AutoCloner

Multiple sequence alignment - TraesCS4A01G498500

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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	TraesCS4A01G498500	chr4A	100.000	2599	0	0	1	2599	743944856	743942258	0.000000e+00	4800.0
1	TraesCS4A01G498500	chr7B	97.507	762	17	2	1	760	635675714	635676475	0.000000e+00	1301.0
2	TraesCS4A01G498500	chr7B	84.015	782	71	23	1	771	543103685	543104423	0.000000e+00	702.0
3	TraesCS4A01G498500	chr4B	96.583	761	23	2	1	760	117290538	117291296	0.000000e+00	1258.0
4	TraesCS4A01G498500	chr4B	93.239	636	29	8	768	1401	469055729	469055106	0.000000e+00	924.0
5	TraesCS4A01G498500	chr4B	92.110	621	45	1	1979	2599	469054464	469053848	0.000000e+00	872.0
6	TraesCS4A01G498500	chr4B	91.002	589	34	3	1397	1985	469055074	469054505	0.000000e+00	776.0
7	TraesCS4A01G498500	chr7D	91.677	781	46	7	1	769	607339361	607340134	0.000000e+00	1064.0
8	TraesCS4A01G498500	chr7D	94.025	636	17	5	768	1398	310285198	310285817	0.000000e+00	944.0
9	TraesCS4A01G498500	chr7D	92.915	621	39	2	1979	2599	310286479	310287094	0.000000e+00	898.0
10	TraesCS4A01G498500	chr7D	93.718	589	35	1	1397	1985	310285852	310286438	0.000000e+00	881.0
11	TraesCS4A01G498500	chr5A	91.041	759	50	5	22	768	680282565	680281813	0.000000e+00	1009.0
12	TraesCS4A01G498500	chr5A	92.640	625	37	3	1979	2599	616143594	616144213	0.000000e+00	891.0
13	TraesCS4A01G498500	chr5A	90.881	636	26	6	768	1398	616142340	616142948	0.000000e+00	824.0
14	TraesCS4A01G498500	chr5A	92.020	589	30	2	1397	1985	616142983	616143554	0.000000e+00	811.0
15	TraesCS4A01G498500	chr5A	86.859	312	21	7	6	310	439020222	439020520	5.360000e-87	331.0
16	TraesCS4A01G498500	chr5A	85.197	304	33	10	400	697	439020550	439020847	4.200000e-78	302.0
17	TraesCS4A01G498500	chr5D	94.340	636	15	5	768	1398	35841237	35841856	0.000000e+00	955.0
18	TraesCS4A01G498500	chr5D	92.605	622	41	2	1979	2599	35842407	35843024	0.000000e+00	889.0
19	TraesCS4A01G498500	chr5D	91.948	621	40	2	1979	2599	174854615	174854005	0.000000e+00	861.0
20	TraesCS4A01G498500	chr5D	96.429	476	14	3	768	1240	174855776	174855301	0.000000e+00	782.0
21	TraesCS4A01G498500	chr5D	89.813	589	34	5	1397	1985	174855218	174854656	0.000000e+00	732.0
22	TraesCS4A01G498500	chr5D	94.118	289	15	2	1397	1685	35841891	35842177	3.070000e-119	438.0
23	TraesCS4A01G498500	chr5D	94.624	93	5	0	1893	1985	35842274	35842366	7.500000e-31	145.0
24	TraesCS4A01G498500	chr5D	98.214	56	1	0	1346	1401	174855305	174855250	5.920000e-17	99.0
25	TraesCS4A01G498500	chr5D	100.000	28	0	0	1676	1703	35842198	35842225	5.000000e-03	52.8
26	TraesCS4A01G498500	chr6D	92.754	621	41	1	1979	2599	12673415	12672799	0.000000e+00	894.0
