AutoCloner

Multiple sequence alignment - TraesCS3B01G282200

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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	TraesCS3B01G282200	chr3B	100.000	4513	0	0	1	4513	452699897	452695385	0.000000e+00	8335.0
1	TraesCS3B01G282200	chr3B	90.763	498	39	4	2684	3176	452564234	452563739	0.000000e+00	658.0
2	TraesCS3B01G282200	chr4B	94.929	2406	69	13	277	2642	24766777	24769169	0.000000e+00	3718.0
3	TraesCS3B01G282200	chr4B	98.356	1034	13	3	2689	3722	24769306	24770335	0.000000e+00	1812.0
4	TraesCS3B01G282200	chr4B	89.833	1141	73	19	3095	4221	25385363	25384252	0.000000e+00	1424.0
5	TraesCS3B01G282200	chr4B	86.887	1243	100	29	301	1509	25388213	25387000	0.000000e+00	1334.0
6	TraesCS3B01G282200	chr4B	91.251	903	63	7	1550	2442	25386995	25386099	0.000000e+00	1216.0
7	TraesCS3B01G282200	chr4B	98.428	636	10	0	3878	4513	24770938	24771573	0.000000e+00	1120.0
8	TraesCS3B01G282200	chr4B	89.308	636	39	7	2467	3097	25386038	25385427	0.000000e+00	771.0
9	TraesCS3B01G282200	chr4B	86.415	714	60	19	2684	3387	24832635	24833321	0.000000e+00	747.0
10	TraesCS3B01G282200	chr4B	99.130	345	3	0	1	345	24766462	24766806	4.960000e-174	621.0
11	TraesCS3B01G282200	chr4B	88.333	420	24	12	2971	3388	25351965	25351569	8.780000e-132	481.0
12	TraesCS3B01G282200	chr4B	95.276	127	4	2	3766	3891	24770308	24770433	2.750000e-47	200.0
13	TraesCS3B01G282200	chr4B	91.912	136	10	1	4	139	25388656	25388522	5.960000e-44	189.0
14	TraesCS3B01G282200	chr4B	100.000	31	0	0	3766	3796	39247066	39247096	1.750000e-04	58.4
15	TraesCS3B01G282200	chr4D	90.728	2556	128	35	895	3388	14401427	14398919	0.000000e+00	3306.0
16	TraesCS3B01G282200	chr4D	93.891	1768	56	10	1421	3158	14926928	14928673	0.000000e+00	2619.0
17	TraesCS3B01G282200	chr4D	86.953	1326	111	27	303	1576	15153679	15152364	0.000000e+00	1434.0
18	TraesCS3B01G282200	chr4D	88.927	876	82	10	1583	2445	15151055	15150182	0.000000e+00	1066.0
19	TraesCS3B01G282200	chr4D	97.814	183	4	0	3203	3385	14928783	14928965	2.620000e-82	316.0
20	TraesCS3B01G282200	chr4D	90.526	190	13	3	3387	3575	15149141	15148956	3.490000e-61	246.0
21	TraesCS3B01G282200	chr4D	91.724	145	10	1	137	281	14402033	14401891	2.750000e-47	200.0
22	TraesCS3B01G282200	chr4D	92.701	137	9	1	4	139	15154056	15153920	3.560000e-46	196.0
23	TraesCS3B01G282200	chr4D	90.000	90	9	0	3860	3949	15148181	15148092	2.850000e-22	117.0
24	TraesCS3B01G282200	chr5A	86.482	2197	209	51	301	2442	40874793	40876956	0.000000e+00	2331.0
25	TraesCS3B01G282200	chr5A	89.961	518	37	7	2666	3173	40877326	40877838	0.000000e+00	654.0
26	TraesCS3B01G282200	chr5A	83.523	176	24	4	2467	2639	40877015	40877188	4.670000e-35	159.0
27	TraesCS3B01G282200	chr4A	89.151	1862	119	35	1344	3158	586674708	586672883	0.000000e+00	2242.0
28	TraesCS3B01G282200	chr4A	89.086	1860	119	39	1346	3158	456401010	456399188	0.000000e+00	2233.0
