AutoCloner

Multiple sequence alignment - TraesCS3B01G379100

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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	TraesCS3B01G379100	chr3B	100.000	2327	0	0	1	2327	597047394	597049720	0.000000e+00	4298.0
1	TraesCS3B01G379100	chr3B	97.091	275	7	1	2038	2311	482184299	482184573	1.630000e-126	462.0
2	TraesCS3B01G379100	chr3B	96.000	275	10	1	2038	2311	712733574	712733848	1.640000e-121	446.0
3	TraesCS3B01G379100	chr3D	89.155	1254	77	21	522	1726	454500249	454501492	0.000000e+00	1507.0
4	TraesCS3B01G379100	chr3D	90.189	530	44	5	1	524	454499401	454499928	0.000000e+00	684.0
5	TraesCS3B01G379100	chr3D	96.078	51	2	0	1769	1819	454501512	454501562	1.480000e-12	84.2
6	TraesCS3B01G379100	chr3A	87.192	1382	82	40	422	1726	596501538	596502901	0.000000e+00	1483.0
7	TraesCS3B01G379100	chr3A	92.063	441	22	3	1	437	596501053	596501484	1.980000e-170	608.0
8	TraesCS3B01G379100	chr3A	92.342	222	11	3	1819	2039	239391	239175	6.240000e-81	311.0
9	TraesCS3B01G379100	chr6B	96.071	280	10	1	2036	2314	101924512	101924233	2.730000e-124	455.0
10	TraesCS3B01G379100	chr6B	92.444	225	11	6	1816	2039	256448357	256448576	1.340000e-82	316.0
11	TraesCS3B01G379100	chr6B	92.105	228	11	4	1813	2039	548176932	548176711	4.830000e-82	315.0
12	TraesCS3B01G379100	chr6B	91.556	225	12	4	1817	2039	460510189	460509970	1.040000e-78	303.0
13	TraesCS3B01G379100	chr4B	94.539	293	15	1	2036	2327	532291965	532292257	3.530000e-123	451.0
14	TraesCS3B01G379100	chr1B	95.423	284	11	2	2033	2314	348605761	348605478	3.530000e-123	451.0
15	TraesCS3B01G379100	chr7B	95.070	284	12	2	2033	2314	497853493	497853210	1.640000e-121	446.0
16	TraesCS3B01G379100	chr7B	91.892	222	12	4	1819	2039	3093973	3093757	2.900000e-79	305.0
17	TraesCS3B01G379100	chr5B	95.070	284	12	2	2033	2314	403644472	403644755	1.640000e-121	446.0
18	TraesCS3B01G379100	chr5B	93.537	294	18	1	2035	2327	91084944	91084651	9.870000e-119	436.0
19	TraesCS3B01G379100	chr5B	91.964	224	11	5	1817	2039	272239126	272238909	8.080000e-80	307.0
20	TraesCS3B01G379100	chr5B	91.518	224	13	3	1817	2039	537787810	537787592	1.040000e-78	303.0
21	TraesCS3B01G379100	chrUn	95.357	280	12	1	2036	2314	69154142	69153863	5.900000e-121	444.0
22	TraesCS3B01G379100	chr6D	95.357	280	12	1	2036	2314	444199922	444200201	5.900000e-121	444.0
23	TraesCS3B01G379100	chr1D	95.357	280	12	1	2036	2314	289804551	289804830	5.900000e-121	444.0
24	TraesCS3B01G379100	chr4A	90.948	232	14	4	1810	2039	672288305	672288079	2.900000e-79	305.0
25	TraesCS3B01G379100	chr2D	91.518	224	13	3	1817	2039	476698491	476698273	1.040000e-78	303.0

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	TraesCS3B01G379100	chr3B	597047394	597049720	2326	False	4298.0	4298	100.000000	1	2327	1	chr3B.!!$F2	2326
1	TraesCS3B01G379100	chr3D	454499401	454501562	2161	False	758.4	1507	91.807333	1	1819	3	chr3D.!!$F1	1818
2	TraesCS3B01G379100	chr3A	596501053	596502901	1848	False	1045.5	1483	89.627500	1	1726	2	chr3A.!!$F1	1725

