AutoCloner

Multiple sequence alignment - TraesCS3B01G296400

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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	TraesCS3B01G296400	chr3B	100.000	2780	0	0	1	2780	474996355	474999134	0.000000e+00	5134.0
1	TraesCS3B01G296400	chr3B	78.824	170	32	1	255	420	238116882	238116713	8.140000e-21	111.0
2	TraesCS3B01G296400	chr3D	95.334	2079	54	13	472	2544	364733634	364735675	0.000000e+00	3262.0
3	TraesCS3B01G296400	chr3D	83.969	524	61	15	1	512	364733129	364733641	5.390000e-132	481.0
4	TraesCS3B01G296400	chr3D	94.089	203	9	1	2578	2780	364735675	364735874	3.480000e-79	305.0
5	TraesCS3B01G296400	chr3D	79.641	167	27	5	243	405	105497306	105497469	2.260000e-21	113.0
6	TraesCS3B01G296400	chr3A	94.448	1801	49	12	423	2218	486044064	486045818	0.000000e+00	2724.0
7	TraesCS3B01G296400	chr3A	94.297	491	19	3	2275	2765	486045818	486046299	0.000000e+00	743.0
8	TraesCS3B01G296400	chr3A	85.612	417	55	4	1	412	486042108	486042524	1.530000e-117	433.0
9	TraesCS3B01G296400	chr1D	83.721	172	21	4	256	421	489752289	489752119	3.710000e-34	156.0
10	TraesCS3B01G296400	chr5B	80.723	166	28	1	256	417	376023377	376023542	2.910000e-25	126.0
11	TraesCS3B01G296400	chr7B	81.410	156	24	2	254	405	446189572	446189418	3.760000e-24	122.0
12	TraesCS3B01G296400	chr2A	79.191	173	32	2	253	421	690720022	690719850	1.750000e-22	117.0
13	TraesCS3B01G296400	chr2B	79.070	172	32	3	253	420	356305689	356305518	6.290000e-22	115.0
14	TraesCS3B01G296400	chr7A	82.051	117	11	7	57	173	279124104	279123998	1.060000e-14	91.6
15	TraesCS3B01G296400	chr6A	90.476	42	4	0	53	94	432710176	432710217	3.870000e-04	56.5
16	TraesCS3B01G296400	chr7D	100.000	28	0	0	57	84	258188483	258188456	5.000000e-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	TraesCS3B01G296400	chr3B	474996355	474999134	2779	False	5134.000000	5134	100.000000	1	2780	1	chr3B.!!$F1	2779
1	TraesCS3B01G296400	chr3D	364733129	364735874	2745	False	1349.333333	3262	91.130667	1	2780	3	chr3D.!!$F2	2779
2	TraesCS3B01G296400	chr3A	486042108	486046299	4191	False	1300.000000	2724	91.452333	1	2765	3	chr3A.!!$F1	2764

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
101	102	0.250234	CCATCCGTGTCCACATGTCT	59.750	55.0	0.0	0.0	0.00	3.41	F
427	1961	0.401395	TGGTGGACTGGGACTTTCCT	60.401	55.0	0.0	0.0	36.57	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1643	3218	1.218316	GAGTCCGGCGTCAAATCCT	59.782	57.895	6.01	0.0	0.0	3.24	R
2344	3920	0.664166	GCAATGCAACAGGTCCAACG	60.664	55.000	0.00	0.0	0.0	4.10	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
28	29	4.932200	GTCTGACAACATTTCTTCTCCGAT	59.068	41.667	2.24	0.00	0.00	4.18
50	51	1.668826	TGAAGGGGCTAGGACATGTT	58.331	50.000	0.00	0.00	0.00	2.71
51	52	1.992557	TGAAGGGGCTAGGACATGTTT	59.007	47.619	0.00	0.00	0.00	2.83
