AutoCloner

Multiple sequence alignment - TraesCS4B01G384500

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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	TraesCS4B01G384500	chr4B	100.000	7368	0	0	1	7368	663802983	663795616	0.000000e+00	13607.0
1	TraesCS4B01G384500	chr4B	97.286	7369	175	15	1	7360	662764360	662771712	0.000000e+00	12477.0
2	TraesCS4B01G384500	chr4B	93.596	3326	190	14	1584	4892	662726535	662729854	0.000000e+00	4940.0
3	TraesCS4B01G384500	chr4B	91.855	1461	113	5	1	1460	662725083	662726538	0.000000e+00	2034.0
4	TraesCS4B01G384500	chr4B	88.138	1214	121	8	387	1581	663783822	663782613	0.000000e+00	1423.0
5	TraesCS4B01G384500	chr4B	94.055	471	26	2	5385	5854	662742207	662742676	0.000000e+00	713.0
6	TraesCS4B01G384500	chr4B	95.567	406	14	3	4895	5297	662741808	662742212	0.000000e+00	647.0
7	TraesCS4B01G384500	chr4B	94.911	393	19	1	6224	6615	663782062	663781670	1.360000e-171	614.0
8	TraesCS4B01G384500	chr4B	81.181	271	40	3	623	891	430052423	430052162	2.690000e-49	207.0
9	TraesCS4B01G384500	chrUn	95.170	6687	289	27	696	7368	41984176	41977510	0.000000e+00	10528.0
10	TraesCS4B01G384500	chrUn	94.286	700	39	1	1	700	41986312	41985614	0.000000e+00	1070.0
11	TraesCS4B01G384500	chrUn	96.615	384	11	2	769	1151	480593147	480592765	2.900000e-178	636.0
12	TraesCS4B01G384500	chrUn	85.458	502	67	6	1	500	285487045	285487542	1.100000e-142	518.0
13	TraesCS4B01G384500	chrUn	85.060	502	69	6	1	500	285493444	285493941	2.370000e-139	507.0
14	TraesCS4B01G384500	chrUn	79.679	374	70	5	6634	7004	41978633	41978263	1.580000e-66	265.0
15	TraesCS4B01G384500	chr3B	95.125	6687	296	24	696	7368	800115365	800108695	0.000000e+00	10515.0
16	TraesCS4B01G384500	chr3B	94.571	700	37	1	1	700	800117495	800116797	0.000000e+00	1081.0
17	TraesCS4B01G384500	chr3B	79.144	374	72	5	6634	7004	800109818	800109448	3.410000e-63	254.0
18	TraesCS4B01G384500	chr5A	92.267	5108	317	40	30	5119	702723243	702718196	0.000000e+00	7173.0
19	TraesCS4B01G384500	chr5A	96.383	1327	46	2	5620	6946	702718145	702716821	0.000000e+00	2183.0
20	TraesCS4B01G384500	chr5A	94.587	351	16	2	7019	7368	702716825	702716477	2.340000e-149	540.0
21	TraesCS4B01G384500	chr5A	73.935	399	89	11	6617	7006	702743041	702742649	5.960000e-31	147.0
22	TraesCS4B01G384500	chr7D	80.738	1246	227	10	1395	2636	630489166	630487930	0.000000e+00	959.0
23	TraesCS4B01G384500	chr4D	77.790	941	176	29	5679	6602	506457752	506456828	3.890000e-152	549.0
24	TraesCS4B01G384500	chr4D	90.698	43	4	0	7316	7358	89051438	89051480	2.870000e-04	58.4
25	TraesCS4B01G384500	chr4A	84.950	505	71	5	1	503	714821847	714822348	2.370000e-139	507.0
26	TraesCS4B01G384500	chr4A	77.066	484	93	10	5803	6270	632023243	632022762	5.670000e-66	263.0
27	TraesCS4B01G384500	chr1B	84.294	503	74	5	1	501	624967218	624966719	3.090000e-133	486.0
