AutoCloner

Multiple sequence alignment - TraesCS3D01G454900

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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	TraesCS3D01G454900	chr3D	100.000	3515	0	0	1	3515	561374931	561378445	0.000000e+00	6492
1	TraesCS3D01G454900	chr3D	94.236	2030	104	4	444	2460	561171862	561173891	0.000000e+00	3088
2	TraesCS3D01G454900	chr3D	93.796	2031	111	8	444	2460	561155488	561157517	0.000000e+00	3038
3	TraesCS3D01G454900	chr3D	91.939	459	22	7	2	446	561154991	561155448	2.300000e-176	628
4	TraesCS3D01G454900	chr3D	90.850	459	27	6	2	446	561171365	561171822	5.020000e-168	601
5	TraesCS3D01G454900	chr3B	95.578	2352	63	8	444	2769	747851212	747853548	0.000000e+00	3729
6	TraesCS3D01G454900	chr3B	95.493	2352	65	8	444	2769	747822209	747824545	0.000000e+00	3718
7	TraesCS3D01G454900	chr3B	95.408	2352	67	7	444	2769	747834685	747837021	0.000000e+00	3707
8	TraesCS3D01G454900	chr3B	95.366	2352	68	7	444	2769	747838737	747841073	0.000000e+00	3701
9	TraesCS3D01G454900	chr3B	94.000	2300	113	11	1229	3515	748414696	748416983	0.000000e+00	3459
10	TraesCS3D01G454900	chr3B	80.435	2162	349	41	451	2563	748453431	748455567	0.000000e+00	1581
11	TraesCS3D01G454900	chr3B	93.342	781	39	5	2741	3515	747824700	747825473	0.000000e+00	1142
12	TraesCS3D01G454900	chr3B	93.342	781	39	5	2741	3515	747841228	747842001	0.000000e+00	1142
13	TraesCS3D01G454900	chr3B	93.342	781	39	5	2741	3515	747853703	747854476	0.000000e+00	1142
14	TraesCS3D01G454900	chr3B	92.958	781	42	5	2741	3515	747837176	747837949	0.000000e+00	1125
15	TraesCS3D01G454900	chr3B	95.302	447	20	1	1	446	747821723	747822169	0.000000e+00	708
16	TraesCS3D01G454900	chr3B	95.302	447	20	1	1	446	747850726	747851172	0.000000e+00	708
17	TraesCS3D01G454900	chr3B	95.078	447	21	1	1	446	747834199	747834645	0.000000e+00	702
18	TraesCS3D01G454900	chr3B	94.930	355	17	1	93	446	747838343	747838697	3.960000e-154	555
19	TraesCS3D01G454900	chr3B	79.234	679	117	18	469	1129	748413842	748414514	5.350000e-123	451
20	TraesCS3D01G454900	chr3A	95.011	2245	95	10	448	2675	697261426	697263670	0.000000e+00	3509
21	TraesCS3D01G454900	chr3A	91.723	737	45	6	2777	3507	697263670	697264396	0.000000e+00	1009
22	TraesCS3D01G454900	chr3A	92.511	454	26	4	1	446	697260928	697261381	0.000000e+00	643
23	TraesCS3D01G454900	chrUn	97.252	1492	34	1	1285	2769	331495088	331496579	0.000000e+00	2521
24	TraesCS3D01G454900	chrUn	93.086	781	41	5	2741	3515	331496734	331497507	0.000000e+00	1131
