AutoCloner

Multiple sequence alignment - TraesCS6B01G068200

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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	TraesCS6B01G068200	chr6B	100.000	3857	0	0	1	3857	46081872	46078016	0.000000e+00	7123
1	TraesCS6B01G068200	chr6B	80.240	3917	683	72	1	3856	658283394	658287280	0.000000e+00	2861
2	TraesCS6B01G068200	chr3B	93.187	3875	238	21	1	3857	666617996	666621862	0.000000e+00	5670
3	TraesCS6B01G068200	chr3B	83.055	3889	600	49	1	3857	790573090	790576951	0.000000e+00	3476
4	TraesCS6B01G068200	chr2B	88.671	3875	409	24	1	3857	797920602	797924464	0.000000e+00	4697
5	TraesCS6B01G068200	chr2B	88.129	1112	123	6	2748	3857	758642665	758641561	0.000000e+00	1314
6	TraesCS6B01G068200	chr2B	85.450	1134	144	14	1	1120	758664589	758663463	0.000000e+00	1160
7	TraesCS6B01G068200	chr4B	87.513	3876	455	21	1	3857	46943618	46947483	0.000000e+00	4449
8	TraesCS6B01G068200	chr4B	78.868	3852	712	76	71	3857	616136724	616140538	0.000000e+00	2510
9	TraesCS6B01G068200	chr4B	89.602	452	43	4	3409	3857	593388057	593388507	4.320000e-159	571
10	TraesCS6B01G068200	chr4A	87.042	3874	475	22	1	3857	691825830	691821967	0.000000e+00	4348
11	TraesCS6B01G068200	chr7B	85.397	3876	526	30	2	3857	658458153	658462008	0.000000e+00	3986
12	TraesCS6B01G068200	chr5B	86.161	3165	400	29	1	3147	609118393	609115249	0.000000e+00	3384
13	TraesCS6B01G068200	chr5B	83.343	3512	540	34	71	3556	710458170	710461662	0.000000e+00	3203
14	TraesCS6B01G068200	chr5B	84.730	1683	235	13	2182	3857	563932117	563930450	0.000000e+00	1664
15	TraesCS6B01G068200	chr5A	87.755	490	56	2	2	487	692007261	692007750	1.550000e-158	569

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	TraesCS6B01G068200	chr6B	46078016	46081872	3856	True	7123	7123	100.000	1	3857	1	chr6B.!!$R1	3856
1	TraesCS6B01G068200	chr6B	658283394	658287280	3886	False	2861	2861	80.240	1	3856	1	chr6B.!!$F1	3855
2	TraesCS6B01G068200	chr3B	666617996	666621862	3866	False	5670	5670	93.187	1	3857	1	chr3B.!!$F1	3856
3	TraesCS6B01G068200	chr3B	790573090	790576951	3861	False	3476	3476	83.055	1	3857	1	chr3B.!!$F2	3856
4	TraesCS6B01G068200	chr2B	797920602	797924464	3862	False	4697	4697	88.671	1	3857	1	chr2B.!!$F1	3856
5	TraesCS6B01G068200	chr2B	758641561	758642665	1104	True	1314	1314	88.129	2748	3857	1	chr2B.!!$R1	1109
