AutoCloner

Multiple sequence alignment - TraesCS3A01G112700

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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	TraesCS3A01G112700	chr3A	100.000	2420	0	0	1	2420	80101807	80104226	0.000000e+00	4470.0
1	TraesCS3A01G112700	chr3A	81.214	346	57	7	715	1056	82744567	82744226	3.070000e-69	272.0
2	TraesCS3A01G112700	chr3A	90.210	143	12	1	671	811	80102230	80102088	4.110000e-43	185.0
3	TraesCS3A01G112700	chr3A	90.210	143	12	1	285	427	80102614	80102474	4.110000e-43	185.0
4	TraesCS3A01G112700	chr3A	72.015	536	132	16	1238	1764	138807706	138808232	2.510000e-30	143.0
5	TraesCS3A01G112700	chr3A	75.000	304	56	16	729	1028	79905458	79905171	3.270000e-24	122.0
6	TraesCS3A01G112700	chr3A	73.899	318	60	18	715	1028	79875911	79875613	3.290000e-19	106.0
7	TraesCS3A01G112700	chr3B	93.287	2428	88	25	21	2420	113929423	113931803	0.000000e+00	3511.0
8	TraesCS3A01G112700	chr3B	83.862	347	48	7	715	1057	116390560	116390218	8.350000e-85	324.0
9	TraesCS3A01G112700	chr3B	82.370	346	53	7	715	1056	116438025	116437684	6.540000e-76	294.0
10	TraesCS3A01G112700	chr3B	74.168	511	113	18	1337	1838	182203950	182204450	6.830000e-46	195.0
11	TraesCS3A01G112700	chr3B	90.909	143	11	1	285	427	113930197	113930057	8.830000e-45	191.0
12	TraesCS3A01G112700	chr3B	71.816	369	77	23	666	1028	182203183	182203530	1.990000e-11	80.5
13	TraesCS3A01G112700	chr3D	95.006	1542	60	7	21	1546	68072967	68071427	0.000000e+00	2405.0
14	TraesCS3A01G112700	chr3D	95.122	1271	41	5	1169	2420	68071404	68070136	0.000000e+00	1984.0
15	TraesCS3A01G112700	chr3D	84.058	345	49	6	715	1056	71116343	71116002	6.450000e-86	327.0
16	TraesCS3A01G112700	chr3D	90.541	148	7	2	668	808	68072548	68072695	3.180000e-44	189.0
17	TraesCS3A01G112700	chr3D	90.000	140	11	1	285	424	68072166	68072302	6.880000e-41	178.0
18	TraesCS3A01G112700	chr3D	76.056	355	73	12	1490	1838	127904682	127905030	8.890000e-40	174.0
19	TraesCS3A01G112700	chr3D	88.182	110	6	4	2292	2400	68069649	68069546	9.080000e-25	124.0
20	TraesCS3A01G112700	chr2B	95.146	206	6	2	1811	2014	557352276	557352073	3.000000e-84	322.0

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	TraesCS3A01G112700	chr3A	80101807	80104226	2419	False	4470.000000	4470	100.000	1	2420	1	chr3A.!!$F1	2419
1	TraesCS3A01G112700	chr3B	113929423	113931803	2380	False	3511.000000	3511	93.287	21	2420	1	chr3B.!!$F1	2399
