AutoCloner

Multiple sequence alignment - TraesCS3B01G519200

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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	TraesCS3B01G519200	chr3B	100.000	2390	0	0	1	2390	762309850	762307461	0.000000e+00	4414.0
1	TraesCS3B01G519200	chr3B	86.842	228	20	5	194	417	762373496	762373275	1.830000e-61	246.0
2	TraesCS3B01G519200	chr3B	88.652	141	15	1	194	333	762592443	762592303	1.140000e-38	171.0
3	TraesCS3B01G519200	chr3A	96.738	1870	57	2	525	2390	707126679	707124810	0.000000e+00	3112.0
4	TraesCS3B01G519200	chr3A	85.246	305	33	10	204	503	707127099	707126802	1.070000e-78	303.0
5	TraesCS3B01G519200	chr3A	93.048	187	12	1	1	187	707127511	707127326	3.030000e-69	272.0
6	TraesCS3B01G519200	chr3A	100.000	43	0	0	487	529	707126750	707126708	1.970000e-11	80.5
7	TraesCS3B01G519200	chr3D	96.787	1774	43	5	621	2390	573121776	573120013	0.000000e+00	2948.0
8	TraesCS3B01G519200	chr3D	88.210	229	16	6	194	417	573123171	573122949	1.820000e-66	263.0
9	TraesCS3B01G519200	chr3D	90.811	185	10	3	439	622	573122302	573122124	8.540000e-60	241.0
10	TraesCS3B01G519200	chr3D	84.507	213	30	3	205	417	573149563	573149354	8.660000e-50	207.0
11	TraesCS3B01G519200	chr1D	93.711	1781	92	8	618	2390	423056983	423058751	0.000000e+00	2651.0
12	TraesCS3B01G519200	chr1B	93.326	1783	92	17	618	2389	572308818	572310584	0.000000e+00	2608.0
13	TraesCS3B01G519200	chr1A	94.153	1642	79	7	755	2390	518986694	518988324	0.000000e+00	2484.0
14	TraesCS3B01G519200	chr7D	93.167	600	33	4	1797	2389	139368876	139369474	0.000000e+00	874.0
15	TraesCS3B01G519200	chr4A	90.365	602	49	4	1797	2389	220627174	220627775	0.000000e+00	782.0
16	TraesCS3B01G519200	chr6A	93.210	162	10	1	1797	1957	395654132	395653971	1.100000e-58	237.0
17	TraesCS3B01G519200	chr2A	92.593	162	11	1	1797	1957	315573836	315573675	5.140000e-57	231.0

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	TraesCS3B01G519200	chr3B	762307461	762309850	2389	True	4414.000000	4414	100.000	1	2390	1	chr3B.!!$R1	2389
1	TraesCS3B01G519200	chr3A	707124810	707127511	2701	True	941.875000	3112	93.758	1	2390	4	chr3A.!!$R1	2389
2	TraesCS3B01G519200	chr3D	573120013	573123171	3158	True	1150.666667	2948	91.936	194	2390	3	chr3D.!!$R2	2196
3	TraesCS3B01G519200	chr1D	423056983	423058751	1768	False	2651.000000	2651	93.711	618	2390	1	chr1D.!!$F1	1772
4	TraesCS3B01G519200	chr1B	572308818	572310584	1766	False	2608.000000	2608	93.326	618	2389	1	chr1B.!!$F1	1771
5	TraesCS3B01G519200	chr1A	518986694	518988324	1630	False	2484.000000	2484	94.153	755	2390	1	chr1A.!!$F1	1635
6	TraesCS3B01G519200	chr7D	139368876	139369474	598	False	874.000000	874	93.167	1797	2389	1	chr7D.!!$F1	592
