AutoCloner

Multiple sequence alignment - TraesCS3B01G241100

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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	TraesCS3B01G241100	chr3B	100.000	2783	0	0	1	2783	380509910	380507128	0.000000e+00	5140
1	TraesCS3B01G241100	chr1D	93.813	889	47	5	1	886	464380666	464379783	0.000000e+00	1330
2	TraesCS3B01G241100	chr2B	93.119	901	44	11	1	885	51995510	51994612	0.000000e+00	1304
3	TraesCS3B01G241100	chr2B	93.265	876	51	7	1	873	701508542	701509412	0.000000e+00	1284
4	TraesCS3B01G241100	chr2B	92.626	895	52	11	1	886	773167246	773166357	0.000000e+00	1275
5	TraesCS3B01G241100	chr2B	92.342	901	48	11	1	885	374804519	374803624	0.000000e+00	1262
6	TraesCS3B01G241100	chr2B	92.368	891	54	9	1	886	489315065	489315946	0.000000e+00	1256
7	TraesCS3B01G241100	chr7B	92.897	901	43	12	1	886	38918793	38919687	0.000000e+00	1290
8	TraesCS3B01G241100	chr7B	92.547	899	49	11	1	883	639081390	639080494	0.000000e+00	1273
9	TraesCS3B01G241100	chr4B	92.497	893	58	8	1	888	603177895	603178783	0.000000e+00	1269
10	TraesCS3B01G241100	chr3D	92.254	865	32	14	1920	2783	287293062	287292232	0.000000e+00	1194
11	TraesCS3B01G241100	chr3D	86.492	992	51	30	884	1806	287294227	287293250	0.000000e+00	1013
12	TraesCS3B01G241100	chr3A	94.165	617	21	6	1914	2526	376782066	376781461	0.000000e+00	926
13	TraesCS3B01G241100	chr3A	82.603	730	45	28	884	1535	376783422	376782697	1.120000e-158	569
14	TraesCS3B01G241100	chr3A	92.632	190	7	3	2592	2781	376781437	376781255	1.640000e-67	267
15	TraesCS3B01G241100	chr3A	81.844	347	27	18	1534	1853	376782650	376782313	2.750000e-65	259

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	TraesCS3B01G241100	chr3B	380507128	380509910	2782	True	5140.00	5140	100.000	1	2783	1	chr3B.!!$R1	2782
1	TraesCS3B01G241100	chr1D	464379783	464380666	883	True	1330.00	1330	93.813	1	886	1	chr1D.!!$R1	885
2	TraesCS3B01G241100	chr2B	51994612	51995510	898	True	1304.00	1304	93.119	1	885	1	chr2B.!!$R1	884
3	TraesCS3B01G241100	chr2B	701508542	701509412	870	False	1284.00	1284	93.265	1	873	1	chr2B.!!$F2	872
4	TraesCS3B01G241100	chr2B	773166357	773167246	889	True	1275.00	1275	92.626	1	886	1	chr2B.!!$R3	885
5	TraesCS3B01G241100	chr2B	374803624	374804519	895	True	1262.00	1262	92.342	1	885	1	chr2B.!!$R2	884