6	TraesCS6B01G068200	chr2B	758663463	758664589	1126	True	1160	1160	85.450	1	1120	1	chr2B.!!$R2	1119
7	TraesCS6B01G068200	chr4B	46943618	46947483	3865	False	4449	4449	87.513	1	3857	1	chr4B.!!$F1	3856
8	TraesCS6B01G068200	chr4B	616136724	616140538	3814	False	2510	2510	78.868	71	3857	1	chr4B.!!$F3	3786
9	TraesCS6B01G068200	chr4A	691821967	691825830	3863	True	4348	4348	87.042	1	3857	1	chr4A.!!$R1	3856
10	TraesCS6B01G068200	chr7B	658458153	658462008	3855	False	3986	3986	85.397	2	3857	1	chr7B.!!$F1	3855
11	TraesCS6B01G068200	chr5B	609115249	609118393	3144	True	3384	3384	86.161	1	3147	1	chr5B.!!$R2	3146
12	TraesCS6B01G068200	chr5B	710458170	710461662	3492	False	3203	3203	83.343	71	3556	1	chr5B.!!$F1	3485
13	TraesCS6B01G068200	chr5B	563930450	563932117	1667	True	1664	1664	84.730	2182	3857	1	chr5B.!!$R1	1675

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
900	955	1.770324	CAGCCCAGGAAAAGGAGGT	59.230	57.895	0.0	0.0	0.0	3.85	F
1574	1647	0.038159	CAAGACCCAGTGACGGAGAC	60.038	60.000	0.0	0.0	0.0	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2331	2408	1.296715	CTTCTCCACTTCCACCCCG	59.703	63.158	0.0	0.0	0.0	5.73	R
3010	3092	1.073923	TCCTTTGTTCCTGAGGCTTCC	59.926	52.381	0.0	0.0	0.0	3.46	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
29	30	3.319198	GGTGTTCCGCTCCCTCCA	61.319	66.667	0.00	0.00	0.00	3.86
36	37	2.421739	CGCTCCCTCCATTACCGG	59.578	66.667	0.00	0.00	0.00	5.28
492	539	5.104569	AGCAAGAGGAAAAATGGGTTCAAAA	60.105	36.000	0.00	0.00	0.00	2.44
691	739	2.548480	GGTTTGAAGAAGACGAGGTTGG	59.452	50.000	0.00	0.00	0.00	3.77
900	955	1.770324	CAGCCCAGGAAAAGGAGGT	59.230	57.895	0.00	0.00	0.00	3.85
1059	1126	0.613260	TCAATCGTGGAGGTGAAGGG	59.387	55.000	0.00	0.00	0.00	3.95
1083	1150	4.195416	GGTTTGCTAGAGGGAGATTCAAG	58.805	47.826	0.00	0.00	0.00	3.02
1121	1188	3.117360	GGTGGATGGAATGGAGGAAGATT	60.117	47.826	0.00	0.00	0.00	2.40
1146	1213	1.070758	ACAACTGACAGATTCGGCAGT	59.929	47.619	10.08	10.09	42.91	4.40
1268	1337	0.615331	TGGCAAGCTAAGACAGGGAG	59.385	55.000	0.00	0.00	0.00	4.30
1274	1343	2.909217	AGCTAAGACAGGGAGGAAAGT	58.091	47.619	0.00	0.00	0.00	2.66
1287	1356	1.072965	AGGAAAGTGGCAGTGGAAGAG	59.927	52.381	0.00	0.00	0.00	2.85
1296	1365	2.026822	GGCAGTGGAAGAGAGGATTGAA	60.027	50.000	0.00	0.00	0.00	2.69
1338	1407	1.207791	GCTCTGGAATGGAGAAGGGA	58.792	55.000	0.00	0.00	33.03	4.20
