AutoCloner

Multiple sequence alignment - TraesCS7B01G048000

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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	TraesCS7B01G048000	chr7B	100.000	2784	0	0	1	2784	47604887	47607670	0.000000e+00	5142
1	TraesCS7B01G048000	chr7B	98.522	2706	37	3	81	2784	253903492	253906196	0.000000e+00	4772
2	TraesCS7B01G048000	chr7B	98.375	2708	40	4	80	2784	202160215	202157509	0.000000e+00	4754
3	TraesCS7B01G048000	chr7B	96.203	79	3	0	6	84	47341720	47341798	2.250000e-26	130
4	TraesCS7B01G048000	chr1B	98.666	2699	34	2	85	2782	500909890	500912587	0.000000e+00	4783
5	TraesCS7B01G048000	chr4B	98.558	2704	35	3	84	2784	468285210	468282508	0.000000e+00	4774
6	TraesCS7B01G048000	chr5B	98.521	2704	35	3	83	2784	579529873	579532573	0.000000e+00	4767
7	TraesCS7B01G048000	chr3B	98.483	2703	39	2	83	2784	761378842	761381543	0.000000e+00	4763
8	TraesCS7B01G048000	chr3B	98.447	2704	38	4	85	2784	183476373	183479076	0.000000e+00	4758
9	TraesCS7B01G048000	chr3B	98.446	2703	39	3	85	2784	766969476	766972178	0.000000e+00	4756
10	TraesCS7B01G048000	chr5A	98.409	2702	41	2	85	2784	549962796	549965497	0.000000e+00	4750

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	TraesCS7B01G048000	chr7B	47604887	47607670	2783	False	5142	5142	100.000	1	2784	1	chr7B.!!$F2	2783
1	TraesCS7B01G048000	chr7B	253903492	253906196	2704	False	4772	4772	98.522	81	2784	1	chr7B.!!$F3	2703
2	TraesCS7B01G048000	chr7B	202157509	202160215	2706	True	4754	4754	98.375	80	2784	1	chr7B.!!$R1	2704
3	TraesCS7B01G048000	chr1B	500909890	500912587	2697	False	4783	4783	98.666	85	2782	1	chr1B.!!$F1	2697
4	TraesCS7B01G048000	chr4B	468282508	468285210	2702	True	4774	4774	98.558	84	2784	1	chr4B.!!$R1	2700
5	TraesCS7B01G048000	chr5B	579529873	579532573	2700	False	4767	4767	98.521	83	2784	1	chr5B.!!$F1	2701
6	TraesCS7B01G048000	chr3B	761378842	761381543	2701	False	4763	4763	98.483	83	2784	1	chr3B.!!$F2	2701
7	TraesCS7B01G048000	chr3B	183476373	183479076	2703	False	4758	4758	98.447	85	2784	1	chr3B.!!$F1	2699
8	TraesCS7B01G048000	chr3B	766969476	766972178	2702	False	4756	4756	98.446	85	2784	1	chr3B.!!$F3	2699
9	TraesCS7B01G048000	chr5A	549962796	549965497	2701	False	4750	4750	98.409	85	2784	1	chr5A.!!$F1	2699

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
48	49	0.101579	GAGAGGCGGAGAGTGCTAAC	59.898	60.0	0.00	0.0	0.0	2.34	F
1421	1427	0.456221	CACCGGTCTTGCTATCGACT	59.544	55.0	2.59	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1750	1756	0.250295	CAAGAGTCGCTGAACCCCAA	60.250	55.000	0.0	0.0	0.00	4.12	R
2341	2347	1.001815	CGGCAAATGAAACTCAACCGT	60.002	47.619	0.0	0.0	32.08	4.83	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
19	20	1.316651	CGGAGTACTACTGTAGCCCC	58.683	60.000	14.55	9.35	0.00	5.80
20	21	1.316651	GGAGTACTACTGTAGCCCCG	58.683	60.000	14.55	0.00	0.00	5.73
