AutoCloner

Multiple sequence alignment - TraesCS2B01G409500

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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	TraesCS2B01G409500	chr2B	100.000	2557	0	0	1	2557	582813253	582810697	0.000000e+00	4723
1	TraesCS2B01G409500	chr2B	82.686	2576	390	33	18	2552	599258006	599260566	0.000000e+00	2235
2	TraesCS2B01G409500	chr2B	84.626	735	100	6	18	752	693443853	693444574	0.000000e+00	719
3	TraesCS2B01G409500	chr2B	84.887	622	60	12	1953	2554	693444596	693445203	4.710000e-167	597
4	TraesCS2B01G409500	chr5D	85.815	2559	302	37	20	2554	476695907	476693386	0.000000e+00	2658
5	TraesCS2B01G409500	chr6D	85.337	2578	317	39	18	2554	146941130	146943687	0.000000e+00	2610
6	TraesCS2B01G409500	chr6D	84.933	750	73	17	1821	2549	456651112	456650382	0.000000e+00	723
7	TraesCS2B01G409500	chr3B	85.247	2596	302	40	18	2557	157906230	157903660	0.000000e+00	2597
8	TraesCS2B01G409500	chr3B	86.863	2139	246	26	443	2557	713994494	713992367	0.000000e+00	2361
9	TraesCS2B01G409500	chr3B	87.322	773	79	7	1801	2554	8126738	8127510	0.000000e+00	867
10	TraesCS2B01G409500	chr3B	79.732	671	112	18	20	682	124817410	124818064	4.980000e-127	464
11	TraesCS2B01G409500	chr3D	84.938	2576	334	30	18	2557	586295614	586293057	0.000000e+00	2558
12	TraesCS2B01G409500	chr3D	84.946	2584	324	40	17	2554	562217304	562219868	0.000000e+00	2556
13	TraesCS2B01G409500	chr3D	85.013	387	34	13	2189	2554	110586491	110586874	3.110000e-99	372
14	TraesCS2B01G409500	chr7D	88.148	2160	208	16	424	2553	585429054	585426913	0.000000e+00	2527
15	TraesCS2B01G409500	chr4D	84.484	2578	322	44	20	2554	51846895	51849437	0.000000e+00	2473
16	TraesCS2B01G409500	chr4D	85.973	221	31	0	2337	2557	319684942	319685162	1.180000e-58	237
17	TraesCS2B01G409500	chr1D	84.056	2584	357	38	16	2557	415632978	415630408	0.000000e+00	2438
18	TraesCS2B01G409500	chr1D	86.697	218	29	0	2337	2554	69527592	69527375	2.540000e-60	243
19	TraesCS2B01G409500	chr4A	85.328	2331	321	16	29	2349	165799077	165796758	0.000000e+00	2390
20	TraesCS2B01G409500	chr4B	87.101	752	75	6	1826	2557	401886628	401885879	0.000000e+00	832
21	TraesCS2B01G409500	chr7B	85.837	233	23	7	18	248	699171512	699171736	3.290000e-59	239

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	TraesCS2B01G409500	chr2B	582810697	582813253	2556	True	4723	4723	100.0000	1	2557	1	chr2B.!!$R1	2556
1	TraesCS2B01G409500	chr2B	599258006	599260566	2560	False	2235	2235	82.6860	18	2552	1	chr2B.!!$F1	2534