29	TraesCS3B01G282200	chr4A	93.107	1059	54	10	301	1346	456402186	456401134	0.000000e+00	1533.0
30	TraesCS3B01G282200	chr4A	92.373	1062	62	9	301	1346	586675888	586674830	0.000000e+00	1495.0
31	TraesCS3B01G282200	chr4A	85.150	1367	127	28	195	1509	585690179	585691521	0.000000e+00	1330.0
32	TraesCS3B01G282200	chr4A	88.078	1082	81	21	360	1406	538490078	538489010	0.000000e+00	1240.0
33	TraesCS3B01G282200	chr4A	87.748	1110	73	22	2576	3669	585692837	585693899	0.000000e+00	1238.0
34	TraesCS3B01G282200	chr4A	90.104	869	76	4	1582	2442	586089515	586090381	0.000000e+00	1120.0
35	TraesCS3B01G282200	chr4A	90.545	550	39	6	3662	4200	585694867	585695414	0.000000e+00	715.0
36	TraesCS3B01G282200	chr4A	89.041	292	24	7	4202	4490	585697866	585698152	5.550000e-94	355.0
37	TraesCS3B01G282200	chr4A	98.387	186	3	0	3203	3388	456399067	456398882	1.210000e-85	327.0
38	TraesCS3B01G282200	chr4A	97.312	186	5	0	3203	3388	586672776	586672591	2.620000e-82	316.0
39	TraesCS3B01G282200	chr4A	86.260	262	25	5	2190	2442	585692325	585692584	1.600000e-69	274.0
40	TraesCS3B01G282200	chr4A	92.350	183	13	1	3393	3575	538487493	538487312	4.480000e-65	259.0
41	TraesCS3B01G282200	chr4A	90.000	190	14	3	3387	3575	586091489	586091674	1.620000e-59	241.0
42	TraesCS3B01G282200	chr4A	94.483	145	8	0	137	281	586676087	586675943	1.630000e-54	224.0
43	TraesCS3B01G282200	chr4A	82.463	268	29	13	3587	3848	456398327	456398072	7.600000e-53	219.0
44	TraesCS3B01G282200	chr4A	81.955	266	33	10	3587	3848	586672036	586671782	1.270000e-50	211.0
45	TraesCS3B01G282200	chr4A	93.617	141	7	1	1	139	586676271	586676131	4.570000e-50	209.0
46	TraesCS3B01G282200	chr4A	92.414	145	11	0	137	281	456402385	456402241	1.650000e-49	207.0
47	TraesCS3B01G282200	chr4A	93.571	140	8	1	1	139	456402568	456402429	1.650000e-49	207.0
48	TraesCS3B01G282200	chr4A	88.889	90	10	0	3860	3949	586092460	586092549	1.330000e-20	111.0
49	TraesCS3B01G282200	chr5D	86.437	1423	129	28	301	1687	51842654	51844048	0.000000e+00	1500.0
50	TraesCS3B01G282200	chr5D	84.671	972	110	26	1678	2641	51844193	51845133	0.000000e+00	933.0
51	TraesCS3B01G282200	chr5D	85.946	185	21	1	3387	3566	51846063	51846247	4.610000e-45	193.0
52	TraesCS3B01G282200	chr5B	87.027	1241	130	18	1222	2442	54826896	54828125	0.000000e+00	1371.0
53	TraesCS3B01G282200	chr5B	86.332	578	50	9	301	852	54825832	54826406	1.800000e-168	603.0
54	TraesCS3B01G282200	chr5B	90.370	135	13	0	4	138	54825458	54825592	1.290000e-40	178.0
55	TraesCS3B01G282200	chr2A	84.919	1366	131	25	195	1509	195821290	195822631	0.000000e+00	1312.0
56	TraesCS3B01G282200	chr2A	88.018	1110	70	22	2576	3669	195823947	195825009	0.000000e+00	1254.0
57	TraesCS3B01G282200	chr2A	88.241	1080	83	17	360	1406	196121697	196122765	0.000000e+00	1251.0
58	TraesCS3B01G282200	chr2A	90.545	550	38	7	3662	4200	195825972	195826518	0.000000e+00	715.0