2	TraesCS3A01G112700	chr3D	68069546	68072967	3421	True	1504.333333	2405	92.770	21	2420	3	chr3D.!!$R2	2399

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
857	879	2.116869	TAATGCATGAGGCCCTCCTA	57.883	50.0	8.62	0.0	44.46	2.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1790	2212	2.159254	TGCTTTCATCCATTTTAGCGCC	60.159	45.455	2.29	0.0	0.0	6.53	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
57	58	7.557358	TGAGGAAGTGACAAATGCATTATGTAT	59.443	33.333	13.39	6.58	0.00	2.29
97	98	8.488651	AATACTAACATAGTTTGAGGTTTCCG	57.511	34.615	0.00	0.00	40.14	4.30
169	170	9.924650	AAGGCGGTATAGTTGTATATCTAAAAG	57.075	33.333	0.00	0.00	0.00	2.27
258	264	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
260	266	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
262	268	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
263	269	5.523588	TCTCTCTCTCTCTCTCTCTCTCTT	58.476	45.833	0.00	0.00	0.00	2.85
266	275	5.960811	TCTCTCTCTCTCTCTCTCTCTTTCT	59.039	44.000	0.00	0.00	0.00	2.52
325	334	9.775539	TCCATATAATATCTAGGAGATATGGCC	57.224	37.037	16.87	0.00	44.74	5.36
332	341	2.622064	AGGAGATATGGCCGACAAAC	57.378	50.000	0.00	0.00	0.00	2.93
424	442	8.291740	GGCATAAAATTTGGCAATAATTCATCC	58.708	33.333	0.00	0.00	39.31	3.51
548	568	6.992123	AGTTGAGACAATGAACTGACACAATA	59.008	34.615	0.00	0.00	0.00	1.90
609	630	9.350357	CAACATTGGTGATATTTCTTCTTCTTG	57.650	33.333	0.00	0.00	0.00	3.02
857	879	2.116869	TAATGCATGAGGCCCTCCTA	57.883	50.000	8.62	0.00	44.46	2.94
1123	1145	1.949525	CTCCTTTATCCATGGCCAACG	59.050	52.381	10.96	3.50	0.00	4.10
1149	1171	7.470192	CCCATAATTCTAATCCCAACCATAGT	58.530	38.462	0.00	0.00	0.00	2.12
1234	1656	6.784031	AGGAACTACTTTGGTTCATCAGATT	58.216	36.000	8.49	0.00	43.20	2.40
1299	1721	0.909610	TCCAAGGAGATCCCGTTGCT	60.910	55.000	4.29	0.00	40.87	3.91
1377	1799	1.145900	TCCCCACCACCCATGTCATT	61.146	55.000	0.00	0.00	0.00	2.57
1439	1861	5.245977	CCTAAATTTTGTCACCCCTTCACAT	59.754	40.000	0.00	0.00	0.00	3.21
1451	1873	7.339466	GTCACCCCTTCACATCAATTACTATTT	59.661	37.037	0.00	0.00	0.00	1.40
1481	1903	1.750193	AAACATACCACATGGAGCGG	58.250	50.000	4.53	0.00	38.94	5.52
1540	1962	1.617322	CTCCATTCATGGCATCCCAG	58.383	55.000	0.00	0.00	46.24	4.45
1562	1984	0.979665	TGGCCTGAGAGAAGACAAGG	59.020	55.000	3.32	0.00	0.00	3.61
1568	1990	1.898472	TGAGAGAAGACAAGGCTCCTG	59.102	52.381	0.00	0.00	0.00	3.86
1675	2097	2.802247	CACGTTCAACTCATCTCAAGCA	59.198	45.455	0.00	0.00	0.00	3.91
1770	2192	5.651139	CCAGACATCCCATGATTATGAATCC	59.349	44.000	0.00	0.00	37.09	3.01
