AutoCloner

Multiple sequence alignment - TraesCS2D01G414500

Loading Multiple Alignment...

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	TraesCS2D01G414500	chr2D	100.000	3011	0	0	1	3011	528591053	528588043	0.000000e+00	5561.0
1	TraesCS2D01G414500	chr2D	87.072	1052	111	13	1000	2028	528473772	528472723	0.000000e+00	1166.0
2	TraesCS2D01G414500	chr2D	80.876	251	18	19	348	584	528474364	528474130	1.440000e-38	171.0
3	TraesCS2D01G414500	chr2D	90.141	71	5	2	741	809	528474042	528473972	1.150000e-14	91.6
4	TraesCS2D01G414500	chr2B	92.749	2565	127	23	1	2536	626885288	626882754	0.000000e+00	3651.0
5	TraesCS2D01G414500	chr2B	88.480	1033	98	8	1000	2014	626651901	626650872	0.000000e+00	1229.0
6	TraesCS2D01G414500	chr2B	95.580	362	11	5	2496	2854	626882764	626882405	2.600000e-160	575.0
7	TraesCS2D01G414500	chr2B	91.250	160	8	2	2853	3011	626882245	626882091	2.350000e-51	213.0
8	TraesCS2D01G414500	chr2B	91.071	56	5	0	754	809	626652178	626652123	3.220000e-10	76.8
9	TraesCS2D01G414500	chr2A	91.492	1857	115	14	303	2126	673278206	673276360	0.000000e+00	2514.0
10	TraesCS2D01G414500	chr2A	88.561	1049	90	18	1000	2019	673196134	673195087	0.000000e+00	1245.0
11	TraesCS2D01G414500	chr2A	86.093	302	31	4	2109	2408	673273737	673273445	6.270000e-82	315.0
12	TraesCS2D01G414500	chr2A	80.658	243	24	17	348	584	673196717	673196492	1.860000e-37	167.0
13	TraesCS2D01G414500	chr2A	94.318	88	3	2	1	87	453522941	453522855	1.880000e-27	134.0
14	TraesCS2D01G414500	chr2A	95.238	84	2	2	1	83	43300741	43300823	6.770000e-27	132.0
15	TraesCS2D01G414500	chr7B	96.429	84	1	2	1	83	296347500	296347582	1.460000e-28	137.0
16	TraesCS2D01G414500	chr3A	82.036	167	25	5	1438	1602	521629603	521629766	1.460000e-28	137.0
17	TraesCS2D01G414500	chrUn	95.238	84	2	2	1	83	88917725	88917807	6.770000e-27	132.0
18	TraesCS2D01G414500	chr6D	95.238	84	2	2	1	83	10026034	10026116	6.770000e-27	132.0
19	TraesCS2D01G414500	chr3D	81.437	167	26	5	1438	1602	401171644	401171807	6.770000e-27	132.0
20	TraesCS2D01G414500	chr3D	94.048	84	3	2	1	83	596215300	596215218	3.150000e-25	126.0
21	TraesCS2D01G414500	chr3D	80.488	164	29	3	1441	1604	330062839	330062679	4.080000e-24	122.0
22	TraesCS2D01G414500	chr7A	94.186	86	3	2	1	85	105519271	105519355	2.440000e-26	130.0
23	TraesCS2D01G414500	chr5D	94.048	84	3	2	1	83	551983532	551983614	3.150000e-25	126.0
