AutoCloner

Multiple sequence alignment - TraesCS5D01G045400

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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	TraesCS5D01G045400	chr5D	100.000	3653	0	0	1	3653	44702659	44699007	0.000000e+00	6746
1	TraesCS5D01G045400	chr5D	91.551	2083	133	19	1404	3473	87541734	87539682	0.000000e+00	2832
2	TraesCS5D01G045400	chr5D	91.057	2091	133	24	1404	3473	122061306	122059249	0.000000e+00	2776
3	TraesCS5D01G045400	chr5D	88.672	768	56	15	2904	3653	44633194	44632440	0.000000e+00	907
4	TraesCS5D01G045400	chr5B	96.769	2538	56	4	830	3364	44467975	44465461	0.000000e+00	4209
5	TraesCS5D01G045400	chr5B	90.031	652	20	17	159	779	44469067	44468430	0.000000e+00	802
6	TraesCS5D01G045400	chr5B	98.264	288	5	0	3366	3653	44465303	44465016	4.210000e-139	505
7	TraesCS5D01G045400	chr5B	89.796	147	14	1	21	167	44469801	44469656	1.730000e-43	187
8	TraesCS5D01G045400	chr5A	90.075	2680	183	38	987	3653	35196041	35193432	0.000000e+00	3398
9	TraesCS5D01G045400	chr5A	90.000	2090	158	23	1402	3473	80511652	80509596	0.000000e+00	2654
10	TraesCS5D01G045400	chr5A	90.482	1765	105	24	1723	3473	121720857	121719142	0.000000e+00	2270
11	TraesCS5D01G045400	chr5A	87.470	415	41	8	1404	1808	121721271	121720858	5.520000e-128	468
12	TraesCS5D01G045400	chr5A	90.189	265	15	5	706	970	35197701	35197448	5.840000e-88	335
13	TraesCS5D01G045400	chr5A	90.909	165	2	1	390	554	35197847	35197696	3.700000e-50	209
14	TraesCS5D01G045400	chr7B	92.946	2013	126	13	1648	3653	726155661	726153658	0.000000e+00	2916
15	TraesCS5D01G045400	chr7B	86.202	645	52	14	987	1623	726156445	726155830	0.000000e+00	664
16	TraesCS5D01G045400	chr7D	92.108	2040	119	17	1649	3653	626378137	626376105	0.000000e+00	2837
17	TraesCS5D01G045400	chr7D	86.202	645	50	15	987	1623	626378938	626378325	0.000000e+00	662
18	TraesCS5D01G045400	chr7D	86.307	241	21	8	233	472	626381988	626381759	6.060000e-63	252
19	TraesCS5D01G045400	chr7A	91.908	2039	124	24	1649	3653	721920473	721918442	0.000000e+00	2813
20	TraesCS5D01G045400	chr7A	86.997	323	23	10	987	1309	721921457	721921154	2.700000e-91	346

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	TraesCS5D01G045400	chr5D	44699007	44702659	3652	True	6746.000000	6746	100.000000	1	3653	1	chr5D.!!$R2	3652
1	TraesCS5D01G045400	chr5D	87539682	87541734	2052	True	2832.000000	2832	91.551000	1404	3473	1	chr5D.!!$R3	2069
2	TraesCS5D01G045400	chr5D	122059249	122061306	2057	True	2776.000000	2776	91.057000	1404	3473	1	chr5D.!!$R4	2069
