AutoCloner

Multiple sequence alignment - TraesCS5B01G087400

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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	TraesCS5B01G087400	chr5B	100.000	4046	0	0	1	4046	112022562	112018517	0.000000e+00	7472.0
1	TraesCS5B01G087400	chr5A	95.066	3648	123	23	418	4046	96983024	96986633	0.000000e+00	5686.0
2	TraesCS5B01G087400	chr5A	91.395	430	33	2	1	426	96982269	96982698	1.620000e-163	586.0
3	TraesCS5B01G087400	chr5A	90.909	44	0	4	3642	3685	27546054	27546015	5.650000e-04	56.5
4	TraesCS5B01G087400	chr5D	96.907	3136	74	8	818	3936	102332305	102329176	0.000000e+00	5232.0
5	TraesCS5B01G087400	chr5D	92.281	570	29	11	140	701	102332982	102332420	0.000000e+00	795.0
6	TraesCS5B01G087400	chr5D	95.312	128	5	1	3919	4046	102328663	102328537	6.860000e-48	202.0
7	TraesCS5B01G087400	chr5D	93.382	136	6	1	1	133	102339578	102339443	8.870000e-47	198.0
8	TraesCS5B01G087400	chr5D	96.639	119	3	1	684	801	102332406	102332288	3.190000e-46	196.0
9	TraesCS5B01G087400	chr3A	84.219	1977	279	24	1075	3036	19988359	19990317	0.000000e+00	1892.0
10	TraesCS5B01G087400	chr1D	84.793	1907	254	22	1165	3044	32738145	32740042	0.000000e+00	1882.0
11	TraesCS5B01G087400	chr3B	85.016	1862	255	21	1191	3039	24019166	24017316	0.000000e+00	1871.0
12	TraesCS5B01G087400	chr3B	76.408	1882	382	57	1196	3037	609801992	609803851	0.000000e+00	959.0
13	TraesCS5B01G087400	chr1B	84.298	1917	258	28	1165	3047	50204094	50206001	0.000000e+00	1832.0
14	TraesCS5B01G087400	chr1A	84.099	1893	254	32	1187	3044	31254306	31252426	0.000000e+00	1784.0
15	TraesCS5B01G087400	chr3D	76.592	1884	375	62	1196	3037	460180050	460181909	0.000000e+00	976.0
16	TraesCS5B01G087400	chr3D	86.207	58	5	3	3638	3693	277152213	277152269	4.370000e-05	60.2
17	TraesCS5B01G087400	chr7D	90.820	512	24	11	3554	4044	608862399	608861890	0.000000e+00	664.0
18	TraesCS5B01G087400	chr7D	82.143	168	29	1	331	497	236640589	236640422	4.220000e-30	143.0
19	TraesCS5B01G087400	chr7D	79.412	170	33	2	330	497	13692498	13692329	7.100000e-23	119.0
20	TraesCS5B01G087400	chr7D	79.290	169	33	2	331	497	13688685	13688517	2.560000e-22	117.0
21	TraesCS5B01G087400	chr7D	79.290	169	33	2	331	497	13691227	13691059	2.560000e-22	117.0
22	TraesCS5B01G087400	chr7D	78.107	169	35	2	331	497	13689955	13689787	5.530000e-19	106.0
23	TraesCS5B01G087400	chr4D	79.833	719	135	9	1217	1930	348564324	348565037	2.160000e-142	516.0
24	TraesCS5B01G087400	chr4B	79.580	715	136	9	1203	1912	428845440	428846149	1.680000e-138	503.0
25	TraesCS5B01G087400	chr4A	79.127	733	143	8	1203	1930	116852161	116851434	7.810000e-137	497.0
26	TraesCS5B01G087400	chr4A	100.000	29	0	0	3596	3624	609567967	609567995	2.000000e-03	54.7
