AutoCloner

Multiple sequence alignment - TraesCS2B01G550900

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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	TraesCS2B01G550900	chr2B	100.000	2400	0	0	1	2400	747076230	747078629	0.000000e+00	4433.0
1	TraesCS2B01G550900	chr2B	86.483	1524	107	34	1	1464	746679508	746680992	0.000000e+00	1581.0
2	TraesCS2B01G550900	chr2D	89.600	1875	101	44	573	2400	612324930	612326757	0.000000e+00	2296.0
3	TraesCS2B01G550900	chr2D	83.743	935	72	41	573	1464	612184273	612185170	0.000000e+00	811.0
4	TraesCS2B01G550900	chr2D	90.175	458	20	5	1	434	612183824	612184280	7.440000e-160	573.0
5	TraesCS2B01G550900	chr2D	93.333	375	20	2	64	434	612324564	612324937	1.250000e-152	549.0
6	TraesCS2B01G550900	chr2D	86.331	139	18	1	438	575	378172984	378172846	1.490000e-32	150.0
7	TraesCS2B01G550900	chr2A	81.969	1747	136	91	590	2245	744408242	744409900	0.000000e+00	1315.0
8	TraesCS2B01G550900	chr2A	83.333	360	45	10	21	368	744407776	744408132	3.850000e-83	318.0
9	TraesCS2B01G550900	chr2A	92.271	207	15	1	2194	2400	744409896	744410101	2.330000e-75	292.0
10	TraesCS2B01G550900	chr2A	86.429	140	18	1	437	575	688016543	688016682	4.130000e-33	152.0
11	TraesCS2B01G550900	chr6D	88.406	138	15	1	438	574	31467887	31468024	5.310000e-37	165.0
12	TraesCS2B01G550900	chr6D	86.957	138	17	1	438	574	31273733	31273596	1.150000e-33	154.0
13	TraesCS2B01G550900	chr4D	87.770	139	15	2	437	574	491004592	491004729	6.870000e-36	161.0
14	TraesCS2B01G550900	chr7D	86.957	138	18	0	437	574	49173066	49173203	3.190000e-34	156.0
15	TraesCS2B01G550900	chr7D	86.232	138	18	1	438	574	7705652	7705789	5.350000e-32	148.0
16	TraesCS2B01G550900	chr5A	86.525	141	18	1	438	577	105127005	105126865	1.150000e-33	154.0
17	TraesCS2B01G550900	chr4A	86.957	138	17	1	438	574	497891035	497890898	1.150000e-33	154.0
18	TraesCS2B01G550900	chr7B	100.000	29	0	0	2262	2290	419247736	419247764	1.000000e-03	54.7
19	TraesCS2B01G550900	chr3B	100.000	29	0	0	2262	2290	130680460	130680432	1.000000e-03	54.7
20	TraesCS2B01G550900	chr3B	100.000	28	0	0	2262	2289	511698719	511698746	4.000000e-03	52.8
21	TraesCS2B01G550900	chr5D	100.000	28	0	0	2262	2289	242691664	242691637	4.000000e-03	52.8

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	TraesCS2B01G550900	chr2B	747076230	747078629	2399	False	4433.000000	4433	100.000000	1	2400	1	chr2B.!!$F2	2399
