AutoCloner

Multiple sequence alignment - TraesCS5B01G026100

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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	TraesCS5B01G026100	chr5B	100.000	4559	0	0	1	4559	24776551	24771993	0.000000e+00	8419.0
1	TraesCS5B01G026100	chr5B	93.733	2904	139	17	769	3670	24107940	24110802	0.000000e+00	4314.0
2	TraesCS5B01G026100	chr5B	90.006	1541	122	19	595	2111	24147721	24146189	0.000000e+00	1964.0
3	TraesCS5B01G026100	chr5B	93.467	1301	58	11	12	1301	24285611	24284327	0.000000e+00	1906.0
4	TraesCS5B01G026100	chr5B	93.075	982	66	2	2689	3670	24145933	24144954	0.000000e+00	1435.0
5	TraesCS5B01G026100	chr5B	93.262	935	48	11	1	926	24805399	24806327	0.000000e+00	1363.0
6	TraesCS5B01G026100	chr5B	93.373	498	23	4	1835	2330	24283662	24283173	0.000000e+00	728.0
7	TraesCS5B01G026100	chr5B	92.790	319	13	2	2354	2672	24283179	24282871	1.930000e-123	453.0
8	TraesCS5B01G026100	chr5B	90.602	266	20	5	2429	2691	497377194	497377457	9.390000e-92	348.0
9	TraesCS5B01G026100	chr5B	89.434	265	24	4	2430	2692	219821873	219821611	9.450000e-87	331.0
10	TraesCS5B01G026100	chr5B	89.474	266	17	5	2172	2432	24146190	24145931	4.400000e-85	326.0
11	TraesCS5B01G026100	chr5D	93.980	4286	194	20	308	4559	37046195	37050450	0.000000e+00	6427.0
12	TraesCS5B01G026100	chr5D	93.408	4308	204	40	311	4559	33049617	33045331	0.000000e+00	6309.0
13	TraesCS5B01G026100	chr5D	93.526	2873	157	16	822	3688	37040322	37043171	0.000000e+00	4248.0
14	TraesCS5B01G026100	chr5D	93.422	2873	159	18	822	3688	33055484	33052636	0.000000e+00	4231.0
15	TraesCS5B01G026100	chr5D	92.562	1694	104	11	434	2111	33658424	33656737	0.000000e+00	2410.0
16	TraesCS5B01G026100	chr5D	91.442	1297	82	13	2689	3980	33656480	33655208	0.000000e+00	1753.0
17	TraesCS5B01G026100	chr5D	86.381	536	58	12	4034	4559	512211718	512212248	5.120000e-159	571.0
18	TraesCS5B01G026100	chr5D	90.672	268	21	2	569	836	37039994	37040257	2.020000e-93	353.0
19	TraesCS5B01G026100	chr5D	90.037	271	23	2	569	839	33055812	33055546	9.390000e-92	348.0
20	TraesCS5B01G026100	chr5D	82.822	326	24	16	12	310	33658867	33658547	3.500000e-66	263.0
21	TraesCS5B01G026100	chr5D	98.000	50	1	0	311	360	33658506	33658457	2.260000e-13	87.9
22	TraesCS5B01G026100	chr5D	95.349	43	2	0	260	302	33049718	33049676	8.180000e-08	69.4
23	TraesCS5B01G026100	chr5D	95.349	43	2	0	260	302	37046096	37046138	8.180000e-08	69.4
24	TraesCS5B01G026100	chr5A	94.028	2813	139	18	882	3688	22059689	22056900	0.000000e+00	4237.0
25	TraesCS5B01G026100	chr5A	93.907	1231	60	6	882	2111	21440619	21439403	0.000000e+00	1844.0
