AutoCloner

Multiple sequence alignment - TraesCS3B01G099500

Loading Multiple Alignment...

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	TraesCS3B01G099500	chr3B	100.000	4493	0	0	1	4493	66589662	66585170	0.000000e+00	8298.0
1	TraesCS3B01G099500	chr3D	96.864	3093	97	0	1017	4109	42747278	42744186	0.000000e+00	5175.0
2	TraesCS3B01G099500	chr3D	93.548	186	12	0	4308	4493	42743480	42743295	1.230000e-70	278.0
3	TraesCS3B01G099500	chr3D	95.000	140	6	1	4164	4303	42743679	42743541	7.570000e-53	219.0
4	TraesCS3B01G099500	chr3D	88.136	59	2	2	4111	4168	42744197	42744143	1.040000e-06	65.8
5	TraesCS3B01G099500	chr3A	97.016	2480	74	0	1017	3496	54669051	54666572	0.000000e+00	4170.0
6	TraesCS3B01G099500	chr3A	94.662	637	28	5	3534	4168	54666575	54665943	0.000000e+00	983.0
7	TraesCS3B01G099500	chr3A	91.429	140	11	1	4164	4303	54665593	54665455	1.650000e-44	191.0
8	TraesCS3B01G099500	chr1B	92.806	2516	178	1	1017	3532	32594741	32592229	0.000000e+00	3640.0
9	TraesCS3B01G099500	chr1B	96.670	1021	29	1	1	1021	503316956	503317971	0.000000e+00	1692.0
10	TraesCS3B01G099500	chr1B	81.649	1019	166	17	8	1019	533614015	533613011	0.000000e+00	826.0
11	TraesCS3B01G099500	chrUn	91.256	2539	183	14	1101	3629	10169503	10172012	0.000000e+00	3422.0
12	TraesCS3B01G099500	chr6B	95.103	1021	45	1	1	1021	417760314	417761329	0.000000e+00	1604.0
13	TraesCS3B01G099500	chr6B	80.882	1020	173	16	8	1019	398880695	398881700	0.000000e+00	784.0
14	TraesCS3B01G099500	chr2A	94.221	1021	54	1	1	1021	34826710	34825695	0.000000e+00	1554.0
15	TraesCS3B01G099500	chr5A	93.928	1021	56	2	1	1021	638548939	638547925	0.000000e+00	1537.0
16	TraesCS3B01G099500	chr4A	93.886	1014	57	1	8	1021	642820869	642819861	0.000000e+00	1524.0
17	TraesCS3B01G099500	chr4D	83.220	1025	159	9	1	1021	464543795	464542780	0.000000e+00	928.0
18	TraesCS3B01G099500	chr7D	82.283	1016	166	10	8	1019	628688235	628687230	0.000000e+00	867.0

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	TraesCS3B01G099500	chr3B	66585170	66589662	4492	True	8298.000000	8298	100.000	1	4493	1	chr3B.!!$R1	4492
1	TraesCS3B01G099500	chr3D	42743295	42747278	3983	True	1434.450000	5175	93.387	1017	4493	4	chr3D.!!$R1	3476
2	TraesCS3B01G099500	chr3A	54665455	54669051	3596	True	1781.333333	4170	94.369	1017	4303	3	chr3A.!!$R1	3286
3	TraesCS3B01G099500	chr1B	32592229	32594741	2512	True	3640.000000	3640	92.806	1017	3532	1	chr1B.!!$R1	2515
