AutoCloner

Multiple sequence alignment - TraesCS2D01G208000

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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	TraesCS2D01G208000	chr2D	100.000	5515	0	0	1	5515	162150977	162156491	0.000000e+00	10185.0
1	TraesCS2D01G208000	chr2B	97.787	5333	93	16	1	5318	221479347	221484669	0.000000e+00	9171.0
2	TraesCS2D01G208000	chr2B	95.929	393	15	1	3468	3859	571193220	571193612	2.170000e-178	636.0
3	TraesCS2D01G208000	chr2B	97.000	100	3	0	3338	3437	571193118	571193217	9.500000e-38	169.0
4	TraesCS2D01G208000	chr2A	96.668	5222	156	11	1	5208	173121707	173126924	0.000000e+00	8663.0
5	TraesCS2D01G208000	chr2A	94.286	245	14	0	5131	5375	173126917	173127161	5.220000e-100	375.0
6	TraesCS2D01G208000	chr2A	96.503	143	3	1	5375	5515	173127264	173127406	9.240000e-58	235.0
7	TraesCS2D01G208000	chr6A	95.929	393	15	1	3468	3859	558773019	558772627	2.170000e-178	636.0
8	TraesCS2D01G208000	chr6A	97.000	100	3	0	3338	3437	558773121	558773022	9.500000e-38	169.0
9	TraesCS2D01G208000	chr4A	95.929	393	15	1	3468	3859	560959024	560958632	2.170000e-178	636.0
10	TraesCS2D01G208000	chr4A	97.000	100	3	0	3338	3437	560959126	560959027	9.500000e-38	169.0
11	TraesCS2D01G208000	chr3A	95.929	393	15	1	3468	3859	41548611	41548219	2.170000e-178	636.0
12	TraesCS2D01G208000	chr3A	97.000	100	3	0	3338	3437	41548713	41548614	9.500000e-38	169.0
13	TraesCS2D01G208000	chr6B	95.674	393	16	1	3468	3859	698422792	698422400	1.010000e-176	630.0
14	TraesCS2D01G208000	chr6B	97.000	100	3	0	3338	3437	698422894	698422795	9.500000e-38	169.0
15	TraesCS2D01G208000	chr4B	96.970	33	0	1	2285	2317	129519941	129519910	3.000000e-03	54.7

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	TraesCS2D01G208000	chr2D	162150977	162156491	5514	False	10185	10185	100.000	1	5515	1	chr2D.!!$F1	5514
1	TraesCS2D01G208000	chr2B	221479347	221484669	5322	False	9171	9171	97.787	1	5318	1	chr2B.!!$F1	5317
2	TraesCS2D01G208000	chr2A	173121707	173127406	5699	False	3091	8663	95.819	1	5515	3	chr2A.!!$F1	5514

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	Hairpin	End Stability	Orientation
708	713	3.246226	CGCCTCATTTATCTCAGGAAACG	59.754	47.826	0.00	0.00	3.60	F
1192	1200	6.969366	TCTGGTAAATCTGTTTGTTCATGTG	58.031	36.000	0.00	0.00	3.21	F
1699	1709	1.662629	CCAGATTGTCTGCGCTGTAAG	59.337	52.381	9.73	42.98	2.34	F
3260	3275	1.329906	CATTCTGGCGATTCTGTCAGC	59.670	52.381	0.00	41.36	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1602	1612	3.256558	TGATCATCTTCTGAAGCACACG	58.743	45.455	12.54	37.44	4.49	R
2960	2975	1.004440	AAGCAGCCTCGGTTCAGAC	60.004	57.895	0.00	0.00	3.51	R
3437	3452	2.218603	ACTGAAACGTGACCATTGACC	58.781	47.619	0.00	0.00	4.02	R
4685	4701	1.342819	CAAGCCCAAACATCCGGAAAA	59.657	47.619	9.01	0.00	2.29	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
