AutoCloner

Multiple sequence alignment - TraesCS1D01G009700

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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	TraesCS1D01G009700	chr1D	100.000	3282	0	0	1	3282	5289664	5292945	0.000000e+00	6061.0
1	TraesCS1D01G009700	chr1D	81.643	621	92	18	2600	3211	486255509	486254902	2.270000e-136	496.0
2	TraesCS1D01G009700	chr1D	79.250	400	66	10	2816	3211	488616386	488616772	2.510000e-66	263.0
3	TraesCS1D01G009700	chr1B	95.497	955	34	4	875	1823	8116585	8117536	0.000000e+00	1517.0
4	TraesCS1D01G009700	chr1B	93.133	830	46	4	1900	2718	8117682	8118511	0.000000e+00	1206.0
5	TraesCS1D01G009700	chr4D	94.044	873	45	4	1	867	232695552	232694681	0.000000e+00	1317.0
6	TraesCS1D01G009700	chr4D	92.792	874	54	5	1	868	461474142	461475012	0.000000e+00	1256.0
7	TraesCS1D01G009700	chr2D	93.578	872	50	2	1	866	306476663	306477534	0.000000e+00	1295.0
8	TraesCS1D01G009700	chr2D	92.395	881	54	7	1	872	346102602	346101726	0.000000e+00	1243.0
9	TraesCS1D01G009700	chr2D	79.268	246	46	5	2578	2821	525519741	525519499	2.030000e-37	167.0
10	TraesCS1D01G009700	chr2D	84.375	96	8	4	1811	1906	636593201	636593113	1.620000e-13	87.9
11	TraesCS1D01G009700	chr7D	93.044	877	53	3	1	870	621971645	621970770	0.000000e+00	1275.0
12	TraesCS1D01G009700	chr2B	93.044	877	51	7	1	869	638015739	638014865	0.000000e+00	1273.0
13	TraesCS1D01G009700	chr2B	84.536	388	51	9	2816	3199	621956990	621957372	3.090000e-100	375.0
14	TraesCS1D01G009700	chr6D	92.922	876	55	2	1	869	191801703	191800828	0.000000e+00	1267.0
15	TraesCS1D01G009700	chr7B	92.808	876	55	3	1	869	267255384	267256258	0.000000e+00	1262.0
16	TraesCS1D01G009700	chr7B	92.580	876	57	4	1	870	168964836	168965709	0.000000e+00	1251.0
17	TraesCS1D01G009700	chr3A	85.075	402	50	8	2816	3211	720412508	720412111	5.100000e-108	401.0
18	TraesCS1D01G009700	chr3A	84.795	171	21	4	3045	3211	468730711	468730880	2.030000e-37	167.0
19	TraesCS1D01G009700	chr4A	84.788	401	52	9	2816	3211	441781522	441781126	8.540000e-106	394.0
20	TraesCS1D01G009700	chr7A	81.572	407	47	13	2808	3211	83300758	83300377	8.840000e-81	311.0
21	TraesCS1D01G009700	chr7A	83.696	92	8	4	1812	1903	678752614	678752698	2.710000e-11	80.5
22	TraesCS1D01G009700	chr1A	81.378	392	57	13	2816	3199	587871958	587872341	4.110000e-79	305.0
23	TraesCS1D01G009700	chr4B	81.963	377	38	16	2816	3188	191211676	191212026	3.200000e-75	292.0
24	TraesCS1D01G009700	chr3D	84.409	186	24	5	3029	3211	350872924	350873107	9.360000e-41	178.0
25	TraesCS1D01G009700	chr3B	85.714	98	10	2	1809	1906	795334321	795334414	2.080000e-17	100.0
26	TraesCS1D01G009700	chr3B	80.208	96	12	3	1811	1906	76514111	76514023	7.600000e-07	65.8
27	TraesCS1D01G009700	chr5A	83.505	97	9	3	1811	1907	32836426	32836515	2.100000e-12	84.2
28	TraesCS1D01G009700	chr5D	83.000	100	8	6	1811	1906	562348446	562348352	7.550000e-12	82.4
29	TraesCS1D01G009700	chr5D	81.818	99	11	3	1812	1910	173749755	173749846	3.510000e-10	76.8
30	TraesCS1D01G009700	chr5B	79.825	114	14	5	1798	1910	324299761	324299866	1.260000e-09	75.0
31	TraesCS1D01G009700	chr6A	95.122	41	2	0	1866	1906	62810623	62810583	7.600000e-07	65.8

