AutoCloner

Multiple sequence alignment - TraesCS7D01G111700

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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	TraesCS7D01G111700	chr7D	100.000	2456	0	0	1	2456	68516948	68519403	0.000000e+00	4536.0
1	TraesCS7D01G111700	chr7D	96.703	455	14	1	2003	2456	610519421	610518967	0.000000e+00	756.0
2	TraesCS7D01G111700	chr7D	95.824	455	18	1	2003	2456	181325471	181325925	0.000000e+00	734.0
3	TraesCS7D01G111700	chr7D	86.623	456	43	6	3	457	399829644	399830082	2.840000e-134	488.0
4	TraesCS7D01G111700	chr7D	95.270	148	7	0	1854	2001	392753319	392753172	4.080000e-58	235.0
5	TraesCS7D01G111700	chr7D	87.879	165	16	4	1841	2003	89291760	89291922	8.960000e-45	191.0
6	TraesCS7D01G111700	chr7D	89.873	79	6	2	382	460	27179643	27179719	1.550000e-17	100.0
7	TraesCS7D01G111700	chr7D	76.543	162	31	7	1845	2002	421882768	421882610	5.630000e-12	82.4
8	TraesCS7D01G111700	chr7B	93.211	1311	66	11	549	1852	9633144	9631850	0.000000e+00	1906.0
9	TraesCS7D01G111700	chr7B	93.243	148	10	0	1854	2001	592347019	592346872	4.110000e-53	219.0
10	TraesCS7D01G111700	chr7A	93.312	1241	44	12	458	1673	71591317	71590091	0.000000e+00	1796.0
11	TraesCS7D01G111700	chr7A	96.774	186	4	2	1667	1852	71391957	71391774	2.370000e-80	309.0
12	TraesCS7D01G111700	chr7A	90.850	153	13	1	1850	2001	722081656	722081504	1.150000e-48	204.0
13	TraesCS7D01G111700	chr7A	79.878	164	28	4	1841	2000	671745447	671745609	5.550000e-22	115.0
14	TraesCS7D01G111700	chr4A	96.703	455	14	1	2003	2456	603684953	603685407	0.000000e+00	756.0
15	TraesCS7D01G111700	chr5D	96.264	455	16	1	2003	2456	517353702	517353248	0.000000e+00	745.0
16	TraesCS7D01G111700	chr5D	95.643	459	19	1	1999	2456	494040592	494040134	0.000000e+00	736.0
17	TraesCS7D01G111700	chr5D	95.824	455	18	1	2003	2456	489734620	489735074	0.000000e+00	734.0
18	TraesCS7D01G111700	chr5D	95.815	454	18	1	2003	2456	564942255	564941803	0.000000e+00	732.0
19	TraesCS7D01G111700	chr5D	84.902	457	65	4	3	455	453133160	453132704	2.230000e-125	459.0
20	TraesCS7D01G111700	chr5D	93.056	144	7	2	1861	2001	217976737	217976594	8.900000e-50	207.0
21	TraesCS7D01G111700	chr3D	96.264	455	16	1	2003	2456	555327859	555327405	0.000000e+00	745.0
22	TraesCS7D01G111700	chr1D	95.643	459	18	2	2000	2456	33833069	33832611	0.000000e+00	736.0
23	TraesCS7D01G111700	chr6D	87.609	460	53	3	4	459	391567157	391566698	4.650000e-147	531.0
24	TraesCS7D01G111700	chr1B	86.710	459	50	7	3	460	581213081	581212633	1.310000e-137	499.0
25	TraesCS7D01G111700	chr1A	86.304	460	58	5	7	462	23118858	23118400	1.700000e-136	496.0
26	TraesCS7D01G111700	chr4D	85.281	462	61	7	3	460	374782872	374783330	1.030000e-128	470.0
27	TraesCS7D01G111700	chr4D	84.749	459	66	4	3	459	6252879	6253335	8.000000e-125	457.0
28	TraesCS7D01G111700	chr2B	85.185	459	63	4	3	457	14355210	14354753	1.330000e-127	466.0
29	TraesCS7D01G111700	chr2B	89.706	68	7	0	395	462	749229378	749229311	1.210000e-13	87.9
30	TraesCS7D01G111700	chr6B	84.449	463	66	6	1	457	691997774	691998236	3.720000e-123	451.0
31	TraesCS7D01G111700	chr3A	93.103	145	10	0	1857	2001	330702096	330702240	1.910000e-51	213.0
32	TraesCS7D01G111700	chr3A	91.892	148	12	0	1854	2001	594019541	594019688	8.900000e-50	207.0
33	TraesCS7D01G111700	chr3A	90.850	153	13	1	1847	1999	63527016	63527167	1.150000e-48	204.0
34	TraesCS7D01G111700	chr5A	90.566	159	11	2	1844	2001	631210494	631210339	8.900000e-50	207.0
35	TraesCS7D01G111700	chr5A	86.093	151	19	2	1854	2003	405029569	405029420	7.030000e-36	161.0
36	TraesCS7D01G111700	chr2A	91.447	152	11	2	1851	2001	102113520	102113370	8.900000e-50	207.0
37	TraesCS7D01G111700	chr3B	85.366	164	20	4	1842	2003	12394063	12394224	1.510000e-37	167.0
38	TraesCS7D01G111700	chr2D	84.663	163	23	2	1842	2003	493617355	493617516	7.030000e-36	161.0