101	102	0.250234	CCATCCGTGTCCACATGTCT	59.750	55.000	0.00	0.00	0.00	3.41
108	109	2.807967	CGTGTCCACATGTCTGTTTGAT	59.192	45.455	0.00	0.00	31.62	2.57
119	120	3.258123	TGTCTGTTTGATGACTCGGATGA	59.742	43.478	0.00	0.00	34.57	2.92
213	215	5.238432	ACACAATACAATCAAAGTCGCTCAA	59.762	36.000	0.00	0.00	0.00	3.02
218	220	5.940192	ACAATCAAAGTCGCTCAAATACA	57.060	34.783	0.00	0.00	0.00	2.29
220	222	4.946784	ATCAAAGTCGCTCAAATACACC	57.053	40.909	0.00	0.00	0.00	4.16
304	306	4.771590	TTTACGAAGTCACCATAGACGT	57.228	40.909	0.00	0.00	43.93	4.34
316	318	1.062148	CATAGACGTCTCGCAGTCGAA	59.938	52.381	23.89	0.52	44.98	3.71
318	320	0.522180	AGACGTCTCGCAGTCGAAAT	59.478	50.000	13.58	0.00	44.98	2.17
346	352	3.469008	TTCACTGAACGAACATCACCT	57.531	42.857	0.00	0.00	0.00	4.00
350	356	3.559655	CACTGAACGAACATCACCTGAAA	59.440	43.478	0.00	0.00	0.00	2.69
360	366	6.094048	CGAACATCACCTGAAACCTGAAATAT	59.906	38.462	0.00	0.00	0.00	1.28
361	367	6.764308	ACATCACCTGAAACCTGAAATATG	57.236	37.500	0.00	0.00	0.00	1.78
376	382	8.621286	ACCTGAAATATGTTTAGGAATAAAGCG	58.379	33.333	13.49	0.00	32.86	4.68
386	392	4.150897	AGGAATAAAGCGAGCACCAATA	57.849	40.909	0.00	0.00	0.00	1.90
397	403	4.786609	GCGAGCACCAATATCAAGTTTAGC	60.787	45.833	0.00	0.00	0.00	3.09
415	421	3.733443	AGCACTTGAATTTTGGTGGAC	57.267	42.857	0.00	0.00	0.00	4.02
416	422	3.299503	AGCACTTGAATTTTGGTGGACT	58.700	40.909	0.00	0.00	0.00	3.85
417	423	3.068590	AGCACTTGAATTTTGGTGGACTG	59.931	43.478	0.00	0.00	0.00	3.51
418	424	3.799917	GCACTTGAATTTTGGTGGACTGG	60.800	47.826	0.00	0.00	0.00	4.00
419	425	2.965147	ACTTGAATTTTGGTGGACTGGG	59.035	45.455	0.00	0.00	0.00	4.45
420	426	3.230134	CTTGAATTTTGGTGGACTGGGA	58.770	45.455	0.00	0.00	0.00	4.37
425	1959	2.358322	TTTGGTGGACTGGGACTTTC	57.642	50.000	0.00	0.00	0.00	2.62
427	1961	0.401395	TGGTGGACTGGGACTTTCCT	60.401	55.000	0.00	0.00	36.57	3.36
430	1964	1.700186	GTGGACTGGGACTTTCCTTCT	59.300	52.381	0.00	0.00	36.57	2.85
431	1965	1.978580	TGGACTGGGACTTTCCTTCTC	59.021	52.381	0.00	0.00	36.57	2.87
435	1969	4.006319	GACTGGGACTTTCCTTCTCAATG	58.994	47.826	0.00	0.00	36.57	2.82
442	1976	5.152623	ACTTTCCTTCTCAATGATCGTCA	57.847	39.130	0.00	0.00	0.00	4.35
452	1986	5.578336	TCTCAATGATCGTCACATGTCTTTC	59.422	40.000	0.00	0.00	0.00	2.62
837	2408	6.015095	CAGCAGGGGTAGAAAAGAAGAAATTT	60.015	38.462	0.00	0.00	0.00	1.82
1596	3171	4.844522	GGCGTCTTATTCGAGTTTTTGTTC	59.155	41.667	0.00	0.00	0.00	3.18
1619	3194	6.815089	TCTTGTTATTGTTGGAATTGCAGTT	58.185	32.000	0.00	0.00	0.00	3.16
1643	3218	0.044092	TGCCCTGGATTGTCCCTAGA	59.956	55.000	0.00	0.00	35.03	2.43
1701	3277	3.721087	AGGAACAAGGGATCGTTTGAT	57.279	42.857	12.98	3.27	37.60	2.57
1702	3278	4.034285	AGGAACAAGGGATCGTTTGATT	57.966	40.909	12.98	5.54	34.09	2.57
1724	3300	1.872388	TCTTGTCGCAATTCGGTTCA	58.128	45.000	0.00	0.00	39.05	3.18
