AutoCloner

Multiple sequence alignment - TraesCS2B01G406000

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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	TraesCS2B01G406000	chr2B	100.000	3814	0	0	1	3814	574715519	574719332	0.000000e+00	7044.0
1	TraesCS2B01G406000	chr2B	95.172	1015	44	4	1280	2290	574676284	574677297	0.000000e+00	1598.0
2	TraesCS2B01G406000	chr2B	95.208	793	35	1	3017	3806	574690049	574690841	0.000000e+00	1251.0
3	TraesCS2B01G406000	chr2B	94.337	618	26	5	559	1174	574675676	574676286	0.000000e+00	939.0
4	TraesCS2B01G406000	chr2B	88.035	794	69	13	1326	2109	575137646	575138423	0.000000e+00	917.0
5	TraesCS2B01G406000	chr2B	95.691	557	21	3	2287	2841	574677335	574677890	0.000000e+00	893.0
6	TraesCS2B01G406000	chr2B	88.740	524	27	4	1	523	574675184	574675676	2.520000e-171	612.0
7	TraesCS2B01G406000	chr2B	88.350	515	52	7	195	707	575136525	575137033	2.520000e-171	612.0
8	TraesCS2B01G406000	chr2B	83.932	585	52	16	2984	3533	575141805	575142382	4.370000e-144	521.0
9	TraesCS2B01G406000	chr2B	83.851	322	50	1	1326	1645	574039951	574039630	4.790000e-79	305.0
10	TraesCS2B01G406000	chr2B	85.959	292	30	6	2287	2575	575138681	575138964	6.190000e-78	302.0
11	TraesCS2B01G406000	chr2B	91.667	156	10	1	2877	3029	574677887	574678042	2.980000e-51	213.0
12	TraesCS2B01G406000	chr2B	88.333	180	14	4	2430	2603	573941947	573941769	3.860000e-50	209.0
13	TraesCS2B01G406000	chr2B	87.805	82	10	0	2782	2863	573941524	573941443	3.140000e-16	97.1
14	TraesCS2B01G406000	chr2B	87.805	82	10	0	2782	2863	574036371	574036290	3.140000e-16	97.1
15	TraesCS2B01G406000	chr2D	93.571	2302	96	13	1	2290	490576524	490578785	0.000000e+00	3384.0
16	TraesCS2B01G406000	chr2D	95.851	1157	39	6	2287	3435	490578823	490579978	0.000000e+00	1862.0
17	TraesCS2B01G406000	chr2D	84.201	1114	121	19	195	1292	490657717	490658791	0.000000e+00	1031.0
18	TraesCS2B01G406000	chr2D	87.173	803	68	14	1326	2109	490658768	490659554	0.000000e+00	880.0
19	TraesCS2B01G406000	chr2D	80.886	790	113	21	1326	2104	490127686	490126924	4.240000e-164	588.0
20	TraesCS2B01G406000	chr2D	83.074	579	59	17	2984	3531	490660612	490661182	1.230000e-134	490.0
21	TraesCS2B01G406000	chr2D	94.631	298	12	2	3513	3807	490579991	490580287	3.470000e-125	459.0
22	TraesCS2B01G406000	chr2D	89.342	319	24	5	2287	2603	490659804	490660114	3.570000e-105	392.0
23	TraesCS2B01G406000	chr2D	83.486	327	23	15	2304	2603	490126059	490125737	3.750000e-70	276.0
24	TraesCS2B01G406000	chr2D	82.007	289	28	11	2671	2959	490660265	490660529	1.380000e-54	224.0
25	TraesCS2B01G406000	chr2D	83.957	187	19	7	2605	2783	490125705	490125522	6.550000e-38	169.0
26	TraesCS2B01G406000	chr2D	90.698	86	5	2	2606	2688	490660173	490660258	1.120000e-20	111.0