3	TraesCS5D01G045400	chr5D	44632440	44633194	754	True	907.000000	907	88.672000	2904	3653	1	chr5D.!!$R1	749
4	TraesCS5D01G045400	chr5B	44465016	44469801	4785	True	1425.750000	4209	93.715000	21	3653	4	chr5B.!!$R1	3632
5	TraesCS5D01G045400	chr5A	80509596	80511652	2056	True	2654.000000	2654	90.000000	1402	3473	1	chr5A.!!$R1	2071
6	TraesCS5D01G045400	chr5A	121719142	121721271	2129	True	1369.000000	2270	88.976000	1404	3473	2	chr5A.!!$R3	2069
7	TraesCS5D01G045400	chr5A	35193432	35197847	4415	True	1314.000000	3398	90.391000	390	3653	3	chr5A.!!$R2	3263
8	TraesCS5D01G045400	chr7B	726153658	726156445	2787	True	1790.000000	2916	89.574000	987	3653	2	chr7B.!!$R1	2666
9	TraesCS5D01G045400	chr7D	626376105	626381988	5883	True	1250.333333	2837	88.205667	233	3653	3	chr7D.!!$R1	3420
10	TraesCS5D01G045400	chr7A	721918442	721921457	3015	True	1579.500000	2813	89.452500	987	3653	2	chr7A.!!$R1	2666

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
163	760	1.140312	TTATGCCTGATGGGAGGTCC	58.860	55.000	0.00	0.0	37.02	4.46	F
1044	5361	1.266989	GGCAAAGGTACTGCTGTTGTC	59.733	52.381	0.09	0.0	40.86	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1142	5459	0.181587	TTCCGACAATGTGTGGTGGT	59.818	50.000	0.00	0.0	0.0	4.16	R
2734	7507	2.279741	GTACCAATTGATCTGCAGCGA	58.720	47.619	9.47	0.0	0.0	4.93	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
28	29	3.118112	AGGCCTCTATGTCAATTCAGGTG	60.118	47.826	0.00	0.00	0.00	4.00
51	52	4.117685	CAGTGGCTACTAACCCGAATTAC	58.882	47.826	0.95	0.00	34.74	1.89
64	65	7.712204	AACCCGAATTACCTGAATAAACATT	57.288	32.000	0.00	0.00	0.00	2.71
76	77	8.201464	ACCTGAATAAACATTTTCGAGGTTTTT	58.799	29.630	10.41	3.01	39.02	1.94
105	106	4.058817	GCTAGCCGTTATAGTGCTTTGAT	58.941	43.478	2.29	0.00	36.57	2.57
123	124	6.969473	GCTTTGATTTCAGGCTATACAAGTTC	59.031	38.462	0.00	0.00	0.00	3.01
125	126	5.116180	TGATTTCAGGCTATACAAGTTCGG	58.884	41.667	0.00	0.00	0.00	4.30
127	128	2.463752	TCAGGCTATACAAGTTCGGGT	58.536	47.619	0.00	0.00	0.00	5.28
137	138	6.920569	ATACAAGTTCGGGTTTCATGTATC	57.079	37.500	0.00	0.00	29.15	2.24
139	140	3.880047	AGTTCGGGTTTCATGTATCGA	57.120	42.857	0.00	0.00	0.00	3.59
141	142	3.194968	AGTTCGGGTTTCATGTATCGAGT	59.805	43.478	0.00	0.00	0.00	4.18
145	146	4.998672	TCGGGTTTCATGTATCGAGTTTTT	59.001	37.500	0.00	0.00	0.00	1.94
146	147	6.164876	TCGGGTTTCATGTATCGAGTTTTTA	58.835	36.000	0.00	0.00	0.00	1.52
147	148	6.819649	TCGGGTTTCATGTATCGAGTTTTTAT	59.180	34.615	0.00	0.00	0.00	1.40
148	149	6.905076	CGGGTTTCATGTATCGAGTTTTTATG	59.095	38.462	0.00	0.00	0.00	1.90