1	TraesCS2B01G550900	chr2B	746679508	746680992	1484	False	1581.000000	1581	86.483000	1	1464	1	chr2B.!!$F1	1463
2	TraesCS2B01G550900	chr2D	612324564	612326757	2193	False	1422.500000	2296	91.466500	64	2400	2	chr2D.!!$F2	2336
3	TraesCS2B01G550900	chr2D	612183824	612185170	1346	False	692.000000	811	86.959000	1	1464	2	chr2D.!!$F1	1463
4	TraesCS2B01G550900	chr2A	744407776	744410101	2325	False	641.666667	1315	85.857667	21	2400	3	chr2A.!!$F2	2379

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
636	739	1.28626	GCTCACCACGTCGTCTCTT	59.714	57.895	0.0	0.0	0.0	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1524	1761	0.617935	TGCACACTAGCCATAGCCAA	59.382	50.0	0.0	0.0	41.25	4.52	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
62	77	6.039941	AGACATAGAGAGACGGTAAAATCCTG	59.960	42.308	0.00	0.00	0.00	3.86
97	112	6.320672	AGAAATGAAGCCTTGTCCATTGATAG	59.679	38.462	0.00	0.00	30.56	2.08
384	456	1.482593	CCCAATTGAGCGGTCTACTCT	59.517	52.381	16.64	0.00	35.12	3.24
399	471	6.651643	CGGTCTACTCTTGCTATAGTACTCAT	59.348	42.308	0.00	0.00	0.00	2.90
401	473	7.662258	GGTCTACTCTTGCTATAGTACTCATCA	59.338	40.741	0.00	0.00	0.00	3.07
403	475	8.433599	TCTACTCTTGCTATAGTACTCATCACT	58.566	37.037	0.00	0.00	0.00	3.41
430	502	5.010617	TGCAACTGTCACTGAATACTACTCA	59.989	40.000	0.00	0.00	0.00	3.41
431	503	5.346281	GCAACTGTCACTGAATACTACTCAC	59.654	44.000	0.00	0.00	0.00	3.51
433	505	6.503589	ACTGTCACTGAATACTACTCACTC	57.496	41.667	0.00	0.00	0.00	3.51
434	506	5.416326	ACTGTCACTGAATACTACTCACTCC	59.584	44.000	0.00	0.00	0.00	3.85
435	507	4.395231	TGTCACTGAATACTACTCACTCCG	59.605	45.833	0.00	0.00	0.00	4.63
440	522	6.089551	CACTGAATACTACTCACTCCGTTTTG	59.910	42.308	0.00	0.00	0.00	2.44
443	525	7.310664	TGAATACTACTCACTCCGTTTTGTAG	58.689	38.462	0.00	0.00	35.07	2.74
445	527	5.373981	ACTACTCACTCCGTTTTGTAGAG	57.626	43.478	0.00	0.00	33.68	2.43
456	538	6.954944	TCCGTTTTGTAGAGATTTCAACAAG	58.045	36.000	0.00	0.00	33.70	3.16
458	540	6.851330	CCGTTTTGTAGAGATTTCAACAAGTC	59.149	38.462	0.00	0.00	33.70	3.01
460	542	7.908082	CGTTTTGTAGAGATTTCAACAAGTCAA	59.092	33.333	0.00	0.00	33.70	3.18
491	573	5.591877	GGGAGCAAAATGAGTGAATCTACAT	59.408	40.000	0.00	0.00	0.00	2.29
588	671	1.823610	GGAGTACCACTCAGTACCACC	59.176	57.143	8.47	0.00	46.79	4.61
636	739	1.286260	GCTCACCACGTCGTCTCTT	59.714	57.895	0.00	0.00	0.00	2.85
876	1039	3.006537	TCACCCAACTGTTAGTCTGCTAC	59.993	47.826	0.00	0.00	0.00	3.58