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	TraesCS1D01G009700	chr1D	5289664	5292945	3281	False	6061.0	6061	100.000	1	3282	1	chr1D.!!$F1	3281
1	TraesCS1D01G009700	chr1D	486254902	486255509	607	True	496.0	496	81.643	2600	3211	1	chr1D.!!$R1	611
2	TraesCS1D01G009700	chr1B	8116585	8118511	1926	False	1361.5	1517	94.315	875	2718	2	chr1B.!!$F1	1843
3	TraesCS1D01G009700	chr4D	232694681	232695552	871	True	1317.0	1317	94.044	1	867	1	chr4D.!!$R1	866
4	TraesCS1D01G009700	chr4D	461474142	461475012	870	False	1256.0	1256	92.792	1	868	1	chr4D.!!$F1	867
5	TraesCS1D01G009700	chr2D	306476663	306477534	871	False	1295.0	1295	93.578	1	866	1	chr2D.!!$F1	865
6	TraesCS1D01G009700	chr2D	346101726	346102602	876	True	1243.0	1243	92.395	1	872	1	chr2D.!!$R1	871
7	TraesCS1D01G009700	chr7D	621970770	621971645	875	True	1275.0	1275	93.044	1	870	1	chr7D.!!$R1	869
8	TraesCS1D01G009700	chr2B	638014865	638015739	874	True	1273.0	1273	93.044	1	869	1	chr2B.!!$R1	868
9	TraesCS1D01G009700	chr6D	191800828	191801703	875	True	1267.0	1267	92.922	1	869	1	chr6D.!!$R1	868
10	TraesCS1D01G009700	chr7B	267255384	267256258	874	False	1262.0	1262	92.808	1	869	1	chr7B.!!$F2	868
11	TraesCS1D01G009700	chr7B	168964836	168965709	873	False	1251.0	1251	92.580	1	870	1	chr7B.!!$F1	869

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
552	558	0.109643	CGTTGATCCGTACGTGGTCA	60.110	55.0	15.21	14.2	33.33	4.02	F
1330	1347	0.108329	TCGGATTTCACGCCTCCTTC	60.108	55.0	0.00	0.0	0.00	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1727	1744	0.307760	GGAGACAAACTGCACGTTGG	59.692	55.0	8.95	5.9	35.61	3.77	R
3242	3342	0.104304	ACGATCTCGCGGCCTTATTT	59.896	50.0	6.13	0.0	44.43	1.40	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	2.285083	CCCGATCAATTACGCTGGAAA	58.715	47.619	0.00	0.00	0.00	3.13
79	80	5.105675	GGAAACTTACTAGGTCTGGAGAGTG	60.106	48.000	0.00	0.00	0.00	3.51
107	108	8.820933	ACAGTTAAATCAATGTATCTCGATGTG	58.179	33.333	0.00	0.00	0.00	3.21
161	162	3.601435	TGTTTCGACAGTCAAAGTTCCA	58.399	40.909	0.41	0.00	0.00	3.53
253	254	4.012374	CGTAACTGGACAGGACCTACTAA	58.988	47.826	4.14	0.00	0.00	2.24
263	264	6.014755	GGACAGGACCTACTAAGTGTAGTTTT	60.015	42.308	0.00	0.00	45.36	2.43
309	310	3.882888	ACACCTTTTTCTTGATTGCTCGA	59.117	39.130	0.00	0.00	0.00	4.04
326	327	3.535561	CTCGATGGCCAAAGTTCTATGT	58.464	45.455	10.96	0.00	0.00	2.29
348	349	2.359900	GGACAGTCCACATAGCCTTTG	58.640	52.381	15.43	0.00	36.28	2.77
366	372	4.275936	CCTTTGACATTTCCGAGTTCTGTT	59.724	41.667	0.00	0.00	0.00	3.16
545	551	1.693083	GCCACTGCGTTGATCCGTAC	61.693	60.000	0.00	0.00	0.00	3.67
552	558	0.109643	CGTTGATCCGTACGTGGTCA	60.110	55.000	15.21	14.20	33.33	4.02
641	647	3.680475	CGGGATATCTTCAACCGGTTTGA	60.680	47.826	19.55	16.31	42.83	2.69
694	700	8.882415	TTAGTTTACCTATCTTTCTTATGCCG	57.118	34.615	0.00	0.00	0.00	5.69
699	705	0.468226	ATCTTTCTTATGCCGGCCGA	59.532	50.000	30.73	8.21	0.00	5.54
800	811	7.597288	AGACCTTGTTAAACCTATTTGCTTT	57.403	32.000	0.00	0.00	0.00	3.51
902	913	6.000891	TCTTGTATTCTTGTGTGACAATGC	57.999	37.500	0.00	0.00	37.48	3.56
906	917	2.524569	TCTTGTGTGACAATGCTCGA	57.475	45.000	0.00	0.00	37.48	4.04
908	919	2.802247	TCTTGTGTGACAATGCTCGAAG	59.198	45.455	0.00	0.00	37.48	3.79
929	940	6.463897	CGAAGAATATAAAAGGGCTAGGTGGA	60.464	42.308	0.00	0.00	0.00	4.02
944	960	1.202770	GGTGGAAAGACCCCCATATCG	60.203	57.143	0.00	0.00	38.00	2.92
949	965	3.630769	GGAAAGACCCCCATATCGAAAAC	59.369	47.826	0.00	0.00	0.00	2.43
956	972	3.434453	CCCCCATATCGAAAACTTGCCTA	60.434	47.826	0.00	0.00	0.00	3.93
957	973	3.564225	CCCCATATCGAAAACTTGCCTAC	59.436	47.826	0.00	0.00	0.00	3.18
967	983	4.347360	AAACTTGCCTACCTACGAGTTT	57.653	40.909	3.15	3.15	42.84	2.66