25	TraesCS3D01G454900	chrUn	95.303	511	17	3	2741	3250	455312332	455311828	0.000000e+00	804
26	TraesCS3D01G454900	chrUn	95.078	447	21	1	1	446	354243093	354243539	0.000000e+00	702
27	TraesCS3D01G454900	chrUn	95.556	315	7	1	2462	2769	455312801	455312487	6.780000e-137	497

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	TraesCS3D01G454900	chr3D	561374931	561378445	3514	False	6492.000000	6492	100.000000	1	3515	1	chr3D.!!$F1	3514
1	TraesCS3D01G454900	chr3D	561171365	561173891	2526	False	1844.500000	3088	92.543000	2	2460	2	chr3D.!!$F3	2458
2	TraesCS3D01G454900	chr3D	561154991	561157517	2526	False	1833.000000	3038	92.867500	2	2460	2	chr3D.!!$F2	2458
3	TraesCS3D01G454900	chr3B	748413842	748416983	3141	False	1955.000000	3459	86.617000	469	3515	2	chr3B.!!$F5	3046
4	TraesCS3D01G454900	chr3B	747850726	747854476	3750	False	1859.666667	3729	94.740667	1	3515	3	chr3B.!!$F4	3514
5	TraesCS3D01G454900	chr3B	747821723	747825473	3750	False	1856.000000	3718	94.712333	1	3515	3	chr3B.!!$F2	3514
6	TraesCS3D01G454900	chr3B	747834199	747842001	7802	False	1822.000000	3707	94.513667	1	3515	6	chr3B.!!$F3	3514
7	TraesCS3D01G454900	chr3B	748453431	748455567	2136	False	1581.000000	1581	80.435000	451	2563	1	chr3B.!!$F1	2112
8	TraesCS3D01G454900	chr3A	697260928	697264396	3468	False	1720.333333	3509	93.081667	1	3507	3	chr3A.!!$F1	3506
9	TraesCS3D01G454900	chrUn	331495088	331497507	2419	False	1826.000000	2521	95.169000	1285	3515	2	chrUn.!!$F2	2230
10	TraesCS3D01G454900	chrUn	455311828	455312801	973	True	650.500000	804	95.429500	2462	3250	2	chrUn.!!$R1	788

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
232	234	1.177401	GGCATCAAACTTCCCTCCAC	58.823	55.000	0.00	0.00	0.00	4.02	F
1120	1201	3.634910	TGGAACTGTTGCCTTAACTTTCC	59.365	43.478	9.61	12.74	44.28	3.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1191	1366	1.803334	TCTGTAATTCGTGGTGCACC	58.197	50.000	29.67	29.67	0.00	5.01	R
2917	7342	1.004440	GTGCCAGTCACTCCTCCAC	60.004	63.158	0.00	0.00	42.38	4.02	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
89	90	4.820894	TCTAAGGAGGCTTGGAAACTAC	57.179	45.455	0.00	0.00	0.00	2.73
209	210	7.798486	AGAGACGTTTATTACATATCGCATC	57.202	36.000	0.00	0.00	0.00	3.91
213	214	7.105494	ACGTTTATTACATATCGCATCAGTG	57.895	36.000	0.00	0.00	0.00	3.66
232	234	1.177401	GGCATCAAACTTCCCTCCAC	58.823	55.000	0.00	0.00	0.00	4.02
1044	1125	8.267620	AGATCAAATCATTAGTAGACATGGGA	57.732	34.615	0.00	0.00	0.00	4.37
1100	1181	6.207417	ACAAGATGTGGTATGACTCTTTTTGG	59.793	38.462	0.00	0.00	0.00	3.28
