AutoCloner

Multiple sequence alignment - TraesCS3A01G086200

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	TraesCS3A01G086200	chr3A	100.000	5253	0	0	1	5253	55715008	55720260	0.000000e+00	9701.0
1	TraesCS3A01G086200	chr3A	96.183	131	5	0	4474	4604	532609643	532609513	1.150000e-51	215.0
2	TraesCS3A01G086200	chr3A	95.420	131	6	0	4478	4608	595058522	595058392	5.330000e-50	209.0
3	TraesCS3A01G086200	chr3D	91.850	2233	102	36	547	2741	43793566	43795756	0.000000e+00	3042.0
4	TraesCS3A01G086200	chr3D	88.235	1479	123	28	2803	4259	43795783	43797232	0.000000e+00	1720.0
5	TraesCS3A01G086200	chr3B	90.684	2265	111	50	528	2741	68449965	68452180	0.000000e+00	2922.0
6	TraesCS3A01G086200	chr3B	89.095	1238	91	25	3262	4480	68452600	68453812	0.000000e+00	1498.0
7	TraesCS3A01G086200	chr3B	86.849	403	37	8	2800	3191	68452204	68452601	2.250000e-118	436.0
8	TraesCS3A01G086200	chr3B	93.671	158	8	2	4603	4759	68453802	68453958	8.790000e-58	235.0
9	TraesCS3A01G086200	chr3B	88.889	189	14	6	5066	5252	68463522	68463705	5.290000e-55	226.0
10	TraesCS3A01G086200	chr3B	96.154	130	4	1	4478	4606	23595106	23594977	1.480000e-50	211.0
11	TraesCS3A01G086200	chr3B	95.122	123	5	1	4950	5071	68454300	68454422	5.370000e-45	193.0
12	TraesCS3A01G086200	chr3B	94.872	78	3	1	4758	4834	68454109	68454186	2.570000e-23	121.0
13	TraesCS3A01G086200	chr3B	100.000	61	0	0	4833	4893	68454238	68454298	4.300000e-21	113.0
14	TraesCS3A01G086200	chrUn	97.638	127	3	0	4477	4603	243391443	243391317	8.860000e-53	219.0
15	TraesCS3A01G086200	chr5D	98.387	124	2	0	4478	4601	303929261	303929138	8.860000e-53	219.0
16	TraesCS3A01G086200	chr5A	98.387	124	2	0	4478	4601	608862350	608862227	8.860000e-53	219.0
17	TraesCS3A01G086200	chr7A	96.212	132	5	0	4476	4607	546640237	546640106	3.190000e-52	217.0
18	TraesCS3A01G086200	chr5B	97.600	125	3	0	4478	4602	399041875	399041999	1.150000e-51	215.0
19	TraesCS3A01G086200	chr5B	95.420	131	6	0	4476	4606	636898708	636898578	5.330000e-50	209.0
20	TraesCS3A01G086200	chr7B	100.000	30	0	0	5152	5181	490356423	490356394	7.350000e-04	56.5

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	TraesCS3A01G086200	chr3A	55715008	55720260	5252	False	9701.000000	9701	100.0000	1	5253	1	chr3A.!!$F1	5252
1	TraesCS3A01G086200	chr3D	43793566	43797232	3666	False	2381.000000	3042	90.0425	547	4259	2	chr3D.!!$F1	3712
2	TraesCS3A01G086200	chr3B	68449965	68454422	4457	False	788.285714	2922	92.8990	528	5071	7	chr3B.!!$F2	4543