28	TraesCS4B01G384500	chr1B	88.636	44	5	0	7317	7360	141021309	141021266	4.000000e-03	54.7
29	TraesCS4B01G384500	chr7A	81.932	559	91	8	2084	2636	726437440	726436886	1.450000e-126	464.0
30	TraesCS4B01G384500	chr7A	83.130	492	72	8	2152	2636	726453081	726452594	8.780000e-119	438.0
31	TraesCS4B01G384500	chr7A	85.422	391	51	5	2249	2636	726439042	726438655	1.150000e-107	401.0
32	TraesCS4B01G384500	chr6D	73.906	640	141	18	1209	1837	9932673	9932049	4.440000e-57	233.0
33	TraesCS4B01G384500	chr5D	75.534	515	101	15	5787	6283	538152713	538152206	5.750000e-56	230.0
34	TraesCS4B01G384500	chr7B	81.250	272	38	6	623	891	382612827	382612566	2.690000e-49	207.0
35	TraesCS4B01G384500	chr7B	100.000	33	0	0	7315	7347	74931724	74931756	2.220000e-05	62.1
36	TraesCS4B01G384500	chr6B	85.385	130	16	3	4091	4218	46035267	46035139	1.670000e-26	132.0
37	TraesCS4B01G384500	chr3D	100.000	36	0	0	7315	7350	587942313	587942348	4.770000e-07	67.6
38	TraesCS4B01G384500	chr2A	90.698	43	4	0	7316	7358	497011392	497011350	2.870000e-04	58.4

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	TraesCS4B01G384500	chr4B	663795616	663802983	7367	True	13607.000000	13607	100.000000	1	7368	1	chr4B.!!$R2	7367
1	TraesCS4B01G384500	chr4B	662764360	662771712	7352	False	12477.000000	12477	97.286000	1	7360	1	chr4B.!!$F1	7359
2	TraesCS4B01G384500	chr4B	662725083	662729854	4771	False	3487.000000	4940	92.725500	1	4892	2	chr4B.!!$F2	4891
3	TraesCS4B01G384500	chr4B	663781670	663783822	2152	True	1018.500000	1423	91.524500	387	6615	2	chr4B.!!$R3	6228
4	TraesCS4B01G384500	chr4B	662741808	662742676	868	False	680.000000	713	94.811000	4895	5854	2	chr4B.!!$F3	959
5	TraesCS4B01G384500	chrUn	41977510	41984176	6666	True	10528.000000	10528	95.170000	696	7368	1	chrUn.!!$R1	6672
6	TraesCS4B01G384500	chrUn	41985614	41986312	698	True	1070.000000	1070	94.286000	1	700	1	chrUn.!!$R3	699
7	TraesCS4B01G384500	chr3B	800108695	800115365	6670	True	10515.000000	10515	95.125000	696	7368	1	chr3B.!!$R1	6672
8	TraesCS4B01G384500	chr3B	800116797	800117495	698	True	1081.000000	1081	94.571000	1	700	1	chr3B.!!$R3	699
9	TraesCS4B01G384500	chr5A	702716477	702723243	6766	True	3298.666667	7173	94.412333	30	7368	3	chr5A.!!$R2	7338
10	TraesCS4B01G384500	chr7D	630487930	630489166	1236	True	959.000000	959	80.738000	1395	2636	1	chr7D.!!$R1	1241
11	TraesCS4B01G384500	chr4D	506456828	506457752	924	True	549.000000	549	77.790000	5679	6602	1	chr4D.!!$R1	923
12	TraesCS4B01G384500	chr4A	714821847	714822348	501	False	507.000000	507	84.950000	1	503	1	chr4A.!!$F1	502
13	TraesCS4B01G384500	chr7A	726436886	726439042	2156	True	432.500000	464	83.677000	2084	2636	2	chr7A.!!$R2	552
14	TraesCS4B01G384500	chr6D	9932049	9932673	624	True	233.000000	233	73.906000	1209	1837	1	chr6D.!!$R1	628
