AutoCloner

Multiple sequence alignment - TraesCS6B01G133500

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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	TraesCS6B01G133500	chr6B	100.000	3209	0	0	1	3209	130319156	130315948	0.000000e+00	5927.0
1	TraesCS6B01G133500	chr6A	92.644	2012	105	24	1073	3077	73385219	73383244	0.000000e+00	2856.0
2	TraesCS6B01G133500	chr6A	93.095	420	19	5	689	1098	73385646	73385227	9.850000e-170	606.0
3	TraesCS6B01G133500	chr6A	92.593	135	3	1	3075	3209	73383162	73383035	1.520000e-43	187.0
4	TraesCS6B01G133500	chr6D	93.369	1674	64	22	687	2327	58061553	58059894	0.000000e+00	2433.0
5	TraesCS6B01G133500	chr6D	93.750	688	41	1	1	686	45802936	45803623	0.000000e+00	1031.0
6	TraesCS6B01G133500	chr6D	84.557	395	37	9	2382	2765	58053429	58053048	1.410000e-98	370.0
7	TraesCS6B01G133500	chr6D	94.595	185	9	1	2752	2936	58049748	58049565	5.240000e-73	285.0
8	TraesCS6B01G133500	chr7D	91.715	688	54	3	1	686	525763135	525763821	0.000000e+00	952.0
9	TraesCS6B01G133500	chr3B	91.424	688	55	4	1	686	575280346	575281031	0.000000e+00	941.0
10	TraesCS6B01G133500	chr3B	91.279	688	55	5	1	686	726434534	726435218	0.000000e+00	933.0
11	TraesCS6B01G133500	chr3B	90.684	687	56	6	1	686	13522833	13523512	0.000000e+00	907.0
12	TraesCS6B01G133500	chr3B	96.970	33	0	1	2374	2406	43718746	43718715	2.000000e-03	54.7
13	TraesCS6B01G133500	chr1B	90.652	706	60	4	1	705	548682987	548682287	0.000000e+00	933.0
14	TraesCS6B01G133500	chr1B	91.279	688	51	4	1	687	539844359	539843680	0.000000e+00	929.0
15	TraesCS6B01G133500	chr1B	91.525	59	5	0	2115	2173	561753080	561753022	7.380000e-12	82.4
16	TraesCS6B01G133500	chr4D	90.738	691	57	4	1	687	488872021	488872708	0.000000e+00	915.0
17	TraesCS6B01G133500	chr5A	90.580	690	63	2	1	689	113805673	113804985	0.000000e+00	913.0
18	TraesCS6B01G133500	chr5A	78.912	147	28	2	1157	1300	537019065	537019211	2.630000e-16	97.1
19	TraesCS6B01G133500	chr2A	77.573	651	135	10	1564	2210	465552651	465552008	1.810000e-102	383.0
20	TraesCS6B01G133500	chr5B	81.022	137	23	2	1167	1300	511346532	511346668	4.380000e-19	106.0
21	TraesCS6B01G133500	chr1A	93.220	59	4	0	2115	2173	513158536	513158478	1.590000e-13	87.9
22	TraesCS6B01G133500	chr1D	89.831	59	6	0	2115	2173	415435091	415435033	3.430000e-10	76.8

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	TraesCS6B01G133500	chr6B	130315948	130319156	3208	True	5927.000000	5927	100.000000	1	3209	1	chr6B.!!$R1	3208
1	TraesCS6B01G133500	chr6A	73383035	73385646	2611	True	1216.333333	2856	92.777333	689	3209	3	chr6A.!!$R1	2520
2	TraesCS6B01G133500	chr6D	58059894	58061553	1659	True	2433.000000	2433	93.369000	687	2327	1	chr6D.!!$R1	1640
