AutoCloner

Multiple sequence alignment - TraesCS6B01G113600

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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	TraesCS6B01G113600	chr6B	100.000	2309	0	0	1	2309	96339364	96341672	0.000000e+00	4265.0
1	TraesCS6B01G113600	chr7D	98.189	1546	27	1	1	1546	135769094	135770638	0.000000e+00	2699.0
2	TraesCS6B01G113600	chr7D	98.122	1544	28	1	1	1544	23563083	23564625	0.000000e+00	2689.0
3	TraesCS6B01G113600	chr7D	98.056	1543	29	1	1	1543	400291675	400290134	0.000000e+00	2682.0
4	TraesCS6B01G113600	chr7D	97.861	1543	32	1	1	1543	135763961	135762420	0.000000e+00	2665.0
5	TraesCS6B01G113600	chr7D	97.798	1544	33	1	1	1544	14171010	14169468	0.000000e+00	2662.0
6	TraesCS6B01G113600	chr3D	97.863	1544	32	1	1	1544	564344209	564345751	0.000000e+00	2667.0
7	TraesCS6B01G113600	chr2D	97.861	1543	32	1	1	1543	70659367	70657826	0.000000e+00	2665.0
8	TraesCS6B01G113600	chr6D	97.860	1542	32	1	1	1542	402531206	402529666	0.000000e+00	2663.0
9	TraesCS6B01G113600	chr6D	97.602	1543	36	1	1	1543	392049938	392048397	0.000000e+00	2643.0
10	TraesCS6B01G113600	chr6D	89.494	514	40	6	1737	2237	41536869	41536357	2.500000e-179	638.0
11	TraesCS6B01G113600	chr6A	80.952	588	65	25	1609	2157	52023730	52023151	2.740000e-114	422.0
12	TraesCS6B01G113600	chr6A	89.744	78	4	2	2234	2309	52023043	52022968	1.890000e-16	97.1
13	TraesCS6B01G113600	chr7A	79.758	331	42	18	1846	2157	43386683	43386359	1.390000e-52	217.0
14	TraesCS6B01G113600	chr7A	78.248	331	47	18	1846	2157	43353173	43352849	3.030000e-44	189.0

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	TraesCS6B01G113600	chr6B	96339364	96341672	2308	False	4265.00	4265	100.000	1	2309	1	chr6B.!!$F1	2308
1	TraesCS6B01G113600	chr7D	135769094	135770638	1544	False	2699.00	2699	98.189	1	1546	1	chr7D.!!$F2	1545
2	TraesCS6B01G113600	chr7D	23563083	23564625	1542	False	2689.00	2689	98.122	1	1544	1	chr7D.!!$F1	1543
3	TraesCS6B01G113600	chr7D	400290134	400291675	1541	True	2682.00	2682	98.056	1	1543	1	chr7D.!!$R3	1542
4	TraesCS6B01G113600	chr7D	135762420	135763961	1541	True	2665.00	2665	97.861	1	1543	1	chr7D.!!$R2	1542
5	TraesCS6B01G113600	chr7D	14169468	14171010	1542	True	2662.00	2662	97.798	1	1544	1	chr7D.!!$R1	1543
6	TraesCS6B01G113600	chr3D	564344209	564345751	1542	False	2667.00	2667	97.863	1	1544	1	chr3D.!!$F1	1543
7	TraesCS6B01G113600	chr2D	70657826	70659367	1541	True	2665.00	2665	97.861	1	1543	1	chr2D.!!$R1	1542