24	TraesCS2D01G414500	chr4A	94.048	84	3	2	1	83	35970221	35970303	3.150000e-25	126.0
25	TraesCS2D01G414500	chr3B	81.013	158	27	3	1441	1598	427590210	427590056	4.080000e-24	122.0

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	TraesCS2D01G414500	chr2D	528588043	528591053	3010	True	5561.000000	5561	100.000000	1	3011	1	chr2D.!!$R1	3010
1	TraesCS2D01G414500	chr2D	528472723	528474364	1641	True	476.200000	1166	86.029667	348	2028	3	chr2D.!!$R2	1680
2	TraesCS2D01G414500	chr2B	626882091	626885288	3197	True	1479.666667	3651	93.193000	1	3011	3	chr2B.!!$R2	3010
3	TraesCS2D01G414500	chr2B	626650872	626652178	1306	True	652.900000	1229	89.775500	754	2014	2	chr2B.!!$R1	1260
4	TraesCS2D01G414500	chr2A	673273445	673278206	4761	True	1414.500000	2514	88.792500	303	2408	2	chr2A.!!$R3	2105
5	TraesCS2D01G414500	chr2A	673195087	673196717	1630	True	706.000000	1245	84.609500	348	2019	2	chr2A.!!$R2	1671

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
246	265	0.468226	GACCGGCTCCCATATTGACA	59.532	55.0	0.00	0.0	0.0	3.58	F
1267	1453	0.106708	GAACTCATATCCGGCTGCCA	59.893	55.0	20.29	0.0	0.0	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1883	2072	3.278592	GACGGCGTCGGAGGAAACT	62.279	63.158	25.42	0.0	41.62	2.66	R
2458	5296	1.687563	AGTTTTTCGGGGGTTGACAG	58.312	50.000	0.00	0.0	0.00	3.51	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
35	36	3.805307	CTCACTCCGCTCGCTCGT	61.805	66.667	0.00	0.00	0.00	4.18
38	39	3.805307	ACTCCGCTCGCTCGTCAG	61.805	66.667	0.00	0.00	0.00	3.51
64	66	9.654663	GAAGTTAGCCTTCTCTTTATACTTGAA	57.345	33.333	0.00	0.00	45.19	2.69
69	71	8.286191	AGCCTTCTCTTTATACTTGAATTTGG	57.714	34.615	0.00	0.00	0.00	3.28
70	72	8.109634	AGCCTTCTCTTTATACTTGAATTTGGA	58.890	33.333	0.00	0.00	0.00	3.53
71	73	8.401709	GCCTTCTCTTTATACTTGAATTTGGAG	58.598	37.037	0.00	0.00	0.00	3.86
72	74	8.401709	CCTTCTCTTTATACTTGAATTTGGAGC	58.598	37.037	0.00	0.00	0.00	4.70
73	75	8.862325	TTCTCTTTATACTTGAATTTGGAGCA	57.138	30.769	0.00	0.00	0.00	4.26
137	156	0.984961	ATGGGGAAGCTGAGCTGCTA	60.985	55.000	13.03	0.00	43.24	3.49
193	212	8.130469	GGAAGTCGGACAATTTTGTTAAGTTAA	58.870	33.333	11.27	0.00	42.43	2.01
202	221	9.593134	ACAATTTTGTTAAGTTAAACAGATGCA	57.407	25.926	0.00	0.00	40.29	3.96
205	224	8.850454	TTTTGTTAAGTTAAACAGATGCAGAC	57.150	30.769	0.00	0.00	40.29	3.51
231	250	3.952323	TGAGGTATAGAGTTGGAAGACCG	59.048	47.826	0.00	0.00	39.42	4.79
