AutoCloner

Multiple sequence alignment - TraesCS3B01G293200

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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	TraesCS3B01G293200	chr3B	100.000	3071	0	0	1	3071	472307984	472304914	0.000000e+00	5672.0
1	TraesCS3B01G293200	chr3B	91.577	1021	79	4	1315	2330	472586375	472587393	0.000000e+00	1402.0
2	TraesCS3B01G293200	chr3B	91.103	517	23	4	822	1315	472584790	472585306	0.000000e+00	678.0
3	TraesCS3B01G293200	chr3B	86.863	373	21	9	444	790	472584423	472584793	2.870000e-105	392.0
4	TraesCS3B01G293200	chr3D	92.688	2366	114	16	1	2330	362425689	362423347	0.000000e+00	3356.0
5	TraesCS3B01G293200	chr3D	90.562	1886	97	29	488	2330	362854910	362856757	0.000000e+00	2422.0
6	TraesCS3B01G293200	chr3A	90.188	2395	156	27	1	2330	482938117	482935737	0.000000e+00	3048.0
7	TraesCS3B01G293200	chr3A	91.101	1843	93	26	547	2330	482929320	482927490	0.000000e+00	2429.0
8	TraesCS3B01G293200	chr3A	90.769	65	3	2	469	530	482929424	482929360	1.960000e-12	84.2
9	TraesCS3B01G293200	chr5D	97.185	746	21	0	2326	3071	298795167	298795912	0.000000e+00	1262.0
10	TraesCS3B01G293200	chr5D	94.444	756	25	4	2326	3064	433930150	433930905	0.000000e+00	1147.0
11	TraesCS3B01G293200	chr2B	97.067	750	18	4	2324	3071	616480491	616481238	0.000000e+00	1260.0
12	TraesCS3B01G293200	chr2D	96.787	747	23	1	2326	3071	590375612	590376358	0.000000e+00	1245.0
13	TraesCS3B01G293200	chr2D	96.118	747	28	1	2326	3071	545604353	545603607	0.000000e+00	1218.0
14	TraesCS3B01G293200	chr2D	86.340	754	76	12	2326	3062	401954227	401953484	0.000000e+00	797.0
15	TraesCS3B01G293200	chr2D	80.021	941	153	26	1099	2029	637802164	637803079	0.000000e+00	664.0
16	TraesCS3B01G293200	chr6B	95.850	747	29	2	2326	3071	240431517	240432262	0.000000e+00	1206.0
17	TraesCS3B01G293200	chr7D	93.421	760	37	5	2325	3071	54052496	54051737	0.000000e+00	1114.0
18	TraesCS3B01G293200	chr5B	92.904	761	36	3	2326	3069	522136159	522135400	0.000000e+00	1090.0
19	TraesCS3B01G293200	chr1A	86.034	759	85	6	2326	3066	572710476	572711231	0.000000e+00	795.0
20	TraesCS3B01G293200	chr1A	82.036	167	30	0	1091	1257	441842041	441842207	3.190000e-30	143.0
21	TraesCS3B01G293200	chr7A	83.425	730	115	5	1298	2024	722767915	722768641	0.000000e+00	673.0
22	TraesCS3B01G293200	chr7B	82.574	746	122	7	1298	2039	727536981	727536240	0.000000e+00	651.0
23	TraesCS3B01G293200	chrUn	78.855	908	163	22	1127	2027	249446248	249447133	1.230000e-163	586.0
24	TraesCS3B01G293200	chr1D	81.437	167	31	0	1091	1257	342170302	342170468	1.490000e-28	137.0
