AutoCloner

Multiple sequence alignment - TraesCS6D01G054700

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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	TraesCS6D01G054700	chr6D	100.000	2545	0	0	1	2545	25857275	25859819	0.000000e+00	4700
1	TraesCS6D01G054700	chr6D	91.522	1616	97	18	589	2185	312544302	312542708	0.000000e+00	2189
2	TraesCS6D01G054700	chr6D	90.943	1612	100	17	589	2185	323166697	323168277	0.000000e+00	2126
3	TraesCS6D01G054700	chr6D	89.963	1614	112	26	591	2185	12108135	12106553	0.000000e+00	2037
4	TraesCS6D01G054700	chr2D	93.584	1621	75	12	589	2185	12544104	12542489	0.000000e+00	2390
5	TraesCS6D01G054700	chr2D	92.834	1228	65	11	584	1795	604079171	604080391	0.000000e+00	1759
6	TraesCS6D01G054700	chr2D	95.184	353	17	0	2183	2535	12542426	12542074	2.210000e-155	558
7	TraesCS6D01G054700	chr2D	95.429	350	16	0	2183	2532	551248445	551248794	2.210000e-155	558
8	TraesCS6D01G054700	chr6A	91.692	1625	106	13	589	2185	574946042	574944419	0.000000e+00	2226
9	TraesCS6D01G054700	chr6A	89.604	606	47	9	1	592	23970788	23971391	0.000000e+00	756
10	TraesCS6D01G054700	chr6A	94.618	353	19	0	2183	2535	574944356	574944004	4.790000e-152	547
11	TraesCS6D01G054700	chr7A	91.240	1621	102	15	589	2185	152034644	152036248	0.000000e+00	2170
12	TraesCS6D01G054700	chr7A	96.694	363	12	0	2183	2545	152036311	152036673	2.800000e-169	604
13	TraesCS6D01G054700	chr4D	91.197	1613	87	23	589	2182	50776934	50778510	0.000000e+00	2141
14	TraesCS6D01G054700	chr4D	90.335	1614	109	28	589	2185	78732769	78731186	0.000000e+00	2073
15	TraesCS6D01G054700	chrUn	91.221	1572	93	27	629	2185	43407879	43409420	0.000000e+00	2097
16	TraesCS6D01G054700	chrUn	95.429	350	16	0	2183	2532	110638367	110638716	2.210000e-155	558
17	TraesCS6D01G054700	chr3B	90.370	1620	114	21	589	2183	124502329	124500727	0.000000e+00	2089
18	TraesCS6D01G054700	chr3B	89.994	1619	123	19	589	2183	124560191	124558588	0.000000e+00	2056
19	TraesCS6D01G054700	chr3D	90.253	1621	92	32	585	2185	447973576	447972002	0.000000e+00	2058
20	TraesCS6D01G054700	chr3D	89.334	1622	103	32	589	2185	573731195	573732771	0.000000e+00	1973
21	TraesCS6D01G054700	chr3D	92.378	656	28	11	1535	2182	4247200	4247841	0.000000e+00	915
22	TraesCS6D01G054700	chr7B	89.561	1619	126	23	589	2187	11744391	11745986	0.000000e+00	2013
23	TraesCS6D01G054700	chr1D	91.743	1308	65	18	896	2185	481625468	481624186	0.000000e+00	1777
24	TraesCS6D01G054700	chr1D	95.184	353	17	0	2183	2535	451671721	451671369	2.210000e-155	558
25	TraesCS6D01G054700	chr2B	91.771	1276	70	17	923	2185	39826203	39827456	0.000000e+00	1742
26	TraesCS6D01G054700	chr4B	90.664	482	25	12	1707	2182	648656685	648657152	7.730000e-175	623
