AutoCloner

Multiple sequence alignment - TraesCS3B01G505500

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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	TraesCS3B01G505500	chr3B	100.000	2867	0	0	1	2867	749650807	749653673	0.000000e+00	5295.0
1	TraesCS3B01G505500	chr3B	76.097	661	133	17	2191	2839	753868746	753868099	3.560000e-84	322.0
2	TraesCS3B01G505500	chr3D	94.291	1086	47	9	783	1861	562439532	562440609	0.000000e+00	1648.0
3	TraesCS3B01G505500	chr3D	94.424	1076	47	8	783	1851	562357938	562359007	0.000000e+00	1642.0
4	TraesCS3B01G505500	chr3D	96.817	911	24	3	1962	2867	562360012	562360922	0.000000e+00	1517.0
5	TraesCS3B01G505500	chr3D	94.943	791	32	6	1110	1899	562359232	562360015	0.000000e+00	1232.0
6	TraesCS3B01G505500	chr3D	97.075	718	10	5	6	712	562355746	562356463	0.000000e+00	1199.0
7	TraesCS3B01G505500	chr3D	96.927	716	13	4	6	712	562437342	562438057	0.000000e+00	1192.0
8	TraesCS3B01G505500	chr3D	85.100	698	91	10	741	1432	562462660	562463350	0.000000e+00	701.0
9	TraesCS3B01G505500	chr3D	77.987	636	106	16	662	1289	562386312	562386921	4.510000e-98	368.0
10	TraesCS3B01G505500	chr3D	81.619	457	73	6	2222	2670	562418224	562418677	4.510000e-98	368.0
11	TraesCS3B01G505500	chr3D	96.244	213	7	1	783	995	562359004	562359215	5.880000e-92	348.0
12	TraesCS3B01G505500	chr3D	78.516	512	96	10	2348	2846	562464877	562465387	9.910000e-85	324.0
13	TraesCS3B01G505500	chr3D	80.374	428	74	4	2450	2867	562419707	562420134	1.660000e-82	316.0
14	TraesCS3B01G505500	chr3D	75.347	576	79	30	73	621	562462041	562462580	4.810000e-53	219.0
15	TraesCS3B01G505500	chr3D	79.681	251	47	4	2167	2417	562419463	562419709	8.160000e-41	178.0
16	TraesCS3B01G505500	chr3D	86.875	160	12	4	1646	1801	562463788	562463942	1.370000e-38	171.0
17	TraesCS3B01G505500	chr3D	97.872	94	2	0	705	798	562357366	562357459	2.290000e-36	163.0
18	TraesCS3B01G505500	chr3D	97.872	94	2	0	705	798	562438960	562439053	2.290000e-36	163.0
19	TraesCS3B01G505500	chr3D	82.873	181	27	3	451	628	562471372	562471551	2.960000e-35	159.0
20	TraesCS3B01G505500	chr3A	87.320	694	71	8	741	1432	697582192	697582870	0.000000e+00	778.0
21	TraesCS3B01G505500	chr3A	76.737	662	128	18	2191	2839	699977328	699976680	2.110000e-91	346.0
22	TraesCS3B01G505500	chr3A	79.775	445	75	11	2426	2862	708539686	708540123	2.770000e-80	309.0
23	TraesCS3B01G505500	chr3A	85.350	157	14	4	1646	1798	697583289	697583440	1.380000e-33	154.0
24	TraesCS3B01G505500	chr3A	90.141	71	7	0	73	143	697575647	697575717	3.040000e-15	93.5
25	TraesCS3B01G505500	chr3A	100.000	33	0	0	6	38	697575619	697575651	8.580000e-06	62.1

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	TraesCS3B01G505500	chr3B	749650807	749653673	2866	False	5295.000000	5295	100.000000	1	2867	1	chr3B.!!$F1	2866
1	TraesCS3B01G505500	chr3B	753868099	753868746	647	True	322.000000	322	76.097000	2191	2839	1	chr3B.!!$R1	648
2	TraesCS3B01G505500	chr3D	562355746	562360922	5176	False	1016.833333	1642	96.229167	6	2867	6	chr3D.!!$F3	2861