8	TraesCS6B01G113600	chr6D	402529666	402531206	1540	True	2663.00	2663	97.860	1	1542	1	chr6D.!!$R3	1541
9	TraesCS6B01G113600	chr6D	392048397	392049938	1541	True	2643.00	2643	97.602	1	1543	1	chr6D.!!$R2	1542
10	TraesCS6B01G113600	chr6D	41536357	41536869	512	True	638.00	638	89.494	1737	2237	1	chr6D.!!$R1	500
11	TraesCS6B01G113600	chr6A	52022968	52023730	762	True	259.55	422	85.348	1609	2309	2	chr6A.!!$R1	700

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
517	518	3.743396	GGTGAGTAAGAAGTTGCAGTCTG	59.257	47.826	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2192	2253	0.038251	GGGTACAGCCAAAGCAAAGC	60.038	55.0	0.0	0.0	43.56	3.51	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
268	269	6.522946	TGCTTGATCATGTTCCAAAAATGAA	58.477	32.000	10.05	0.00	34.21	2.57
269	270	6.990939	TGCTTGATCATGTTCCAAAAATGAAA	59.009	30.769	10.05	0.00	34.21	2.69
329	330	6.703607	CGAATAAAGAGTGTTCAGGCTATCAT	59.296	38.462	0.00	0.00	0.00	2.45
355	356	4.394729	TCAAGCACCCGAGTTAAGAAAAT	58.605	39.130	0.00	0.00	0.00	1.82
452	453	8.003784	CGCACTTGAGAAATTTGAATTTTTACC	58.996	33.333	0.00	0.00	38.64	2.85
465	466	5.105392	TGAATTTTTACCTGGCATGGTCATC	60.105	40.000	11.17	4.72	41.22	2.92
517	518	3.743396	GGTGAGTAAGAAGTTGCAGTCTG	59.257	47.826	0.00	0.00	0.00	3.51
831	832	8.563502	TCCCTAACTACTAGATTTGAGGAACTA	58.436	37.037	0.00	0.00	41.55	2.24
933	934	7.927629	AGATGTTGCACTAATTTTGTCAACAAT	59.072	29.630	20.42	14.51	44.26	2.71
1035	1036	2.679336	CACATTCATGTCAGCGGATCAA	59.321	45.455	0.00	0.00	39.39	2.57
1107	1108	4.025979	GCTTATCGTATCCTTTTGACCGTG	60.026	45.833	0.00	0.00	0.00	4.94
1241	1242	7.173032	TGCATTGAGAAGAATATGCTGGATAT	58.827	34.615	0.00	0.00	42.85	1.63
1277	1278	6.931838	ACACTCTCATTGATGATTTTGCATT	58.068	32.000	0.00	0.00	36.02	3.56
1334	1335	4.164988	ACTGGAGGTTAGCATGCTATTTCT	59.835	41.667	27.35	22.24	0.00	2.52
1555	1556	3.636231	CCCTGCCTCCACGGTGAA	61.636	66.667	10.28	0.00	34.25	3.18
1556	1557	2.046892	CCTGCCTCCACGGTGAAG	60.047	66.667	10.28	0.00	34.25	3.02
1557	1558	2.743928	CTGCCTCCACGGTGAAGC	60.744	66.667	10.28	9.63	34.25	3.86
1558	1559	4.329545	TGCCTCCACGGTGAAGCC	62.330	66.667	10.28	0.00	34.25	4.35
1559	1560	4.329545	GCCTCCACGGTGAAGCCA	62.330	66.667	10.28	0.00	36.97	4.75
1560	1561	2.429930	CCTCCACGGTGAAGCCAA	59.570	61.111	10.28	0.00	36.97	4.52
1561	1562	1.672356	CCTCCACGGTGAAGCCAAG	60.672	63.158	10.28	0.00	36.97	3.61
1562	1563	1.672356	CTCCACGGTGAAGCCAAGG	60.672	63.158	10.28	0.00	36.97	3.61