27	TraesCS6D01G054700	chr4B	88.360	189	7	8	1707	1893	648642269	648642444	1.980000e-51	213
28	TraesCS6D01G054700	chr5D	96.143	363	13	1	2183	2545	486704443	486704082	2.180000e-165	592
29	TraesCS6D01G054700	chr5D	94.618	353	19	0	2183	2535	18406346	18405994	4.790000e-152	547
30	TraesCS6D01G054700	chr3A	95.592	363	16	0	2183	2545	634658178	634657816	1.310000e-162	582
31	TraesCS6D01G054700	chr6B	88.377	456	47	5	99	549	42289267	42289721	6.190000e-151	544

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	TraesCS6D01G054700	chr6D	25857275	25859819	2544	False	4700.0	4700	100.000	1	2545	1	chr6D.!!$F1	2544
1	TraesCS6D01G054700	chr6D	312542708	312544302	1594	True	2189.0	2189	91.522	589	2185	1	chr6D.!!$R2	1596
2	TraesCS6D01G054700	chr6D	323166697	323168277	1580	False	2126.0	2126	90.943	589	2185	1	chr6D.!!$F2	1596
3	TraesCS6D01G054700	chr6D	12106553	12108135	1582	True	2037.0	2037	89.963	591	2185	1	chr6D.!!$R1	1594
4	TraesCS6D01G054700	chr2D	604079171	604080391	1220	False	1759.0	1759	92.834	584	1795	1	chr2D.!!$F2	1211
5	TraesCS6D01G054700	chr2D	12542074	12544104	2030	True	1474.0	2390	94.384	589	2535	2	chr2D.!!$R1	1946
6	TraesCS6D01G054700	chr6A	574944004	574946042	2038	True	1386.5	2226	93.155	589	2535	2	chr6A.!!$R1	1946
7	TraesCS6D01G054700	chr6A	23970788	23971391	603	False	756.0	756	89.604	1	592	1	chr6A.!!$F1	591
8	TraesCS6D01G054700	chr7A	152034644	152036673	2029	False	1387.0	2170	93.967	589	2545	2	chr7A.!!$F1	1956
9	TraesCS6D01G054700	chr4D	50776934	50778510	1576	False	2141.0	2141	91.197	589	2182	1	chr4D.!!$F1	1593
10	TraesCS6D01G054700	chr4D	78731186	78732769	1583	True	2073.0	2073	90.335	589	2185	1	chr4D.!!$R1	1596
11	TraesCS6D01G054700	chrUn	43407879	43409420	1541	False	2097.0	2097	91.221	629	2185	1	chrUn.!!$F1	1556
12	TraesCS6D01G054700	chr3B	124500727	124502329	1602	True	2089.0	2089	90.370	589	2183	1	chr3B.!!$R1	1594
13	TraesCS6D01G054700	chr3B	124558588	124560191	1603	True	2056.0	2056	89.994	589	2183	1	chr3B.!!$R2	1594
14	TraesCS6D01G054700	chr3D	447972002	447973576	1574	True	2058.0	2058	90.253	585	2185	1	chr3D.!!$R1	1600
15	TraesCS6D01G054700	chr3D	573731195	573732771	1576	False	1973.0	1973	89.334	589	2185	1	chr3D.!!$F2	1596
16	TraesCS6D01G054700	chr3D	4247200	4247841	641	False	915.0	915	92.378	1535	2182	1	chr3D.!!$F1	647
17	TraesCS6D01G054700	chr7B	11744391	11745986	1595	False	2013.0	2013	89.561	589	2187	1	chr7B.!!$F1	1598
18	TraesCS6D01G054700	chr1D	481624186	481625468	1282	True	1777.0	1777	91.743	896	2185	1	chr1D.!!$R2	1289
19	TraesCS6D01G054700	chr2B	39826203	39827456	1253	False	1742.0	1742	91.771	923	2185	1	chr2B.!!$F1	1262

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