94	95	6.920758	TCCTTGTCCAATTTGTTTTTCATACG	59.079	34.615	0.00	0.00	0.00	3.06
281	282	4.142038	AGGTACTCCCATGTTTTCACAAC	58.858	43.478	0.00	0.00	36.16	3.32
398	400	9.013229	TGCAAAGAGATAAATGACTAATGTTGT	57.987	29.630	0.00	0.00	0.00	3.32
485	490	8.566260	GCTATAGGGGTACACATATATTCGTAG	58.434	40.741	9.79	0.91	0.00	3.51
708	713	3.246226	CGCCTCATTTATCTCAGGAAACG	59.754	47.826	0.00	0.00	0.00	3.60
1120	1128	7.584122	TGGACTAATATACTCTGTGTCCTTC	57.416	40.000	0.00	0.00	41.93	3.46
1192	1200	6.969366	TCTGGTAAATCTGTTTGTTCATGTG	58.031	36.000	0.00	0.00	0.00	3.21
1602	1612	4.145052	AGGGAATTTTCAGGACACACTTC	58.855	43.478	0.00	0.00	0.00	3.01
1699	1709	1.662629	CCAGATTGTCTGCGCTGTAAG	59.337	52.381	9.73	0.00	42.98	2.34
1972	1982	9.969001	GAAGTTCTATCCTACTACTATGGAGAT	57.031	37.037	0.00	0.00	32.95	2.75
2264	2274	6.528537	TCATTAGCACAGCCACAATATTTT	57.471	33.333	0.00	0.00	0.00	1.82
2723	2738	6.088749	CGCTTTCGTCTGGAGATATCATAAAG	59.911	42.308	5.32	4.25	0.00	1.85
2960	2975	3.473367	CGATGTCTTGAGAAAAGTTGCG	58.527	45.455	0.00	0.00	0.00	4.85
3215	3230	7.561722	TCACTAAGAAATCTACCTACAGATGCT	59.438	37.037	0.00	0.00	35.42	3.79
3260	3275	1.329906	CATTCTGGCGATTCTGTCAGC	59.670	52.381	0.00	0.00	41.36	4.26
3437	3452	2.292828	TTTCTTCCTTTCCAGGCAGG	57.707	50.000	0.00	0.00	40.58	4.85
3972	3987	7.504926	ACTACAAGTTATATCCAACCTCCAA	57.495	36.000	0.00	0.00	0.00	3.53
3987	4002	4.012374	ACCTCCAACTGACAATAATGCAG	58.988	43.478	0.00	0.00	37.00	4.41
4491	4506	3.244422	TGGCATGAAAACGAGTAAGGAGT	60.244	43.478	0.00	0.00	0.00	3.85
4587	4603	6.072112	TGATCTTGTGGTAGAAAGCAAAAC	57.928	37.500	0.00	0.00	34.25	2.43
4685	4701	0.679505	TTCAGCTGTAGTTCGGTGCT	59.320	50.000	14.67	0.00	0.00	4.40
4771	4787	3.049912	GTTTGCCGTCATTCCTTTTGAC	58.950	45.455	0.00	0.00	40.06	3.18
4779	4795	4.036262	CGTCATTCCTTTTGACACCAGAAA	59.964	41.667	4.86	0.00	42.90	2.52
5035	5056	5.966636	AATTCAAAAGGAGAACGCAAAAC	57.033	34.783	0.00	0.00	0.00	2.43
5098	5119	2.033299	AGTGCTGTGTTCCAAATGTTCG	59.967	45.455	0.00	0.00	0.00	3.95
5108	5129	5.982516	TGTTCCAAATGTTCGAAATTTCTGG	59.017	36.000	15.92	13.77	0.00	3.86
5180	5271	4.351874	AGATTTGCTTAGCCGGCTATTA	57.648	40.909	35.60	21.45	0.00	0.98
5204	5295	9.953565	TTATGGCTCTGTAACATTTACTAGTTT	57.046	29.630	0.00	0.00	0.00	2.66
5213	5304	6.947644	AACATTTACTAGTTTTGGAACCGT	57.052	33.333	0.00	0.00	36.39	4.83
5284	5375	4.966965	TGCGTCCTAGTTCTAGAGAAAG	57.033	45.455	8.26	0.00	35.58	2.62
5285	5376	3.128938	TGCGTCCTAGTTCTAGAGAAAGC	59.871	47.826	8.26	11.48	35.58	3.51
5308	5399	5.009710	GCCTACATTAAGGAGTATTTTGGCC	59.990	44.000	0.00	0.00	39.15	5.36
5329	5420	3.305335	CCCTGCTTTTATGTCGCAAAACT	60.305	43.478	0.00	0.00	32.66	2.66
5338	5429	7.861176	TTTATGTCGCAAAACTTATGTTTCC	57.139	32.000	7.15	2.15	44.70	3.13
5343	5434	6.483974	TGTCGCAAAACTTATGTTTCCTAAGA	59.516	34.615	7.15	1.97	44.70	2.10
