AutoCloner

Multiple sequence alignment - TraesCS2B01G089300

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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	TraesCS2B01G089300	chr2B	100.000	3142	0	0	1	3142	50400492	50403633	0.000000e+00	5803
1	TraesCS2B01G089300	chr2B	75.528	1373	250	50	943	2272	50494959	50493630	2.090000e-166	595
2	TraesCS2B01G089300	chr2B	81.439	695	112	11	1453	2146	50524181	50523503	1.270000e-153	553
3	TraesCS2B01G089300	chr2D	91.347	2219	155	22	942	3142	30612076	30614275	0.000000e+00	3000
4	TraesCS2B01G089300	chr2D	79.628	1129	185	28	1176	2277	30619248	30620358	0.000000e+00	769
5	TraesCS2B01G089300	chr2D	87.425	167	21	0	1893	2059	402929024	402928858	3.200000e-45	193
6	TraesCS2B01G089300	chr2A	95.094	1121	50	2	942	2060	32773354	32774471	0.000000e+00	1760
7	TraesCS2B01G089300	chr2A	99.045	942	9	0	1	942	653285555	653284614	0.000000e+00	1690
8	TraesCS2B01G089300	chr2A	90.237	1096	88	10	1537	2630	32857039	32858117	0.000000e+00	1413
9	TraesCS2B01G089300	chr2A	91.476	962	76	4	1678	2636	32818042	32819000	0.000000e+00	1317
10	TraesCS2B01G089300	chr2A	84.238	958	98	30	1085	2020	32554760	32555686	0.000000e+00	883
11	TraesCS2B01G089300	chr2A	90.188	693	46	9	2459	3142	32778397	32779076	0.000000e+00	883
12	TraesCS2B01G089300	chr2A	79.254	1099	185	27	1205	2277	32875911	32876992	0.000000e+00	726
13	TraesCS2B01G089300	chr2A	85.203	615	64	13	942	1539	32820945	32821549	9.640000e-170	606
14	TraesCS2B01G089300	chr2A	92.000	325	25	1	2127	2451	32774774	32775097	3.690000e-124	455
15	TraesCS2B01G089300	chr2A	88.674	362	30	8	2016	2374	32578137	32578490	6.230000e-117	431
16	TraesCS2B01G089300	chr2A	85.849	212	22	5	2666	2870	32860317	32860527	5.280000e-53	219
17	TraesCS2B01G089300	chr2A	85.782	211	22	7	2489	2693	32756036	32756244	1.900000e-52	217
18	TraesCS2B01G089300	chr2A	97.345	113	2	1	2053	2164	32774662	32774774	1.150000e-44	191
19	TraesCS2B01G089300	chr2A	89.655	145	15	0	942	1086	32554534	32554678	5.350000e-43	185
20	TraesCS2B01G089300	chr4A	98.943	946	9	1	1	945	618866151	618865206	0.000000e+00	1690
21	TraesCS2B01G089300	chrUn	99.044	941	9	0	1	941	17574503	17575443	0.000000e+00	1688
22	TraesCS2B01G089300	chr5B	98.942	945	9	1	1	944	439371131	439370187	0.000000e+00	1688
23	TraesCS2B01G089300	chr1A	99.045	942	8	1	1	941	461340996	461340055	0.000000e+00	1688
24	TraesCS2B01G089300	chr3B	98.938	942	10	0	1	942	812911229	812910288	0.000000e+00	1685
25	TraesCS2B01G089300	chr7B	98.937	941	10	0	1	941	697386580	697385640	0.000000e+00	1683
26	TraesCS2B01G089300	chr1B	98.937	941	10	0	1	941	651483899	651482959	0.000000e+00	1683