1784	2206	9.300681	TGATTATGAATCCTGGGACAAATATTC	57.699	33.333	0.00	0.00	37.09	1.75
1790	2212	5.630415	TCCTGGGACAAATATTCCTACTG	57.370	43.478	0.00	0.00	38.70	2.74
1825	2247	4.890158	TGAAAGCACAGAGGTTCTATCA	57.110	40.909	0.00	0.00	36.83	2.15
1826	2248	5.227569	TGAAAGCACAGAGGTTCTATCAA	57.772	39.130	0.00	0.00	36.83	2.57
1910	2332	7.603784	GCATAGGATTGGAAAAATTGTTCTGTT	59.396	33.333	8.27	0.00	0.00	3.16
2386	2838	6.778069	TCTCTCTATCATCGAAAACCCTATGT	59.222	38.462	0.00	0.00	0.00	2.29
2416	2868	8.559536	CAACGTGAAAAATAGATACATGGCTAT	58.440	33.333	0.00	0.00	0.00	2.97

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.384056	AGCGAACAAGCATGCTATTATCT	58.616	39.130	23.00	14.55	40.15	1.98
1	2	4.739046	AGCGAACAAGCATGCTATTATC	57.261	40.909	23.00	15.44	40.15	1.75
2	3	4.261322	CCAAGCGAACAAGCATGCTATTAT	60.261	41.667	23.00	7.82	40.15	1.28
3	4	3.065233	CCAAGCGAACAAGCATGCTATTA	59.935	43.478	23.00	0.00	40.15	0.98
4	5	2.159338	CCAAGCGAACAAGCATGCTATT	60.159	45.455	23.00	18.43	40.15	1.73
5	6	1.402968	CCAAGCGAACAAGCATGCTAT	59.597	47.619	23.00	9.85	40.15	2.97
6	7	0.804364	CCAAGCGAACAAGCATGCTA	59.196	50.000	23.00	0.00	40.15	3.49
7	8	1.582968	CCAAGCGAACAAGCATGCT	59.417	52.632	16.30	16.30	40.15	3.79
8	9	1.444895	CCCAAGCGAACAAGCATGC	60.445	57.895	10.51	10.51	40.15	4.06
9	10	0.109597	GTCCCAAGCGAACAAGCATG	60.110	55.000	0.00	0.00	40.15	4.06
10	11	0.537143	TGTCCCAAGCGAACAAGCAT	60.537	50.000	0.00	0.00	40.15	3.79
11	12	0.749818	TTGTCCCAAGCGAACAAGCA	60.750	50.000	0.00	0.00	40.15	3.91
12	13	0.598065	ATTGTCCCAAGCGAACAAGC	59.402	50.000	0.00	0.00	36.44	4.01
13	14	1.879380	TCATTGTCCCAAGCGAACAAG	59.121	47.619	0.00	0.00	36.44	3.16
14	15	1.879380	CTCATTGTCCCAAGCGAACAA	59.121	47.619	0.00	0.00	37.32	2.83
15	16	1.522668	CTCATTGTCCCAAGCGAACA	58.477	50.000	0.00	0.00	0.00	3.18
16	17	0.804989	CCTCATTGTCCCAAGCGAAC	59.195	55.000	0.00	0.00	0.00	3.95
17	18	0.690192	TCCTCATTGTCCCAAGCGAA	59.310	50.000	0.00	0.00	0.00	4.70
18	19	0.690192	TTCCTCATTGTCCCAAGCGA	59.310	50.000	0.00	0.00	0.00	4.93
19	20	1.089920	CTTCCTCATTGTCCCAAGCG	58.910	55.000	0.00	0.00	0.00	4.68
30	31	6.379133	ACATAATGCATTTGTCACTTCCTCAT	59.621	34.615	18.75	0.00	0.00	2.90
31	32	5.711506	ACATAATGCATTTGTCACTTCCTCA	59.288	36.000	18.75	0.00	0.00	3.86
85	86	2.888414	GGGAATTCACGGAAACCTCAAA	59.112	45.455	7.93	0.00	0.00	2.69
258	264	8.238060	AGGAGAATAATGGATCCTAGAAAGAGA	58.762	37.037	14.23	0.00	40.42	3.10
260	266	8.805145	AAGGAGAATAATGGATCCTAGAAAGA	57.195	34.615	14.23	0.00	41.36	2.52