6	TraesCS3B01G241100	chr2B	489315065	489315946	881	False	1256.00	1256	92.368	1	886	1	chr2B.!!$F1	885
7	TraesCS3B01G241100	chr7B	38918793	38919687	894	False	1290.00	1290	92.897	1	886	1	chr7B.!!$F1	885
8	TraesCS3B01G241100	chr7B	639080494	639081390	896	True	1273.00	1273	92.547	1	883	1	chr7B.!!$R1	882
9	TraesCS3B01G241100	chr4B	603177895	603178783	888	False	1269.00	1269	92.497	1	888	1	chr4B.!!$F1	887
10	TraesCS3B01G241100	chr3D	287292232	287294227	1995	True	1103.50	1194	89.373	884	2783	2	chr3D.!!$R1	1899
11	TraesCS3B01G241100	chr3A	376781255	376783422	2167	True	505.25	926	87.811	884	2781	4	chr3A.!!$R1	1897

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
914	940	1.900486	GTGGCAGTAACTCTAGGTGGT	59.1	52.381	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2463	2879	0.105964	TTGTGCAGTTCCACTACGCT	59.894	50.0	0.0	0.0	36.68	5.07	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
97	99	4.142004	TGTTTAATCCTAAGGCGTCTCTCC	60.142	45.833	0.00	0.00	0.00	3.71
254	272	3.007398	GTGGGGTGTTTATTTGCAATCCA	59.993	43.478	0.00	0.00	0.00	3.41
290	308	4.634199	ACGAAAGGAAAACGGATCTTACA	58.366	39.130	0.00	0.00	0.00	2.41
753	774	2.356695	ACGCAGGGACTTTTGTGTAAAC	59.643	45.455	0.00	0.00	34.60	2.01
757	778	5.640357	CGCAGGGACTTTTGTGTAAACTATA	59.360	40.000	0.00	0.00	34.60	1.31
788	814	6.148315	ACGATCCGTTTTAACTTAAAAGAGGG	59.852	38.462	18.90	14.64	36.35	4.30
855	881	2.413837	CATGACGGACGAAAGAAACCT	58.586	47.619	0.00	0.00	0.00	3.50
914	940	1.900486	GTGGCAGTAACTCTAGGTGGT	59.100	52.381	0.00	0.00	0.00	4.16
1025	1068	0.322975	AGCAGGCAAGAATCGTCAGT	59.677	50.000	0.00	0.00	0.00	3.41
1027	1070	1.941209	GCAGGCAAGAATCGTCAGTCA	60.941	52.381	0.00	0.00	0.00	3.41
1114	1166	2.260844	CCTCCCAGGTACGTACGATA	57.739	55.000	24.41	7.86	0.00	2.92
1172	1251	0.037590	TCCCCTGAACCCGAATTGTG	59.962	55.000	0.00	0.00	0.00	3.33
1186	1265	3.123621	CGAATTGTGCCTACTGAGTTGTC	59.876	47.826	0.00	0.00	0.00	3.18
1189	1272	1.270305	TGTGCCTACTGAGTTGTCTGC	60.270	52.381	0.00	0.00	0.00	4.26
1210	1296	4.776837	TGCCATTATGTTGATCAAGGGTTT	59.223	37.500	8.80	0.00	0.00	3.27
1222	1308	4.910458	TCAAGGGTTTAAGAAGGAGGAG	57.090	45.455	0.00	0.00	0.00	3.69
1324	1410	1.002033	CTGCACAAGGTGTTTCAGCTC	60.002	52.381	2.02	0.00	41.59	4.09
1341	1428	0.105593	CTCCATCCACATCCGACCTG	59.894	60.000	0.00	0.00	0.00	4.00
1437	1551	2.355481	GACGTCGGCGACAAACCT	60.355	61.111	35.62	14.70	42.00	3.50
