AutoCloner

Multiple sequence alignment - TraesCS7D01G081700

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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	TraesCS7D01G081700	chr7D	100.000	7878	0	0	1	7878	48527336	48535213	0.000000e+00	14549
1	TraesCS7D01G081700	chr7D	94.571	571	28	3	294	862	503804485	503805054	0.000000e+00	880
2	TraesCS7D01G081700	chr7D	98.976	293	3	0	1	293	170515000	170515292	7.380000e-145	525
3	TraesCS7D01G081700	chr7D	98.976	293	3	0	1	293	586280659	586280367	7.380000e-145	525
4	TraesCS7D01G081700	chr7D	94.355	124	6	1	6966	7089	33478447	33478569	1.100000e-43	189
5	TraesCS7D01G081700	chr7D	100.000	59	0	0	8240	8298	48535575	48535633	8.810000e-20	110
6	TraesCS7D01G081700	chr4A	93.146	5311	252	61	882	6131	663276662	663281921	0.000000e+00	7688
7	TraesCS7D01G081700	chr4A	93.593	796	46	3	7086	7878	663282744	663283537	0.000000e+00	1182
8	TraesCS7D01G081700	chr4A	90.036	833	39	23	6182	6975	663281921	663282748	0.000000e+00	1038
9	TraesCS7D01G081700	chr7A	97.355	3478	69	13	1402	4873	51367677	51371137	0.000000e+00	5891
10	TraesCS7D01G081700	chr7A	95.260	2152	53	11	4866	6975	51371462	51373606	0.000000e+00	3363
11	TraesCS7D01G081700	chr7A	90.061	815	56	13	7086	7878	51373602	51374413	0.000000e+00	1033
12	TraesCS7D01G081700	chr7A	94.957	575	25	4	294	864	538376340	538376914	0.000000e+00	898
13	TraesCS7D01G081700	chr7A	94.431	413	20	3	883	1294	51366963	51367373	4.230000e-177	632
14	TraesCS7D01G081700	chr7A	98.438	64	0	1	7578	7641	51374068	51374130	2.450000e-20	111
15	TraesCS7D01G081700	chr4D	95.447	571	25	1	294	863	8142928	8142358	0.000000e+00	909
16	TraesCS7D01G081700	chr4D	98.980	294	3	0	1	294	291784682	291784975	2.050000e-145	527
17	TraesCS7D01G081700	chr4D	98.976	293	3	0	1	293	163814315	163814023	7.380000e-145	525
18	TraesCS7D01G081700	chr4D	98.976	293	3	0	1	293	412231902	412231610	7.380000e-145	525
19	TraesCS7D01G081700	chr5D	95.752	565	21	3	303	865	375212329	375212892	0.000000e+00	907
20	TraesCS7D01G081700	chr5D	84.571	175	25	2	6481	6653	297309721	297309547	1.110000e-38	172
21	TraesCS7D01G081700	chr3B	94.930	572	28	1	294	864	766959500	766960071	0.000000e+00	894
22	TraesCS7D01G081700	chr3B	91.304	138	9	3	6959	7096	605645719	605645585	1.420000e-42	185
23	TraesCS7D01G081700	chr2D	94.755	572	29	1	294	864	569112481	569111910	0.000000e+00	889
24	TraesCS7D01G081700	chr2D	98.976	293	3	0	1	293	496716057	496715765	7.380000e-145	525
25	TraesCS7D01G081700	chr2D	98.976	293	3	0	1	293	597699610	597699318	7.380000e-145	525
26	TraesCS7D01G081700	chr2D	91.176	136	9	2	6967	7101	158283415	158283282	1.840000e-41	182
27	TraesCS7D01G081700	chr3D	94.746	571	28	2	294	862	126221291	126220721	0.000000e+00	887