1344	1413	2.308866	TGGAATGGAGAAGGGAAAGGAC	59.691	50.000	0.00	0.00	0.00	3.85
1347	1416	3.728385	ATGGAGAAGGGAAAGGACAAG	57.272	47.619	0.00	0.00	0.00	3.16
1393	1462	0.321034	TGCTCAGCAACAGCTACTGG	60.321	55.000	0.00	0.00	36.70	4.00
1471	1540	4.657013	AGAAGGAGTGATTGGAAAACCTC	58.343	43.478	0.00	0.00	0.00	3.85
1491	1564	2.110188	TCTGGAGGTTCAGTCTGGTAGT	59.890	50.000	0.00	0.00	36.25	2.73
1550	1623	2.103771	TGCAGAAAGCTGACAAGAGAGT	59.896	45.455	0.00	0.00	45.17	3.24
1551	1624	2.479656	GCAGAAAGCTGACAAGAGAGTG	59.520	50.000	0.00	0.00	45.17	3.51
1574	1647	0.038159	CAAGACCCAGTGACGGAGAC	60.038	60.000	0.00	0.00	0.00	3.36
1623	1696	3.596214	GCAGTTGAATTTAGACGAGGGA	58.404	45.455	0.00	0.00	0.00	4.20
1656	1729	7.660208	GGAATGGAGAGACTTAACAAACAAGTA	59.340	37.037	0.00	0.00	36.38	2.24
1731	1805	3.461085	ACTGCTTGATATGTGGAAGGGAT	59.539	43.478	0.00	0.00	0.00	3.85
1740	1814	8.230848	TGATATGTGGAAGGGATAACCATATT	57.769	34.615	0.00	0.00	43.89	1.28
2017	2091	3.250617	AGATTCCCCAACAAGGCAAAAT	58.749	40.909	0.00	0.00	35.39	1.82
2034	2108	4.675408	GCAAAATTGGTAGAGCTGGCTAAC	60.675	45.833	0.00	0.00	0.00	2.34
2036	2110	3.550437	ATTGGTAGAGCTGGCTAACTG	57.450	47.619	0.00	0.00	0.00	3.16
2145	2219	1.909700	CCTGGGTTAAGCTGAGCAAA	58.090	50.000	7.39	0.00	0.00	3.68
2228	2305	6.466326	CCTGTGTTGGAAGTGGATATGGATAT	60.466	42.308	0.00	0.00	0.00	1.63
2279	2356	4.582869	TGTGGAATCAGAGATGTGGAAAG	58.417	43.478	0.00	0.00	0.00	2.62
2331	2408	6.222389	CCCTGATCTACTCATGTTCAGAATC	58.778	44.000	0.00	0.00	36.72	2.52
2463	2540	4.624913	AGAGATTCAGGGTGGAAGATACA	58.375	43.478	0.00	0.00	0.00	2.29
2484	2561	9.542462	GATACAGAACATAAAGGCATTACACTA	57.458	33.333	0.00	0.00	0.00	2.74
2562	2640	7.436118	TGAAAGCACAATTAGAAGAAAGCATT	58.564	30.769	0.00	0.00	0.00	3.56
2713	2791	8.924511	TGAACAAAGAATTAAGGATCTTGAGT	57.075	30.769	0.00	2.99	36.09	3.41
2815	2895	4.202398	GGGAACAATATGAGATGGAGCTGA	60.202	45.833	0.00	0.00	0.00	4.26
2854	2934	6.836007	GGAAGATTATGAGAAGGAAACCCAAT	59.164	38.462	0.00	0.00	0.00	3.16
2934	3014	3.202151	GTCAGGAATCAATTGGGACCCTA	59.798	47.826	13.00	4.14	0.00	3.53
3010	3092	8.628630	AGAGGAGAAAGAAGTGGAAATAAAAG	57.371	34.615	0.00	0.00	0.00	2.27
3358	3441	7.407729	AGATGTGGATATTGATGGATTATGCA	58.592	34.615	0.00	0.00	0.00	3.96
3444	3528	3.080319	CTCTGGAAAGAAAGGAGGCAAG	58.920	50.000	0.00	0.00	0.00	4.01
3546	3636	9.802039	ACTGATTAGTCTCTAACCTAGGAATAG	57.198	37.037	17.98	16.63	28.79	1.73