238	257	2.528127	TTGGAAGACCGGCTCCCA	60.528	61.111	13.72	7.46	39.42	4.37
243	262	1.543429	GGAAGACCGGCTCCCATATTG	60.543	57.143	0.00	0.00	0.00	1.90
245	264	0.759346	AGACCGGCTCCCATATTGAC	59.241	55.000	0.00	0.00	0.00	3.18
246	265	0.468226	GACCGGCTCCCATATTGACA	59.532	55.000	0.00	0.00	0.00	3.58
249	268	1.072173	CCGGCTCCCATATTGACATCA	59.928	52.381	0.00	0.00	0.00	3.07
250	269	2.487086	CCGGCTCCCATATTGACATCAA	60.487	50.000	0.00	0.00	40.51	2.57
252	271	3.822735	CGGCTCCCATATTGACATCAATT	59.177	43.478	12.16	0.00	43.48	2.32
253	272	4.279169	CGGCTCCCATATTGACATCAATTT	59.721	41.667	12.16	2.35	43.48	1.82
255	274	6.348786	CGGCTCCCATATTGACATCAATTTAG	60.349	42.308	12.16	3.72	43.48	1.85
295	314	9.036671	CAAATACCGTGTCCATTTTAAAAGTTT	57.963	29.630	6.79	0.00	0.00	2.66
324	343	1.141657	GATGCCCTAAGCTGATGGACA	59.858	52.381	0.00	0.00	44.23	4.02
325	344	1.216064	TGCCCTAAGCTGATGGACAT	58.784	50.000	0.00	0.00	44.23	3.06
337	356	6.757237	AGCTGATGGACATTGAGAATACTAG	58.243	40.000	0.00	0.00	0.00	2.57
450	477	2.691409	TGGCAAGCTCTGGTATGTAC	57.309	50.000	0.00	0.00	0.00	2.90
498	525	6.358118	TCTGCGCGTCATATTAAATTTCTT	57.642	33.333	8.43	0.00	0.00	2.52
575	612	1.883926	TCTTCATTGACACGACTCCGA	59.116	47.619	0.00	0.00	39.50	4.55
621	658	6.528072	GCAAGTCAAAATTATCAACTGCCTAC	59.472	38.462	0.00	0.00	0.00	3.18
664	701	0.757512	TGCCCACAAATTGCACATGT	59.242	45.000	0.00	0.00	0.00	3.21
665	702	1.966354	TGCCCACAAATTGCACATGTA	59.034	42.857	0.00	0.00	0.00	2.29
666	703	2.288702	TGCCCACAAATTGCACATGTAC	60.289	45.455	0.00	0.00	0.00	2.90
863	979	2.961741	TCTCTCAGCTGGCCTATAAGTG	59.038	50.000	15.13	3.06	0.00	3.16
1019	1181	2.509561	GGAGTTCGCCGGAGAAGC	60.510	66.667	21.74	15.50	0.00	3.86
1056	1218	2.584418	CTCATCCGCGAGCACCTG	60.584	66.667	8.23	0.00	0.00	4.00
1098	1260	1.883084	GGCGACGGCTAACCATGAG	60.883	63.158	15.00	0.00	39.81	2.90
1267	1453	0.106708	GAACTCATATCCGGCTGCCA	59.893	55.000	20.29	0.00	0.00	4.92
1718	1907	3.926616	ACAAACGTAAGAGATCACAGGG	58.073	45.455	0.00	0.00	43.62	4.45
1769	1958	1.737793	GGTCATAAACAAGGCCGTGAG	59.262	52.381	26.25	9.20	0.00	3.51
1902	2091	3.296836	TTTCCTCCGACGCCGTCA	61.297	61.111	18.40	0.00	32.09	4.35
1922	2114	4.463879	CTCGGGCTGGGAGCAGTG	62.464	72.222	0.00	0.00	44.75	3.66
2046	2238	6.525121	TCATTAAGCGATAGAATGTTTCCG	57.475	37.500	7.77	0.00	39.76	4.30
2084	2276	0.320771	GAGTAGGCACCCACACACAG	60.321	60.000	0.00	0.00	0.00	3.66