25	TraesCS3B01G293200	chr2A	84.946	93	12	2	2303	2394	65952061	65951970	3.260000e-15	93.5
26	TraesCS3B01G293200	chr6A	91.111	45	1	2	638	679	599757461	599757505	1.190000e-04	58.4

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	TraesCS3B01G293200	chr3B	472304914	472307984	3070	True	5672.0	5672	100.000000	1	3071	1	chr3B.!!$R1	3070
1	TraesCS3B01G293200	chr3B	472584423	472587393	2970	False	824.0	1402	89.847667	444	2330	3	chr3B.!!$F1	1886
2	TraesCS3B01G293200	chr3D	362423347	362425689	2342	True	3356.0	3356	92.688000	1	2330	1	chr3D.!!$R1	2329
3	TraesCS3B01G293200	chr3D	362854910	362856757	1847	False	2422.0	2422	90.562000	488	2330	1	chr3D.!!$F1	1842
4	TraesCS3B01G293200	chr3A	482935737	482938117	2380	True	3048.0	3048	90.188000	1	2330	1	chr3A.!!$R1	2329
5	TraesCS3B01G293200	chr3A	482927490	482929424	1934	True	1256.6	2429	90.935000	469	2330	2	chr3A.!!$R2	1861
6	TraesCS3B01G293200	chr5D	298795167	298795912	745	False	1262.0	1262	97.185000	2326	3071	1	chr5D.!!$F1	745
7	TraesCS3B01G293200	chr5D	433930150	433930905	755	False	1147.0	1147	94.444000	2326	3064	1	chr5D.!!$F2	738
8	TraesCS3B01G293200	chr2B	616480491	616481238	747	False	1260.0	1260	97.067000	2324	3071	1	chr2B.!!$F1	747
9	TraesCS3B01G293200	chr2D	590375612	590376358	746	False	1245.0	1245	96.787000	2326	3071	1	chr2D.!!$F1	745
10	TraesCS3B01G293200	chr2D	545603607	545604353	746	True	1218.0	1218	96.118000	2326	3071	1	chr2D.!!$R2	745
11	TraesCS3B01G293200	chr2D	401953484	401954227	743	True	797.0	797	86.340000	2326	3062	1	chr2D.!!$R1	736
12	TraesCS3B01G293200	chr2D	637802164	637803079	915	False	664.0	664	80.021000	1099	2029	1	chr2D.!!$F2	930
13	TraesCS3B01G293200	chr6B	240431517	240432262	745	False	1206.0	1206	95.850000	2326	3071	1	chr6B.!!$F1	745
14	TraesCS3B01G293200	chr7D	54051737	54052496	759	True	1114.0	1114	93.421000	2325	3071	1	chr7D.!!$R1	746
15	TraesCS3B01G293200	chr5B	522135400	522136159	759	True	1090.0	1090	92.904000	2326	3069	1	chr5B.!!$R1	743
16	TraesCS3B01G293200	chr1A	572710476	572711231	755	False	795.0	795	86.034000	2326	3066	1	chr1A.!!$F2	740
17	TraesCS3B01G293200	chr7A	722767915	722768641	726	False	673.0	673	83.425000	1298	2024	1	chr7A.!!$F1	726
18	TraesCS3B01G293200	chr7B	727536240	727536981	741	True	651.0	651	82.574000	1298	2039	1	chr7B.!!$R1	741
19	TraesCS3B01G293200	chrUn	249446248	249447133	885	False	586.0	586	78.855000	1127	2027	1	chrUn.!!$F1	900

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
176	177	0.534412	AGGTGTCCAATCTGCTCTCG	59.466	55.0	0.0	0.0	0.0	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2108	3342	0.108329	TTCGCTTGTACTAGGCCAGC	60.108	55.0	5.01	1.39	0.0	4.85	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