27	TraesCS2B01G089300	chr4B	98.629	948	13	0	1	948	486090743	486091690	0.000000e+00	1679

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	TraesCS2B01G089300	chr2B	50400492	50403633	3141	False	5803.00	5803	100.00000	1	3142	1	chr2B.!!$F1	3141
1	TraesCS2B01G089300	chr2B	50493630	50494959	1329	True	595.00	595	75.52800	943	2272	1	chr2B.!!$R1	1329
2	TraesCS2B01G089300	chr2B	50523503	50524181	678	True	553.00	553	81.43900	1453	2146	1	chr2B.!!$R2	693
3	TraesCS2B01G089300	chr2D	30612076	30614275	2199	False	3000.00	3000	91.34700	942	3142	1	chr2D.!!$F1	2200
4	TraesCS2B01G089300	chr2D	30619248	30620358	1110	False	769.00	769	79.62800	1176	2277	1	chr2D.!!$F2	1101
5	TraesCS2B01G089300	chr2A	653284614	653285555	941	True	1690.00	1690	99.04500	1	942	1	chr2A.!!$R1	941
6	TraesCS2B01G089300	chr2A	32818042	32821549	3507	False	961.50	1317	88.33950	942	2636	2	chr2A.!!$F6	1694
7	TraesCS2B01G089300	chr2A	32773354	32779076	5722	False	822.25	1760	93.65675	942	3142	4	chr2A.!!$F5	2200
8	TraesCS2B01G089300	chr2A	32857039	32860527	3488	False	816.00	1413	88.04300	1537	2870	2	chr2A.!!$F7	1333
9	TraesCS2B01G089300	chr2A	32875911	32876992	1081	False	726.00	726	79.25400	1205	2277	1	chr2A.!!$F3	1072
10	TraesCS2B01G089300	chr2A	32554534	32555686	1152	False	534.00	883	86.94650	942	2020	2	chr2A.!!$F4	1078
11	TraesCS2B01G089300	chr4A	618865206	618866151	945	True	1690.00	1690	98.94300	1	945	1	chr4A.!!$R1	944
12	TraesCS2B01G089300	chrUn	17574503	17575443	940	False	1688.00	1688	99.04400	1	941	1	chrUn.!!$F1	940
13	TraesCS2B01G089300	chr5B	439370187	439371131	944	True	1688.00	1688	98.94200	1	944	1	chr5B.!!$R1	943
14	TraesCS2B01G089300	chr1A	461340055	461340996	941	True	1688.00	1688	99.04500	1	941	1	chr1A.!!$R1	940
15	TraesCS2B01G089300	chr3B	812910288	812911229	941	True	1685.00	1685	98.93800	1	942	1	chr3B.!!$R1	941
16	TraesCS2B01G089300	chr7B	697385640	697386580	940	True	1683.00	1683	98.93700	1	941	1	chr7B.!!$R1	940
17	TraesCS2B01G089300	chr1B	651482959	651483899	940	True	1683.00	1683	98.93700	1	941	1	chr1B.!!$R1	940
18	TraesCS2B01G089300	chr4B	486090743	486091690	947	False	1679.00	1679	98.62900	1	948	1	chr4B.!!$F1	947

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
201	202	1.067295	TGCACCCTCCAGTTGAATCT	58.933	50.0	0.0	0.0	0.0	2.4	F
1039	1041	0.535335	GGATGCGGACTTCAGGTACA	59.465	55.0	0.0	0.0	0.0	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1838	1990	0.107459	CCACTAGCTCTTCCTTGCCC	60.107	60.0	0.00	0.0	0.00	5.36	R
