AutoCloner

Multiple sequence alignment - TraesCS3D01G297100

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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	TraesCS3D01G297100	chr3D	100.000	2596	0	0	1	2596	410899024	410901619	0.000000e+00	4795
1	TraesCS3D01G297100	chr3D	94.613	297	7	2	2300	2596	527511338	527511625	3.940000e-123	451
2	TraesCS3D01G297100	chr2D	94.647	2055	80	8	568	2596	331197175	331199225	0.000000e+00	3158
3	TraesCS3D01G297100	chr2D	95.960	297	12	0	2300	2596	218366382	218366678	1.400000e-132	483
4	TraesCS3D01G297100	chr5D	94.393	2051	80	8	572	2596	336262624	336264665	0.000000e+00	3118
5	TraesCS3D01G297100	chr5D	94.149	2051	88	16	572	2596	520497539	520495495	0.000000e+00	3094
6	TraesCS3D01G297100	chr5D	93.520	571	34	3	1	570	193739599	193740167	0.000000e+00	846
7	TraesCS3D01G297100	chr5D	93.019	573	39	1	1	572	266405531	266406103	0.000000e+00	835
8	TraesCS3D01G297100	chr5D	92.995	571	39	1	3	572	257144274	257144844	0.000000e+00	832
9	TraesCS3D01G297100	chr1A	94.363	2040	98	13	562	2596	71245448	71243421	0.000000e+00	3114
10	TraesCS3D01G297100	chr7D	94.344	2051	77	12	572	2596	574727118	574725081	0.000000e+00	3109
11	TraesCS3D01G297100	chr7D	93.543	573	35	2	1	572	518002488	518001917	0.000000e+00	852
12	TraesCS3D01G297100	chr7D	93.194	573	37	2	1	572	266992887	266993458	0.000000e+00	841
13	TraesCS3D01G297100	chr7D	93.007	572	39	1	1	571	349715706	349716277	0.000000e+00	833
14	TraesCS3D01G297100	chr3A	93.898	2032	109	13	572	2596	696312540	696310517	0.000000e+00	3051
15	TraesCS3D01G297100	chr3A	94.158	291	17	0	2306	2596	706124066	706123776	6.590000e-121	444
16	TraesCS3D01G297100	chr5A	93.517	2036	111	16	566	2596	30204981	30207000	0.000000e+00	3009
17	TraesCS3D01G297100	chr5A	93.939	297	11	2	2300	2596	553436179	553435890	2.370000e-120	442
18	TraesCS3D01G297100	chr2A	93.415	2035	114	15	568	2596	659814579	659816599	0.000000e+00	2998
19	TraesCS3D01G297100	chrUn	93.120	2035	113	13	568	2596	87140323	87142336	0.000000e+00	2957
20	TraesCS3D01G297100	chr6D	93.357	572	36	2	1	571	222287619	222287049	0.000000e+00	845
21	TraesCS3D01G297100	chr4D	93.170	571	36	3	1	570	324052979	324053547	0.000000e+00	835
22	TraesCS3D01G297100	chr4D	92.334	574	40	4	1	572	400884799	400885370	0.000000e+00	813

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	TraesCS3D01G297100	chr3D	410899024	410901619	2595	False	4795	4795	100.000	1	2596	1	chr3D.!!$F1	2595
