AutoCloner

Multiple sequence alignment - TraesCS3B01G085600

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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	TraesCS3B01G085600	chr3B	100.000	2801	0	0	1	2801	54141270	54138470	0.000000e+00	5173.0
1	TraesCS3B01G085600	chr3B	94.111	2802	162	2	1	2801	54132254	54135053	0.000000e+00	4257.0
2	TraesCS3B01G085600	chr3B	92.893	2617	165	8	195	2801	53943657	53946262	0.000000e+00	3783.0
3	TraesCS3B01G085600	chr3B	95.766	2291	80	4	1	2291	53992224	53989951	0.000000e+00	3677.0
4	TraesCS3B01G085600	chr3B	91.736	2662	189	13	154	2801	54293484	54296128	0.000000e+00	3668.0
5	TraesCS3B01G085600	chr3B	96.567	1340	45	1	1	1339	54065374	54064035	0.000000e+00	2218.0
6	TraesCS3B01G085600	chr3B	92.787	1331	93	2	1	1331	54062690	54064017	0.000000e+00	1923.0
7	TraesCS3B01G085600	chr3B	96.970	33	1	0	3	35	54293416	54293448	3.900000e-04	56.5
8	TraesCS3B01G085600	chr3D	92.665	2822	173	12	7	2801	31762589	31765403	0.000000e+00	4034.0
9	TraesCS3B01G085600	chr5A	86.349	608	45	7	236	834	667063169	667062591	1.830000e-176	628.0
10	TraesCS3B01G085600	chr2D	86.631	374	43	3	22	393	19878676	19879044	9.340000e-110	407.0
11	TraesCS3B01G085600	chr6D	89.492	295	23	4	20	311	435557475	435557186	1.590000e-97	366.0
12	TraesCS3B01G085600	chr1D	87.814	279	29	3	201	479	20356618	20356345	3.480000e-84	322.0
13	TraesCS3B01G085600	chr7B	85.484	310	38	3	28	336	31433867	31433564	1.620000e-82	316.0
14	TraesCS3B01G085600	chrUn	85.507	276	21	6	563	834	30407640	30407380	1.280000e-68	270.0

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	TraesCS3B01G085600	chr3B	54138470	54141270	2800	True	5173.00	5173	100.000	1	2801	1	chr3B.!!$R3	2800
1	TraesCS3B01G085600	chr3B	54132254	54135053	2799	False	4257.00	4257	94.111	1	2801	1	chr3B.!!$F3	2800
2	TraesCS3B01G085600	chr3B	53943657	53946262	2605	False	3783.00	3783	92.893	195	2801	1	chr3B.!!$F1	2606
3	TraesCS3B01G085600	chr3B	53989951	53992224	2273	True	3677.00	3677	95.766	1	2291	1	chr3B.!!$R1	2290
4	TraesCS3B01G085600	chr3B	54064035	54065374	1339	True	2218.00	2218	96.567	1	1339	1	chr3B.!!$R2	1338
5	TraesCS3B01G085600	chr3B	54062690	54064017	1327	False	1923.00	1923	92.787	1	1331	1	chr3B.!!$F2	1330
6	TraesCS3B01G085600	chr3B	54293416	54296128	2712	False	1862.25	3668	94.353	3	2801	2	chr3B.!!$F4	2798