2485	6166	0.333312	AACCAACCACCAACTGGACA	59.667	50.0	1.86	0.0	43.95	4.02	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
201	202	1.067295	TGCACCCTCCAGTTGAATCT	58.933	50.000	0.00	0.00	0.00	2.40
561	563	2.364579	TAGGTCGTGGCCCGGAAT	60.365	61.111	0.73	3.17	37.11	3.01
927	929	1.092921	ACACCAACAACGTCGCATGT	61.093	50.000	0.00	0.00	0.00	3.21
1039	1041	0.535335	GGATGCGGACTTCAGGTACA	59.465	55.000	0.00	0.00	0.00	2.90
1104	1189	2.896685	GGTGTTTGTGATCCCAAATCCA	59.103	45.455	6.63	0.00	36.75	3.41
1188	1273	3.967467	ATGGAGAAATCTGAATGGCCT	57.033	42.857	3.32	0.00	0.00	5.19
1262	1347	5.894393	AGGAGAGGTCTTTTATTCGAGATGA	59.106	40.000	0.00	0.00	0.00	2.92
1363	1448	1.218875	TGCACTTTACGTCCACTGCG	61.219	55.000	0.00	0.00	0.00	5.18
1387	1472	7.829378	GAAACTGATTTCGTAATGAGGTAGT	57.171	36.000	6.23	0.00	35.18	2.73
1388	1473	8.922058	GAAACTGATTTCGTAATGAGGTAGTA	57.078	34.615	6.23	0.00	35.18	1.82
1389	1474	8.699283	AAACTGATTTCGTAATGAGGTAGTAC	57.301	34.615	6.23	0.00	30.24	2.73
1408	1502	9.962783	GGTAGTACCTAATAACTTACACATCAG	57.037	37.037	12.41	0.00	34.73	2.90
1544	1656	1.367471	TGAACTCGGTGAGTGCAGG	59.633	57.895	3.47	0.00	42.67	4.85
1631	1767	4.946160	TCTTATGGTTTGGGTCCTTGAT	57.054	40.909	0.00	0.00	0.00	2.57
1673	1809	6.374333	TGAATTGGGTCTTGAAGTATAACAGC	59.626	38.462	0.00	0.00	0.00	4.40
1777	1929	1.203237	AGAGAGAAAGGAGGGCACTGA	60.203	52.381	0.00	0.00	0.00	3.41
1780	1932	1.625818	GAGAAAGGAGGGCACTGAAGA	59.374	52.381	0.00	0.00	0.00	2.87
1782	1934	2.026449	AGAAAGGAGGGCACTGAAGATG	60.026	50.000	0.00	0.00	0.00	2.90
1783	1935	1.661463	AAGGAGGGCACTGAAGATGA	58.339	50.000	0.00	0.00	0.00	2.92
1792	1944	5.310068	AGGGCACTGAAGATGATGAAGATAT	59.690	40.000	0.00	0.00	0.00	1.63
1979	2131	9.784531	TTCCATCCATATAAAGAGATTGTCTTC	57.215	33.333	0.00	0.00	45.44	2.87
1984	2136	6.429385	CCATATAAAGAGATTGTCTTCCTGGC	59.571	42.308	0.00	0.00	45.44	4.85
2152	2540	4.096732	GGCACCAGTAAGCAATTAACAG	57.903	45.455	0.00	0.00	0.00	3.16
2174	2562	4.349342	AGGAATGTAGAAGGGCATCTTAGG	59.651	45.833	0.00	0.00	35.50	2.69
2177	2565	3.731431	TGTAGAAGGGCATCTTAGGGAA	58.269	45.455	0.00	0.00	35.50	3.97
2225	2614	7.099266	TGAACATCACAATAAATGGCCTAAG	57.901	36.000	3.32	0.00	0.00	2.18
2252	2641	8.711457	CATGTTTAAGGCCTTGTTCATTTTTAG	58.289	33.333	28.77	11.77	0.00	1.85
2348	2737	8.946085	GTAACAGTGTATCATGAGAAAAATGGA	58.054	33.333	0.09	0.00	0.00	3.41
2349	2738	8.408043	AACAGTGTATCATGAGAAAAATGGAA	57.592	30.769	0.09	0.00	0.00	3.53
2389	2778	5.723295	ACTTCATTGCTTTGTTCAACAACT	58.277	33.333	1.28	0.00	37.90	3.16
2401	2790	5.167121	TGTTCAACAACTCCAATGTGTTTG	58.833	37.500	0.00	0.00	33.17	2.93
2485	6166	9.554395	CCTATTAATTTTGTTGTTGTTTTCCCT	57.446	29.630	0.00	0.00	0.00	4.20
