AutoCloner

Multiple sequence alignment - TraesCS6B01G446600

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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	TraesCS6B01G446600	chr6B	100.000	2381	0	0	1	2381	707702988	707705368	0.000000e+00	4397
1	TraesCS6B01G446600	chr6B	93.425	1673	66	15	1	1650	707599228	707600879	0.000000e+00	2440
2	TraesCS6B01G446600	chr6B	93.353	1670	74	13	1	1650	707335946	707337598	0.000000e+00	2435
3	TraesCS6B01G446600	chr6B	88.054	745	75	5	1	732	599517836	599518579	0.000000e+00	870
4	TraesCS6B01G446600	chr6B	88.521	514	33	13	1870	2381	707338035	707338524	1.220000e-167	599
5	TraesCS6B01G446600	chr6B	85.470	585	39	15	1801	2381	707601009	707601551	3.430000e-158	568
6	TraesCS6B01G446600	chr6B	86.517	534	47	10	1663	2193	707507326	707507837	4.440000e-157	564
7	TraesCS6B01G446600	chr6B	84.687	431	60	3	1019	1443	707421149	707421579	2.190000e-115	425
8	TraesCS6B01G446600	chr6B	90.400	250	21	3	1801	2049	707337728	707337975	2.280000e-85	326
9	TraesCS6B01G446600	chrUn	88.375	757	70	9	1	742	289136749	289137502	0.000000e+00	894
10	TraesCS6B01G446600	chrUn	84.793	434	60	3	1019	1446	428550366	428549933	4.700000e-117	431
11	TraesCS6B01G446600	chr5B	88.375	757	70	9	1	742	22112866	22113619	0.000000e+00	894
12	TraesCS6B01G446600	chr5B	88.375	757	70	9	1	742	22120225	22120978	0.000000e+00	894
13	TraesCS6B01G446600	chr3A	87.550	755	76	13	1	743	661804101	661804849	0.000000e+00	857
14	TraesCS6B01G446600	chr7A	87.805	738	70	15	15	739	90442735	90443465	0.000000e+00	846
15	TraesCS6B01G446600	chr2A	87.399	746	76	13	18	751	33580702	33579963	0.000000e+00	841
16	TraesCS6B01G446600	chr6D	89.522	649	44	8	990	1637	464119518	464120143	0.000000e+00	800
17	TraesCS6B01G446600	chr6D	87.123	365	47	0	1019	1383	464166343	464166707	4.740000e-112	414
18	TraesCS6B01G446600	chr6D	88.953	344	25	9	1663	2002	464138778	464139112	1.700000e-111	412
19	TraesCS6B01G446600	chr6D	92.857	182	11	2	2201	2381	464139900	464140080	1.810000e-66	263
20	TraesCS6B01G446600	chr4D	86.721	738	54	10	1	723	427519045	427518337	0.000000e+00	780
21	TraesCS6B01G446600	chr6A	89.234	548	30	8	741	1279	610526856	610527383	0.000000e+00	658
22	TraesCS6B01G446600	chr6A	86.269	386	51	1	1019	1402	610557555	610557940	3.660000e-113	418
23	TraesCS6B01G446600	chr6A	83.121	314	22	16	1691	2002	610527620	610527904	8.440000e-65	257