7	TraesCS3B01G085600	chr3D	31762589	31765403	2814	False	4034.00	4034	92.665	7	2801	1	chr3D.!!$F1	2794
8	TraesCS3B01G085600	chr5A	667062591	667063169	578	True	628.00	628	86.349	236	834	1	chr5A.!!$R1	598

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
93	107	0.946221	GTGTGAGGCGACAGACAAGG	60.946	60.0	0.0	0.0	34.8	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1943	1987	0.325671	TTTCCCAAGTGGCCCAAACA	60.326	50.0	0.0	0.0	0.0	2.83	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
88	102	1.212751	CATCGTGTGAGGCGACAGA	59.787	57.895	0.00	0.00	41.33	3.41
89	103	1.073216	CATCGTGTGAGGCGACAGAC	61.073	60.000	0.00	5.32	41.33	3.51
90	104	1.524008	ATCGTGTGAGGCGACAGACA	61.524	55.000	13.07	0.00	41.33	3.41
91	105	1.299850	CGTGTGAGGCGACAGACAA	60.300	57.895	13.07	0.00	34.42	3.18
92	106	1.278172	CGTGTGAGGCGACAGACAAG	61.278	60.000	13.07	0.00	34.42	3.16
93	107	0.946221	GTGTGAGGCGACAGACAAGG	60.946	60.000	0.00	0.00	34.80	3.61
94	108	2.029844	GTGAGGCGACAGACAAGGC	61.030	63.158	0.00	0.00	0.00	4.35
95	109	2.811317	GAGGCGACAGACAAGGCG	60.811	66.667	0.00	0.00	35.47	5.52
96	110	4.379243	AGGCGACAGACAAGGCGG	62.379	66.667	0.00	0.00	35.47	6.13
97	111	4.681978	GGCGACAGACAAGGCGGT	62.682	66.667	0.00	0.00	0.00	5.68
98	112	3.414700	GCGACAGACAAGGCGGTG	61.415	66.667	0.00	0.00	0.00	4.94
99	113	2.738521	CGACAGACAAGGCGGTGG	60.739	66.667	0.00	0.00	0.00	4.61
152	166	2.347490	GGAAGCAGGGCGAGACAA	59.653	61.111	0.00	0.00	0.00	3.18
415	444	6.198216	CGATCTGTTAAAGTTGGTGGTTTTTG	59.802	38.462	0.00	0.00	0.00	2.44
506	535	4.089408	TGTACACAAGGGTAGGGAAAAC	57.911	45.455	0.00	0.00	0.00	2.43
583	613	7.384115	TCTGTCAATTTAACCTTGTTCTCGTAG	59.616	37.037	0.00	0.00	0.00	3.51
713	745	7.467557	ACTGTGCATTATTTTGTTGTTTCTG	57.532	32.000	0.00	0.00	0.00	3.02
716	748	8.932945	TGTGCATTATTTTGTTGTTTCTGTAA	57.067	26.923	0.00	0.00	0.00	2.41
776	808	9.512588	ACATTATCTGACTCACTTCATCTTTTT	57.487	29.630	0.00	0.00	0.00	1.94
1118	1153	1.172180	CCTTTGAGGGCAAGTTCGCA	61.172	55.000	0.00	0.00	35.04	5.10
1142	1177	2.481952	CCTCTCTTTGCAAGAAGTTCGG	59.518	50.000	0.00	1.39	37.02	4.30
1149	1184	1.168714	GCAAGAAGTTCGGCATCCTT	58.831	50.000	15.04	0.00	0.00	3.36
1274	1309	2.235898	GTGATCTGGTTCTCTTCAGGCT	59.764	50.000	0.00	0.00	0.00	4.58
1449	1484	1.601759	GAAGGCTGTGGCTGAGCAA	60.602	57.895	6.82	0.00	38.81	3.91
1463	1498	2.609459	CTGAGCAACGTGTGTTCTTTCT	59.391	45.455	12.83	0.00	38.25	2.52