27	TraesCS4A01G498500	chr6D	96.421	475	15	2	768	1240	12674513	12674039	0.000000e+00	782.0
28	TraesCS4A01G498500	chr6D	89.032	465	25	5	1397	1861	12673956	12673518	1.050000e-153	553.0
29	TraesCS4A01G498500	chr6D	95.312	64	3	0	1922	1985	12673519	12673456	4.580000e-18	102.0
30	TraesCS4A01G498500	chr6D	98.214	56	1	0	1346	1401	12674043	12673988	5.920000e-17	99.0
31	TraesCS4A01G498500	chr3B	92.271	621	44	1	1979	2599	571907393	571908009	0.000000e+00	878.0
32	TraesCS4A01G498500	chr3B	85.734	715	75	15	1	697	678002691	678003396	0.000000e+00	730.0
33	TraesCS4A01G498500	chr3B	83.356	721	81	21	1	697	201229029	201228324	4.720000e-177	630.0
34	TraesCS4A01G498500	chr3B	89.200	500	36	9	1486	1985	571906871	571907352	2.210000e-170	608.0
35	TraesCS4A01G498500	chr3B	86.166	506	42	16	1	500	758923816	758924299	2.960000e-144	521.0
36	TraesCS4A01G498500	chr1B	90.229	655	35	8	768	1401	135262850	135262204	0.000000e+00	828.0
37	TraesCS4A01G498500	chr1B	91.751	594	44	3	1978	2571	135261523	135260935	0.000000e+00	821.0
38	TraesCS4A01G498500	chr1B	87.480	639	52	14	1397	2012	135262172	135261539	0.000000e+00	712.0
39	TraesCS4A01G498500	chr2A	84.231	780	67	22	1	772	689814849	689814118	0.000000e+00	708.0
40	TraesCS4A01G498500	chr2A	92.888	464	32	1	2137	2599	733659683	733660146	0.000000e+00	673.0
41	TraesCS4A01G498500	chr2D	84.292	643	60	16	6	620	489363935	489364564	8.010000e-165	590.0
42	TraesCS4A01G498500	chr3A	81.780	708	68	28	1	697	532642633	532643290	1.060000e-148	536.0
43	TraesCS4A01G498500	chr3A	86.667	300	17	10	1	289	574501863	574501576	6.980000e-81	311.0
44	TraesCS4A01G498500	chr3A	86.333	300	18	10	1	289	574501255	574500968	3.250000e-79	305.0
45	TraesCS4A01G498500	chr3A	85.333	300	21	10	1	289	574502473	574502186	3.270000e-74	289.0

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	TraesCS4A01G498500	chr4A	743942258	743944856	2598	True	4800.000000	4800	100.000000	1	2599	1	chr4A.!!$R1	2598
1	TraesCS4A01G498500	chr7B	635675714	635676475	761	False	1301.000000	1301	97.507000	1	760	1	chr7B.!!$F2	759
2	TraesCS4A01G498500	chr7B	543103685	543104423	738	False	702.000000	702	84.015000	1	771	1	chr7B.!!$F1	770
3	TraesCS4A01G498500	chr4B	117290538	117291296	758	False	1258.000000	1258	96.583000	1	760	1	chr4B.!!$F1	759
4	TraesCS4A01G498500	chr4B	469053848	469055729	1881	True	857.333333	924	92.117000	768	2599	3	chr4B.!!$R1	1831
5	TraesCS4A01G498500	chr7D	607339361	607340134	773	False	1064.000000	1064	91.677000	1	769	1	chr7D.!!$F1	768
6	TraesCS4A01G498500	chr7D	310285198	310287094	1896	False	907.666667	944	93.552667	768	2599	3	chr7D.!!$F2	1831
7	TraesCS4A01G498500	chr5A	680281813	680282565	752	True	1009.000000	1009	91.041000	22	768	1	chr5A.!!$R1	746