5491	5685	5.215160	CGAAATAATGAACTTATGCTGCCC	58.785	41.667	0.00	0.00	30.26	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	95	7.699812	GTCTTAACAGATCATCCTTTTGCATTC	59.300	37.037	0.00	0.00	0.00	2.67
318	319	2.288395	GCACAAGGTTTTGCTAGCACAT	60.288	45.455	19.17	0.06	37.85	3.21
396	398	6.391537	TGAGAAATGTACGTGCATAGTTACA	58.608	36.000	19.74	12.86	0.00	2.41
397	399	6.880822	TGAGAAATGTACGTGCATAGTTAC	57.119	37.500	19.74	10.69	0.00	2.50
398	400	8.192110	TGTATGAGAAATGTACGTGCATAGTTA	58.808	33.333	19.74	6.31	0.00	2.24
448	451	8.275758	TGTGTACCCCTATAGCAAATAATTGAA	58.724	33.333	0.00	0.00	38.94	2.69
466	469	7.063074	GCACATTCTACGAATATATGTGTACCC	59.937	40.741	13.17	0.00	44.80	3.69
1120	1128	9.196552	TCAAGATAATTCATCTGTAACATAGCG	57.803	33.333	0.00	0.00	43.56	4.26
1259	1269	2.543445	CCATCTGCGCACACAAAAGAAA	60.543	45.455	5.66	0.00	0.00	2.52
1260	1270	1.001487	CCATCTGCGCACACAAAAGAA	60.001	47.619	5.66	0.00	0.00	2.52
1402	1412	1.345715	CCACCTGGTACTCATCCCCC	61.346	65.000	0.00	0.00	0.00	5.40
1436	1446	2.146342	CATGCGTTCCTCTTCTGTTGT	58.854	47.619	0.00	0.00	0.00	3.32
1602	1612	3.256558	TGATCATCTTCTGAAGCACACG	58.743	45.455	12.54	0.00	37.44	4.49
1699	1709	6.938596	TCTCACCATGATCATCATATTCAACC	59.061	38.462	4.86	0.00	34.28	3.77
2264	2274	7.051000	TGATTGTAATGATCGTACCATGGAAA	58.949	34.615	21.47	2.58	0.00	3.13
2723	2738	8.547967	TTAGTCTGAAATCACCAGTCAAATAC	57.452	34.615	0.00	0.00	33.57	1.89
2960	2975	1.004440	AAGCAGCCTCGGTTCAGAC	60.004	57.895	0.00	0.00	0.00	3.51
3215	3230	2.637382	TGAAGAACTGTAGCCATGACCA	59.363	45.455	0.00	0.00	0.00	4.02
3260	3275	4.984785	TCTGAATGTTCTTCTGAGTTCACG	59.015	41.667	0.00	0.00	0.00	4.35
3437	3452	2.218603	ACTGAAACGTGACCATTGACC	58.781	47.619	0.00	0.00	0.00	4.02
3972	3987	7.012704	GTCCATGATTACTGCATTATTGTCAGT	59.987	37.037	14.60	14.60	40.70	3.41
3987	4002	6.540189	GGATGCATAGGTATGTCCATGATTAC	59.460	42.308	0.00	0.00	39.02	1.89
4491	4506	3.507103	ATGAAATTGCTGCGCATGTAA	57.493	38.095	12.24	11.63	38.76	2.41
4685	4701	1.342819	CAAGCCCAAACATCCGGAAAA	59.657	47.619	9.01	0.00	0.00	2.29
5098	5119	5.131594	AGAGCAAAAGCTCCAGAAATTTC	57.868	39.130	10.33	10.33	37.53	2.17
5108	5129	6.499172	ACTCAAACTAAAAGAGCAAAAGCTC	58.501	36.000	9.34	9.34	37.11	4.09
5180	5271	8.730680	CAAAACTAGTAAATGTTACAGAGCCAT	58.269	33.333	0.00	0.00	0.00	4.40
5204	5295	2.028130	ACATTCAAAGCACGGTTCCAA	58.972	42.857	0.00	0.00	0.00	3.53
5213	5304	1.614903	CCTCAGCCAACATTCAAAGCA	59.385	47.619	0.00	0.00	0.00	3.91
5284	5375	5.009710	GGCCAAAATACTCCTTAATGTAGGC	59.990	44.000	0.00	0.00	35.15	3.93
5285	5376	5.535030	GGGCCAAAATACTCCTTAATGTAGG	59.465	44.000	4.39	0.00	36.59	3.18
5308	5399	3.900941	AGTTTTGCGACATAAAAGCAGG	58.099	40.909	0.00	0.00	42.19	4.85
5382	5576	3.853671	GCATCCACACGTTTCATGATTTC	59.146	43.478	0.00	0.00	0.00	2.17
5460	5654	7.326063	GCATAAGTTCATTATTTCGGGCATTAC	59.674	37.037	0.00	0.00	31.40	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.