1438	1552	2.654912	GACGTCGGCGACAAACCTG	61.655	63.158	35.62	22.01	42.00	4.00
1439	1553	2.660552	CGTCGGCGACAAACCTGT	60.661	61.111	35.62	0.00	41.33	4.00
1440	1554	2.241880	CGTCGGCGACAAACCTGTT	61.242	57.895	35.62	0.00	41.33	3.16
1441	1555	1.278637	GTCGGCGACAAACCTGTTG	59.721	57.895	33.07	0.00	39.65	3.33
1442	1556	1.890041	TCGGCGACAAACCTGTTGG	60.890	57.895	4.99	0.00	37.42	3.77
1558	1720	0.037232	GGACGACAGGAAACAGGAGG	60.037	60.000	0.00	0.00	0.00	4.30
1561	1723	1.376037	GACAGGAAACAGGAGGCCG	60.376	63.158	0.00	0.00	0.00	6.13
1568	1730	3.553095	AACAGGAGGCCGAGGCAAC	62.553	63.158	16.65	8.64	44.11	4.17
1595	1757	1.269778	GGCAGAAAAGGTGGTGAAAGC	60.270	52.381	0.00	0.00	0.00	3.51
1608	1779	1.604278	GTGAAAGCTCAGGACCACAAC	59.396	52.381	0.00	0.00	30.14	3.32
1611	1782	0.249911	AAGCTCAGGACCACAACGAC	60.250	55.000	0.00	0.00	0.00	4.34
1673	1871	1.002011	GCTGGAAGGAGGGGTTCAC	60.002	63.158	0.00	0.00	0.00	3.18
1684	1882	3.124921	GGTTCACGTGGGCGGATG	61.125	66.667	17.00	0.00	43.45	3.51
1797	1995	7.832685	TCCAGAAACTGAAAATCATCATCATCT	59.167	33.333	0.00	0.00	32.44	2.90
1814	2030	1.742761	TCTCTAAATGTGCTGCTGCC	58.257	50.000	13.47	5.20	38.71	4.85
1824	2040	4.694233	CTGCTGCCTGCGTCCACT	62.694	66.667	0.00	0.00	46.63	4.00
1835	2051	3.869246	CCTGCGTCCACTTAATAACGATT	59.131	43.478	0.00	0.00	37.31	3.34
1836	2052	5.045215	CCTGCGTCCACTTAATAACGATTA	58.955	41.667	0.00	0.00	37.31	1.75
1837	2053	5.051240	CCTGCGTCCACTTAATAACGATTAC	60.051	44.000	0.00	0.00	37.31	1.89
1870	2123	8.543774	GGATGTACTGAATAAATTCTCGTCAAG	58.456	37.037	4.45	0.00	37.67	3.02
1910	2236	7.472543	ACTATCACAAAATTGATAAACGCTCC	58.527	34.615	0.00	0.00	37.89	4.70
1943	2351	4.529109	TTTTTATAAGGTGCAAGGCCAC	57.471	40.909	5.01	0.00	35.00	5.01
1957	2365	4.743018	CCACGAGGCTTGGGAAAT	57.257	55.556	5.28	0.00	0.00	2.17
2039	2447	9.995003	AAGTTCCATTTGATAATGCAGTAAAAA	57.005	25.926	0.00	3.00	39.87	1.94
2305	2721	2.203470	TGTGCCATCATCAAAGCAGA	57.797	45.000	0.00	0.00	35.56	4.26
2313	2729	3.648339	TCATCAAAGCAGACCTTTTGC	57.352	42.857	0.00	0.00	41.75	3.68
2463	2879	3.126858	GCCTCATGTATGCGAAGAAAACA	59.873	43.478	0.00	0.00	0.00	2.83
2526	2942	5.818336	GCTCCCACCTTAAATTCTAGAGTTC	59.182	44.000	0.40	0.00	0.00	3.01
2527	2943	6.576442	GCTCCCACCTTAAATTCTAGAGTTCA	60.576	42.308	0.40	0.00	0.00	3.18
2528	2944	6.708285	TCCCACCTTAAATTCTAGAGTTCAC	58.292	40.000	0.40	0.00	0.00	3.18