3557	3647	8.603304	TCTAACCTAGGAATAGATTAATTGCCC	58.397	37.037	17.98	0.00	0.00	5.36
3574	3665	3.078837	TGCCCGGACAGAAAAGTAATTC	58.921	45.455	0.73	0.00	0.00	2.17
3792	3900	4.535526	AAAATTACCAATGGTGCTGGAC	57.464	40.909	16.41	0.00	36.19	4.02
3820	3928	3.834231	CCAAAGGAATGTCTGGTGGAATT	59.166	43.478	0.00	0.00	0.00	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	95	4.758251	CATCACCACCGCCTGCGA	62.758	66.667	13.94	0.00	42.83	5.10
290	336	2.027561	CAGTAACCAGAAACGGATCCCA	60.028	50.000	6.06	0.00	0.00	4.37
295	341	0.035739	GGCCAGTAACCAGAAACGGA	59.964	55.000	0.00	0.00	0.00	4.69
331	377	2.204705	ACTCCCCCTCCTCCTCCT	60.205	66.667	0.00	0.00	0.00	3.69
492	539	2.769893	GCAGTCATTTGCAATTTGGGT	58.230	42.857	0.00	0.00	43.53	4.51
504	551	3.152341	CAGAAACTCCCTTGCAGTCATT	58.848	45.455	0.00	0.00	0.00	2.57
570	617	9.816354	ACAATTATTTTCAATAATTTCTCCCCG	57.184	29.630	10.47	3.21	33.37	5.73
599	646	5.222079	TCTGTGCATCAAAACCAGTACTA	57.778	39.130	0.00	0.00	0.00	1.82
604	651	5.633830	AACTATCTGTGCATCAAAACCAG	57.366	39.130	0.00	0.00	0.00	4.00
666	714	3.134081	ACCTCGTCTTCTTCAAACCAAGA	59.866	43.478	0.00	0.00	0.00	3.02
900	955	1.003646	TTTTATACCTGCCAGCCCCA	58.996	50.000	0.00	0.00	0.00	4.96
994	1061	2.160022	CCAAATTTCCAGCCATTTTGCG	59.840	45.455	0.00	0.00	36.02	4.85
1059	1126	1.512735	ATCTCCCTCTAGCAAACCCC	58.487	55.000	0.00	0.00	0.00	4.95
1083	1150	1.553704	CCACCTCCCCTGTTACTGTAC	59.446	57.143	0.00	0.00	0.00	2.90
1121	1188	4.021807	TGCCGAATCTGTCAGTTGTAGTAA	60.022	41.667	0.00	0.00	0.00	2.24
1146	1213	3.593942	TCTACCACTTCCTCTCCCAAAA	58.406	45.455	0.00	0.00	0.00	2.44
1268	1337	1.072331	TCTCTTCCACTGCCACTTTCC	59.928	52.381	0.00	0.00	0.00	3.13
1274	1343	1.280133	CAATCCTCTCTTCCACTGCCA	59.720	52.381	0.00	0.00	0.00	4.92
1287	1356	4.460382	TCACCATTTGCTCTTTCAATCCTC	59.540	41.667	0.00	0.00	0.00	3.71
1296	1365	1.988107	TCTCCCTCACCATTTGCTCTT	59.012	47.619	0.00	0.00	0.00	2.85
1338	1407	6.331042	TCTGGATCATCATATCCTTGTCCTTT	59.669	38.462	4.63	0.00	44.98	3.11
1344	1413	6.372103	GCTCTTTCTGGATCATCATATCCTTG	59.628	42.308	4.63	0.00	44.98	3.61
1347	1416	5.802465	TGCTCTTTCTGGATCATCATATCC	58.198	41.667	0.00	0.00	44.96	2.59
1393	1462	1.185315	AACTGAGAGAGCAGAGAGGC	58.815	55.000	0.00	0.00	39.20	4.70
1471	1540	2.232452	CACTACCAGACTGAACCTCCAG	59.768	54.545	3.32	0.00	39.93	3.86