21	22	1.316651	GAGTACTACTGTAGCCCCGG	58.683	60.000	14.55	0.00	0.00	5.73
22	23	0.754587	AGTACTACTGTAGCCCCGGC	60.755	60.000	14.55	0.00	42.33	6.13
23	24	1.039233	GTACTACTGTAGCCCCGGCA	61.039	60.000	14.55	0.00	44.88	5.69
24	25	0.324552	TACTACTGTAGCCCCGGCAA	60.325	55.000	14.55	0.00	44.88	4.52
25	26	0.981277	ACTACTGTAGCCCCGGCAAT	60.981	55.000	14.55	0.00	44.88	3.56
26	27	0.532862	CTACTGTAGCCCCGGCAATG	60.533	60.000	8.74	0.00	44.88	2.82
27	28	0.978667	TACTGTAGCCCCGGCAATGA	60.979	55.000	8.74	0.00	44.88	2.57
28	29	1.819632	CTGTAGCCCCGGCAATGAC	60.820	63.158	8.74	1.16	44.88	3.06
29	30	2.895372	GTAGCCCCGGCAATGACG	60.895	66.667	0.00	0.00	44.88	4.35
30	31	3.078196	TAGCCCCGGCAATGACGA	61.078	61.111	11.36	0.00	44.88	4.20
31	32	3.088941	TAGCCCCGGCAATGACGAG	62.089	63.158	11.36	0.00	44.88	4.18
32	33	4.467084	GCCCCGGCAATGACGAGA	62.467	66.667	11.36	0.00	35.20	4.04
33	34	2.202932	CCCCGGCAATGACGAGAG	60.203	66.667	11.36	0.00	35.20	3.20
34	35	2.202932	CCCGGCAATGACGAGAGG	60.203	66.667	11.36	0.00	35.20	3.69
35	36	2.892425	CCGGCAATGACGAGAGGC	60.892	66.667	11.36	0.00	35.20	4.70
43	44	2.795297	GACGAGAGGCGGAGAGTG	59.205	66.667	0.00	0.00	46.49	3.51
44	45	3.404141	GACGAGAGGCGGAGAGTGC	62.404	68.421	0.00	0.00	46.49	4.40
45	46	3.137459	CGAGAGGCGGAGAGTGCT	61.137	66.667	0.00	0.00	36.03	4.40
46	47	1.820056	CGAGAGGCGGAGAGTGCTA	60.820	63.158	0.00	0.00	36.03	3.49
47	48	1.377366	CGAGAGGCGGAGAGTGCTAA	61.377	60.000	0.00	0.00	36.03	3.09
48	49	0.101579	GAGAGGCGGAGAGTGCTAAC	59.898	60.000	0.00	0.00	0.00	2.34
49	50	1.142097	GAGGCGGAGAGTGCTAACC	59.858	63.158	0.00	0.00	0.00	2.85
50	51	2.187163	GGCGGAGAGTGCTAACCC	59.813	66.667	0.00	0.00	0.00	4.11
51	52	2.202756	GCGGAGAGTGCTAACCCG	60.203	66.667	0.00	0.00	42.74	5.28
52	53	2.202756	CGGAGAGTGCTAACCCGC	60.203	66.667	0.00	0.00	33.47	6.13
53	54	2.202756	GGAGAGTGCTAACCCGCG	60.203	66.667	0.00	0.00	0.00	6.46
54	55	2.202756	GAGAGTGCTAACCCGCGG	60.203	66.667	21.04	21.04	0.00	6.46
55	56	2.678934	AGAGTGCTAACCCGCGGA	60.679	61.111	30.73	5.58	0.00	5.54
56	57	2.221906	GAGAGTGCTAACCCGCGGAA	62.222	60.000	30.73	10.96	0.00	4.30
57	58	1.810030	GAGTGCTAACCCGCGGAAG	60.810	63.158	30.73	21.35	0.00	3.46
58	59	2.818274	GTGCTAACCCGCGGAAGG	60.818	66.667	30.73	13.32	0.00	3.46
59	60	4.770874	TGCTAACCCGCGGAAGGC	62.771	66.667	30.73	23.73	38.69	4.35
60	61	4.770874	GCTAACCCGCGGAAGGCA	62.771	66.667	30.73	5.67	43.84	4.75
61	62	2.511600	CTAACCCGCGGAAGGCAG	60.512	66.667	30.73	11.56	43.84	4.85
62	63	4.770874	TAACCCGCGGAAGGCAGC	62.771	66.667	30.73	0.00	43.84	5.25
274	276	4.740822	GTCCAGTTGCGGCCCCAT	62.741	66.667	0.00	0.00	0.00	4.00
299	301	1.812922	CTGTGCAGCGCCTAAGAGG	60.813	63.158	2.29	0.00	38.80	3.69
480	484	6.183360	CCTCTCAGATCTGAAGATTTGATCCA	60.183	42.308	25.09	0.00	42.40	3.41
1421	1427	0.456221	CACCGGTCTTGCTATCGACT	59.544	55.000	2.59	0.00	0.00	4.18
