e-151	545.0
21	TraesCS3D01G420200	chr5D	84.083	289	39	6	1740	2023	563401335	563401049	3.030000e-69	272.0
22	TraesCS3D01G420200	chr5D	78.014	141	21	6	422	554	8541077	8541215	1.970000e-11	80.5
23	TraesCS3D01G420200	chr6A	86.420	81	11	0	422	502	595049088	595049008	3.270000e-14	89.8
24	TraesCS3D01G420200	chr1B	80.189	106	19	2	422	525	429700248	429700143	7.080000e-11	78.7
25	TraesCS3D01G420200	chr6B	85.915	71	8	2	457	525	552398555	552398485	9.160000e-10	75.0

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	TraesCS3D01G420200	chr3D	532582400	532584788	2388	True	4412.0	4412	100.00000	1	2389	1	chr3D.!!$R2	2388
1	TraesCS3D01G420200	chr3D	532343098	532343845	747	True	924.0	924	89.41800	970	1701	1	chr3D.!!$R1	731
2	TraesCS3D01G420200	chr3B	704652692	704654784	2092	True	3192.0	3192	94.34400	312	2389	1	chr3B.!!$R2	2077
3	TraesCS3D01G420200	chr3B	704577143	704577853	710	True	968.0	968	91.60800	970	1666	1	chr3B.!!$R1	696
4	TraesCS3D01G420200	chr3A	667704172	667706244	2072	True	621.5	1380	91.86775	1	1667	4	chr3A.!!$R2	1666
5	TraesCS3D01G420200	chr3A	667512994	667514136	1142	True	482.5	562	91.53600	970	1668	2	chr3A.!!$R1	698
6	TraesCS3D01G420200	chr7A	3354538	3355177	639	True	671.0	671	85.64900	1740	2389	1	chr7A.!!$R1	649
7	TraesCS3D01G420200	chr2B	54344541	54345179	638	True	658.0	658	85.31700	1747	2389	1	chr2B.!!$R1	642
8	TraesCS3D01G420200	chr4A	607184570	607185206	636	True	634.0	634	84.75900	1740	2376	1	chr4A.!!$R2	636
9	TraesCS3D01G420200	chr2A	773373790	773374360	570	False	601.0	601	85.73900	1812	2389	1	chr2A.!!$F1	577

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
144	147	0.034896	CTTGGACGCACCCTACTGTT	59.965	55.0	0.0	0.0	38.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1766	2649	0.179012	TTTCCCCCTTCGTGTTGGAC	60.179	55.0	0.0	0.0	0.0	4.02	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
50	53	4.379499	GCCCAGTAAAAACAGAGAAATCCG	60.379	45.833	0.00	0.00	0.00	4.18
59	62	4.830826	ACAGAGAAATCCGGTGAAAAAC	57.169	40.909	0.00	0.00	0.00	2.43
60	63	3.568430	ACAGAGAAATCCGGTGAAAAACC	59.432	43.478	0.00	0.00	46.60	3.27
129	132	3.439129	CCGGCTCTTTTACCTTTACTTGG	59.561	47.826	0.00	0.00	0.00	3.61
130	133	4.320870	CGGCTCTTTTACCTTTACTTGGA	58.679	43.478	0.00	0.00	0.00	3.53
134	137	4.706035	TCTTTTACCTTTACTTGGACGCA	58.294	39.130	0.00	0.00	0.00	5.24
144	147	0.034896	CTTGGACGCACCCTACTGTT	59.965	55.000	0.00	0.00	38.00	3.16
145	148	0.470766	TTGGACGCACCCTACTGTTT	59.529	50.000	0.00	0.00	38.00	2.83
158	161	4.003648	CCTACTGTTTCATCACAACTCCC	58.996	47.826	0.00	0.00	0.00	4.30