2172	5004	5.673337	TGTTGTCAAGCTAGTGTTTGATC	57.327	39.130	8.86	0.00	43.37	2.92
2343	5181	1.635487	TGGGGAGGGAATGACAAAGAG	59.365	52.381	0.00	0.00	0.00	2.85
2346	5184	1.373570	GAGGGAATGACAAAGAGCGG	58.626	55.000	0.00	0.00	0.00	5.52
2369	5207	3.123050	GTTTGCTGGCAGTTTTAGTTGG	58.877	45.455	17.16	0.00	0.00	3.77
2428	5266	2.376518	TGCTGACAATTTCCTTCCTCCT	59.623	45.455	0.00	0.00	0.00	3.69
2439	5277	4.127918	TCCTTCCTCCTAGAAACTGTCA	57.872	45.455	0.00	0.00	0.00	3.58
2449	5287	7.310113	CCTCCTAGAAACTGTCATACTCTTGTT	60.310	40.741	0.00	0.00	0.00	2.83
2458	5296	7.920738	ACTGTCATACTCTTGTTGAAGAAAAC	58.079	34.615	0.00	0.00	37.77	2.43
2473	5311	2.025898	GAAAACTGTCAACCCCCGAAA	58.974	47.619	0.00	0.00	0.00	3.46
2508	5346	2.411904	TCAAAATGTTCGCAAATGCCC	58.588	42.857	0.00	0.00	37.91	5.36
2517	5355	2.280079	CAAATGCCCCTCCCTCCC	59.720	66.667	0.00	0.00	0.00	4.30
2518	5356	2.204448	AAATGCCCCTCCCTCCCA	60.204	61.111	0.00	0.00	0.00	4.37
2529	5367	2.342279	CCTCCCAGCGAACGTTCA	59.658	61.111	26.71	6.35	0.00	3.18
2531	5369	2.027625	CTCCCAGCGAACGTTCACC	61.028	63.158	26.71	16.82	0.00	4.02
2655	5525	9.616156	TTTTAAAACAGTGGACAAGATGTAGTA	57.384	29.630	0.00	0.00	0.00	1.82
2907	5939	7.382488	CCATCCTATAGTTTGTATCGTTCACTG	59.618	40.741	0.00	0.00	0.00	3.66
2923	5955	8.986477	TCGTTCACTGATATATGTATCAATGG	57.014	34.615	17.39	7.94	44.48	3.16
2924	5956	7.545615	TCGTTCACTGATATATGTATCAATGGC	59.454	37.037	17.39	11.39	44.48	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	1.540407	CTAACTTCTGACGAGCGAGC	58.460	55.000	0.00	0.00	0.00	5.03
64	66	8.863086	AGCATGTATTATGTTATTGCTCCAAAT	58.137	29.630	0.00	0.00	0.00	2.32
65	67	8.236585	AGCATGTATTATGTTATTGCTCCAAA	57.763	30.769	0.00	0.00	0.00	3.28
66	68	7.822161	AGCATGTATTATGTTATTGCTCCAA	57.178	32.000	0.00	0.00	0.00	3.53
67	69	7.285172	ACAAGCATGTATTATGTTATTGCTCCA	59.715	33.333	0.00	0.00	38.24	3.86
68	70	7.592533	CACAAGCATGTATTATGTTATTGCTCC	59.407	37.037	0.00	0.00	37.82	4.70
69	71	8.131100	ACACAAGCATGTATTATGTTATTGCTC	58.869	33.333	0.00	0.00	37.82	4.26
70	72	7.999679	ACACAAGCATGTATTATGTTATTGCT	58.000	30.769	0.00	0.00	37.82	3.91
71	73	8.533965	CAACACAAGCATGTATTATGTTATTGC	58.466	33.333	8.49	0.00	37.82	3.56
72	74	9.571810	ACAACACAAGCATGTATTATGTTATTG	57.428	29.630	8.49	8.65	37.82	1.90
73	75	9.571810	CACAACACAAGCATGTATTATGTTATT	57.428	29.630	8.49	0.00	37.82	1.40
85	87	2.143008	ATGCACACAACACAAGCATG	57.857	45.000	0.00	0.00	43.60	4.06