2515	6196	2.698274	GGTGGTTGGTTTCATCCTTGTT	59.302	45.455	0.00	0.00	34.61	2.83
2532	6213	7.873719	TCCTTGTTTGTTGTCTGAATTCTTA	57.126	32.000	7.05	0.00	0.00	2.10
2537	6218	8.099364	TGTTTGTTGTCTGAATTCTTATCCTC	57.901	34.615	7.05	0.00	0.00	3.71
2566	6255	6.798427	ATTCTGACTCTTGTATGCCTAAGA	57.202	37.500	0.00	0.00	0.00	2.10
2660	7900	4.098960	ACAATCAGAATAAATGGCCTGCTG	59.901	41.667	3.32	0.00	0.00	4.41
2664	8524	2.626743	AGAATAAATGGCCTGCTGATGC	59.373	45.455	3.32	0.00	40.20	3.91
2691	8551	3.309954	GGCCTTGTTCAATCTTACTAGCG	59.690	47.826	0.00	0.00	0.00	4.26
2736	8601	9.829507	TCCATTTGAATCAAGTTACAATGTTTT	57.170	25.926	0.00	0.00	0.00	2.43
2739	8604	9.829507	ATTTGAATCAAGTTACAATGTTTTCCA	57.170	25.926	0.00	0.00	0.00	3.53
2740	8605	9.829507	TTTGAATCAAGTTACAATGTTTTCCAT	57.170	25.926	0.00	0.00	34.36	3.41
2814	8689	5.705905	AGAGCCATTTACTTGTTCTGTTACC	59.294	40.000	0.00	0.00	0.00	2.85
2919	8796	6.699575	ATATTTTGCTCAGCGGTATCTTTT	57.300	33.333	0.00	0.00	0.00	2.27
2920	8797	4.846779	TTTTGCTCAGCGGTATCTTTTT	57.153	36.364	0.00	0.00	0.00	1.94
2936	8817	3.052490	TCTTTTTCCCCCTCTTGGTTTCA	60.052	43.478	0.00	0.00	0.00	2.69
2978	8859	9.567776	TCAGTTTTATAGTTTGTTTCATCCTGA	57.432	29.630	0.00	0.00	0.00	3.86
2989	8870	9.710900	GTTTGTTTCATCCTGATTTTTCCTTAT	57.289	29.630	0.00	0.00	0.00	1.73
3006	8887	3.127030	CCTTATTTTCGGTTCCTGCTGTC	59.873	47.826	0.00	0.00	0.00	3.51
3046	8927	6.360370	TCTTTTGAGCTTAAGCCTCTAGAA	57.640	37.500	23.71	10.37	43.38	2.10
3050	8931	7.440523	TTTGAGCTTAAGCCTCTAGAAAAAG	57.559	36.000	23.71	0.00	43.38	2.27
3058	8939	3.118075	AGCCTCTAGAAAAAGATGCTCCC	60.118	47.826	0.00	0.00	41.79	4.30
3059	8940	3.462021	CCTCTAGAAAAAGATGCTCCCG	58.538	50.000	0.00	0.00	0.00	5.14
3088	8969	5.280830	GGTGGGGGTCTCTAAGAAACAAATA	60.281	44.000	0.00	0.00	0.00	1.40
3135	9016	7.541783	TCGAATTTTGGCTTATTTTCTGTGATG	59.458	33.333	0.00	0.00	0.00	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
201	202	4.520874	GTGGCTAGATGAGTACATAGAGCA	59.479	45.833	0.00	0.00	41.81	4.26
515	517	3.393970	CTCCGCTTCAGCCTCCCA	61.394	66.667	0.00	0.00	37.91	4.37
927	929	6.942005	CCACATAATAATGGGTGAATAGCTCA	59.058	38.462	0.00	0.00	34.42	4.26
1104	1189	2.335011	GGCTTCGTTTTGCGCCTT	59.665	55.556	4.18	0.00	39.42	4.35
1161	1246	5.368145	CATTCAGATTTCTCCATAACGGGA	58.632	41.667	0.00	0.00	34.36	5.14
1188	1273	1.855213	GCAAAGCGCACACAGATGGA	61.855	55.000	11.47	0.00	41.79	3.41
1262	1347	2.833604	GATGGTGCCTGCAGCCTTCT	62.834	60.000	17.68	1.34	43.08	2.85
1363	1448	7.829378	ACTACCTCATTACGAAATCAGTTTC	57.171	36.000	0.00	0.00	40.25	2.78