26	TraesCS5B01G026100	chr5A	93.388	983	64	1	2689	3670	21439146	21438164	0.000000e+00	1454.0
27	TraesCS5B01G026100	chr5A	92.471	518	31	3	311	822	22060319	22059804	0.000000e+00	734.0
28	TraesCS5B01G026100	chr5A	88.390	267	19	5	2172	2432	21439404	21439144	1.230000e-80	311.0
29	TraesCS5B01G026100	chr5A	93.846	130	8	0	501	630	22052604	22052475	3.600000e-46	196.0
30	TraesCS5B01G026100	chr5A	87.234	94	5	2	367	454	22052706	22052614	2.900000e-17	100.0
31	TraesCS5B01G026100	chr5A	95.556	45	2	0	260	304	22060389	22060345	6.330000e-09	73.1
32	TraesCS5B01G026100	chr5A	95.455	44	2	0	469	512	21440997	21440954	2.280000e-08	71.3
33	TraesCS5B01G026100	chr5A	100.000	34	0	0	313	346	22061300	22061267	3.810000e-06	63.9
34	TraesCS5B01G026100	chr5A	100.000	30	0	0	832	861	26809390	26809361	6.370000e-04	56.5
35	TraesCS5B01G026100	chr1D	89.326	534	48	3	4034	4559	480997519	480998051	0.000000e+00	662.0
36	TraesCS5B01G026100	chr7D	88.534	532	56	5	4032	4559	543352731	543353261	1.380000e-179	640.0
37	TraesCS5B01G026100	chr7D	81.614	533	87	10	4034	4559	596974211	596974739	9.060000e-117	431.0
38	TraesCS5B01G026100	chr3D	87.476	527	59	4	4039	4559	398411945	398412470	6.530000e-168	601.0
39	TraesCS5B01G026100	chr3D	86.517	534	63	7	4032	4559	333004975	333005505	3.060000e-161	579.0
40	TraesCS5B01G026100	chr3D	100.000	28	0	0	3673	3700	19538036	19538063	8.000000e-03	52.8
41	TraesCS5B01G026100	chr6A	86.965	537	61	6	4030	4559	430921577	430922111	3.040000e-166	595.0
42	TraesCS5B01G026100	chr6A	100.000	30	0	0	832	861	609610069	609610040	6.370000e-04	56.5
43	TraesCS5B01G026100	chrUn	86.891	534	58	10	4034	4559	21650230	21649701	5.080000e-164	588.0
44	TraesCS5B01G026100	chrUn	95.349	43	2	0	260	302	478151435	478151477	8.180000e-08	69.4
45	TraesCS5B01G026100	chr1B	86.542	535	63	6	4031	4559	564857971	564858502	8.500000e-162	580.0

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	TraesCS5B01G026100	chr5B	24771993	24776551	4558	True	8419.000000	8419	100.000000	1	4559	1	chr5B.!!$R1	4558
1	TraesCS5B01G026100	chr5B	24107940	24110802	2862	False	4314.000000	4314	93.733000	769	3670	1	chr5B.!!$F1	2901
2	TraesCS5B01G026100	chr5B	24805399	24806327	928	False	1363.000000	1363	93.262000	1	926	1	chr5B.!!$F2	925
3	TraesCS5B01G026100	chr5B	24144954	24147721	2767	True	1241.666667	1964	90.851667	595	3670	3	chr5B.!!$R3	3075
4	TraesCS5B01G026100	chr5B	24282871	24285611	2740	True	1029.000000	1906	93.210000	12	2672	3	chr5B.!!$R4	2660
5	TraesCS5B01G026100	chr5D	37039994	37050450	10456	False	2774.350000	6427	93.381750	260	4559	4	chr5D.!!$F2	4299
