AutoCloner

Multiple sequence alignment - TraesCS3B01G144200

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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	TraesCS3B01G144200	chr3B	100.000	5507	0	0	1	5507	132719007	132724513	0.000000e+00	10170.0
1	TraesCS3B01G144200	chr3B	88.095	588	57	9	4924	5506	71218041	71217462	0.000000e+00	686.0
2	TraesCS3B01G144200	chr3B	84.810	79	11	1	4925	5003	698627284	698627207	1.640000e-10	78.7
3	TraesCS3B01G144200	chr3B	83.784	74	11	1	4925	4998	698690462	698690390	9.900000e-08	69.4
4	TraesCS3B01G144200	chr3D	94.230	4194	191	20	583	4731	83829860	83825673	0.000000e+00	6357.0
5	TraesCS3B01G144200	chr3D	85.662	272	38	1	267	537	83830130	83829859	9.030000e-73	285.0
6	TraesCS3B01G144200	chr3D	82.569	109	19	0	418	526	180593337	180593229	4.540000e-16	97.1
7	TraesCS3B01G144200	chr3D	86.567	67	8	1	4722	4788	27936629	27936564	7.650000e-09	73.1
8	TraesCS3B01G144200	chr3D	77.419	124	26	2	430	552	136043559	136043437	7.650000e-09	73.1
9	TraesCS3B01G144200	chr3D	93.750	48	3	0	4743	4790	417211776	417211729	7.650000e-09	73.1
10	TraesCS3B01G144200	chr3A	95.448	3932	123	17	754	4643	99626086	99622169	0.000000e+00	6218.0
11	TraesCS3B01G144200	chr3A	89.391	443	34	9	5067	5504	685814016	685814450	3.750000e-151	545.0
12	TraesCS3B01G144200	chr3A	86.123	454	55	8	5057	5507	131407319	131407767	2.980000e-132	483.0
13	TraesCS3B01G144200	chr3A	84.507	213	30	3	376	586	99628069	99627858	2.010000e-49	207.0
14	TraesCS3B01G144200	chr6B	84.103	585	72	14	4926	5507	71846615	71846049	3.750000e-151	545.0
15	TraesCS3B01G144200	chr7A	91.003	389	29	5	5121	5507	76116342	76115958	2.270000e-143	520.0
16	TraesCS3B01G144200	chr7A	82.119	151	22	3	423	568	375898469	375898619	2.080000e-24	124.0
17	TraesCS3B01G144200	chr7A	79.545	132	24	3	418	547	264338567	264338437	2.110000e-14	91.6
18	TraesCS3B01G144200	chr4D	85.540	491	60	10	5022	5507	338014139	338013655	2.290000e-138	503.0
19	TraesCS3B01G144200	chr4D	84.694	490	61	13	5022	5507	385673897	385674376	1.390000e-130	477.0
20	TraesCS3B01G144200	chr5A	87.215	438	40	13	5071	5506	121421114	121421537	8.290000e-133	484.0
21	TraesCS3B01G144200	chr5A	88.136	59	5	2	4734	4791	382759472	382759529	9.900000e-08	69.4
22	TraesCS3B01G144200	chr2A	84.663	489	63	10	5022	5507	761300081	761300560	1.390000e-130	477.0
23	TraesCS3B01G144200	chr2A	78.912	147	28	3	420	564	122043939	122043794	4.540000e-16	97.1
24	TraesCS3B01G144200	chr7D	81.457	151	22	4	423	568	311863038	311862889	9.690000e-23	119.0
25	TraesCS3B01G144200	chr1D	81.169	154	24	3	418	568	479605518	479605669	9.690000e-23	119.0
26	TraesCS3B01G144200	chr1D	81.538	130	22	2	418	546	459274891	459275019	7.540000e-19	106.0
27	TraesCS3B01G144200	chr6D	81.379	145	26	1	418	561	451892531	451892387	3.490000e-22	117.0
28	TraesCS3B01G144200	chr6D	90.741	54	4	1	4722	4775	7985400	7985348	2.750000e-08	71.3
29	TraesCS3B01G144200	chr1B	79.355	155	22	6	418	567	667828781	667828930	3.510000e-17	100.0
30	TraesCS3B01G144200	chr6A	77.381	168	34	3	418	582	184947076	184946910	4.540000e-16	97.1
31	TraesCS3B01G144200	chr2D	88.889	72	6	2	420	490	129958044	129958114	2.730000e-13	87.9
32	TraesCS3B01G144200	chr2B	92.453	53	3	1	4728	4779	639246820	639246872	2.130000e-09	75.0
33	TraesCS3B01G144200	chr7B	92.157	51	3	1	4725	4775	585509018	585508969	2.750000e-08	71.3
34	TraesCS3B01G144200	chr5D	89.286	56	5	1	4733	4788	447251951	447252005	9.900000e-08	69.4
35	TraesCS3B01G144200	chr5B	87.931	58	7	0	4734	4791	381355204	381355261	9.900000e-08	69.4
36	TraesCS3B01G144200	chr1A	83.333	72	11	1	4722	4793	70977641	70977571	1.280000e-06	65.8