877	1040	3.006967	CACCCAACTGTTAGTCTGCTACT	59.993	47.826	0.00	0.00	42.62	2.57
878	1041	4.219944	CACCCAACTGTTAGTCTGCTACTA	59.780	45.833	0.00	0.00	39.80	1.82
879	1042	4.463186	ACCCAACTGTTAGTCTGCTACTAG	59.537	45.833	0.00	0.00	41.70	2.57
880	1043	4.425520	CCAACTGTTAGTCTGCTACTAGC	58.574	47.826	0.61	0.61	41.70	3.42
881	1044	4.158764	CCAACTGTTAGTCTGCTACTAGCT	59.841	45.833	9.49	0.00	42.97	3.32
882	1045	5.336849	CCAACTGTTAGTCTGCTACTAGCTT	60.337	44.000	9.49	0.00	42.97	3.74
912	1076	4.947388	GCTATATCTCCTACTGCTAGCTGT	59.053	45.833	27.37	27.37	0.00	4.40
964	1129	5.670835	GCTCGATAGGTACGTACATAAGCTC	60.671	48.000	24.55	17.22	0.00	4.09
1175	1367	2.623416	ACCAAAGTACCAGCTGCTTTTC	59.377	45.455	8.66	0.00	32.86	2.29
1236	1452	3.682696	TCACTGAGAGTTAGCCTTCGTA	58.317	45.455	0.00	0.00	0.00	3.43
1487	1720	4.934942	TGCGTCCGTGACACCGTG	62.935	66.667	0.00	0.00	32.09	4.94
1524	1761	2.693864	AGCTAGCATGCCCCTGGT	60.694	61.111	18.83	4.89	0.00	4.00
1538	1775	0.839946	CCTGGTTGGCTATGGCTAGT	59.160	55.000	0.00	0.00	38.73	2.57
1543	1780	0.617935	TTGGCTATGGCTAGTGTGCA	59.382	50.000	0.00	0.00	38.73	4.57
1577	1814	1.003223	ACGTACGTGCAAGCCTTTTTC	60.003	47.619	22.14	0.00	0.00	2.29
1646	1908	1.134401	TGGATTGGATTGCGAGAGGTC	60.134	52.381	0.00	0.00	0.00	3.85
1904	2178	1.136828	TCCTTATTATGGGCCACGCT	58.863	50.000	9.28	0.00	0.00	5.07
1905	2179	1.071699	TCCTTATTATGGGCCACGCTC	59.928	52.381	9.28	0.00	0.00	5.03
1935	2209	1.757118	AGCTAGCGCTCTTGGATGTAA	59.243	47.619	16.34	0.00	45.15	2.41
1968	2244	1.267532	CGTGTCTTGTGTCTTGTGTGC	60.268	52.381	0.00	0.00	0.00	4.57
1982	2260	1.202475	TGTGTGCGTGACTGTGTGTAT	60.202	47.619	0.00	0.00	0.00	2.29
2020	2298	6.309494	GTGTGTTGTGTACGCTTTATCATCTA	59.691	38.462	8.10	0.00	38.12	1.98
2052	2330	4.701956	TTTTGGAGCACAATTAGCTAGC	57.298	40.909	6.62	6.62	43.58	3.42
2055	2333	4.753516	TGGAGCACAATTAGCTAGCTAA	57.246	40.909	33.35	33.35	43.58	3.09
2074	2352	2.910688	AGGGCGATGATTTGTACGAT	57.089	45.000	0.00	0.00	0.00	3.73
2079	2357	3.555956	GGCGATGATTTGTACGATGAACT	59.444	43.478	0.00	0.00	0.00	3.01
2093	2375	4.154918	ACGATGAACTTGCCTCAAGAAATC	59.845	41.667	12.89	10.50	43.42	2.17
2104	2386	6.672593	TGCCTCAAGAAATCAATATTAGGGT	58.327	36.000	0.00	0.00	0.00	4.34
2120	2404	9.881773	AATATTAGGGTATGTTTGGTTCATGAT	57.118	29.630	0.00	0.00	0.00	2.45
2156	2440	6.038936	ACAACTAATTTTAAGCAGACAACGGT	59.961	34.615	0.00	0.00	0.00	4.83
2197	2481	0.467804	ACAAAATGGCCACCACAACC	59.532	50.000	8.16	0.00	35.80	3.77
