AutoCloner

Multiple sequence alignment - TraesCS3D01G108400

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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	TraesCS3D01G108400	chr3D	100.000	3092	0	0	1	3092	61689861	61686770	0.000000e+00	5710
1	TraesCS3D01G108400	chr3D	73.431	685	130	34	2419	3092	61681272	61680629	3.120000e-50	209
2	TraesCS3D01G108400	chr3A	96.467	2434	60	9	667	3092	70715083	70712668	0.000000e+00	3995
3	TraesCS3D01G108400	chr3B	92.784	1663	60	14	667	2301	99131354	99129724	0.000000e+00	2351
4	TraesCS3D01G108400	chr3B	95.776	805	28	2	2294	3092	99127813	99127009	0.000000e+00	1293
5	TraesCS3D01G108400	chr3B	72.470	672	137	24	2429	3092	99118847	99118216	4.100000e-39	172
6	TraesCS3D01G108400	chr2D	98.551	621	8	1	1	620	565131659	565131039	0.000000e+00	1096
7	TraesCS3D01G108400	chr1D	98.390	621	8	2	1	620	406845576	406846195	0.000000e+00	1090
8	TraesCS3D01G108400	chr1D	97.907	621	11	2	1	620	440872162	440872781	0.000000e+00	1074
9	TraesCS3D01G108400	chrUn	98.068	621	11	1	1	620	97653874	97654494	0.000000e+00	1079
10	TraesCS3D01G108400	chr1B	95.974	621	24	1	1	620	555555284	555555904	0.000000e+00	1007
11	TraesCS3D01G108400	chr1B	95.390	629	26	2	1	628	37293498	37294124	0.000000e+00	998
12	TraesCS3D01G108400	chr5B	95.498	622	27	1	1	621	523381271	523380650	0.000000e+00	992
13	TraesCS3D01G108400	chr6B	95.169	621	21	4	1	620	298139313	298139925	0.000000e+00	972
14	TraesCS3D01G108400	chr7B	94.534	622	32	2	1	620	705535030	705534409	0.000000e+00	959

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	TraesCS3D01G108400	chr3D	61686770	61689861	3091	True	5710	5710	100.000	1	3092	1	chr3D.!!$R2	3091
1	TraesCS3D01G108400	chr3D	61680629	61681272	643	True	209	209	73.431	2419	3092	1	chr3D.!!$R1	673
2	TraesCS3D01G108400	chr3A	70712668	70715083	2415	True	3995	3995	96.467	667	3092	1	chr3A.!!$R1	2425
3	TraesCS3D01G108400	chr3B	99127009	99131354	4345	True	1822	2351	94.280	667	3092	2	chr3B.!!$R2	2425
4	TraesCS3D01G108400	chr2D	565131039	565131659	620	True	1096	1096	98.551	1	620	1	chr2D.!!$R1	619
5	TraesCS3D01G108400	chr1D	406845576	406846195	619	False	1090	1090	98.390	1	620	1	chr1D.!!$F1	619
6	TraesCS3D01G108400	chr1D	440872162	440872781	619	False	1074	1074	97.907	1	620	1	chr1D.!!$F2	619
7	TraesCS3D01G108400	chrUn	97653874	97654494	620	False	1079	1079	98.068	1	620	1	chrUn.!!$F1	619
8	TraesCS3D01G108400	chr1B	555555284	555555904	620	False	1007	1007	95.974	1	620	1	chr1B.!!$F2	619