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
829	1235	0.107116	TCTCTACTCCCGAGCTCACC	60.107	60.0	15.4	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1846	2325	0.033796	ATGTGGCATGCTTAGCACCT	60.034	50.0	18.92	7.18	43.04	4.0	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
195	196	0.394938	TCCAAAGTTGACCGCAGCTA	59.605	50.000	0.00	0.00	34.21	3.32
220	221	4.202253	TGGATGGTGACTGATGCTGTATAC	60.202	45.833	0.00	0.00	0.00	1.47
221	222	4.039730	GGATGGTGACTGATGCTGTATACT	59.960	45.833	4.17	0.00	0.00	2.12
249	254	4.208047	CGAAAGCTGACGGATAGATTCTTG	59.792	45.833	5.12	0.00	0.00	3.02
257	264	4.504858	ACGGATAGATTCTTGCTTTTCGT	58.495	39.130	0.00	0.00	0.00	3.85
304	311	2.592102	ATGCTCCTGGTTTGTCATGT	57.408	45.000	0.00	0.00	0.00	3.21
336	346	5.100943	GGACTTTAGGTCGTCAGTCATTAC	58.899	45.833	0.00	0.00	45.35	1.89
395	405	6.150641	CACTCCAACAGATGTCATCTTTCATT	59.849	38.462	12.88	3.08	37.58	2.57
445	524	7.839680	AGAAGAAGAAGAAGAAAGTCTCTCT	57.160	36.000	0.00	0.00	31.02	3.10
463	542	6.950842	TCTCTCTTGATTATTTTGAGAGGCA	58.049	36.000	15.41	0.00	46.20	4.75
589	991	1.000938	GCTGGAGCCAGTTCAAAAGTG	60.001	52.381	17.23	0.00	45.24	3.16
641	1043	1.383963	ACCTGTAGAGTCCCTCTCCA	58.616	55.000	0.00	0.00	43.71	3.86
705	1107	2.774007	CTTTAAAGCGAACCGATGCTG	58.226	47.619	1.47	0.00	41.46	4.41
753	1155	3.182967	CAAAAGTTTGCCGTTGCTTGTA	58.817	40.909	0.00	0.00	38.71	2.41
758	1160	3.317993	AGTTTGCCGTTGCTTGTAGAAAT	59.682	39.130	0.00	0.00	38.71	2.17
768	1170	6.147164	CGTTGCTTGTAGAAATGAGAAAGGTA	59.853	38.462	0.00	0.00	0.00	3.08
777	1179	3.895232	ATGAGAAAGGTACAGACGCAT	57.105	42.857	0.00	0.00	0.00	4.73
802	1204	8.582657	TTATATAAGCTCCAGGATACAGAGAC	57.417	38.462	0.00	0.00	40.62	3.36
818	1224	5.007682	ACAGAGACTGAAACCTCTCTACTC	58.992	45.833	5.76	0.00	41.15	2.59
820	1226	3.697542	GAGACTGAAACCTCTCTACTCCC	59.302	52.174	0.00	0.00	31.74	4.30
823	1229	2.685897	CTGAAACCTCTCTACTCCCGAG	59.314	54.545	0.00	0.00	0.00	4.63
824	1230	1.406180	GAAACCTCTCTACTCCCGAGC	59.594	57.143	0.00	0.00	0.00	5.03
828	1234	1.305201	CTCTCTACTCCCGAGCTCAC	58.695	60.000	15.40	0.00	0.00	3.51
829	1235	0.107116	TCTCTACTCCCGAGCTCACC	60.107	60.000	15.40	0.00	0.00	4.02
831	1237	1.451567	CTACTCCCGAGCTCACCGA	60.452	63.158	15.40	4.40	0.00	4.69

Showing 1 to 25 of 448 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
29	30	3.499737	CCTCGTGCATCCCAACGC	61.500	66.667	0.00	0.00	4.84
140	141	3.120580	GCCATTTGCAACAATTTCTTCGG	60.121	43.478	0.00	40.77	4.30
178	179	2.414559	CCAATAGCTGCGGTCAACTTTG	60.415	50.000	0.00	0.00	2.77
195	196	2.025605	ACAGCATCAGTCACCATCCAAT	60.026	45.455	0.00	0.00	3.16
220	221	1.640428	TCCGTCAGCTTTCGCATAAG	58.360	50.000	2.24	39.10	1.73
221	222	2.309528	ATCCGTCAGCTTTCGCATAA	57.690	45.000	2.24	39.10	1.90
304	311	2.288825	CGACCTAAAGTCCTGTGCAGAA	60.289	50.000	0.02	43.08	3.02
336	346	9.829507	AGATGATCTGAATAAAACTGGACTAAG	57.170	33.333	0.00	0.00	2.18
360	370	3.572642	TCTGTTGGAGTGTCAAGGTAGA	58.427	45.455	0.00	0.00	2.59
395	405	7.644490	AGTAACGTGCAATACAAAAAGAATCA	58.356	30.769	0.00	0.00	2.57
405	415	6.916440	TCTTCTTCTAGTAACGTGCAATACA	58.084	36.000	0.00	0.00	2.29
445	524	6.721318	AGTAGGTGCCTCTCAAAATAATCAA	58.279	36.000	0.00	0.00	2.57
463	542	6.901081	TTCATCATCATCGTCATAGTAGGT	57.099	37.500	0.00	0.00	3.08
491	570	4.265073	ACCAGAGGCTTACACATGATTTC	58.735	43.478	0.00	0.00	2.17
589	991	1.538276	CATGAAACGCGCAAGAATCC	58.462	50.000	5.73	43.02	3.01
641	1043	5.535333	CATTGGAGCATTTCTTTCACACTT	58.465	37.500	0.00	0.00	3.16
705	1107	1.333619	ACCGTGAATGACAAAGCACAC	59.666	47.619	0.00	0.00	3.82
753	1155	4.246458	GCGTCTGTACCTTTCTCATTTCT	58.754	43.478	0.00	0.00	2.52
758	1160	3.678056	AATGCGTCTGTACCTTTCTCA	57.322	42.857	0.00	0.00	3.27
768	1170	5.468540	TGGAGCTTATATAATGCGTCTGT	57.531	39.130	0.00	0.00	3.41
777	1179	8.394822	AGTCTCTGTATCCTGGAGCTTATATAA	58.605	37.037	1.52	0.00	0.98
802	1204	2.685897	CTCGGGAGTAGAGAGGTTTCAG	59.314	54.545	0.00	37.93	3.02
818	1224	1.030488	TACTTCTCGGTGAGCTCGGG	61.030	60.000	9.64	0.00	5.14
820	1226	1.469308	ACTTACTTCTCGGTGAGCTCG	59.531	52.381	9.64	0.00	5.03
823	1229	1.272769	ACCACTTACTTCTCGGTGAGC	59.727	52.381	0.00	32.12	4.26

Showing 1 to 25 of 428 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.