1563	1564	2.672996	CCACGGTGAAGCCAAGGG	60.673	66.667	10.28	0.00	36.97	3.95
1564	1565	2.429930	CACGGTGAAGCCAAGGGA	59.570	61.111	0.74	0.00	36.97	4.20
1565	1566	1.672356	CACGGTGAAGCCAAGGGAG	60.672	63.158	0.74	0.00	36.97	4.30
1566	1567	2.747855	CGGTGAAGCCAAGGGAGC	60.748	66.667	0.00	0.00	36.97	4.70
1567	1568	2.759795	GGTGAAGCCAAGGGAGCT	59.240	61.111	0.00	0.00	44.19	4.09
1568	1569	1.377856	GGTGAAGCCAAGGGAGCTC	60.378	63.158	4.71	4.71	40.49	4.09
1569	1570	1.743252	GTGAAGCCAAGGGAGCTCG	60.743	63.158	7.83	0.00	40.49	5.03
1570	1571	2.124942	GAAGCCAAGGGAGCTCGG	60.125	66.667	7.83	4.19	40.49	4.63
1571	1572	3.689002	GAAGCCAAGGGAGCTCGGG	62.689	68.421	7.83	7.76	40.49	5.14
1572	1573	4.722535	AGCCAAGGGAGCTCGGGA	62.723	66.667	7.83	0.00	34.91	5.14
1573	1574	3.717294	GCCAAGGGAGCTCGGGAA	61.717	66.667	7.83	0.00	0.00	3.97
1574	1575	2.586792	CCAAGGGAGCTCGGGAAG	59.413	66.667	7.83	0.00	0.00	3.46
1632	1633	2.043450	AGCTGGGAGACGGGAGAG	60.043	66.667	0.00	0.00	0.00	3.20
1658	1659	3.966930	GAGGCGAGAGGACCTGGGT	62.967	68.421	0.00	0.00	36.05	4.51
1666	1667	0.325671	GAGGACCTGGGTGAGGATGA	60.326	60.000	0.00	0.00	46.33	2.92
1668	1669	1.517832	GACCTGGGTGAGGATGACG	59.482	63.158	0.00	0.00	46.33	4.35
1669	1670	2.187946	CCTGGGTGAGGATGACGC	59.812	66.667	0.00	0.00	46.33	5.19
1670	1671	2.202797	CTGGGTGAGGATGACGCG	60.203	66.667	3.53	3.53	38.15	6.01
1792	1806	3.751175	CCTGCCACTCAGAAATAACGAAA	59.249	43.478	0.00	0.00	45.72	3.46
1914	1944	1.751162	CGTCTCCTTCTCCTCCGCT	60.751	63.158	0.00	0.00	0.00	5.52
2024	2085	1.774217	AGCCACCCTCTTCCACCAA	60.774	57.895	0.00	0.00	0.00	3.67
2031	2092	1.815421	CTCTTCCACCAATCGCCGG	60.815	63.158	0.00	0.00	0.00	6.13
2161	2222	1.350193	AGTGAACTTATCTGCGTGCG	58.650	50.000	0.00	0.00	0.00	5.34
2170	2231	1.790755	ATCTGCGTGCGTAAAAGTGA	58.209	45.000	0.00	0.00	0.00	3.41
2172	2233	0.859232	CTGCGTGCGTAAAAGTGAGT	59.141	50.000	0.00	0.00	0.00	3.41
2174	2235	0.721483	GCGTGCGTAAAAGTGAGTGC	60.721	55.000	0.00	0.00	0.00	4.40
2176	2237	2.055838	CGTGCGTAAAAGTGAGTGCTA	58.944	47.619	0.00	0.00	0.00	3.49
2225	2286	1.271871	TGTACCCCTGCACTGATTTGG	60.272	52.381	0.00	0.00	0.00	3.28
2229	2290	1.318158	CCCTGCACTGATTTGGCCTC	61.318	60.000	3.32	0.00	0.00	4.70
2240	2353	0.324614	TTTGGCCTCTCTGAATCGCA	59.675	50.000	3.32	0.00	0.00	5.10
2255	2368	9.643652	CTCTGAATCGCAGTATTTTTAGAATTC	57.356	33.333	0.00	0.00	45.14	2.17
2262	2375	7.328982	TCGCAGTATTTTTAGAATTCGTGTGTA	59.671	33.333	0.00	0.00	0.00	2.90