6	TraesCS5B01G026100	chr5D	33045331	33055812	10481	True	2739.350000	6309	93.054000	260	4559	4	chr5D.!!$R1	4299
7	TraesCS5B01G026100	chr5D	33655208	33658867	3659	True	1128.475000	2410	91.206500	12	3980	4	chr5D.!!$R2	3968
8	TraesCS5B01G026100	chr5D	512211718	512212248	530	False	571.000000	571	86.381000	4034	4559	1	chr5D.!!$F1	525
9	TraesCS5B01G026100	chr5A	22056900	22061300	4400	True	1277.000000	4237	95.513750	260	3688	4	chr5A.!!$R4	3428
10	TraesCS5B01G026100	chr5A	21438164	21440997	2833	True	920.075000	1844	92.785000	469	3670	4	chr5A.!!$R2	3201
11	TraesCS5B01G026100	chr1D	480997519	480998051	532	False	662.000000	662	89.326000	4034	4559	1	chr1D.!!$F1	525
12	TraesCS5B01G026100	chr7D	543352731	543353261	530	False	640.000000	640	88.534000	4032	4559	1	chr7D.!!$F1	527
13	TraesCS5B01G026100	chr7D	596974211	596974739	528	False	431.000000	431	81.614000	4034	4559	1	chr7D.!!$F2	525
14	TraesCS5B01G026100	chr3D	398411945	398412470	525	False	601.000000	601	87.476000	4039	4559	1	chr3D.!!$F3	520
15	TraesCS5B01G026100	chr3D	333004975	333005505	530	False	579.000000	579	86.517000	4032	4559	1	chr3D.!!$F2	527
16	TraesCS5B01G026100	chr6A	430921577	430922111	534	False	595.000000	595	86.965000	4030	4559	1	chr6A.!!$F1	529
17	TraesCS5B01G026100	chrUn	21649701	21650230	529	True	588.000000	588	86.891000	4034	4559	1	chrUn.!!$R1	525
18	TraesCS5B01G026100	chr1B	564857971	564858502	531	False	580.000000	580	86.542000	4031	4559	1	chr1B.!!$F1	528

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
744	6687	2.100087	TCGCGATGTGCCATACTTTAGA	59.900	45.455	3.71	0.00	42.08	2.10	F
807	6773	2.275134	ATGTGTGAATGTGCAGGACA	57.725	45.000	0.00	0.00	39.53	4.02	F
2066	8565	2.098934	TCATTGTTGAACAGGTGCACAC	59.901	45.455	20.43	8.23	0.00	3.82	F
3301	9872	1.781429	CTCTCAGTTCGTGTGTTGTCG	59.219	52.381	0.00	0.00	0.00	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1818	8317	0.109272	TCGGCTCTAGTTGTGCTTCG	60.109	55.000	0.00	0.00	35.67	3.79	R
2128	8629	1.065709	GGTAGGGGAACAATTCGAGCA	60.066	52.381	0.00	0.00	0.00	4.26	R
3502	10073	1.939255	GATAGAGGCAAGCTCAAGCAC	59.061	52.381	4.59	2.34	45.16	4.40	R
4427	11079	3.078594	GGCAACGTTTGAACAGTTCAT	57.921	42.857	16.89	0.00	39.84	2.57	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
713	6650	7.045126	TGACATTCCGTATCATGTGTATGTA	57.955	36.000	0.00	0.00	33.62	2.29
744	6687	2.100087	TCGCGATGTGCCATACTTTAGA	59.900	45.455	3.71	0.00	42.08	2.10
807	6773	2.275134	ATGTGTGAATGTGCAGGACA	57.725	45.000	0.00	0.00	39.53	4.02
947	7071	3.746751	GCTCCACTCATGCCATAATCTGT	60.747	47.826	0.00	0.00	0.00	3.41