1	TraesCS3D01G297100	chr2D	331197175	331199225	2050	False	3158	3158	94.647	568	2596	1	chr2D.!!$F2	2028
2	TraesCS3D01G297100	chr5D	336262624	336264665	2041	False	3118	3118	94.393	572	2596	1	chr5D.!!$F4	2024
3	TraesCS3D01G297100	chr5D	520495495	520497539	2044	True	3094	3094	94.149	572	2596	1	chr5D.!!$R1	2024
4	TraesCS3D01G297100	chr5D	193739599	193740167	568	False	846	846	93.520	1	570	1	chr5D.!!$F1	569
5	TraesCS3D01G297100	chr5D	266405531	266406103	572	False	835	835	93.019	1	572	1	chr5D.!!$F3	571
6	TraesCS3D01G297100	chr5D	257144274	257144844	570	False	832	832	92.995	3	572	1	chr5D.!!$F2	569
7	TraesCS3D01G297100	chr1A	71243421	71245448	2027	True	3114	3114	94.363	562	2596	1	chr1A.!!$R1	2034
8	TraesCS3D01G297100	chr7D	574725081	574727118	2037	True	3109	3109	94.344	572	2596	1	chr7D.!!$R2	2024
9	TraesCS3D01G297100	chr7D	518001917	518002488	571	True	852	852	93.543	1	572	1	chr7D.!!$R1	571
10	TraesCS3D01G297100	chr7D	266992887	266993458	571	False	841	841	93.194	1	572	1	chr7D.!!$F1	571
11	TraesCS3D01G297100	chr7D	349715706	349716277	571	False	833	833	93.007	1	571	1	chr7D.!!$F2	570
12	TraesCS3D01G297100	chr3A	696310517	696312540	2023	True	3051	3051	93.898	572	2596	1	chr3A.!!$R1	2024
13	TraesCS3D01G297100	chr5A	30204981	30207000	2019	False	3009	3009	93.517	566	2596	1	chr5A.!!$F1	2030
14	TraesCS3D01G297100	chr2A	659814579	659816599	2020	False	2998	2998	93.415	568	2596	1	chr2A.!!$F1	2028
15	TraesCS3D01G297100	chrUn	87140323	87142336	2013	False	2957	2957	93.120	568	2596	1	chrUn.!!$F1	2028
16	TraesCS3D01G297100	chr6D	222287049	222287619	570	True	845	845	93.357	1	571	1	chr6D.!!$R1	570
17	TraesCS3D01G297100	chr4D	324052979	324053547	568	False	835	835	93.170	1	570	1	chr4D.!!$F1	569
18	TraesCS3D01G297100	chr4D	400884799	400885370	571	False	813	813	92.334	1	572	1	chr4D.!!$F2	571

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
324	325	0.246360	TGACGTGAGCCATGACGATT	59.754	50.0	11.17	0.0	38.94	3.34	F
1119	1127	0.472471	GGAGGGTTTCTCACACACCA	59.528	55.0	0.00	0.0	44.19	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1264	1274	0.035881	CAGAGTCTTGGCCAGAGCAA	59.964	55.000	5.11	0.00	42.56	3.91	R
2018	2036	1.134907	GCTGAGGCACATTTTCCATGG	60.135	52.381	4.97	4.97	38.54	3.66	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
207	208	0.693049	AAGGCATTCAAGACCCTCGT	59.307	50.000	0.00	0.00	0.00	4.18
324	325	0.246360	TGACGTGAGCCATGACGATT	59.754	50.000	11.17	0.00	38.94	3.34
388	390	2.671070	GTGCTAAGGAGGCCAGCA	59.329	61.111	10.49	10.49	42.77	4.41