2263	2376	8.114290	CGCAGTATTTTTAGAATTCGTGTGTAT	58.886	33.333	0.00	0.00	0.00	2.29
2264	2377	9.210426	GCAGTATTTTTAGAATTCGTGTGTATG	57.790	33.333	0.00	0.00	0.00	2.39
2297	2410	5.836821	TGCAAATTGTAGTTGGTTGTGTA	57.163	34.783	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
174	175	3.957497	TGCACAACACCAAAGAAGGTAAT	59.043	39.130	0.00	0.00	40.77	1.89
268	269	7.546667	TCGAGTGTTACACAAAGACTTAACTTT	59.453	33.333	18.19	0.00	41.53	2.66
269	270	7.037438	TCGAGTGTTACACAAAGACTTAACTT	58.963	34.615	18.19	0.00	41.53	2.66
329	330	6.474140	TTCTTAACTCGGGTGCTTGATATA	57.526	37.500	0.00	0.00	0.00	0.86
355	356	8.553459	GAAGTTCTCTTCAATTCCAGTAATGA	57.447	34.615	0.00	0.00	46.50	2.57
381	382	2.851263	TAGTCTTGGCGTCATTGGTT	57.149	45.000	0.00	0.00	0.00	3.67
385	386	2.622436	GCTCTTAGTCTTGGCGTCATT	58.378	47.619	0.00	0.00	0.00	2.57
452	453	0.467474	ATGCCAGATGACCATGCCAG	60.467	55.000	0.00	0.00	0.00	4.85
465	466	3.985279	CAGTGAACAAAATGTCATGCCAG	59.015	43.478	0.00	0.00	0.00	4.85
517	518	5.762045	AGTAACATCAATGCACACAAACTC	58.238	37.500	0.00	0.00	0.00	3.01
831	832	5.484998	ACCAAATATGCTCCCAAATGTCTTT	59.515	36.000	0.00	0.00	0.00	2.52
933	934	4.040339	TCTGCTGACTTACCATGAGTGAAA	59.960	41.667	0.00	0.00	0.00	2.69
994	995	2.364647	TGTTTGGCAATGTCATCTGCAA	59.635	40.909	16.59	7.34	40.46	4.08
1035	1036	7.552687	TCCGCATCTCTAACAAACTCAAATATT	59.447	33.333	0.00	0.00	0.00	1.28
1107	1108	0.520404	CTGATGCAACAGTCACAGGC	59.480	55.000	15.39	0.00	33.73	4.85
1241	1242	9.106070	CATCAATGAGAGTGTCAAGATCAATAA	57.894	33.333	0.00	0.00	39.19	1.40
1472	1473	4.230502	TGGGCCCAATAGAGAGAAAATTCT	59.769	41.667	26.33	0.00	41.00	2.40
1475	1476	3.529319	AGTGGGCCCAATAGAGAGAAAAT	59.471	43.478	30.64	0.00	0.00	1.82
1504	1505	4.796495	GAAGGCCCCGGTGCGAAT	62.796	66.667	1.83	0.00	0.00	3.34
1546	1547	2.672996	CCCTTGGCTTCACCGTGG	60.673	66.667	0.00	0.00	43.94	4.94
1547	1548	1.672356	CTCCCTTGGCTTCACCGTG	60.672	63.158	0.00	0.00	43.94	4.94
1548	1549	2.750350	CTCCCTTGGCTTCACCGT	59.250	61.111	0.00	0.00	43.94	4.83
1549	1550	2.747855	GCTCCCTTGGCTTCACCG	60.748	66.667	0.00	0.00	43.94	4.94
1550	1551	1.377856	GAGCTCCCTTGGCTTCACC	60.378	63.158	0.87	0.00	40.40	4.02
1551	1552	1.743252	CGAGCTCCCTTGGCTTCAC	60.743	63.158	8.47	0.00	40.40	3.18
1552	1553	2.665000	CGAGCTCCCTTGGCTTCA	59.335	61.111	8.47	0.00	40.40	3.02
1553	1554	2.124942	CCGAGCTCCCTTGGCTTC	60.125	66.667	8.47	0.00	40.40	3.86
1554	1555	3.721706	CCCGAGCTCCCTTGGCTT	61.722	66.667	8.47	0.00	40.78	4.35