2529	2945	5.880887	CCCACCTTAAATTCTAGAGTTCACC	59.119	44.000	0.40	0.00	0.00	4.02
2530	2946	5.880887	CCACCTTAAATTCTAGAGTTCACCC	59.119	44.000	0.40	0.00	0.00	4.61
2531	2947	5.581085	CACCTTAAATTCTAGAGTTCACCCG	59.419	44.000	0.40	0.00	0.00	5.28
2532	2948	5.482878	ACCTTAAATTCTAGAGTTCACCCGA	59.517	40.000	0.40	0.00	0.00	5.14
2533	2949	6.013984	ACCTTAAATTCTAGAGTTCACCCGAA	60.014	38.462	0.40	0.00	0.00	4.30
2534	2950	6.877322	CCTTAAATTCTAGAGTTCACCCGAAA	59.123	38.462	0.40	0.00	31.43	3.46
2535	2951	7.389607	CCTTAAATTCTAGAGTTCACCCGAAAA	59.610	37.037	0.40	0.00	31.43	2.29
2536	2952	8.680039	TTAAATTCTAGAGTTCACCCGAAAAA	57.320	30.769	0.40	0.00	31.43	1.94
2716	3132	1.538047	AGAATCATGTGCAAAGCCGT	58.462	45.000	0.00	0.00	0.00	5.68
2717	3133	1.200716	AGAATCATGTGCAAAGCCGTG	59.799	47.619	0.00	0.00	0.00	4.94
2718	3134	0.244450	AATCATGTGCAAAGCCGTGG	59.756	50.000	0.00	0.00	0.00	4.94
2719	3135	2.216750	ATCATGTGCAAAGCCGTGGC	62.217	55.000	1.67	1.67	42.33	5.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	99	4.179599	GGGAGGGAGGGAGGGAGG	62.180	77.778	0.00	0.00	0.00	4.30
230	248	3.742433	TTGCAAATAAACACCCCACTG	57.258	42.857	0.00	0.00	0.00	3.66
411	429	9.939802	ATCTGTATCTTTTAAACCGTAACTTCT	57.060	29.630	0.00	0.00	0.00	2.85
670	691	6.306117	CACCCGAACCGTTATTTTACATTTTC	59.694	38.462	0.00	0.00	0.00	2.29
734	755	5.959618	ATAGTTTACACAAAAGTCCCTGC	57.040	39.130	0.00	0.00	32.81	4.85
768	793	5.458015	CAGCCCTCTTTTAAGTTAAAACGG	58.542	41.667	15.29	16.46	34.27	4.44
784	810	1.657751	GAATTCAACCCGCAGCCCTC	61.658	60.000	0.00	0.00	0.00	4.30
788	814	0.449388	CAGAGAATTCAACCCGCAGC	59.551	55.000	8.44	0.00	0.00	5.25
914	940	1.684983	GATCGATCGGGTTTGGAGGTA	59.315	52.381	16.41	0.00	0.00	3.08
923	949	1.653115	GCGTACTGATCGATCGGGT	59.347	57.895	32.19	26.43	37.50	5.28
952	978	0.592148	CGATCAGACGGTACCTAGCC	59.408	60.000	10.90	0.00	0.00	3.93
985	1015	3.773117	CCATGTCGTTTCACTTGGC	57.227	52.632	0.00	0.00	35.46	4.52
1172	1251	0.321671	TGGCAGACAACTCAGTAGGC	59.678	55.000	0.00	0.00	0.00	3.93
1186	1265	3.956199	ACCCTTGATCAACATAATGGCAG	59.044	43.478	3.38	0.00	0.00	4.85
1189	1272	8.292444	TCTTAAACCCTTGATCAACATAATGG	57.708	34.615	3.38	3.06	0.00	3.16
1210	1296	1.078324	ACCCGGAACTCCTCCTTCTTA	59.922	52.381	0.73	0.00	42.85	2.10
1222	1308	4.612412	TCCACGTGCACCCGGAAC	62.612	66.667	17.35	0.00	0.00	3.62