1991	3567	9.112725	GGAGTTGGTGAGTAGTTTAAAGTTAAA	57.887	33.333	0.00	0.00	0.00	1.52
2155	3731	2.418197	GCTTCATTGTAGCGGTGAGGTA	60.418	50.000	0.00	0.00	0.00	3.08
2170	3746	6.369615	GCGGTGAGGTATTTTAAGTGTTCTTA	59.630	38.462	0.00	0.00	35.36	2.10
2196	3772	6.583427	TGCATTGATCACATTTCTTTTCTTCG	59.417	34.615	0.00	0.00	0.00	3.79
2415	3991	5.131475	TGATCCTTATTAGGTGGGGTGTAAC	59.869	44.000	0.00	0.00	42.60	2.50
2449	4027	2.297701	ACATGGGCATTAATCCGTGAC	58.702	47.619	17.93	0.00	41.33	3.67
2450	4028	2.092429	ACATGGGCATTAATCCGTGACT	60.092	45.455	17.93	0.00	41.33	3.41
2470	4048	9.825972	CGTGACTGTTTCTTATATGAAATTGTT	57.174	29.630	14.74	3.33	38.09	2.83
2569	4147	4.852134	TTGCTTGTTGTGATTGCATACT	57.148	36.364	0.00	0.00	33.50	2.12
2570	4148	4.852134	TGCTTGTTGTGATTGCATACTT	57.148	36.364	0.00	0.00	0.00	2.24
2571	4149	5.199024	TGCTTGTTGTGATTGCATACTTT	57.801	34.783	0.00	0.00	0.00	2.66
2572	4150	5.221880	TGCTTGTTGTGATTGCATACTTTC	58.778	37.500	0.00	0.00	0.00	2.62
2573	4151	4.622740	GCTTGTTGTGATTGCATACTTTCC	59.377	41.667	0.00	0.00	0.00	3.13
2602	4180	7.594714	TCGGCTTAGCAAACATAAAACAATAA	58.405	30.769	6.53	0.00	0.00	1.40
2672	4250	8.033038	TGTACTCTGATAGGTTACACATGTTTC	58.967	37.037	0.00	0.00	0.00	2.78
2765	4344	1.635487	TGGCCATCTCCTAGTTTTGCT	59.365	47.619	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	4.893608	TCATCGGAGAAGAAATGTTGTCA	58.106	39.130	0.00	0.00	43.58	3.58
28	29	1.770658	CATGTCCTAGCCCCTTCATCA	59.229	52.381	0.00	0.00	0.00	3.07
50	51	2.630580	GGTGCTACCCCATTTGAAACAA	59.369	45.455	0.00	0.00	30.04	2.83
51	52	2.243810	GGTGCTACCCCATTTGAAACA	58.756	47.619	0.00	0.00	30.04	2.83
101	102	4.001618	TGTTCATCCGAGTCATCAAACA	57.998	40.909	0.00	0.00	0.00	2.83
133	135	2.037511	AGACCCAAACGGACACGAAATA	59.962	45.455	0.00	0.00	44.60	1.40
213	215	2.171870	CGTTCATAGGGGTGGGTGTATT	59.828	50.000	0.00	0.00	0.00	1.89
218	220	1.921346	TGCGTTCATAGGGGTGGGT	60.921	57.895	0.00	0.00	0.00	4.51
220	222	1.813753	CGTGCGTTCATAGGGGTGG	60.814	63.158	0.00	0.00	0.00	4.61
252	254	5.825679	AGATGCTATGTCGACTTAGTCTCTT	59.174	40.000	28.88	16.30	0.00	2.85
316	318	5.584649	TGTTCGTTCAGTGAAAGAAGACATT	59.415	36.000	27.57	0.00	39.71	2.71
318	320	4.500127	TGTTCGTTCAGTGAAAGAAGACA	58.500	39.130	27.57	22.09	39.71	3.41
350	356	8.621286	CGCTTTATTCCTAAACATATTTCAGGT	58.379	33.333	0.00	0.00	0.00	4.00
360	366	3.687698	GGTGCTCGCTTTATTCCTAAACA	59.312	43.478	0.00	0.00	0.00	2.83
361	367	3.687698	TGGTGCTCGCTTTATTCCTAAAC	59.312	43.478	0.00	0.00	0.00	2.01
373	379	2.698855	ACTTGATATTGGTGCTCGCT	57.301	45.000	0.00	0.00	0.00	4.93
376	382	5.355350	AGTGCTAAACTTGATATTGGTGCTC	59.645	40.000	0.00	0.00	34.57	4.26
397	403	3.243839	CCCAGTCCACCAAAATTCAAGTG	60.244	47.826	0.00	0.00	0.00	3.16
405	411	2.661718	GAAAGTCCCAGTCCACCAAAA	58.338	47.619	0.00	0.00	0.00	2.44
407	413	0.476771	GGAAAGTCCCAGTCCACCAA	59.523	55.000	0.00	0.00	0.00	3.67