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	TraesCS7D01G111700	chr7D	68516948	68519403	2455	False	4536	4536	100.000	1	2456	1	chr7D.!!$F2	2455
1	TraesCS7D01G111700	chr7B	9631850	9633144	1294	True	1906	1906	93.211	549	1852	1	chr7B.!!$R1	1303
2	TraesCS7D01G111700	chr7A	71590091	71591317	1226	True	1796	1796	93.312	458	1673	1	chr7A.!!$R2	1215

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
760	782	0.036164	CCACTCCATCCACGGAAACA	59.964	55.0	0.0	0.0	33.65	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2199	2227	0.032217	ACCAATGGTTATGGGCCAGG	60.032	55.0	13.78	7.57	42.48	4.45	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
18	19	3.713902	CTGTATGGGGCATCAGTCC	57.286	57.895	0.00	0.00	39.43	3.85
19	20	0.250038	CTGTATGGGGCATCAGTCCG	60.250	60.000	0.00	0.00	41.80	4.79
20	21	1.071471	GTATGGGGCATCAGTCCGG	59.929	63.158	0.00	0.00	41.80	5.14
21	22	2.146724	TATGGGGCATCAGTCCGGG	61.147	63.158	0.00	0.00	41.80	5.73
36	37	3.799755	GGGCGACGCAACCACATC	61.800	66.667	23.09	0.62	0.00	3.06
37	38	4.147322	GGCGACGCAACCACATCG	62.147	66.667	23.09	0.00	37.63	3.84
38	39	3.411351	GCGACGCAACCACATCGT	61.411	61.111	16.42	0.00	39.33	3.73
39	40	2.469847	CGACGCAACCACATCGTG	59.530	61.111	0.00	0.00	36.50	4.35
66	67	2.844839	GGCGGCTGGTCCCTAGAT	60.845	66.667	0.00	0.00	0.00	1.98
67	68	2.423446	GCGGCTGGTCCCTAGATG	59.577	66.667	0.00	0.00	0.00	2.90
68	69	3.142393	CGGCTGGTCCCTAGATGG	58.858	66.667	0.00	0.00	0.00	3.51
69	70	1.457643	CGGCTGGTCCCTAGATGGA	60.458	63.158	0.00	0.00	38.35	3.41
70	71	0.833834	CGGCTGGTCCCTAGATGGAT	60.834	60.000	0.00	0.00	36.63	3.41
71	72	0.980423	GGCTGGTCCCTAGATGGATC	59.020	60.000	0.00	0.00	36.63	3.36
72	73	0.980423	GCTGGTCCCTAGATGGATCC	59.020	60.000	4.20	4.20	34.38	3.36
73	74	1.261480	CTGGTCCCTAGATGGATCCG	58.739	60.000	7.39	0.00	34.38	4.18
74	75	0.561184	TGGTCCCTAGATGGATCCGT	59.439	55.000	6.04	6.04	34.38	4.69
75	76	1.258676	GGTCCCTAGATGGATCCGTC	58.741	60.000	24.30	24.30	36.63	4.79
76	77	1.480683	GGTCCCTAGATGGATCCGTCA	60.481	57.143	31.14	17.98	36.63	4.35
77	78	2.530701	GTCCCTAGATGGATCCGTCAT	58.469	52.381	31.14	19.77	36.63	3.06
78	79	2.494073	GTCCCTAGATGGATCCGTCATC	59.506	54.545	31.14	17.65	40.79	2.92
79	80	1.474478	CCCTAGATGGATCCGTCATCG	59.526	57.143	31.14	19.37	44.04	3.84
80	81	2.437413	CCTAGATGGATCCGTCATCGA	58.563	52.381	31.14	13.49	44.04	3.59
81	82	3.020274	CCTAGATGGATCCGTCATCGAT	58.980	50.000	31.14	15.61	44.04	3.59
82	83	3.066064	CCTAGATGGATCCGTCATCGATC	59.934	52.174	31.14	15.64	43.72	3.69