300	309	8.690884	CGGCCATATCTCCTAGATATTATATGG	58.309	40.741	2.24	12.67	43.44	2.74
305	314	6.669631	TGTCGGCCATATCTCCTAGATATTA	58.330	40.000	2.24	0.00	43.44	0.98
371	385	8.644374	AAGATGGCAAGTATTAGTTTACCAAA	57.356	30.769	0.00	0.00	0.00	3.28
453	471	5.522097	GTCCAAGCTACTATTTGCTTCTCTC	59.478	44.000	0.00	0.00	46.29	3.20
535	555	9.944663	TTAAACAAGTGATTATTGTGTCAGTTC	57.055	29.630	0.00	0.00	39.91	3.01
578	598	9.685276	AGAAGAAATATCACCAATGTTGATACA	57.315	29.630	2.57	0.00	38.95	2.29
600	620	4.091220	GTCACTCGATCTTGCAAGAAGAAG	59.909	45.833	31.55	26.54	38.77	2.85
609	630	5.578727	AGAAACATAAGTCACTCGATCTTGC	59.421	40.000	0.00	0.00	0.00	4.01
810	831	9.349713	TCAATTGTGTCATTAACTAGAAGGTTT	57.650	29.630	5.13	0.00	0.00	3.27
892	914	8.468547	AGGGATGTTATGGGAAGTGATATTAT	57.531	34.615	0.00	0.00	0.00	1.28
1060	1082	1.007842	TGGTGGTAGTGCTGATAGGGA	59.992	52.381	0.00	0.00	0.00	4.20
1123	1145	4.479158	TGGTTGGGATTAGAATTATGGGC	58.521	43.478	0.00	0.00	0.00	5.36
1149	1171	3.760151	CTGGCTGGTTCTCAATGATTTCA	59.240	43.478	0.00	0.00	0.00	2.69
1299	1721	2.666272	TAAGGTGGGCATGAACAACA	57.334	45.000	0.00	0.00	0.00	3.33
1451	1873	5.235850	TGTGGTATGTTTTGCTTCTCCTA	57.764	39.130	0.00	0.00	0.00	2.94
1457	1879	3.056607	GCTCCATGTGGTATGTTTTGCTT	60.057	43.478	0.00	0.00	36.34	3.91
1459	1881	2.731968	CGCTCCATGTGGTATGTTTTGC	60.732	50.000	0.00	0.00	36.34	3.68
1481	1903	4.067896	CCATCAGTAGCATCATGGGTTAC	58.932	47.826	0.00	0.00	33.37	2.50
1539	1961	0.540923	GTCTTCTCTCAGGCCATGCT	59.459	55.000	5.01	0.00	0.00	3.79
1540	1962	0.251354	TGTCTTCTCTCAGGCCATGC	59.749	55.000	5.01	0.00	0.00	4.06
1562	1984	2.137177	TTTGGGCCACCTACAGGAGC	62.137	60.000	5.23	4.49	38.94	4.70
1568	1990	0.322187	ACGACATTTGGGCCACCTAC	60.322	55.000	5.23	0.00	37.76	3.18
1675	2097	4.018506	TGGAACTTCATGTGACCACCATAT	60.019	41.667	0.00	0.00	33.39	1.78
1770	2192	4.137543	GCCAGTAGGAATATTTGTCCCAG	58.862	47.826	0.00	0.00	35.59	4.45
1784	2206	2.325583	TCCATTTTAGCGCCAGTAGG	57.674	50.000	2.29	0.00	38.23	3.18
1790	2212	2.159254	TGCTTTCATCCATTTTAGCGCC	60.159	45.455	2.29	0.00	0.00	6.53
1825	2247	7.839680	AACCATAATGACTTTCTCCACTTTT	57.160	32.000	0.00	0.00	0.00	2.27
1826	2248	7.839680	AAACCATAATGACTTTCTCCACTTT	57.160	32.000	0.00	0.00	0.00	2.66
2153	2596	6.049149	GCATCCATGTAAGAGCAAACTACTA	58.951	40.000	0.00	0.00	0.00	1.82
2386	2838	8.670135	CCATGTATCTATTTTTCACGTTGGTTA	58.330	33.333	0.00	0.00	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.