1490	1496	6.393171	CAGATGATTGCTCTTATCGGTATGA	58.607	40.000	0.00	0.00	0.00	2.15
1750	1756	3.448686	CGTCTTCGATAGCAAATGGAGT	58.551	45.455	0.00	0.00	39.71	3.85
1781	1787	2.094649	GCGACTCTTGCCTACTTGTACT	60.095	50.000	0.00	0.00	0.00	2.73
1799	1805	1.344763	ACTGACAGGTAGTTGGTCTGC	59.655	52.381	7.51	0.00	34.90	4.26
2341	2347	1.408683	GCCCACTGATATGCAACTGGA	60.409	52.381	0.00	0.00	29.47	3.86
2540	2546	1.376037	GACAGGAGAAGGCAACGGG	60.376	63.158	0.00	0.00	46.39	5.28
2553	2559	2.280628	GCAACGGGAGATAAAGGACTG	58.719	52.381	0.00	0.00	0.00	3.51
2623	2630	2.421877	AAGCTCGTAGCACTGCACGT	62.422	55.000	18.89	0.00	45.56	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.316651	GGGGCTACAGTAGTACTCCG	58.683	60.000	9.42	0.00	0.00	4.63
5	6	0.324552	TTGCCGGGGCTACAGTAGTA	60.325	55.000	11.55	0.00	42.51	1.82
6	7	0.981277	ATTGCCGGGGCTACAGTAGT	60.981	55.000	11.55	0.00	42.51	2.73
7	8	0.532862	CATTGCCGGGGCTACAGTAG	60.533	60.000	11.55	2.85	42.51	2.57
8	9	0.978667	TCATTGCCGGGGCTACAGTA	60.979	55.000	11.55	0.00	42.51	2.74
9	10	2.272146	CATTGCCGGGGCTACAGT	59.728	61.111	11.55	0.00	42.51	3.55
10	11	1.819632	GTCATTGCCGGGGCTACAG	60.820	63.158	11.55	0.49	42.51	2.74
11	12	2.270850	GTCATTGCCGGGGCTACA	59.729	61.111	11.55	0.00	42.51	2.74
12	13	2.895372	CGTCATTGCCGGGGCTAC	60.895	66.667	11.55	3.54	42.51	3.58
13	14	3.078196	TCGTCATTGCCGGGGCTA	61.078	61.111	11.55	3.45	42.51	3.93
14	15	4.473520	CTCGTCATTGCCGGGGCT	62.474	66.667	11.55	0.00	42.51	5.19
15	16	4.467084	TCTCGTCATTGCCGGGGC	62.467	66.667	2.18	1.86	42.35	5.80
16	17	2.202932	CTCTCGTCATTGCCGGGG	60.203	66.667	2.18	0.00	0.00	5.73
17	18	2.202932	CCTCTCGTCATTGCCGGG	60.203	66.667	2.18	0.00	0.00	5.73
18	19	2.892425	GCCTCTCGTCATTGCCGG	60.892	66.667	0.00	0.00	0.00	6.13
19	20	3.257561	CGCCTCTCGTCATTGCCG	61.258	66.667	0.00	0.00	0.00	5.69
20	21	2.892425	CCGCCTCTCGTCATTGCC	60.892	66.667	0.00	0.00	36.19	4.52
21	22	1.880340	CTCCGCCTCTCGTCATTGC	60.880	63.158	0.00	0.00	36.19	3.56
22	23	0.248825	CTCTCCGCCTCTCGTCATTG	60.249	60.000	0.00	0.00	36.19	2.82
23	24	0.681564	ACTCTCCGCCTCTCGTCATT	60.682	55.000	0.00	0.00	36.19	2.57
24	25	1.077357	ACTCTCCGCCTCTCGTCAT	60.077	57.895	0.00	0.00	36.19	3.06
25	26	2.041115	CACTCTCCGCCTCTCGTCA	61.041	63.158	0.00	0.00	36.19	4.35
26	27	2.795297	CACTCTCCGCCTCTCGTC	59.205	66.667	0.00	0.00	36.19	4.20
27	28	2.538512	TAGCACTCTCCGCCTCTCGT	62.539	60.000	0.00	0.00	36.19	4.18
28	29	1.377366	TTAGCACTCTCCGCCTCTCG	61.377	60.000	0.00	0.00	38.08	4.04
29	30	0.101579	GTTAGCACTCTCCGCCTCTC	59.898	60.000	0.00	0.00	0.00	3.20
30	31	1.324005	GGTTAGCACTCTCCGCCTCT	61.324	60.000	0.00	0.00	0.00	3.69
31	32	1.142097	GGTTAGCACTCTCCGCCTC	59.858	63.158	0.00	0.00	0.00	4.70
32	33	2.359967	GGGTTAGCACTCTCCGCCT	61.360	63.158	0.00	0.00	0.00	5.52
33	34	2.187163	GGGTTAGCACTCTCCGCC	59.813	66.667	0.00	0.00	0.00	6.13
34	35	2.202756	CGGGTTAGCACTCTCCGC	60.203	66.667	0.00	0.00	34.17	5.54