27	TraesCS2B01G406000	chr2A	95.103	1797	81	5	1	1794	634106092	634107884	0.000000e+00	2824.0
28	TraesCS2B01G406000	chr2A	94.902	1530	48	15	2287	3807	634108467	634109975	0.000000e+00	2366.0
29	TraesCS2B01G406000	chr2A	85.276	1107	116	17	195	1292	634606135	634607203	0.000000e+00	1098.0
30	TraesCS2B01G406000	chr2A	87.760	768	75	9	1345	2109	634607205	634607956	0.000000e+00	880.0
31	TraesCS2B01G406000	chr2A	91.304	506	18	2	1786	2290	634107950	634108430	0.000000e+00	667.0
32	TraesCS2B01G406000	chr2A	82.906	585	57	20	2984	3531	634609103	634609681	1.590000e-133	486.0
33	TraesCS2B01G406000	chr2A	87.500	320	28	7	2287	2603	634608206	634608516	3.620000e-95	359.0
34	TraesCS2B01G406000	chr2A	83.944	355	32	6	2606	2959	634608577	634608907	2.210000e-82	316.0
35	TraesCS2B01G406000	chrUn	81.562	781	115	16	1330	2103	259671365	259670607	5.410000e-173	617.0
36	TraesCS2B01G406000	chrUn	84.259	324	24	12	2304	2603	259669778	259669458	1.340000e-74	291.0
37	TraesCS2B01G406000	chrUn	85.714	147	12	8	2605	2742	259669421	259669275	3.070000e-31	147.0
38	TraesCS2B01G406000	chr3B	91.837	49	3	1	143	190	785044381	785044333	2.460000e-07	67.6

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	TraesCS2B01G406000	chr2B	574715519	574719332	3813	False	7044.000000	7044	100.000000	1	3814	1	chr2B.!!$F2	3813
1	TraesCS2B01G406000	chr2B	574690049	574690841	792	False	1251.000000	1251	95.208000	3017	3806	1	chr2B.!!$F1	789
2	TraesCS2B01G406000	chr2B	574675184	574678042	2858	False	851.000000	1598	93.121400	1	3029	5	chr2B.!!$F3	3028
3	TraesCS2B01G406000	chr2B	575136525	575142382	5857	False	588.000000	917	86.569000	195	3533	4	chr2B.!!$F4	3338
4	TraesCS2B01G406000	chr2B	574036290	574039951	3661	True	201.050000	305	85.828000	1326	2863	2	chr2B.!!$R2	1537
5	TraesCS2B01G406000	chr2D	490576524	490580287	3763	False	1901.666667	3384	94.684333	1	3807	3	chr2D.!!$F1	3806
6	TraesCS2B01G406000	chr2D	490657717	490661182	3465	False	521.333333	1031	86.082500	195	3531	6	chr2D.!!$F2	3336
7	TraesCS2B01G406000	chr2D	490125522	490127686	2164	True	344.333333	588	82.776333	1326	2783	3	chr2D.!!$R1	1457
8	TraesCS2B01G406000	chr2A	634106092	634109975	3883	False	1952.333333	2824	93.769667	1	3807	3	chr2A.!!$F1	3806
9	TraesCS2B01G406000	chr2A	634606135	634609681	3546	False	627.800000	1098	85.477200	195	3531	5	chr2A.!!$F2	3336
10	TraesCS2B01G406000	chrUn	259669275	259671365	2090	True	351.666667	617	83.845000	1330	2742	3	chrUn.!!$R1	1412

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
275	277	0.034574	ACTGCACAACCCAAGTGTCA	60.035	50.0	0.0	0.00	39.17	3.58	F
1465	1579	0.036010	ACGCTGCTTGACAAGGCTAT	60.036	50.0	16.8	1.66	0.00	2.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1502	1616	0.604578	TGTAGTACTTCACGCCACCC	59.395	55.0	0.0	0.0	0.0	4.61	R
