AutoCloner

Multiple sequence alignment - TraesCS5A01G550100

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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	TraesCS5A01G550100	chr5A	100.000	2940	0	0	1	2940	703937140	703934201	0.000000e+00	5430
1	TraesCS5A01G550100	chr5A	95.822	1532	39	3	334	1841	703952808	703951278	0.000000e+00	2451
2	TraesCS5A01G550100	chr5A	94.713	1532	52	5	334	1841	703964520	703962994	0.000000e+00	2353
3	TraesCS5A01G550100	chr5A	94.582	1532	54	5	334	1841	703958653	703957127	0.000000e+00	2342
4	TraesCS5A01G550100	chr5A	95.541	1413	50	8	437	1841	704100566	704099159	0.000000e+00	2248
5	TraesCS5A01G550100	chr5A	95.541	1413	50	8	437	1841	704261360	704259953	0.000000e+00	2248
6	TraesCS5A01G550100	chr5A	93.856	1416	64	15	437	1841	704016758	704015355	0.000000e+00	2111
7	TraesCS5A01G550100	chr5A	93.079	1416	74	15	437	1841	703970242	703968840	0.000000e+00	2050
8	TraesCS5A01G550100	chr5A	97.455	1100	27	1	1841	2940	462143561	462142463	0.000000e+00	1875
9	TraesCS5A01G550100	chr5A	97.195	1105	27	4	1838	2940	700871663	700872765	0.000000e+00	1866
10	TraesCS5A01G550100	chr5A	95.940	1059	36	3	786	1841	704208887	704207833	0.000000e+00	1711
11	TraesCS5A01G550100	chr5A	86.556	662	53	8	1	640	703846982	703846335	0.000000e+00	697
12	TraesCS5A01G550100	chr5A	93.204	309	16	1	1	309	704004054	704003751	1.610000e-122	449
13	TraesCS5A01G550100	chr5A	92.759	290	15	5	437	721	704130473	704130185	5.860000e-112	414
14	TraesCS5A01G550100	chr6A	97.545	1100	27	0	1841	2940	565266208	565265109	0.000000e+00	1882
15	TraesCS5A01G550100	chr6A	82.192	219	35	4	146	361	431245806	431246023	5.000000e-43	185
16	TraesCS5A01G550100	chr7A	97.455	1100	28	0	1841	2940	12870360	12869261	0.000000e+00	1877
17	TraesCS5A01G550100	chr4A	97.455	1100	28	0	1841	2940	15333330	15332231	0.000000e+00	1877
18	TraesCS5A01G550100	chr4A	83.582	201	30	3	194	393	92902483	92902681	5.000000e-43	185
19	TraesCS5A01G550100	chr1A	97.288	1106	29	1	1835	2940	3709537	3710641	0.000000e+00	1875
20	TraesCS5A01G550100	chr3A	97.364	1100	29	0	1841	2940	119326662	119327761	0.000000e+00	1871
21	TraesCS5A01G550100	chr3A	97.364	1100	28	1	1841	2940	30372453	30373551	0.000000e+00	1869
22	TraesCS5A01G550100	chr2A	97.364	1100	29	0	1841	2940	30114155	30113056	0.000000e+00	1871
23	TraesCS5A01G550100	chrUn	88.776	1470	120	29	393	1841	109056040	109057485	0.000000e+00	1759
24	TraesCS5A01G550100	chr4B	82.353	255	40	5	105	355	363997558	363997811	1.770000e-52	217