638	660	0.183492	TGTGCTCAGTTTTGCCCTCT	59.817	50.0	0.0	0.0	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2047	2232	1.89115	CCAGAGCTGAGGCACATTTTT	59.109	47.619	0.0	0.0	41.7	1.94	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
22	23	3.190874	GCATCTGTAGTGTTGGAGTAGC	58.809	50.000	0.00	0.00	0.00	3.58
35	36	1.153489	AGTAGCATGCTCACCGCTG	60.153	57.895	26.57	0.00	40.11	5.18
37	38	1.153568	TAGCATGCTCACCGCTGAC	60.154	57.895	26.57	0.00	40.11	3.51
150	151	2.826128	GTTCCCCTGATGGTTTTCCTTC	59.174	50.000	0.00	0.00	42.38	3.46
169	170	5.069781	TCCTTCGGAATTTTGTGTTTTCCAT	59.930	36.000	0.00	0.00	39.09	3.41
204	205	6.831727	TTTCTTATTCGTGTTTCTCGTGAA	57.168	33.333	0.00	0.00	0.00	3.18
225	230	6.259829	GTGAAGAGAGCTTTCAATAAGATCCC	59.740	42.308	7.06	0.00	33.46	3.85
363	374	7.985634	TTTGAAACTTGAACTTGATACAAGC	57.014	32.000	10.78	0.00	42.93	4.01
367	378	3.746492	ACTTGAACTTGATACAAGCGACC	59.254	43.478	10.78	0.54	42.93	4.79
368	379	3.394674	TGAACTTGATACAAGCGACCA	57.605	42.857	10.78	2.71	0.00	4.02
369	380	3.325870	TGAACTTGATACAAGCGACCAG	58.674	45.455	10.78	0.00	0.00	4.00
377	389	4.631377	TGATACAAGCGACCAGAAAATCAG	59.369	41.667	0.00	0.00	0.00	2.90
390	402	6.091437	CCAGAAAATCAGAAGTTTCAGATGC	58.909	40.000	10.91	0.00	40.92	3.91
392	404	7.143340	CAGAAAATCAGAAGTTTCAGATGCAA	58.857	34.615	10.91	0.00	40.92	4.08
393	405	7.326305	CAGAAAATCAGAAGTTTCAGATGCAAG	59.674	37.037	10.91	0.00	40.92	4.01
396	408	6.680874	ATCAGAAGTTTCAGATGCAAGATC	57.319	37.500	0.00	0.00	32.99	2.75
397	409	5.802465	TCAGAAGTTTCAGATGCAAGATCT	58.198	37.500	0.00	0.00	0.00	2.75
405	417	6.492007	TTCAGATGCAAGATCTCAAGTTTC	57.508	37.500	0.00	0.00	0.00	2.78
442	454	3.389983	ACAACTTACTGTTCCCTAGTGCA	59.610	43.478	0.00	0.00	36.63	4.57
476	488	2.109799	CGGATGGCGAGGCAATCT	59.890	61.111	2.86	0.00	38.88	2.40
477	489	2.249535	CGGATGGCGAGGCAATCTG	61.250	63.158	2.86	2.44	38.88	2.90
480	492	1.155042	GATGGCGAGGCAATCTGATC	58.845	55.000	2.86	0.00	36.18	2.92
485	497	1.220169	CGAGGCAATCTGATCGCTGG	61.220	60.000	0.01	0.00	0.00	4.85
503	515	1.973812	GGAAGGGCTTGACAGGTGC	60.974	63.158	0.00	0.00	0.00	5.01
510	522	3.832237	CTTGACAGGTGCGTGCCCT	62.832	63.158	0.00	0.00	0.00	5.19
520	532	1.801512	GCGTGCCCTTGCGAATTTC	60.802	57.895	0.00	0.00	41.78	2.17
530	545	4.201950	CCCTTGCGAATTTCCAGTATTGAG	60.202	45.833	0.00	0.00	0.00	3.02
574	589	3.994392	GGAACTAAGTGCGATCTCAACAA	59.006	43.478	0.00	0.00	0.00	2.83
638	660	0.183492	TGTGCTCAGTTTTGCCCTCT	59.817	50.000	0.00	0.00	0.00	3.69
796	819	3.707700	CGTTGCACGCGTGGCTTA	61.708	61.111	37.47	19.24	33.65	3.09
875	899	1.803943	GACAGAGAGCGACGGTGAT	59.196	57.895	3.31	0.00	0.00	3.06
943	1044	2.045242	ACAGAGAGAGCGGCGGTA	60.045	61.111	13.22	0.00	0.00	4.02