3	TraesCS3B01G505500	chr3D	562437342	562440609	3267	False	1001.000000	1648	96.363333	6	1861	3	chr3D.!!$F5	1855
4	TraesCS3B01G505500	chr3D	562386312	562386921	609	False	368.000000	368	77.987000	662	1289	1	chr3D.!!$F1	627
5	TraesCS3B01G505500	chr3D	562462041	562465387	3346	False	353.750000	701	81.459500	73	2846	4	chr3D.!!$F6	2773
6	TraesCS3B01G505500	chr3D	562418224	562420134	1910	False	287.333333	368	80.558000	2167	2867	3	chr3D.!!$F4	700
7	TraesCS3B01G505500	chr3A	697582192	697583440	1248	False	466.000000	778	86.335000	741	1798	2	chr3A.!!$F3	1057
8	TraesCS3B01G505500	chr3A	699976680	699977328	648	True	346.000000	346	76.737000	2191	2839	1	chr3A.!!$R1	648

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
946	2381	3.777465	TTCTACACGTCACAGCTATCC	57.223	47.619	0.0	0.0	0.0	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2689	7037	0.17576	GCGGAGATCAAGGTGCAGTA	59.824	55.0	0.0	0.0	0.0	2.74	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
103	104	6.881065	GCAGAGGTATATTGCAAGATATCCAA	59.119	38.462	18.43	0.00	37.75	3.53
104	105	7.555554	GCAGAGGTATATTGCAAGATATCCAAT	59.444	37.037	18.43	10.50	37.75	3.16
282	292	5.324784	GGAAGTTTCCTTTTGTGTTCACT	57.675	39.130	3.63	0.00	44.11	3.41
519	538	5.172053	CGCAACTGAGAAAAAGAAATGTGAC	59.828	40.000	0.00	0.00	0.00	3.67
739	1673	4.283978	TGTTAGTAATGACCAAAGTCCCGA	59.716	41.667	0.00	0.00	42.81	5.14
814	2249	9.609346	TCATAAAATAGTACAAAAGACTAGCCC	57.391	33.333	0.00	0.00	33.03	5.19
904	2339	5.529800	TGCTAGAACAGAACCTTTTAACACC	59.470	40.000	0.00	0.00	0.00	4.16
946	2381	3.777465	TTCTACACGTCACAGCTATCC	57.223	47.619	0.00	0.00	0.00	2.59
1035	2472	1.132453	CATCACCATCACAAGCTGCAG	59.868	52.381	10.11	10.11	0.00	4.41
1071	2508	5.667539	ATAGCTAGCTCAAGTGAAGTGAA	57.332	39.130	23.26	0.00	0.00	3.18
1178	2621	1.092345	GTGATCTTTGGGGCGAGCTC	61.092	60.000	2.73	2.73	0.00	4.09
1341	2784	1.498865	CGGTATTCATCTGTGGCGCC	61.499	60.000	22.73	22.73	0.00	6.53
1475	3001	8.718734	GTTTATCAGTTGTACCTCTTGTTAAGG	58.281	37.037	0.00	0.00	39.96	2.69
1484	3010	3.923425	ACCTCTTGTTAAGGGAAGGGAAT	59.077	43.478	0.00	0.00	38.29	3.01
1489	3015	8.279361	CCTCTTGTTAAGGGAAGGGAATAATTA	58.721	37.037	0.00	0.00	0.00	1.40
1525	3224	7.533426	AGTGTTCATTCTGATGCTGATTAAAC	58.467	34.615	0.00	0.00	33.14	2.01
1527	3226	7.972277	GTGTTCATTCTGATGCTGATTAAACAT	59.028	33.333	0.00	0.00	33.14	2.71
1556	3255	7.443879	TGCTTAATTTAGACACAAGACATCACA	59.556	33.333	0.00	0.00	0.00	3.58
1606	3305	8.169977	AGAGAGAGTGTTCATTCTGATAGATC	57.830	38.462	2.71	0.00	0.00	2.75
1621	3320	5.371526	TGATAGATCCCATGAAGAGTTTGC	58.628	41.667	0.00	0.00	0.00	3.68
1626	3325	1.879380	CCCATGAAGAGTTTGCGTGAA	59.121	47.619	0.00	0.00	0.00	3.18
1710	3412	5.779806	ATGCGAATGTGTAGAGTTTGTAC	57.220	39.130	0.00	0.00	0.00	2.90
1749	3451	7.182817	TGTAGAACACTAGGTATTGCAATCT	57.817	36.000	16.86	10.52	0.00	2.40
1787	3489	1.728971	GAGCCTCTGTTCATGTCAACG	59.271	52.381	0.00	0.00	0.00	4.10