28	TraesCS7D01G081700	chr7B	95.035	564	26	2	303	864	457644469	457643906	0.000000e+00	885
29	TraesCS7D01G081700	chr7B	93.651	126	8	0	6964	7089	252178047	252178172	1.100000e-43	189
30	TraesCS7D01G081700	chr2A	94.561	570	30	1	294	862	494904297	494903728	0.000000e+00	880
31	TraesCS7D01G081700	chr2A	82.822	163	25	3	6490	6651	569587006	569587166	8.680000e-30	143
32	TraesCS7D01G081700	chr6D	98.976	293	3	0	1	293	189558579	189558287	7.380000e-145	525
33	TraesCS7D01G081700	chr1D	98.976	293	3	0	1	293	47670737	47671029	7.380000e-145	525
34	TraesCS7D01G081700	chr6B	93.939	132	7	1	6958	7089	183271168	183271298	1.830000e-46	198
35	TraesCS7D01G081700	chr3A	85.789	190	24	3	6475	6661	528529304	528529493	1.830000e-46	198
36	TraesCS7D01G081700	chr1B	93.701	127	8	0	6970	7096	667395282	667395156	3.060000e-44	191
37	TraesCS7D01G081700	chr1B	79.121	182	29	6	6481	6653	678263512	678263693	5.260000e-22	117
38	TraesCS7D01G081700	chr5B	92.537	134	7	3	6960	7091	90181683	90181815	1.100000e-43	189
39	TraesCS7D01G081700	chr2B	91.304	138	10	2	6959	7096	612672747	612672882	3.950000e-43	187
40	TraesCS7D01G081700	chr2B	92.913	127	9	0	6971	7097	182719478	182719604	1.420000e-42	185
41	TraesCS7D01G081700	chr4B	87.179	156	19	1	6490	6644	22850696	22850851	8.560000e-40	176
42	TraesCS7D01G081700	chr5A	84.000	175	26	2	6481	6653	401760745	401760919	5.150000e-37	167
43	TraesCS7D01G081700	chr6A	84.553	123	17	2	6490	6611	104117703	104117824	4.070000e-23	121

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	TraesCS7D01G081700	chr7D	48527336	48535633	8297	False	7329.500000	14549	100.000000	1	8298	2	chr7D.!!$F4	8297
1	TraesCS7D01G081700	chr7D	503804485	503805054	569	False	880.000000	880	94.571000	294	862	1	chr7D.!!$F3	568
2	TraesCS7D01G081700	chr4A	663276662	663283537	6875	False	3302.666667	7688	92.258333	882	7878	3	chr4A.!!$F1	6996
3	TraesCS7D01G081700	chr7A	51366963	51374413	7450	False	2206.000000	5891	95.109000	883	7878	5	chr7A.!!$F2	6995
4	TraesCS7D01G081700	chr7A	538376340	538376914	574	False	898.000000	898	94.957000	294	864	1	chr7A.!!$F1	570
5	TraesCS7D01G081700	chr4D	8142358	8142928	570	True	909.000000	909	95.447000	294	863	1	chr4D.!!$R1	569
6	TraesCS7D01G081700	chr5D	375212329	375212892	563	False	907.000000	907	95.752000	303	865	1	chr5D.!!$F1	562
7	TraesCS7D01G081700	chr3B	766959500	766960071	571	False	894.000000	894	94.930000	294	864	1	chr3B.!!$F1	570
8	TraesCS7D01G081700	chr2D	569111910	569112481	571	True	889.000000	889	94.755000	294	864	1	chr2D.!!$R3	570
9	TraesCS7D01G081700	chr3D	126220721	126221291	570	True	887.000000	887	94.746000	294	862	1	chr3D.!!$R1	568
10	TraesCS7D01G081700	chr7B	457643906	457644469	563	True	885.000000	885	95.035000	303	864	1	chr7B.!!$R1	561