8	TraesCS4A01G498500	chr5A	616142340	616144213	1873	False	842.000000	891	91.847000	768	2599	3	chr5A.!!$F2	1831
9	TraesCS4A01G498500	chr5A	439020222	439020847	625	False	316.500000	331	86.028000	6	697	2	chr5A.!!$F1	691
10	TraesCS4A01G498500	chr5D	174854005	174855776	1771	True	618.500000	861	94.101000	768	2599	4	chr5D.!!$R1	1831
11	TraesCS4A01G498500	chr5D	35841237	35843024	1787	False	495.960000	955	95.137400	768	2599	5	chr5D.!!$F1	1831
12	TraesCS4A01G498500	chr6D	12672799	12674513	1714	True	486.000000	894	94.346600	768	2599	5	chr6D.!!$R1	1831
13	TraesCS4A01G498500	chr3B	571906871	571908009	1138	False	743.000000	878	90.735500	1486	2599	2	chr3B.!!$F3	1113
14	TraesCS4A01G498500	chr3B	678002691	678003396	705	False	730.000000	730	85.734000	1	697	1	chr3B.!!$F1	696
15	TraesCS4A01G498500	chr3B	201228324	201229029	705	True	630.000000	630	83.356000	1	697	1	chr3B.!!$R1	696
16	TraesCS4A01G498500	chr1B	135260935	135262850	1915	True	787.000000	828	89.820000	768	2571	3	chr1B.!!$R1	1803
17	TraesCS4A01G498500	chr2A	689814118	689814849	731	True	708.000000	708	84.231000	1	772	1	chr2A.!!$R1	771
18	TraesCS4A01G498500	chr2D	489363935	489364564	629	False	590.000000	590	84.292000	6	620	1	chr2D.!!$F1	614
19	TraesCS4A01G498500	chr3A	532642633	532643290	657	False	536.000000	536	81.780000	1	697	1	chr3A.!!$F1	696
20	TraesCS4A01G498500	chr3A	574500968	574502473	1505	True	301.666667	311	86.111000	1	289	3	chr3A.!!$R1	288

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
779	1465	0.684153	CCGCCCCTGATTTGACCAAT	60.684	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2576	3427	1.153549	CTAACGGGAGGTGCTGCTC	60.154	63.158	0.0	0.0	0.0	4.26	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
779	1465	0.684153	CCGCCCCTGATTTGACCAAT	60.684	55.000	0.00	0.00	0.00	3.16
802	1488	5.120054	TGGACATGTAGCTGTAGGTACTA	57.880	43.478	18.63	8.57	46.08	1.82
1004	1692	3.696548	GCTCCAGGCTAAGTAAAAATGCT	59.303	43.478	0.00	0.00	38.06	3.79
1067	1755	0.322816	CCCACTGCACCTAAGCACAT	60.323	55.000	0.00	0.00	40.11	3.21
1161	1851	3.107601	TGCTCCTAAACCATCTGCTAGT	58.892	45.455	0.00	0.00	0.00	2.57
1169	1859	1.343478	ACCATCTGCTAGTAGTGCCCT	60.343	52.381	7.77	0.00	0.00	5.19
1309	2018	7.759489	TTCTGTGCAATAACACTCCTTTATT	57.241	32.000	0.00	0.00	41.30	1.40
1310	2019	7.759489	TCTGTGCAATAACACTCCTTTATTT	57.241	32.000	0.00	0.00	41.30	1.40
1311	2020	8.856153	TCTGTGCAATAACACTCCTTTATTTA	57.144	30.769	0.00	0.00	41.30	1.40
1312	2021	9.461312	TCTGTGCAATAACACTCCTTTATTTAT	57.539	29.630	0.00	0.00	41.30	1.40
1412	2160	6.264067	AGAGAAAAGCTTCAAATGTTAGCAGT	59.736	34.615	0.00	0.00	37.37	4.40
1465	2213	0.995024	ACTGCTACCTCAAAGGCCAT	59.005	50.000	5.01	0.00	39.63	4.40