3	TraesCS6B01G133500	chr6D	45802936	45803623	687	False	1031.000000	1031	93.750000	1	686	1	chr6D.!!$F1	685
4	TraesCS6B01G133500	chr6D	58049565	58053429	3864	True	327.500000	370	89.576000	2382	2936	2	chr6D.!!$R2	554
5	TraesCS6B01G133500	chr7D	525763135	525763821	686	False	952.000000	952	91.715000	1	686	1	chr7D.!!$F1	685
6	TraesCS6B01G133500	chr3B	575280346	575281031	685	False	941.000000	941	91.424000	1	686	1	chr3B.!!$F2	685
7	TraesCS6B01G133500	chr3B	726434534	726435218	684	False	933.000000	933	91.279000	1	686	1	chr3B.!!$F3	685
8	TraesCS6B01G133500	chr3B	13522833	13523512	679	False	907.000000	907	90.684000	1	686	1	chr3B.!!$F1	685
9	TraesCS6B01G133500	chr1B	548682287	548682987	700	True	933.000000	933	90.652000	1	705	1	chr1B.!!$R2	704
10	TraesCS6B01G133500	chr1B	539843680	539844359	679	True	929.000000	929	91.279000	1	687	1	chr1B.!!$R1	686
11	TraesCS6B01G133500	chr4D	488872021	488872708	687	False	915.000000	915	90.738000	1	687	1	chr4D.!!$F1	686
12	TraesCS6B01G133500	chr5A	113804985	113805673	688	True	913.000000	913	90.580000	1	689	1	chr5A.!!$R1	688
13	TraesCS6B01G133500	chr2A	465552008	465552651	643	True	383.000000	383	77.573000	1564	2210	1	chr2A.!!$R1	646

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
812	820	0.595588	TGCACAAATGTAACCCTGCG	59.404	50.0	0.0	0.0	0.0	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2479	2557	0.388659	TTGTTGCATGGTGAGTTGGC	59.611	50.0	0.0	0.0	0.0	4.52	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
82	85	7.648908	CAGAAAAACAATTACAGATCTGTTGCA	59.351	33.333	32.14	17.44	41.83	4.08
83	86	8.362639	AGAAAAACAATTACAGATCTGTTGCAT	58.637	29.630	32.14	18.79	41.83	3.96
163	166	2.126307	CGACGCTGCTGCTACACT	60.126	61.111	14.03	0.00	36.97	3.55
186	189	0.608130	CCTCACAATCGTCTGGGACA	59.392	55.000	0.00	0.00	32.09	4.02
228	231	1.264826	GGTTTTCGACCGCAAAGCTAA	59.735	47.619	8.86	0.00	39.00	3.09
315	318	2.509336	CTCCAAGCGATTCGGCGT	60.509	61.111	6.85	0.00	38.18	5.68
351	354	2.032634	GCCGCCATGAACGAAGACA	61.033	57.895	9.34	0.00	0.00	3.41
531	537	1.133181	TGGTGGGCCAGATCTGTCAA	61.133	55.000	21.11	4.26	40.46	3.18
628	634	7.281991	CTGAAGTTTTTGGTCAGTTTTCAAG	57.718	36.000	0.00	0.00	35.17	3.02
756	764	4.710423	TCATCCAGAGACGAAGAAGAAG	57.290	45.455	0.00	0.00	0.00	2.85
812	820	0.595588	TGCACAAATGTAACCCTGCG	59.404	50.000	0.00	0.00	0.00	5.18
982	994	2.668550	GGTGGTTCCGGCTCACAC	60.669	66.667	18.45	14.04	33.45	3.82
1336	1387	3.812262	GGTATGTACCCACCACCATTAC	58.188	50.000	7.86	0.00	40.53	1.89
1337	1388	3.434024	GGTATGTACCCACCACCATTACC	60.434	52.174	7.86	0.00	40.53	2.85
1338	1389	0.993470	TGTACCCACCACCATTACCC	59.007	55.000	0.00	0.00	0.00	3.69
1339	1390	0.993470	GTACCCACCACCATTACCCA	59.007	55.000	0.00	0.00	0.00	4.51