11	TraesCS7D01G081700	chr2A	494903728	494904297	569	True	880.000000	880	94.561000	294	862	1	chr2A.!!$R1	568

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
68	69	0.107459	TGTGCGCCATTAGTATGCCA	60.107	50.000	4.18	0.00	0.00	4.92	F
159	160	0.108585	CTGGGGTGCGCCATTAGTAT	59.891	55.000	19.98	0.00	36.17	2.12	F
1309	1319	0.176680	CCTCGACAAGCTGCAGGTAT	59.823	55.000	20.51	10.77	0.00	2.73	F
1341	1351	0.260230	TGCCCCCTTCTCAAAACACA	59.740	50.000	0.00	0.00	0.00	3.72	F
2284	2493	0.632294	GAGGTCTCCAGGTCCCTAGT	59.368	60.000	0.00	0.00	0.00	2.57	F
3684	3899	0.667487	CCCAGCATGAGTATACGGCG	60.667	60.000	4.80	4.80	39.69	6.46	F
3831	4052	3.865745	CGAACACCTTTCAGCGATTCTAT	59.134	43.478	0.00	0.00	0.00	1.98	F
4987	5559	1.212688	TGAATATGACCCCTGGTGCAG	59.787	52.381	0.00	0.00	35.25	4.41	F
6552	7163	0.662619	CTTTCTGACCAAAGCGCACA	59.337	50.000	11.47	0.00	0.00	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1322	1332	0.260230	TGTGTTTTGAGAAGGGGGCA	59.740	50.000	0.00	0.00	0.00	5.36	R
1723	1929	0.892755	TCTTAGCACACACGGTAGGG	59.107	55.000	0.00	0.00	0.00	3.53	R
2523	2732	1.065701	ACGCTCGATAACAGCAGGTAG	59.934	52.381	0.00	0.00	36.61	3.18	R
2558	2767	3.814504	ACAGGTGAATCACAATTCCCT	57.185	42.857	15.86	0.00	40.40	4.20	R
4097	4319	0.804364	GATGATGCAAGAACACCGCA	59.196	50.000	0.00	0.00	40.50	5.69	R
4981	5553	0.105778	GCTGGATAGAGACCTGCACC	59.894	60.000	0.00	0.00	46.54	5.01	R
5229	5811	3.876274	AGTGATACGAAGCTGTCACAT	57.124	42.857	14.66	1.36	42.51	3.21	R
6975	7641	0.032813	AGTATTTCCGGACGGAGGGA	60.033	55.000	13.64	4.95	46.06	4.20	R
7422	8090	0.102844	GAAAGCCTGCAGTGCAACAA	59.897	50.000	20.22	0.00	41.43	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.299541	ACAGTGCGCCATTAGTATGC	58.700	50.000	4.18	0.00	0.00	3.14
21	22	0.588252	CAGTGCGCCATTAGTATGCC	59.412	55.000	4.18	0.00	0.00	4.40
22	23	0.880278	AGTGCGCCATTAGTATGCCG	60.880	55.000	4.18	0.00	35.84	5.69
23	24	0.878523	GTGCGCCATTAGTATGCCGA	60.879	55.000	4.18	0.00	34.77	5.54
24	25	0.179070	TGCGCCATTAGTATGCCGAA	60.179	50.000	4.18	0.00	34.77	4.30
25	26	0.512952	GCGCCATTAGTATGCCGAAG	59.487	55.000	0.00	0.00	34.77	3.79
26	27	1.865865	CGCCATTAGTATGCCGAAGT	58.134	50.000	0.00	0.00	34.77	3.01
27	28	2.210116	CGCCATTAGTATGCCGAAGTT	58.790	47.619	0.00	0.00	34.77	2.66
28	29	3.386486	CGCCATTAGTATGCCGAAGTTA	58.614	45.455	0.00	0.00	34.77	2.24
29	30	3.183775	CGCCATTAGTATGCCGAAGTTAC	59.816	47.826	0.00	0.00	34.77	2.50
30	31	4.377897	GCCATTAGTATGCCGAAGTTACT	58.622	43.478	0.00	0.00	0.00	2.24
31	32	5.535333	GCCATTAGTATGCCGAAGTTACTA	58.465	41.667	0.00	0.00	0.00	1.82
32	33	5.987347	GCCATTAGTATGCCGAAGTTACTAA	59.013	40.000	4.74	4.74	40.66	2.24
33	34	6.649557	GCCATTAGTATGCCGAAGTTACTAAT	59.350	38.462	8.16	8.16	44.24	1.73
36	37	4.377897	AGTATGCCGAAGTTACTAATGGC	58.622	43.478	13.29	13.29	42.76	4.40