59	TraesCS3B01G282200	chr2A	90.613	522	38	6	2645	3158	196125181	196125699	0.000000e+00	682.0
60	TraesCS3B01G282200	chr2A	90.411	292	21	7	4202	4490	195829208	195829495	1.190000e-100	377.0
61	TraesCS3B01G282200	chr2A	99.429	175	1	0	3203	3377	196345009	196344835	7.290000e-83	318.0
62	TraesCS3B01G282200	chr2A	98.857	175	2	0	3203	3377	196348843	196348669	3.390000e-81	313.0
63	TraesCS3B01G282200	chr2A	86.260	262	25	5	2190	2442	195823435	195823694	1.600000e-69	274.0
64	TraesCS3B01G282200	chr2A	82.772	267	28	13	3587	3848	196314556	196314303	5.880000e-54	222.0
65	TraesCS3B01G282200	chr2A	92.763	152	10	1	3424	3575	196126050	196126200	7.600000e-53	219.0
66	TraesCS3B01G282200	chr2A	88.889	153	13	4	2467	2616	196124381	196124532	7.710000e-43	185.0
67	TraesCS3B01G282200	chr2A	94.444	54	3	0	2389	2442	196124197	196124250	2.890000e-12	84.2
68	TraesCS3B01G282200	chr1D	85.949	975	101	14	305	1248	320387545	320388514	0.000000e+00	1009.0
69	TraesCS3B01G282200	chr1D	86.339	732	71	15	2666	3392	320390396	320391103	0.000000e+00	771.0
70	TraesCS3B01G282200	chr1D	88.034	117	14	0	22	138	320387185	320387301	6.090000e-29	139.0
71	TraesCS3B01G282200	chr1B	85.920	973	99	20	305	1248	433424591	433425554	0.000000e+00	1003.0
72	TraesCS3B01G282200	chr1B	87.395	119	11	3	22	138	433424228	433424344	2.830000e-27	134.0

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	TraesCS3B01G282200	chr3B	452695385	452699897	4512	True	8335.000000	8335	100.000000	1	4513	1	chr3B.!!$R2	4512
1	TraesCS3B01G282200	chr4B	24766462	24771573	5111	False	1494.200000	3718	97.223800	1	4513	5	chr4B.!!$F3	4512
2	TraesCS3B01G282200	chr4B	25384252	25388656	4404	True	986.800000	1424	89.838200	4	4221	5	chr4B.!!$R2	4217
3	TraesCS3B01G282200	chr4B	24832635	24833321	686	False	747.000000	747	86.415000	2684	3387	1	chr4B.!!$F1	703
4	TraesCS3B01G282200	chr4D	14398919	14402033	3114	True	1753.000000	3306	91.226000	137	3388	2	chr4D.!!$R1	3251
5	TraesCS3B01G282200	chr4D	14926928	14928965	2037	False	1467.500000	2619	95.852500	1421	3385	2	chr4D.!!$F1	1964
6	TraesCS3B01G282200	chr4D	15148092	15154056	5964	True	611.800000	1434	89.821400	4	3949	5	chr4D.!!$R2	3945
7	TraesCS3B01G282200	chr5A	40874793	40877838	3045	False	1048.000000	2331	86.655333	301	3173	3	chr5A.!!$F1	2872
8	TraesCS3B01G282200	chr4A	456398072	456402568	4496	True	787.666667	2233	91.504667	1	3848	6	chr4A.!!$R1	3847
9	TraesCS3B01G282200	chr4A	586671782	586676271	4489	True	782.833333	2242	91.481833	1	3848	6	chr4A.!!$R3	3847
10	TraesCS3B01G282200	chr4A	585690179	585698152	7973	False	782.400000	1330	87.748800	195	4490	5	chr4A.!!$F1	4295
11	TraesCS3B01G282200	chr4A	538487312	538490078	2766	True	749.500000	1240	90.214000	360	3575	2	chr4A.!!$R2	3215
12	TraesCS3B01G282200	chr4A	586089515	586092549	3034	False	490.666667	1120	89.664333	1582	3949	3	chr4A.!!$F2	2367