1491	1564	2.699321	CTCTTCTCTCCTCATGCCATCA	59.301	50.000	0.00	0.00	0.00	3.07
1550	1623	1.754380	CGTCACTGGGTCTTGGTCCA	61.754	60.000	0.00	0.00	0.00	4.02
1551	1624	1.004918	CGTCACTGGGTCTTGGTCC	60.005	63.158	0.00	0.00	0.00	4.46
1617	1690	1.559682	TCCATTCCCTTCTTTCCCTCG	59.440	52.381	0.00	0.00	0.00	4.63
1623	1696	6.044404	TGTTAAGTCTCTCCATTCCCTTCTTT	59.956	38.462	0.00	0.00	0.00	2.52
1656	1729	3.505386	TGGGTCTTTGCATTTACCACAT	58.495	40.909	12.37	0.00	33.46	3.21
1731	1805	9.899661	AAGTTGCATTCACTAGTAATATGGTTA	57.100	29.630	0.00	0.00	0.00	2.85
2017	2091	2.257207	ACAGTTAGCCAGCTCTACCAA	58.743	47.619	0.00	0.00	0.00	3.67
2034	2108	5.163683	CCCAAGCAGATTGAAGTCATTACAG	60.164	44.000	0.00	0.00	41.83	2.74
2036	2110	4.943705	TCCCAAGCAGATTGAAGTCATTAC	59.056	41.667	0.00	0.00	41.83	1.89
2249	2326	4.916041	TCTCTGATTCCACATTTGACCT	57.084	40.909	0.00	0.00	0.00	3.85
2303	2380	1.765314	ACATGAGTAGATCAGGGGCAC	59.235	52.381	0.00	0.00	44.08	5.01
2331	2408	1.296715	CTTCTCCACTTCCACCCCG	59.703	63.158	0.00	0.00	0.00	5.73
2463	2540	7.195374	TCCTAGTGTAATGCCTTTATGTTCT	57.805	36.000	0.00	0.00	0.00	3.01
2508	2585	4.846940	ACCAGTTTTCCATCTACTTCCTCT	59.153	41.667	0.00	0.00	0.00	3.69
2562	2640	7.335171	GCATACATCTCATCTTGCCATTGTATA	59.665	37.037	0.00	0.00	30.25	1.47
2637	2715	4.023622	GCTTTGTCTTCTTCCAAGGTCTTC	60.024	45.833	0.00	0.00	0.00	2.87
2713	2791	2.036089	TCTGCATTGCTTGTTGATTGCA	59.964	40.909	10.49	0.00	37.73	4.08
3010	3092	1.073923	TCCTTTGTTCCTGAGGCTTCC	59.926	52.381	0.00	0.00	0.00	3.46
3291	3374	2.079925	GTGTCTCTGCATTCTTCCACC	58.920	52.381	0.00	0.00	0.00	4.61
3329	3412	6.653790	ATCCATCAATATCCACATCTCCAT	57.346	37.500	0.00	0.00	0.00	3.41
3444	3528	3.005155	AGTTCAATGCTGGTGAGCTTTTC	59.995	43.478	0.00	0.00	46.39	2.29
3546	3636	4.157840	ACTTTTCTGTCCGGGCAATTAATC	59.842	41.667	11.40	0.00	0.00	1.75
3549	3639	3.149005	ACTTTTCTGTCCGGGCAATTA	57.851	42.857	11.40	0.00	0.00	1.40
3557	3647	9.151471	TCTCAATAAGAATTACTTTTCTGTCCG	57.849	33.333	0.00	0.00	39.72	4.79
3628	3730	3.548745	TGACCTATGCCTCTCACATTG	57.451	47.619	0.00	0.00	0.00	2.82
3684	3786	8.477256	TCCCAATAAAATCCAATTTGTGATCTC	58.523	33.333	0.00	0.00	31.77	2.75
3760	3862	2.625639	TGGTAATTTTTGCCCCCACAT	58.374	42.857	0.00	0.00	34.10	3.21
3820	3928	9.905713	AACATCTCTTTATTAATGCCAACTAGA	57.094	29.630	0.00	0.00	0.00	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.