35	36	2.202756	GCGGGTTAGCACTCTCCG	60.203	66.667	0.00	0.00	43.13	4.63
36	37	2.202756	CGCGGGTTAGCACTCTCC	60.203	66.667	0.00	0.00	36.85	3.71
37	38	2.202756	CCGCGGGTTAGCACTCTC	60.203	66.667	20.10	0.00	36.85	3.20
38	39	2.227089	CTTCCGCGGGTTAGCACTCT	62.227	60.000	27.83	0.00	36.85	3.24
39	40	1.810030	CTTCCGCGGGTTAGCACTC	60.810	63.158	27.83	0.00	36.85	3.51
40	41	2.264794	CTTCCGCGGGTTAGCACT	59.735	61.111	27.83	0.00	36.85	4.40
41	42	2.818274	CCTTCCGCGGGTTAGCAC	60.818	66.667	27.83	0.00	36.85	4.40
42	43	4.770874	GCCTTCCGCGGGTTAGCA	62.771	66.667	27.83	0.17	36.85	3.49
43	44	4.770874	TGCCTTCCGCGGGTTAGC	62.771	66.667	27.83	22.53	42.08	3.09
44	45	2.511600	CTGCCTTCCGCGGGTTAG	60.512	66.667	27.83	19.34	40.51	2.34
45	46	4.770874	GCTGCCTTCCGCGGGTTA	62.771	66.667	27.83	10.41	44.79	2.85
62	63	3.376935	AATCTCCTCGTGCCGCCTG	62.377	63.158	0.00	0.00	0.00	4.85
63	64	3.077556	AATCTCCTCGTGCCGCCT	61.078	61.111	0.00	0.00	0.00	5.52
64	65	2.892425	CAATCTCCTCGTGCCGCC	60.892	66.667	0.00	0.00	0.00	6.13
65	66	2.892425	CCAATCTCCTCGTGCCGC	60.892	66.667	0.00	0.00	0.00	6.53
66	67	2.892425	GCCAATCTCCTCGTGCCG	60.892	66.667	0.00	0.00	0.00	5.69
67	68	2.892425	CGCCAATCTCCTCGTGCC	60.892	66.667	0.00	0.00	0.00	5.01
68	69	2.892425	CCGCCAATCTCCTCGTGC	60.892	66.667	0.00	0.00	0.00	5.34
69	70	2.892425	GCCGCCAATCTCCTCGTG	60.892	66.667	0.00	0.00	0.00	4.35
70	71	3.376935	CTGCCGCCAATCTCCTCGT	62.377	63.158	0.00	0.00	0.00	4.18
71	72	2.578163	TTCTGCCGCCAATCTCCTCG	62.578	60.000	0.00	0.00	0.00	4.63
72	73	0.392998	TTTCTGCCGCCAATCTCCTC	60.393	55.000	0.00	0.00	0.00	3.71
73	74	0.257039	ATTTCTGCCGCCAATCTCCT	59.743	50.000	0.00	0.00	0.00	3.69
74	75	0.665298	GATTTCTGCCGCCAATCTCC	59.335	55.000	0.00	0.00	0.00	3.71
75	76	1.064654	GTGATTTCTGCCGCCAATCTC	59.935	52.381	7.97	2.71	0.00	2.75
76	77	1.098050	GTGATTTCTGCCGCCAATCT	58.902	50.000	7.97	0.00	0.00	2.40
77	78	0.810648	TGTGATTTCTGCCGCCAATC	59.189	50.000	0.00	0.00	0.00	2.67
78	79	0.813184	CTGTGATTTCTGCCGCCAAT	59.187	50.000	0.00	0.00	0.00	3.16
79	80	0.250684	TCTGTGATTTCTGCCGCCAA	60.251	50.000	0.00	0.00	0.00	4.52
80	81	0.035152	ATCTGTGATTTCTGCCGCCA	60.035	50.000	0.00	0.00	0.00	5.69
81	82	1.098050	AATCTGTGATTTCTGCCGCC	58.902	50.000	0.00	0.00	0.00	6.13
299	301	1.866925	GTCAAAGTGTGGCGCCTAC	59.133	57.895	29.70	25.10	0.00	3.18
377	379	0.037790	AGAGACGAAGAACTGCCTGC	60.038	55.000	0.00	0.00	0.00	4.85
1421	1427	2.251818	GCTCATACATAGAGGCCTCCA	58.748	52.381	29.54	17.52	33.72	3.86
1750	1756	0.250295	CAAGAGTCGCTGAACCCCAA	60.250	55.000	0.00	0.00	0.00	4.12
1781	1787	1.717032	AGCAGACCAACTACCTGTCA	58.283	50.000	0.00	0.00	0.00	3.58
2341	2347	1.001815	CGGCAAATGAAACTCAACCGT	60.002	47.619	0.00	0.00	32.08	4.83
2540	2546	2.924421	CTTGGCCCAGTCCTTTATCTC	58.076	52.381	0.00	0.00	0.00	2.75
2553	2559	1.440476	GCAGAATGATGCTTGGCCC	59.560	57.895	0.00	0.00	43.07	5.80

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.