116	118	1.523258	CAGCTCAGCTTCCCCATCG	60.523	63.158	0.00	0.00	36.40	3.84
137	156	2.629656	GCAACTTCCGCCATGCAGT	61.630	57.895	0.00	0.00	38.63	4.40
158	177	1.982395	TCCGACTTCCGCCATCACT	60.982	57.895	0.00	0.00	36.84	3.41
168	187	9.505995	TTTAACTTAACAAAATTGTCCGACTTC	57.494	29.630	0.00	0.00	41.31	3.01
172	191	8.675504	TCTGTTTAACTTAACAAAATTGTCCGA	58.324	29.630	0.00	0.00	41.31	4.55
193	212	3.759581	ACCTCAAATGTCTGCATCTGTT	58.240	40.909	0.00	0.00	33.50	3.16
202	221	7.400339	TCTTCCAACTCTATACCTCAAATGTCT	59.600	37.037	0.00	0.00	0.00	3.41
205	224	6.763610	GGTCTTCCAACTCTATACCTCAAATG	59.236	42.308	0.00	0.00	0.00	2.32
231	250	5.796424	AAATTGATGTCAATATGGGAGCC	57.204	39.130	8.54	0.00	45.06	4.70
243	262	8.778358	GTCCATAGACCAATCTAAATTGATGTC	58.222	37.037	0.00	0.86	40.88	3.06
245	264	8.681486	TGTCCATAGACCAATCTAAATTGATG	57.319	34.615	0.00	0.00	41.53	3.07
246	265	9.699410	TTTGTCCATAGACCAATCTAAATTGAT	57.301	29.630	0.00	0.00	41.53	2.57
250	269	9.574516	GGTATTTGTCCATAGACCAATCTAAAT	57.425	33.333	0.00	0.00	42.81	1.40
251	270	7.713507	CGGTATTTGTCCATAGACCAATCTAAA	59.286	37.037	0.00	0.00	42.81	1.85
252	271	7.147620	ACGGTATTTGTCCATAGACCAATCTAA	60.148	37.037	0.00	0.00	42.81	2.10
253	272	6.325545	ACGGTATTTGTCCATAGACCAATCTA	59.674	38.462	0.00	0.00	42.81	1.98
255	274	5.236478	CACGGTATTTGTCCATAGACCAATC	59.764	44.000	0.00	0.00	42.81	2.67
295	314	1.202533	GCTTAGGGCATCTCTAACGCA	60.203	52.381	0.00	0.00	41.35	5.24
324	343	7.129425	ACTGAAGGGTCTCTAGTATTCTCAAT	58.871	38.462	0.00	0.00	0.00	2.57
325	344	6.494952	ACTGAAGGGTCTCTAGTATTCTCAA	58.505	40.000	0.00	0.00	0.00	3.02
337	356	8.261522	AGTTTCATTCTTATACTGAAGGGTCTC	58.738	37.037	0.00	0.00	31.11	3.36
376	399	5.026038	TCTTCCTCGTACACAAAAAGGAA	57.974	39.130	0.00	0.00	42.37	3.36
390	417	3.384789	TCTCTCTCTCTCTCTCTTCCTCG	59.615	52.174	0.00	0.00	0.00	4.63
472	499	7.247728	AGAAATTTAATATGACGCGCAGAAAA	58.752	30.769	5.73	1.95	0.00	2.29
498	525	2.224426	ACCATTCCGCTCACACTTTACA	60.224	45.455	0.00	0.00	0.00	2.41
523	550	3.474600	GCATACATCCATGACAAGAGCT	58.525	45.455	0.00	0.00	0.00	4.09
621	658	6.624710	TTTTCGTTGTCAAACTCAAACATG	57.375	33.333	0.00	0.00	33.87	3.21
664	701	2.232696	TGCGCTGAGATGTTTACTGGTA	59.767	45.455	9.73	0.00	0.00	3.25
665	702	1.001974	TGCGCTGAGATGTTTACTGGT	59.998	47.619	9.73	0.00	0.00	4.00
666	703	1.662629	CTGCGCTGAGATGTTTACTGG	59.337	52.381	9.73	0.00	0.00	4.00