2	TraesCS2B01G409500	chr2B	693443853	693445203	1350	False	658	719	84.7565	18	2554	2	chr2B.!!$F2	2536
3	TraesCS2B01G409500	chr5D	476693386	476695907	2521	True	2658	2658	85.8150	20	2554	1	chr5D.!!$R1	2534
4	TraesCS2B01G409500	chr6D	146941130	146943687	2557	False	2610	2610	85.3370	18	2554	1	chr6D.!!$F1	2536
5	TraesCS2B01G409500	chr6D	456650382	456651112	730	True	723	723	84.9330	1821	2549	1	chr6D.!!$R1	728
6	TraesCS2B01G409500	chr3B	157903660	157906230	2570	True	2597	2597	85.2470	18	2557	1	chr3B.!!$R1	2539
7	TraesCS2B01G409500	chr3B	713992367	713994494	2127	True	2361	2361	86.8630	443	2557	1	chr3B.!!$R2	2114
8	TraesCS2B01G409500	chr3B	8126738	8127510	772	False	867	867	87.3220	1801	2554	1	chr3B.!!$F1	753
9	TraesCS2B01G409500	chr3B	124817410	124818064	654	False	464	464	79.7320	20	682	1	chr3B.!!$F2	662
10	TraesCS2B01G409500	chr3D	586293057	586295614	2557	True	2558	2558	84.9380	18	2557	1	chr3D.!!$R1	2539
11	TraesCS2B01G409500	chr3D	562217304	562219868	2564	False	2556	2556	84.9460	17	2554	1	chr3D.!!$F2	2537
12	TraesCS2B01G409500	chr7D	585426913	585429054	2141	True	2527	2527	88.1480	424	2553	1	chr7D.!!$R1	2129
13	TraesCS2B01G409500	chr4D	51846895	51849437	2542	False	2473	2473	84.4840	20	2554	1	chr4D.!!$F1	2534
14	TraesCS2B01G409500	chr1D	415630408	415632978	2570	True	2438	2438	84.0560	16	2557	1	chr1D.!!$R2	2541
15	TraesCS2B01G409500	chr4A	165796758	165799077	2319	True	2390	2390	85.3280	29	2349	1	chr4A.!!$R1	2320
16	TraesCS2B01G409500	chr4B	401885879	401886628	749	True	832	832	87.1010	1826	2557	1	chr4B.!!$R1	731

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
73	74	0.390735	GCGTGTCCATTTAGGTCGGT	60.391	55.0	0.0	0.0	39.02	4.69	F
1178	1247	0.255318	TCCAGAGGACTACGGACTCC	59.745	60.0	0.0	0.0	31.70	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1388	1464	0.317854	CGCTCATGGAACTCGCGATA	60.318	55.0	10.36	0.0	45.99	2.92	R
2226	2329	0.172803	GCCATAGGTCACTCGTCGTT	59.827	55.0	0.00	0.0	0.00	3.85	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
66	67	0.785378	CGTTCACGCGTGTCCATTTA	59.215	50.000	35.74	14.71	0.00	1.40
73	74	0.390735	GCGTGTCCATTTAGGTCGGT	60.391	55.000	0.00	0.00	39.02	4.69
168	171	1.391933	CCCGGCCTATTTTTGAGCCC	61.392	60.000	0.00	0.00	42.66	5.19
172	175	1.688735	GGCCTATTTTTGAGCCCCATC	59.311	52.381	0.00	0.00	39.60	3.51
266	270	1.212935	ACCCCTTCATCATTTCCCTCG	59.787	52.381	0.00	0.00	0.00	4.63
338	367	2.434884	CAACCTCGATGCTGCCGT	60.435	61.111	0.00	0.00	0.00	5.68
392	421	4.033776	CGCCCCCTCCAGCAAAGA	62.034	66.667	0.00	0.00	0.00	2.52
393	422	2.685999	GCCCCCTCCAGCAAAGAT	59.314	61.111	0.00	0.00	0.00	2.40