13	TraesCS3B01G282200	chr5D	51842654	51846247	3593	False	875.333333	1500	85.684667	301	3566	3	chr5D.!!$F1	3265
14	TraesCS3B01G282200	chr5B	54825458	54828125	2667	False	717.333333	1371	87.909667	4	2442	3	chr5B.!!$F1	2438
15	TraesCS3B01G282200	chr2A	195821290	195829495	8205	False	786.400000	1312	88.030600	195	4490	5	chr2A.!!$F1	4295
16	TraesCS3B01G282200	chr2A	196121697	196126200	4503	False	484.240000	1251	90.990000	360	3575	5	chr2A.!!$F2	3215
17	TraesCS3B01G282200	chr2A	196344835	196348843	4008	True	315.500000	318	99.143000	3203	3377	2	chr2A.!!$R2	174
18	TraesCS3B01G282200	chr1D	320387185	320391103	3918	False	639.666667	1009	86.774000	22	3392	3	chr1D.!!$F1	3370
19	TraesCS3B01G282200	chr1B	433424228	433425554	1326	False	568.500000	1003	86.657500	22	1248	2	chr1B.!!$F1	1226

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
877	1247	1.136891	GGCTAAAATGGGCATGTCCAC	59.863	52.381	24.12	7.59	39.97	4.02	F
1664	3803	0.918799	TGTAGGTGCCCCATGTGGAT	60.919	55.000	0.00	0.00	37.39	3.41	F
1847	4142	3.272574	TCTTGAAGCCAGCCTTATGAG	57.727	47.619	0.00	0.00	32.78	2.90	F
2888	7503	1.482748	CCAAGGGGGCTTGCACATTT	61.483	55.000	0.00	0.00	33.30	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1978	4282	1.427819	GCCAATTCCGTAACTGCCG	59.572	57.895	5.69	R
2511	6087	4.041567	TCAGTAGCCAAAGTCCATCAGAAA	59.958	41.667	2.52	R
2976	7599	5.733226	TCCAACAATCATATTACACTGCG	57.267	39.130	5.18	R
4302	18269	1.063764	GTCTCACCGTCAGTATCGTCC	59.936	57.143	4.79	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
349	569	1.995542	ACATCAAATCCCCTGTCTGGT	59.004	47.619	0.00	0.00	0.00	4.00
422	643	6.239036	AGAACACCTTTTGTGCTTTATCTTCC	60.239	38.462	0.00	0.00	42.17	3.46
423	644	5.712152	CACCTTTTGTGCTTTATCTTCCT	57.288	39.130	0.00	0.00	38.34	3.36
877	1247	1.136891	GGCTAAAATGGGCATGTCCAC	59.863	52.381	24.12	7.59	39.97	4.02
1062	1485	2.158608	CCAAGAAACAGGGAGTTGGAGT	60.159	50.000	0.00	0.00	41.19	3.85
1176	1611	5.520376	AGTTTGTCTGAACTTCATTTGGG	57.480	39.130	0.00	0.00	36.49	4.12
1219	1673	2.949644	ACACCTTTCTCTTTGGGAAACG	59.050	45.455	0.00	0.00	0.00	3.60
1275	1755	9.295825	AGTTGGAATTTGAATAACTGTGATGTA	57.704	29.630	0.00	0.00	31.00	2.29
1486	2319	4.764679	TGCGATAACTCTTTTTGCACAT	57.235	36.364	0.00	0.00	0.00	3.21
1577	2414	6.147164	TCGCTGCTTACAATTGGTTATATAGC	59.853	38.462	10.83	9.31	0.00	2.97
1664	3803	0.918799	TGTAGGTGCCCCATGTGGAT	60.919	55.000	0.00	0.00	37.39	3.41
1847	4142	3.272574	TCTTGAAGCCAGCCTTATGAG	57.727	47.619	0.00	0.00	32.78	2.90
1978	4282	8.716646	ATAATAGGGCTTAAAAATGCAAACAC	57.283	30.769	0.00	0.00	0.00	3.32
2072	4383	8.783660	ATCTAGTTTTGGATAGACTGATGGTA	57.216	34.615	0.00	0.00	31.09	3.25
2112	4423	7.894376	ATGATATTGTTGCACCAAAAAGAAG	57.106	32.000	0.00	0.00	0.00	2.85
2139	4450	8.854117	CAAAGCTATAAGAATATCTGCCCTTTT	58.146	33.333	0.00	0.00	0.00	2.27
2461	6021	5.048782	CAGCAAAGTGATGGTTTTAGTGCTA	60.049	40.000	0.00	0.00	28.61	3.49