15	TraesCS4B01G384500	chr5D	538152206	538152713	507	True	230.000000	230	75.534000	5787	6283	1	chr5D.!!$R1	496

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
252	253	0.896940	GGTGTGTGACCTAGTCCCGA	60.897	60.000	0.00	0.00	42.25	5.14	F
1203	1223	0.461516	ATGACCTCATCAGCACGCTG	60.462	55.000	12.91	12.91	41.91	5.18	F
2032	2200	0.179048	TGTCTGCTTCACACAGGTGG	60.179	55.000	4.24	0.00	45.32	4.61	F
2936	3922	0.836400	AGCTTTCCTCTCCAACCGGA	60.836	55.000	9.46	0.00	39.79	5.14	F
3111	4098	4.701956	ATCGGAATTAGTGCACTTTTGG	57.298	40.909	27.06	12.69	0.00	3.28	F
4219	5217	2.642154	TTCTCTAGCCCTAGACCTCG	57.358	55.000	0.97	0.00	37.28	4.63	F
4252	5250	3.579151	GGTCTCCTCTTTCAACTAGTGGT	59.421	47.826	0.00	0.00	0.00	4.16	F
5195	6316	3.667497	TTAATGCGCCAAACATTCCAA	57.333	38.095	4.18	0.00	38.62	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1500	1648	0.387565	GGACGAAGATGAGCTCCTCC	59.612	60.000	12.15	0.00	0.00	4.30	R
3040	4027	0.874390	TGCAGAAGCTTTAGGTTGCG	59.126	50.000	0.00	0.00	42.74	4.85	R
3872	4862	2.835764	ACGACCTGAATGGCTACCTTTA	59.164	45.455	0.00	0.00	40.22	1.85	R
4219	5217	1.675720	GAGGAGACCAGAGCTCAGGC	61.676	65.000	24.06	16.43	34.07	4.85	R
5043	6163	0.895100	GCTGGTGGCATCTTGGTTGA	60.895	55.000	0.00	0.00	41.35	3.18	R
6188	7330	3.906720	TGGAGCCCAACTTAGTATCAC	57.093	47.619	0.00	0.00	0.00	3.06	R
6271	7413	7.759489	ACAAATTCTGTAAATACTCTTGGCA	57.241	32.000	0.00	0.00	36.10	4.92	R
6444	7587	4.264352	TGGAAAATATTCTTGCCACTCCCT	60.264	41.667	0.00	0.00	35.79	4.20	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
26	27	2.628657	GGAGGAGCGGTGTTACATCTAT	59.371	50.000	0.00	0.00	0.00	1.98
229	230	4.441695	CCTCTGAGAGCGCGCCAA	62.442	66.667	30.33	10.12	0.00	4.52
252	253	0.896940	GGTGTGTGACCTAGTCCCGA	60.897	60.000	0.00	0.00	42.25	5.14
334	335	3.824443	TGATATTAGGCTCGGACATTCGA	59.176	43.478	0.00	0.00	37.60	3.71
493	496	5.593909	TCGGTGGTATATCCTCGTTTTCTTA	59.406	40.000	0.00	0.00	35.99	2.10
551	561	2.203280	CGTTGTTGCCCCTGTCCA	60.203	61.111	0.00	0.00	0.00	4.02
565	575	2.045634	TCCATCCCGTCGTCGAGT	60.046	61.111	2.98	0.00	39.71	4.18
600	610	3.265221	TGCCATCAAGAGAGACCTTCAAT	59.735	43.478	0.00	0.00	0.00	2.57
799	809	7.531857	TTGCATAAAAGGATGGTTGTTTAGA	57.468	32.000	0.00	0.00	0.00	2.10
868	878	3.623060	AGCGCATGATTTAGATCGTTTGT	59.377	39.130	11.47	0.00	34.91	2.83
991	1010	6.260271	CGGTAAAAGAAGGAAAGGTGGATATC	59.740	42.308	0.00	0.00	0.00	1.63
1000	1019	4.889409	GGAAAGGTGGATATCATTGCTTCA	59.111	41.667	4.83	0.00	0.00	3.02
1016	1036	2.522436	CATGGGCCGCAATGGGAT	60.522	61.111	0.00	0.00	38.63	3.85
1178	1198	2.745037	GGCACAGGGTTGTACGGA	59.255	61.111	0.00	0.00	35.25	4.69
1203	1223	0.461516	ATGACCTCATCAGCACGCTG	60.462	55.000	12.91	12.91	41.91	5.18
1464	1612	2.099062	CATGACGAAGCGCTTGCC	59.901	61.111	30.47	13.48	40.41	4.52
1477	1625	1.211743	GCTTGCCAAGAAGTTGTTGC	58.788	50.000	9.04	4.16	30.95	4.17