3237	8340	1.742308	ACAAGGAGAAACTGGGGCTA	58.258	50.0	0.0	0.0	0.0	3.93	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
116	117	6.091718	TGTAAGCATAATGTAGCGATACCA	57.908	37.500	8.59	0.00	35.48	3.25
140	141	3.430471	TGGATGGGCCATCTTGCT	58.570	55.556	37.80	10.83	43.33	3.91
212	214	8.826293	AAAAATCCCGTTAAATCTACCCATAA	57.174	30.769	0.00	0.00	0.00	1.90
214	216	8.459911	AAATCCCGTTAAATCTACCCATAAAG	57.540	34.615	0.00	0.00	0.00	1.85
275	277	0.034574	ACTGCACAACCCAAGTGTCA	60.035	50.000	0.00	0.00	39.17	3.58
289	291	2.557869	AGTGTCATAAACCCTAGCCCA	58.442	47.619	0.00	0.00	0.00	5.36
416	418	4.973168	TCATCATTCCTTCCTAAATCCCG	58.027	43.478	0.00	0.00	0.00	5.14
449	451	6.913545	AGGCCTAACTAGTAGTCAACTATCT	58.086	40.000	1.29	0.00	39.96	1.98
473	475	1.827969	AGGGTGGAGATTTGACTCGAG	59.172	52.381	11.84	11.84	37.74	4.04
502	504	3.733443	AATTGCAGTCACCCAAGTTTC	57.267	42.857	0.00	0.00	0.00	2.78
510	512	4.035675	CAGTCACCCAAGTTTCAGTCTTTC	59.964	45.833	0.00	0.00	0.00	2.62
526	542	1.000060	CTTTCGACCTCGTTGGGTACA	60.000	52.381	0.00	0.00	40.06	2.90
549	565	7.263496	ACACATCTTCTTAATTACCGAGTACC	58.737	38.462	0.00	0.00	0.00	3.34
574	590	2.821969	GCTCTGACCCAATTGTCAACAT	59.178	45.455	4.43	0.00	44.19	2.71
575	591	4.009675	GCTCTGACCCAATTGTCAACATA	58.990	43.478	4.43	0.00	44.19	2.29
576	592	4.095483	GCTCTGACCCAATTGTCAACATAG	59.905	45.833	4.43	3.25	44.19	2.23
662	678	5.896073	ATTTGGTCTCATAGGGTTCCTAG	57.104	43.478	0.06	0.00	39.70	3.02
667	683	3.643792	GTCTCATAGGGTTCCTAGCATGT	59.356	47.826	0.00	0.00	39.70	3.21
686	702	2.012673	GTCCTCTGCTGCCAAGTTATG	58.987	52.381	0.00	0.00	0.00	1.90
756	845	4.219115	TGGAGAATTTAAGGCCACAACAA	58.781	39.130	5.01	0.00	0.00	2.83
787	877	3.227614	GGGGTGTGACAACAAATAGGTT	58.772	45.455	1.89	0.00	38.27	3.50
1025	1123	6.000840	TGGCAAAAAGGAAACAAGTTTTTCT	58.999	32.000	0.00	0.00	36.02	2.52
1026	1124	6.072783	TGGCAAAAAGGAAACAAGTTTTTCTG	60.073	34.615	0.00	0.00	36.02	3.02
1049	1151	3.645884	TGGTAAAGACGAGCACTAACAC	58.354	45.455	0.00	0.00	0.00	3.32
1288	1394	7.757941	TCATTGTTTCACAGGAATTACATGA	57.242	32.000	0.00	0.00	34.19	3.07
1441	1555	4.337264	AACCATTTAGCCAGGGAGAATT	57.663	40.909	0.00	0.00	0.00	2.17
1465	1579	0.036010	ACGCTGCTTGACAAGGCTAT	60.036	50.000	16.80	1.66	0.00	2.97
1502	1616	2.820330	ACAATGAAAAGGCAAACACGG	58.180	42.857	0.00	0.00	0.00	4.94
1530	1644	4.980434	GCGTGAAGTACTACAACTCTGAAA	59.020	41.667	0.00	0.00	0.00	2.69
1624	1744	5.627499	TGTTCATTGGACTTCTGTTATGC	57.373	39.130	0.00	0.00	0.00	3.14
1705	3117	7.273381	CACATGGCTAAAGTAACTTTTATGCAC	59.727	37.037	0.00	0.00	35.21	4.57
1794	3285	1.082756	GTGGTTGTCTTTGCTCGCG	60.083	57.895	0.00	0.00	0.00	5.87
1799	3290	1.194547	GTTGTCTTTGCTCGCGATTGA	59.805	47.619	10.36	0.64	0.00	2.57
1822	3314	7.563906	TGACATTTCCTTTTGAACCTTGAAAT	58.436	30.769	0.00	0.00	33.89	2.17
2434	4801	8.275015	TGTTCAAGAAACACTGATTCTTACAA	57.725	30.769	12.52	7.33	43.41	2.41