Showing 1 to 25 of 150 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	4.661247	ACACTCTCCAGACCTAGTAAGT	57.339	45.455	0.00	0.00	0.00	2.24
107	108	9.855021	GAACTAGGAATAGAGCTAGAATTGATC	57.145	37.037	0.00	0.00	0.00	2.92
145	146	4.811555	TTCAATGGAACTTTGACTGTCG	57.188	40.909	2.98	0.00	0.00	4.35
161	162	9.589111	AACCACGTAAACACTTTAATTTTCAAT	57.411	25.926	0.00	0.00	0.00	2.57
181	182	6.050454	TGACTTGTTTATGTACAAACCACG	57.950	37.500	0.00	0.00	37.55	4.94
253	254	4.345859	TCCCGATCACAAAAACTACACT	57.654	40.909	0.00	0.00	0.00	3.55
263	264	5.351948	TGATAGTTTCATCCCGATCACAA	57.648	39.130	0.00	0.00	0.00	3.33
309	310	2.238646	TCCGACATAGAACTTTGGCCAT	59.761	45.455	6.09	0.00	0.00	4.40
326	327	0.324368	AGGCTATGTGGACTGTCCGA	60.324	55.000	21.15	11.21	40.17	4.55
348	349	3.994392	TGCTAACAGAACTCGGAAATGTC	59.006	43.478	0.00	0.00	0.00	3.06
545	551	0.168348	CGGAGTGAGTAGTGACCACG	59.832	60.000	0.00	0.00	34.07	4.94
552	558	3.156157	CTCCGTCGGAGTGAGTAGT	57.844	57.895	29.66	0.00	44.25	2.73
641	647	4.640771	ATCCTATTACATGACCGCCATT	57.359	40.909	0.00	0.00	31.94	3.16
699	705	4.141733	ACAAACTAGCCAAAAAGCCACAAT	60.142	37.500	0.00	0.00	0.00	2.71
800	811	5.899120	TGCATACGGCCAACTTTATAAAA	57.101	34.783	2.24	0.00	43.89	1.52
869	880	8.446273	CACACAAGAATACAAGATAACAAGAGG	58.554	37.037	0.00	0.00	0.00	3.69
870	881	9.208022	TCACACAAGAATACAAGATAACAAGAG	57.792	33.333	0.00	0.00	0.00	2.85
871	882	8.988934	GTCACACAAGAATACAAGATAACAAGA	58.011	33.333	0.00	0.00	0.00	3.02
872	883	8.773645	TGTCACACAAGAATACAAGATAACAAG	58.226	33.333	0.00	0.00	0.00	3.16
873	884	8.669946	TGTCACACAAGAATACAAGATAACAA	57.330	30.769	0.00	0.00	0.00	2.83
878	889	6.432162	AGCATTGTCACACAAGAATACAAGAT	59.568	34.615	0.00	0.00	41.94	2.40
902	913	6.647067	CACCTAGCCCTTTTATATTCTTCGAG	59.353	42.308	0.00	0.00	0.00	4.04
906	917	6.841781	TCCACCTAGCCCTTTTATATTCTT	57.158	37.500	0.00	0.00	0.00	2.52
908	919	7.228906	GTCTTTCCACCTAGCCCTTTTATATTC	59.771	40.741	0.00	0.00	0.00	1.75
929	940	4.586306	AGTTTTCGATATGGGGGTCTTT	57.414	40.909	0.00	0.00	0.00	2.52

Showing 1 to 25 of 184 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.