1599	1634	0.582005	GTGTGTTCCGCTCACTTGTC	59.418	55.000	0.00	0.00	38.25	3.18
1605	1640	0.539669	TCCGCTCACTTGTCTCTGGA	60.540	55.000	0.00	0.00	0.00	3.86
1715	1750	5.306532	GATGCTGTCATCACATTCAACTT	57.693	39.130	7.05	0.00	46.44	2.66
1803	1838	5.013599	GCCCCAGATCTTATACCTCTGATTT	59.986	44.000	0.00	0.00	38.96	2.17
1861	1896	5.163478	GGCAAAGCATTCTATGAGGTGAATT	60.163	40.000	0.00	0.00	31.35	2.17
1943	1987	1.306141	TCCGCTCTGATGGGGAACT	60.306	57.895	9.37	0.00	44.43	3.01
1995	2039	9.178758	AGTTTCACCATTCACTCCTATATTTTC	57.821	33.333	0.00	0.00	0.00	2.29
2026	2070	1.067173	TGGGCCATGGGATGAGCATA	61.067	55.000	15.13	0.00	0.00	3.14
2029	2073	1.005097	GGCCATGGGATGAGCATATGA	59.995	52.381	15.13	0.00	0.00	2.15
2052	2096	4.652881	ACCATCACATCTGAAGAGCTATGA	59.347	41.667	0.00	0.00	0.00	2.15
2151	2195	4.393371	GCATACTTTTTGGTCTCAGAGTCC	59.607	45.833	6.76	6.76	0.00	3.85
2208	2252	8.283291	GTCACAATTCAGTTAAGTACCAAGAAG	58.717	37.037	0.00	0.00	0.00	2.85
2222	2266	2.069273	CAAGAAGGTGCTCGTAGTTGG	58.931	52.381	0.00	0.00	0.00	3.77
2295	2339	5.667539	TGATCGAGGAAAAGTCTCATCTT	57.332	39.130	0.00	0.00	0.00	2.40
2445	2491	5.237344	AGTGTTGGATAATCGAAATAGCTGC	59.763	40.000	0.00	0.00	0.00	5.25
2539	2586	7.148623	CCTCTTAACTTCGTGAATAGGTTGTTC	60.149	40.741	0.00	0.00	0.00	3.18
2582	2629	4.335647	AGCCCTCGTTGCCTGGTG	62.336	66.667	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	102	2.764637	GATTCCACCCACCGCCTTGT	62.765	60.000	0.00	0.00	0.00	3.16
89	103	2.035626	ATTCCACCCACCGCCTTG	59.964	61.111	0.00	0.00	0.00	3.61
90	104	2.231380	AGATTCCACCCACCGCCTT	61.231	57.895	0.00	0.00	0.00	4.35
91	105	2.610859	AGATTCCACCCACCGCCT	60.611	61.111	0.00	0.00	0.00	5.52
92	106	2.438434	CAGATTCCACCCACCGCC	60.438	66.667	0.00	0.00	0.00	6.13
93	107	3.134127	GCAGATTCCACCCACCGC	61.134	66.667	0.00	0.00	0.00	5.68
94	108	1.002134	AAGCAGATTCCACCCACCG	60.002	57.895	0.00	0.00	0.00	4.94
95	109	0.038166	TGAAGCAGATTCCACCCACC	59.962	55.000	0.00	0.00	37.08	4.61
96	110	1.541588	GTTGAAGCAGATTCCACCCAC	59.458	52.381	0.00	0.00	37.08	4.61
97	111	1.144708	TGTTGAAGCAGATTCCACCCA	59.855	47.619	0.47	0.00	37.08	4.51
98	112	1.541588	GTGTTGAAGCAGATTCCACCC	59.458	52.381	0.47	0.00	37.08	4.61
99	113	1.541588	GGTGTTGAAGCAGATTCCACC	59.458	52.381	10.08	10.08	40.66	4.61
152	166	3.692406	GGTGAAGGGGTCGAGCGT	61.692	66.667	8.77	0.00	0.00	5.07
415	444	0.454196	ACAACAACGTTTGCCACTCC	59.546	50.000	0.00	0.00	0.00	3.85
