AutoCloner

Multiple sequence alignment - TraesCS3B01G383300

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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	TraesCS3B01G383300	chr3B	100.000	5089	0	0	1	5089	603447215	603452303	0.000000e+00	9398.0
1	TraesCS3B01G383300	chr3B	88.561	271	23	4	2424	2693	330679942	330680205	6.360000e-84	322.0
2	TraesCS3B01G383300	chr3B	77.128	376	83	2	4717	5089	650953126	650953501	1.110000e-51	215.0
3	TraesCS3B01G383300	chr3B	75.266	376	90	1	4717	5089	651258447	651258072	5.240000e-40	176.0
4	TraesCS3B01G383300	chr3B	95.181	83	4	0	1824	1906	526495893	526495811	1.150000e-26	132.0
5	TraesCS3B01G383300	chr3B	93.103	87	6	0	1823	1909	99019527	99019441	1.490000e-25	128.0
6	TraesCS3B01G383300	chr3B	91.667	60	5	0	3748	3807	736650678	736650619	3.270000e-12	84.2
7	TraesCS3B01G383300	chr3D	92.667	1500	59	9	2041	3520	456594280	456595748	0.000000e+00	2113.0
8	TraesCS3B01G383300	chr3D	92.358	1374	55	9	1908	3235	456594121	456595490	0.000000e+00	1910.0
9	TraesCS3B01G383300	chr3D	88.861	1203	52	21	431	1557	456592617	456593813	0.000000e+00	1404.0
10	TraesCS3B01G383300	chr3D	94.222	675	29	7	3620	4292	456595809	456596475	0.000000e+00	1022.0
11	TraesCS3B01G383300	chr3D	96.735	490	16	0	4600	5089	456596750	456597239	0.000000e+00	817.0
12	TraesCS3B01G383300	chr3D	84.636	371	45	6	1463	1825	456593755	456594121	4.840000e-95	359.0
13	TraesCS3B01G383300	chr3D	85.978	271	20	3	1	254	456591873	456592142	1.810000e-69	274.0
14	TraesCS3B01G383300	chr3D	76.596	376	85	2	4717	5089	488117910	488118285	2.400000e-48	204.0
15	TraesCS3B01G383300	chr3D	74.734	376	92	1	4717	5089	488236052	488235677	1.130000e-36	165.0
16	TraesCS3B01G383300	chr3D	93.182	88	5	1	1820	1906	329496861	329496948	1.490000e-25	128.0
17	TraesCS3B01G383300	chr3D	96.970	33	0	1	2367	2399	414906178	414906209	3.000000e-03	54.7
18	TraesCS3B01G383300	chr3A	89.145	1299	81	28	3007	4292	599381707	599382958	0.000000e+00	1563.0
19	TraesCS3B01G383300	chr3A	92.634	991	47	8	1908	2872	599380720	599381710	0.000000e+00	1402.0
20	TraesCS3B01G383300	chr3A	85.385	1300	83	28	601	1825	599379453	599380720	0.000000e+00	1249.0
21	TraesCS3B01G383300	chr3A	96.735	490	16	0	4600	5089	599384462	599384951	0.000000e+00	817.0
22	TraesCS3B01G383300	chr3A	91.403	221	19	0	2424	2644	666820362	666820142	2.300000e-78	303.0
23	TraesCS3B01G383300	chr3A	76.517	379	83	4	4717	5089	631727890	631728268	8.640000e-48	202.0
24	TraesCS3B01G383300	chr3A	88.571	140	13	3	1	138	599378733	599378871	3.150000e-37	167.0
25	TraesCS3B01G383300	chr3A	89.655	58	5	1	197	254	599379189	599379245	7.070000e-09	73.1
26	TraesCS3B01G383300	chr3A	100.000	29	0	0	2372	2400	600316558	600316530	3.000000e-03	54.7
27	TraesCS3B01G383300	chr5D	86.824	296	34	4	2688	2979	404748626	404748920	4.910000e-85	326.0
