AutoCloner

Multiple sequence alignment - TraesCS4B01G316200

Loading Multiple Alignment...

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	TraesCS4B01G316200	chr4B	100.000	2867	0	0	1	2867	605694239	605691373	0.000000e+00	5295
1	TraesCS4B01G316200	chr4B	81.250	304	53	4	1137	1438	605682888	605683189	2.850000e-60	243
2	TraesCS4B01G316200	chr4D	95.045	2886	93	19	1	2867	479000351	478997497	0.000000e+00	4492
3	TraesCS4B01G316200	chr4D	84.328	268	34	6	1156	1419	382738013	382738276	3.670000e-64	255
4	TraesCS4B01G316200	chr4D	79.245	265	40	14	1154	1412	52763827	52764082	1.370000e-38	171
5	TraesCS4B01G316200	chr4A	90.824	2899	157	41	53	2867	685382574	685379701	0.000000e+00	3779
6	TraesCS4B01G316200	chr4A	82.566	304	49	4	1137	1438	685372125	685372426	6.090000e-67	265
7	TraesCS4B01G316200	chr4A	84.586	266	37	4	1156	1419	64956723	64956986	7.880000e-66	261
8	TraesCS4B01G316200	chr4A	100.000	57	0	0	2	58	685402995	685402939	3.910000e-19	106
9	TraesCS4B01G316200	chr6D	87.132	272	33	2	1150	1420	462273020	462272750	9.980000e-80	307
10	TraesCS4B01G316200	chr6A	87.085	271	35	0	1150	1420	609107553	609107283	9.980000e-80	307
11	TraesCS4B01G316200	chr6B	86.765	272	34	2	1150	1420	704751360	704751630	4.640000e-78	302
12	TraesCS4B01G316200	chr3D	75.000	260	41	22	1143	1392	511726697	511726452	6.540000e-17	99
13	TraesCS4B01G316200	chr3A	75.000	260	41	22	1143	1392	647755513	647755268	6.540000e-17	99

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	TraesCS4B01G316200	chr4B	605691373	605694239	2866	True	5295	5295	100.000	1	2867	1	chr4B.!!$R1	2866
1	TraesCS4B01G316200	chr4D	478997497	479000351	2854	True	4492	4492	95.045	1	2867	1	chr4D.!!$R1	2866
2	TraesCS4B01G316200	chr4A	685379701	685382574	2873	True	3779	3779	90.824	53	2867	1	chr4A.!!$R1	2814

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
985	1020	1.208293	CTCTTTCCCCCTTCCTCTTCG	59.792	57.143	0.0	0.0	0.0	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2404	2459	1.566703	ACTGGAGGAGCTAGCTAGTCA	59.433	52.381	19.38	12.56	0.0	3.41	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	4.982916	CCTACCTACACGATTTAGTCATGC	59.017	45.833	0.00	0.00	0.00	4.06
281	285	2.893489	GTTCCAATCTTTCCTGCAGGTT	59.107	45.455	31.58	15.93	36.34	3.50
531	550	4.437682	TTCCCATCACATATTGTCTCCC	57.562	45.455	0.00	0.00	0.00	4.30
623	642	5.722441	TGCTTGTATATGTATTATCCCCGGA	59.278	40.000	0.73	0.00	0.00	5.14
683	702	4.772100	ACCCATCCCAACTAATCACAAAAG	59.228	41.667	0.00	0.00	0.00	2.27
869	904	1.384989	CCTTAGCGGAAGAGGCGAGA	61.385	60.000	3.23	0.00	37.33	4.04
952	987	4.231890	TGTTTATTCCCTCAGGCCCTAATT	59.768	41.667	0.00	0.00	0.00	1.40
953	988	5.208890	GTTTATTCCCTCAGGCCCTAATTT	58.791	41.667	0.00	0.00	0.00	1.82
968	1003	4.019174	CCTAATTTCCAACCATGCACTCT	58.981	43.478	0.00	0.00	0.00	3.24
969	1004	4.463891	CCTAATTTCCAACCATGCACTCTT	59.536	41.667	0.00	0.00	0.00	2.85
985	1020	1.208293	CTCTTTCCCCCTTCCTCTTCG	59.792	57.143	0.00	0.00	0.00	3.79
1034	1069	1.548081	CCATTGCACTCCAACCATCA	58.452	50.000	0.00	0.00	35.99	3.07
1038	1073	2.812836	TGCACTCCAACCATCATCAT	57.187	45.000	0.00	0.00	0.00	2.45
1039	1074	2.646930	TGCACTCCAACCATCATCATC	58.353	47.619	0.00	0.00	0.00	2.92
1040	1075	2.026075	TGCACTCCAACCATCATCATCA	60.026	45.455	0.00	0.00	0.00	3.07
1041	1076	3.220110	GCACTCCAACCATCATCATCAT	58.780	45.455	0.00	0.00	0.00	2.45
1042	1077	3.252701	GCACTCCAACCATCATCATCATC	59.747	47.826	0.00	0.00	0.00	2.92
1043	1078	4.457466	CACTCCAACCATCATCATCATCA	58.543	43.478	0.00	0.00	0.00	3.07
1044	1079	5.070685	CACTCCAACCATCATCATCATCAT	58.929	41.667	0.00	0.00	0.00	2.45
1092	1137	4.636249	GGAGAGAGACAACACAATCAGTT	58.364	43.478	0.00	0.00	0.00	3.16
1094	1139	4.636249	AGAGAGACAACACAATCAGTTCC	58.364	43.478	0.00	0.00	0.00	3.62
1112	1157	1.300465	CATCACCGAGCGATCCAGG	60.300	63.158	0.00	0.00	0.00	4.45
1180	1225	0.524392	CGGTGCGTGCAAGTTTTTGA	60.524	50.000	0.59	0.00	36.36	2.69
1701	1749	0.806102	ACATGATGTACCACGCGCTC	60.806	55.000	5.73	0.00	0.00	5.03
1887	1935	6.128063	CGTAAGAACCACTACAACTAGCTAGT	60.128	42.308	20.95	20.95	43.02	2.57