1051	7175	6.525578	TGAGACTAACACGGAATAATGACT	57.474	37.500	0.00	0.00	0.00	3.41
1073	7197	4.985538	TGGGTTCTAAGATTGCTCTTTGT	58.014	39.130	0.00	0.00	41.91	2.83
1409	7533	3.549423	CGTCTTACTCAACGTGGTGAGAA	60.549	47.826	21.09	9.96	46.76	2.87
1696	8188	5.030874	ACTCGGAAAATCAAACGACATTC	57.969	39.130	0.00	0.00	0.00	2.67
1909	8408	3.941483	GGTACATTCTGCAACTGCTATGT	59.059	43.478	16.22	16.22	42.66	2.29
1985	8484	9.915629	GGTACAACTATATGGATATATAGCAGC	57.084	37.037	12.08	0.00	46.74	5.25
2066	8565	2.098934	TCATTGTTGAACAGGTGCACAC	59.901	45.455	20.43	8.23	0.00	3.82
2152	8653	2.500098	TCGAATTGTTCCCCTACCTCTG	59.500	50.000	0.00	0.00	0.00	3.35
2181	8743	9.014297	GTTTGATATAGGGTTGAAATCATAGGG	57.986	37.037	0.00	0.00	0.00	3.53
2228	8790	8.850454	TTTGCGCTATAGTTTATTGAAATTCC	57.150	30.769	9.73	0.00	0.00	3.01
2252	8814	6.294731	CCATTCACTTCAACCTTTTAGGAAGG	60.295	42.308	0.00	3.35	40.72	3.46
2274	8836	3.686691	GCTCCTATGCTTTTCCTGTCCAT	60.687	47.826	0.00	0.00	0.00	3.41
2340	8907	5.409826	ACACTCTAATCTTGTGCTTTAGTGC	59.590	40.000	0.00	0.00	36.21	4.40
2393	8961	4.111916	GTCAAACATTTGAGGTGTTGGTG	58.888	43.478	7.30	0.00	46.80	4.17
2394	8962	4.019858	TCAAACATTTGAGGTGTTGGTGA	58.980	39.130	2.89	0.00	41.88	4.02
2395	8963	4.648762	TCAAACATTTGAGGTGTTGGTGAT	59.351	37.500	2.89	0.00	41.88	3.06
2396	8964	4.589216	AACATTTGAGGTGTTGGTGATG	57.411	40.909	0.00	0.00	38.31	3.07
2397	8965	2.892852	ACATTTGAGGTGTTGGTGATGG	59.107	45.455	0.00	0.00	0.00	3.51
2398	8966	2.746279	TTTGAGGTGTTGGTGATGGT	57.254	45.000	0.00	0.00	0.00	3.55
2425	8993	2.019984	GGCACCACCTTGATGATCTTC	58.980	52.381	1.67	1.67	34.51	2.87
2649	9218	8.927721	GGTGAAAGTAGAGATACTTTGACTTTC	58.072	37.037	21.43	15.12	46.26	2.62
2708	9278	6.857956	AGGAGTATCAGTATATGCATTCGTC	58.142	40.000	3.54	0.00	36.25	4.20
3301	9872	1.781429	CTCTCAGTTCGTGTGTTGTCG	59.219	52.381	0.00	0.00	0.00	4.35
3343	9914	2.325583	TCAACTCTTTCGTGGCAGTT	57.674	45.000	0.00	0.00	0.00	3.16
3426	9997	5.009610	GCATTTGAAGTTCAAGGTAGGTCAA	59.990	40.000	17.36	1.24	37.70	3.18
3502	10073	3.050619	GGGTACGACTATCAGCAAATCG	58.949	50.000	0.00	0.00	38.71	3.34
3633	10204	7.148983	CGTGTGTTGCCATAGAAAACAAATAAG	60.149	37.037	0.00	0.00	35.70	1.73
3921	10529	8.626057	TCACACGTGAAAGAGTCAAATGACTAC	61.626	40.741	25.01	9.20	44.89	2.73
3992	10601	9.884636	ACTTAAGATGTACTGTATGTGCAATTA	57.115	29.630	10.09	0.00	44.04	1.40
4037	10646	5.708697	TGATTGTCACTACCGTCTTTAGAGA	59.291	40.000	0.00	0.00	0.00	3.10
4054	10663	2.358247	AAACTCCAACGCGCCGAT	60.358	55.556	5.73	0.00	0.00	4.18
4355	11006	1.636148	ATTGGTTGCCAACATGAGCT	58.364	45.000	10.18	0.00	46.95	4.09