28	TraesCS3B01G383300	chr5D	95.181	83	4	0	1824	1906	382868411	382868493	1.150000e-26	132.0
29	TraesCS3B01G383300	chr5D	93.023	86	6	0	1824	1909	411995116	411995031	5.350000e-25	126.0
30	TraesCS3B01G383300	chr7A	86.149	296	35	5	2688	2979	477604580	477604287	1.060000e-81	315.0
31	TraesCS3B01G383300	chr7A	93.103	87	6	0	1824	1910	596726035	596725949	1.490000e-25	128.0
32	TraesCS3B01G383300	chr7A	96.875	32	1	0	2372	2403	501067493	501067462	3.000000e-03	54.7
33	TraesCS3B01G383300	chr1B	85.859	297	35	6	2688	2979	80103784	80103490	4.950000e-80	309.0
34	TraesCS3B01G383300	chr2B	87.500	272	25	5	2424	2693	599830795	599830531	6.400000e-79	305.0
35	TraesCS3B01G383300	chr2B	84.672	137	13	2	4921	5057	627652435	627652307	4.130000e-26	130.0
36	TraesCS3B01G383300	chr6B	91.403	221	19	0	2424	2644	172705731	172705511	2.300000e-78	303.0
37	TraesCS3B01G383300	chr6B	85.473	296	38	4	2688	2979	221738493	221738199	2.300000e-78	303.0
38	TraesCS3B01G383300	chr6B	96.429	84	3	0	1823	1906	8403635	8403552	6.870000e-29	139.0
39	TraesCS3B01G383300	chr6B	93.750	64	3	1	3748	3810	605554236	605554299	1.510000e-15	95.3
40	TraesCS3B01G383300	chr6B	94.286	35	1	1	2372	2406	123500541	123500508	9.000000e-03	52.8
41	TraesCS3B01G383300	chr2A	85.473	296	38	4	2688	2979	741419800	741420094	2.300000e-78	303.0
42	TraesCS3B01G383300	chr2A	91.892	37	3	0	2372	2408	695313933	695313897	9.000000e-03	52.8
43	TraesCS3B01G383300	chr7B	86.813	273	31	5	2688	2958	478040671	478040402	2.980000e-77	300.0
44	TraesCS3B01G383300	chr7B	97.222	36	1	0	3777	3812	521143273	521143308	1.530000e-05	62.1
45	TraesCS3B01G383300	chr1D	82.216	343	59	2	4709	5050	394670660	394671001	1.390000e-75	294.0
46	TraesCS3B01G383300	chr1D	94.318	88	5	0	1822	1909	363804258	363804171	8.890000e-28	135.0
47	TraesCS3B01G383300	chr1D	91.954	87	6	1	1823	1909	97862744	97862659	2.490000e-23	121.0
48	TraesCS3B01G383300	chr4B	88.889	216	22	2	2688	2902	560902965	560903179	1.090000e-66	265.0
49	TraesCS3B01G383300	chr4B	96.970	33	1	0	3786	3818	139702010	139702042	7.120000e-04	56.5
50	TraesCS3B01G383300	chr6A	94.318	88	4	1	1819	1906	27782697	27782783	3.200000e-27	134.0
51	TraesCS3B01G383300	chr4A	94.048	84	5	0	1823	1906	113335691	113335608	1.490000e-25	128.0
52	TraesCS3B01G383300	chr4A	96.875	32	0	1	3786	3817	175550106	175550136	9.000000e-03	52.8
53	TraesCS3B01G383300	chr2D	91.860	86	7	0	1824	1909	454026263	454026178	2.490000e-23	121.0
54	TraesCS3B01G383300	chr2D	84.146	82	11	2	197	277	498865869	498865789	1.520000e-10	78.7
55	TraesCS3B01G383300	chr2D	100.000	32	0	0	3787	3818	616935200	616935169	5.500000e-05	60.2
56	TraesCS3B01G383300	chr2D	94.286	35	2	0	2366	2400	166738807	166738841	3.000000e-03	54.7
57	TraesCS3B01G383300	chr4D	90.909	88	8	0	1819	1906	266786405	266786492	8.950000e-23	119.0