9	TraesCS3D01G108400	chr1B	37293498	37294124	626	False	998	998	95.390	1	628	1	chr1B.!!$F1	627
10	TraesCS3D01G108400	chr5B	523380650	523381271	621	True	992	992	95.498	1	621	1	chr5B.!!$R1	620
11	TraesCS3D01G108400	chr6B	298139313	298139925	612	False	972	972	95.169	1	620	1	chr6B.!!$F1	619
12	TraesCS3D01G108400	chr7B	705534409	705535030	621	True	959	959	94.534	1	620	1	chr7B.!!$R1	619

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
633	636	0.179056	GCCCTATGCGCAACCTAAGA	60.179	55.0	17.11	0.0	0.0	2.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2390	4349	0.319641	GCCTACTATGTGCCGTAGCC	60.32	60.0	0.0	0.0	38.69	3.93	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
82	83	4.547406	TCGATCTCGAGCTAATTTCGAA	57.453	40.909	7.81	0.00	45.35	3.71
148	149	4.655963	AGCAAGATAGACCACAACACAAT	58.344	39.130	0.00	0.00	0.00	2.71
266	267	5.404366	CAGCTCTCAAACATTGACCAAAATG	59.596	40.000	0.00	0.00	42.21	2.32
621	624	2.096496	CGAGTTTTCTTGCAGCCCTATG	59.904	50.000	0.00	0.00	0.00	2.23
631	634	4.551729	GCCCTATGCGCAACCTAA	57.448	55.556	17.11	0.00	0.00	2.69
632	635	2.321213	GCCCTATGCGCAACCTAAG	58.679	57.895	17.11	7.14	0.00	2.18
633	636	0.179056	GCCCTATGCGCAACCTAAGA	60.179	55.000	17.11	0.00	0.00	2.10
634	637	1.543429	GCCCTATGCGCAACCTAAGAT	60.543	52.381	17.11	0.00	0.00	2.40
635	638	2.146342	CCCTATGCGCAACCTAAGATG	58.854	52.381	17.11	0.00	0.00	2.90
636	639	2.224281	CCCTATGCGCAACCTAAGATGA	60.224	50.000	17.11	0.00	0.00	2.92
637	640	3.557898	CCCTATGCGCAACCTAAGATGAT	60.558	47.826	17.11	0.00	0.00	2.45
638	641	4.067896	CCTATGCGCAACCTAAGATGATT	58.932	43.478	17.11	0.00	0.00	2.57
639	642	4.516698	CCTATGCGCAACCTAAGATGATTT	59.483	41.667	17.11	0.00	0.00	2.17
640	643	5.700832	CCTATGCGCAACCTAAGATGATTTA	59.299	40.000	17.11	0.00	0.00	1.40
641	644	4.875544	TGCGCAACCTAAGATGATTTAC	57.124	40.909	8.16	0.00	0.00	2.01
642	645	4.257731	TGCGCAACCTAAGATGATTTACA	58.742	39.130	8.16	0.00	0.00	2.41
643	646	4.094294	TGCGCAACCTAAGATGATTTACAC	59.906	41.667	8.16	0.00	0.00	2.90
644	647	4.094294	GCGCAACCTAAGATGATTTACACA	59.906	41.667	0.30	0.00	0.00	3.72
645	648	5.560148	CGCAACCTAAGATGATTTACACAC	58.440	41.667	0.00	0.00	0.00	3.82
646	649	5.447279	CGCAACCTAAGATGATTTACACACC	60.447	44.000	0.00	0.00	0.00	4.16
647	650	5.648092	GCAACCTAAGATGATTTACACACCT	59.352	40.000	0.00	0.00	0.00	4.00
648	651	6.821665	GCAACCTAAGATGATTTACACACCTA	59.178	38.462	0.00	0.00	0.00	3.08
649	652	7.011482	GCAACCTAAGATGATTTACACACCTAG	59.989	40.741	0.00	0.00	0.00	3.02
650	653	7.973048	ACCTAAGATGATTTACACACCTAGA	57.027	36.000	0.00	0.00	0.00	2.43