1952	2107	8.860088	AGTCCTTGTTAATAGCTTCAACAAATT	58.140	29.630	16.27	2.33	40.54	1.82
2032	2200	0.179048	TGTCTGCTTCACACAGGTGG	60.179	55.000	4.24	0.00	45.32	4.61
2080	2248	1.697982	GGTTGTCCCTCCAACACTACT	59.302	52.381	6.41	0.00	45.16	2.57
2472	3454	1.202114	GGGAAAGATGCATGTTCGCAA	59.798	47.619	22.24	0.00	46.87	4.85
2772	3758	5.165961	AGTCTCCAGTTAGCTAAATGCAA	57.834	39.130	24.81	15.20	45.94	4.08
2784	3770	4.711355	AGCTAAATGCAATTTCCTAAGGCA	59.289	37.500	0.00	0.00	44.81	4.75
2931	3917	1.277557	GAGAGCAGCTTTCCTCTCCAA	59.722	52.381	18.53	0.00	45.24	3.53
2936	3922	0.836400	AGCTTTCCTCTCCAACCGGA	60.836	55.000	9.46	0.00	39.79	5.14
3040	4027	9.011095	AGTATTTAGTAGGGAAGTTGCTTTTTC	57.989	33.333	0.00	0.00	0.00	2.29
3111	4098	4.701956	ATCGGAATTAGTGCACTTTTGG	57.298	40.909	27.06	12.69	0.00	3.28
3319	4306	7.549842	AGCAAGCATCATAGATAGCAAATCTAG	59.450	37.037	12.62	6.92	34.50	2.43
3965	4961	6.151480	CCCAATAAAAAGGATTGCAGCAAATT	59.849	34.615	12.97	4.87	33.70	1.82
4135	5132	5.221925	GGGCCATCCAGAGAGTGAATTAATA	60.222	44.000	4.39	0.00	35.00	0.98
4219	5217	2.642154	TTCTCTAGCCCTAGACCTCG	57.358	55.000	0.97	0.00	37.28	4.63
4252	5250	3.579151	GGTCTCCTCTTTCAACTAGTGGT	59.421	47.826	0.00	0.00	0.00	4.16
4417	5415	3.910627	ACACCCTTCTGTAGTCTTTCCAT	59.089	43.478	0.00	0.00	0.00	3.41
4845	5846	3.714798	TCTAACCAGGTCAAAAGTCACCT	59.285	43.478	0.00	0.00	44.42	4.00
5195	6316	3.667497	TTAATGCGCCAAACATTCCAA	57.333	38.095	4.18	0.00	38.62	3.53
5353	6474	4.403113	TGTGCGACTTCCCTATAATGTGTA	59.597	41.667	0.00	0.00	0.00	2.90
5590	6713	7.308408	CGGTAGTACTAGCTCATTATGCAAGTA	60.308	40.741	25.25	0.00	0.00	2.24
5601	6724	9.173939	GCTCATTATGCAAGTAATGTTATGAAC	57.826	33.333	16.07	0.00	40.97	3.18
6188	7330	6.292757	GGATCATGAGATTGATTTCGTGACAG	60.293	42.308	0.09	0.00	40.89	3.51
6490	7633	0.185901	AGGGGATGCAAGTTGTGTGT	59.814	50.000	4.48	0.00	0.00	3.72
6541	7684	9.420551	GGAACTTCTATTACCTGTAATATTCCG	57.579	37.037	16.64	6.25	35.72	4.30
6704	7847	5.825532	TCATATGTTTTTGTCATCCTCCCA	58.174	37.500	1.90	0.00	0.00	4.37
6775	7918	2.627699	GGTGCAAGGTGATCCTGAAAAA	59.372	45.455	0.00	0.00	44.35	1.94
7010	8154	7.780008	TCTCGTCTCATTCTTGTTTTAAACA	57.220	32.000	6.41	6.41	40.21	2.83
7227	8372	6.824305	AGAAACATCAAAGGTGACCAATAG	57.176	37.500	3.63	0.00	36.31	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	2.355363	CGTTGTCGGTCCTTGCGA	60.355	61.111	0.00	0.00	0.00	5.10
252	253	0.687354	CCCTAGCCGAGCCACAATAT	59.313	55.000	0.00	0.00	0.00	1.28
551	561	2.125391	TCGACTCGACGACGGGAT	60.125	61.111	15.33	0.00	43.41	3.85
868	878	4.062293	CGTGTATCCTTTGTGTTCTCCAA	58.938	43.478	0.00	0.00	0.00	3.53
964	983	2.817844	CACCTTTCCTTCTTTTACCGGG	59.182	50.000	6.32	0.00	0.00	5.73
991	1010	2.105528	GCGGCCCATGAAGCAATG	59.894	61.111	0.00	1.16	0.00	2.82
1000	1019	2.135581	CAATCCCATTGCGGCCCAT	61.136	57.895	0.00	0.00	32.92	4.00