58	TraesCS3B01G383300	chr1A	90.698	86	8	0	1824	1909	439847104	439847019	1.160000e-21	115.0
59	TraesCS3B01G383300	chr1A	100.000	34	0	0	3777	3810	578016642	578016675	4.250000e-06	63.9
60	TraesCS3B01G383300	chrUn	86.667	75	10	0	3737	3811	217865590	217865516	3.270000e-12	84.2
61	TraesCS3B01G383300	chrUn	85.897	78	11	0	3734	3811	218107981	218108058	3.270000e-12	84.2
62	TraesCS3B01G383300	chrUn	85.897	78	11	0	3734	3811	478575281	478575358	3.270000e-12	84.2
63	TraesCS3B01G383300	chr5A	94.118	34	2	0	2372	2405	326533321	326533288	9.000000e-03	52.8

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	TraesCS3B01G383300	chr3B	603447215	603452303	5088	False	9398.000000	9398	100.000000	1	5089	1	chr3B.!!$F2	5088
1	TraesCS3B01G383300	chr3D	456591873	456597239	5366	False	1128.428571	2113	90.779571	1	5089	7	chr3D.!!$F4	5088
2	TraesCS3B01G383300	chr3A	599378733	599384951	6218	False	878.516667	1563	90.354167	1	5089	6	chr3A.!!$F2	5088

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 end TH	Hairpin	End Stability	Orientation
69	70	0.240678	TGTTGCACGGACATGAATGC	59.759	50.0	4.0	38.59	3.56	F
1190	1826	0.179142	GGTACGTCGCCTCTTCTTCC	60.179	60.0	0.0	0.00	3.46	F
1906	2632	0.178932	TATCATGGGACGGAGGGAGG	60.179	60.0	0.0	0.00	4.30	F
2751	3504	0.973632	ACACATTAGCCAGGACGTGA	59.026	50.0	0.0	0.00	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1887	2613	0.178932	CCTCCCTCCGTCCCATGATA	60.179	60.0	2.15	R
3095	3867	0.780637	TGGCCCTTAACCCACAATGA	59.219	50.0	2.57	R
3564	4336	0.106268	TGTGTTGGCCCAGTGTCATT	60.106	50.0	2.57	R
4563	5430	0.108138	CCCTCGTTCTTTCGCCAGAT	60.108	55.0	2.90	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	0.606096	TTCGCCATCTCCAAAGTCGA	59.394	50.000	0.00	0.00	0.00	4.20
48	49	2.416836	CCATCTCCAAAGTCGACGCTAA	60.417	50.000	10.46	0.00	0.00	3.09
54	55	2.096909	CCAAAGTCGACGCTAAGTGTTG	60.097	50.000	10.46	5.77	0.00	3.33
69	70	0.240678	TGTTGCACGGACATGAATGC	59.759	50.000	0.00	4.00	38.59	3.56
75	76	2.599973	GCACGGACATGAATGCATTTTC	59.400	45.455	14.33	2.94	38.00	2.29
177	181	3.991536	GAGTTCGGCTCGGTGCTCC	62.992	68.421	1.77	0.00	42.39	4.70
254	527	8.685838	AAATGTTTGAGCCACTAACTTAAGTA	57.314	30.769	8.92	0.00	35.79	2.24
258	531	9.953565	TGTTTGAGCCACTAACTTAAGTATATT	57.046	29.630	8.92	0.00	35.79	1.28
261	534	7.792032	TGAGCCACTAACTTAAGTATATTGCT	58.208	34.615	8.92	13.98	0.00	3.91
262	535	7.710907	TGAGCCACTAACTTAAGTATATTGCTG	59.289	37.037	20.07	6.52	0.00	4.41
292	652	4.546829	TGTCCCTGTAGACACATTTACC	57.453	45.455	0.00	0.00	41.78	2.85
299	659	5.421056	CCTGTAGACACATTTACCAGTAGGA	59.579	44.000	0.00	0.00	34.49	2.94
300	660	6.098409	CCTGTAGACACATTTACCAGTAGGAT	59.902	42.308	0.00	0.00	34.49	3.24
305	665	5.175859	ACACATTTACCAGTAGGATCAACG	58.824	41.667	0.00	0.00	38.69	4.10
309	669	1.267121	ACCAGTAGGATCAACGCACT	58.733	50.000	0.00	0.00	38.69	4.40