651	654	7.783042	ACCTAAGATGATTTACACACCTAGAC	58.217	38.462	0.00	0.00	0.00	2.59
652	655	6.918569	CCTAAGATGATTTACACACCTAGACG	59.081	42.308	0.00	0.00	0.00	4.18
653	656	4.683832	AGATGATTTACACACCTAGACGC	58.316	43.478	0.00	0.00	0.00	5.19
654	657	4.402793	AGATGATTTACACACCTAGACGCT	59.597	41.667	0.00	0.00	0.00	5.07
655	658	5.593095	AGATGATTTACACACCTAGACGCTA	59.407	40.000	0.00	0.00	0.00	4.26
656	659	5.244785	TGATTTACACACCTAGACGCTAG	57.755	43.478	6.85	6.85	0.00	3.42
657	660	4.945543	TGATTTACACACCTAGACGCTAGA	59.054	41.667	13.37	0.00	0.00	2.43
658	661	4.691860	TTTACACACCTAGACGCTAGAC	57.308	45.455	13.37	0.00	0.00	2.59
679	682	1.478916	GGAGGGAGTACTCTGCACTTC	59.521	57.143	21.88	10.89	35.00	3.01
813	824	0.464373	GCAGCATCTCGAATTGGGGA	60.464	55.000	0.00	0.00	0.00	4.81
814	825	1.590932	CAGCATCTCGAATTGGGGAG	58.409	55.000	0.00	0.00	0.00	4.30
1513	1525	0.596083	CATGAGCATCTCCGACGACC	60.596	60.000	0.00	0.00	34.92	4.79
1526	1538	3.697747	CGACCTGTACGCCCCCAA	61.698	66.667	0.00	0.00	0.00	4.12
1716	1728	1.153549	CTTCTCCTTCGCCTTCCCG	60.154	63.158	0.00	0.00	0.00	5.14
1921	1947	0.248134	GTTCGAGGAGATGACGACGG	60.248	60.000	0.00	0.00	35.82	4.79
1922	1948	0.392060	TTCGAGGAGATGACGACGGA	60.392	55.000	0.00	0.00	35.82	4.69
1923	1949	0.810426	TCGAGGAGATGACGACGGAG	60.810	60.000	0.00	0.00	0.00	4.63
2126	2155	2.403252	ACACTAGAAATGGCGGGAAG	57.597	50.000	0.00	0.00	0.00	3.46
2258	2292	2.229784	GACAGGGAATTCAAAGTGCAGG	59.770	50.000	7.93	0.00	0.00	4.85
2292	2326	4.911514	TGTTAGGACAAAGCAAAAGGAC	57.088	40.909	0.00	0.00	31.49	3.85
2302	4254	6.101997	ACAAAGCAAAAGGACTTTCAGAAAG	58.898	36.000	19.71	19.71	44.10	2.62
2357	4315	8.979574	GTACATAATCTAGCAAGACAACCATAC	58.020	37.037	0.00	0.00	33.57	2.39
2360	4318	9.060347	CATAATCTAGCAAGACAACCATACATT	57.940	33.333	0.00	0.00	33.57	2.71
2390	4349	4.751098	CATGTTGGAACATTTTTCCACAGG	59.249	41.667	3.74	4.65	46.95	4.00
2399	4358	2.058125	TTTTCCACAGGGCTACGGCA	62.058	55.000	0.00	0.00	40.87	5.69
2421	4380	2.011741	TAGTAGGCACACATCCGGCG	62.012	60.000	0.00	0.00	0.00	6.46
2516	4476	2.583520	AGGCACTGCTAGCTCTGC	59.416	61.111	22.12	22.12	37.18	4.26
2741	4701	1.195448	GAACGGACAAGCAGTGATGTG	59.805	52.381	6.72	0.00	0.00	3.21
2790	4750	2.357517	AAACGGCCTGCAGACTCG	60.358	61.111	17.39	17.32	0.00	4.18
2799	4759	0.987715	CTGCAGACTCGTGATTCGTG	59.012	55.000	8.42	0.00	40.80	4.35
2958	4921	6.100404	AGCTCAAGATCTAATGTCCTGATC	57.900	41.667	0.00	0.00	37.46	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
266	267	5.108027	GCAACCGTGTGTTCAATATTTTGTC	60.108	40.000	0.00	0.00	34.00	3.18