752	820	0.389948	ATCTCGTCACTTTCCGTGGC	60.390	55.000	0.00	0.00	44.75	5.01
863	979	5.415701	TGTGATATTCCTTGAGGACAAAAGC	59.584	40.000	0.00	0.00	45.39	3.51
1098	1260	3.302344	TCGCAAAAAGGGCCCTGC	61.302	61.111	29.50	24.51	0.00	4.85
1464	1653	4.692475	GCGTACTTGCCCCACGGT	62.692	66.667	0.00	0.00	36.23	4.83
1883	2072	3.278592	GACGGCGTCGGAGGAAACT	62.279	63.158	25.42	0.00	41.62	2.66
1920	2112	4.479993	ATCAGCGCCTCCCAGCAC	62.480	66.667	2.29	0.00	35.48	4.40
1921	2113	4.478371	CATCAGCGCCTCCCAGCA	62.478	66.667	2.29	0.00	35.48	4.41
2046	2238	7.415229	CCTACTCTGTTTTTCTTACAAACACC	58.585	38.462	0.00	0.00	38.84	4.16
2172	5004	5.643348	TGGTTGTTGCACTGATGTAATAGAG	59.357	40.000	0.00	0.00	32.67	2.43
2343	5181	2.627510	AAACTGCCAGCAAACACCGC	62.628	55.000	0.00	0.00	0.00	5.68
2346	5184	3.436700	ACTAAAACTGCCAGCAAACAC	57.563	42.857	0.00	0.00	0.00	3.32
2369	5207	3.098636	GCAATTGTTTAATCTCGCGTCC	58.901	45.455	5.77	0.00	0.00	4.79
2409	5247	5.683876	TCTAGGAGGAAGGAAATTGTCAG	57.316	43.478	0.00	0.00	0.00	3.51
2428	5266	8.638873	TCTTCAACAAGAGTATGACAGTTTCTA	58.361	33.333	0.00	0.00	33.38	2.10
2439	5277	8.398665	GTTGACAGTTTTCTTCAACAAGAGTAT	58.601	33.333	8.46	0.00	41.61	2.12
2449	5287	2.661718	GGGGGTTGACAGTTTTCTTCA	58.338	47.619	0.00	0.00	0.00	3.02
2458	5296	1.687563	AGTTTTTCGGGGGTTGACAG	58.312	50.000	0.00	0.00	0.00	3.51
2473	5311	9.458374	CGAACATTTTGATGGTAGTTTTAGTTT	57.542	29.630	0.00	0.00	0.00	2.66
2498	5336	2.830370	GAGGGAGGGGCATTTGCG	60.830	66.667	0.00	0.00	43.26	4.85
2508	5346	4.148825	CGTTCGCTGGGAGGGAGG	62.149	72.222	0.00	0.00	38.45	4.30
2517	5355	1.990799	TATCTGGTGAACGTTCGCTG	58.009	50.000	33.54	26.56	37.80	5.18
2518	5356	2.230508	TCTTATCTGGTGAACGTTCGCT	59.769	45.455	33.54	20.45	37.80	4.93
2529	5367	2.765502	GGAAGGACCCTCTTATCTGGT	58.234	52.381	0.00	0.00	34.33	4.00
2601	5471	9.757227	TGCTTGTTTTAAAGTATGTAGCAAAAT	57.243	25.926	0.00	0.00	33.63	1.82
2632	5502	8.590204	TGATACTACATCTTGTCCACTGTTTTA	58.410	33.333	0.00	0.00	0.00	1.52
2874	5906	9.273016	CGATACAAACTATAGGATGGACATTTT	57.727	33.333	4.43	0.00	0.00	1.82
2875	5907	8.429641	ACGATACAAACTATAGGATGGACATTT	58.570	33.333	4.43	0.00	0.00	2.32
2876	5908	7.963532	ACGATACAAACTATAGGATGGACATT	58.036	34.615	4.43	0.00	0.00	2.71
2938	5971	1.953559	TATGACATTGGCCTTCTCGC	58.046	50.000	3.32	0.00	0.00	5.03
2969	6002	2.514458	ATAGTCTTGCAAGGGTTGGG	57.486	50.000	25.73	0.00	0.00	4.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.