459	489	1.835494	AGAAGATGACGGACGAGGAA	58.165	50.000	0.00	0.00	0.00	3.36
527	557	0.678048	GCAAGGAAGGAAGCCATCGT	60.678	55.000	0.00	0.00	0.00	3.73
620	650	3.799232	GCGCTGATGTACCTAGGGTTAAG	60.799	52.174	14.81	4.04	37.09	1.85
653	683	3.554692	CCTCGTCAATGCCGTCGC	61.555	66.667	0.00	0.00	0.00	5.19
775	805	3.403558	AAGCTTCCCGGCTCTCCC	61.404	66.667	0.00	0.00	42.24	4.30
847	902	3.485346	GACCTCAACGCCACCCCAA	62.485	63.158	0.00	0.00	0.00	4.12
910	966	4.314440	ACATGCCAGCCGACGTGT	62.314	61.111	0.00	0.00	0.00	4.49
944	1000	1.336440	CAACCTGTTTGACGGAATGCA	59.664	47.619	0.00	0.00	37.39	3.96
999	1059	0.327924	TCTTCGAGGGTGGTACGGTA	59.672	55.000	0.00	0.00	0.00	4.02
1033	1095	3.227276	CGGGGCTGGCTACGATCT	61.227	66.667	11.89	0.00	0.00	2.75
1064	1127	3.881019	AAGCCAGGACGTCGAGGGA	62.881	63.158	21.77	0.00	0.00	4.20
1066	1129	2.675423	CCAGGACGTCGAGGGACA	60.675	66.667	9.92	0.00	43.61	4.02
1126	1195	1.048160	TGCATGATCAGGTCGGCCTA	61.048	55.000	9.07	0.00	44.97	3.93
1178	1247	0.255318	TCCAGAGGACTACGGACTCC	59.745	60.000	0.00	0.00	31.70	3.85
1231	1300	1.532868	CCTTTGTTCGAGGACAAGCTG	59.467	52.381	3.13	0.00	40.33	4.24
1269	1341	1.028868	GGGAAGAAGCGCAAGAGCAT	61.029	55.000	11.47	0.00	42.27	3.79
1334	1410	2.304761	GAGTGTTGGAGGTACATTGGGA	59.695	50.000	0.00	0.00	0.00	4.37
1388	1464	4.411256	TTAACCTTTTGGACTCGTGTCT	57.589	40.909	16.45	0.00	44.07	3.41
1537	1615	2.053865	CATCAAGGCACGCCCCATT	61.054	57.895	3.95	0.00	36.58	3.16
1540	1618	1.378514	CAAGGCACGCCCCATTAGT	60.379	57.895	3.95	0.00	36.58	2.24
1642	1729	6.952938	TCCATATCCATTTGCCAATATGCTTA	59.047	34.615	0.00	0.00	32.96	3.09
1644	1731	4.566545	TCCATTTGCCAATATGCTTACG	57.433	40.909	0.00	0.00	0.00	3.18
1655	1742	5.626543	CCAATATGCTTACGTGCAATTCATC	59.373	40.000	4.54	0.00	46.61	2.92
1701	1788	3.005684	GCATTCAAGGTCCAACACAATGA	59.994	43.478	0.00	0.00	0.00	2.57
1723	1810	0.318762	AGTCCTTCAACCTCTCGCAC	59.681	55.000	0.00	0.00	0.00	5.34
1760	1847	4.341235	TCAAAGACGAGGAGAAGTTCAAGA	59.659	41.667	5.50	0.00	0.00	3.02
1787	1879	3.853330	CCGCCTTCATGTCGCGTG	61.853	66.667	5.77	0.00	44.29	5.34
1890	1989	2.173669	CGGGATGCAGCGTCGAATT	61.174	57.895	8.57	0.00	0.00	2.17
1902	2001	1.256376	CGTCGAATTCCTTGATCGCAG	59.744	52.381	0.00	0.00	36.56	5.18
1976	2078	5.279156	GCAAGACAAGGGAGAACAAATGAAT	60.279	40.000	0.00	0.00	0.00	2.57
2030	2132	1.302511	GGAGGCGGAGAAGCAAACA	60.303	57.895	0.00	0.00	39.27	2.83
2138	2240	1.001746	CTCGCTAGCATGATGATGGGT	59.998	52.381	16.45	0.00	0.00	4.51
2142	2244	2.486013	GCTAGCATGATGATGGGTGTGA	60.486	50.000	10.63	0.00	0.00	3.58