621	624	4.094294	TGTGTAAATCATCTTAGGTTGCGC	59.906	41.667	0.00	0.00	0.00	6.09
628	631	6.418226	GCGTCTAGGTGTGTAAATCATCTTAG	59.582	42.308	0.00	0.00	0.00	2.18
629	632	6.096423	AGCGTCTAGGTGTGTAAATCATCTTA	59.904	38.462	0.00	0.00	0.00	2.10
630	633	5.105310	AGCGTCTAGGTGTGTAAATCATCTT	60.105	40.000	0.00	0.00	0.00	2.40
631	634	4.402793	AGCGTCTAGGTGTGTAAATCATCT	59.597	41.667	0.00	0.00	0.00	2.90
632	635	4.683832	AGCGTCTAGGTGTGTAAATCATC	58.316	43.478	0.00	0.00	0.00	2.92
633	636	4.737855	AGCGTCTAGGTGTGTAAATCAT	57.262	40.909	0.00	0.00	0.00	2.45
634	637	4.945543	TCTAGCGTCTAGGTGTGTAAATCA	59.054	41.667	12.09	0.00	0.00	2.57
635	638	5.272397	GTCTAGCGTCTAGGTGTGTAAATC	58.728	45.833	12.09	0.00	0.00	2.17
636	639	4.201891	CGTCTAGCGTCTAGGTGTGTAAAT	60.202	45.833	12.09	0.00	35.54	1.40
637	640	3.125829	CGTCTAGCGTCTAGGTGTGTAAA	59.874	47.826	12.09	0.00	35.54	2.01
638	641	2.674852	CGTCTAGCGTCTAGGTGTGTAA	59.325	50.000	12.09	0.00	35.54	2.41
639	642	2.274437	CGTCTAGCGTCTAGGTGTGTA	58.726	52.381	12.09	0.00	35.54	2.90
640	643	1.085091	CGTCTAGCGTCTAGGTGTGT	58.915	55.000	12.09	0.00	35.54	3.72
641	644	0.377554	CCGTCTAGCGTCTAGGTGTG	59.622	60.000	12.09	3.07	39.32	3.82
642	645	0.251354	TCCGTCTAGCGTCTAGGTGT	59.749	55.000	12.09	0.00	39.32	4.16
643	646	0.938713	CTCCGTCTAGCGTCTAGGTG	59.061	60.000	12.09	6.66	39.32	4.00
644	647	0.179051	CCTCCGTCTAGCGTCTAGGT	60.179	60.000	12.09	0.00	39.32	3.08
645	648	0.885596	CCCTCCGTCTAGCGTCTAGG	60.886	65.000	12.09	8.47	39.32	3.02
646	649	0.106335	TCCCTCCGTCTAGCGTCTAG	59.894	60.000	7.36	7.36	39.32	2.43
647	650	0.106335	CTCCCTCCGTCTAGCGTCTA	59.894	60.000	5.97	0.00	39.32	2.59
648	651	1.153127	CTCCCTCCGTCTAGCGTCT	60.153	63.158	5.97	0.00	39.32	4.18
649	652	0.179062	TACTCCCTCCGTCTAGCGTC	60.179	60.000	5.97	0.00	39.32	5.19
650	653	0.463474	GTACTCCCTCCGTCTAGCGT	60.463	60.000	5.97	0.00	39.32	5.07
651	654	0.179051	AGTACTCCCTCCGTCTAGCG	60.179	60.000	0.00	0.33	40.95	4.26
652	655	1.141455	AGAGTACTCCCTCCGTCTAGC	59.859	57.143	19.38	0.00	31.53	3.42
653	656	2.841215	CAGAGTACTCCCTCCGTCTAG	58.159	57.143	19.38	0.00	31.53	2.43
654	657	1.134159	GCAGAGTACTCCCTCCGTCTA	60.134	57.143	19.38	0.00	31.53	2.59
655	658	0.394625	GCAGAGTACTCCCTCCGTCT	60.395	60.000	19.38	0.00	31.53	4.18
656	659	0.680280	TGCAGAGTACTCCCTCCGTC	60.680	60.000	19.38	2.11	31.53	4.79
657	660	0.966370	GTGCAGAGTACTCCCTCCGT	60.966	60.000	19.38	0.00	31.53	4.69
658	661	0.681564	AGTGCAGAGTACTCCCTCCG	60.682	60.000	19.38	4.59	31.53	4.63
659	662	1.478916	GAAGTGCAGAGTACTCCCTCC	59.521	57.143	19.38	5.76	31.53	4.30