37	38	1.647346	TGCCGAAGTTACTAATGGCG	58.353	50.000	14.62	2.53	45.34	5.69
38	39	0.303796	GCCGAAGTTACTAATGGCGC	59.696	55.000	0.00	0.00	32.14	6.53
39	40	1.647346	CCGAAGTTACTAATGGCGCA	58.353	50.000	10.83	0.00	0.00	6.09
40	41	2.210116	CCGAAGTTACTAATGGCGCAT	58.790	47.619	10.83	0.00	0.00	4.73
41	42	2.221055	CCGAAGTTACTAATGGCGCATC	59.779	50.000	10.83	0.00	0.00	3.91
42	43	2.221055	CGAAGTTACTAATGGCGCATCC	59.779	50.000	10.83	0.00	0.00	3.51
43	44	3.467803	GAAGTTACTAATGGCGCATCCT	58.532	45.455	10.83	0.00	35.26	3.24
44	45	2.838736	AGTTACTAATGGCGCATCCTG	58.161	47.619	10.83	0.00	35.26	3.86
45	46	2.170607	AGTTACTAATGGCGCATCCTGT	59.829	45.455	10.83	4.70	35.26	4.00
46	47	2.943033	GTTACTAATGGCGCATCCTGTT	59.057	45.455	10.83	0.00	35.26	3.16

Showing 1 to 25 of 403 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.670811	GCATACTAATGGCGCACTGTT	59.329	47.619	10.83	0.00	33.38	3.16
1	2	1.299541	GCATACTAATGGCGCACTGT	58.700	50.000	10.83	2.73	33.38	3.55
11	12	6.649557	GCCATTAGTAACTTCGGCATACTAAT	59.350	38.462	10.20	10.20	46.23	1.73
13	14	5.535333	GCCATTAGTAACTTCGGCATACTA	58.465	41.667	8.76	0.00	39.38	1.82
14	15	4.377897	GCCATTAGTAACTTCGGCATACT	58.622	43.478	8.76	0.00	39.38	2.12
15	16	3.183775	CGCCATTAGTAACTTCGGCATAC	59.816	47.826	12.43	0.00	39.56	2.39
16	17	3.386486	CGCCATTAGTAACTTCGGCATA	58.614	45.455	12.43	0.00	39.56	3.14
17	18	2.210116	CGCCATTAGTAACTTCGGCAT	58.790	47.619	12.43	0.00	39.56	4.40
18	19	1.647346	CGCCATTAGTAACTTCGGCA	58.353	50.000	12.43	0.00	39.56	5.69
19	20	0.303796	GCGCCATTAGTAACTTCGGC	59.696	55.000	0.00	0.00	36.16	5.54
20	21	1.647346	TGCGCCATTAGTAACTTCGG	58.353	50.000	4.18	0.00	0.00	4.30
21	22	2.221055	GGATGCGCCATTAGTAACTTCG	59.779	50.000	4.18	0.00	36.34	3.79
22	23	3.248602	CAGGATGCGCCATTAGTAACTTC	59.751	47.826	4.18	0.00	40.02	3.01
23	24	3.206150	CAGGATGCGCCATTAGTAACTT	58.794	45.455	4.18	0.00	40.02	2.66
24	25	2.170607	ACAGGATGCGCCATTAGTAACT	59.829	45.455	4.18	0.00	42.53	2.24
25	26	2.561569	ACAGGATGCGCCATTAGTAAC	58.438	47.619	4.18	0.00	42.53	2.50
26	27	2.942376	CAACAGGATGCGCCATTAGTAA	59.058	45.455	4.18	0.00	42.53	2.24
27	28	2.093181	ACAACAGGATGCGCCATTAGTA	60.093	45.455	4.18	0.00	42.53	1.82
28	29	1.340017	ACAACAGGATGCGCCATTAGT	60.340	47.619	4.18	0.00	42.53	2.24
29	30	1.382522	ACAACAGGATGCGCCATTAG	58.617	50.000	4.18	0.00	42.53	1.73
30	31	1.472082	CAACAACAGGATGCGCCATTA	59.528	47.619	4.18	0.00	42.53	1.90
31	32	0.244450	CAACAACAGGATGCGCCATT	59.756	50.000	4.18	0.00	42.53	3.16
32	33	0.895100	ACAACAACAGGATGCGCCAT	60.895	50.000	4.18	0.00	42.53	4.40
33	34	1.528076	ACAACAACAGGATGCGCCA	60.528	52.632	4.18	0.00	42.53	5.69
34	35	1.081242	CACAACAACAGGATGCGCC	60.081	57.895	4.18	0.00	42.53	6.53

Showing 1 to 25 of 425 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.