25	TraesCS5A01G550100	chr1B	82.061	262	40	5	118	377	201457565	201457309	1.770000e-52	217
26	TraesCS5A01G550100	chr3B	85.238	210	27	4	171	377	716960830	716960622	2.300000e-51	213
27	TraesCS5A01G550100	chr3B	79.508	244	44	6	118	359	405959581	405959342	5.040000e-38	169
28	TraesCS5A01G550100	chr3D	82.063	223	36	3	140	359	2913762	2913541	1.390000e-43	187
29	TraesCS5A01G550100	chr1D	81.148	244	36	5	118	359	237920614	237920379	1.390000e-43	187

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	TraesCS5A01G550100	chr5A	703934201	703937140	2939	True	5430	5430	100.000	1	2940	1	chr5A.!!$R3	2939
1	TraesCS5A01G550100	chr5A	703951278	703952808	1530	True	2451	2451	95.822	334	1841	1	chr5A.!!$R4	1507
2	TraesCS5A01G550100	chr5A	703962994	703964520	1526	True	2353	2353	94.713	334	1841	1	chr5A.!!$R6	1507
3	TraesCS5A01G550100	chr5A	703957127	703958653	1526	True	2342	2342	94.582	334	1841	1	chr5A.!!$R5	1507
4	TraesCS5A01G550100	chr5A	704099159	704100566	1407	True	2248	2248	95.541	437	1841	1	chr5A.!!$R10	1404
5	TraesCS5A01G550100	chr5A	704259953	704261360	1407	True	2248	2248	95.541	437	1841	1	chr5A.!!$R13	1404
6	TraesCS5A01G550100	chr5A	704015355	704016758	1403	True	2111	2111	93.856	437	1841	1	chr5A.!!$R9	1404
7	TraesCS5A01G550100	chr5A	703968840	703970242	1402	True	2050	2050	93.079	437	1841	1	chr5A.!!$R7	1404
8	TraesCS5A01G550100	chr5A	462142463	462143561	1098	True	1875	1875	97.455	1841	2940	1	chr5A.!!$R1	1099
9	TraesCS5A01G550100	chr5A	700871663	700872765	1102	False	1866	1866	97.195	1838	2940	1	chr5A.!!$F1	1102
10	TraesCS5A01G550100	chr5A	704207833	704208887	1054	True	1711	1711	95.940	786	1841	1	chr5A.!!$R12	1055
11	TraesCS5A01G550100	chr5A	703846335	703846982	647	True	697	697	86.556	1	640	1	chr5A.!!$R2	639
12	TraesCS5A01G550100	chr6A	565265109	565266208	1099	True	1882	1882	97.545	1841	2940	1	chr6A.!!$R1	1099
13	TraesCS5A01G550100	chr7A	12869261	12870360	1099	True	1877	1877	97.455	1841	2940	1	chr7A.!!$R1	1099
14	TraesCS5A01G550100	chr4A	15332231	15333330	1099	True	1877	1877	97.455	1841	2940	1	chr4A.!!$R1	1099
15	TraesCS5A01G550100	chr1A	3709537	3710641	1104	False	1875	1875	97.288	1835	2940	1	chr1A.!!$F1	1105
16	TraesCS5A01G550100	chr3A	119326662	119327761	1099	False	1871	1871	97.364	1841	2940	1	chr3A.!!$F2	1099
17	TraesCS5A01G550100	chr3A	30372453	30373551	1098	False	1869	1869	97.364	1841	2940	1	chr3A.!!$F1	1099
18	TraesCS5A01G550100	chr2A	30113056	30114155	1099	True	1871	1871	97.364	1841	2940	1	chr2A.!!$R1	1099