1466	2214	1.065126	ACTGCTACCTCAAAGGCCATC	60.065	52.381	5.01	0.00	39.63	3.51
1492	2240	7.269084	CGTGAAGAATGTTCATGTCAATGTTAC	59.731	37.037	4.39	0.00	35.15	2.50
1493	2241	8.292448	GTGAAGAATGTTCATGTCAATGTTACT	58.708	33.333	0.00	0.00	35.15	2.24
1502	2250	3.511699	TGTCAATGTTACTAGCAGCTCG	58.488	45.455	0.00	0.00	0.00	5.03
1604	2352	1.601759	GCTGCTTGAGTGAGGCCAA	60.602	57.895	5.01	0.00	0.00	4.52
1616	2364	2.095853	GTGAGGCCAATGTGTATGTTCG	59.904	50.000	5.01	0.00	0.00	3.95
1655	2403	8.352942	GTTTGTTTCCTTCTTATCTCATGTGTT	58.647	33.333	0.00	0.00	0.00	3.32
1656	2404	8.463930	TTGTTTCCTTCTTATCTCATGTGTTT	57.536	30.769	0.00	0.00	0.00	2.83
1704	2452	7.039644	TGTTTGTTTCCTTCAGAAAACCTGTTA	60.040	33.333	0.00	0.00	45.93	2.41
1870	2659	7.250032	TCAAGCCAATATGTAGAGCATAGAT	57.750	36.000	0.00	0.00	42.68	1.98
1920	2709	9.890629	AGTGCTTATAATGTCAACTGAAATAGA	57.109	29.630	0.00	0.00	0.00	1.98
2012	2851	3.450817	TCCAATAAGCACAGCTAGCACTA	59.549	43.478	18.83	4.40	38.25	2.74
2017	2856	3.126001	AGCACAGCTAGCACTACAAAA	57.874	42.857	18.83	0.00	36.99	2.44
2108	2947	7.289310	TCATTGCCTTCATCTTGGATAACATA	58.711	34.615	0.00	0.00	0.00	2.29
2144	2983	6.884280	TTCTTCTCTTTTTCTTCCATGTCC	57.116	37.500	0.00	0.00	0.00	4.02
2193	3032	7.148018	GCTCCAATTCCATCTTACAATCTTCAA	60.148	37.037	0.00	0.00	0.00	2.69
2232	3077	7.976135	ACATAAAGTGCATTGATAGATCTCC	57.024	36.000	0.00	0.00	0.00	3.71
2238	3083	2.257894	CATTGATAGATCTCCGCGCTC	58.742	52.381	5.56	0.00	0.00	5.03
2244	3089	4.435436	ATCTCCGCGCTCGTGCAA	62.435	61.111	5.56	0.00	39.64	4.08
2267	3112	4.722220	ACCATTCAGGATCATACCACATG	58.278	43.478	0.00	0.00	41.22	3.21
2356	3201	9.901172	ACCGTATAGATTTGGTAGAAAGAAATT	57.099	29.630	0.00	0.00	31.60	1.82
2391	3236	3.803082	CACCTCCCGCATGCAACG	61.803	66.667	19.57	3.77	0.00	4.10
2480	3327	5.358298	ACAACTAAAATTGCTCTCGGTTC	57.642	39.130	0.00	0.00	32.47	3.62
2543	3394	1.209261	TGCCAGATATCAGTTCGGCAA	59.791	47.619	15.91	5.07	46.04	4.52
2576	3427	0.722282	TTCAACGACACACAACACCG	59.278	50.000	0.00	0.00	0.00	4.94
2578	3429	0.300491	CAACGACACACAACACCGAG	59.700	55.000	0.00	0.00	0.00	4.63

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
640	1325	3.370978	GCGACACAACTACACAAGCATAT	59.629	43.478	0.00	0.00	0.00	1.78
724	1410	1.559682	TGAGAGGGGGCAAAGATGTAC	59.440	52.381	0.00	0.00	0.00	2.90
779	1465	4.350245	AGTACCTACAGCTACATGTCCAA	58.650	43.478	0.00	0.00	34.56	3.53
947	1635	2.629617	CTGTTGGATTCAGGCCAAGTTT	59.370	45.455	5.01	0.00	45.42	2.66
990	1678	5.885912	TGGCCTTCCTAGCATTTTTACTTAG	59.114	40.000	3.32	0.00	0.00	2.18
993	1681	4.316025	TGGCCTTCCTAGCATTTTTACT	57.684	40.909	3.32	0.00	0.00	2.24
1004	1692	1.078823	TCTCAGTCCTTGGCCTTCCTA	59.921	52.381	3.32	0.00	0.00	2.94
1067	1755	2.666272	TGTGCCAACTTTACCCATCA	57.334	45.000	0.00	0.00	0.00	3.07