27	TraesCS5B01G087400	chr7B	82.143	168	29	1	331	497	213248073	213247906	4.220000e-30	143.0
28	TraesCS5B01G087400	chr7B	92.683	41	0	3	3643	3683	191676487	191676450	5.650000e-04	56.5
29	TraesCS5B01G087400	chr7A	80.952	168	31	1	331	497	251743508	251743341	9.120000e-27	132.0
30	TraesCS5B01G087400	chr2A	83.133	83	8	5	3615	3693	210060836	210060916	2.020000e-08	71.3
31	TraesCS5B01G087400	chr2A	92.157	51	3	1	3643	3693	309688835	309688884	2.020000e-08	71.3
32	TraesCS5B01G087400	chr6B	100.000	29	0	0	3644	3672	155228725	155228753	2.000000e-03	54.7

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	TraesCS5B01G087400	chr5B	112018517	112022562	4045	True	7472.00	7472	100.00000	1	4046	1	chr5B.!!$R1	4045
1	TraesCS5B01G087400	chr5A	96982269	96986633	4364	False	3136.00	5686	93.23050	1	4046	2	chr5A.!!$F1	4045
2	TraesCS5B01G087400	chr5D	102328537	102332982	4445	True	1606.25	5232	95.28475	140	4046	4	chr5D.!!$R2	3906
3	TraesCS5B01G087400	chr3A	19988359	19990317	1958	False	1892.00	1892	84.21900	1075	3036	1	chr3A.!!$F1	1961
4	TraesCS5B01G087400	chr1D	32738145	32740042	1897	False	1882.00	1882	84.79300	1165	3044	1	chr1D.!!$F1	1879
5	TraesCS5B01G087400	chr3B	24017316	24019166	1850	True	1871.00	1871	85.01600	1191	3039	1	chr3B.!!$R1	1848
6	TraesCS5B01G087400	chr3B	609801992	609803851	1859	False	959.00	959	76.40800	1196	3037	1	chr3B.!!$F1	1841
7	TraesCS5B01G087400	chr1B	50204094	50206001	1907	False	1832.00	1832	84.29800	1165	3047	1	chr1B.!!$F1	1882
8	TraesCS5B01G087400	chr1A	31252426	31254306	1880	True	1784.00	1784	84.09900	1187	3044	1	chr1A.!!$R1	1857
9	TraesCS5B01G087400	chr3D	460180050	460181909	1859	False	976.00	976	76.59200	1196	3037	1	chr3D.!!$F2	1841
10	TraesCS5B01G087400	chr7D	608861890	608862399	509	True	664.00	664	90.82000	3554	4044	1	chr7D.!!$R2	490
11	TraesCS5B01G087400	chr4D	348564324	348565037	713	False	516.00	516	79.83300	1217	1930	1	chr4D.!!$F1	713
12	TraesCS5B01G087400	chr4B	428845440	428846149	709	False	503.00	503	79.58000	1203	1912	1	chr4B.!!$F1	709
13	TraesCS5B01G087400	chr4A	116851434	116852161	727	True	497.00	497	79.12700	1203	1930	1	chr4A.!!$R1	727

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
778	1156	0.600557	ACTCTGGCACTCGAGTTCAG	59.399	55.000	27.22	27.22	37.19	3.02	F
1698	2090	1.447140	GAGCGCGTTCATGGTGGTA	60.447	57.895	18.62	0.00	0.00	3.25	F
2646	3077	0.395862	TCCTCGCCTACTTCCTCCTG	60.396	60.000	0.00	0.00	0.00	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1737	2129	0.035152	GCTGGTGGATGGTCATCACA	60.035	55.000	12.33	7.41	39.54	3.58	R
2967	3401	1.813753	GAAGCCGAATGCCGCAGTA	60.814	57.895	0.00	0.00	42.71	2.74	R