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	TraesCS3B01G144200	chr3B	132719007	132724513	5506	False	10170.0	10170	100.0000	1	5507	1	chr3B.!!$F1	5506
1	TraesCS3B01G144200	chr3B	71217462	71218041	579	True	686.0	686	88.0950	4924	5506	1	chr3B.!!$R1	582
2	TraesCS3B01G144200	chr3D	83825673	83830130	4457	True	3321.0	6357	89.9460	267	4731	2	chr3D.!!$R5	4464
3	TraesCS3B01G144200	chr3A	99622169	99628069	5900	True	3212.5	6218	89.9775	376	4643	2	chr3A.!!$R1	4267
4	TraesCS3B01G144200	chr6B	71846049	71846615	566	True	545.0	545	84.1030	4926	5507	1	chr6B.!!$R1	581

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
137	138	0.039074	GGCTGGTCCGATCGTGATAG	60.039	60.0	15.09	13.23	0.00	2.08	F
138	139	0.039074	GCTGGTCCGATCGTGATAGG	60.039	60.0	15.09	2.87	35.25	2.57	F
576	578	0.108585	GTGAAGGGGCAACTCAGACA	59.891	55.0	0.00	0.00	42.85	3.41	F
940	2547	0.246635	GTCGCTTCCTAGCCAAGTCA	59.753	55.0	0.00	0.00	44.86	3.41	F
1169	2780	0.389166	CGAGCCGAGCACTTCTTTCT	60.389	55.0	0.00	0.00	0.00	2.52	F
2791	4424	1.074872	GGCGTACGACTACACCAAGC	61.075	60.0	21.65	0.00	0.00	4.01	F
3564	5212	0.036388	ACATCAAGGCGAACACGGAT	60.036	50.0	0.00	0.00	0.00	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1938	3571	1.052617	TCTTGTCGTGGGTGATTGGA	58.947	50.000	0.00	0.00	0.00	3.53	R
1998	3631	2.277437	CGTATGGTGCGCGTCGTA	60.277	61.111	8.43	0.00	0.00	3.43	R
2315	3948	2.640989	CGTCCACCGACTTGTCGA	59.359	61.111	22.54	1.73	39.56	4.20	R
2724	4357	0.249868	CGAACCTGTTCCACAGCTCA	60.250	55.000	4.54	0.00	44.63	4.26	R
3157	4805	0.391597	AACAGGACCGACACGTTCAT	59.608	50.000	0.00	0.00	0.00	2.57	R
4108	5756	0.972983	TAGCTCTTCTTCAGCGGCCT	60.973	55.000	0.00	0.00	42.14	5.19	R
5074	6750	0.042535	GCGATGTAATTTAGCGCGCA	60.043	50.000	35.10	16.82	42.21	6.09	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
20	21	4.839706	GCCCGGGGCCACAATCAT	62.840	66.667	28.23	0.00	44.06	2.45
21	22	2.834505	CCCGGGGCCACAATCATG	60.835	66.667	14.71	0.00	0.00	3.07
22	23	3.530260	CCGGGGCCACAATCATGC	61.530	66.667	5.46	0.00	0.00	4.06
23	24	2.755064	CGGGGCCACAATCATGCA	60.755	61.111	5.46	0.00	0.00	3.96
24	25	2.777972	CGGGGCCACAATCATGCAG	61.778	63.158	5.46	0.00	0.00	4.41
25	26	1.683365	GGGGCCACAATCATGCAGT	60.683	57.895	4.39	0.00	0.00	4.40
26	27	1.259840	GGGGCCACAATCATGCAGTT	61.260	55.000	4.39	0.00	0.00	3.16
27	28	0.609662	GGGCCACAATCATGCAGTTT	59.390	50.000	4.39	0.00	0.00	2.66
28	29	1.824230	GGGCCACAATCATGCAGTTTA	59.176	47.619	4.39	0.00	0.00	2.01
29	30	2.431782	GGGCCACAATCATGCAGTTTAT	59.568	45.455	4.39	0.00	0.00	1.40
30	31	3.118665	GGGCCACAATCATGCAGTTTATT	60.119	43.478	4.39	0.00	0.00	1.40
31	32	4.506758	GGCCACAATCATGCAGTTTATTT	58.493	39.130	0.00	0.00	0.00	1.40
32	33	4.330620	GGCCACAATCATGCAGTTTATTTG	59.669	41.667	0.00	0.00	0.00	2.32
33	34	4.931002	GCCACAATCATGCAGTTTATTTGT	59.069	37.500	0.00	0.00	0.00	2.83
34	35	5.163933	GCCACAATCATGCAGTTTATTTGTG	60.164	40.000	15.22	15.22	0.00	3.33
35	36	5.927689	CCACAATCATGCAGTTTATTTGTGT	59.072	36.000	18.23	1.37	0.00	3.72
36	37	6.089820	CCACAATCATGCAGTTTATTTGTGTC	59.910	38.462	18.23	0.00	0.00	3.67
37	38	6.641723	CACAATCATGCAGTTTATTTGTGTCA	59.358	34.615	14.48	0.00	0.00	3.58
38	39	6.642131	ACAATCATGCAGTTTATTTGTGTCAC	59.358	34.615	0.00	0.00	0.00	3.67
39	40	4.782156	TCATGCAGTTTATTTGTGTCACG	58.218	39.130	0.00	0.00	0.00	4.35
40	41	2.993545	TGCAGTTTATTTGTGTCACGC	58.006	42.857	0.00	0.00	0.00	5.34
41	42	2.616376	TGCAGTTTATTTGTGTCACGCT	59.384	40.909	0.00	0.00	0.00	5.07
42	43	3.226347	GCAGTTTATTTGTGTCACGCTC	58.774	45.455	0.00	0.00	0.00	5.03
43	44	3.303725	GCAGTTTATTTGTGTCACGCTCA	60.304	43.478	0.00	0.00	0.00	4.26
44	45	4.211389	CAGTTTATTTGTGTCACGCTCAC	58.789	43.478	0.00	0.00	36.48	3.51

