AutoCloner

Multiple sequence alignment - TraesCS2B01G495300

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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	TraesCS2B01G495300	chr2B	100.000	2748	0	0	1	2748	692114276	692117023	0.000000e+00	5075.0
1	TraesCS2B01G495300	chr2B	96.742	798	19	4	1956	2748	3046911	3046116	0.000000e+00	1323.0
2	TraesCS2B01G495300	chr2B	96.742	798	18	4	1955	2748	671061065	671060272	0.000000e+00	1323.0
3	TraesCS2B01G495300	chr2B	90.000	1020	74	9	850	1863	692148752	692149749	0.000000e+00	1293.0
4	TraesCS2B01G495300	chr2B	81.116	932	158	16	467	1390	692128559	692129480	0.000000e+00	730.0
5	TraesCS2B01G495300	chr2B	80.363	331	48	13	1386	1704	692141510	692141835	4.580000e-58	235.0
6	TraesCS2B01G495300	chr2B	90.909	99	2	2	1862	1954	692150008	692150105	2.870000e-25	126.0
7	TraesCS2B01G495300	chr2D	94.265	1552	81	7	1	1546	575946612	575945063	0.000000e+00	2366.0
8	TraesCS2B01G495300	chr2D	86.245	1185	134	22	466	1638	575969853	575968686	0.000000e+00	1258.0
9	TraesCS2B01G495300	chr2D	82.377	1220	191	18	475	1683	575831237	575832443	0.000000e+00	1040.0
10	TraesCS2B01G495300	chr2D	86.167	347	37	8	1614	1952	575945044	575944701	5.590000e-97	364.0
11	TraesCS2B01G495300	chr2A	90.048	1246	100	16	727	1952	714059594	714058353	0.000000e+00	1592.0
12	TraesCS2B01G495300	chr3B	96.871	799	15	5	1955	2748	684341808	684341015	0.000000e+00	1328.0
13	TraesCS2B01G495300	chr3B	96.754	801	15	6	1955	2748	21782500	21783296	0.000000e+00	1325.0
14	TraesCS2B01G495300	chr6B	96.393	804	17	5	1954	2748	488530066	488529266	0.000000e+00	1314.0
15	TraesCS2B01G495300	chr5B	96.269	804	21	5	1952	2748	9409166	9408365	0.000000e+00	1310.0
16	TraesCS2B01G495300	chr5B	92.105	38	3	0	17	54	439263420	439263457	1.000000e-03	54.7
17	TraesCS2B01G495300	chr7B	96.273	805	14	7	1955	2748	666655183	666654384	0.000000e+00	1306.0
18	TraesCS2B01G495300	chr4B	96.273	805	15	6	1955	2748	649160400	649161200	0.000000e+00	1306.0
19	TraesCS2B01G495300	chr1B	96.370	799	19	5	1955	2748	217704958	217705751	0.000000e+00	1306.0
20	TraesCS2B01G495300	chrUn	70.032	634	173	16	887	1513	30047929	30048552	4.840000e-18	102.0
21	TraesCS2B01G495300	chr4D	90.000	70	6	1	1	70	470125938	470126006	3.770000e-14	89.8
22	TraesCS2B01G495300	chr7D	85.333	75	8	3	1	72	203950146	203950220	1.060000e-09	75.0
23	TraesCS2B01G495300	chr7A	87.037	54	6	1	20	72	215573218	215573271	2.960000e-05	60.2
24	TraesCS2B01G495300	chr4A	83.333	66	10	1	8	72	676455602	676455667	2.960000e-05	60.2

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	TraesCS2B01G495300	chr2B	692114276	692117023	2747	False	5075.0	5075	100.0000	1	2748	1	chr2B.!!$F1	2747