19	TraesCS5A01G550100	chrUn	109056040	109057485	1445	False	1759	1759	88.776	393	1841	1	chrUn.!!$F1	1448

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
70	71	0.987294	ACAATGGCCACTGCTACTCT	59.013	50.000	15.51	0.0	37.74	3.24	F
1128	1168	1.153647	CACCATCAAGAGCGGCGTA	60.154	57.895	9.37	0.0	0.00	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1663	1707	0.108804	CCGTGACGCTAAGTGATGGT	60.109	55.0	0.0	0.0	38.18	3.55	R
2682	2729	0.391927	TAGGGTCGGTTGGCATTTCG	60.392	55.0	0.0	0.0	0.00	3.46	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
36	37	5.738619	TCTTAATAGTGTTCCACTCTGCA	57.261	39.130	0.00	0.00	41.21	4.41
59	60	3.438781	TGATGAAAGACGTAACAATGGCC	59.561	43.478	0.00	0.00	0.00	5.36
69	70	1.826385	AACAATGGCCACTGCTACTC	58.174	50.000	15.51	0.00	37.74	2.59
70	71	0.987294	ACAATGGCCACTGCTACTCT	59.013	50.000	15.51	0.00	37.74	3.24
71	72	2.187958	ACAATGGCCACTGCTACTCTA	58.812	47.619	15.51	0.00	37.74	2.43
72	73	2.093447	ACAATGGCCACTGCTACTCTAC	60.093	50.000	15.51	0.00	37.74	2.59
73	74	2.166907	ATGGCCACTGCTACTCTACT	57.833	50.000	8.16	0.00	37.74	2.57
78	79	2.732597	GCCACTGCTACTCTACTGTTCG	60.733	54.545	0.00	0.00	33.53	3.95
97	98	8.811378	ACTGTTCGAACTACTAAAAGTTGTTAC	58.189	33.333	27.32	0.00	42.52	2.50
98	99	8.700722	TGTTCGAACTACTAAAAGTTGTTACA	57.299	30.769	27.32	0.00	42.52	2.41
110	111	4.939052	AGTTGTTACAGTCACTGCTACT	57.061	40.909	4.13	0.00	34.37	2.57
143	144	6.920569	ACTAAAAGTTGTTACTGTCACTGG	57.079	37.500	0.00	0.00	34.01	4.00
147	148	5.609533	AAGTTGTTACTGTCACTGGTACT	57.390	39.130	0.00	0.00	34.01	2.73
148	149	6.720112	AAGTTGTTACTGTCACTGGTACTA	57.280	37.500	0.00	0.00	34.01	1.82
151	152	8.413309	AGTTGTTACTGTCACTGGTACTATTA	57.587	34.615	0.00	0.00	31.99	0.98
177	178	9.896263	ACTATTTTTACTCTTAGCGCTACTATC	57.104	33.333	18.63	0.00	0.00	2.08
197	198	5.991933	ATCAGATTATCATACTCCTGCGT	57.008	39.130	0.00	0.00	0.00	5.24
210	211	4.430908	ACTCCTGCGTACTAATACTTTGC	58.569	43.478	0.00	0.00	0.00	3.68
212	213	4.679662	TCCTGCGTACTAATACTTTGCTC	58.320	43.478	0.00	0.00	0.00	4.26
295	296	2.122783	TTTTGGCTCCCCTTATGTCG	57.877	50.000	0.00	0.00	0.00	4.35
310	311	6.978080	CCCTTATGTCGAACCAATAAATTTGG	59.022	38.462	0.00	2.87	44.91	3.28
311	312	6.978080	CCTTATGTCGAACCAATAAATTTGGG	59.022	38.462	9.06	2.51	43.71	4.12
319	320	9.857957	TCGAACCAATAAATTTGGGTAAAATAC	57.142	29.630	9.06	0.00	40.13	1.89
368	370	9.530633	CCTCTATACTTGTGTGTTAATAAGACC	57.469	37.037	0.00	0.00	0.00	3.85
700	732	7.494625	AGTTTCTGAATTTCGTTGACTTGAGTA	59.505	33.333	0.00	0.00	0.00	2.59
