AutoCloner

Multiple sequence alignment - TraesCS2D01G437900

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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	TraesCS2D01G437900	chr2D	100.000	2801	0	0	514	3314	547760306	547763106	0.000000e+00	5173.0
1	TraesCS2D01G437900	chr2D	90.605	926	51	16	979	1890	547694487	547695390	0.000000e+00	1195.0
2	TraesCS2D01G437900	chr2D	94.768	669	20	6	1971	2633	547695598	547696257	0.000000e+00	1027.0
3	TraesCS2D01G437900	chr2D	92.558	215	12	1	2714	2924	547696514	547696728	4.150000e-79	305.0
4	TraesCS2D01G437900	chr2D	100.000	118	0	0	1	118	547759793	547759910	5.570000e-53	219.0
5	TraesCS2D01G437900	chr2D	93.985	133	8	0	3174	3306	74862947	74863079	5.610000e-48	202.0
6	TraesCS2D01G437900	chr2B	90.785	1682	104	23	977	2630	654355160	654356818	0.000000e+00	2200.0
7	TraesCS2D01G437900	chr2B	89.610	1386	83	24	514	1858	654323301	654324666	0.000000e+00	1705.0
8	TraesCS2D01G437900	chr2B	88.263	639	38	20	1887	2517	654324827	654325436	0.000000e+00	730.0
9	TraesCS2D01G437900	chr2B	97.214	359	6	1	2959	3313	654357366	654357724	3.660000e-169	604.0
10	TraesCS2D01G437900	chr2B	88.737	293	17	5	2636	2924	654352673	654352953	8.800000e-91	344.0
11	TraesCS2D01G437900	chr2B	86.777	242	23	5	2714	2955	654357090	654357322	9.120000e-66	261.0
12	TraesCS2D01G437900	chr2B	92.857	154	10	1	3161	3314	113613210	113613362	4.300000e-54	222.0
13	TraesCS2D01G437900	chr2B	85.484	124	12	2	577	695	43068675	43068797	1.250000e-24	124.0
14	TraesCS2D01G437900	chr2B	94.872	78	4	0	2556	2633	654352372	654352449	4.490000e-24	122.0
15	TraesCS2D01G437900	chr2A	90.576	1337	84	23	570	1884	691186195	691184879	0.000000e+00	1733.0
16	TraesCS2D01G437900	chr2A	87.393	936	68	20	975	1890	691216899	691215994	0.000000e+00	1029.0
17	TraesCS2D01G437900	chr2A	87.124	699	53	16	1883	2573	691184595	691183926	0.000000e+00	758.0
18	TraesCS2D01G437900	chr2A	97.207	358	7	2	2959	3314	691183310	691182954	1.320000e-168	603.0
19	TraesCS2D01G437900	chr2A	92.623	366	21	1	1971	2336	691215812	691215453	3.790000e-144	521.0
20	TraesCS2D01G437900	chr2A	86.402	353	17	4	2636	2960	691183698	691183349	1.130000e-94	357.0
21	TraesCS2D01G437900	chr2A	91.525	118	9	1	1	118	691186419	691186303	9.520000e-36	161.0
22	TraesCS2D01G437900	chr2A	92.857	56	4	0	514	569	691186274	691186219	7.620000e-12	82.4
23	TraesCS2D01G437900	chr5B	100.000	30	0	0	1945	1974	659987210	659987181	4.620000e-04	56.5

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	TraesCS2D01G437900	chr2D	547759793	547763106	3313	False	2696.000000	5173	100.000000	1	3314	2	chr2D.!!$F3	3313
1	TraesCS2D01G437900	chr2D	547694487	547696728	2241	False	842.333333	1195	92.643667	979	2924	3	chr2D.!!$F2	1945