1	TraesCS2B01G495300	chr2B	3046116	3046911	795	True	1323.0	1323	96.7420	1956	2748	1	chr2B.!!$R1	792
2	TraesCS2B01G495300	chr2B	671060272	671061065	793	True	1323.0	1323	96.7420	1955	2748	1	chr2B.!!$R2	793
3	TraesCS2B01G495300	chr2B	692128559	692129480	921	False	730.0	730	81.1160	467	1390	1	chr2B.!!$F2	923
4	TraesCS2B01G495300	chr2B	692148752	692150105	1353	False	709.5	1293	90.4545	850	1954	2	chr2B.!!$F4	1104
5	TraesCS2B01G495300	chr2D	575944701	575946612	1911	True	1365.0	2366	90.2160	1	1952	2	chr2D.!!$R2	1951
6	TraesCS2B01G495300	chr2D	575968686	575969853	1167	True	1258.0	1258	86.2450	466	1638	1	chr2D.!!$R1	1172
7	TraesCS2B01G495300	chr2D	575831237	575832443	1206	False	1040.0	1040	82.3770	475	1683	1	chr2D.!!$F1	1208
8	TraesCS2B01G495300	chr2A	714058353	714059594	1241	True	1592.0	1592	90.0480	727	1952	1	chr2A.!!$R1	1225
9	TraesCS2B01G495300	chr3B	684341015	684341808	793	True	1328.0	1328	96.8710	1955	2748	1	chr3B.!!$R1	793
10	TraesCS2B01G495300	chr3B	21782500	21783296	796	False	1325.0	1325	96.7540	1955	2748	1	chr3B.!!$F1	793
11	TraesCS2B01G495300	chr6B	488529266	488530066	800	True	1314.0	1314	96.3930	1954	2748	1	chr6B.!!$R1	794
12	TraesCS2B01G495300	chr5B	9408365	9409166	801	True	1310.0	1310	96.2690	1952	2748	1	chr5B.!!$R1	796
13	TraesCS2B01G495300	chr7B	666654384	666655183	799	True	1306.0	1306	96.2730	1955	2748	1	chr7B.!!$R1	793
14	TraesCS2B01G495300	chr4B	649160400	649161200	800	False	1306.0	1306	96.2730	1955	2748	1	chr4B.!!$F1	793
15	TraesCS2B01G495300	chr1B	217704958	217705751	793	False	1306.0	1306	96.3700	1955	2748	1	chr1B.!!$F1	793

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
955	966	0.038599	AGAAGATGTGCACATGGCCA	59.961	50.0	35.92	8.56	43.89	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1962	2260	1.095807	GGTGCTATTGCCCGGTTCTC	61.096	60.0	0.0	0.0	38.71	2.87	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
48	49	3.180584	GCTCGTATATGTGAGCGACTTTG	59.819	47.826	13.23	0.00	47.00	2.77
55	56	3.660501	TGTGAGCGACTTTGAGTGTAT	57.339	42.857	0.00	0.00	0.00	2.29
56	57	3.990092	TGTGAGCGACTTTGAGTGTATT	58.010	40.909	0.00	0.00	0.00	1.89
59	60	4.211374	GTGAGCGACTTTGAGTGTATTGTT	59.789	41.667	0.00	0.00	0.00	2.83
62	63	6.131544	AGCGACTTTGAGTGTATTGTTTTT	57.868	33.333	0.00	0.00	0.00	1.94
63	64	7.011576	TGAGCGACTTTGAGTGTATTGTTTTTA	59.988	33.333	0.00	0.00	0.00	1.52
89	90	5.728637	AAAAATCTTTAGGCTGAACCCAG	57.271	39.130	0.00	0.00	43.22	4.45
144	145	5.385198	AGCCAGGATCAGTTTGTAGAAAAA	58.615	37.500	0.00	0.00	0.00	1.94
145	146	6.012745	AGCCAGGATCAGTTTGTAGAAAAAT	58.987	36.000	0.00	0.00	0.00	1.82