166	169	4.305539	TCATCACAACTCCCACATTGAT	57.694	40.909	0.00	0.00	0.00	2.57
167	170	4.011698	TCATCACAACTCCCACATTGATG	58.988	43.478	0.00	0.00	41.04	3.07
184	187	4.293662	TGATGTACTGGTTTGTGGCATA	57.706	40.909	0.00	0.00	0.00	3.14
198	201	4.771903	TGTGGCATAACGCTTTATCCTAA	58.228	39.130	0.00	1.13	41.91	2.69
202	205	5.526111	TGGCATAACGCTTTATCCTAAAGAC	59.474	40.000	10.12	2.35	41.91	3.01
212	215	6.457159	TTTATCCTAAAGACCTGGGTTCAA	57.543	37.500	0.00	0.00	0.00	2.69
216	219	3.010138	CCTAAAGACCTGGGTTCAATCCA	59.990	47.826	0.00	0.00	0.00	3.41
225	229	3.091545	TGGGTTCAATCCATTGCTTCTC	58.908	45.455	0.00	0.00	37.68	2.87
227	231	2.428530	GGTTCAATCCATTGCTTCTCCC	59.571	50.000	0.00	0.00	37.68	4.30
229	233	3.008835	TCAATCCATTGCTTCTCCCTG	57.991	47.619	0.00	0.00	37.68	4.45
279	283	0.464036	CTGGGCCGCTCATTACTGTA	59.536	55.000	0.00	0.00	0.00	2.74
280	284	0.177141	TGGGCCGCTCATTACTGTAC	59.823	55.000	0.00	0.00	0.00	2.90
282	286	1.287425	GGCCGCTCATTACTGTACAC	58.713	55.000	0.00	0.00	0.00	2.90
289	293	3.845178	CTCATTACTGTACACGCCTCAA	58.155	45.455	0.00	0.00	0.00	3.02
627	708	8.158789	TGATGTTGCAGATGAATTATCCATAGA	58.841	33.333	0.00	0.00	36.40	1.98
888	1304	2.485122	GGCGTTCCAATGGCTTCG	59.515	61.111	0.00	0.19	37.49	3.79
982	1398	3.081409	CTACTCCCCACCACCCCG	61.081	72.222	0.00	0.00	0.00	5.73
1069	1487	0.315869	CGCGAATAATCCACCGCAAC	60.316	55.000	0.00	0.00	46.99	4.17
1081	1499	2.288152	CCACCGCAACAAGCAAATAACT	60.288	45.455	0.00	0.00	46.13	2.24
1089	1507	4.098914	ACAAGCAAATAACTCACCTCCA	57.901	40.909	0.00	0.00	0.00	3.86
1307	1729	0.249489	AGCATGAATACCGCCGAGAC	60.249	55.000	0.00	0.00	0.00	3.36
1548	2423	9.274065	GATTAGGTATCGTGATTTTTGTTTGTC	57.726	33.333	0.00	0.00	0.00	3.18
1634	2509	1.435577	GGCCGTCTGTTCGTTTGTAT	58.564	50.000	0.00	0.00	0.00	2.29
1707	2590	4.613167	CGTAGGTGGTCATTAGAGATACGC	60.613	50.000	0.00	0.00	0.00	4.42
1737	2620	5.912528	ACACGATAAAGAAATCAACACGAC	58.087	37.500	0.00	0.00	0.00	4.34
1744	2627	3.792401	AGAAATCAACACGACAGACACA	58.208	40.909	0.00	0.00	0.00	3.72
1757	2640	5.107607	ACGACAGACACATGATTTTAACGTC	60.108	40.000	0.00	0.00	0.00	4.34
1766	2649	7.112844	ACACATGATTTTAACGTCGAAAACATG	59.887	33.333	26.78	26.78	38.89	3.21
1788	2672	1.967779	CCAACACGAAGGGGGAAAAAT	59.032	47.619	0.00	0.00	0.00	1.82
1790	2674	3.574826	CCAACACGAAGGGGGAAAAATAA	59.425	43.478	0.00	0.00	0.00	1.40
1791	2675	4.552355	CAACACGAAGGGGGAAAAATAAC	58.448	43.478	0.00	0.00	0.00	1.89
1792	2676	3.834938	ACACGAAGGGGGAAAAATAACA	58.165	40.909	0.00	0.00	0.00	2.41
1793	2677	4.216708	ACACGAAGGGGGAAAAATAACAA	58.783	39.130	0.00	0.00	0.00	2.83
1794	2678	4.279922	ACACGAAGGGGGAAAAATAACAAG	59.720	41.667	0.00	0.00	0.00	3.16