4494	11155	2.777692	TCTCACCCTGAAACTGAAACCT	59.222	45.455	0.00	0.00	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
713	6650	2.417379	GGCACATCGCGATATACTGGAT	60.417	50.000	23.22	0.00	43.84	3.41
744	6687	7.727181	TCTAAATCTTCTATTTAAGCTCGGCT	58.273	34.615	0.00	0.00	42.56	5.52
787	6753	3.415457	TGTCCTGCACATTCACACATA	57.585	42.857	0.00	0.00	0.00	2.29
964	7088	7.175104	AGAATAATCTACAGAAGGCCAAAACA	58.825	34.615	5.01	0.00	32.88	2.83
1051	7175	4.985538	ACAAAGAGCAATCTTAGAACCCA	58.014	39.130	0.00	0.00	0.00	4.51
1696	8188	7.251704	TGTGCAGTTTAGAAAGAAGAAGAAG	57.748	36.000	0.00	0.00	0.00	2.85
1814	8313	1.336887	GCTCTAGTTGTGCTTCGTGGA	60.337	52.381	0.00	0.00	32.89	4.02
1815	8314	1.071605	GCTCTAGTTGTGCTTCGTGG	58.928	55.000	0.00	0.00	32.89	4.94
1818	8317	0.109272	TCGGCTCTAGTTGTGCTTCG	60.109	55.000	0.00	0.00	35.67	3.79
1985	8484	4.136678	CAATGAATCATAACGATCACGCG	58.863	43.478	3.53	3.53	43.96	6.01
2024	8523	1.957177	TGGGATCATCTCTGCTACGAC	59.043	52.381	0.00	0.00	0.00	4.34
2052	8551	3.348119	TGTAAAAGTGTGCACCTGTTCA	58.652	40.909	15.69	9.48	0.00	3.18
2128	8629	1.065709	GGTAGGGGAACAATTCGAGCA	60.066	52.381	0.00	0.00	0.00	4.26
2181	8743	7.311408	CAAATGAATCCCAAGAGAGAGAAAAC	58.689	38.462	0.00	0.00	0.00	2.43
2228	8790	6.681777	CCTTCCTAAAAGGTTGAAGTGAATG	58.318	40.000	0.00	0.00	36.53	2.67
2252	8814	2.293170	GGACAGGAAAAGCATAGGAGC	58.707	52.381	0.00	0.00	0.00	4.70
2274	8836	7.939039	ACAAGAGACTGAAAGGATGTTTGATTA	59.061	33.333	0.00	0.00	39.30	1.75
2340	8907	4.057406	TGCAGGATTCCAAAAAGTGTTG	57.943	40.909	5.29	0.00	0.00	3.33
2657	9226	6.691388	CGGTCCTTTTTAGTTTGCATATAAGC	59.309	38.462	0.00	0.00	0.00	3.09
2708	9278	5.518847	CCTCAAAGCACATGAATTTGCATAG	59.481	40.000	0.00	1.88	41.48	2.23
2718	9288	6.888105	TGTATAAGATCCTCAAAGCACATGA	58.112	36.000	0.00	0.00	0.00	3.07
2777	9348	6.939730	TCATGCAAAGATAACTAACCACAGAA	59.060	34.615	0.00	0.00	0.00	3.02
3343	9914	5.129634	TCTTAAGCCACATGACTCAACAAA	58.870	37.500	0.00	0.00	0.00	2.83
3502	10073	1.939255	GATAGAGGCAAGCTCAAGCAC	59.061	52.381	4.59	2.34	45.16	4.40
4037	10646	2.358247	ATCGGCGCGTTGGAGTTT	60.358	55.556	8.43	0.00	0.00	2.66
4054	10663	3.142951	ACAAAATCATCGTCCGTTTGGA	58.857	40.909	0.00	0.00	43.88	3.53
4321	10971	6.712095	TGGCAACCAATAGATGTATCTTCATC	59.288	38.462	0.00	0.00	42.96	2.92
4323	10973	6.000246	TGGCAACCAATAGATGTATCTTCA	58.000	37.500	0.00	0.00	38.32	3.02
4355	11006	7.492020	GCAAAATGATTTGGTTAGCATATGTGA	59.508	33.333	4.29	0.00	44.93	3.58
4427	11079	3.078594	GGCAACGTTTGAACAGTTCAT	57.921	42.857	16.89	0.00	39.84	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.