1077	1178	2.145397	TGCCTATCTTCGTCTGTCCT	57.855	50.000	0.00	0.00	0.00	3.85
1155	1269	0.228742	CGTTGTACGTGTGCAGTGAC	59.771	55.000	0.00	0.00	36.74	3.67
1175	1289	1.493022	CAATGGGGTAAGAATCGGGGA	59.507	52.381	0.00	0.00	0.00	4.81
1220	1335	4.889409	GGATCTTTGAGCAATGGGTTGATA	59.111	41.667	0.00	0.00	37.53	2.15
1282	1404	1.202394	CGAGGCCAAGACTCTGATGAG	60.202	57.143	5.01	0.00	45.43	2.90
1425	1556	5.745312	TGAGCTTAGGATGTTGAAGAAGA	57.255	39.130	0.00	0.00	0.00	2.87
1426	1557	6.114187	TGAGCTTAGGATGTTGAAGAAGAA	57.886	37.500	0.00	0.00	0.00	2.52
1427	1558	6.169094	TGAGCTTAGGATGTTGAAGAAGAAG	58.831	40.000	0.00	0.00	0.00	2.85
1435	1566	6.216456	AGGATGTTGAAGAAGAAGGTTAGGAT	59.784	38.462	0.00	0.00	0.00	3.24
1471	1602	6.619329	AGCACAAATACCAATACCCATTTT	57.381	33.333	0.00	0.00	0.00	1.82
1549	1680	8.947055	AAATTGTATGGAAAGGCATGAATTAC	57.053	30.769	0.00	0.00	0.00	1.89
1854	2017	3.198068	GGCAAATGAGATCTCTTGCGTA	58.802	45.455	29.05	10.96	39.91	4.42
1944	2125	9.369904	GCTAATTGAATTATTTCAGAGCCAAAA	57.630	29.630	14.16	0.00	42.60	2.44
2131	2317	6.690530	TGAAGGGCATTACATTGAGAAAAAG	58.309	36.000	0.00	0.00	0.00	2.27
2190	2444	1.255882	AAAATTGGTGCGGCAGATGA	58.744	45.000	1.18	0.00	0.00	2.92
2341	2595	4.294347	TGAACTTTTGGAGGGTTGGAAAT	58.706	39.130	0.00	0.00	0.00	2.17
2353	2607	4.531732	AGGGTTGGAAATGTATGTTTGCAT	59.468	37.500	0.00	0.00	38.83	3.96
2416	2670	8.344831	GGATTTAAAGGGAATAAATTTGCATGC	58.655	33.333	11.82	11.82	34.09	4.06
2461	2715	4.637483	AGAAATGATATGTTTGGGCACG	57.363	40.909	0.00	0.00	0.00	5.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	1.734465	GTGAGCATGCTACTCCAACAC	59.266	52.381	22.74	18.11	32.98	3.32
41	42	7.931407	TGTCTTCTCTTTACAGCTTACATCAAA	59.069	33.333	0.00	0.00	0.00	2.69
115	116	1.478654	GGGGAACACACACAGACCATT	60.479	52.381	0.00	0.00	0.00	3.16
150	151	5.527951	TCAGATGGAAAACACAAAATTCCG	58.472	37.500	0.00	0.00	44.48	4.30
178	179	6.477688	TCACGAGAAACACGAATAAGAAAACT	59.522	34.615	0.00	0.00	34.70	2.66
186	187	5.366829	TCTCTTCACGAGAAACACGAATA	57.633	39.130	0.00	0.00	45.55	1.75
187	188	4.238761	TCTCTTCACGAGAAACACGAAT	57.761	40.909	0.00	0.00	45.55	3.34
204	205	5.965033	TGGGATCTTATTGAAAGCTCTCT	57.035	39.130	0.00	0.00	0.00	3.10
270	278	5.403466	GGTCACTCGTACTAAATTCAAACGT	59.597	40.000	0.00	0.00	35.21	3.99
279	287	4.566545	TTTGTCGGTCACTCGTACTAAA	57.433	40.909	0.00	0.00	0.00	1.85
349	360	3.585862	TCTGGTCGCTTGTATCAAGTTC	58.414	45.455	10.49	3.08	0.00	3.01
363	374	5.466728	TCTGAAACTTCTGATTTTCTGGTCG	59.533	40.000	13.99	0.00	33.68	4.79
367	378	6.675026	TGCATCTGAAACTTCTGATTTTCTG	58.325	36.000	8.60	10.90	41.87	3.02
368	379	6.889301	TGCATCTGAAACTTCTGATTTTCT	57.111	33.333	8.60	0.00	41.87	2.52
369	380	7.365741	TCTTGCATCTGAAACTTCTGATTTTC	58.634	34.615	8.60	5.67	41.87	2.29