2	TraesCS2D01G437900	chr2B	654323301	654325436	2135	False	1217.500000	1705	88.936500	514	2517	2	chr2B.!!$F3	2003
3	TraesCS2D01G437900	chr2B	654352372	654357724	5352	False	706.200000	2200	91.677000	977	3313	5	chr2B.!!$F4	2336
4	TraesCS2D01G437900	chr2A	691215453	691216899	1446	True	775.000000	1029	90.008000	975	2336	2	chr2A.!!$R2	1361
5	TraesCS2D01G437900	chr2A	691182954	691186419	3465	True	615.733333	1733	90.948500	1	3314	6	chr2A.!!$R1	3313

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
902	940	0.390603	CACCGTTGCTGGTATCGGAA	60.391	55.0	13.37	0.0	44.86	4.30	F
1737	3571	0.319555	TACAAGGCGTCTCAGCACAC	60.320	55.0	0.00	0.0	39.27	3.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2088	4330	0.253630	TTATCACCTTCCCTGCCCCT	60.254	55.0	0.0	0.0	0.0	4.79	R
2581	4861	2.260844	TCAAGTTCCTCAAGCACCAG	57.739	50.0	0.0	0.0	0.0	4.00	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
33	34	6.764877	TCGTGCTTTACTCTAGAAAACAAG	57.235	37.500	0.00	0.00	0.00	3.16
46	47	8.786826	TCTAGAAAACAAGAAGAAGTTTGACA	57.213	30.769	0.00	0.00	37.94	3.58
77	78	3.885901	TCAATGGAATTTGACCGAACACA	59.114	39.130	0.00	0.00	31.22	3.72
109	110	2.986290	TCCGCCATGGACATCGTT	59.014	55.556	18.40	0.00	43.74	3.85
622	646	2.681421	CAAGGGGAAAGCAGGGGC	60.681	66.667	0.00	0.00	41.61	5.80
757	786	4.135747	TGCGGAGTATCATGTTTGATGA	57.864	40.909	0.00	0.00	42.60	2.92
766	795	8.352137	AGTATCATGTTTGATGACAAAATGGA	57.648	30.769	0.00	0.00	45.65	3.41
795	824	3.234630	CTGAGGGTCGGCGTTGGAA	62.235	63.158	6.85	0.00	0.00	3.53
797	826	2.281276	AGGGTCGGCGTTGGAAAC	60.281	61.111	6.85	0.00	45.31	2.78
833	862	7.659290	CGGATACCGTGTTTTATTTTGATTC	57.341	36.000	1.80	0.00	42.73	2.52
902	940	0.390603	CACCGTTGCTGGTATCGGAA	60.391	55.000	13.37	0.00	44.86	4.30
1014	2830	1.631405	CCAAAATGGCCACCTCAAGA	58.369	50.000	8.16	0.00	0.00	3.02
1230	3046	1.227674	GATGCTAGCCGTGGAAGGG	60.228	63.158	13.29	0.00	46.87	3.95
1231	3047	2.666596	GATGCTAGCCGTGGAAGGGG	62.667	65.000	13.29	0.00	43.56	4.79
1267	3083	0.531532	CGTGGATGTGGATGCTCCTC	60.532	60.000	4.21	1.67	37.46	3.71
1449	3271	3.379445	TTCCAGAGGGACGGCGAC	61.379	66.667	16.62	7.58	44.89	5.19
1539	3370	0.884704	AGTTCAACGCGCTGGTGAAT	60.885	50.000	26.77	16.83	0.00	2.57
1554	3385	0.982852	TGAATGAGGCGATGGGGTCT	60.983	55.000	0.00	0.00	0.00	3.85
1562	3393	2.659063	CGATGGGGTCTGACAGCCA	61.659	63.158	10.38	9.74	45.63	4.75
1565	3396	1.136329	ATGGGGTCTGACAGCCAGTT	61.136	55.000	10.38	0.00	45.63	3.16
1566	3397	1.352622	TGGGGTCTGACAGCCAGTTT	61.353	55.000	10.38	0.00	45.63	2.66
1737	3571	0.319555	TACAAGGCGTCTCAGCACAC	60.320	55.000	0.00	0.00	39.27	3.82
1859	3715	7.147707	ACAGTAGTTAAGAAAGACACACTTCCT	60.148	37.037	0.00	0.00	37.93	3.36
1867	3723	2.906354	AGACACACTTCCTGTTCACAC	58.094	47.619	0.00	0.00	0.00	3.82