1555	1556	4.722535	TCCCGAGCTCCCTTGGCT	62.723	66.667	8.47	0.00	40.78	4.75
1556	1557	3.689002	CTTCCCGAGCTCCCTTGGC	62.689	68.421	8.47	0.00	40.78	4.52
1557	1558	2.586792	CTTCCCGAGCTCCCTTGG	59.413	66.667	8.47	3.02	41.65	3.61
1658	1659	4.451150	GGTGCCGCGTCATCCTCA	62.451	66.667	4.92	0.00	0.00	3.86
1721	1729	3.982316	TAAGAGAGTCCCGCGCCGA	62.982	63.158	0.00	0.00	0.00	5.54
1723	1731	2.104530	GTAAGAGAGTCCCGCGCC	59.895	66.667	0.00	0.00	0.00	6.53
1724	1732	2.104530	GGTAAGAGAGTCCCGCGC	59.895	66.667	0.00	0.00	0.00	6.86
1725	1733	2.783288	GGGGTAAGAGAGTCCCGCG	61.783	68.421	0.00	0.00	41.92	6.46
1726	1734	2.433146	GGGGGTAAGAGAGTCCCGC	61.433	68.421	0.00	0.00	44.64	6.13
1727	1735	3.951765	GGGGGTAAGAGAGTCCCG	58.048	66.667	0.00	0.00	41.92	5.14
1728	1736	0.325016	TTCGGGGGTAAGAGAGTCCC	60.325	60.000	0.00	0.00	40.41	4.46
1731	1739	1.900486	CAACTTCGGGGGTAAGAGAGT	59.100	52.381	0.00	0.00	0.00	3.24
1734	1748	0.252197	CCCAACTTCGGGGGTAAGAG	59.748	60.000	0.00	0.00	43.21	2.85
1754	1768	1.132453	GCAGGAAGCGGGTAATTTCAC	59.868	52.381	0.00	0.00	0.00	3.18
1766	1780	1.831580	ATTTCTGAGTGGCAGGAAGC	58.168	50.000	0.00	0.00	45.13	3.86
1768	1782	3.007506	TCGTTATTTCTGAGTGGCAGGAA	59.992	43.478	0.00	0.00	45.96	3.36
2010	2071	1.299976	GCGATTGGTGGAAGAGGGT	59.700	57.895	0.00	0.00	0.00	4.34
2016	2077	3.851897	TTGCCGGCGATTGGTGGAA	62.852	57.895	23.90	3.60	0.00	3.53
2017	2078	4.337177	TTGCCGGCGATTGGTGGA	62.337	61.111	23.90	0.00	0.00	4.02
2147	2208	3.122948	CACTTTTACGCACGCAGATAAGT	59.877	43.478	0.00	0.00	0.00	2.24
2157	2218	3.927142	AGATAGCACTCACTTTTACGCAC	59.073	43.478	0.00	0.00	0.00	5.34
2174	2235	5.920273	GCAAAGCTTCTACAGAGCTAGATAG	59.080	44.000	0.00	0.00	38.01	2.08
2176	2237	4.405358	AGCAAAGCTTCTACAGAGCTAGAT	59.595	41.667	0.00	0.00	33.89	1.98
2192	2253	0.038251	GGGTACAGCCAAAGCAAAGC	60.038	55.000	0.00	0.00	43.56	3.51
2225	2286	2.810439	ATACTGCGATTCAGAGAGGC	57.190	50.000	0.00	0.00	45.72	4.70
2229	2290	9.643652	GAATTCTAAAAATACTGCGATTCAGAG	57.356	33.333	0.00	0.00	45.72	3.35
2255	2368	5.684850	TGCAACTAATTCAACATACACACG	58.315	37.500	0.00	0.00	0.00	4.49
2262	2375	9.762933	AACTACAATTTGCAACTAATTCAACAT	57.237	25.926	0.00	0.00	0.00	2.71
2263	2376	9.029243	CAACTACAATTTGCAACTAATTCAACA	57.971	29.630	0.00	0.00	0.00	3.33
2264	2377	8.487176	CCAACTACAATTTGCAACTAATTCAAC	58.513	33.333	0.00	0.00	0.00	3.18
2265	2378	8.200792	ACCAACTACAATTTGCAACTAATTCAA	58.799	29.630	0.00	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.