515	518	0.825010	CAGCACCAGAGCCCTTTTGT	60.825	55.000	0.00	0.00	34.23	2.83
553	556	7.476540	TTTTGTCAGGATAGCTTGTACTAGA	57.523	36.000	8.60	0.00	0.00	2.43
602	605	3.772387	TCATTTTGCCCTCAATGGTGTA	58.228	40.909	0.00	0.00	32.17	2.90
659	662	1.351017	TCAGTTTTGCCCCTAGTCTGG	59.649	52.381	0.00	0.00	0.00	3.86
724	727	1.633945	ACCTTTTGACTCGGCCCTTAT	59.366	47.619	0.00	0.00	0.00	1.73
776	779	2.106477	TATTCAGACCGTTGCATGCA	57.894	45.000	18.46	18.46	0.00	3.96
810	813	3.184683	GCAGAGAGCCGTTGAGCG	61.185	66.667	0.00	0.00	38.01	5.03
863	867	4.662961	CAGCAGCGGTGACCACGA	62.663	66.667	20.69	0.00	32.22	4.35
903	911	1.450491	CCACGGCGAGAGAGAGAGA	60.450	63.158	16.62	0.00	0.00	3.10
904	912	0.817634	CCACGGCGAGAGAGAGAGAT	60.818	60.000	16.62	0.00	0.00	2.75
1085	1093	4.293648	CGTCTGTCCGTGGTGCCA	62.294	66.667	0.00	0.00	0.00	4.92
1119	1127	0.472471	GGAGGGTTTCTCACACACCA	59.528	55.000	0.00	0.00	44.19	4.17
1236	1246	4.037923	GGTTGATCTGTTTGGTGTTCATGT	59.962	41.667	0.00	0.00	0.00	3.21
1264	1274	2.341846	TGCTTCTTTCTTTGGGTCGT	57.658	45.000	0.00	0.00	0.00	4.34
1313	1323	3.336468	ACTGCAAGAAGAGCATGAAGAG	58.664	45.455	0.00	0.00	41.82	2.85
1348	1358	1.667830	CACGAATGGCAGTGGTCGT	60.668	57.895	0.00	6.08	46.95	4.34
1370	1380	0.319555	CACGAGCTCCGGAAGAACAA	60.320	55.000	5.23	0.00	43.93	2.83
1397	1407	2.553268	GAAGCACGCACTGACAGC	59.447	61.111	1.25	0.00	0.00	4.40
1406	1416	1.518133	CACTGACAGCGAGCTAGCC	60.518	63.158	15.76	1.79	38.01	3.93
1469	1479	5.045942	TGAAGATCAAGCACTACCAATACCA	60.046	40.000	0.00	0.00	0.00	3.25
1547	1557	4.757594	TGAAAATGTATGGAAAGGCATGC	58.242	39.130	9.90	9.90	0.00	4.06
1716	1729	7.432869	TCGGAAACTTTTGATCAATGAAATGT	58.567	30.769	9.40	0.00	0.00	2.71
1775	1790	1.203038	TCTTGGGCCAAATTCAGAGCA	60.203	47.619	21.28	0.00	0.00	4.26
1780	1795	3.117398	TGGGCCAAATTCAGAGCATAGAT	60.117	43.478	2.13	0.00	0.00	1.98
1811	1826	2.704065	GGCTAGACTAATGGGCCAACTA	59.296	50.000	11.89	4.22	42.08	2.24
2018	2036	9.739786	CGTGATTTAAATTAAAGACCAAAATGC	57.260	29.630	1.43	0.00	0.00	3.56
2081	2100	6.430616	CCTGGTGCCAAAATAAATGAACATTT	59.569	34.615	15.41	15.41	42.95	2.32
2082	2101	7.040548	CCTGGTGCCAAAATAAATGAACATTTT	60.041	33.333	16.12	4.33	40.99	1.82
2211	2234	1.599797	GTGGTGTTTAGGGCTGCGT	60.600	57.895	0.00	0.00	0.00	5.24
2220	2243	1.481901	TAGGGCTGCGTTGGTAACCA	61.482	55.000	0.00	0.00	0.00	3.67
2291	2315	7.426929	ACATAGTGAGACTGTGAAATTTGTC	57.573	36.000	7.40	0.00	39.34	3.18
2515	2592	2.610859	GGCTTCTCACCCCCTCCA	60.611	66.667	0.00	0.00	0.00	3.86