2345	4593	7.182749	CCATGGATAGTCCTTTTCCCTCATATA	59.817	40.741	5.56	0.00	37.46	0.86
2346	4594	8.776119	CATGGATAGTCCTTTTCCCTCATATAT	58.224	37.037	0.00	0.00	37.46	0.86
2354	4602	9.905713	GTCCTTTTCCCTCATATATATATTGCA	57.094	33.333	2.28	0.00	0.00	4.08
2356	4604	9.911788	CCTTTTCCCTCATATATATATTGCAGT	57.088	33.333	2.28	0.00	0.00	4.40
2498	4777	4.373527	TCACTCAAAAGTCCGAATTCGAA	58.626	39.130	28.76	5.90	35.85	3.71
2581	4861	8.741101	TTTCAACAACAATATCAATGCTACAC	57.259	30.769	0.00	0.00	0.00	2.90
2589	4869	2.566833	TCAATGCTACACTGGTGCTT	57.433	45.000	0.17	0.00	0.00	3.91
2633	4919	1.153147	GACCCTTTGGATCTCGGCC	60.153	63.158	0.00	0.00	34.81	6.13
2634	4920	1.616628	ACCCTTTGGATCTCGGCCT	60.617	57.895	0.00	0.00	34.81	5.19
2665	5170	3.561725	GGATACATAGCCAACAACTCTGC	59.438	47.826	0.00	0.00	0.00	4.26
2672	5177	6.209391	ACATAGCCAACAACTCTGCTTTTATT	59.791	34.615	0.00	0.00	35.34	1.40
2673	5178	7.393234	ACATAGCCAACAACTCTGCTTTTATTA	59.607	33.333	0.00	0.00	35.34	0.98
2674	5179	6.840780	AGCCAACAACTCTGCTTTTATTAT	57.159	33.333	0.00	0.00	0.00	1.28
2675	5180	7.232118	AGCCAACAACTCTGCTTTTATTATT	57.768	32.000	0.00	0.00	0.00	1.40
2728	5257	2.540973	GCAACTCCGGTTTTCAGTTGAC	60.541	50.000	27.98	18.36	46.74	3.18
2773	5302	0.179234	TGCCTCCAGTGTTCGAAACA	59.821	50.000	0.00	0.00	39.52	2.83
2877	5410	2.943036	TTGGTGTTGGTACTCTTCCC	57.057	50.000	0.00	0.00	0.00	3.97
2893	5426	5.736616	ACTCTTCCCTATAAATTTGGTCCCT	59.263	40.000	0.00	0.00	0.00	4.20
2927	5460	3.863142	AACTGCCTTTCATTGCTCATC	57.137	42.857	0.00	0.00	0.00	2.92
2957	5490	1.462670	GCAGAGAAAGAAAGAGGCACG	59.537	52.381	0.00	0.00	0.00	5.34
3151	5725	5.675970	TCGTTTCGCAATAAAGAAGACTTG	58.324	37.500	0.00	0.00	36.39	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	2.595386	GGCATGTGTTCGGTCAAATTC	58.405	47.619	0.00	0.00	0.00	2.17
526	527	4.403137	CCCACCAATGCGCGTGTG	62.403	66.667	8.43	8.08	0.00	3.82
574	598	1.336609	GCACCTTCCTCGTCTAACGTT	60.337	52.381	5.88	5.88	43.14	3.99
579	603	2.035961	GCATATGCACCTTCCTCGTCTA	59.964	50.000	22.84	0.00	41.59	2.59
622	646	4.498009	CCGATCCATTTTTCTTCCAATCCG	60.498	45.833	0.00	0.00	0.00	4.18
710	739	0.542702	AGGCAATTTGTGGGGTGAGG	60.543	55.000	0.00	0.00	0.00	3.86
757	786	4.466370	TCAGACCGTCTAGATCCATTTTGT	59.534	41.667	0.00	0.00	0.00	2.83
766	795	1.475392	CGACCCTCAGACCGTCTAGAT	60.475	57.143	0.00	0.00	0.00	1.98
833	862	4.142403	ACCATGCCATGTTTAATGTCTTCG	60.142	41.667	3.63	0.00	0.00	3.79
902	940	8.677870	AATCTCAGCTAGGGATGATTTATAGT	57.322	34.615	0.09	0.00	37.24	2.12
1539	3370	2.038813	TCAGACCCCATCGCCTCA	59.961	61.111	0.00	0.00	0.00	3.86
1562	3393	0.179108	GACGAGCTCCGCCATAAACT	60.179	55.000	8.47	0.00	43.32	2.66
1565	3396	2.332362	GACGACGAGCTCCGCCATAA	62.332	60.000	8.47	0.00	43.32	1.90
1566	3397	2.827190	ACGACGAGCTCCGCCATA	60.827	61.111	8.47	0.00	43.32	2.74