Showing 1 to 25 of 43 entries

Previous1 2Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	7.806487	CCATGCTTATCACTAAATTACATGCAG	59.194	37.037	0.00	0.00	32.91	4.41
281	285	2.094182	CGGCTGCTCTAAACTAAGTGGA	60.094	50.000	0.00	0.00	0.00	4.02
531	550	3.045601	TCAGCTCCTTTCTTTTCCTCG	57.954	47.619	0.00	0.00	0.00	4.63
623	642	4.012374	CCAGCACAGTCCAGTTGATAAAT	58.988	43.478	0.00	0.00	0.00	1.40
662	681	6.588719	TTCTTTTGTGATTAGTTGGGATGG	57.411	37.500	0.00	0.00	0.00	3.51
683	702	1.468054	GCTTGCCCGTGTGATGATTTC	60.468	52.381	0.00	0.00	0.00	2.17
869	904	0.895100	TTTGAGCTTCCAATGGCGCT	60.895	50.000	14.15	14.15	33.33	5.92
912	947	1.079127	CAATTCCGGCGTGTCTCCT	60.079	57.895	6.01	0.00	0.00	3.69
941	976	2.230130	TGGTTGGAAATTAGGGCCTG	57.770	50.000	18.53	0.00	0.00	4.85
952	987	2.238521	GGAAAGAGTGCATGGTTGGAA	58.761	47.619	0.00	0.00	0.00	3.53
953	988	1.547675	GGGAAAGAGTGCATGGTTGGA	60.548	52.381	0.00	0.00	0.00	3.53
968	1003	0.981943	GACGAAGAGGAAGGGGGAAA	59.018	55.000	0.00	0.00	0.00	3.13
969	1004	0.116541	AGACGAAGAGGAAGGGGGAA	59.883	55.000	0.00	0.00	0.00	3.97
985	1020	2.224314	GCGCCATTGCTTATAAGGAGAC	59.776	50.000	14.28	1.93	34.43	3.36
1034	1069	2.155279	GCTGCTGCTGATGATGATGAT	58.845	47.619	10.92	0.00	36.03	2.45
1038	1073	0.106149	ATCGCTGCTGCTGATGATGA	59.894	50.000	14.03	1.95	36.97	2.92
1039	1074	0.513385	GATCGCTGCTGCTGATGATG	59.487	55.000	20.90	3.53	34.47	3.07
1040	1075	0.106149	TGATCGCTGCTGCTGATGAT	59.894	50.000	20.90	13.31	34.47	2.45
1041	1076	0.808847	GTGATCGCTGCTGCTGATGA	60.809	55.000	20.90	13.60	34.47	2.92
1042	1077	1.642215	GTGATCGCTGCTGCTGATG	59.358	57.895	20.90	5.08	34.47	3.07
1043	1078	1.523258	GGTGATCGCTGCTGCTGAT	60.523	57.895	17.71	17.71	36.02	2.90
1044	1079	2.125391	GGTGATCGCTGCTGCTGA	60.125	61.111	14.03	12.39	36.97	4.26
1092	1137	1.738346	CTGGATCGCTCGGTGATGGA	61.738	60.000	4.92	0.00	32.57	3.41
1094	1139	1.300465	CCTGGATCGCTCGGTGATG	60.300	63.158	4.92	0.00	32.57	3.07
1164	1209	0.527385	GCCTCAAAAACTTGCACGCA	60.527	50.000	0.00	0.00	0.00	5.24

Showing 1 to 25 of 50 entries

Previous1 2Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.