412	418	1.978580	TGAGAAGGAAAGTCCCAGTCC	59.021	52.381	0.00	0.00	37.19	3.85
415	421	4.292186	TCATTGAGAAGGAAAGTCCCAG	57.708	45.455	0.00	0.00	37.19	4.45
416	422	4.623886	CGATCATTGAGAAGGAAAGTCCCA	60.624	45.833	0.00	0.00	37.19	4.37
417	423	3.873952	CGATCATTGAGAAGGAAAGTCCC	59.126	47.826	0.00	0.00	37.19	4.46
418	424	4.508662	ACGATCATTGAGAAGGAAAGTCC	58.491	43.478	0.00	0.00	36.58	3.85
419	425	5.062809	GTGACGATCATTGAGAAGGAAAGTC	59.937	44.000	0.00	0.00	34.54	3.01
420	426	4.932200	GTGACGATCATTGAGAAGGAAAGT	59.068	41.667	0.00	0.00	0.00	2.66
425	1959	4.186926	ACATGTGACGATCATTGAGAAGG	58.813	43.478	0.00	0.00	0.00	3.46
427	1961	5.077134	AGACATGTGACGATCATTGAGAA	57.923	39.130	1.15	0.00	0.00	2.87
430	1964	5.120674	GTGAAAGACATGTGACGATCATTGA	59.879	40.000	1.15	0.00	0.00	2.57
431	1965	5.319139	GTGAAAGACATGTGACGATCATTG	58.681	41.667	1.15	0.00	0.00	2.82
435	1969	2.673368	GGGTGAAAGACATGTGACGATC	59.327	50.000	1.15	0.00	0.00	3.69
442	1976	2.999185	ATTGGGGGTGAAAGACATGT	57.001	45.000	0.00	0.00	0.00	3.21
452	1986	2.478831	CACAACGAAAAATTGGGGGTG	58.521	47.619	0.00	0.00	0.00	4.61
837	2408	2.227194	GAAAGGCCAGTTTCTTCCGAA	58.773	47.619	5.01	0.00	34.19	4.30
912	2483	1.811679	CGGAAGGAAGCGAGGAAGC	60.812	63.158	0.00	0.00	37.41	3.86
916	2487	4.840005	GGGCGGAAGGAAGCGAGG	62.840	72.222	0.00	0.00	0.00	4.63
1047	2622	2.124653	GAGGGAGACGGCGAGAGA	60.125	66.667	16.62	0.00	0.00	3.10
1596	3171	6.564499	GCAACTGCAATTCCAACAATAACAAG	60.564	38.462	0.00	0.00	41.59	3.16
1619	3194	1.303561	GACAATCCAGGGCACAGCA	60.304	57.895	0.00	0.00	0.00	4.41
1643	3218	1.218316	GAGTCCGGCGTCAAATCCT	59.782	57.895	6.01	0.00	0.00	3.24
1701	3277	2.489971	ACCGAATTGCGACAAGAAGAA	58.510	42.857	0.00	0.00	44.57	2.52
1702	3278	2.163818	ACCGAATTGCGACAAGAAGA	57.836	45.000	0.00	0.00	44.57	2.87
1724	3300	6.906157	TCTTCAGAGCCAAATCAAAGAAAT	57.094	33.333	0.00	0.00	0.00	2.17
1991	3567	5.422012	CCTACAAGCCCAATAACCAAATTCT	59.578	40.000	0.00	0.00	0.00	2.40
2170	3746	7.274904	CGAAGAAAAGAAATGTGATCAATGCAT	59.725	33.333	0.00	0.00	0.00	3.96
2220	3796	7.095144	CCACAACAACACCACTTACGAATTATA	60.095	37.037	0.00	0.00	0.00	0.98
2228	3804	3.630312	ACATCCACAACAACACCACTTAC	59.370	43.478	0.00	0.00	0.00	2.34
2240	3816	8.556213	TGTACCTTATCTAAAACATCCACAAC	57.444	34.615	0.00	0.00	0.00	3.32
2344	3920	0.664166	GCAATGCAACAGGTCCAACG	60.664	55.000	0.00	0.00	0.00	4.10
2398	3974	3.776417	GGACAGTTACACCCCACCTAATA	59.224	47.826	0.00	0.00	0.00	0.98
2399	3975	2.574824	GGACAGTTACACCCCACCTAAT	59.425	50.000	0.00	0.00	0.00	1.73
2400	3976	1.980036	GGACAGTTACACCCCACCTAA	59.020	52.381	0.00	0.00	0.00	2.69
2415	3991	4.269183	TGCCCATGTAAATAACAGGACAG	58.731	43.478	0.00	0.00	42.55	3.51
2573	4151	4.530094	TTATGTTTGCTAAGCCGATTCG	57.470	40.909	0.00	0.00	0.00	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.