1340	1391	0.993470	TACCCACCACCATTACCCAC	59.007	55.000	0.00	0.00	0.00	4.61
1341	1392	0.774491	ACCCACCACCATTACCCACT	60.774	55.000	0.00	0.00	0.00	4.00
1342	1393	1.291109	CCCACCACCATTACCCACTA	58.709	55.000	0.00	0.00	0.00	2.74
1343	1394	1.064979	CCCACCACCATTACCCACTAC	60.065	57.143	0.00	0.00	0.00	2.73
1402	1462	1.180029	CCCAAACAGCCAAGGATCAG	58.820	55.000	0.00	0.00	0.00	2.90
1491	1558	0.914644	TGAAGAAGGGCCTCTCCATG	59.085	55.000	6.46	0.00	36.21	3.66
1642	1709	2.268920	GCAGCATCCCGGACAAGA	59.731	61.111	0.73	0.00	0.00	3.02
1667	1734	0.108992	TACTTCATCGTCACGGGCAC	60.109	55.000	0.00	0.00	0.00	5.01
1887	1954	4.988598	ACGGACCGCAACCAGCTG	62.989	66.667	15.39	6.78	42.61	4.24
1979	2046	2.490509	TGGTGAACGTCGACATCTACAT	59.509	45.455	17.16	0.00	0.00	2.29
1996	2063	1.226974	ATCATCTTCGCCGACGTGG	60.227	57.895	0.00	0.00	41.18	4.94
2167	2234	1.152440	AGGGGCTACCAGATCCTCG	60.152	63.158	0.97	0.00	43.89	4.63
2212	2279	2.814269	TCAGATTCATGCACTAGCGAC	58.186	47.619	0.00	0.00	46.23	5.19
2236	2303	5.179182	CAGCAACTTTCTTTTCTCTCTCTCC	59.821	44.000	0.00	0.00	0.00	3.71
2237	2304	5.071653	AGCAACTTTCTTTTCTCTCTCTCCT	59.928	40.000	0.00	0.00	0.00	3.69
2255	2325	5.505780	TCTCCTCTCTCTCTCTTTTGGTAG	58.494	45.833	0.00	0.00	0.00	3.18
2256	2326	4.020543	TCCTCTCTCTCTCTTTTGGTAGC	58.979	47.826	0.00	0.00	0.00	3.58
2257	2327	3.766591	CCTCTCTCTCTCTTTTGGTAGCA	59.233	47.826	0.00	0.00	0.00	3.49
2264	2334	7.946207	TCTCTCTCTTTTGGTAGCATAGTATG	58.054	38.462	5.73	5.73	0.00	2.39
2327	2403	4.013050	AGGAGTGCTCTGCCTTTTATTTC	58.987	43.478	3.47	0.00	32.28	2.17
2410	2488	8.504815	GTCCTCACTAACTCCAAATTCTTTTAC	58.495	37.037	0.00	0.00	0.00	2.01
2421	2499	8.429237	TCCAAATTCTTTTACCATACAACCAT	57.571	30.769	0.00	0.00	0.00	3.55
2422	2500	8.310382	TCCAAATTCTTTTACCATACAACCATG	58.690	33.333	0.00	0.00	0.00	3.66
2423	2501	8.093927	CCAAATTCTTTTACCATACAACCATGT	58.906	33.333	0.00	0.00	43.74	3.21
2424	2502	9.487790	CAAATTCTTTTACCATACAACCATGTT	57.512	29.630	0.00	0.00	41.05	2.71
2441	2519	4.456911	CCATGTTTGTCAACTCACTATGCT	59.543	41.667	0.00	0.00	33.58	3.79
2503	2581	3.648339	ACTCACCATGCAACAATTCAC	57.352	42.857	0.00	0.00	0.00	3.18
2512	2590	5.406175	CCATGCAACAATTCACGAAAAAGAT	59.594	36.000	0.00	0.00	0.00	2.40
2523	2601	6.308371	TCACGAAAAAGATCCACCTTTAAC	57.692	37.500	0.00	0.00	35.50	2.01
2524	2602	5.049954	TCACGAAAAAGATCCACCTTTAACG	60.050	40.000	0.00	0.00	38.91	3.18
2546	2624	3.450893	GCATCATGCATGATACTCGTG	57.549	47.619	35.47	26.03	45.23	4.35
2667	2754	9.806203	CAAATCTCATTTAGATAATTGCAACCA	57.194	29.630	0.00	0.00	44.56	3.67
2674	2761	7.487822	TTTAGATAATTGCAACCAATTCCCA	57.512	32.000	0.00	0.00	45.99	4.37
2684	2771	1.288752	CAATTCCCACGGCAACACC	59.711	57.895	0.00	0.00	0.00	4.16
2707	2794	4.831155	CCGGGGTATCATCTCTAGTTGTAA	59.169	45.833	0.00	0.00	0.00	2.41