7	TraesCS3B01G519200	chr4A	220627174	220627775	601	False	782.000000	782	90.365	1797	2389	1	chr4A.!!$F1	592

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
916	2214	0.178068	TGTTTCTATCCTGCCTCGCC	59.822	55.0	0.0	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1896	3198	1.446907	CTGCCATTCACACAGTCCTC	58.553	55.0	0.0	0.0	0.0	3.71	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
22	23	5.156608	TCTCATCTGCTTTTGTGAGATGA	57.843	39.130	0.00	0.00	46.29	2.92
24	25	3.688185	TCATCTGCTTTTGTGAGATGAGC	59.312	43.478	0.00	0.00	44.55	4.26
27	28	1.881973	TGCTTTTGTGAGATGAGCCAC	59.118	47.619	0.00	0.00	32.53	5.01
132	133	1.684734	GGGGAACACTCTCGGCCTA	60.685	63.158	0.00	0.00	0.00	3.93
135	136	0.530870	GGAACACTCTCGGCCTATGC	60.531	60.000	0.00	0.00	0.00	3.14
160	161	4.215399	GCGTGCCTTTATATAAGGATGCAA	59.785	41.667	12.61	0.00	39.81	4.08
162	163	6.317088	CGTGCCTTTATATAAGGATGCAATG	58.683	40.000	14.34	2.02	39.81	2.82
187	188	4.226427	TCTCCTGCTCAATACTTGCATT	57.774	40.909	0.00	0.00	36.07	3.56
188	189	5.357742	TCTCCTGCTCAATACTTGCATTA	57.642	39.130	0.00	0.00	36.07	1.90
189	190	5.363101	TCTCCTGCTCAATACTTGCATTAG	58.637	41.667	0.00	0.00	36.07	1.73
190	191	5.102953	TCCTGCTCAATACTTGCATTAGT	57.897	39.130	0.00	0.00	36.07	2.24
192	193	6.649155	TCCTGCTCAATACTTGCATTAGTAA	58.351	36.000	2.47	0.00	34.50	2.24
194	195	7.227314	TCCTGCTCAATACTTGCATTAGTAATG	59.773	37.037	17.09	17.09	41.85	1.90
195	196	7.263100	TGCTCAATACTTGCATTAGTAATGG	57.737	36.000	21.56	9.78	39.31	3.16
196	197	6.262944	TGCTCAATACTTGCATTAGTAATGGG	59.737	38.462	21.56	10.24	35.83	4.00
197	198	6.486657	GCTCAATACTTGCATTAGTAATGGGA	59.513	38.462	21.56	5.22	35.07	4.37
199	200	6.998074	TCAATACTTGCATTAGTAATGGGAGG	59.002	38.462	21.56	8.92	39.31	4.30
201	202	3.053693	ACTTGCATTAGTAATGGGAGGCA	60.054	43.478	21.56	11.75	39.31	4.75
254	466	1.722011	AACGCATGGACTAACCGAAG	58.278	50.000	0.00	0.00	42.61	3.79
256	468	0.739462	CGCATGGACTAACCGAAGCA	60.739	55.000	0.00	0.00	42.61	3.91
300	512	5.719563	AGTACTTTTGGGGGTGGAAATATTG	59.280	40.000	0.00	0.00	0.00	1.90
337	551	2.233922	TCAGCAACTAGGTTAGTGCCTC	59.766	50.000	0.00	0.00	39.39	4.70
339	553	2.234908	AGCAACTAGGTTAGTGCCTCAG	59.765	50.000	0.00	0.00	39.39	3.35
340	554	2.028020	GCAACTAGGTTAGTGCCTCAGT	60.028	50.000	0.00	0.00	39.39	3.41
341	555	3.589988	CAACTAGGTTAGTGCCTCAGTG	58.410	50.000	0.00	0.00	39.39	3.66
343	557	3.507411	ACTAGGTTAGTGCCTCAGTGAA	58.493	45.455	0.00	0.00	39.94	3.18
344	558	2.841442	AGGTTAGTGCCTCAGTGAAC	57.159	50.000	0.00	0.00	32.39	3.18
345	559	1.000955	AGGTTAGTGCCTCAGTGAACG	59.999	52.381	0.00	0.00	32.39	3.95
346	560	1.429463	GTTAGTGCCTCAGTGAACGG	58.571	55.000	0.00	0.00	0.00	4.44
382	596	1.789464	GCAAGTCGTGTCTGAACTCTG	59.211	52.381	0.00	0.00	0.00	3.35
383	597	2.799917	GCAAGTCGTGTCTGAACTCTGT	60.800	50.000	0.00	0.00	0.00	3.41