4	TraesCS3B01G099500	chr1B	503316956	503317971	1015	False	1692.000000	1692	96.670	1	1021	1	chr1B.!!$F1	1020
5	TraesCS3B01G099500	chr1B	533613011	533614015	1004	True	826.000000	826	81.649	8	1019	1	chr1B.!!$R2	1011
6	TraesCS3B01G099500	chrUn	10169503	10172012	2509	False	3422.000000	3422	91.256	1101	3629	1	chrUn.!!$F1	2528
7	TraesCS3B01G099500	chr6B	417760314	417761329	1015	False	1604.000000	1604	95.103	1	1021	1	chr6B.!!$F2	1020
8	TraesCS3B01G099500	chr6B	398880695	398881700	1005	False	784.000000	784	80.882	8	1019	1	chr6B.!!$F1	1011
9	TraesCS3B01G099500	chr2A	34825695	34826710	1015	True	1554.000000	1554	94.221	1	1021	1	chr2A.!!$R1	1020
10	TraesCS3B01G099500	chr5A	638547925	638548939	1014	True	1537.000000	1537	93.928	1	1021	1	chr5A.!!$R1	1020
11	TraesCS3B01G099500	chr4A	642819861	642820869	1008	True	1524.000000	1524	93.886	8	1021	1	chr4A.!!$R1	1013
12	TraesCS3B01G099500	chr4D	464542780	464543795	1015	True	928.000000	928	83.220	1	1021	1	chr4D.!!$R1	1020
13	TraesCS3B01G099500	chr7D	628687230	628688235	1005	True	867.000000	867	82.283	8	1019	1	chr7D.!!$R1	1011

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	Hairpin	End Stability	Orientation
625	630	1.277557	CCAACAGGAGAGGAGTGGAAG	59.722	57.143	0.00	0.00	3.46	F
1547	1552	1.271108	TGGTTGCATTAGTGAGGCGAA	60.271	47.619	0.00	0.00	4.70	F
2607	2612	0.532573	TTCACTCAGATGAGGCGACC	59.467	55.000	14.09	46.13	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1695	1700	1.948834	CATGCACCAAGAACACTGACA	59.051	47.619	0.00	0.00	3.58	R
2797	2802	2.236146	TGGAGTTCCATAACGTGATGCT	59.764	45.455	7.45	42.01	3.79	R
4452	4993	0.038159	GTTCAGAGGACCGTGTGGAG	60.038	60.000	0.00	39.21	3.86	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
250	251	3.513912	TGTCAGTAACCATAGACACTGGG	59.486	47.826	0.00	0.00	39.09	4.45
423	424	3.826157	TCCACAAAGTCCATGGAAATGTC	59.174	43.478	18.20	3.21	39.60	3.06
440	441	6.239714	GGAAATGTCTCTCCAAGCCATATCTA	60.240	42.308	0.00	0.00	0.00	1.98
572	574	7.353525	TGGCCAATAGAAAATCCTCTTGATTA	58.646	34.615	0.61	0.00	42.97	1.75
625	630	1.277557	CCAACAGGAGAGGAGTGGAAG	59.722	57.143	0.00	0.00	0.00	3.46
654	659	2.945668	GCAGTTTCTGTTGGAAGTCAGT	59.054	45.455	0.00	0.00	35.16	3.41
1324	1329	1.375908	GCGCAACAGAGTGGGATCA	60.376	57.895	0.30	0.00	33.45	2.92
1353	1358	6.650120	TGAGGTCTTTGGATTGTATAAGGAC	58.350	40.000	0.00	0.00	31.87	3.85
1452	1457	1.865340	GTTGAAGGTCGACAGTTCCAC	59.135	52.381	18.91	16.12	31.07	4.02