151	152	7.415206	GGTTTCATGTATCGAGTTTTTATGCCT	60.415	37.037	0.00	0.00	0.00	4.75
152	153	6.603237	TCATGTATCGAGTTTTTATGCCTG	57.397	37.500	0.00	0.00	0.00	4.85
153	154	6.345298	TCATGTATCGAGTTTTTATGCCTGA	58.655	36.000	0.00	0.00	0.00	3.86
154	155	6.992123	TCATGTATCGAGTTTTTATGCCTGAT	59.008	34.615	0.00	0.00	0.00	2.90
157	158	3.278574	TCGAGTTTTTATGCCTGATGGG	58.721	45.455	0.00	0.00	38.36	4.00
163	760	1.140312	TTATGCCTGATGGGAGGTCC	58.860	55.000	0.00	0.00	37.02	4.46
174	771	1.997874	GGAGGTCCATGGTCCTGCT	60.998	63.158	32.45	13.93	38.34	4.24
185	782	4.396166	CCATGGTCCTGCTTGTAACTTTAG	59.604	45.833	2.57	0.00	0.00	1.85
230	845	2.175202	ACTCCCTCTGATCCATATCGC	58.825	52.381	0.00	0.00	34.60	4.58
481	2818	5.200483	GGAATCACCTGATATTTTCCCACA	58.800	41.667	0.00	0.00	33.73	4.17
507	2844	4.051922	AGAAATAGTAAGCCTTGATCGCG	58.948	43.478	0.00	0.00	0.00	5.87
579	2929	2.336809	GCTGGAGCGGAGATACGG	59.663	66.667	0.00	0.00	0.00	4.02
619	2969	3.384014	CTGGTCGAGTCGAGTCGCC	62.384	68.421	32.58	32.05	39.90	5.54
716	3066	4.717313	GGCGAACCCCTCCACCAC	62.717	72.222	0.00	0.00	0.00	4.16
985	5302	4.484872	GGCCCGGCTGACCCTAAC	62.485	72.222	9.86	0.00	0.00	2.34
1039	5356	1.956477	AGTTTGGCAAAGGTACTGCTG	59.044	47.619	13.94	0.00	40.86	4.41
1043	5360	1.318576	GGCAAAGGTACTGCTGTTGT	58.681	50.000	0.09	0.00	40.86	3.32
1044	5361	1.266989	GGCAAAGGTACTGCTGTTGTC	59.733	52.381	0.09	0.00	40.86	3.18
1045	5362	1.946768	GCAAAGGTACTGCTGTTGTCA	59.053	47.619	0.09	0.00	40.86	3.58
1046	5363	2.357637	GCAAAGGTACTGCTGTTGTCAA	59.642	45.455	0.09	0.00	40.86	3.18
1047	5364	3.181491	GCAAAGGTACTGCTGTTGTCAAA	60.181	43.478	0.09	0.00	40.86	2.69
1048	5365	4.676723	GCAAAGGTACTGCTGTTGTCAAAA	60.677	41.667	0.09	0.00	40.86	2.44
1049	5366	5.406649	CAAAGGTACTGCTGTTGTCAAAAA	58.593	37.500	0.09	0.00	40.86	1.94
1126	5443	4.345859	TGCCTCCGTAATTAACTATGGG	57.654	45.455	2.47	0.00	0.00	4.00
1162	5480	1.202879	ACCACCACACATTGTCGGAAT	60.203	47.619	8.45	0.00	0.00	3.01
1410	5914	6.412214	GTGGGTTACTGGATTATGTTACACT	58.588	40.000	0.00	0.00	0.00	3.55
1532	6042	5.572896	CAGTTTTCAAACTTGGACAGTCAAC	59.427	40.000	2.17	0.00	46.52	3.18
1797	6563	7.093992	GCTGGTAGTCCATAATATGACTCTTC	58.906	42.308	1.10	0.00	43.43	2.87
2235	7003	2.802816	CGAAAAGTGAGTCCAAGGACAG	59.197	50.000	20.52	0.00	46.76	3.51
2640	7412	3.377172	CCAAAACCGATGAGATGGGTAAC	59.623	47.826	0.00	0.00	40.77	2.50
3117	7961	0.107831	CGTCAGTTTTGGACCTGGGA	59.892	55.000	0.00	0.00	31.55	4.37
3404	8437	4.664139	CGCAGTTTACTCAGTGATGTTTCG	60.664	45.833	0.00	0.00	0.00	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.946478	ATTGACATAGAGGCCTAGTCAC	57.054	45.455	22.22	4.98	35.16	3.67