1076	1116	4.899239	GGCGCAGATGTCCCCGAG	62.899	72.222	10.83	0.00	0.00	4.63
1128	1168	1.153647	CACCATCAAGAGCGGCGTA	60.154	57.895	9.37	0.00	0.00	4.42
1223	1263	4.067896	CAAGCAAGTCCTTCACACACTAT	58.932	43.478	0.00	0.00	0.00	2.12
1283	1324	1.602605	GTTAACCCGTGCCTGGCTT	60.603	57.895	21.03	7.80	0.00	4.35
1447	1488	4.814294	GCCGACATCCTCGCCGTT	62.814	66.667	0.00	0.00	41.46	4.44
1499	1540	6.784031	AGAACTAACATGATCTTTCAACCCT	58.216	36.000	0.00	0.00	34.96	4.34
1663	1707	3.872603	AACCGTGACCTGCCTGCA	61.873	61.111	0.00	0.00	0.00	4.41
1681	1725	0.992072	CACCATCACTTAGCGTCACG	59.008	55.000	0.00	0.00	0.00	4.35
1702	1746	2.185350	CTCATCACCCGCTTCGCT	59.815	61.111	0.00	0.00	0.00	4.93
1752	1796	2.267006	CCTCTCTGGTGCGCACAT	59.733	61.111	38.60	0.00	0.00	3.21
1809	1856	2.166459	TCTACAGCGAGGAGAACATTGG	59.834	50.000	0.00	0.00	0.00	3.16
1845	1892	4.715523	GCGCCAGGCCACCACTAA	62.716	66.667	5.01	0.00	34.80	2.24
1865	1912	6.015434	CACTAATAGAAAACAGGGCTTTGGTT	60.015	38.462	0.00	0.00	0.00	3.67
2033	2080	3.264845	AACCGGGACCAATGGGCT	61.265	61.111	4.56	0.00	37.90	5.19
2056	2103	2.362889	CCTGGCCCACCACCATTC	60.363	66.667	0.00	0.00	42.67	2.67
2217	2264	1.205460	GGGGAGAGGGCTTTGTGGTA	61.205	60.000	0.00	0.00	0.00	3.25
2311	2358	3.798758	AGCTCGACCTCCAAGCTT	58.201	55.556	0.00	0.00	43.67	3.74
2410	2457	1.067669	CGATCTCATCACCGACACCAT	59.932	52.381	0.00	0.00	0.00	3.55
2573	2620	2.103263	GCCCTCGTCCTGTCTATGATTT	59.897	50.000	0.00	0.00	0.00	2.17
2574	2621	3.800604	GCCCTCGTCCTGTCTATGATTTC	60.801	52.174	0.00	0.00	0.00	2.17
2909	2957	4.527564	GCTTGGTATCATTATGTCGTTGC	58.472	43.478	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	7.733773	TGGAACACTATTAAGAAGATCTCCA	57.266	36.000	0.00	0.00	0.00	3.86
36	37	4.096382	GGCCATTGTTACGTCTTTCATCAT	59.904	41.667	0.00	0.00	0.00	2.45
59	60	4.083217	AGTTCGAACAGTAGAGTAGCAGTG	60.083	45.833	28.78	0.00	0.00	3.66
69	70	8.571461	ACAACTTTTAGTAGTTCGAACAGTAG	57.429	34.615	28.78	16.76	36.24	2.57
70	71	8.931385	AACAACTTTTAGTAGTTCGAACAGTA	57.069	30.769	28.78	17.85	36.24	2.74
71	72	7.838771	AACAACTTTTAGTAGTTCGAACAGT	57.161	32.000	28.78	18.19	36.24	3.55
72	73	8.810427	TGTAACAACTTTTAGTAGTTCGAACAG	58.190	33.333	28.78	17.57	36.24	3.16
73	74	8.700722	TGTAACAACTTTTAGTAGTTCGAACA	57.299	30.769	28.78	12.97	36.24	3.18
78	79	9.310716	AGTGACTGTAACAACTTTTAGTAGTTC	57.689	33.333	0.00	0.00	36.24	3.01
98	99	4.408182	AGTTCAAACAGTAGCAGTGACT	57.592	40.909	0.00	0.00	0.00	3.41
114	115	9.090692	GTGACAGTAACAACTTTTAGTAGTTCA	57.909	33.333	0.00	0.00	36.24	3.18
115	116	9.310716	AGTGACAGTAACAACTTTTAGTAGTTC	57.689	33.333	0.00	0.00	36.24	3.01