331	691	8.598924	GCACTAGAATAATAACCATCATCGATG	58.401	37.037	19.61	19.61	39.52	3.84
344	704	6.313905	ACCATCATCGATGAAAAGAAGTGTAC	59.686	38.462	30.41	0.00	42.09	2.90
386	746	2.357034	ACACAAGCGCGGACGAAT	60.357	55.556	8.83	0.00	43.93	3.34
429	1000	6.703319	TCCATTAAAGATAAACACTGACCGA	58.297	36.000	0.00	0.00	0.00	4.69
452	1023	3.334691	TCCGACGAGATGCAAATTCTTT	58.665	40.909	0.00	0.00	0.00	2.52
475	1057	1.052617	TCATCACCTCCAAACCGTCA	58.947	50.000	0.00	0.00	0.00	4.35
533	1126	0.248458	CACCACCACGCAAACAGTTC	60.248	55.000	0.00	0.00	0.00	3.01
595	1189	3.963383	ACAAACGAGTGACCACAAATC	57.037	42.857	2.78	0.00	0.00	2.17
704	1300	0.389948	GCGTCACGAGGATCCAAAGT	60.390	55.000	15.82	7.75	0.00	2.66
743	1340	1.302832	CGCACAAGCCTTCCTTCCT	60.303	57.895	0.00	0.00	37.52	3.36

Showing 1 to 25 of 284 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.236147	CGAAGCCATGATGATGAGTCTAG	58.764	47.826	0.00	0.00	0.00	2.43
42	43	1.068417	TCCGTGCAACACTTAGCGT	59.932	52.632	0.00	0.00	35.74	5.07
48	49	1.536766	CATTCATGTCCGTGCAACACT	59.463	47.619	0.00	0.00	35.74	3.55
54	55	2.282701	AAATGCATTCATGTCCGTGC	57.717	45.000	13.38	0.21	38.05	5.34
118	122	7.938563	TGGAGTTATTTTTGGAAAACATTCG	57.061	32.000	0.00	0.00	0.00	3.34
177	181	9.775854	AATTATCTAGTTTCCATCAGTGATCTG	57.224	33.333	1.56	0.00	42.54	2.90
229	502	7.582667	ACTTAAGTTAGTGGCTCAAACATTT	57.417	32.000	1.12	0.00	0.00	2.32
230	503	8.863872	ATACTTAAGTTAGTGGCTCAAACATT	57.136	30.769	14.49	0.00	0.00	2.71
235	508	8.265055	AGCAATATACTTAAGTTAGTGGCTCAA	58.735	33.333	14.49	0.00	0.00	3.02
277	620	6.666113	TGATCCTACTGGTAAATGTGTCTACA	59.334	38.462	0.00	0.00	36.52	2.74
288	648	2.829720	AGTGCGTTGATCCTACTGGTAA	59.170	45.455	0.00	0.00	34.23	2.85
292	652	4.371855	TTCTAGTGCGTTGATCCTACTG	57.628	45.455	0.00	0.00	0.00	2.74
299	659	7.931407	TGATGGTTATTATTCTAGTGCGTTGAT	59.069	33.333	0.00	0.00	0.00	2.57
300	660	7.269316	TGATGGTTATTATTCTAGTGCGTTGA	58.731	34.615	0.00	0.00	0.00	3.18
305	665	8.598924	CATCGATGATGGTTATTATTCTAGTGC	58.401	37.037	21.02	0.00	36.51	4.40
361	721	1.218875	CCGCGCTTGTGTGTCTGTAA	61.219	55.000	5.56	0.00	0.00	2.41
363	723	2.967076	CCGCGCTTGTGTGTCTGT	60.967	61.111	5.56	0.00	0.00	3.41
410	770	5.808540	CGGATTCGGTCAGTGTTTATCTTTA	59.191	40.000	0.00	0.00	0.00	1.85
411	771	4.630069	CGGATTCGGTCAGTGTTTATCTTT	59.370	41.667	0.00	0.00	0.00	2.52
416	776	2.669113	CGTCGGATTCGGTCAGTGTTTA	60.669	50.000	0.00	0.00	36.95	2.01
419	779	1.211969	CGTCGGATTCGGTCAGTGT	59.788	57.895	0.00	0.00	36.95	3.55
422	782	0.663688	ATCTCGTCGGATTCGGTCAG	59.336	55.000	0.00	0.00	36.95	3.51
423	783	0.380733	CATCTCGTCGGATTCGGTCA	59.619	55.000	0.00	0.00	36.95	4.02
429	1000	3.535561	AGAATTTGCATCTCGTCGGATT	58.464	40.909	0.00	0.00	0.00	3.01
452	1023	2.039746	ACGGTTTGGAGGTGATGATTCA	59.960	45.455	0.00	0.00	0.00	2.57

Showing 1 to 25 of 339 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.