2199	2483	1.045911	AAAATGGCCACCACAACCGT	61.046	50.000	8.16	0.00	35.80	4.83
2237	2564	3.895232	AAACTCAGCCTATGACGACAT	57.105	42.857	5.56	5.56	40.16	3.06
2246	2573	1.665679	CTATGACGACATGCCAACCAC	59.334	52.381	10.69	0.00	37.87	4.16
2297	2626	4.549458	CTGCAAACCAAACATGTCCTTAG	58.451	43.478	0.00	0.00	0.00	2.18
2321	2650	0.800631	GTTACGGCCCTGCTTTACAC	59.199	55.000	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	5.151632	TGTCTAAGTTGACTGCGTTTTTC	57.848	39.130	6.89	0.00	37.79	2.29
62	77	5.397142	AGGCTTCATTTCTGAATCCAAAC	57.603	39.130	9.99	0.00	45.92	2.93
118	137	6.737720	TCAATGTCTCCTAGTGCATAATCT	57.262	37.500	0.00	0.00	0.00	2.40
362	405	3.081554	AGACCGCTCAATTGGGCT	58.918	55.556	27.02	10.40	39.40	5.19
384	456	5.737349	GCAGCAGTGATGAGTACTATAGCAA	60.737	44.000	13.68	0.00	0.00	3.91
399	471	0.178767	AGTGACAGTTGCAGCAGTGA	59.821	50.000	2.71	0.00	0.00	3.41
401	473	0.178767	TCAGTGACAGTTGCAGCAGT	59.821	50.000	2.55	0.00	0.00	4.40
403	475	1.971481	ATTCAGTGACAGTTGCAGCA	58.029	45.000	2.55	0.00	0.00	4.41
430	502	6.053005	TGTTGAAATCTCTACAAAACGGAGT	58.947	36.000	0.00	0.00	36.97	3.85
431	503	6.539649	TGTTGAAATCTCTACAAAACGGAG	57.460	37.500	0.00	0.00	34.88	4.63
433	505	6.725246	ACTTGTTGAAATCTCTACAAAACGG	58.275	36.000	0.00	0.00	43.56	4.44
434	506	7.406553	TGACTTGTTGAAATCTCTACAAAACG	58.593	34.615	0.00	0.00	43.56	3.60
435	507	9.736023	ATTGACTTGTTGAAATCTCTACAAAAC	57.264	29.630	0.00	0.00	43.56	2.43
456	538	8.725148	CACTCATTTTGCTCCCTATATATTGAC	58.275	37.037	0.00	0.00	0.00	3.18
458	540	8.853077	TCACTCATTTTGCTCCCTATATATTG	57.147	34.615	0.00	0.00	0.00	1.90
460	542	9.678260	GATTCACTCATTTTGCTCCCTATATAT	57.322	33.333	0.00	0.00	0.00	0.86
467	549	4.943705	TGTAGATTCACTCATTTTGCTCCC	59.056	41.667	0.00	0.00	0.00	4.30
469	551	8.976986	AAAATGTAGATTCACTCATTTTGCTC	57.023	30.769	17.26	0.00	40.40	4.26
548	630	9.628500	GTACTCCCTCCATTTCTAAATATTTGT	57.372	33.333	11.05	0.00	0.00	2.83
549	631	9.067986	GGTACTCCCTCCATTTCTAAATATTTG	57.932	37.037	11.05	1.65	0.00	2.32
560	643	2.840651	CTGAGTGGTACTCCCTCCATTT	59.159	50.000	6.52	0.00	44.44	2.32
563	646	0.784495	ACTGAGTGGTACTCCCTCCA	59.216	55.000	6.52	0.00	44.44	3.86
588	671	0.179134	GCAGCACCACTCTACTACCG	60.179	60.000	0.00	0.00	0.00	4.02
636	739	2.552155	GGGCTGTAAATGTGTGACAGGA	60.552	50.000	3.65	0.00	40.78	3.86
880	1043	7.556275	AGCAGTAGGAGATATAGCTTAGCTAAG	59.444	40.741	26.20	26.20	44.62	2.18