149	150	9.846248	CCAGGATCAGTTTGTAGAAAAATAAAG	57.154	33.333	0.00	0.00	0.00	1.85
206	209	4.282703	ACTGTTACGGAAAGCCTCTTCTAA	59.717	41.667	0.00	0.00	0.00	2.10
207	210	5.046520	ACTGTTACGGAAAGCCTCTTCTAAT	60.047	40.000	0.00	0.00	0.00	1.73
211	214	5.678955	ACGGAAAGCCTCTTCTAATAGTT	57.321	39.130	0.00	0.00	0.00	2.24
212	215	5.662456	ACGGAAAGCCTCTTCTAATAGTTC	58.338	41.667	0.00	0.00	0.00	3.01
218	221	7.430760	AAGCCTCTTCTAATAGTTCATGTCT	57.569	36.000	0.00	0.00	0.00	3.41
235	238	2.234661	TGTCTCCCTACAAGTCAGCATG	59.765	50.000	0.00	0.00	37.54	4.06
239	242	2.040278	TCCCTACAAGTCAGCATGCTTT	59.960	45.455	19.98	7.48	31.75	3.51
244	247	4.660789	ACAAGTCAGCATGCTTTTTCTT	57.339	36.364	19.98	16.02	31.75	2.52
303	308	2.134789	ATAGGGACTCACGTTACGGT	57.865	50.000	10.20	0.00	41.75	4.83
306	311	0.387750	GGGACTCACGTTACGGTCAC	60.388	60.000	10.20	4.38	0.00	3.67
307	312	0.311790	GGACTCACGTTACGGTCACA	59.688	55.000	10.20	0.00	0.00	3.58
319	324	5.170270	CGTTACGGTCACAGATATAAACGTC	59.830	44.000	0.00	0.00	34.22	4.34
344	349	3.058224	CCTTCCAGGTCGATTTGTGAAAC	60.058	47.826	0.00	0.00	37.35	2.78
431	436	1.301716	GTTGCTCTTCGGTCAGGCA	60.302	57.895	0.00	0.00	0.00	4.75
444	449	3.330720	AGGCAGCAGTACCCACCC	61.331	66.667	0.00	0.00	0.00	4.61
600	605	1.070275	GGGAAAGTTCACCGTCGGT	59.930	57.895	12.23	12.23	35.62	4.69
633	638	3.442076	GGATCTCCACTTATACCCCGAT	58.558	50.000	0.00	0.00	35.64	4.18
847	852	2.169561	TGGGGCTTTGAAAAGTTTGTCC	59.830	45.455	4.80	0.00	38.28	4.02
950	958	1.003928	TCAGGCAGAAGATGTGCACAT	59.996	47.619	31.82	31.82	43.12	3.21
955	966	0.038599	AGAAGATGTGCACATGGCCA	59.961	50.000	35.92	8.56	43.89	5.36
994	1005	1.750778	CCAACCTGCACAAACACTTCT	59.249	47.619	0.00	0.00	0.00	2.85
995	1006	2.480073	CCAACCTGCACAAACACTTCTG	60.480	50.000	0.00	0.00	0.00	3.02
1059	1070	2.032681	GCAGGCCAGTCGTTCCTT	59.967	61.111	5.01	0.00	0.00	3.36
1118	1129	0.912486	AAGGCCGAGCTCTTTGGTAT	59.088	50.000	12.85	0.00	32.26	2.73
1203	1214	4.991056	GCACTTCTTCACTTCATCTACACA	59.009	41.667	0.00	0.00	0.00	3.72
1257	1271	0.742281	GACACACGGAGATGCAGCAT	60.742	55.000	7.91	7.91	0.00	3.79
1392	1406	2.030412	CACCACTGCGTGCACCTA	59.970	61.111	12.15	0.00	31.34	3.08
1560	1576	5.419471	GGTATTGCATGGTTTAGGGTTTACA	59.581	40.000	0.00	0.00	0.00	2.41
1565	1581	5.068460	TGCATGGTTTAGGGTTTACATATGC	59.932	40.000	1.58	0.00	35.90	3.14
1584	1600	1.818674	GCCGGATGGATGTTCAAACTT	59.181	47.619	5.05	0.00	37.49	2.66
1592	1608	5.275067	TGGATGTTCAAACTTCTTTTGGG	57.725	39.130	8.21	0.00	44.30	4.12
1600	1616	7.930865	TGTTCAAACTTCTTTTGGGATTAATGG	59.069	33.333	0.00	0.00	44.30	3.16
1622	1646	4.278419	GGGTGCTTTTGACTTAATGACACT	59.722	41.667	0.00	0.00	0.00	3.55