660	663	1.133407	CGAAGTGCAGAGTACTCCCTC	59.867	57.143	19.38	11.31	0.00	4.30
661	664	1.178276	CGAAGTGCAGAGTACTCCCT	58.822	55.000	19.38	7.60	0.00	4.20
662	665	0.173708	CCGAAGTGCAGAGTACTCCC	59.826	60.000	19.38	11.28	0.00	4.30
663	666	0.458716	GCCGAAGTGCAGAGTACTCC	60.459	60.000	19.38	5.74	0.00	3.85
664	667	0.243907	TGCCGAAGTGCAGAGTACTC	59.756	55.000	15.41	15.41	36.04	2.59
665	668	0.898320	ATGCCGAAGTGCAGAGTACT	59.102	50.000	0.00	0.00	45.93	2.73
934	946	6.070596	TGAGTTCTCTGCCTAAGATCAATCAA	60.071	38.462	0.00	0.00	33.29	2.57
935	947	5.423290	TGAGTTCTCTGCCTAAGATCAATCA	59.577	40.000	0.00	0.00	33.29	2.57
936	948	5.911752	TGAGTTCTCTGCCTAAGATCAATC	58.088	41.667	0.00	0.00	33.29	2.67
937	949	5.946942	TGAGTTCTCTGCCTAAGATCAAT	57.053	39.130	0.00	0.00	33.29	2.57
1174	1186	2.978010	CTGGAAAACGCACCCGCT	60.978	61.111	0.00	0.00	38.22	5.52
1175	1187	4.038080	CCTGGAAAACGCACCCGC	62.038	66.667	0.00	0.00	38.22	6.13
1495	1507	0.753479	AGGTCGTCGGAGATGCTCAT	60.753	55.000	0.00	0.00	44.51	2.90
1513	1525	2.046314	CCTGTTGGGGGCGTACAG	60.046	66.667	0.00	0.00	39.13	2.74
1526	1538	1.203025	AGTAGTCGAAGTGGGACCTGT	60.203	52.381	0.00	0.00	34.97	4.00
1583	1595	4.373116	GCAGCTTCCCGTCCGTGA	62.373	66.667	0.00	0.00	0.00	4.35
1716	1728	2.656328	GCGGGGCGTACGTACATC	60.656	66.667	24.50	15.03	0.00	3.06
2046	2075	2.575993	CAGGTCGGACAGGAGCAG	59.424	66.667	10.76	0.00	36.90	4.24
2090	2119	0.612174	TGTAGCTCTCGCCACCTCTT	60.612	55.000	0.00	0.00	36.60	2.85
2099	2128	3.376540	GCCATTTCTAGTGTAGCTCTCG	58.623	50.000	0.00	0.00	0.00	4.04
2101	2130	2.101582	CCGCCATTTCTAGTGTAGCTCT	59.898	50.000	0.00	0.00	0.00	4.09
2126	2155	4.564041	TGAAAGATCAGCTCTGTGTTCTC	58.436	43.478	0.00	0.00	33.29	2.87
2258	2292	5.682943	TGTCCTAACAAAACAGTACATGC	57.317	39.130	0.00	0.00	30.70	4.06
2292	2326	7.672983	TGACCTGCTAAATACTTTCTGAAAG	57.327	36.000	24.58	24.58	44.10	2.62
2302	4254	7.621428	ATGATGCATATGACCTGCTAAATAC	57.379	36.000	6.97	0.00	40.34	1.89
2390	4349	0.319641	GCCTACTATGTGCCGTAGCC	60.320	60.000	0.00	0.00	38.69	3.93
2399	4358	1.412710	CCGGATGTGTGCCTACTATGT	59.587	52.381	0.00	0.00	0.00	2.29
2516	4476	4.925646	TCATTCGAAGGCTATCATGAATCG	59.074	41.667	4.63	3.98	0.00	3.34
2741	4701	0.601311	GGTCCATCTACCAGCATCGC	60.601	60.000	0.00	0.00	39.50	4.58
2790	4750	4.284123	TGCCTCTGCACGAATCAC	57.716	55.556	0.00	0.00	44.23	3.06
2799	4759	1.370810	GAGCCTCCTATGCCTCTGC	59.629	63.158	0.00	0.00	38.26	4.26
2958	4921	1.466167	CTGTTTGCAAGTGATCGGGAG	59.534	52.381	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.