506	535	2.001872	TGTACAATGACGAGCATGCTG	58.998	47.619	28.27	19.26	37.28	4.41
583	613	1.202336	CGGATTGCAGATTGCCCTTTC	60.202	52.381	0.00	0.00	44.23	2.62
713	745	7.756722	GCAAGATGTCATAATAATGCCCATTAC	59.243	37.037	3.04	0.00	36.24	1.89
716	748	5.776208	TGCAAGATGTCATAATAATGCCCAT	59.224	36.000	0.00	0.00	32.76	4.00
973	1008	7.882791	TGATCAGCAGATTAAAACAGGTTTAGA	59.117	33.333	0.00	0.00	33.22	2.10
1142	1177	0.820226	GGCAAGGAGGAAAAGGATGC	59.180	55.000	0.00	0.00	0.00	3.91
1149	1184	2.351276	GGCTCGGCAAGGAGGAAA	59.649	61.111	1.58	0.00	34.56	3.13
1449	1484	2.093658	AGTGTCCAGAAAGAACACACGT	60.094	45.455	7.52	0.00	44.46	4.49
1463	1498	2.457598	GGATGAGTCCTACAGTGTCCA	58.542	52.381	0.00	0.00	41.60	4.02
1599	1634	2.621998	GCCATCACCATCATTTCCAGAG	59.378	50.000	0.00	0.00	0.00	3.35
1605	1640	3.118186	CCCATTTGCCATCACCATCATTT	60.118	43.478	0.00	0.00	0.00	2.32
1715	1750	8.363390	TGTAATAGTTGATCCAACAAATGCAAA	58.637	29.630	11.73	0.00	45.66	3.68
1803	1838	3.972133	TCTAGGACGGTCAACAATAGGA	58.028	45.455	10.76	0.00	0.00	2.94
1861	1896	3.285982	CATGGCGCACACACCACA	61.286	61.111	10.83	0.00	39.19	4.17
1943	1987	0.325671	TTTCCCAAGTGGCCCAAACA	60.326	50.000	0.00	0.00	0.00	2.83
1995	2039	1.350351	CATGGCCCATCTTAGGAGGAG	59.650	57.143	0.00	0.00	0.00	3.69
2026	2070	3.455177	AGCTCTTCAGATGTGATGGTCAT	59.545	43.478	5.99	0.00	30.85	3.06
2029	2073	4.652881	TCATAGCTCTTCAGATGTGATGGT	59.347	41.667	5.99	2.86	31.81	3.55
2052	2096	8.097662	GGCAGACCTATATATCTGTTTAAAGCT	58.902	37.037	12.72	0.00	43.60	3.74
2151	2195	3.485877	CCTTGCTATTTTCTTCTTCGGCG	60.486	47.826	0.00	0.00	0.00	6.46
2208	2252	0.249398	ATGGACCAACTACGAGCACC	59.751	55.000	0.00	0.00	0.00	5.01
2222	2266	7.716998	TGCCTTCTTCTCTTGAAATATATGGAC	59.283	37.037	0.00	0.00	0.00	4.02
2295	2339	5.045578	CCTGGAGGAAATGAAACTCCTTAGA	60.046	44.000	10.86	0.00	42.34	2.10
2412	2458	6.820335	TCGATTATCCAACACTGAGATCAAT	58.180	36.000	0.00	0.00	0.00	2.57
2413	2459	6.220726	TCGATTATCCAACACTGAGATCAA	57.779	37.500	0.00	0.00	0.00	2.57
2454	2501	4.065088	TCAGTGGACTTTGCTATTGTCAC	58.935	43.478	0.00	0.00	32.84	3.67
2539	2586	7.067737	TGGAGTTTTGTTCTAAAACACTAAGGG	59.932	37.037	15.15	0.00	44.90	3.95
2646	2695	8.023128	GCTTCAATTTTACATGCTCACTTTCTA	58.977	33.333	0.00	0.00	0.00	2.10
2695	2744	0.603707	TGGTGCTGCAACAGAGCTAC	60.604	55.000	17.83	0.00	37.35	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.