24	TraesCS6B01G446600	chr6A	92.308	182	12	2	2201	2381	610528693	610528873	8.440000e-65	257
25	TraesCS6B01G446600	chr6A	89.655	87	7	2	1721	1806	610598596	610598681	2.500000e-20	110

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	TraesCS6B01G446600	chr6B	707702988	707705368	2380	False	4397.000000	4397	100.0000	1	2381	1	chr6B.!!$F4	2380
1	TraesCS6B01G446600	chr6B	707599228	707601551	2323	False	1504.000000	2440	89.4475	1	2381	2	chr6B.!!$F6	2380
2	TraesCS6B01G446600	chr6B	707335946	707338524	2578	False	1120.000000	2435	90.7580	1	2381	3	chr6B.!!$F5	2380
3	TraesCS6B01G446600	chr6B	599517836	599518579	743	False	870.000000	870	88.0540	1	732	1	chr6B.!!$F1	731
4	TraesCS6B01G446600	chr6B	707507326	707507837	511	False	564.000000	564	86.5170	1663	2193	1	chr6B.!!$F3	530
5	TraesCS6B01G446600	chrUn	289136749	289137502	753	False	894.000000	894	88.3750	1	742	1	chrUn.!!$F1	741
6	TraesCS6B01G446600	chr5B	22112866	22113619	753	False	894.000000	894	88.3750	1	742	1	chr5B.!!$F1	741
7	TraesCS6B01G446600	chr5B	22120225	22120978	753	False	894.000000	894	88.3750	1	742	1	chr5B.!!$F2	741
8	TraesCS6B01G446600	chr3A	661804101	661804849	748	False	857.000000	857	87.5500	1	743	1	chr3A.!!$F1	742
9	TraesCS6B01G446600	chr7A	90442735	90443465	730	False	846.000000	846	87.8050	15	739	1	chr7A.!!$F1	724
10	TraesCS6B01G446600	chr2A	33579963	33580702	739	True	841.000000	841	87.3990	18	751	1	chr2A.!!$R1	733
11	TraesCS6B01G446600	chr6D	464119518	464120143	625	False	800.000000	800	89.5220	990	1637	1	chr6D.!!$F1	647
12	TraesCS6B01G446600	chr6D	464138778	464140080	1302	False	337.500000	412	90.9050	1663	2381	2	chr6D.!!$F3	718
13	TraesCS6B01G446600	chr4D	427518337	427519045	708	True	780.000000	780	86.7210	1	723	1	chr4D.!!$R1	722
14	TraesCS6B01G446600	chr6A	610526856	610528873	2017	False	390.666667	658	88.2210	741	2381	3	chr6A.!!$F3	1640

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
364	385	1.139734	GAAGATCCAGCTCGCGTCA	59.86	57.895	5.77	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2191	3118	0.179702	TGGATCTGCACATGGCTCTC	59.82	55.0	0.0	0.0	45.15	3.2	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
234	255	2.020720	TCGCACAGGTGTTCATGTTTT	58.979	42.857	0.91	0.00	36.41	2.43
241	262	5.527214	CACAGGTGTTCATGTTTTAGAGTGA	59.473	40.000	0.00	0.00	36.41	3.41
364	385	1.139734	GAAGATCCAGCTCGCGTCA	59.860	57.895	5.77	0.00	0.00	4.35