Showing 1 to 25 of 355 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.834505	CATGATTGTGGCCCCGGG	60.835	66.667	15.80	15.80	0.00	5.73
5	6	3.530260	GCATGATTGTGGCCCCGG	61.530	66.667	0.00	0.00	0.00	5.73
6	7	2.755064	TGCATGATTGTGGCCCCG	60.755	61.111	0.00	0.00	0.00	5.73
7	8	1.259840	AACTGCATGATTGTGGCCCC	61.260	55.000	0.00	0.00	0.00	5.80
8	9	0.609662	AAACTGCATGATTGTGGCCC	59.390	50.000	0.00	0.00	0.00	5.80
9	10	3.806625	ATAAACTGCATGATTGTGGCC	57.193	42.857	0.00	0.00	0.00	5.36
10	11	4.931002	ACAAATAAACTGCATGATTGTGGC	59.069	37.500	0.00	0.00	0.00	5.01
11	12	5.927689	ACACAAATAAACTGCATGATTGTGG	59.072	36.000	21.29	10.92	46.26	4.17
12	13	6.641723	TGACACAAATAAACTGCATGATTGTG	59.358	34.615	18.28	18.28	46.95	3.33
13	14	6.642131	GTGACACAAATAAACTGCATGATTGT	59.358	34.615	0.00	0.00	0.00	2.71
14	15	6.183359	CGTGACACAAATAAACTGCATGATTG	60.183	38.462	6.37	0.00	0.00	2.67
15	16	5.858049	CGTGACACAAATAAACTGCATGATT	59.142	36.000	6.37	0.00	0.00	2.57
16	17	5.393124	CGTGACACAAATAAACTGCATGAT	58.607	37.500	6.37	0.00	0.00	2.45
17	18	4.782156	CGTGACACAAATAAACTGCATGA	58.218	39.130	6.37	0.00	0.00	3.07
18	19	3.361644	GCGTGACACAAATAAACTGCATG	59.638	43.478	6.37	0.00	0.00	4.06
19	20	3.253188	AGCGTGACACAAATAAACTGCAT	59.747	39.130	6.37	0.00	0.00	3.96
20	21	2.616376	AGCGTGACACAAATAAACTGCA	59.384	40.909	6.37	0.00	0.00	4.41
21	22	3.226347	GAGCGTGACACAAATAAACTGC	58.774	45.455	6.37	0.00	0.00	4.40
22	23	4.211389	GTGAGCGTGACACAAATAAACTG	58.789	43.478	6.37	0.00	38.05	3.16
23	24	3.874543	TGTGAGCGTGACACAAATAAACT	59.125	39.130	6.37	0.00	43.73	2.66
24	25	4.203950	TGTGAGCGTGACACAAATAAAC	57.796	40.909	6.37	0.00	43.73	2.01
44	45	1.492873	CAACACGAGACACCGCATG	59.507	57.895	0.00	0.00	0.00	4.06
45	46	2.317609	GCAACACGAGACACCGCAT	61.318	57.895	0.00	0.00	0.00	4.73
46	47	2.964925	GCAACACGAGACACCGCA	60.965	61.111	0.00	0.00	0.00	5.69
47	48	3.712881	GGCAACACGAGACACCGC	61.713	66.667	0.00	0.00	0.00	5.68

Showing 1 to 25 of 348 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.