1	2	4.962362	TGAATTGACATAGAGGCCTAGTCA	59.038	41.667	19.88	19.88	34.41	3.41
2	3	5.510520	CCTGAATTGACATAGAGGCCTAGTC	60.511	48.000	4.42	12.59	0.00	2.59
3	4	4.346418	CCTGAATTGACATAGAGGCCTAGT	59.654	45.833	4.42	1.48	0.00	2.57
4	5	4.346418	ACCTGAATTGACATAGAGGCCTAG	59.654	45.833	4.42	0.00	0.00	3.02
5	6	4.101585	CACCTGAATTGACATAGAGGCCTA	59.898	45.833	4.42	0.00	0.00	3.93
6	7	3.118112	CACCTGAATTGACATAGAGGCCT	60.118	47.826	3.86	3.86	0.00	5.19
7	8	3.209410	CACCTGAATTGACATAGAGGCC	58.791	50.000	0.00	0.00	0.00	5.19
8	9	2.615912	GCACCTGAATTGACATAGAGGC	59.384	50.000	0.00	0.00	0.00	4.70
9	10	3.875727	CTGCACCTGAATTGACATAGAGG	59.124	47.826	0.00	0.00	0.00	3.69
10	11	4.331992	CACTGCACCTGAATTGACATAGAG	59.668	45.833	0.00	0.00	0.00	2.43
11	12	4.256110	CACTGCACCTGAATTGACATAGA	58.744	43.478	0.00	0.00	0.00	1.98
12	13	3.376234	CCACTGCACCTGAATTGACATAG	59.624	47.826	0.00	0.00	0.00	2.23
13	14	3.346315	CCACTGCACCTGAATTGACATA	58.654	45.455	0.00	0.00	0.00	2.29
14	15	2.165167	CCACTGCACCTGAATTGACAT	58.835	47.619	0.00	0.00	0.00	3.06
15	16	1.608055	CCACTGCACCTGAATTGACA	58.392	50.000	0.00	0.00	0.00	3.58
16	17	0.242017	GCCACTGCACCTGAATTGAC	59.758	55.000	0.00	0.00	37.47	3.18
17	18	0.111061	AGCCACTGCACCTGAATTGA	59.889	50.000	0.00	0.00	41.13	2.57
18	19	1.470098	GTAGCCACTGCACCTGAATTG	59.530	52.381	0.00	0.00	41.13	2.32
19	20	1.352352	AGTAGCCACTGCACCTGAATT	59.648	47.619	0.00	0.00	41.13	2.17
28	29	0.248289	TTCGGGTTAGTAGCCACTGC	59.752	55.000	5.32	0.00	42.23	4.40
51	52	8.487176	CAAAAACCTCGAAAATGTTTATTCAGG	58.513	33.333	0.00	0.00	32.26	3.86
64	65	4.712122	AGCAGTTTCAAAAACCTCGAAA	57.288	36.364	0.00	0.00	0.00	3.46
76	77	4.430007	CACTATAACGGCTAGCAGTTTCA	58.570	43.478	32.90	19.63	35.99	2.69
105	106	3.262405	ACCCGAACTTGTATAGCCTGAAA	59.738	43.478	0.00	0.00	0.00	2.69
123	124	4.939509	AAAACTCGATACATGAAACCCG	57.060	40.909	0.00	0.00	0.00	5.28
125	126	6.691388	GGCATAAAAACTCGATACATGAAACC	59.309	38.462	0.00	0.00	0.00	3.27
127	128	7.335673	TCAGGCATAAAAACTCGATACATGAAA	59.664	33.333	0.00	0.00	0.00	2.69
137	138	3.278574	TCCCATCAGGCATAAAAACTCG	58.721	45.455	0.00	0.00	34.51	4.18
139	140	3.011708	ACCTCCCATCAGGCATAAAAACT	59.988	43.478	0.00	0.00	36.98	2.66
141	142	3.627237	GGACCTCCCATCAGGCATAAAAA	60.627	47.826	0.00	0.00	36.98	1.94
145	146	0.030195	TGGACCTCCCATCAGGCATA	60.030	55.000	0.00	0.00	40.82	3.14
146	147	1.308128	TGGACCTCCCATCAGGCAT	60.308	57.895	0.00	0.00	40.82	4.40
147	148	2.124768	TGGACCTCCCATCAGGCA	59.875	61.111	0.00	0.00	40.82	4.75