1016	1036	4.015406	ATCCGTCACGCAGCCCAA	62.015	61.111	0.00	0.00	0.00	4.12
1203	1223	4.148825	AGGAGCATGTCGTCCGGC	62.149	66.667	0.00	0.00	37.97	6.13
1464	1612	1.480205	CCTTGCGCAACAACTTCTTG	58.520	50.000	21.02	5.96	33.68	3.02
1500	1648	0.387565	GGACGAAGATGAGCTCCTCC	59.612	60.000	12.15	0.00	0.00	4.30
1952	2107	0.874390	CGGCAGCTCAGCAGTAAAAA	59.126	50.000	0.00	0.00	35.83	1.94
2032	2200	3.378427	AGTGCCAAGAATTTATCTTCCGC	59.622	43.478	0.00	0.00	45.42	5.54
2080	2248	0.904649	AGATCGAGGATGGTGCAACA	59.095	50.000	7.04	7.04	39.98	3.33
2472	3454	1.677552	GACATGAACACGAGGGGGT	59.322	57.895	0.00	0.00	0.00	4.95
2592	3578	9.866655	ATCCTAAATAGCATCCAACTGATAAAA	57.133	29.630	0.00	0.00	30.56	1.52
2772	3758	7.486407	AATGACTTTGAATGCCTTAGGAAAT	57.514	32.000	0.69	0.00	0.00	2.17
2784	3770	6.427853	TCATTGTCTGTCGAATGACTTTGAAT	59.572	34.615	16.56	7.95	45.70	2.57
2856	3842	9.430399	GGTTGCCTACCTACTATCCATATATAA	57.570	37.037	0.00	0.00	44.10	0.98
2931	3917	7.509546	ACAACATTATTGAGAGAATATCCGGT	58.490	34.615	0.00	0.00	0.00	5.28
3040	4027	0.874390	TGCAGAAGCTTTAGGTTGCG	59.126	50.000	0.00	0.00	42.74	4.85
3111	4098	7.561237	TCTTTTGCATGAAAATTAACTACGC	57.439	32.000	0.00	0.00	32.98	4.42
3252	4239	5.798125	TTGATTATTGGTTTGTGCCTTGA	57.202	34.783	0.00	0.00	0.00	3.02
3319	4306	8.466617	TTCACCTCTCCTCTTCAATATAGTAC	57.533	38.462	0.00	0.00	0.00	2.73
3872	4862	2.835764	ACGACCTGAATGGCTACCTTTA	59.164	45.455	0.00	0.00	40.22	1.85
3965	4961	4.467795	AGAGAGCCTCTAATGCTACAAACA	59.532	41.667	0.00	0.00	39.28	2.83
4135	5132	4.281657	GCCAACCATAGAAGGAGGAAAAT	58.718	43.478	0.00	0.00	31.87	1.82
4219	5217	1.675720	GAGGAGACCAGAGCTCAGGC	61.676	65.000	24.06	16.43	34.07	4.85
4417	5415	7.664082	TGTTGCAAGAGAAAATTTCAAAACA	57.336	28.000	8.55	6.24	0.00	2.83
5043	6163	0.895100	GCTGGTGGCATCTTGGTTGA	60.895	55.000	0.00	0.00	41.35	3.18
5195	6316	6.539826	TCAGTGTCTCGATGAATTGCATATTT	59.460	34.615	0.00	0.00	37.34	1.40
5451	6572	4.928615	GCAACATAAAAGCTTATTGTGGCA	59.071	37.500	21.75	0.00	31.98	4.92
5590	6713	4.647611	TCGTGTTCCTGGTTCATAACATT	58.352	39.130	1.82	0.00	34.62	2.71
6188	7330	3.906720	TGGAGCCCAACTTAGTATCAC	57.093	47.619	0.00	0.00	0.00	3.06
6271	7413	7.759489	ACAAATTCTGTAAATACTCTTGGCA	57.241	32.000	0.00	0.00	36.10	4.92
6305	7447	7.373493	AGATAAACGAAGGAGTTAACGAAAGA	58.627	34.615	0.00	0.00	33.41	2.52
6444	7587	4.264352	TGGAAAATATTCTTGCCACTCCCT	60.264	41.667	0.00	0.00	35.79	4.20
6704	7847	6.897986	AGCTGAGATAAATGAAGGAGTTGAT	58.102	36.000	0.00	0.00	0.00	2.57
6775	7918	5.647658	TGTTTTGAATCGTTCTCATAGCCAT	59.352	36.000	0.00	0.00	0.00	4.40
7010	8154	8.232913	TCAAATGTGCTAAGGAACTAAAAAGT	57.767	30.769	0.00	0.00	38.49	2.66
7227	8372	2.871633	CAACCACTTGAAAAACATGGGC	59.128	45.455	0.00	0.00	34.11	5.36
7281	8426	1.248101	ATGGGGCGCCACAAACTTAC	61.248	55.000	38.92	10.67	0.00	2.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.