2560	2638	4.653806	GTTCTCGAACTTCATGACTTGG	57.346	45.455	0.00	0.00	38.25	3.61
2564	2642	4.511454	TCTCGAACTTCATGACTTGGTTTG	59.489	41.667	0.00	3.28	0.00	2.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	1.270625	CCAAAGGTCAAGTACGGAGCA	60.271	52.381	17.85	0.00	35.30	4.26
412	414	1.681264	CCGATATGGAAACCTTTGCCC	59.319	52.381	0.00	0.00	42.00	5.36
498	500	1.168714	CTACAAAAGGGCTCTGGTGC	58.831	55.000	0.00	0.00	0.00	5.01
524	527	1.017387	GCTATCCTGACAAAAGCGGG	58.983	55.000	0.00	0.00	0.00	6.13
602	605	3.181445	TGAGGGTAAAACTGAGCACATGT	60.181	43.478	0.00	0.00	0.00	3.21
776	779	2.765969	CTGGGTCCCACAAGCCAT	59.234	61.111	6.47	0.00	45.28	4.40
810	813	1.598130	ACACTTGCAACGGCTCTCC	60.598	57.895	0.00	0.00	41.91	3.71
863	867	4.406173	CGCCGTGCTCTCTGTCGT	62.406	66.667	0.00	0.00	0.00	4.34
903	911	1.344953	TAGCTTCCCACCGCCATGAT	61.345	55.000	0.00	0.00	0.00	2.45
904	912	1.971505	CTAGCTTCCCACCGCCATGA	61.972	60.000	0.00	0.00	0.00	3.07
997	1005	1.407989	GGAGCTTGAGGAAGACATGGG	60.408	57.143	0.00	0.00	0.00	4.00
1236	1246	4.761739	CCAAAGAAAGAAGCATGTCACCTA	59.238	41.667	0.00	0.00	0.00	3.08
1264	1274	0.035881	CAGAGTCTTGGCCAGAGCAA	59.964	55.000	5.11	0.00	42.56	3.91
1370	1380	2.436646	CGTGCTTCGCCCTCCATT	60.437	61.111	0.00	0.00	0.00	3.16
1397	1407	2.492090	AGCTCAACGGCTAGCTCG	59.508	61.111	15.72	18.12	45.92	5.03
1406	1416	4.245660	TCTTCAACATCCTAAGCTCAACG	58.754	43.478	0.00	0.00	0.00	4.10
1469	1479	6.897706	AATGCCCAAAAGTATTTGCAAATT	57.102	29.167	28.45	10.21	43.73	1.82
1584	1594	8.356657	TGACCAACATTTAAACTAGGTGAATTG	58.643	33.333	7.84	0.00	0.00	2.32
1775	1790	3.323403	GTCTAGCCTGCACTTGGATCTAT	59.677	47.826	0.00	0.00	0.00	1.98
1780	1795	2.231716	TAGTCTAGCCTGCACTTGGA	57.768	50.000	0.00	0.00	0.00	3.53
1811	1826	2.586425	CGAATGGGCCTAATTGGATGT	58.414	47.619	4.53	0.00	38.35	3.06
2004	2022	5.815233	TTTCCATGGCATTTTGGTCTTTA	57.185	34.783	6.96	0.00	34.48	1.85
2018	2036	1.134907	GCTGAGGCACATTTTCCATGG	60.135	52.381	4.97	4.97	38.54	3.66
2081	2100	9.838339	TTTTTCTCAATGTAATGCCCTTAAAAA	57.162	25.926	0.00	0.00	0.00	1.94
2211	2234	3.517901	CCATCTGTCCTAGTGGTTACCAA	59.482	47.826	5.33	0.00	34.18	3.67
2220	2243	2.826488	AGTCTTGCCATCTGTCCTAGT	58.174	47.619	0.00	0.00	0.00	2.57
2302	2328	1.872952	TGCAAACATTCACGGTCTCAG	59.127	47.619	0.00	0.00	0.00	3.35
2560	2638	6.818142	CCAAACATATCATTTCTTCCCCAAAC	59.182	38.462	0.00	0.00	0.00	2.93
2564	2642	4.202253	GCCCAAACATATCATTTCTTCCCC	60.202	45.833	0.00	0.00	0.00	4.81

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.