3771	4225	2.108168	AGGTAGCTATGGTCGCAGAAA	58.892	47.619	0.00	0.00	39.69	2.52	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
20	21	1.006102	GGGCGATGGTCGGATACAG	60.006	63.158	1.29	0.00	40.84	2.74
27	28	0.681887	TGGTCGGATACAGCGGAAGA	60.682	55.000	0.00	0.00	0.00	2.87
52	53	3.416955	GCAAAAGGTAATGCGGGTG	57.583	52.632	0.00	0.00	32.17	4.61
82	86	5.066764	AGCTCCTAGAAGAGTAAAGTAAGCG	59.933	44.000	0.00	0.00	36.20	4.68
91	95	1.392510	GTAAAGTAAGCGGTCCTTGCG	59.607	52.381	0.00	0.00	40.60	4.85
133	137	3.442625	CGTTCACTGGACTAGGTGTATCA	59.557	47.826	0.00	0.00	35.26	2.15
171	175	1.972872	ATCACGCAATCCCTCATTCC	58.027	50.000	0.00	0.00	0.00	3.01
223	227	3.736126	CGACGGTTGAGGTTAGGGTTATC	60.736	52.174	0.00	0.00	0.00	1.75
235	239	1.209747	AGGGTTATCCTTGTCTTCCGC	59.790	52.381	0.00	0.00	45.47	5.54
237	241	1.065709	GGTTATCCTTGTCTTCCGCCA	60.066	52.381	0.00	0.00	0.00	5.69
268	273	2.019807	TTGAAGTCTCCCCCGTAAGT	57.980	50.000	0.00	0.00	0.00	2.24
275	280	1.358787	TCTCCCCCGTAAGTCAAGGTA	59.641	52.381	0.00	0.00	0.00	3.08
302	308	1.205417	GGGAAGCACAAACATCATGGG	59.795	52.381	0.00	0.00	0.00	4.00
305	311	1.549203	AGCACAAACATCATGGGGAC	58.451	50.000	0.00	0.00	0.00	4.46
350	356	5.587043	TCATTGTCCCCAAATTATGTCGTAC	59.413	40.000	0.00	0.00	33.44	3.67
352	358	4.509616	TGTCCCCAAATTATGTCGTACAG	58.490	43.478	0.00	0.00	0.00	2.74
355	361	5.465724	GTCCCCAAATTATGTCGTACAGATC	59.534	44.000	0.00	0.00	0.00	2.75
388	394	8.674263	AATGTCAATGCTTTCCAAATTAAACA	57.326	26.923	0.00	0.00	0.00	2.83
778	1156	0.600557	ACTCTGGCACTCGAGTTCAG	59.399	55.000	27.22	27.22	37.19	3.02
783	1161	1.684450	TGGCACTCGAGTTCAGTTGTA	59.316	47.619	17.26	0.00	0.00	2.41
785	1163	1.714460	GCACTCGAGTTCAGTTGTACG	59.286	52.381	17.26	1.25	0.00	3.67
787	1165	3.607775	GCACTCGAGTTCAGTTGTACGTA	60.608	47.826	17.26	0.00	0.00	3.57
789	1167	5.672073	GCACTCGAGTTCAGTTGTACGTATA	60.672	44.000	17.26	0.00	0.00	1.47
791	1169	4.885838	TCGAGTTCAGTTGTACGTATACG	58.114	43.478	23.24	23.24	46.33	3.06
805	1183	4.386716	CGTATACGTAGCGATCTTGTCT	57.613	45.455	17.16	0.00	34.11	3.41
806	1184	4.384529	CGTATACGTAGCGATCTTGTCTC	58.615	47.826	17.16	0.00	34.11	3.36
807	1185	4.084693	CGTATACGTAGCGATCTTGTCTCA	60.085	45.833	17.16	0.00	34.11	3.27
808	1186	4.895224	ATACGTAGCGATCTTGTCTCAA	57.105	40.909	0.08	0.00	0.00	3.02
810	1188	3.502920	ACGTAGCGATCTTGTCTCAAAG	58.497	45.455	0.00	0.00	0.00	2.77
813	1191	4.621460	CGTAGCGATCTTGTCTCAAAGAAA	59.379	41.667	0.00	0.00	39.54	2.52
814	1192	5.118664	CGTAGCGATCTTGTCTCAAAGAAAA	59.881	40.000	0.00	0.00	39.54	2.29
815	1193	6.346598	CGTAGCGATCTTGTCTCAAAGAAAAA	60.347	38.462	0.00	0.00	39.54	1.94
875	1255	5.339990	CAAAGTTCAAACCAAACACGAGAT	58.660	37.500	0.00	0.00	0.00	2.75