69	70	1.338579	GGAAGAGGAGTTGGAGCACTG	60.339	57.143	0.00	0.00	0.00	3.66
72	73	1.152030	AGGAGTTGGAGCACTGGGA	60.152	57.895	0.00	0.00	0.00	4.37
86	87	2.196776	GGGATGCTCCACCCCATG	59.803	66.667	0.00	0.00	38.64	3.66
170	171	3.981071	TGAACCTAGGTGTCCAATCTG	57.019	47.619	17.14	0.00	0.00	2.90
176	177	0.534412	AGGTGTCCAATCTGCTCTCG	59.466	55.000	0.00	0.00	0.00	4.04
198	199	6.415702	TCGTGTGAAGTTTCGTGAAAAATAG	58.584	36.000	0.00	0.00	31.33	1.73
272	279	7.931578	AAAATACTGTTTGGATGGATCGTAA	57.068	32.000	0.00	0.00	0.00	3.18
290	297	1.168714	AAGCCGGACTGCATTTTCTC	58.831	50.000	5.05	0.00	0.00	2.87
296	303	1.464997	GGACTGCATTTTCTCCGACAC	59.535	52.381	0.00	0.00	0.00	3.67
333	340	7.687941	TGATATCTTTTCAGGAAACTTCACC	57.312	36.000	3.98	0.00	40.21	4.02
352	359	1.825474	CCCGTGAGTAGATTGGACACT	59.175	52.381	0.00	0.00	0.00	3.55
376	383	3.719871	GGTTTGATACCCCCAAATTCCT	58.280	45.455	0.00	0.00	41.43	3.36
377	384	4.101114	GGTTTGATACCCCCAAATTCCTT	58.899	43.478	0.00	0.00	41.43	3.36
452	478	2.457598	CACCCAGGAGCTCTAGTGTAA	58.542	52.381	14.64	0.00	0.00	2.41
456	482	4.536489	ACCCAGGAGCTCTAGTGTAATTTT	59.464	41.667	14.64	0.00	0.00	1.82
467	493	8.653338	GCTCTAGTGTAATTTTCGTTGTAATGA	58.347	33.333	0.00	0.00	0.00	2.57
810	926	5.344743	TTCCATTAGTGATCACTGACTCC	57.655	43.478	33.76	3.83	42.52	3.85
818	934	4.013728	GTGATCACTGACTCCTCTGTAGT	58.986	47.826	18.83	0.00	0.00	2.73
1014	1139	1.717791	CTGGCACACACACACCACTG	61.718	60.000	0.00	0.00	0.00	3.66
1406	2630	0.033781	ACAACTACGGCGCCTTTGTA	59.966	50.000	26.68	18.03	0.00	2.41
1817	3041	2.959372	TCGAGCCACGACGTGATT	59.041	55.556	28.83	15.92	46.45	2.57
2100	3334	7.604927	TCTCTAAATACTGTAACAATGGCGTTT	59.395	33.333	0.00	0.00	0.00	3.60
2248	3487	6.309494	GCCCGACTTTAAATTAATGAAACCAC	59.691	38.462	5.76	0.00	0.00	4.16
2268	3507	3.353370	CCAACCGGGTAGGATACAAAA	57.647	47.619	6.32	0.00	45.43	2.44
2277	3516	5.277974	CGGGTAGGATACAAAATGCAGATTG	60.278	44.000	11.53	11.53	45.43	2.67
2278	3517	5.827797	GGGTAGGATACAAAATGCAGATTGA	59.172	40.000	18.13	5.45	45.43	2.57
2287	3526	4.637483	AAATGCAGATTGATACAACGGG	57.363	40.909	0.00	0.00	0.00	5.28
2443	3684	5.642063	AGATAACACAAACACAATCGGGTAG	59.358	40.000	0.00	0.00	0.00	3.18
2684	3925	7.445402	ACCCATTCTGTACAAGCAATATATGTC	59.555	37.037	0.00	0.00	0.00	3.06
2809	4066	2.446435	CGGACACATCCCTTCCATTTT	58.554	47.619	0.00	0.00	42.83	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	7.716998	ACAGACATTTCACATGTTAAGAACTCT	59.283	33.333	0.00	0.00	31.52	3.24