432	456	1.152204	TTCAACCAGGGGTCCTCGA	60.152	57.895	0.00	0.00	33.12	4.04
433	457	1.192146	TTCAACCAGGGGTCCTCGAG	61.192	60.000	5.13	5.13	33.12	4.04
446	470	1.495148	TCCTCGAGGAGCTAGATTGGA	59.505	52.381	30.49	3.57	39.78	3.53
814	844	1.303282	CACCTACCCTGCCTTTCCC	59.697	63.158	0.00	0.00	0.00	3.97
832	862	4.463050	TCCCCAACAGTCCTAATTTGTT	57.537	40.909	0.00	0.00	35.56	2.83
874	904	3.793797	TTTACTTCATCATCGAGCCGA	57.206	42.857	0.00	0.00	41.13	5.54
971	1001	3.957497	AGCTCGTCTCCATATCCATATCC	59.043	47.826	0.00	0.00	0.00	2.59
972	1002	3.243234	GCTCGTCTCCATATCCATATCCG	60.243	52.174	0.00	0.00	0.00	4.18
974	1004	5.106876	TCGTCTCCATATCCATATCCGTA	57.893	43.478	0.00	0.00	0.00	4.02
979	1009	6.546403	GTCTCCATATCCATATCCGTAGCTAA	59.454	42.308	0.00	0.00	0.00	3.09
1123	1180	2.930019	CTCTCTGCACCACCCCCA	60.930	66.667	0.00	0.00	0.00	4.96
1213	1270	2.983592	CCACCACAAAGACCGCCC	60.984	66.667	0.00	0.00	0.00	6.13
1483	1541	2.755929	GAGCATGTTGGTCGTCTCC	58.244	57.895	0.00	0.00	35.04	3.71
1484	1542	1.078759	GAGCATGTTGGTCGTCTCCG	61.079	60.000	0.00	0.00	35.04	4.63
1485	1543	2.740714	GCATGTTGGTCGTCTCCGC	61.741	63.158	0.00	0.00	0.00	5.54
1505	1563	1.216941	CCGTTAGGTTGCGACGTTGT	61.217	55.000	4.30	0.00	35.17	3.32
1565	1628	8.045507	TCTGAATCTCTATCCAATTATGCATCC	58.954	37.037	0.19	0.00	0.00	3.51
1566	1629	7.925622	TGAATCTCTATCCAATTATGCATCCT	58.074	34.615	0.19	0.00	0.00	3.24
1567	1630	8.388589	TGAATCTCTATCCAATTATGCATCCTT	58.611	33.333	0.19	0.00	0.00	3.36
1568	1631	8.577048	AATCTCTATCCAATTATGCATCCTTG	57.423	34.615	0.19	8.31	0.00	3.61
1569	1632	7.083062	TCTCTATCCAATTATGCATCCTTGT	57.917	36.000	0.19	0.00	0.00	3.16
1570	1633	7.164122	TCTCTATCCAATTATGCATCCTTGTC	58.836	38.462	0.19	0.00	0.00	3.18
1571	1634	6.840527	TCTATCCAATTATGCATCCTTGTCA	58.159	36.000	0.19	0.00	0.00	3.58
1630	1693	4.322080	TCGAGTTGACAACTTGAGATGT	57.678	40.909	27.51	3.45	44.89	3.06
1637	1700	4.717877	TGACAACTTGAGATGTGTGGAAT	58.282	39.130	0.00	0.00	30.95	3.01
1653	1719	6.989759	TGTGTGGAATTGTTATATGTATCGCT	59.010	34.615	0.00	0.00	0.00	4.93
1656	1722	6.797033	GTGGAATTGTTATATGTATCGCTTGC	59.203	38.462	0.00	0.00	0.00	4.01
1657	1723	6.484977	TGGAATTGTTATATGTATCGCTTGCA	59.515	34.615	0.00	0.00	0.00	4.08
1659	1725	8.023128	GGAATTGTTATATGTATCGCTTGCATT	58.977	33.333	0.00	0.00	32.43	3.56
1660	1726	8.732413	AATTGTTATATGTATCGCTTGCATTG	57.268	30.769	0.00	0.00	32.43	2.82