151	152	9.896263	GATAGTAGCGCTAAGAGTAAAAATAGT	57.104	33.333	20.73	0.00	32.72	2.12
167	168	7.012894	AGGAGTATGATAATCTGATAGTAGCGC	59.987	40.741	0.00	0.00	0.00	5.92
168	169	8.341903	CAGGAGTATGATAATCTGATAGTAGCG	58.658	40.741	0.00	0.00	0.00	4.26
177	178	6.260870	AGTACGCAGGAGTATGATAATCTG	57.739	41.667	0.00	0.00	0.00	2.90
276	277	1.631388	TCGACATAAGGGGAGCCAAAA	59.369	47.619	0.00	0.00	0.00	2.44
279	280	0.539986	GTTCGACATAAGGGGAGCCA	59.460	55.000	0.00	0.00	0.00	4.75
281	282	0.539986	TGGTTCGACATAAGGGGAGC	59.460	55.000	0.00	0.00	0.00	4.70
290	291	5.993748	ACCCAAATTTATTGGTTCGACAT	57.006	34.783	6.48	0.00	37.88	3.06
310	311	7.392418	ACACTCTTTGAGGGTAGTATTTTACC	58.608	38.462	0.05	0.00	45.28	2.85
311	312	8.718734	CAACACTCTTTGAGGGTAGTATTTTAC	58.281	37.037	2.70	0.00	46.54	2.01
319	320	4.073293	ACACAACACTCTTTGAGGGTAG	57.927	45.455	2.70	0.18	46.54	3.18
379	381	5.798125	ATCATATGATCCTCGTCAACAGT	57.202	39.130	12.62	0.00	0.00	3.55
589	618	4.498177	GCTTTGTTCCAAGTCAACTTCTCC	60.498	45.833	0.00	0.00	33.11	3.71
700	732	5.665916	TCGATGTATCATGCATAGATGGT	57.334	39.130	16.93	0.00	0.00	3.55
926	964	0.473755	TGGATGCGGATGTAATGGCT	59.526	50.000	0.00	0.00	0.00	4.75
1223	1263	6.806751	TGAAACCGATCCAAACAATAACAAA	58.193	32.000	0.00	0.00	0.00	2.83
1423	1464	3.371097	GAGGATGTCGGCGCAGGAA	62.371	63.158	10.83	0.00	0.00	3.36
1633	1677	2.425592	CGGTTGGCCAGTGTCTCA	59.574	61.111	5.11	0.00	34.09	3.27
1663	1707	0.108804	CCGTGACGCTAAGTGATGGT	60.109	55.000	0.00	0.00	38.18	3.55
1681	1725	1.153349	GAAGCGGGTGATGAGGTCC	60.153	63.158	0.00	0.00	0.00	4.46
1752	1796	2.687200	ACTGCACCCGCCCTATGA	60.687	61.111	0.00	0.00	37.32	2.15
1832	1879	4.331968	TGTTTTCTATTAGTGGTGGCCTG	58.668	43.478	3.32	0.00	0.00	4.85
1845	1892	4.479158	TGAACCAAAGCCCTGTTTTCTAT	58.521	39.130	0.00	0.00	0.00	1.98
2002	2049	1.074072	CGGTTCATCCCACCAACCA	59.926	57.895	0.00	0.00	39.79	3.67
2084	2131	2.724454	GGAACTAAAGGGGAGCCTTTC	58.276	52.381	0.00	0.00	40.11	2.62
2217	2264	2.091610	TGCATAGGAGGTGAGCTAGAGT	60.092	50.000	0.00	0.00	0.00	3.24
2311	2358	7.170393	TCTAGACAAATCTCGAGGAAAATGA	57.830	36.000	13.56	0.00	36.29	2.57
2410	2457	1.899814	AGAACAATAGGCTCACCACGA	59.100	47.619	0.00	0.00	39.06	4.35
2423	2470	9.799106	TCCTTTCAGAAAGAAGATAAGAACAAT	57.201	29.630	22.55	0.00	41.02	2.71
2682	2729	0.391927	TAGGGTCGGTTGGCATTTCG	60.392	55.000	0.00	0.00	0.00	3.46
2909	2957	3.919804	CGCAACCAAGGTAACAATTGATG	59.080	43.478	13.59	1.39	41.41	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.