377	389	6.149142	ACTTGAGATCTTGCATCTGAAACTTC	59.851	38.462	0.00	0.00	0.00	3.01
422	434	3.008049	CCTGCACTAGGGAACAGTAAGTT	59.992	47.826	0.00	0.00	43.33	2.66
442	454	3.644966	TCCGCAAATTAGTTGGATCCT	57.355	42.857	14.23	0.00	37.73	3.24
467	479	0.883814	CCCAGCGATCAGATTGCCTC	60.884	60.000	17.91	0.00	40.67	4.70
476	488	2.300967	AAGCCCTTCCCAGCGATCA	61.301	57.895	0.00	0.00	0.00	2.92
477	489	1.821332	CAAGCCCTTCCCAGCGATC	60.821	63.158	0.00	0.00	0.00	3.69
480	492	2.747855	GTCAAGCCCTTCCCAGCG	60.748	66.667	0.00	0.00	0.00	5.18
485	497	1.973812	GCACCTGTCAAGCCCTTCC	60.974	63.158	0.00	0.00	0.00	3.46
503	515	1.154035	GGAAATTCGCAAGGGCACG	60.154	57.895	0.00	0.00	41.24	5.34
510	522	4.584874	TCCTCAATACTGGAAATTCGCAA	58.415	39.130	0.00	0.00	0.00	4.85
546	561	7.342769	TGAGATCGCACTTAGTTCCTATAAA	57.657	36.000	0.00	0.00	0.00	1.40
567	582	5.163416	ACCCCAAAAGAATTCTGTTGTTGAG	60.163	40.000	28.61	18.93	39.09	3.02
574	589	8.758829	GGATAATTAACCCCAAAAGAATTCTGT	58.241	33.333	9.17	0.00	0.00	3.41
638	660	0.108662	ACTGAGCACGATTCGCATCA	60.109	50.000	5.86	7.08	0.00	3.07
796	819	1.000396	GCTCTTTGCTGGGTCCCAT	60.000	57.895	12.23	0.00	38.95	4.00
853	877	3.805307	CGTCGCTCTCTGTCGCCT	61.805	66.667	0.00	0.00	0.00	5.52
875	899	1.499688	CGCTCTCTCTATCGCCGTGA	61.500	60.000	0.00	0.00	0.00	4.35
943	1044	1.799933	CCCTCCACAGCTATCTTCCT	58.200	55.000	0.00	0.00	0.00	3.36
1140	1254	1.194547	CCATTGTCACTGCACACGTAC	59.805	52.381	0.00	0.00	0.00	3.67
1155	1269	1.493022	TCCCCGATTCTTACCCCATTG	59.507	52.381	0.00	0.00	0.00	2.82
1220	1335	0.244450	CCTGCATGAACGCCAAACAT	59.756	50.000	0.00	0.00	0.00	2.71
1282	1404	2.810274	TCATGCTCTTCTTGCAGTTCAC	59.190	45.455	0.00	0.00	44.04	3.18
1425	1556	5.441718	TGATCTTCAAGCATCCTAACCTT	57.558	39.130	0.00	0.00	0.00	3.50
1426	1557	5.435291	CTTGATCTTCAAGCATCCTAACCT	58.565	41.667	4.46	0.00	46.03	3.50
1427	1558	5.747951	CTTGATCTTCAAGCATCCTAACC	57.252	43.478	4.46	0.00	46.03	2.85
1471	1602	6.268847	ACCTACAAATGCCCAAAAGTAATTGA	59.731	34.615	0.00	0.00	31.84	2.57
1549	1680	5.371115	TTTCAAGCTTACAAATTCCTCCG	57.629	39.130	0.00	0.00	0.00	4.63
2038	2223	5.393352	GCTGAGGCACATTTTTCATGACATA	60.393	40.000	0.00	0.00	38.54	2.29
2047	2232	1.891150	CCAGAGCTGAGGCACATTTTT	59.109	47.619	0.00	0.00	41.70	1.94
2190	2444	4.082125	CCCTAGCCATGTCAAAGTCTTTT	58.918	43.478	0.00	0.00	0.00	2.27
2341	2595	3.586892	CATGTGGCAATGCAAACATACA	58.413	40.909	20.36	10.09	35.98	2.29
2353	2607	2.107378	TCTAACCAGAACCATGTGGCAA	59.893	45.455	0.00	0.00	43.76	4.52
2416	2670	6.049955	TCCCTAAACCAAGTCATGAACTAG	57.950	41.667	0.00	0.00	37.17	2.57
2461	2715	9.691362	AGTTATTATGTGTGTTCAAAAATGTCC	57.309	29.630	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.