1661	1727	5.688823	TGTTATATGTATCGCTTGCATTGC	58.311	37.500	0.46	0.46	32.43	3.56
1668	1807	2.054687	TCGCTTGCATTGCTTCTTTG	57.945	45.000	10.49	0.00	0.00	2.77
1669	1808	1.608109	TCGCTTGCATTGCTTCTTTGA	59.392	42.857	10.49	0.00	0.00	2.69
1719	1858	0.395311	AGAGCCGGGAACTGACGATA	60.395	55.000	2.18	0.00	36.31	2.92
1725	1864	3.676873	GCCGGGAACTGACGATAACTTTA	60.677	47.826	2.18	0.00	36.31	1.85
1746	1885	1.074319	GCTGCGACAACAATGCATGG	61.074	55.000	0.00	0.00	38.07	3.66
1748	1887	0.672889	TGCGACAACAATGCATGGTT	59.327	45.000	13.98	13.98	32.86	3.67
1761	1900	2.922704	ATGGTTGGGTCCCTGGCTG	61.923	63.158	10.00	0.00	0.00	4.85
1858	1999	3.083997	GCCCACCTCCATCCGACT	61.084	66.667	0.00	0.00	0.00	4.18
1875	2254	6.349243	TCCGACTTGAGTAATCTAACCAAA	57.651	37.500	0.00	0.00	0.00	3.28
1888	2267	3.058160	CCAAAGCCCGAGCCAGTG	61.058	66.667	0.00	0.00	41.25	3.66
1890	2269	1.003839	CAAAGCCCGAGCCAGTGTA	60.004	57.895	0.00	0.00	41.25	2.90
1902	2281	2.712057	CCAGTGTAAAAGGCAAGCTG	57.288	50.000	0.00	0.00	0.00	4.24
1928	2308	2.770048	CCGGCAGGGGGAGATTCT	60.770	66.667	0.00	0.00	0.00	2.40
1960	2340	2.496470	AGGGCTAGAGTTTTCACCTACG	59.504	50.000	0.00	0.00	0.00	3.51
1963	2343	2.353406	GCTAGAGTTTTCACCTACGCCA	60.353	50.000	0.00	0.00	0.00	5.69
1980	2364	3.054802	ACGCCAATCTTCTTTCTCTCCAT	60.055	43.478	0.00	0.00	0.00	3.41
1983	2367	3.559242	CCAATCTTCTTTCTCTCCATCGC	59.441	47.826	0.00	0.00	0.00	4.58
1984	2368	2.969628	TCTTCTTTCTCTCCATCGCC	57.030	50.000	0.00	0.00	0.00	5.54
1985	2369	1.135139	TCTTCTTTCTCTCCATCGCCG	59.865	52.381	0.00	0.00	0.00	6.46
2029	2927	5.574891	AGAATAGATCTTCCCATCGATCG	57.425	43.478	9.36	9.36	40.65	3.69
2031	2929	4.710423	ATAGATCTTCCCATCGATCGTG	57.290	45.455	15.94	12.28	40.65	4.35
2071	2969	2.032799	TCGAGCAACACAACCATCAAAC	59.967	45.455	0.00	0.00	0.00	2.93
2104	3030	5.770663	AGGATCTTATTCTTCTCGATCGGAA	59.229	40.000	16.41	15.69	33.15	4.30
2118	3044	4.344865	GGAAGGCCCGAACCTGCA	62.345	66.667	0.00	0.00	39.93	4.41
2191	3118	6.366332	CCCCTCGAATAAATTTGTCTATCTCG	59.634	42.308	0.00	0.42	0.00	4.04
2192	3119	7.145985	CCCTCGAATAAATTTGTCTATCTCGA	58.854	38.462	0.00	4.89	0.00	4.04
2199	3182	5.543507	AATTTGTCTATCTCGAGAGCCAT	57.456	39.130	21.52	6.38	0.00	4.40
2229	3212	3.573967	TCCAATTGATCGGATCGAGATGA	59.426	43.478	18.48	10.44	39.91	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	62	2.165030	GGTTGATGCCTCTGGTTTCATG	59.835	50.000	0.00	0.00	0.00	3.07