2144	2246	3.090210	AGCATGATGATGGGTGTGAAA	57.910	42.857	0.00	0.00	0.00	2.69
2154	2256	5.078949	TGATGGGTGTGAAAATCATGAAGT	58.921	37.500	0.00	0.00	0.00	3.01
2226	2329	0.955428	GGCCGACATGCTCAAGTTCA	60.955	55.000	0.00	0.00	0.00	3.18
2251	2354	2.185867	GTGACCTATGGCGGCGAA	59.814	61.111	12.98	0.00	0.00	4.70
2323	2449	4.353437	GCGTGGTCGAACTCCCGT	62.353	66.667	0.33	0.00	39.71	5.28
2363	2510	0.721718	GTGTGCCGACTGAACTATGC	59.278	55.000	0.00	0.00	0.00	3.14
2405	2554	2.180204	GTATGTCGGCGCTGGCATT	61.180	57.895	38.41	23.03	42.47	3.56
2421	2571	2.886523	GGCATTATGCTGGCATGAACTA	59.113	45.455	17.13	0.00	44.28	2.24
2463	2633	1.678123	GCATGATCTATGGCTGCGGAT	60.678	52.381	0.00	0.00	37.26	4.18
2464	2634	2.277969	CATGATCTATGGCTGCGGATC	58.722	52.381	0.00	12.89	36.21	3.36
2465	2635	0.610174	TGATCTATGGCTGCGGATCC	59.390	55.000	0.00	0.00	35.18	3.36
2473	2664	1.106285	GGCTGCGGATCCTTTTCAAT	58.894	50.000	10.75	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.755330	CTCTTACGAGAGCTTTTTGACTC	57.245	43.478	0.00	0.00	42.72	3.36
12	13	2.351447	CGTTGGAGTTGCTCTTACGAGA	60.351	50.000	0.00	0.00	39.74	4.04
13	14	1.986378	CGTTGGAGTTGCTCTTACGAG	59.014	52.381	13.76	0.00	38.46	4.18
14	15	1.933500	GCGTTGGAGTTGCTCTTACGA	60.934	52.381	19.24	0.00	38.46	3.43
66	67	0.834612	TTTTCTGTCCACACCGACCT	59.165	50.000	0.00	0.00	31.35	3.85
73	74	0.534203	GGCCGACTTTTCTGTCCACA	60.534	55.000	0.00	0.00	33.70	4.17
156	159	2.023673	CGCAGATGGGGCTCAAAAATA	58.976	47.619	0.00	0.00	0.00	1.40
247	251	1.490490	TCGAGGGAAATGATGAAGGGG	59.510	52.381	0.00	0.00	0.00	4.79
250	254	4.333926	GGAAAGTCGAGGGAAATGATGAAG	59.666	45.833	0.00	0.00	0.00	3.02
266	270	1.629043	GGGAGGGTTTTGGGAAAGTC	58.371	55.000	0.00	0.00	0.00	3.01
459	489	2.342648	GTCGACTTCCTTGCCCGT	59.657	61.111	8.70	0.00	0.00	5.28
469	499	1.270893	GCCCTTTCTCTTGGTCGACTT	60.271	52.381	16.46	0.00	0.00	3.01
591	621	1.522569	GTACATCAGCGCCTCCCTT	59.477	57.895	2.29	0.00	0.00	3.95
738	768	2.582978	GGGTAGACGTGGAAGCCC	59.417	66.667	0.00	0.00	0.00	5.19
775	805	2.492090	CTCAGGGGAGCGTTCTCG	59.508	66.667	0.00	0.00	40.26	4.04
777	807	2.120718	ACCTCAGGGGAGCGTTCT	59.879	61.111	0.00	0.00	39.96	3.01
847	902	0.392998	GATGACGAGCCACCAACCAT	60.393	55.000	0.00	0.00	0.00	3.55
910	966	0.534877	AGGTTGCATGCACTCGACAA	60.535	50.000	22.58	0.00	0.00	3.18
1033	1095	0.318699	CTGGCTTTGTGTCTCGTCGA	60.319	55.000	0.00	0.00	0.00	4.20
1064	1127	2.358247	GGTGGACGGCGTGAATGT	60.358	61.111	21.19	0.00	0.00	2.71
1066	1129	1.072505	AAAGGTGGACGGCGTGAAT	59.927	52.632	21.19	0.00	0.00	2.57