1113	1194	4.953579	ACTCTTTTTGGAACTGTTGCCTTA	59.046	37.500	9.61	0.00	0.00	2.69
1120	1201	3.634910	TGGAACTGTTGCCTTAACTTTCC	59.365	43.478	9.61	12.74	44.28	3.13
1188	1363	7.648142	TGATTTATGGGAATTAGTTGATTCGC	58.352	34.615	7.47	7.47	44.59	4.70
1191	1366	7.962964	TTATGGGAATTAGTTGATTCGCTAG	57.037	36.000	13.41	0.00	44.61	3.42
1294	1475	7.815549	TGTATATGAAAACACTTACGCTCTTCA	59.184	33.333	0.00	0.00	0.00	3.02
1734	1915	4.464008	TGCCAATTGAGAATAGATCACCC	58.536	43.478	7.12	0.00	0.00	4.61
1744	1925	4.657969	AGAATAGATCACCCCTTCTTCCTG	59.342	45.833	0.00	0.00	0.00	3.86
1749	1930	2.356667	CCCCTTCTTCCTGTGCCC	59.643	66.667	0.00	0.00	0.00	5.36
1764	1945	2.031870	GTGCCCCCAAAGACCATATTC	58.968	52.381	0.00	0.00	0.00	1.75
2505	6739	0.108186	CGGTCAAGTCAGCTATGGCA	60.108	55.000	3.10	0.00	41.70	4.92
2614	6849	7.326454	TGATTTGATGTTGTTTTCAAGACCAA	58.674	30.769	0.00	0.00	40.74	3.67
2746	6988	6.919721	TGAAATTAGTGAACACAATAAGGGC	58.080	36.000	7.68	0.00	29.93	5.19
2754	6996	3.237268	ACACAATAAGGGCAAAGGACA	57.763	42.857	0.00	0.00	0.00	4.02
2791	7216	5.344066	CATGGAAGCCTATATACTACAGCG	58.656	45.833	0.00	0.00	0.00	5.18
2917	7342	5.664457	TGTACATATTGCACAGGAGAGAAG	58.336	41.667	0.00	0.00	0.00	2.85
2932	7357	1.548269	GAGAAGTGGAGGAGTGACTGG	59.452	57.143	0.00	0.00	0.00	4.00
2933	7358	0.036858	GAAGTGGAGGAGTGACTGGC	60.037	60.000	0.00	0.00	0.00	4.85
2934	7359	0.764369	AAGTGGAGGAGTGACTGGCA	60.764	55.000	0.00	0.00	0.00	4.92
3029	7454	6.493458	AGATAGTCCTCTCTATGCCTTTTCTC	59.507	42.308	0.00	0.00	31.71	2.87
3262	7688	4.733850	TGTACTAGACGTTGCATCTGAAG	58.266	43.478	0.00	0.00	0.00	3.02
3279	7705	8.924691	GCATCTGAAGATAATCTTGCTAACTAG	58.075	37.037	0.00	0.00	36.73	2.57
3280	7706	9.979578	CATCTGAAGATAATCTTGCTAACTAGT	57.020	33.333	0.00	0.00	36.73	2.57
3364	7790	7.166167	AGGATTTAAGACGTGTAAATTCAGGT	58.834	34.615	16.52	0.00	38.78	4.00
3454	7885	0.307760	CAGGTGAACAAAGGTCGTGC	59.692	55.000	0.00	0.00	0.00	5.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	7.560626	AGACCTAGTTCTTACTAACCTACATGG	59.439	40.741	0.00	0.00	36.46	3.66
109	110	9.280174	CAATGTGGTTTAGTTCTTTAAGACCTA	57.720	33.333	0.00	0.00	0.00	3.08
188	189	7.220604	CACTGATGCGATATGTAATAAACGTC	58.779	38.462	0.00	0.00	35.94	4.34
209	210	1.815003	GAGGGAAGTTTGATGCCACTG	59.185	52.381	0.00	0.00	0.00	3.66
213	214	1.177401	GTGGAGGGAAGTTTGATGCC	58.823	55.000	0.00	0.00	0.00	4.40
232	234	3.539604	CCACTCTTCCTGAGGCTATTTG	58.460	50.000	0.00	0.00	46.72	2.32