1547	1552	1.271108	TGGTTGCATTAGTGAGGCGAA	60.271	47.619	0.00	0.00	0.00	4.70
1550	1555	2.010145	TGCATTAGTGAGGCGAAGTC	57.990	50.000	0.00	0.00	0.00	3.01
1695	1700	2.224281	TGAGGCTGATGAGTTCACGTTT	60.224	45.455	0.00	0.00	0.00	3.60
1937	1942	3.563390	GCACATAATGGAGAAGAGGAAGC	59.437	47.826	0.00	0.00	0.00	3.86
1982	1987	4.415881	TGAATGCGGATGGTATAACACT	57.584	40.909	0.00	0.00	0.00	3.55
2088	2093	7.537596	AGCAATGAAGTATAGTATCTGCTCT	57.462	36.000	0.00	0.00	32.35	4.09
2212	2217	3.067180	CCCAATAAATGCTCTGATTGCGT	59.933	43.478	0.00	0.00	0.00	5.24
2227	2232	1.083401	GCGTGTCTTGTGCAGAACG	60.083	57.895	1.75	1.75	38.25	3.95
2275	2280	5.482908	TGTTTCAGCAGGTTCTTAGAGATC	58.517	41.667	0.00	0.00	0.00	2.75
2390	2395	4.450419	CACAATGAAGTCTGGTCTTCTGAC	59.550	45.833	7.72	0.00	42.76	3.51
2492	2497	4.008330	ACAGAGATGCCAGATCACAAAAG	58.992	43.478	0.00	0.00	0.00	2.27
2546	2551	6.295067	GGGTATGCTCAAAATGGTTACAGTTT	60.295	38.462	0.00	0.00	44.80	2.66
2557	2562	4.880759	TGGTTACAGTTTGCAATCATTGG	58.119	39.130	10.05	0.00	0.00	3.16
2607	2612	0.532573	TTCACTCAGATGAGGCGACC	59.467	55.000	14.09	0.00	46.13	4.79
2637	2642	7.118390	GCTAGTATTCTCAAAGCTTGTTCAGAA	59.882	37.037	0.00	5.95	0.00	3.02
2797	2802	6.808008	TCAAACAATTGGAAAACAAGCAAA	57.192	29.167	10.83	0.00	43.48	3.68
2856	2861	4.379394	GCAAAGAATGGTTATGCTGACGAA	60.379	41.667	0.00	0.00	34.29	3.85
2907	2912	4.319177	AGTCACAACTAAAGCCTGATGAC	58.681	43.478	0.00	0.00	36.34	3.06
3096	3101	6.303839	TGAAGAAGTTATTAACCAGTTGCCT	58.696	36.000	2.92	0.00	0.00	4.75
3137	3142	1.819632	GGGCGACATACCTTGCAGG	60.820	63.158	0.00	1.16	42.49	4.85
3664	3678	6.017109	TCTGACCACTTTATTTTCTGCAGTTC	60.017	38.462	14.67	0.00	0.00	3.01
3720	3734	0.608035	GGTTTCACCCTGCATTCCGA	60.608	55.000	0.00	0.00	30.04	4.55
3818	3833	8.051901	AGTAATTTTCACTATGGTTGTAAGCC	57.948	34.615	0.00	0.00	0.00	4.35
3826	3841	2.024176	TGGTTGTAAGCCTCTGAGGA	57.976	50.000	27.53	3.46	37.67	3.71
3849	3864	7.770897	AGGACTCGCAAAATTTCATATCTAGTT	59.229	33.333	0.00	0.00	0.00	2.24
3929	3944	2.838202	GGTACCAGTGAAGATTCAGGGA	59.162	50.000	7.15	1.88	37.98	4.20
3945	3960	3.196469	TCAGGGAGCAACTAGAACTCATG	59.804	47.826	0.00	3.67	31.88	3.07
4236	4721	7.959658	TTGGAACTTGATGAATGGTATCATT	57.040	32.000	0.00	0.00	45.45	2.57
4243	4728	5.065235	TGATGAATGGTATCATTGCACGAT	58.935	37.500	5.79	3.45	43.08	3.73
4257	4742	1.931906	CACGATGCACAGTGAGCTAT	58.068	50.000	15.91	5.76	40.56	2.97