1157	1226	2.657143	GAGTCCGTAGTCCTCTGGAAT	58.343	52.381	0.00	0.00	31.38	3.01
1178	1247	4.226427	TGTCCAATTCATCCTCTTCCTG	57.774	45.455	0.00	0.00	0.00	3.86
1269	1341	0.673333	CGTGTATGCCTTGGTCTGCA	60.673	55.000	0.00	0.00	42.52	4.41
1334	1410	0.678048	GCGCAGATCTTGGGGTCTTT	60.678	55.000	0.30	0.00	39.95	2.52
1368	1444	5.620654	CGATAGACACGAGTCCAAAAGGTTA	60.621	44.000	9.50	0.00	46.15	2.85
1388	1464	0.317854	CGCTCATGGAACTCGCGATA	60.318	55.000	10.36	0.00	45.99	2.92
1484	1560	4.390297	GGCACAAAACTTGTTGCACTTTTA	59.610	37.500	12.61	0.00	43.23	1.52
1487	1563	2.289320	TGGCACAAAACTTGTTGCACTT	60.289	40.909	12.61	0.00	43.23	3.16
1642	1729	2.009774	GCCTACAGATGAATTGCACGT	58.990	47.619	0.00	0.00	0.00	4.49
1644	1731	4.498682	GGAATGCCTACAGATGAATTGCAC	60.499	45.833	0.00	0.00	0.00	4.57
1655	1742	3.498927	CAAAGCTTGGAATGCCTACAG	57.501	47.619	0.00	0.00	37.80	2.74
1701	1788	1.270358	GCGAGAGGTTGAAGGACTTGT	60.270	52.381	0.00	0.00	0.00	3.16
1723	1810	3.677121	CGTCTTTGATGACTCTCCAACAG	59.323	47.826	0.00	0.00	35.00	3.16
1760	1847	0.819259	ATGAAGGCGGCATATTGCGT	60.819	50.000	13.08	0.00	46.21	5.24
1890	1989	2.125552	CACGGCTGCGATCAAGGA	60.126	61.111	0.00	0.00	0.00	3.36
1902	2001	0.811616	GTCATCATGTCCTCCACGGC	60.812	60.000	0.00	0.00	0.00	5.68
1976	2078	3.010472	TCTTTTGGATCTCCATGAAGGCA	59.990	43.478	16.54	3.36	46.97	4.75
2030	2132	1.133853	GCCTCCATCTCAAGCATCCTT	60.134	52.381	0.00	0.00	0.00	3.36
2138	2240	6.716173	TGAGATCCAACTTCATGATTTTCACA	59.284	34.615	0.00	0.00	0.00	3.58
2154	2256	1.067846	CGAGACGGTGTTGAGATCCAA	60.068	52.381	0.00	0.00	0.00	3.53
2226	2329	0.172803	GCCATAGGTCACTCGTCGTT	59.827	55.000	0.00	0.00	0.00	3.85
2266	2369	1.155889	CAGCACACTTGTCGGCATAA	58.844	50.000	0.00	0.00	0.00	1.90
2274	2377	1.174712	GGTCATGCCAGCACACTTGT	61.175	55.000	0.00	0.00	37.17	3.16
2303	2413	2.737376	GGAGTTCGACCACGCCAC	60.737	66.667	5.27	0.00	36.66	5.01
2323	2449	1.761449	TGCCAGCACACAAAAAGAGA	58.239	45.000	0.00	0.00	0.00	3.10
2363	2510	1.600413	GCCAGCTTCAGAAAAACACCG	60.600	52.381	0.00	0.00	0.00	4.94
2405	2554	2.442878	ACCCATAGTTCATGCCAGCATA	59.557	45.455	4.52	0.00	34.91	3.14
2421	2571	1.218047	CGGTCATGTCGTCACCCAT	59.782	57.895	0.00	0.00	0.00	4.00
2463	2633	4.936411	TCCGCACGTAAATATTGAAAAGGA	59.064	37.500	0.00	0.00	0.00	3.36
2464	2634	5.025826	GTCCGCACGTAAATATTGAAAAGG	58.974	41.667	0.00	0.00	0.00	3.11
2465	2635	5.623335	TGTCCGCACGTAAATATTGAAAAG	58.377	37.500	0.00	0.00	0.00	2.27
2473	2664	4.034626	CCATTTCATGTCCGCACGTAAATA	59.965	41.667	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.