1686	1710	9.932207	TCGTTCTCTTGTCTTTATTTTGGTATA	57.068	29.630	0.00	0.00	0.00	1.47
1717	1742	2.902705	TCTATGGCCATAACGTGACC	57.097	50.000	25.38	0.00	0.00	4.02
1726	1751	4.438200	GGCCATAACGTGACCTAAAATGTG	60.438	45.833	0.00	0.00	0.00	3.21
1925	2223	7.648039	TGTTAAAAGTTAGATGTTGGTTGGT	57.352	32.000	0.00	0.00	0.00	3.67
1962	2260	0.252197	GGTGCCCCTTACACTAGTGG	59.748	60.000	26.12	8.85	38.14	4.00
1992	2290	2.992063	GCAATAGCACCGGTTCGTAAGA	60.992	50.000	2.97	0.00	43.36	2.10
2008	2306	0.323957	AAGACCCTTTAGTGCCGGTC	59.676	55.000	1.90	0.00	44.31	4.79
2473	2797	2.485426	AGCACGATGACAATTGGAAGTG	59.515	45.455	10.83	12.57	0.00	3.16
2474	2798	2.414559	GCACGATGACAATTGGAAGTGG	60.415	50.000	10.83	0.00	0.00	4.00
2639	2963	5.961396	AAGAAGGAGATCAATATGCATGC	57.039	39.130	11.82	11.82	0.00	4.06
2713	3037	5.049954	GTGTTTTGACAAGCGTACCTATTCA	60.050	40.000	0.00	0.00	0.00	2.57
2734	3058	4.958581	TCATGTCTTTGAGATCTGCTCCTA	59.041	41.667	0.00	0.00	43.26	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	7.050970	AGCATACACTCATTCCTATAAACGA	57.949	36.000	0.00	0.00	0.00	3.85
15	16	6.981722	TCACATATACGAGCATACACTCATT	58.018	36.000	0.00	0.00	36.42	2.57
89	90	0.381801	CCGAGCCACCATGTTATTGC	59.618	55.000	0.00	0.00	0.00	3.56
94	95	1.224592	GGATCCGAGCCACCATGTT	59.775	57.895	0.00	0.00	0.00	2.71
98	99	1.335132	GGTTAGGATCCGAGCCACCA	61.335	60.000	20.60	0.00	0.00	4.17
144	145	8.344939	TGGATCCCTCCTAAATACAACTTTAT	57.655	34.615	9.90	0.00	42.59	1.40
145	146	7.758820	TGGATCCCTCCTAAATACAACTTTA	57.241	36.000	9.90	0.00	42.59	1.85
149	150	8.437575	TCTTATTGGATCCCTCCTAAATACAAC	58.562	37.037	9.90	0.00	42.59	3.32
150	151	8.575736	TCTTATTGGATCCCTCCTAAATACAA	57.424	34.615	9.90	0.00	42.59	2.41
151	152	7.794683	ACTCTTATTGGATCCCTCCTAAATACA	59.205	37.037	9.90	0.00	42.59	2.29
152	153	8.208575	ACTCTTATTGGATCCCTCCTAAATAC	57.791	38.462	9.90	0.00	42.59	1.89
154	155	6.273495	GGACTCTTATTGGATCCCTCCTAAAT	59.727	42.308	9.90	3.59	42.59	1.40
160	163	5.373812	TTTGGACTCTTATTGGATCCCTC	57.626	43.478	9.90	0.00	0.00	4.30
206	209	5.958380	TGACTTGTAGGGAGACATGAACTAT	59.042	40.000	0.00	0.00	0.00	2.12
207	210	5.330233	TGACTTGTAGGGAGACATGAACTA	58.670	41.667	0.00	0.00	0.00	2.24
211	214	2.497675	GCTGACTTGTAGGGAGACATGA	59.502	50.000	0.00	0.00	0.00	3.07
212	215	2.234661	TGCTGACTTGTAGGGAGACATG	59.765	50.000	0.00	0.00	0.00	3.21
218	221	1.279496	AGCATGCTGACTTGTAGGGA	58.721	50.000	21.98	0.00	0.00	4.20
244	247	2.604139	GACTTCCCCACCCATGAAAAA	58.396	47.619	0.00	0.00	0.00	1.94
250	253	3.728373	GCCGACTTCCCCACCCAT	61.728	66.667	0.00	0.00	0.00	4.00
303	308	5.068723	GGAAGGGAGACGTTTATATCTGTGA	59.931	44.000	0.00	0.00	38.82	3.58