2789	6189	2.632377	AGCATGTACCATAGCACACAC	58.368	47.619	0.00	0.00	0.00	3.82
2854	6254	7.012044	ACACGTACTAAGCAACAAGATTTCTTT	59.988	33.333	0.00	0.00	33.11	2.52
3026	6427	1.194121	ACTCCAAAGGCAAATGGGGC	61.194	55.000	3.33	0.00	41.12	5.80
3038	6439	1.366319	AATGGGGCCCTAGAGCATAG	58.634	55.000	25.93	0.00	0.00	2.23
3106	6591	8.815565	ATAAGTAGTGATTCTCTCAAGTCTCA	57.184	34.615	0.00	0.00	35.07	3.27
3107	6592	7.531857	AAGTAGTGATTCTCTCAAGTCTCAA	57.468	36.000	0.00	0.00	35.07	3.02
3193	6678	4.701651	AGCACAACAACAGTATATGCACAT	59.298	37.500	0.00	0.00	34.03	3.21
3196	6681	7.067372	AGCACAACAACAGTATATGCACATATT	59.933	33.333	8.37	0.00	35.71	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	85	4.891727	CTGGCGGCGCGAGGTAAT	62.892	66.667	32.26	0.00	30.86	1.89
163	166	1.215382	CAGACGATTGTGAGGCGGA	59.785	57.895	0.00	0.00	0.00	5.54
186	189	0.619832	TCCCAGCCTCAATCTCAGCT	60.620	55.000	0.00	0.00	35.52	4.24
365	368	1.227664	CTCTCCCCCGAGCTCACTA	59.772	63.158	15.40	0.00	35.94	2.74
483	489	2.962253	GGCCGCGCTAACAGCTAG	60.962	66.667	5.56	0.00	39.60	3.42
628	634	3.535561	CATCCCACAGAACTACCACATC	58.464	50.000	0.00	0.00	0.00	3.06
756	764	3.616317	GCTCTCTGTCTCTCTGGGTTTTC	60.616	52.174	0.00	0.00	0.00	2.29
982	994	2.125753	GTGAGTGGCAGCGAGAGG	60.126	66.667	0.00	0.00	0.00	3.69
1016	1034	2.885113	CGGAGATCACGCCAGACA	59.115	61.111	0.00	0.00	35.72	3.41
1281	1332	2.005451	CTGATCTTGCCGTTGGAGAAG	58.995	52.381	0.00	0.00	0.00	2.85
1330	1381	4.638865	GGCAAAAGTAGTAGTGGGTAATGG	59.361	45.833	0.00	0.00	0.00	3.16
1331	1382	5.250200	TGGCAAAAGTAGTAGTGGGTAATG	58.750	41.667	0.00	0.00	0.00	1.90
1333	1384	4.978438	TGGCAAAAGTAGTAGTGGGTAA	57.022	40.909	0.00	0.00	0.00	2.85
1334	1385	4.532916	TCATGGCAAAAGTAGTAGTGGGTA	59.467	41.667	0.00	0.00	0.00	3.69
1335	1386	3.329520	TCATGGCAAAAGTAGTAGTGGGT	59.670	43.478	0.00	0.00	0.00	4.51
1336	1387	3.950397	TCATGGCAAAAGTAGTAGTGGG	58.050	45.455	0.00	0.00	0.00	4.61
1337	1388	5.957842	TTTCATGGCAAAAGTAGTAGTGG	57.042	39.130	0.00	0.00	0.00	4.00
1338	1389	7.370383	ACATTTTCATGGCAAAAGTAGTAGTG	58.630	34.615	0.00	0.00	34.27	2.74
1339	1390	7.524717	ACATTTTCATGGCAAAAGTAGTAGT	57.475	32.000	0.00	0.00	34.27	2.73
1342	1393	9.777297	AAAATACATTTTCATGGCAAAAGTAGT	57.223	25.926	0.00	6.65	35.18	2.73
1369	1420	4.396790	GCTGTTTGGGAAATTATACCGTGA	59.603	41.667	0.00	0.00	0.00	4.35
1373	1433	5.395214	CCTTGGCTGTTTGGGAAATTATACC	60.395	44.000	0.00	0.00	0.00	2.73
1374	1434	5.420739	TCCTTGGCTGTTTGGGAAATTATAC	59.579	40.000	0.00	0.00	0.00	1.47
1402	1462	2.596343	CGCACGCATTTCCAAAACAAAC	60.596	45.455	0.00	0.00	0.00	2.93
1501	1568	2.811317	GAAGCTCACGCCGGTCTG	60.811	66.667	1.90	0.00	36.60	3.51
1642	1709	1.202043	CGTGACGATGAAGTAGAGCGT	60.202	52.381	0.00	0.00	37.97	5.07