947	1329	1.951130	CCCACCAATCGATCGAGCG	60.951	63.158	23.84	18.51	0.00	5.03
960	1347	4.738345	GAGCGCTCGTCGTGTCGT	62.738	66.667	23.61	0.00	41.07	4.34
963	1350	3.157523	CGCTCGTCGTGTCGTGTC	61.158	66.667	0.00	0.00	0.00	3.67
964	1351	3.157523	GCTCGTCGTGTCGTGTCG	61.158	66.667	0.00	0.00	0.00	4.35
965	1352	3.157523	CTCGTCGTGTCGTGTCGC	61.158	66.667	0.00	0.00	0.00	5.19
966	1353	4.999532	TCGTCGTGTCGTGTCGCG	63.000	66.667	0.00	0.00	41.75	5.87
1698	2090	1.447140	GAGCGCGTTCATGGTGGTA	60.447	57.895	18.62	0.00	0.00	3.25
1803	2195	2.441901	CGCCTCCTGCTCCTCTCT	60.442	66.667	0.00	0.00	38.05	3.10
2209	2640	1.153309	CGCCTGAGCACCATCATGA	60.153	57.895	0.00	0.00	39.83	3.07
2646	3077	0.395862	TCCTCGCCTACTTCCTCCTG	60.396	60.000	0.00	0.00	0.00	3.86
2886	3320	3.354678	GGCACAAACATGACGGCT	58.645	55.556	0.00	0.00	0.00	5.52
2967	3401	1.136329	AGTGGATGTGCCTCCTGGTT	61.136	55.000	0.00	0.00	36.20	3.67
2970	3404	0.912486	GGATGTGCCTCCTGGTTACT	59.088	55.000	0.00	0.00	35.27	2.24
3332	3768	5.964887	TTTTTCAGAATTCGCTGTTTTGG	57.035	34.783	0.00	0.00	37.20	3.28
3392	3829	5.664457	CTGCTACAATGTCTCAACTATCCA	58.336	41.667	0.00	0.00	0.00	3.41
3393	3830	5.419542	TGCTACAATGTCTCAACTATCCAC	58.580	41.667	0.00	0.00	0.00	4.02
3418	3855	7.231925	ACGTAATAATTTCCAAACAACCTCCTT	59.768	33.333	0.00	0.00	0.00	3.36
3434	3871	3.181439	CCTCCTTTCCTTTGTTCTGGAGT	60.181	47.826	0.00	0.00	38.24	3.85
3640	4077	8.000780	ACTTGTCTTTCTTTTTAAGCACTGAT	57.999	30.769	0.00	0.00	0.00	2.90
3750	4204	6.318900	AGAGTATTCGTCACATGACATAGACA	59.681	38.462	12.32	3.23	44.99	3.41
3889	4344	9.992442	TTCTAGAAGAAGATTAAACTCCTCCTA	57.008	33.333	0.00	0.00	29.50	2.94
3915	4370	2.427232	GCAAATCTGAAGCACTTGCA	57.573	45.000	3.62	0.00	45.16	4.08
3927	4382	7.121020	TCTGAAGCACTTGCATTGTATTATGAA	59.879	33.333	3.62	0.00	45.16	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	1.371758	CCGCTGTATCCGACCATCG	60.372	63.158	0.00	0.00	40.07	3.84
27	28	1.539827	GCATTACCTTTTGCGGTGTCT	59.460	47.619	0.00	0.00	37.93	3.41
42	43	2.499205	CTCCGAGCACCCGCATTA	59.501	61.111	0.00	0.00	42.27	1.90
52	53	0.951558	CTCTTCTAGGAGCTCCGAGC	59.048	60.000	31.84	12.80	42.84	5.03
133	137	5.059161	GTGATATGTACATGCATGAGTGGT	58.941	41.667	32.75	12.71	0.00	4.16
171	175	0.370273	CGCTTTCGTCGATTCCTTGG	59.630	55.000	0.00	0.00	0.00	3.61
204	208	2.770232	AGGATAACCCTAACCTCAACCG	59.230	50.000	0.00	0.00	45.48	4.44
235	239	6.229733	GGAGACTTCAATATGATCCTCTTGG	58.770	44.000	0.00	0.00	0.00	3.61
237	241	5.309282	GGGGAGACTTCAATATGATCCTCTT	59.691	44.000	0.00	0.00	0.00	2.85
268	273	1.263356	CTTCCCCGACTGTACCTTGA	58.737	55.000	0.00	0.00	0.00	3.02
275	280	0.818040	GTTTGTGCTTCCCCGACTGT	60.818	55.000	0.00	0.00	0.00	3.55