Showing 1 to 25 of 705 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.250038	CGGACTGATGCCCCATACAG	60.250	60.000	0.00	0.00	36.58	2.74
1	2	1.695114	CCGGACTGATGCCCCATACA	61.695	60.000	0.00	0.00	0.00	2.29
2	3	1.071471	CCGGACTGATGCCCCATAC	59.929	63.158	0.00	0.00	0.00	2.39
3	4	2.146724	CCCGGACTGATGCCCCATA	61.147	63.158	0.73	0.00	0.00	2.74
4	5	3.492353	CCCGGACTGATGCCCCAT	61.492	66.667	0.73	0.00	0.00	4.00
19	20	3.799755	GATGTGGTTGCGTCGCCC	61.800	66.667	15.88	10.25	0.00	6.13
20	21	4.147322	CGATGTGGTTGCGTCGCC	62.147	66.667	15.88	0.00	40.32	5.54
49	50	2.844839	ATCTAGGGACCAGCCGCC	60.845	66.667	0.00	0.00	37.63	6.13
50	51	2.423446	CATCTAGGGACCAGCCGC	59.577	66.667	0.00	0.00	37.63	6.53
51	52	0.833834	ATCCATCTAGGGACCAGCCG	60.834	60.000	0.00	0.00	40.44	5.52
52	53	0.980423	GATCCATCTAGGGACCAGCC	59.020	60.000	0.00	0.00	40.44	4.85
53	54	0.980423	GGATCCATCTAGGGACCAGC	59.020	60.000	6.95	0.00	40.44	4.85
54	55	1.261480	CGGATCCATCTAGGGACCAG	58.739	60.000	13.41	0.00	40.44	4.00
55	56	0.561184	ACGGATCCATCTAGGGACCA	59.439	55.000	13.41	0.00	40.44	4.02
56	57	1.258676	GACGGATCCATCTAGGGACC	58.741	60.000	13.41	0.00	40.44	4.46
57	58	1.996798	TGACGGATCCATCTAGGGAC	58.003	55.000	13.41	0.00	40.44	4.46
58	59	2.808919	GATGACGGATCCATCTAGGGA	58.191	52.381	13.41	0.00	42.21	4.20
59	60	1.474478	CGATGACGGATCCATCTAGGG	59.526	57.143	13.41	0.00	38.53	3.53
60	61	2.437413	TCGATGACGGATCCATCTAGG	58.563	52.381	13.41	0.00	38.53	3.02
61	62	3.944650	AGATCGATGACGGATCCATCTAG	59.055	47.826	13.41	2.09	37.29	2.43
62	63	3.691609	CAGATCGATGACGGATCCATCTA	59.308	47.826	13.41	0.00	37.03	1.98
63	64	2.491298	CAGATCGATGACGGATCCATCT	59.509	50.000	13.41	7.59	39.02	2.90
64	65	2.489722	TCAGATCGATGACGGATCCATC	59.510	50.000	13.41	6.74	40.21	3.51
65	66	2.230025	GTCAGATCGATGACGGATCCAT	59.770	50.000	13.41	0.00	40.18	3.41
66	67	1.609072	GTCAGATCGATGACGGATCCA	59.391	52.381	13.41	0.00	40.18	3.41

Showing 1 to 25 of 625 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.