1803	3505	2.872245	TCAACGAAGAAGCCTGAAGTTG	59.128	45.455	0.00	0.00	38.87	3.16
1835	4494	7.447243	AGATTTTAACGTAGCGATCAGTAAC	57.553	36.000	0.00	0.00	0.00	2.50
1876	4552	5.009854	AGCGGCAACTGCAATAAAAATAT	57.990	34.783	1.45	0.00	44.36	1.28
1912	4596	2.047061	AGTACTGCTTGTGGTGAGGAA	58.953	47.619	0.00	0.00	0.00	3.36
1922	4606	2.886523	TGTGGTGAGGAAGCTTCATTTG	59.113	45.455	27.02	0.00	0.00	2.32
1924	4608	2.886523	TGGTGAGGAAGCTTCATTTGTG	59.113	45.455	27.02	0.00	0.00	3.33
1927	4611	4.540824	GTGAGGAAGCTTCATTTGTGTTC	58.459	43.478	27.02	7.70	0.00	3.18
1928	4612	4.276926	GTGAGGAAGCTTCATTTGTGTTCT	59.723	41.667	27.02	11.78	0.00	3.01
1929	4613	4.276678	TGAGGAAGCTTCATTTGTGTTCTG	59.723	41.667	27.02	0.00	0.00	3.02
1931	4615	3.569701	GGAAGCTTCATTTGTGTTCTGGA	59.430	43.478	27.02	0.00	0.00	3.86
1932	4616	4.540824	GAAGCTTCATTTGTGTTCTGGAC	58.459	43.478	21.67	0.00	0.00	4.02
1933	4617	3.554934	AGCTTCATTTGTGTTCTGGACA	58.445	40.909	0.00	0.00	35.42	4.02
1935	4619	4.044426	GCTTCATTTGTGTTCTGGACAAC	58.956	43.478	0.00	0.00	40.65	3.32
1936	4620	4.610945	CTTCATTTGTGTTCTGGACAACC	58.389	43.478	0.00	0.00	40.65	3.77
1947	4652	1.376683	GGACAACCAGGTGCGCATA	60.377	57.895	15.91	0.00	35.97	3.14
1955	4660	1.202290	CCAGGTGCGCATATTTTCACC	60.202	52.381	15.91	7.44	46.93	4.02
1961	4666	5.164954	GGTGCGCATATTTTCACCTTAAAA	58.835	37.500	15.91	0.00	44.09	1.52
2103	4836	9.412460	ACTTTATTTTCTGATATCCTTGCATCA	57.588	29.630	0.00	0.00	0.00	3.07
2146	5154	6.702716	AAGAAGACCTAGAGATAAACGAGG	57.297	41.667	0.00	0.00	0.00	4.63
2165	5173	8.649973	AACGAGGAACATAATTCTTCTATGAC	57.350	34.615	0.00	0.00	32.20	3.06
2467	5551	8.545229	ACTCACTCAACAATCTTTAGATGAAG	57.455	34.615	0.00	0.00	34.49	3.02
2470	5554	6.656693	CACTCAACAATCTTTAGATGAAGGGT	59.343	38.462	0.00	0.00	34.49	4.34
2482	5570	2.489938	TGAAGGGTGGAGCATTACAC	57.510	50.000	0.00	0.00	36.89	2.90
2487	5575	1.271926	GGGTGGAGCATTACACAACCT	60.272	52.381	0.00	0.00	37.71	3.50
2649	6991	1.077429	GAGCAACTCACCATCCCCC	60.077	63.158	0.00	0.00	0.00	5.40
2689	7037	4.382685	CCAACCTACCGTCATACTTGTCAT	60.383	45.833	0.00	0.00	0.00	3.06
2842	7193	1.135859	CCATCTCAAACAAGTCAGCGC	60.136	52.381	0.00	0.00	0.00	5.92
2863	7214	1.414919	AGTGAGTAACAACGGGAGCAA	59.585	47.619	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.537300	TTGACTGCAATATCTACTCCCTC	57.463	43.478	0.00	0.00	0.00	4.30
3	4	4.926238	CCGATTGACTGCAATATCTACTCC	59.074	45.833	0.00	0.00	44.47	3.85
4	5	5.533482	ACCGATTGACTGCAATATCTACTC	58.467	41.667	0.00	0.00	44.47	2.59
103	104	8.854614	ACTTAAAAGATTCAGTGCAGTTCTAT	57.145	30.769	0.00	0.00	0.00	1.98
104	105	8.677148	AACTTAAAAGATTCAGTGCAGTTCTA	57.323	30.769	0.00	0.00	0.00	2.10
216	220	5.649395	CCTCTTTCAGATGCTGGTCATTTTA	59.351	40.000	0.00	0.00	35.05	1.52
282	292	2.112297	GTCGTTTCAGCCACCCCA	59.888	61.111	0.00	0.00	0.00	4.96
519	538	0.729116	GGAGTTGTGGACATCATGCG	59.271	55.000	0.00	0.00	0.00	4.73
624	644	1.004044	CTCCAGGCTCCAGTTGTTGAT	59.996	52.381	0.00	0.00	0.00	2.57