157	158	0.393537	CAAGCAGGACCATGGACCTC	60.394	60.000	29.97	23.11	38.15	3.85
163	760	5.003804	ACTAAAGTTACAAGCAGGACCATG	58.996	41.667	0.00	0.00	0.00	3.66
185	782	7.362802	AGTAGAAAGATCCCATAGGTGTAAC	57.637	40.000	0.00	0.00	0.00	2.50
230	845	1.944177	ACTCCCTCCGATCCATATGG	58.056	55.000	16.25	16.25	0.00	2.74
298	913	4.002982	TGCGTTAATTGCTCTGACAGATT	58.997	39.130	5.42	0.00	0.00	2.40
299	914	3.372206	GTGCGTTAATTGCTCTGACAGAT	59.628	43.478	5.42	0.00	0.00	2.90
481	2818	5.812642	CGATCAAGGCTTACTATTTCTGTGT	59.187	40.000	0.00	0.00	0.00	3.72
507	2844	1.209504	TGGATTGGATCTCACGGTTCC	59.790	52.381	0.00	0.00	35.06	3.62
555	2892	3.965539	CTCCGCTCCAGCAGGTTGG	62.966	68.421	0.00	0.00	42.21	3.77
579	2929	0.247974	CATGTCGGTCTCGGTCGTAC	60.248	60.000	0.00	0.00	36.95	3.67
619	2969	1.277557	GCAGGGGCAGAGGATACATAG	59.722	57.143	0.00	0.00	40.72	2.23
985	5302	0.820226	TCCATCAGACTGAAGCTCGG	59.180	55.000	9.70	5.68	0.00	4.63
1039	5356	6.645700	TCTGCATTTTGAGTTTTTGACAAC	57.354	33.333	0.00	0.00	0.00	3.32
1043	5360	7.903995	ACTTTTCTGCATTTTGAGTTTTTGA	57.096	28.000	0.00	0.00	0.00	2.69
1044	5361	8.872845	ACTACTTTTCTGCATTTTGAGTTTTTG	58.127	29.630	0.00	0.00	0.00	2.44
1126	5443	8.948145	TGTGTGGTGGTATAATTGTATAAACAC	58.052	33.333	7.78	7.78	34.61	3.32
1142	5459	0.181587	TTCCGACAATGTGTGGTGGT	59.818	50.000	0.00	0.00	0.00	4.16
1143	5460	1.533625	ATTCCGACAATGTGTGGTGG	58.466	50.000	0.00	0.00	0.00	4.61
1144	5461	3.004210	TCAAATTCCGACAATGTGTGGTG	59.996	43.478	0.00	0.00	0.00	4.17
1162	5480	9.142014	TCTTTAAAGGTGAGAAATCCATTCAAA	57.858	29.630	15.13	0.00	40.72	2.69
1313	5817	8.846211	TCAAAAGACAGATACCTTACAAAAAGG	58.154	33.333	2.23	2.23	43.05	3.11
1510	6019	4.862574	GGTTGACTGTCCAAGTTTGAAAAC	59.137	41.667	5.17	0.00	40.07	2.43
1532	6042	9.793252	CTCAAAATATCAAATGTAGGACAAAGG	57.207	33.333	0.00	0.00	0.00	3.11
1619	6295	5.221880	TGCACAACAGAAAATATTGCTGTC	58.778	37.500	18.95	10.72	41.65	3.51
1940	6706	5.247564	TCCTTCTCCTTTCCGAATTTCAGTA	59.752	40.000	0.00	0.00	0.00	2.74
2070	6836	2.436173	AGGGTAAATCTACTGGAGCAGC	59.564	50.000	0.00	0.00	34.37	5.25
2640	7412	6.388278	AGAAAAGTGTAGCTAACTAAGTCCG	58.612	40.000	0.00	0.00	0.00	4.79
2734	7507	2.279741	GTACCAATTGATCTGCAGCGA	58.720	47.619	9.47	0.00	0.00	4.93
3117	7961	7.814264	AGTGAGACTGAAGAAATGAAATTGT	57.186	32.000	0.00	0.00	36.10	2.71
3214	8073	7.752239	CCATATATTAAAGAAAATCAGCAGGCG	59.248	37.037	0.00	0.00	0.00	5.52
3404	8437	6.129009	GCAAATGGCATATGATGATTTCGAAC	60.129	38.462	6.97	0.00	43.97	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.