1324	1410	1.146930	CCAGGTCGGATGTGGATGG	59.853	63.158	3.13	0.00	36.56	3.51
1437	1551	3.244735	TGGATTTCTCATCCGTTCCAACA	60.245	43.478	0.00	0.00	41.03	3.33
1438	1552	3.343617	TGGATTTCTCATCCGTTCCAAC	58.656	45.455	0.00	0.00	41.03	3.77
1439	1553	3.712016	TGGATTTCTCATCCGTTCCAA	57.288	42.857	0.00	0.00	41.03	3.53
1440	1554	3.609853	CTTGGATTTCTCATCCGTTCCA	58.390	45.455	0.00	0.00	41.03	3.53
1441	1555	2.945668	CCTTGGATTTCTCATCCGTTCC	59.054	50.000	0.00	0.00	41.03	3.62
1442	1556	3.610911	ACCTTGGATTTCTCATCCGTTC	58.389	45.455	0.00	0.00	41.03	3.95
1568	1730	3.788766	CCTTTTCTGCCGGCGTCG	61.789	66.667	23.90	13.07	0.00	5.12
1569	1731	2.668550	ACCTTTTCTGCCGGCGTC	60.669	61.111	23.90	0.00	0.00	5.19
1570	1732	2.978010	CACCTTTTCTGCCGGCGT	60.978	61.111	23.90	8.70	0.00	5.68
1571	1733	3.737172	CCACCTTTTCTGCCGGCG	61.737	66.667	23.90	16.91	0.00	6.46
1572	1734	2.597510	ACCACCTTTTCTGCCGGC	60.598	61.111	22.73	22.73	0.00	6.13
1573	1735	0.821711	TTCACCACCTTTTCTGCCGG	60.822	55.000	0.00	0.00	0.00	6.13
1574	1736	1.001378	CTTTCACCACCTTTTCTGCCG	60.001	52.381	0.00	0.00	0.00	5.69
1575	1737	1.269778	GCTTTCACCACCTTTTCTGCC	60.270	52.381	0.00	0.00	0.00	4.85
1576	1738	1.683385	AGCTTTCACCACCTTTTCTGC	59.317	47.619	0.00	0.00	0.00	4.26
1595	1757	1.502231	CTTGTCGTTGTGGTCCTGAG	58.498	55.000	0.00	0.00	0.00	3.35
1608	1779	1.929836	GCCTCATACTCAAGCTTGTCG	59.070	52.381	25.19	18.96	0.00	4.35
1611	1782	1.293924	CCGCCTCATACTCAAGCTTG	58.706	55.000	20.81	20.81	0.00	4.01
1644	1827	0.886563	CCTTCCAGCAGCCTTTCTTG	59.113	55.000	0.00	0.00	0.00	3.02
1684	1882	3.118884	TCCTTGTTCTTACGACCTATGGC	60.119	47.826	0.00	0.00	0.00	4.40
1691	1889	3.655276	TCACCTCCTTGTTCTTACGAC	57.345	47.619	0.00	0.00	0.00	4.34
1692	1890	3.119602	CGATCACCTCCTTGTTCTTACGA	60.120	47.826	0.00	0.00	0.00	3.43
1693	1891	3.179830	CGATCACCTCCTTGTTCTTACG	58.820	50.000	0.00	0.00	0.00	3.18
1797	1995	1.456296	CAGGCAGCAGCACATTTAGA	58.544	50.000	2.65	0.00	44.61	2.10
1800	1998	2.654877	GCAGGCAGCAGCACATTT	59.345	55.556	2.65	0.00	44.61	2.32
1814	2030	5.517411	TGTAATCGTTATTAAGTGGACGCAG	59.483	40.000	0.00	0.00	35.63	5.18
1824	2040	6.535865	ACATCCGCTTGTGTAATCGTTATTAA	59.464	34.615	0.00	0.00	29.41	1.40
1835	2051	3.945981	TTCAGTACATCCGCTTGTGTA	57.054	42.857	0.00	0.00	0.00	2.90
1836	2052	2.831685	TTCAGTACATCCGCTTGTGT	57.168	45.000	0.00	0.00	0.00	3.72