216	234	4.275936	ACTCTAAAACATGAACACCTGTGC	59.724	41.667	0.00	0.00	0.00	4.57
234	255	6.406692	AAACACTAGCTCTGTTTCACTCTA	57.593	37.500	14.03	0.00	37.27	2.43
241	262	4.067972	TCCGAAAACACTAGCTCTGTTT	57.932	40.909	14.03	14.03	42.41	2.83
415	436	1.609501	CTCGAGGACCCCTGGTTGA	60.610	63.158	3.91	0.00	35.25	3.18
432	456	3.678965	TCAGACTCCAATCTAGCTCCT	57.321	47.619	0.00	0.00	0.00	3.69
433	457	3.258123	GGATCAGACTCCAATCTAGCTCC	59.742	52.174	0.00	0.00	35.24	4.70
446	470	1.504912	CCAGATGGTGGGATCAGACT	58.495	55.000	0.00	0.00	43.63	3.24
645	674	2.007608	CATAGCCGTCCGATCGATCTA	58.992	52.381	22.43	8.41	0.00	1.98
814	844	9.840427	CTACAATTAACAAATTAGGACTGTTGG	57.160	33.333	3.27	0.00	35.09	3.77
832	862	9.801873	GTAAATTACGTACCTGGACTACAATTA	57.198	33.333	0.00	0.00	0.00	1.40
971	1001	2.271800	CTGCCTGGAAAGTTAGCTACG	58.728	52.381	0.00	0.00	0.00	3.51
972	1002	2.010497	GCTGCCTGGAAAGTTAGCTAC	58.990	52.381	0.00	0.00	0.00	3.58
974	1004	0.322906	GGCTGCCTGGAAAGTTAGCT	60.323	55.000	12.43	0.00	0.00	3.32
979	1009	2.759795	GGAGGCTGCCTGGAAAGT	59.240	61.111	28.82	0.00	31.76	2.66
1107	1164	3.249189	GTGGGGGTGGTGCAGAGA	61.249	66.667	0.00	0.00	0.00	3.10
1366	1423	2.781595	CTTGTCTACCGGCGCCACTT	62.782	60.000	28.98	12.23	0.00	3.16
1368	1425	2.216750	TACTTGTCTACCGGCGCCAC	62.217	60.000	28.98	17.32	0.00	5.01
1417	1474	1.852157	AAGTGCATCCATGGTCCGGT	61.852	55.000	12.58	0.00	0.00	5.28
1418	1475	1.077501	AAGTGCATCCATGGTCCGG	60.078	57.895	12.58	0.00	0.00	5.14
1422	1479	2.372264	CTAAGCAAGTGCATCCATGGT	58.628	47.619	12.58	0.00	45.16	3.55
1484	1542	3.484547	CGTCGCAACCTAACGGGC	61.485	66.667	0.00	0.00	39.10	6.13
1485	1543	1.665599	AACGTCGCAACCTAACGGG	60.666	57.895	0.00	0.00	40.58	5.28
1505	1563	4.286032	ACTGCTGGACCTAAACAGAACATA	59.714	41.667	9.60	0.00	36.86	2.29
1535	1593	9.364989	GCATAATTGGATAGAGATTCAGACTAC	57.635	37.037	0.00	0.00	0.00	2.73
1565	1628	1.063912	ACACGCACACACAATGACAAG	59.936	47.619	0.00	0.00	0.00	3.16
1566	1629	1.090728	ACACGCACACACAATGACAA	58.909	45.000	0.00	0.00	0.00	3.18
1567	1630	0.376502	CACACGCACACACAATGACA	59.623	50.000	0.00	0.00	0.00	3.58
1568	1631	0.376852	ACACACGCACACACAATGAC	59.623	50.000	0.00	0.00	0.00	3.06
1569	1632	1.090728	AACACACGCACACACAATGA	58.909	45.000	0.00	0.00	0.00	2.57
1570	1633	2.638673	CTAACACACGCACACACAATG	58.361	47.619	0.00	0.00	0.00	2.82
1571	1634	1.002900	GCTAACACACGCACACACAAT	60.003	47.619	0.00	0.00	0.00	2.71