302	308	2.798148	ATTGTGTTCCTCGCGGGTCC	62.798	60.000	4.71	2.16	36.25	4.46
305	311	0.673644	AAGATTGTGTTCCTCGCGGG	60.674	55.000	6.13	0.59	0.00	6.13
317	323	3.524095	TGGGGACAATGACAAGATTGT	57.476	42.857	0.00	0.00	46.89	2.71
352	358	9.508567	GGAAAGCATTGACATTTTAACTAGATC	57.491	33.333	0.00	0.00	0.00	2.75
355	361	9.474920	TTTGGAAAGCATTGACATTTTAACTAG	57.525	29.630	0.00	0.00	0.00	2.57
682	1028	1.343465	CCACCAGTACAACTCCGTCTT	59.657	52.381	0.00	0.00	0.00	3.01
785	1163	5.340010	TGAGACAAGATCGCTACGTATAC	57.660	43.478	0.00	0.00	0.00	1.47
787	1165	4.895224	TTGAGACAAGATCGCTACGTAT	57.105	40.909	0.00	0.00	0.00	3.06
789	1167	3.190744	TCTTTGAGACAAGATCGCTACGT	59.809	43.478	0.00	0.00	0.00	3.57
791	1169	6.467723	TTTTCTTTGAGACAAGATCGCTAC	57.532	37.500	0.00	0.00	0.00	3.58
875	1255	1.367659	GTGGTTTGCTTTGCTTTGCA	58.632	45.000	0.00	0.00	36.47	4.08
947	1329	3.157523	CGACACGACACGACGAGC	61.158	66.667	0.00	0.00	37.03	5.03
960	1347	0.588980	CGATGATCTTCGACGCGACA	60.589	55.000	22.68	0.00	41.62	4.35
963	1350	4.589967	TCGATGATCTTCGACGCG	57.410	55.556	24.91	3.53	42.81	6.01
967	1354	1.359117	GGCGGTCGATGATCTTCGA	59.641	57.895	24.91	24.91	45.27	3.71
1519	1911	3.075005	GGTGAGGCCGAGCTGGTA	61.075	66.667	0.00	0.00	41.21	3.25
1737	2129	0.035152	GCTGGTGGATGGTCATCACA	60.035	55.000	12.33	7.41	39.54	3.58
2197	2628	3.391736	CCGTCATCATGATGGTGCT	57.608	52.632	30.54	0.00	46.07	4.40
2209	2640	2.446848	CCAGGATGAGCCCCGTCAT	61.447	63.158	0.00	0.00	39.69	3.06
2337	2768	1.602605	TCGCTCCTGGACGAAGACA	60.603	57.895	15.61	0.00	34.93	3.41
2340	2771	1.444553	GTGTCGCTCCTGGACGAAG	60.445	63.158	18.32	0.35	40.47	3.79
2646	3077	2.386661	TGATGAAGAAGCCGGAGAAC	57.613	50.000	5.05	0.00	0.00	3.01
2967	3401	1.813753	GAAGCCGAATGCCGCAGTA	60.814	57.895	0.00	0.00	42.71	2.74
2970	3404	2.359850	AAGAAGCCGAATGCCGCA	60.360	55.556	0.00	0.00	42.71	5.69
3315	3751	5.717038	AAAAACCAAAACAGCGAATTCTG	57.283	34.783	3.52	0.00	39.86	3.02
3353	3790	7.776933	TTGTAGCAGCTGAGTAATATCAAAG	57.223	36.000	20.43	0.00	0.00	2.77
3392	3829	6.717997	AGGAGGTTGTTTGGAAATTATTACGT	59.282	34.615	0.00	0.00	0.00	3.57
3393	3830	7.153217	AGGAGGTTGTTTGGAAATTATTACG	57.847	36.000	0.00	0.00	0.00	3.18
3418	3855	4.165372	ACCAACTACTCCAGAACAAAGGAA	59.835	41.667	0.00	0.00	32.57	3.36
3434	3871	2.976882	AGGTAGAAGGTTGCACCAACTA	59.023	45.455	7.88	7.41	43.14	2.24
3453	3890	4.520492	AGATTGTGTTCCACTAGCAAAAGG	59.480	41.667	0.00	0.00	35.11	3.11
3695	4148	7.429340	GTCAGCGACAAGTAATATGGATTTTTG	59.571	37.037	4.20	0.00	32.09	2.44
3771	4225	2.108168	AGGTAGCTATGGTCGCAGAAA	58.892	47.619	0.00	0.00	39.69	2.52
3889	4344	5.909621	AGTGCTTCAGATTTGCAATACAT	57.090	34.783	0.00	0.00	38.50	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.