1795	2679	4.279922	CACGAAGGGGGAAAAATAACAAGT	59.720	41.667	0.00	0.00	0.00	3.16
1860	2746	4.074970	GCCGGGATCTACAATTGATCAAT	58.925	43.478	15.36	15.36	41.35	2.57
1925	2811	8.424918	CAGGTAACCTATGTCAATACTGATCTT	58.575	37.037	0.00	0.00	29.78	2.40
1984	2872	2.415625	CGCTCGCCTGTTAGAAGTTAGT	60.416	50.000	0.00	0.00	0.00	2.24
2110	3000	1.134551	ACACTTTTGGCGCCAAACAAT	60.135	42.857	45.43	32.28	44.39	2.71
2138	3028	8.368668	ACTAGGGCTAATGTGTTATATCAACTC	58.631	37.037	0.00	0.00	0.00	3.01
2143	3033	7.171678	GGCTAATGTGTTATATCAACTCAGTCC	59.828	40.741	0.00	0.00	0.00	3.85
2254	3144	0.890683	CCTTGCTCAACAATGTCCCC	59.109	55.000	0.00	0.00	37.72	4.81
2331	3221	4.021016	CCTTAGTGAGGTATATGGCACTCC	60.021	50.000	0.00	0.00	41.43	3.85
2350	3240	1.433534	CGGCTCTCAGAAAACAGGTC	58.566	55.000	0.00	0.00	0.00	3.85
2356	3246	3.149196	TCTCAGAAAACAGGTCAATGCC	58.851	45.455	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	7.929245	TCTGTTTTTACTGGGCCTTTTATTTTC	59.071	33.333	4.53	0.00	0.00	2.29
129	132	2.000447	GATGAAACAGTAGGGTGCGTC	59.000	52.381	0.00	0.00	0.00	5.19
130	133	1.346395	TGATGAAACAGTAGGGTGCGT	59.654	47.619	0.00	0.00	0.00	5.24
134	137	4.505039	GGAGTTGTGATGAAACAGTAGGGT	60.505	45.833	0.00	0.00	0.00	4.34
144	147	4.097551	TCAATGTGGGAGTTGTGATGAA	57.902	40.909	0.00	0.00	0.00	2.57
145	148	3.786368	TCAATGTGGGAGTTGTGATGA	57.214	42.857	0.00	0.00	0.00	2.92
158	161	4.797471	CCACAAACCAGTACATCAATGTG	58.203	43.478	5.89	11.76	41.89	3.21
166	169	2.809119	CGTTATGCCACAAACCAGTACA	59.191	45.455	0.00	0.00	0.00	2.90
167	170	2.413634	GCGTTATGCCACAAACCAGTAC	60.414	50.000	0.00	0.00	37.76	2.73
184	187	4.514401	CCAGGTCTTTAGGATAAAGCGTT	58.486	43.478	4.72	0.00	0.00	4.84
198	201	3.434309	CAATGGATTGAACCCAGGTCTT	58.566	45.455	0.00	0.00	40.14	3.01
202	205	1.856629	AGCAATGGATTGAACCCAGG	58.143	50.000	3.47	0.00	40.14	4.45
212	215	3.011032	AGAAACAGGGAGAAGCAATGGAT	59.989	43.478	0.00	0.00	0.00	3.41
216	219	4.379302	AGAAGAAACAGGGAGAAGCAAT	57.621	40.909	0.00	0.00	0.00	3.56
247	251	1.822990	CGGCCCAGTAGTGAAGACTTA	59.177	52.381	0.00	0.00	33.21	2.24
252	256	1.153549	GAGCGGCCCAGTAGTGAAG	60.154	63.158	0.00	0.00	0.00	3.02
260	264	0.464036	TACAGTAATGAGCGGCCCAG	59.536	55.000	0.00	0.00	0.00	4.45
289	293	3.657956	GCAAGAGCTATGTCTCGCT	57.342	52.632	0.00	0.00	38.12	4.93
365	444	9.974750	TTGTTTTTCGAAACATTACCATTTTTC	57.025	25.926	10.79	0.00	41.69	2.29
389	469	1.004745	AGGTATGCTTCCCACACCTTG	59.995	52.381	0.00	0.00	36.16	3.61
397	477	9.000486	GTATGAAATAGTTTAGGTATGCTTCCC	58.000	37.037	0.00	0.00	0.00	3.97
398	478	9.780186	AGTATGAAATAGTTTAGGTATGCTTCC	57.220	33.333	0.00	0.00	0.00	3.46