1737	3571	0.508641	CAGCAAACTCAACCGACTCG	59.491	55.000	0.00	0.00	0.00	4.18
1832	3677	7.169476	GGAAGTGTGTCTTTCTTAACTACTGTC	59.831	40.741	0.00	0.00	36.40	3.51
1841	3686	5.815740	GTGAACAGGAAGTGTGTCTTTCTTA	59.184	40.000	0.00	0.00	39.79	2.10
1859	3715	6.653320	GTGAGGAATTGGTATAAGTGTGAACA	59.347	38.462	0.00	0.00	0.00	3.18
1867	3723	8.576442	ACTTGTTTTGTGAGGAATTGGTATAAG	58.424	33.333	0.00	0.00	0.00	1.73
1899	4087	5.110940	TGCACCCGTTTATTCTTGTTAAC	57.889	39.130	0.00	0.00	0.00	2.01
1967	4209	9.262358	ACAAGTCAAAAACTATCACTAAGAGAC	57.738	33.333	0.00	0.00	37.17	3.36
1975	4217	6.575162	ATCCCACAAGTCAAAAACTATCAC	57.425	37.500	0.00	0.00	37.17	3.06
2087	4329	0.988145	TATCACCTTCCCTGCCCCTG	60.988	60.000	0.00	0.00	0.00	4.45
2088	4330	0.253630	TTATCACCTTCCCTGCCCCT	60.254	55.000	0.00	0.00	0.00	4.79
2089	4331	0.853530	ATTATCACCTTCCCTGCCCC	59.146	55.000	0.00	0.00	0.00	5.80
2090	4332	1.494721	TGATTATCACCTTCCCTGCCC	59.505	52.381	0.00	0.00	0.00	5.36
2091	4333	3.416156	GATGATTATCACCTTCCCTGCC	58.584	50.000	0.00	0.00	33.38	4.85
2092	4334	3.070018	CGATGATTATCACCTTCCCTGC	58.930	50.000	0.00	0.00	32.67	4.85
2351	4599	9.555727	GGAAAGTATAAAATGGATAGTACTGCA	57.444	33.333	5.39	0.00	0.00	4.41
2352	4600	8.709646	CGGAAAGTATAAAATGGATAGTACTGC	58.290	37.037	5.39	0.00	0.00	4.40
2353	4601	8.709646	GCGGAAAGTATAAAATGGATAGTACTG	58.290	37.037	5.39	0.00	0.00	2.74
2354	4602	8.648693	AGCGGAAAGTATAAAATGGATAGTACT	58.351	33.333	0.00	0.00	0.00	2.73
2355	4603	8.828688	AGCGGAAAGTATAAAATGGATAGTAC	57.171	34.615	0.00	0.00	0.00	2.73
2356	4604	9.485206	GAAGCGGAAAGTATAAAATGGATAGTA	57.515	33.333	0.00	0.00	0.00	1.82
2479	4758	4.378459	CCCTTTCGAATTCGGACTTTTGAG	60.378	45.833	26.47	11.63	40.29	3.02
2581	4861	2.260844	TCAAGTTCCTCAAGCACCAG	57.739	50.000	0.00	0.00	0.00	4.00
2589	4869	3.840666	AGCTAGGACAATCAAGTTCCTCA	59.159	43.478	0.00	0.00	32.43	3.86
2672	5177	8.298854	CACATTGAACAATCCAACAGAGAAATA	58.701	33.333	0.00	0.00	0.00	1.40
2673	5178	7.149973	CACATTGAACAATCCAACAGAGAAAT	58.850	34.615	0.00	0.00	0.00	2.17
2674	5179	6.506147	CACATTGAACAATCCAACAGAGAAA	58.494	36.000	0.00	0.00	0.00	2.52
2675	5180	5.507817	GCACATTGAACAATCCAACAGAGAA	60.508	40.000	0.00	0.00	0.00	2.87
2728	5257	5.396484	CAGAACTTAATGTGGTTGCATCAG	58.604	41.667	0.00	0.00	0.00	2.90
2844	5377	4.082787	CCAACACCAAATAAGCACCTACTG	60.083	45.833	0.00	0.00	0.00	2.74
2877	5410	9.627123	TGTCTAATGAAGGGACCAAATTTATAG	57.373	33.333	0.00	0.00	0.00	1.31
2893	5426	6.096141	TGAAAGGCAGTTTTGTGTCTAATGAA	59.904	34.615	0.00	0.00	30.14	2.57
2927	5460	3.818961	TCTTTCTCTGCGAAATTGCTG	57.181	42.857	0.00	0.00	40.62	4.41
2957	5490	3.003480	GTTGCACTGGATTACCTGAGAC	58.997	50.000	0.00	0.00	38.29	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.