1887	1954	1.973812	GTGGTTGAAGAGCAGGGCC	60.974	63.158	0.00	0.00	36.22	5.80
1979	2046	2.180769	CCACGTCGGCGAAGATGA	59.819	61.111	28.54	0.00	42.00	2.92
2212	2279	5.179182	GGAGAGAGAGAAAAGAAAGTTGCTG	59.821	44.000	0.00	0.00	0.00	4.41
2236	2303	5.596836	ATGCTACCAAAAGAGAGAGAGAG	57.403	43.478	0.00	0.00	0.00	3.20
2237	2304	6.191315	ACTATGCTACCAAAAGAGAGAGAGA	58.809	40.000	0.00	0.00	0.00	3.10
2255	2325	5.704888	ACTCGCTAGTGAATCATACTATGC	58.295	41.667	7.52	0.00	33.57	3.14
2256	2326	8.581057	AAAACTCGCTAGTGAATCATACTATG	57.419	34.615	7.52	0.00	35.62	2.23
2410	2488	5.009510	TGAGTTGACAAACATGGTTGTATGG	59.990	40.000	28.43	2.39	41.78	2.74
2414	2492	4.016444	AGTGAGTTGACAAACATGGTTGT	58.984	39.130	28.72	28.72	44.38	3.32
2421	2499	7.561021	TTTTAGCATAGTGAGTTGACAAACA	57.439	32.000	0.00	0.00	38.88	2.83
2422	2500	7.061094	GCATTTTAGCATAGTGAGTTGACAAAC	59.939	37.037	0.00	0.00	36.47	2.93
2423	2501	7.083858	GCATTTTAGCATAGTGAGTTGACAAA	58.916	34.615	0.00	0.00	0.00	2.83
2424	2502	6.611381	GCATTTTAGCATAGTGAGTTGACAA	58.389	36.000	0.00	0.00	0.00	3.18
2479	2557	0.388659	TTGTTGCATGGTGAGTTGGC	59.611	50.000	0.00	0.00	0.00	4.52
2503	2581	5.144359	CACGTTAAAGGTGGATCTTTTTCG	58.856	41.667	0.00	0.00	37.96	3.46
2512	2590	2.552599	TGATGCACGTTAAAGGTGGA	57.447	45.000	9.27	7.18	38.59	4.02
2654	2741	4.111916	CGTGGGAATTGGTTGCAATTATC	58.888	43.478	0.59	0.00	35.18	1.75
2667	2754	1.906333	GGGTGTTGCCGTGGGAATT	60.906	57.895	0.00	0.00	38.44	2.17
2684	2771	3.231818	ACAACTAGAGATGATACCCCGG	58.768	50.000	0.00	0.00	0.00	5.73
2707	2794	7.148239	CGAAAATAGAAGCCACAAAGGAGTAAT	60.148	37.037	0.00	0.00	41.22	1.89
2789	6189	5.978919	TCTTATGCTTGCAGTTTTTGACTTG	59.021	36.000	0.87	0.00	36.10	3.16
2829	6229	6.467723	AGAAATCTTGTTGCTTAGTACGTG	57.532	37.500	0.00	0.00	0.00	4.49
2959	6360	8.702819	TCCATGAGGAATAGCTTGAGATATATG	58.297	37.037	0.00	0.00	42.23	1.78
2990	6391	3.069586	TGGAGTGTTGTAGGAACTCTGTG	59.930	47.826	0.00	0.00	41.75	3.66
3026	6427	7.059788	TCATCTATAGCTTCTATGCTCTAGGG	58.940	42.308	0.00	0.00	42.97	3.53
3089	6574	5.535753	TGTGTTGAGACTTGAGAGAATCA	57.464	39.130	0.00	0.00	37.82	2.57
3101	6586	5.986135	AGTAAGAGACATGTTGTGTTGAGAC	59.014	40.000	0.00	0.00	42.36	3.36
3102	6587	6.161855	AGTAAGAGACATGTTGTGTTGAGA	57.838	37.500	0.00	0.00	42.36	3.27
3103	6588	7.115520	CACTAGTAAGAGACATGTTGTGTTGAG	59.884	40.741	0.00	0.00	42.36	3.02
3104	6589	6.923508	CACTAGTAAGAGACATGTTGTGTTGA	59.076	38.462	0.00	0.00	42.36	3.18
3105	6590	6.146184	CCACTAGTAAGAGACATGTTGTGTTG	59.854	42.308	0.00	0.00	42.36	3.33
3106	6591	6.183360	ACCACTAGTAAGAGACATGTTGTGTT	60.183	38.462	0.00	0.00	42.36	3.32
3107	6592	5.304614	ACCACTAGTAAGAGACATGTTGTGT	59.695	40.000	0.00	0.00	45.83	3.72

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.