431	1271	2.496070	AGACTGCATACGCTACAGGAAA	59.504	45.455	0.00	0.00	39.64	3.13
433	1273	3.670625	ACTGCATACGCTACAGGAAAAA	58.329	40.909	0.00	0.00	39.64	1.94
533	1475	6.238402	GCAAAGGCCTTAATAAGTACTAGCAC	60.238	42.308	20.84	0.00	0.00	4.40
569	1511	6.322201	CCTCATCTTACCTTTGCATATGGTTT	59.678	38.462	4.56	0.00	35.92	3.27
645	1938	3.291809	TCTTGCTGCACAATTCACATG	57.708	42.857	0.00	0.00	37.72	3.21
916	2214	0.178068	TGTTTCTATCCTGCCTCGCC	59.822	55.000	0.00	0.00	0.00	5.54
958	2260	9.206870	GAAAAGAACAGGCAAAAATAATCATCA	57.793	29.630	0.00	0.00	0.00	3.07
1029	2331	7.553044	ACTGAACTAAAAATACAGAGGTATGCC	59.447	37.037	0.00	0.00	40.09	4.40
1104	2406	0.815734	CCTTTGCAGCCTCCAGAATG	59.184	55.000	0.00	0.00	0.00	2.67
1212	2514	1.745115	ATCCATGTGGTTCACGGCG	60.745	57.895	4.80	4.80	37.14	6.46
1257	2559	1.450312	GCCAAGGGACACCGATGAG	60.450	63.158	0.00	0.00	43.47	2.90
1310	2612	1.751927	GGAGGGCCATGAGTGCAAG	60.752	63.158	6.18	0.00	0.00	4.01
1311	2613	1.001641	GAGGGCCATGAGTGCAAGT	60.002	57.895	6.18	0.00	0.00	3.16
1329	2631	1.890041	TGCCGAGACAACAAACCCG	60.890	57.895	0.00	0.00	0.00	5.28
1611	2913	5.452776	CCTTCGCCATGGTATCTTTACAGTA	60.453	44.000	14.67	0.00	0.00	2.74
1626	2928	1.138266	ACAGTACGAGGTGCAACAACT	59.862	47.619	3.64	0.00	39.98	3.16
1644	2946	0.459237	CTCCTACTGACTGCGCCTTG	60.459	60.000	4.18	0.00	0.00	3.61
2362	3678	6.037830	CACGAATATTTACCAGGGTTTACCAG	59.962	42.308	0.00	0.00	43.89	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	4.988598	ACTCAACGGTGGCTGCGG	62.989	66.667	0.00	0.00	0.00	5.69
36	37	1.013596	TGTGTGCTTCAACTCAACGG	58.986	50.000	0.00	0.00	0.00	4.44
99	100	5.899547	AGTGTTCCCCTCTTTTCTGAAAAAT	59.100	36.000	15.67	0.00	34.00	1.82
116	117	0.530870	GCATAGGCCGAGAGTGTTCC	60.531	60.000	0.00	0.00	0.00	3.62
135	136	3.034721	TCCTTATATAAAGGCACGCGG	57.965	47.619	12.47	0.00	37.34	6.46
137	138	3.751175	TGCATCCTTATATAAAGGCACGC	59.249	43.478	3.08	7.03	37.34	5.34
160	161	2.776536	AGTATTGAGCAGGAGAAGGCAT	59.223	45.455	0.00	0.00	0.00	4.40
162	163	2.998316	AGTATTGAGCAGGAGAAGGC	57.002	50.000	0.00	0.00	0.00	4.35
187	188	4.816126	ACTACAGATGCCTCCCATTACTA	58.184	43.478	0.00	0.00	33.29	1.82
188	189	3.658725	ACTACAGATGCCTCCCATTACT	58.341	45.455	0.00	0.00	33.29	2.24
189	190	4.141711	TGAACTACAGATGCCTCCCATTAC	60.142	45.833	0.00	0.00	33.29	1.89
190	191	4.037222	TGAACTACAGATGCCTCCCATTA	58.963	43.478	0.00	0.00	33.29	1.90
192	193	2.481441	TGAACTACAGATGCCTCCCAT	58.519	47.619	0.00	0.00	36.70	4.00
194	195	3.567478	AATGAACTACAGATGCCTCCC	57.433	47.619	0.00	0.00	0.00	4.30
195	196	4.345257	TCCTAATGAACTACAGATGCCTCC	59.655	45.833	0.00	0.00	0.00	4.30
196	197	5.537300	TCCTAATGAACTACAGATGCCTC	57.463	43.478	0.00	0.00	0.00	4.70
197	198	5.957771	TTCCTAATGAACTACAGATGCCT	57.042	39.130	0.00	0.00	0.00	4.75