2749	7637	5.824624	CCTGTTAAAGATCATGCTGGTACAT	59.175	40.000	0.00	0.00	38.20	2.29
2879	7805	9.185192	CCTAGTTCACTTTTGCAAAAGATAAAG	57.815	33.333	43.34	31.16	46.39	1.85
2960	7886	6.940739	AGTATGTGCCAGCTTCTTATATAGG	58.059	40.000	0.00	0.00	0.00	2.57
3012	8110	6.269769	GGATTTCCCTATCAAATGGCCAATTA	59.730	38.462	10.96	0.00	0.00	1.40
3082	8184	3.786553	TGTACTGACCTGTGTCCCTAAT	58.213	45.455	0.00	0.00	41.01	1.73
3237	8340	1.134280	CCTTCTCGATTGAGGTGGCAT	60.134	52.381	10.19	0.00	42.79	4.40
3379	8496	7.408756	TCACTCCCCAAAATCAATTATCTTG	57.591	36.000	0.00	0.00	0.00	3.02
3449	8586	8.262227	AGAAGGTTTATGGACGACAATGTATTA	58.738	33.333	0.00	0.00	0.00	0.98
3527	8665	3.777106	TCTCATGGAAGAGCAAGTGTT	57.223	42.857	0.00	0.00	35.59	3.32
3566	8704	2.334977	TGGGAAAACCACTCTCTAGCA	58.665	47.619	0.00	0.00	46.80	3.49
3633	8771	1.407936	TCTGGGATCTAGCTGCTGTC	58.592	55.000	13.43	7.63	0.00	3.51
3643	8781	1.882912	AGCTGCTGTCGAATTTGACA	58.117	45.000	24.02	24.02	46.15	3.58
3652	8790	3.639094	TGTCGAATTTGACATGGGGTTTT	59.361	39.130	22.25	0.00	43.62	2.43
3692	8830	6.306199	AGCACTCTAGATCTCATGATGTACT	58.694	40.000	0.00	0.00	32.19	2.73
3770	8911	5.734855	TCGATTTATGCAGAAAACTAGCC	57.265	39.130	11.02	0.00	0.00	3.93
3807	8948	3.403737	AGGGATGATTGATTAAGGGCCAT	59.596	43.478	6.18	0.00	0.00	4.40
3808	8949	3.512724	GGGATGATTGATTAAGGGCCATG	59.487	47.826	6.18	0.00	0.00	3.66
3809	8950	4.410099	GGATGATTGATTAAGGGCCATGA	58.590	43.478	6.18	0.00	0.00	3.07
3810	8951	4.834496	GGATGATTGATTAAGGGCCATGAA	59.166	41.667	6.18	0.00	0.00	2.57
3811	8952	5.279156	GGATGATTGATTAAGGGCCATGAAC	60.279	44.000	6.18	0.00	0.00	3.18
3812	8953	4.608269	TGATTGATTAAGGGCCATGAACA	58.392	39.130	6.18	0.00	0.00	3.18
3813	8954	5.022122	TGATTGATTAAGGGCCATGAACAA	58.978	37.500	6.18	1.95	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	1.710809	ACCTAGTCAATGCCCCAAAGT	59.289	47.619	0.00	0.00	0.00	2.66
19	20	2.237392	GCTCTGAACCCACCTAGTCAAT	59.763	50.000	0.00	0.00	0.00	2.57
116	117	3.772715	TGGCCCATCCATGTCCAT	58.227	55.556	0.00	0.00	40.72	3.41
321	323	9.970395	CATTACACATATTGGCATAATTTGAGT	57.030	29.630	9.28	9.48	0.00	3.41
416	418	6.121590	ACTACTAGTTAGGCCTTCTAGACAC	58.878	44.000	32.68	13.94	36.17	3.67
449	451	0.038166	GTCAAATCTCCACCCTGCCA	59.962	55.000	0.00	0.00	0.00	4.92
473	475	4.083003	TGGGTGACTGCAATTATTTCGAAC	60.083	41.667	0.00	0.00	0.00	3.95
481	483	4.211125	TGAAACTTGGGTGACTGCAATTA	58.789	39.130	0.00	0.00	0.00	1.40
510	512	0.245539	ATGTGTACCCAACGAGGTCG	59.754	55.000	0.00	0.00	41.58	4.79
526	542	7.341256	TCTGGTACTCGGTAATTAAGAAGATGT	59.659	37.037	0.00	0.00	0.00	3.06
549	565	2.289882	TGACAATTGGGTCAGAGCTCTG	60.290	50.000	33.73	33.73	42.56	3.35
595	611	1.004745	ACCACGAGGCATTTCCAAGAT	59.995	47.619	0.00	0.00	39.06	2.40