330	332	5.111989	TGAAGTGAGCAATAGGATTTCTCG	58.888	41.667	0.00	0.00	0.00	4.04
587	653	8.967664	AGGTACATGTCTAACTTTGTTGTTTA	57.032	30.769	0.00	0.00	0.00	2.01
655	726	5.481105	TGCTTCCCAATTTATGCTTGAAAG	58.519	37.500	0.00	0.00	0.00	2.62
697	770	6.556212	TGAGAATGACTTCATTACGAGAGTC	58.444	40.000	4.42	0.00	45.72	3.36
797	871	6.615726	TGAATAGCCCAGACTACCTAAGAAAT	59.384	38.462	0.00	0.00	0.00	2.17
854	929	5.986135	CACATATAGGGACGGAGAAAAGAAG	59.014	44.000	0.00	0.00	0.00	2.85
1044	1125	7.709613	GCCATATTTGCTTCATCTTCAGAAAAT	59.290	33.333	0.00	0.00	0.00	1.82
1100	1181	5.515797	AAGGAAAGTTAAGGCAACAGTTC	57.484	39.130	0.00	0.00	39.81	3.01
1120	1201	8.837788	ATTTAAGATGCCTTTCTTGGAAAAAG	57.162	30.769	4.44	0.00	36.63	2.27
1188	1363	2.930040	CTGTAATTCGTGGTGCACCTAG	59.070	50.000	34.75	26.90	36.82	3.02
1191	1366	1.803334	TCTGTAATTCGTGGTGCACC	58.197	50.000	29.67	29.67	0.00	5.01
1500	1681	7.297391	GTTGCAAATAACCTGGCAAATTAAAG	58.703	34.615	0.00	0.00	46.50	1.85
1734	1915	2.080336	TTGGGGGCACAGGAAGAAGG	62.080	60.000	0.00	0.00	0.00	3.46
1744	1925	2.031870	GAATATGGTCTTTGGGGGCAC	58.968	52.381	0.00	0.00	0.00	5.01
1749	1930	2.222027	GCCTCGAATATGGTCTTTGGG	58.778	52.381	0.00	0.00	0.00	4.12
1764	1945	2.620251	TGTAATGAGGGAATGCCTCG	57.380	50.000	16.02	0.00	37.14	4.63
1992	2173	5.413213	ACCGAGTAGATATTCCATCTCTTCG	59.587	44.000	10.77	10.77	35.63	3.79
2505	6739	7.661847	GTGCTACAATAATTAGGCTACATCCTT	59.338	37.037	0.00	0.00	37.66	3.36
2614	6849	4.641094	TCGTCTACACAAACCACCAAATTT	59.359	37.500	0.00	0.00	0.00	1.82
2731	6973	3.572255	GTCCTTTGCCCTTATTGTGTTCA	59.428	43.478	0.00	0.00	0.00	3.18
2791	7216	6.205658	AGGTTGACTGCAGAAAAAGATAAGAC	59.794	38.462	23.35	0.31	0.00	3.01
2917	7342	1.004440	GTGCCAGTCACTCCTCCAC	60.004	63.158	0.00	0.00	42.38	4.02
3020	7445	4.454504	TGAAACATTCTACCGAGAAAAGGC	59.545	41.667	0.00	0.00	44.85	4.35
3029	7454	7.757526	TGGTATGAAAATGAAACATTCTACCG	58.242	34.615	0.00	0.00	33.88	4.02
3205	7631	8.053963	CCCCTCCGAAAGAGAGATAATATAGTA	58.946	40.741	0.00	0.00	46.50	1.82
3262	7688	6.858993	CGACTCCACTAGTTAGCAAGATTATC	59.141	42.308	0.00	0.00	39.07	1.75
3279	7705	2.822764	ACAACAGAAACTCGACTCCAC	58.177	47.619	0.00	0.00	0.00	4.02
3280	7706	3.118920	TCAACAACAGAAACTCGACTCCA	60.119	43.478	0.00	0.00	0.00	3.86
3448	7879	2.280119	TCACTGCCACTGCACGAC	60.280	61.111	0.00	0.00	44.23	4.34
3454	7885	2.106566	AGGTATCTCTCACTGCCACTG	58.893	52.381	0.00	0.00	0.00	3.66
3466	7897	2.439507	TGGGAGGCAATCAAGGTATCTC	59.560	50.000	0.00	0.00	0.00	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.