199	200	5.471456	CCCATTCCTAATGAACTACAGATGC	59.529	44.000	1.23	0.00	41.46	3.91
201	202	6.043706	CCTCCCATTCCTAATGAACTACAGAT	59.956	42.308	1.23	0.00	41.46	2.90
337	551	7.317842	TCTCTTATAGTACTTCCGTTCACTG	57.682	40.000	0.00	0.00	0.00	3.66
339	553	6.183360	TGCTCTCTTATAGTACTTCCGTTCAC	60.183	42.308	0.00	0.00	0.00	3.18
340	554	5.884232	TGCTCTCTTATAGTACTTCCGTTCA	59.116	40.000	0.00	0.00	0.00	3.18
341	555	6.374565	TGCTCTCTTATAGTACTTCCGTTC	57.625	41.667	0.00	0.00	0.00	3.95
343	557	5.887035	ACTTGCTCTCTTATAGTACTTCCGT	59.113	40.000	0.00	0.00	0.00	4.69
344	558	6.380095	ACTTGCTCTCTTATAGTACTTCCG	57.620	41.667	0.00	0.00	0.00	4.30
345	559	6.038492	ACGACTTGCTCTCTTATAGTACTTCC	59.962	42.308	0.00	0.00	0.00	3.46
346	560	6.908284	CACGACTTGCTCTCTTATAGTACTTC	59.092	42.308	0.00	0.00	0.00	3.01
350	564	6.037281	CAGACACGACTTGCTCTCTTATAGTA	59.963	42.308	0.00	0.00	0.00	1.82
351	565	4.944930	AGACACGACTTGCTCTCTTATAGT	59.055	41.667	0.00	0.00	0.00	2.12
352	566	5.065346	TCAGACACGACTTGCTCTCTTATAG	59.935	44.000	0.00	0.00	0.00	1.31
382	596	7.592903	CCTTTTCTGAATTTCTTTCTGTAGCAC	59.407	37.037	0.00	0.00	35.44	4.40
383	597	7.502226	TCCTTTTCTGAATTTCTTTCTGTAGCA	59.498	33.333	0.00	0.00	35.44	3.49
540	1482	7.335422	CCATATGCAAAGGTAAGATGAGGATAC	59.665	40.741	0.00	0.00	0.00	2.24
545	1487	6.949352	AACCATATGCAAAGGTAAGATGAG	57.051	37.500	8.30	0.00	34.63	2.90
577	1519	7.286316	AGGAAGCCTGAAATATTATGGTCAAAG	59.714	37.037	0.00	0.00	29.57	2.77
670	1965	5.822519	TGGGCATACATCATCTCTGTTTTAC	59.177	40.000	0.00	0.00	0.00	2.01
671	1966	6.000246	TGGGCATACATCATCTCTGTTTTA	58.000	37.500	0.00	0.00	0.00	1.52
742	2037	7.675161	TGATCCTATGACTCTGTTATTCCAA	57.325	36.000	0.00	0.00	0.00	3.53
916	2214	3.187637	TCTTTTCTTGTCATTTACGGGCG	59.812	43.478	0.00	0.00	0.00	6.13
958	2260	7.560368	ACTGGTGAGAAGATTTTCGAATAGAT	58.440	34.615	0.00	0.00	38.38	1.98
1029	2331	4.095782	TGGAAAACAGTCTTCTTTGTTCCG	59.904	41.667	0.00	0.00	36.56	4.30
1104	2406	2.741211	GTCGGCCTCACGGGAAAC	60.741	66.667	0.00	0.00	37.23	2.78
1119	2421	1.523938	GGCTGGGATAGTTGGCGTC	60.524	63.158	0.00	0.00	0.00	5.19
1310	2612	1.652563	GGGTTTGTTGTCTCGGCAC	59.347	57.895	0.00	0.00	0.00	5.01
1311	2613	1.890041	CGGGTTTGTTGTCTCGGCA	60.890	57.895	0.00	0.00	0.00	5.69
1329	2631	3.636153	AGGAAGCTCCTTAACACCATC	57.364	47.619	0.00	0.00	46.91	3.51
1611	2913	1.045407	TAGGAGTTGTTGCACCTCGT	58.955	50.000	0.00	0.00	34.42	4.18
1626	2928	0.898326	TCAAGGCGCAGTCAGTAGGA	60.898	55.000	10.83	0.00	0.00	2.94
1644	2946	3.153919	AGTAGCATCTCGGGAGAAGATC	58.846	50.000	2.00	0.00	41.36	2.75
1896	3198	1.446907	CTGCCATTCACACAGTCCTC	58.553	55.000	0.00	0.00	0.00	3.71
2362	3678	4.461198	TGGAAGGAAGAAAGACAGGTTTC	58.539	43.478	0.00	0.00	36.79	2.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.