15	16	7.865707	ACAGACATTTCACATGTTAAGAACTC	58.134	34.615	0.00	0.00	31.52	3.01
25	26	6.094719	CCCATTACAACAGACATTTCACATG	58.905	40.000	0.00	0.00	0.00	3.21
35	36	3.263425	TCCTCTTCCCCATTACAACAGAC	59.737	47.826	0.00	0.00	0.00	3.51
37	38	3.264450	ACTCCTCTTCCCCATTACAACAG	59.736	47.826	0.00	0.00	0.00	3.16
72	73	1.422781	CTCATACATGGGGTGGAGCAT	59.577	52.381	0.00	0.00	0.00	3.79
142	143	3.974642	GGACACCTAGGTTCAATATCCCT	59.025	47.826	13.15	0.00	0.00	4.20
150	151	2.027192	GCAGATTGGACACCTAGGTTCA	60.027	50.000	13.15	8.47	0.00	3.18
151	152	2.237392	AGCAGATTGGACACCTAGGTTC	59.763	50.000	13.15	13.01	0.00	3.62
170	171	1.190323	CACGAAACTTCACACGAGAGC	59.810	52.381	0.00	0.00	0.00	4.09
176	177	5.968848	TGCTATTTTTCACGAAACTTCACAC	59.031	36.000	0.00	0.00	0.00	3.82
198	199	8.728088	TTTTTCTTCGAGAATACATTTTCTGC	57.272	30.769	0.00	0.00	36.10	4.26
272	279	0.678048	GGAGAAAATGCAGTCCGGCT	60.678	55.000	0.00	0.00	34.04	5.52
296	303	8.607441	TGAAAAGATATCAGGAAATGTATCCG	57.393	34.615	5.32	0.00	44.60	4.18
333	340	2.492088	TGAGTGTCCAATCTACTCACGG	59.508	50.000	0.00	0.00	44.10	4.94
436	462	5.411781	ACGAAAATTACACTAGAGCTCCTG	58.588	41.667	10.93	6.04	0.00	3.86
437	463	5.662674	ACGAAAATTACACTAGAGCTCCT	57.337	39.130	10.93	0.10	0.00	3.69
439	465	6.707599	ACAACGAAAATTACACTAGAGCTC	57.292	37.500	5.27	5.27	0.00	4.09
441	467	8.653338	TCATTACAACGAAAATTACACTAGAGC	58.347	33.333	0.00	0.00	0.00	4.09
452	478	7.925993	TGAACAGTCTTCATTACAACGAAAAT	58.074	30.769	0.00	0.00	0.00	1.82
456	482	7.817478	ACATATGAACAGTCTTCATTACAACGA	59.183	33.333	10.38	0.00	39.59	3.85
486	514	2.159382	CCGACCAGGCAAACTATGTTT	58.841	47.619	0.00	0.00	0.00	2.83
810	926	5.677612	CGATTCGTGTAAGCTAACTACAGAG	59.322	44.000	0.00	0.00	0.00	3.35
818	934	4.177165	TGTTCCGATTCGTGTAAGCTAA	57.823	40.909	5.20	0.00	0.00	3.09
2100	3334	2.105993	TGTACTAGGCCAGCTCTATCGA	59.894	50.000	5.01	0.00	0.00	3.59
2108	3342	0.108329	TTCGCTTGTACTAGGCCAGC	60.108	55.000	5.01	1.39	0.00	4.85
2111	3345	3.746492	CCATTATTCGCTTGTACTAGGCC	59.254	47.826	6.46	0.00	0.00	5.19
2149	3388	5.609696	GCATTATAATCGACTACACACGCAC	60.610	44.000	0.00	0.00	0.00	5.34
2248	3487	3.353370	TTTTGTATCCTACCCGGTTGG	57.647	47.619	11.56	11.56	41.37	3.77
2268	3507	2.945008	CACCCGTTGTATCAATCTGCAT	59.055	45.455	0.00	0.00	0.00	3.96
2277	3516	1.087202	TCATGCGCACCCGTTGTATC	61.087	55.000	14.90	0.00	36.67	2.24
2278	3517	1.078778	TCATGCGCACCCGTTGTAT	60.079	52.632	14.90	0.00	36.67	2.29
2640	3881	3.454812	TGGGTATAAGTCAAGGAAGAGGC	59.545	47.826	0.00	0.00	0.00	4.70
2684	3925	9.499585	CTTTGATGAGAAGTATTTGTGCTAATG	57.500	33.333	0.00	0.00	0.00	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.