306	311	5.531122	TGGAAGGGAGACGTTTATATCTG	57.469	43.478	0.00	0.00	38.82	2.90
307	312	5.793030	CTGGAAGGGAGACGTTTATATCT	57.207	43.478	0.00	0.00	38.82	1.98
414	419	1.004560	CTGCCTGACCGAAGAGCAA	60.005	57.895	0.00	0.00	32.14	3.91
431	436	0.693049	CTTCTTGGGTGGGTACTGCT	59.307	55.000	0.00	0.00	0.00	4.24
473	478	1.211818	GCATCTCGACCATGTCTCGC	61.212	60.000	5.38	0.00	0.00	5.03
600	605	2.685017	AGATCCCACTCGCAGCCA	60.685	61.111	0.00	0.00	0.00	4.75
633	638	0.547471	TGTGCTCCTCCTTCCATCCA	60.547	55.000	0.00	0.00	0.00	3.41
847	852	2.847901	CTGTCGCAGCTTTGATTTCTG	58.152	47.619	0.00	0.00	0.00	3.02
994	1005	2.509548	CCCCACCCTTCAACATATCTCA	59.490	50.000	0.00	0.00	0.00	3.27
995	1006	2.777692	TCCCCACCCTTCAACATATCTC	59.222	50.000	0.00	0.00	0.00	2.75
1059	1070	1.147557	CGAGCACACATCTATGCGCA	61.148	55.000	14.96	14.96	46.74	6.09
1118	1129	1.472201	GCGCCAGAGTCTCATTCATCA	60.472	52.381	0.00	0.00	0.00	3.07
1177	1188	4.363991	AGATGAAGTGAAGAAGTGCCTT	57.636	40.909	0.00	0.00	0.00	4.35
1392	1406	6.602803	ACAAAAATTCAAGACATGCCCTTTTT	59.397	30.769	0.00	0.00	30.57	1.94
1560	1576	3.507162	TTGAACATCCATCCGGCATAT	57.493	42.857	0.00	0.00	0.00	1.78
1565	1581	3.347216	AGAAGTTTGAACATCCATCCGG	58.653	45.455	0.00	0.00	0.00	5.14
1584	1600	4.059773	AGCACCCATTAATCCCAAAAGA	57.940	40.909	0.00	0.00	0.00	2.52
1592	1608	8.250332	TCATTAAGTCAAAAGCACCCATTAATC	58.750	33.333	0.00	0.00	0.00	1.75
1600	1616	5.215160	CAGTGTCATTAAGTCAAAAGCACC	58.785	41.667	0.00	0.00	0.00	5.01
1686	1710	8.567948	CGTTATGGCCATAGAAAAATTACAGAT	58.432	33.333	24.19	0.00	0.00	2.90
1687	1711	7.554835	ACGTTATGGCCATAGAAAAATTACAGA	59.445	33.333	24.19	3.27	0.00	3.41
1694	1718	5.554822	GTCACGTTATGGCCATAGAAAAA	57.445	39.130	24.19	9.63	0.00	1.94
1709	1734	5.570234	AAACACACATTTTAGGTCACGTT	57.430	34.783	0.00	0.00	0.00	3.99
1717	1742	8.229137	CCAATATGCCAAAAACACACATTTTAG	58.771	33.333	0.00	0.00	31.50	1.85
1726	1751	3.397482	TGTGCCAATATGCCAAAAACAC	58.603	40.909	0.00	0.00	0.00	3.32
1925	2223	2.096248	ACCACTTTCGCTCCAAAAACA	58.904	42.857	0.00	0.00	0.00	2.83
1962	2260	1.095807	GGTGCTATTGCCCGGTTCTC	61.096	60.000	0.00	0.00	38.71	2.87
1992	2290	2.599757	GGGACCGGCACTAAAGGGT	61.600	63.158	0.00	0.00	34.94	4.34
2008	2306	2.014128	CACTTTAGTGCCGGTTATGGG	58.986	52.381	1.90	0.00	39.39	4.00
2473	2797	3.074369	CGCCCCCATGAAAACCCC	61.074	66.667	0.00	0.00	0.00	4.95
2474	2798	2.502329	TACCGCCCCCATGAAAACCC	62.502	60.000	0.00	0.00	0.00	4.11
2639	2963	8.493547	TCGATATCTAGTCACACAACTAATACG	58.506	37.037	0.34	0.00	31.56	3.06
2713	3037	5.278907	CGATAGGAGCAGATCTCAAAGACAT	60.279	44.000	0.00	0.00	43.70	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.