4303	4788	9.176460	TCATGCAAAGTATTTCACTCATGATTA	57.824	29.630	0.00	0.00	35.03	1.75
4304	4789	9.961265	CATGCAAAGTATTTCACTCATGATTAT	57.039	29.630	0.00	0.00	35.03	1.28
4340	4881	8.840200	TGTAAATCTCTATTGTCCTTAGTCCT	57.160	34.615	0.00	0.00	0.00	3.85
4345	4886	5.419155	TCTCTATTGTCCTTAGTCCTGTGTG	59.581	44.000	0.00	0.00	0.00	3.82
4459	5000	6.920569	TTTTTCTACTTCTGAACTCCACAC	57.079	37.500	0.00	0.00	0.00	3.82
4473	5014	1.745890	CACACGGTCCTCTGAACCA	59.254	57.895	0.00	0.00	36.53	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
250	251	6.560253	AATGTGTTCAAACTACATGGTCTC	57.440	37.500	0.00	0.00	33.83	3.36
297	298	9.799106	CCCTATCTCATCCATTTACTGTAAATT	57.201	33.333	20.16	6.60	36.29	1.82
299	300	7.147391	TGCCCTATCTCATCCATTTACTGTAAA	60.147	37.037	14.73	14.73	0.00	2.01
423	424	5.598005	CCTATCCTAGATATGGCTTGGAGAG	59.402	48.000	11.83	11.83	43.81	3.20
440	441	3.900601	CTGCTTGATCCACTACCTATCCT	59.099	47.826	0.00	0.00	0.00	3.24
595	597	2.172483	CTCCTGTTGGGGGACACTCG	62.172	65.000	0.00	0.00	37.96	4.18
625	630	2.223805	CCAACAGAAACTGCTTTCCACC	60.224	50.000	0.00	0.00	37.12	4.61
654	659	4.410481	AGGATCTACATAGGATCTGCCA	57.590	45.455	0.00	0.00	39.41	4.92
789	794	9.790344	CCTAGTTGGATAGATCAAATTGAAGAT	57.210	33.333	0.00	0.00	38.35	2.40
790	795	8.772250	ACCTAGTTGGATAGATCAAATTGAAGA	58.228	33.333	0.00	0.00	39.71	2.87
941	946	7.865820	TGAACAAAGGATATCAGAAGGAATCT	58.134	34.615	4.83	0.00	39.68	2.40
1274	1279	1.444119	GACAGCGTTCCAAGCAACCA	61.444	55.000	0.00	0.00	37.01	3.67
1324	1329	3.771216	ACAATCCAAAGACCTCATGCTT	58.229	40.909	0.00	0.00	0.00	3.91
1353	1358	3.418995	CCATAATCCCTGCCTCTTCATG	58.581	50.000	0.00	0.00	0.00	3.07
1430	1435	2.135933	GGAACTGTCGACCTTCAACAG	58.864	52.381	14.12	4.80	44.68	3.16
1547	1552	4.755123	CACGGGAGAAATAAAACACAGACT	59.245	41.667	0.00	0.00	0.00	3.24
1550	1555	4.994852	TCTCACGGGAGAAATAAAACACAG	59.005	41.667	16.79	0.00	46.94	3.66
1695	1700	1.948834	CATGCACCAAGAACACTGACA	59.051	47.619	0.00	0.00	0.00	3.58
1982	1987	5.246203	ACAGTAGCAAAAGACACCTCATCTA	59.754	40.000	0.00	0.00	0.00	1.98
2088	2093	4.406972	AGAGAGCTACCAACAGCATGATTA	59.593	41.667	0.00	0.00	44.35	1.75
2212	2217	3.506067	TCTCTATCGTTCTGCACAAGACA	59.494	43.478	0.00	0.00	33.46	3.41
2227	2232	9.571810	CAACTGTATAGCTTCATCATCTCTATC	57.428	37.037	0.00	0.00	0.00	2.08
2275	2280	3.249687	AGCTGGAGGGCTTTAAACG	57.750	52.632	0.00	0.00	39.86	3.60
2390	2395	3.960571	ACACCAAGGGAAGAATCATCAG	58.039	45.455	0.00	0.00	0.00	2.90