1117	1806	6.146216	CAGTACACTTTGTTTTGTTGTGACA	58.854	36.000	0.00	0.00	33.41	3.58
1169	1859	5.932619	TGCACTAGAATTCCTAGCAGTTA	57.067	39.130	0.65	0.00	46.98	2.24
1315	2024	8.445493	GCAAGCATTTTCATTAAGCTATGTTTT	58.555	29.630	0.00	0.00	34.66	2.43
1412	2160	3.103742	AGGTGGTTTGAAAGGCTTGAAA	58.896	40.909	0.00	0.15	0.00	2.69
1465	2213	5.469760	ACATTGACATGAACATTCTTCACGA	59.530	36.000	0.00	0.00	34.11	4.35
1466	2214	5.692814	ACATTGACATGAACATTCTTCACG	58.307	37.500	0.00	0.00	34.11	4.35
1492	2240	1.394618	AGTAACTCCCGAGCTGCTAG	58.605	55.000	0.15	1.49	0.00	3.42
1493	2241	2.723322	TAGTAACTCCCGAGCTGCTA	57.277	50.000	0.15	0.00	0.00	3.49
1502	2250	7.281100	CCAGAACTGAAATTCATAGTAACTCCC	59.719	40.741	0.00	0.00	0.00	4.30
1540	2288	4.503741	TTATTTGCTCCAGTGAAGTTGC	57.496	40.909	0.00	0.00	0.00	4.17
1604	2352	5.240623	ACACATGTTTTCCGAACATACACAT	59.759	36.000	0.00	0.00	38.69	3.21
1673	2421	7.119116	GGTTTTCTGAAGGAAACAAACAACAAT	59.881	33.333	14.63	0.00	42.80	2.71
1674	2422	6.425417	GGTTTTCTGAAGGAAACAAACAACAA	59.575	34.615	14.63	0.00	42.80	2.83
1704	2452	6.772716	AGGTTCATCTTGTTCAGTACACAAAT	59.227	34.615	0.00	0.00	36.21	2.32
1965	2757	6.942576	ACTGAAAATGTAACAGGCTAAGATGT	59.057	34.615	0.00	0.00	36.17	3.06
2041	2880	6.636454	AGGATCTGTTTATCTGGGTGTTAA	57.364	37.500	0.00	0.00	0.00	2.01
2042	2881	6.443849	AGAAGGATCTGTTTATCTGGGTGTTA	59.556	38.462	0.00	0.00	33.59	2.41
2043	2882	5.251700	AGAAGGATCTGTTTATCTGGGTGTT	59.748	40.000	0.00	0.00	33.59	3.32
2044	2883	4.785376	AGAAGGATCTGTTTATCTGGGTGT	59.215	41.667	0.00	0.00	33.59	4.16
2108	2947	6.721704	AAAGAGAAGAAAAGCCAACAGAAT	57.278	33.333	0.00	0.00	0.00	2.40
2144	2983	5.063186	GCTCATGTTGGCTGATAAGATATCG	59.937	44.000	0.00	0.00	0.00	2.92
2193	3032	8.100791	TGCACTTTATGTAGATAAGTTGAAGGT	58.899	33.333	6.69	0.00	0.00	3.50
2208	3053	6.648310	CGGAGATCTATCAATGCACTTTATGT	59.352	38.462	0.00	0.00	0.00	2.29
2232	3077	3.593551	AATGGTTTGCACGAGCGCG	62.594	57.895	8.75	8.75	46.23	6.86
2238	3083	1.811965	TGATCCTGAATGGTTTGCACG	59.188	47.619	0.00	0.00	37.07	5.34
2244	3089	4.860802	TGTGGTATGATCCTGAATGGTT	57.139	40.909	0.00	0.00	37.07	3.67
2267	3112	5.803967	GGATGAACAAGCATGTGATTTTCTC	59.196	40.000	0.00	0.00	40.46	2.87
2356	3201	5.353123	GGAGGTGAATTTAGTTGTCGCATTA	59.647	40.000	0.00	0.00	0.00	1.90
2391	3236	2.508526	ACACTGGCAGAAGGTTCATTC	58.491	47.619	23.66	0.00	0.00	2.67
2480	3327	2.037136	CAGAGTTCTGCGGCCTTGG	61.037	63.158	0.00	0.00	37.15	3.61
2543	3394	6.040504	TGTGTCGTTGAATAGGTCTATATGCT	59.959	38.462	0.00	0.00	0.00	3.79
2576	3427	1.153549	CTAACGGGAGGTGCTGCTC	60.154	63.158	0.00	0.00	0.00	4.26
2578	3429	1.448013	GACTAACGGGAGGTGCTGC	60.448	63.158	0.00	0.00	0.00	5.25

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.