1502	1614	6.316640	CACCATGTATCGGTGGTTTAATTACA	59.683	38.462	1.25	0.00	46.22	2.41
1631	1767	1.902938	TCATTTGGCCACACGATTCA	58.097	45.000	3.88	0.00	0.00	2.57
1673	1809	3.483954	CAGTATGGGTGGAAGGCAG	57.516	57.895	0.00	0.00	0.00	4.85
1770	1910	7.609960	TCTATATCTTCATCATCTTCAGTGCC	58.390	38.462	0.00	0.00	0.00	5.01
1838	1990	0.107459	CCACTAGCTCTTCCTTGCCC	60.107	60.000	0.00	0.00	0.00	5.36
2152	2540	4.505742	CCCTAAGATGCCCTTCTACATTCC	60.506	50.000	0.00	0.00	36.34	3.01
2174	2562	2.427095	GTTCCAACCAGCATACCATTCC	59.573	50.000	0.00	0.00	0.00	3.01
2225	2614	3.658757	TGAACAAGGCCTTAAACATGC	57.341	42.857	20.00	4.31	0.00	4.06
2302	2691	6.315642	TGTTACGTCACATGTTTTTAGAACCA	59.684	34.615	0.00	0.00	0.00	3.67
2357	2746	9.624697	TGAACAAAGCAATGAAGTATATTTGAC	57.375	29.630	0.00	0.00	32.12	3.18
2389	2778	9.072375	TGATACATAAGAAACAAACACATTGGA	57.928	29.630	0.00	0.00	43.66	3.53
2401	2790	6.978659	TCCGACACAGATGATACATAAGAAAC	59.021	38.462	0.00	0.00	0.00	2.78
2419	2808	3.126343	AGCGAAATATTGGTTTCCGACAC	59.874	43.478	0.00	0.00	35.23	3.67
2485	6166	0.333312	AACCAACCACCAACTGGACA	59.667	50.000	1.86	0.00	43.95	4.02
2515	6196	7.020827	AGGAGGATAAGAATTCAGACAACAA	57.979	36.000	8.44	0.00	0.00	2.83
2532	6213	9.836179	ATACAAGAGTCAGAATATAAGGAGGAT	57.164	33.333	0.00	0.00	0.00	3.24
2537	6218	7.675062	AGGCATACAAGAGTCAGAATATAAGG	58.325	38.462	0.00	0.00	0.00	2.69
2566	6255	4.042435	TCCGTAAACCTTTTCCTGGAGAAT	59.958	41.667	0.00	0.00	33.44	2.40
2660	7900	4.340381	AGATTGAACAAGGCCATAAGCATC	59.660	41.667	5.01	0.00	46.50	3.91
2664	8524	7.254932	GCTAGTAAGATTGAACAAGGCCATAAG	60.255	40.741	5.01	0.00	0.00	1.73
2737	8602	9.935682	GGTATCATGTTTATATAATCGCAATGG	57.064	33.333	0.00	0.00	0.00	3.16
2740	8605	9.936759	TGAGGTATCATGTTTATATAATCGCAA	57.063	29.630	0.00	0.00	0.00	4.85
2781	8654	9.129209	GAACAAGTAAATGGCTCTATGTTTTTC	57.871	33.333	0.00	0.00	30.58	2.29
2847	8722	6.166279	AGAGACATACATGTGTGTAGTTTGG	58.834	40.000	25.81	0.00	43.62	3.28
2919	8796	2.178984	ACAATGAAACCAAGAGGGGGAA	59.821	45.455	0.00	0.00	42.91	3.97
2920	8797	1.786441	ACAATGAAACCAAGAGGGGGA	59.214	47.619	0.00	0.00	42.91	4.81
2978	8859	6.014584	AGCAGGAACCGAAAATAAGGAAAAAT	60.015	34.615	0.00	0.00	0.00	1.82
2989	8870	1.872237	CGAGACAGCAGGAACCGAAAA	60.872	52.381	0.00	0.00	0.00	2.29
3006	8887	7.900352	GCTCAAAAGAAGTAACACAATATCGAG	59.100	37.037	0.00	0.00	0.00	4.04
3046	8927	4.743018	CCCACGGGAGCATCTTTT	57.257	55.556	0.00	0.00	37.50	2.27
3059	8940	2.776053	TTAGAGACCCCCACCCCCAC	62.776	65.000	0.00	0.00	0.00	4.61
3088	8969	5.181245	TCGAAAAGCTGAAAAGAATCGGAAT	59.819	36.000	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.