670	892	6.005198	ACACTATGTTCCAAAATACCCGAAA	58.995	36.000	0.00	0.00	0.00	3.46
888	1304	5.179555	GCGTGGATCCTAAATTCCTAATGTC	59.820	44.000	14.23	0.00	32.95	3.06
1069	1487	4.096984	GGATGGAGGTGAGTTATTTGCTTG	59.903	45.833	0.00	0.00	0.00	4.01
1081	1499	2.923426	GATTGCGCGGATGGAGGTGA	62.923	60.000	8.83	0.00	0.00	4.02
1089	1507	1.069823	AGATTGAGAGATTGCGCGGAT	59.930	47.619	8.83	0.00	0.00	4.18
1132	1554	1.498865	CGCAGCTCGTTGTTCCTTGT	61.499	55.000	0.00	0.00	0.00	3.16
1188	1610	4.996434	GCGGTGTGGCTCAGCAGT	62.996	66.667	17.55	0.00	43.83	4.40
1372	1800	4.614555	TTTAATTAGTACTCGACGCCGA	57.385	40.909	0.00	0.00	43.35	5.54
1548	2423	5.337554	CATCTGCACATCCAAATTACACAG	58.662	41.667	0.00	0.00	0.00	3.66
1634	2509	3.455543	TCATAATGATCAGTGAGGCCACA	59.544	43.478	5.01	0.25	45.54	4.17
1683	2566	4.514441	CGTATCTCTAATGACCACCTACGT	59.486	45.833	0.00	0.00	0.00	3.57
1737	2620	5.509605	TCGACGTTAAAATCATGTGTCTG	57.490	39.130	0.00	0.00	0.00	3.51
1744	2627	6.799925	GGACATGTTTTCGACGTTAAAATCAT	59.200	34.615	0.00	11.42	0.00	2.45
1757	2640	3.288242	CTTCGTGTTGGACATGTTTTCG	58.712	45.455	0.00	0.44	36.53	3.46
1766	2649	0.179012	TTTCCCCCTTCGTGTTGGAC	60.179	55.000	0.00	0.00	0.00	4.02
1788	2672	2.340210	TTGCTGGCTGACACTTGTTA	57.660	45.000	0.00	0.00	0.00	2.41
1790	2674	1.696063	ATTTGCTGGCTGACACTTGT	58.304	45.000	0.00	0.00	0.00	3.16
1791	2675	2.806608	AATTTGCTGGCTGACACTTG	57.193	45.000	0.00	0.00	0.00	3.16
1792	2676	3.132646	TGAAAATTTGCTGGCTGACACTT	59.867	39.130	0.00	0.00	0.00	3.16
1793	2677	2.694628	TGAAAATTTGCTGGCTGACACT	59.305	40.909	0.00	0.00	0.00	3.55
1794	2678	2.796593	GTGAAAATTTGCTGGCTGACAC	59.203	45.455	0.00	0.00	0.00	3.67
1795	2679	2.694628	AGTGAAAATTTGCTGGCTGACA	59.305	40.909	0.00	0.00	0.00	3.58
1860	2746	5.878332	TGTAAGTCACCGTACGAGATAAA	57.122	39.130	18.76	0.00	0.00	1.40
1904	2790	8.083828	AGTGAAGATCAGTATTGACATAGGTT	57.916	34.615	0.00	0.00	35.83	3.50
1910	2796	5.410924	CCGAAGTGAAGATCAGTATTGACA	58.589	41.667	0.00	0.00	35.83	3.58
2006	2895	9.520515	AAGGTGAAGTTTGTTATGTTATGATCT	57.479	29.630	0.00	0.00	0.00	2.75
2110	3000	7.849322	TGATATAACACATTAGCCCTAGTGA	57.151	36.000	5.03	0.00	35.97	3.41
2184	3074	6.114089	ACTCATGATAATCCTGCTGATATGC	58.886	40.000	0.00	0.00	31.83	3.14
2270	3160	5.300034	TGAGAGAACAAAGCACATTGATGTT	59.700	36.000	4.22	0.00	39.39	2.71
2331	3221	1.270305	TGACCTGTTTTCTGAGAGCCG	60.270	52.381	0.00	0.00	0.00	5.52
2350	3240	3.631686	TCGTGGAGATAATTTGGGCATTG	59.368	43.478	0.00	0.00	0.00	2.82
2356	3246	4.191544	TGAGCTTCGTGGAGATAATTTGG	58.808	43.478	0.00	0.00	0.00	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.