1837	2053	5.794687	TTTATTCAGTACATCCGCTTGTG	57.205	39.130	0.00	0.00	0.00	3.33
1943	2351	2.432444	TGTGTAATTTCCCAAGCCTCG	58.568	47.619	0.00	0.00	0.00	4.63
1957	2365	4.385447	GCACCGTCGTTAACTATTGTGTAA	59.615	41.667	3.71	0.00	0.00	2.41
2205	2621	2.351455	GCTGAAAAGCTAGACCTGGAC	58.649	52.381	0.00	0.00	0.00	4.02
2229	2645	7.404980	TGTTATTACCCCTGTTCCTCTTTCTAT	59.595	37.037	0.00	0.00	0.00	1.98
2305	2721	2.632028	TGCATATGGTTGTGCAAAAGGT	59.368	40.909	4.56	0.00	45.56	3.50
2313	2729	5.239306	CCCTATTACTGTGCATATGGTTGTG	59.761	44.000	4.56	0.00	0.00	3.33
2463	2879	0.105964	TTGTGCAGTTCCACTACGCT	59.894	50.000	0.00	0.00	36.68	5.07
2538	2954	9.495572	CTATTTCAGACCTCAACTCTAGTTTTT	57.504	33.333	0.00	0.00	35.83	1.94
2539	2955	8.652290	ACTATTTCAGACCTCAACTCTAGTTTT	58.348	33.333	0.00	0.00	35.83	2.43
2540	2956	8.091449	CACTATTTCAGACCTCAACTCTAGTTT	58.909	37.037	0.00	0.00	35.83	2.66
2541	2957	7.310113	CCACTATTTCAGACCTCAACTCTAGTT	60.310	40.741	0.00	0.00	39.12	2.24
2542	2958	6.153680	CCACTATTTCAGACCTCAACTCTAGT	59.846	42.308	0.00	0.00	0.00	2.57
2543	2959	6.568869	CCACTATTTCAGACCTCAACTCTAG	58.431	44.000	0.00	0.00	0.00	2.43
2544	2960	5.105310	GCCACTATTTCAGACCTCAACTCTA	60.105	44.000	0.00	0.00	0.00	2.43
2545	2961	4.323104	GCCACTATTTCAGACCTCAACTCT	60.323	45.833	0.00	0.00	0.00	3.24
2546	2962	3.935828	GCCACTATTTCAGACCTCAACTC	59.064	47.826	0.00	0.00	0.00	3.01
2547	2963	3.327757	TGCCACTATTTCAGACCTCAACT	59.672	43.478	0.00	0.00	0.00	3.16
2548	2964	3.437049	GTGCCACTATTTCAGACCTCAAC	59.563	47.826	0.00	0.00	0.00	3.18
2549	2965	3.072330	TGTGCCACTATTTCAGACCTCAA	59.928	43.478	0.00	0.00	0.00	3.02
2550	2966	2.637382	TGTGCCACTATTTCAGACCTCA	59.363	45.455	0.00	0.00	0.00	3.86
2557	2973	2.038952	AGCTCTGTGTGCCACTATTTCA	59.961	45.455	0.00	0.00	35.11	2.69
2648	3064	2.418368	TGAACAACTTGTGAGTGCCT	57.582	45.000	0.00	0.00	35.91	4.75
2693	3109	5.049198	CACGGCTTTGCACATGATTCTATAT	60.049	40.000	0.00	0.00	0.00	0.86
2716	3132	2.671619	GCGCTAACCAACCAGCCA	60.672	61.111	0.00	0.00	34.15	4.75
2717	3133	0.746563	TATGCGCTAACCAACCAGCC	60.747	55.000	9.73	0.00	34.15	4.85
2718	3134	1.308998	ATATGCGCTAACCAACCAGC	58.691	50.000	9.73	0.00	0.00	4.85
2719	3135	4.370364	AAAATATGCGCTAACCAACCAG	57.630	40.909	9.73	0.00	0.00	4.00
2723	3139	5.106118	TGCTTGTAAAATATGCGCTAACCAA	60.106	36.000	9.73	0.15	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.