631	651	1.203441	TCAATGCTCCAGGCTCCAGT	61.203	55.000	0.00	0.00	42.39	4.00
739	1673	6.821388	ACGAATAAGATCCAAGATAAGCTGT	58.179	36.000	0.00	0.00	0.00	4.40
798	2229	5.123979	CAGAATTGGGGCTAGTCTTTTGTAC	59.876	44.000	0.00	0.00	0.00	2.90
801	2236	3.445096	CCAGAATTGGGGCTAGTCTTTTG	59.555	47.826	0.00	0.00	41.05	2.44
849	2284	1.158227	ATTGCTTTTGGGAGGGGCA	59.842	52.632	0.00	0.00	0.00	5.36
904	2339	7.272978	AGAAAATCGGGGATAATATACATCCG	58.727	38.462	9.20	0.00	42.57	4.18
946	2381	3.118738	AGTGCTTAATCGAGGTGTAAGGG	60.119	47.826	0.00	0.00	0.00	3.95
1035	2472	2.925594	GCTATAGGCTGCTGCTTCC	58.074	57.895	15.64	1.72	39.59	3.46
1071	2508	4.000325	CCTCTGTATCTCGATCGATCAGT	59.000	47.826	24.40	7.52	0.00	3.41
1178	2621	2.034532	TGTGGGACATGCAGCAGG	59.965	61.111	5.26	5.26	44.52	4.85
1416	2859	1.964223	ACATATCAGGACTACAGGGCG	59.036	52.381	0.00	0.00	0.00	6.13
1475	3001	8.980481	TCTCTCACAAATAATTATTCCCTTCC	57.020	34.615	11.08	0.00	0.00	3.46
1489	3015	6.528321	TCAGAATGAACACTCTCTCACAAAT	58.472	36.000	0.00	0.00	45.97	2.32
1548	3247	2.988010	TGGGAGCTATGTGTGATGTC	57.012	50.000	0.00	0.00	0.00	3.06
1606	3305	1.522668	TCACGCAAACTCTTCATGGG	58.477	50.000	0.00	0.00	0.00	4.00
1621	3320	4.794248	TCAGAATGAACACTGTTTCACG	57.206	40.909	0.00	0.00	45.97	4.35
1749	3451	8.950210	CAGAGGCTCTTAAGATCAAAATTACAA	58.050	33.333	15.90	0.00	0.00	2.41
1803	3505	4.648970	GCTACGTTAAAATCTTCAGTGCC	58.351	43.478	0.00	0.00	0.00	5.01
1850	4526	1.533625	TATTGCAGTTGCCGCTCTTT	58.466	45.000	1.06	0.00	41.18	2.52
1904	4588	2.887152	ACACAAATGAAGCTTCCTCACC	59.113	45.455	23.42	0.00	0.00	4.02
1912	4596	3.554934	TGTCCAGAACACAAATGAAGCT	58.445	40.909	0.00	0.00	31.20	3.74
1928	4612	2.118233	TATGCGCACCTGGTTGTCCA	62.118	55.000	14.90	0.00	42.05	4.02
1929	4613	0.748005	ATATGCGCACCTGGTTGTCC	60.748	55.000	14.90	0.00	0.00	4.02
1931	4615	1.544724	AAATATGCGCACCTGGTTGT	58.455	45.000	14.90	0.00	0.00	3.32
1932	4616	2.094803	TGAAAATATGCGCACCTGGTTG	60.095	45.455	14.90	0.00	0.00	3.77
1933	4617	2.094752	GTGAAAATATGCGCACCTGGTT	60.095	45.455	14.90	3.12	0.00	3.67
1935	4619	1.202290	GGTGAAAATATGCGCACCTGG	60.202	52.381	14.90	0.00	45.58	4.45
1936	4620	2.193306	GGTGAAAATATGCGCACCTG	57.807	50.000	14.90	0.00	45.58	4.00
2006	4739	6.891361	ACTGGTAATGAATTTGTGATGATGGA	59.109	34.615	0.00	0.00	0.00	3.41
2467	5551	1.173913	GGTTGTGTAATGCTCCACCC	58.826	55.000	0.00	0.00	0.00	4.61
2470	5554	3.788227	AGAAGGTTGTGTAATGCTCCA	57.212	42.857	0.00	0.00	0.00	3.86
2482	5570	6.216750	CTTCTTTTCGACACTAGAAGGTTG	57.783	41.667	13.30	0.00	39.77	3.77
2487	5575	5.007332	GCAAACCTTCTTTTCGACACTAGAA	59.993	40.000	0.00	0.00	0.00	2.10
2531	5619	7.668492	AGAAGTCGGTCTTAGTCACTTTAATT	58.332	34.615	0.00	0.00	36.40	1.40
2649	6991	0.887247	TGGATTTGATGGTTGTGCCG	59.113	50.000	0.00	0.00	41.21	5.69
2689	7037	0.175760	GCGGAGATCAAGGTGCAGTA	59.824	55.000	0.00	0.00	0.00	2.74
2842	7193	1.270094	TGCTCCCGTTGTTACTCACTG	60.270	52.381	0.00	0.00	0.00	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.