2492	2497	2.331132	GCTGTCCACTCAAGCAGGC	61.331	63.158	0.00	0.00	0.00	4.85
2546	2551	6.380560	TCTCCAAAATGATACCAATGATTGCA	59.619	34.615	0.00	0.00	0.00	4.08
2547	2552	6.808829	TCTCCAAAATGATACCAATGATTGC	58.191	36.000	0.00	0.00	0.00	3.56
2557	2562	4.201950	ACTGCGCATTCTCCAAAATGATAC	60.202	41.667	12.24	0.00	38.64	2.24
2607	2612	5.578727	ACAAGCTTTGAGAATACTAGCGAAG	59.421	40.000	0.00	0.00	36.96	3.79
2637	2642	2.607187	CCGTCGTTAAGAGCTGTCATT	58.393	47.619	0.00	0.00	0.00	2.57
2797	2802	2.236146	TGGAGTTCCATAACGTGATGCT	59.764	45.455	7.45	0.00	42.01	3.79
2884	2889	4.757149	GTCATCAGGCTTTAGTTGTGACTT	59.243	41.667	0.00	0.00	37.33	3.01
2907	2912	3.053831	AGGACACCAAGGAATGTAACG	57.946	47.619	0.00	0.00	0.00	3.18
3192	3197	3.879932	GAGTTTTCTGGTTCCAACTCG	57.120	47.619	5.89	0.00	36.73	4.18
3514	3524	6.034591	CCTCATTCTTAAGCAGAGCATTTTG	58.965	40.000	0.00	0.00	31.12	2.44
3573	3584	2.483188	CCTCGGTAACCAAGCATCTACC	60.483	54.545	0.00	0.00	0.00	3.18
3664	3678	1.949465	TGCTGATGCAGTGATGCTAG	58.051	50.000	0.00	0.00	45.31	3.42
3720	3734	3.456277	CAGGTAATTAGGCTCCCTTGAGT	59.544	47.826	0.00	0.00	40.95	3.41
3818	3833	3.748048	TGAAATTTTGCGAGTCCTCAGAG	59.252	43.478	0.00	0.00	0.00	3.35
3826	3841	8.177663	CACAACTAGATATGAAATTTTGCGAGT	58.822	33.333	0.00	0.00	0.00	4.18
3849	3864	3.003394	CAAGCCATCTTGGTATCCACA	57.997	47.619	0.00	0.00	44.53	4.17
3929	3944	5.105187	TGAGCATACATGAGTTCTAGTTGCT	60.105	40.000	0.00	0.00	40.35	3.91
3945	3960	1.012841	GCTGAAGCACCTGAGCATAC	58.987	55.000	0.00	0.00	41.59	2.39
4046	4061	9.211485	CATCTGCAAATTTTTAGACAGGAAATT	57.789	29.630	3.86	0.00	35.22	1.82
4168	4185	6.195244	GCAACATAAACATCAAGCTTCATACG	59.805	38.462	0.00	0.00	0.00	3.06
4243	4728	4.893608	TCAAGTTTATAGCTCACTGTGCA	58.106	39.130	2.12	0.00	0.00	4.57
4324	4865	5.407407	ACACACAGGACTAAGGACAATAG	57.593	43.478	0.00	0.00	0.00	1.73
4326	4867	4.102524	TGAACACACAGGACTAAGGACAAT	59.897	41.667	0.00	0.00	0.00	2.71
4340	4881	8.791327	ATATCTGTCAATAACATGAACACACA	57.209	30.769	0.00	0.00	37.23	3.72
4374	4915	8.557029	ACAAGACTAATAACCTGAAAAAGAACG	58.443	33.333	0.00	0.00	0.00	3.95
4401	4942	3.763897	ACAAAGTTGTCTTTTGTGCTCCT	59.236	39.130	2.86	0.00	41.31	3.69
4448	4989	0.469331	AGAGGACCGTGTGGAGTTCA	60.469	55.000	0.00	0.00	39.21	3.18
4452	4993	0.038159	GTTCAGAGGACCGTGTGGAG	60.038	60.000	0.00	0.00	39.21	3.86
4459	5000	2.906354	CCTAAATGGTTCAGAGGACCG	58.094	52.381	0.00	0.00	40.13	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.