2462	6022	5.711976	AGCAAAGTGATGGTTTTAGTGCTAT	59.288	36.000	0.00	0.00	0.00	2.97
2511	6087	8.965172	CGTATTTATAGAGTACAAGCATTCGTT	58.035	33.333	0.00	0.00	0.00	3.85
2642	6962	8.341903	TGTTTTCACACACATGTATAGAAACTG	58.658	33.333	0.00	0.00	36.72	3.16
2751	7358	3.519107	TCTCTGCCATCCTAATGTGTTGA	59.481	43.478	0.00	0.00	0.00	3.18
2758	7365	4.577693	CCATCCTAATGTGTTGACCATCAG	59.422	45.833	0.00	0.00	0.00	2.90
2888	7503	1.482748	CCAAGGGGGCTTGCACATTT	61.483	55.000	0.00	0.00	33.30	2.32
2955	7574	6.418057	TCTGAAATTTATTTGGTGCCTGTT	57.582	33.333	0.00	0.00	0.00	3.16
2976	7599	9.528018	CCTGTTAGAAAGATTCTGATAGAAGAC	57.472	37.037	9.27	0.00	40.94	3.01

Showing 1 to 25 of 32 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
877	1247	0.242825	CAGCTGCCACCACAAGAATG	59.757	55.000	0.00	0.00	0.00	2.67
1062	1485	5.935789	GGCCACAGACAAGTTACTGTAATAA	59.064	40.000	12.44	0.00	44.07	1.40
1176	1611	7.254932	GGTGTCAATTTCTTCAGGCTATATGAC	60.255	40.741	0.00	0.00	35.30	3.06
1460	2293	5.284660	GTGCAAAAAGAGTTATCGCATTCAG	59.715	40.000	0.00	0.00	0.00	3.02
1486	2319	6.154192	TGCAATATGAGTTGGAAGGCAATAAA	59.846	34.615	0.00	0.00	0.00	1.40
1633	3772	3.873910	GGCACCTACATGACATACAAGT	58.126	45.455	0.00	0.00	34.72	3.16
1664	3803	7.884877	AGGATAGATGAAACATGTTGAAAGACA	59.115	33.333	12.82	6.58	0.00	3.41
1847	4142	2.210116	TCTCCGTTTGACTTTCTGCAC	58.790	47.619	0.00	0.00	0.00	4.57
1966	4268	2.307934	AACTGCCGTGTTTGCATTTT	57.692	40.000	0.00	0.00	38.22	1.82
1978	4282	1.427819	GCCAATTCCGTAACTGCCG	59.572	57.895	0.00	0.00	0.00	5.69
2082	4393	7.459795	TTTGGTGCAACAATATCATTACTCA	57.540	32.000	19.74	0.00	39.98	3.41
2102	4413	8.992835	ATTCTTATAGCTTTGCTTCTTTTTGG	57.007	30.769	0.00	0.00	40.44	3.28
2112	4423	5.942826	AGGGCAGATATTCTTATAGCTTTGC	59.057	40.000	0.00	0.00	30.76	3.68
2461	6021	6.073765	CGGCTGAATTCGCTACTACAATTTAT	60.074	38.462	17.53	0.00	0.00	1.40
2462	6022	5.233476	CGGCTGAATTCGCTACTACAATTTA	59.767	40.000	17.53	0.00	0.00	1.40
2511	6087	4.041567	TCAGTAGCCAAAGTCCATCAGAAA	59.958	41.667	0.00	0.00	0.00	2.52
2654	6974	7.613411	AGAGCCAACTCAAAGCTAGAATTTAAT	59.387	33.333	0.00	0.00	46.09	1.40
2655	6975	6.942576	AGAGCCAACTCAAAGCTAGAATTTAA	59.057	34.615	0.00	0.00	46.09	1.52
2955	7574	7.067615	ACTGCGTCTTCTATCAGAATCTTTCTA	59.932	37.037	0.00	0.00	38.11	2.10
2976	7599	5.733226	TCCAACAATCATATTACACTGCG	57.267	39.130	0.00	0.00	0.00	5.18
3731	14103	8.519526	CAAGCTTTAACATGGTAGTTAATGGAA	58.480	33.333	0.00	0.00	41.89	3.53
3806	14181	8.303156	TCCATGTAACAAAATGATCGTCAAAAT	58.697	29.630	0.00	0.00	0.00	1.82
3847	14237	2.238521	TCCTTTGGCTGGTGATTGAAC	58.761	47.619	0.00	0.00	0.00	3.18
4011	15280	3.815809	ACACCAGAACGGAAAGAAATCA	58.184	40.909	0.00	0.00	38.63	2.57
4018	15287	2.614983	GCAAAGTACACCAGAACGGAAA	59.385	45.455	0.00	0.00	38.63	3.13

Showing 1 to 25 of 27 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.