1630	1693	7.519809	GCAAGCGATACATATAACAATTCCACA	60.520	37.037	0.00	0.00	0.00	4.17
1637	1700	6.017192	AGCAATGCAAGCGATACATATAACAA	60.017	34.615	8.35	0.00	37.01	2.83
1650	1716	2.054687	TCAAAGAAGCAATGCAAGCG	57.945	45.000	8.35	0.00	37.01	4.68
1653	1719	4.799949	GCGAATATCAAAGAAGCAATGCAA	59.200	37.500	8.35	0.00	0.00	4.08
1656	1722	3.419922	GCGCGAATATCAAAGAAGCAATG	59.580	43.478	12.10	0.00	0.00	2.82
1657	1723	3.548818	GGCGCGAATATCAAAGAAGCAAT	60.549	43.478	12.10	0.00	0.00	3.56
1659	1725	1.330521	GGCGCGAATATCAAAGAAGCA	59.669	47.619	12.10	0.00	0.00	3.91
1660	1726	1.330521	TGGCGCGAATATCAAAGAAGC	59.669	47.619	12.10	0.00	0.00	3.86
1661	1727	3.063997	AGTTGGCGCGAATATCAAAGAAG	59.936	43.478	12.10	0.00	0.00	2.85
1668	1807	0.233332	GCAGAGTTGGCGCGAATATC	59.767	55.000	12.10	9.93	0.00	1.63
1669	1808	1.160329	GGCAGAGTTGGCGCGAATAT	61.160	55.000	12.10	0.00	40.30	1.28
1719	1858	1.961793	TGTTGTCGCAGCCTAAAGTT	58.038	45.000	0.00	0.00	0.00	2.66
1725	1864	1.246056	ATGCATTGTTGTCGCAGCCT	61.246	50.000	0.00	0.00	39.39	4.58
1761	1900	2.574450	TCGTTGGTTAACAAGGTTCCC	58.426	47.619	8.10	0.00	43.55	3.97
1858	1999	4.020039	TCGGGCTTTGGTTAGATTACTCAA	60.020	41.667	0.00	0.00	0.00	3.02
1875	2254	0.321653	CTTTTACACTGGCTCGGGCT	60.322	55.000	7.48	0.00	38.73	5.19
1888	2267	1.177401	CTCCCCAGCTTGCCTTTTAC	58.823	55.000	0.00	0.00	0.00	2.01
1890	2269	1.228988	CCTCCCCAGCTTGCCTTTT	60.229	57.895	0.00	0.00	0.00	2.27
1923	2303	6.717289	TCTAGCCCTAGAGTGATCTAGAATC	58.283	44.000	12.75	0.00	41.56	2.52
1947	2327	3.418684	AGATTGGCGTAGGTGAAAACT	57.581	42.857	0.00	0.00	0.00	2.66
1960	2340	3.559242	CGATGGAGAGAAAGAAGATTGGC	59.441	47.826	0.00	0.00	0.00	4.52
1963	2343	3.739519	CGGCGATGGAGAGAAAGAAGATT	60.740	47.826	0.00	0.00	0.00	2.40
1984	2368	3.014085	TTACAAGCTCCCGGCCTCG	62.014	63.158	0.00	0.00	43.05	4.63
1985	2369	1.449778	GTTACAAGCTCCCGGCCTC	60.450	63.158	0.00	0.00	43.05	4.70
2071	2969	7.807433	CGAGAAGAATAAGATCCTACTCATGTG	59.193	40.741	0.00	0.00	0.00	3.21
2104	3030	0.258774	ATTTATGCAGGTTCGGGCCT	59.741	50.000	0.84	0.00	39.99	5.19
2111	3037	4.210331	GGGACAGATGATTTATGCAGGTT	58.790	43.478	0.00	0.00	0.00	3.50
2191	3118	0.179702	TGGATCTGCACATGGCTCTC	59.820	55.000	0.00	0.00	45.15	3.20
2192	3119	0.622136	TTGGATCTGCACATGGCTCT	59.378	50.000	0.00	0.00	45.15	4.09
2199	3182	3.434024	ATCCGATCAATTGGATCTGCACA	60.434	43.478	5.42	0.00	45.94	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.