881	1044	7.406916	AGCAGTAGGAGATATAGCTTAGCTAA	58.593	38.462	18.34	5.94	44.62	3.09
882	1045	6.964464	AGCAGTAGGAGATATAGCTTAGCTA	58.036	40.000	16.76	16.76	45.55	3.32
912	1076	2.772191	AGTGCCCACTCCCACACA	60.772	61.111	0.00	0.00	36.92	3.72
1041	1217	1.429825	CGAGATGGACGTCGAGCTT	59.570	57.895	19.39	3.78	38.50	3.74
1048	1224	3.921521	GTCCTCCGAGATGGACGT	58.078	61.111	0.00	0.00	43.74	4.34
1175	1367	2.160205	CATCAGCTGCCTATTCATGGG	58.840	52.381	9.47	0.00	0.00	4.00
1214	1427	2.891580	ACGAAGGCTAACTCTCAGTGAA	59.108	45.455	0.00	0.00	0.00	3.18
1236	1452	1.665442	GCCGAACCCTGCAAACAAT	59.335	52.632	0.00	0.00	0.00	2.71
1369	1587	3.842923	CTCCTGATGACGGCGGCT	61.843	66.667	16.45	0.00	0.00	5.52
1469	1702	4.936823	ACGGTGTCACGGACGCAC	62.937	66.667	16.66	6.54	43.87	5.34
1496	1733	4.321750	GGGCATGCTAGCTCGTAGTATTAA	60.322	45.833	18.92	0.00	32.09	1.40
1498	1735	2.028930	GGGCATGCTAGCTCGTAGTATT	60.029	50.000	18.92	0.00	32.09	1.89
1524	1761	0.617935	TGCACACTAGCCATAGCCAA	59.382	50.000	0.00	0.00	41.25	4.52
1538	1775	2.415491	CGTACACTAGCTAGCTTGCACA	60.415	50.000	24.88	2.79	34.99	4.57
1543	1780	3.063180	CACGTACGTACACTAGCTAGCTT	59.937	47.826	24.88	7.28	0.00	3.74
1577	1814	2.549329	GCAAATGCAAAAACCTCAAGGG	59.451	45.455	0.00	0.00	41.59	3.95
1904	2178	1.139989	GCGCTAGCTGCAATTATCGA	58.860	50.000	21.32	0.00	43.06	3.59
1905	2179	3.646520	GCGCTAGCTGCAATTATCG	57.353	52.632	21.32	1.34	43.06	2.92
1968	2244	5.541098	TGAGTACTATACACACAGTCACG	57.459	43.478	0.00	0.00	0.00	4.35
1982	2260	6.704289	ACACAACACACTACTTGAGTACTA	57.296	37.500	0.00	0.00	35.64	1.82
2052	2330	3.713288	TCGTACAAATCATCGCCCTTAG	58.287	45.455	0.00	0.00	0.00	2.18
2055	2333	2.102420	TCATCGTACAAATCATCGCCCT	59.898	45.455	0.00	0.00	0.00	5.19
2074	2352	7.707624	ATATTGATTTCTTGAGGCAAGTTCA	57.292	32.000	7.02	6.60	41.66	3.18
2079	2357	7.125391	ACCCTAATATTGATTTCTTGAGGCAA	58.875	34.615	0.00	0.00	0.00	4.52
2093	2375	9.130661	TCATGAACCAAACATACCCTAATATTG	57.869	33.333	0.00	0.00	0.00	1.90
2128	2412	7.803189	CGTTGTCTGCTTAAAATTAGTTGTGAT	59.197	33.333	0.00	0.00	0.00	3.06
2139	2423	2.223618	GGCAACCGTTGTCTGCTTAAAA	60.224	45.455	12.77	0.00	36.32	1.52
2156	2440	1.000283	CGCCACACTTTTTATGGGCAA	60.000	47.619	0.00	0.00	41.41	4.52
2297	2626	1.746470	AAGCAGGGCCGTAACAATAC	58.254	50.000	0.00	0.00	0.00	1.89
2365	2694	2.029073	ACGTACGCTTGCTGCAGT	59.971	55.556	16.72	0.00	43.06	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.