662	678	1.654954	CTTGGCAGCAGAGGACATGC	61.655	60.000	0.00	0.00	44.18	4.06
667	683	1.908619	TCATAACTTGGCAGCAGAGGA	59.091	47.619	0.00	0.00	0.00	3.71
686	702	9.612620	GCAAACATATAATGGTATAAGCAAGTC	57.387	33.333	0.00	0.00	33.60	3.01
756	845	2.956132	TGTCACACCCCAAATGATTGT	58.044	42.857	0.00	0.00	34.60	2.71
905	1001	5.544176	CAGGTATCTGGTGGGAGTATATGTT	59.456	44.000	0.00	0.00	37.36	2.71
1025	1123	4.021807	TGTTAGTGCTCGTCTTTACCATCA	60.022	41.667	0.00	0.00	0.00	3.07
1026	1124	4.326548	GTGTTAGTGCTCGTCTTTACCATC	59.673	45.833	0.00	0.00	0.00	3.51
1240	1342	8.556194	TGAATTTACCACGATTTATGAGTATGC	58.444	33.333	0.00	0.00	0.00	3.14
1250	1352	8.293114	GTGAAACAATGAATTTACCACGATTT	57.707	30.769	0.00	0.00	36.32	2.17
1306	1414	5.531634	ACACATGTGGTAAGCAATTCAAAG	58.468	37.500	28.64	0.00	34.19	2.77
1441	1555	2.076100	CCTTGTCAAGCAGCGTATCAA	58.924	47.619	7.09	0.00	0.00	2.57
1477	1591	2.941720	GTTTGCCTTTTCATTGTTGCCA	59.058	40.909	0.00	0.00	0.00	4.92
1502	1616	0.604578	TGTAGTACTTCACGCCACCC	59.395	55.000	0.00	0.00	0.00	4.61
1530	1644	7.622713	TCAAAATATGATGGTTGCCTTTCATT	58.377	30.769	8.61	0.00	32.44	2.57
1560	1674	3.449746	AAAAGCAAGCATACCTGGGTA	57.550	42.857	1.70	1.70	34.87	3.69
1794	3285	7.209475	TCAAGGTTCAAAAGGAAATGTCAATC	58.791	34.615	0.00	0.00	37.23	2.67
1799	3290	8.676401	CAAATTTCAAGGTTCAAAAGGAAATGT	58.324	29.630	0.00	0.00	37.23	2.71
1822	3314	2.687700	ACACAATGTTGGCTTGCAAA	57.312	40.000	0.00	0.00	0.00	3.68
2051	3550	7.441017	TGCAAGCTTTGTATTTTACCAAAGAT	58.559	30.769	14.41	6.68	36.94	2.40
2058	3557	8.693542	ATTGAGATGCAAGCTTTGTATTTTAC	57.306	30.769	0.00	0.00	40.42	2.01
2319	4519	7.651808	TGGAAAGATAACTTCTCAAGCAAAAG	58.348	34.615	0.00	0.00	35.05	2.27
2434	4801	8.524870	AAAACGTGTTGATTAATAGTACGACT	57.475	30.769	16.08	0.00	34.52	4.18
2603	7449	3.004752	ACAACAGGTGGAGCCATTATC	57.995	47.619	0.00	0.00	40.61	1.75
2879	7805	3.910648	AGTTACTCCGTTGTGAACTAGC	58.089	45.455	0.00	0.00	0.00	3.42
2960	7886	2.987355	TTTTTGCGGGGAGGGACCAC	62.987	60.000	0.00	0.00	41.20	4.16
2998	8096	5.929058	TTGCTATGTAATTGGCCATTTGA	57.071	34.783	20.62	9.19	0.00	2.69
3082	8184	8.855804	ATTCTACAAAGGAAGGGAGTAGATTA	57.144	34.615	0.00	0.00	40.35	1.75
3184	8286	8.908786	TCTTCTGTAATTCTGTTTGTGATCTT	57.091	30.769	0.00	0.00	0.00	2.40
3237	8340	1.742308	ACAAGGAGAAACTGGGGCTA	58.258	50.000	0.00	0.00	0.00	3.93
3379	8496	5.742255	GCAAACTATGGTATACCCCTGTCTC	60.742	48.000	19.42	0.00	34.29	3.36
3527	8665	3.768757	CCCATCCAAAGGCTGATTTGTAA	59.231	43.478	0.00	0.00	38.28	2.41
3633	8771	3.584834	GGAAAACCCCATGTCAAATTCG	58.415	45.455	0.00	0.00	0.00	3.34
3652	8790	2.219080	TGCTCAATTTCAGCATGGGA	57.781	45.000	4.94	0.00	42.09	4.37
3757	8898	3.565516	CTTTTTCGGGCTAGTTTTCTGC	58.434	45.455	0.00	0.00	0.00	4.26
3770	8911	3.694072	TCATCCCTTGTATGCTTTTTCGG	59.306	43.478	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.