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
132	133	0.029567	CTCGCCGTCATCCACTAGAC	59.970	60.0	0.00	0.00	0.00	2.59	F
392	393	0.031721	GACGACCGAAGACCACAAGT	59.968	55.0	0.00	0.00	0.00	3.16	F
489	490	0.035317	CTTGCACTCCCAGTACTGCA	59.965	55.0	17.86	9.22	0.00	4.41	F
2311	2387	0.393808	ACGTGTCCTGGCAGTTTGTT	60.394	50.0	14.43	0.00	0.00	2.83	F
3322	3418	0.456653	CAATAGCCTTGTGCCGTTGC	60.457	55.0	0.00	0.00	42.71	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1847	1911	0.248843	CACCCAGCTCTGTCTTCCTC	59.751	60.000	0.00	0.00	0.00	3.71	R
2381	2457	1.127582	GACAAAGCTCACGTGCTCATC	59.872	52.381	11.67	0.82	43.24	2.92	R
2460	2536	1.000163	TCTTGAGCACGTTGGAGTCTC	60.000	52.381	0.00	0.00	0.00	3.36	R
3393	3489	0.258774	AACTGCCAGGGTGTTCTGTT	59.741	50.000	0.00	0.00	33.14	3.16	R
5228	5550	0.031857	TTTGTTGCGCACCATCCAAG	59.968	50.000	11.12	0.00	0.00	3.61	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
18	19	3.715871	TCTCATCGGTGGCACAAAA	57.284	47.368	20.82	4.02	44.16	2.44
19	20	1.522668	TCTCATCGGTGGCACAAAAG	58.477	50.000	20.82	8.93	44.16	2.27
20	21	1.202758	TCTCATCGGTGGCACAAAAGT	60.203	47.619	20.82	0.00	44.16	2.66
21	22	2.037902	TCTCATCGGTGGCACAAAAGTA	59.962	45.455	20.82	0.00	44.16	2.24
22	23	3.009723	CTCATCGGTGGCACAAAAGTAT	58.990	45.455	20.82	0.10	44.16	2.12
23	24	2.746904	TCATCGGTGGCACAAAAGTATG	59.253	45.455	20.82	12.19	44.16	2.39
24	25	2.552599	TCGGTGGCACAAAAGTATGA	57.447	45.000	20.82	0.86	44.16	2.15
25	26	2.852449	TCGGTGGCACAAAAGTATGAA	58.148	42.857	20.82	0.00	44.16	2.57
26	27	3.215151	TCGGTGGCACAAAAGTATGAAA	58.785	40.909	20.82	0.00	44.16	2.69
27	28	3.252215	TCGGTGGCACAAAAGTATGAAAG	59.748	43.478	20.82	0.00	44.16	2.62
28	29	3.611530	CGGTGGCACAAAAGTATGAAAGG	60.612	47.826	20.82	0.00	44.16	3.11
29	30	3.317150	GTGGCACAAAAGTATGAAAGGC	58.683	45.455	13.86	0.00	44.16	4.35
30	31	2.961741	TGGCACAAAAGTATGAAAGGCA	59.038	40.909	0.00	0.00	31.92	4.75
31	32	3.386078	TGGCACAAAAGTATGAAAGGCAA	59.614	39.130	0.00	0.00	31.92	4.52
32	33	4.141846	TGGCACAAAAGTATGAAAGGCAAA	60.142	37.500	0.00	0.00	31.92	3.68
33	34	4.996758	GGCACAAAAGTATGAAAGGCAAAT	59.003	37.500	0.00	0.00	0.00	2.32
34	35	5.106987	GGCACAAAAGTATGAAAGGCAAATG	60.107	40.000	0.00	0.00	0.00	2.32
35	36	5.106987	GCACAAAAGTATGAAAGGCAAATGG	60.107	40.000	0.00	0.00	0.00	3.16
36	37	6.222389	CACAAAAGTATGAAAGGCAAATGGA	58.778	36.000	0.00	0.00	0.00	3.41
37	38	6.705381	CACAAAAGTATGAAAGGCAAATGGAA	59.295	34.615	0.00	0.00	0.00	3.53
38	39	7.226325	CACAAAAGTATGAAAGGCAAATGGAAA	59.774	33.333	0.00	0.00	0.00	3.13
39	40	7.772757	ACAAAAGTATGAAAGGCAAATGGAAAA	59.227	29.630	0.00	0.00	0.00	2.29
40	41	7.728847	AAAGTATGAAAGGCAAATGGAAAAC	57.271	32.000	0.00	0.00	0.00	2.43
41	42	5.793817	AGTATGAAAGGCAAATGGAAAACC	58.206	37.500	0.00	0.00	0.00	3.27
42	43	3.483808	TGAAAGGCAAATGGAAAACCC	57.516	42.857	0.00	0.00	0.00	4.11

Showing 1 to 25 of 832 entries

Previous1 2 3 4 5…34Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
0	1	1.202758	ACTTTTGTGCCACCGATGAGA	60.203	47.619	0.00	3.27
1	2	1.238439	ACTTTTGTGCCACCGATGAG	58.762	50.000	0.00	2.90
2	3	2.552599	TACTTTTGTGCCACCGATGA	57.447	45.000	0.00	2.92
3	4	2.746904	TCATACTTTTGTGCCACCGATG	59.253	45.455	0.00	3.84
4	5	3.066291	TCATACTTTTGTGCCACCGAT	57.934	42.857	0.00	4.18
5	6	2.552599	TCATACTTTTGTGCCACCGA	57.447	45.000	0.00	4.69
6	7	3.564511	CTTTCATACTTTTGTGCCACCG	58.435	45.455	0.00	4.94
7	8	3.860754	GCCTTTCATACTTTTGTGCCACC	60.861	47.826	0.00	4.61
8	9	3.243704	TGCCTTTCATACTTTTGTGCCAC	60.244	43.478	0.00	5.01
9	10	2.961741	TGCCTTTCATACTTTTGTGCCA	59.038	40.909	0.00	4.92
10	11	3.658757	TGCCTTTCATACTTTTGTGCC	57.341	42.857	0.00	5.01
11	12	5.106987	CCATTTGCCTTTCATACTTTTGTGC	60.107	40.000	0.00	4.57
12	13	6.222389	TCCATTTGCCTTTCATACTTTTGTG	58.778	36.000	0.00	3.33
13	14	6.418057	TCCATTTGCCTTTCATACTTTTGT	57.582	33.333	0.00	2.83
14	15	7.727331	TTTCCATTTGCCTTTCATACTTTTG	57.273	32.000	0.00	2.44
15	16	7.228507	GGTTTTCCATTTGCCTTTCATACTTTT	59.771	33.333	40.31	2.27
16	17	6.710295	GGTTTTCCATTTGCCTTTCATACTTT	59.290	34.615	40.31	2.66
17	18	6.230472	GGTTTTCCATTTGCCTTTCATACTT	58.770	36.000	40.31	2.24
18	19	5.279960	GGGTTTTCCATTTGCCTTTCATACT	60.280	40.000	42.91	2.12
19	20	4.935205	GGGTTTTCCATTTGCCTTTCATAC	59.065	41.667	42.91	2.39
20	21	4.843516	AGGGTTTTCCATTTGCCTTTCATA	59.156	37.500	42.91	2.15
21	22	3.652387	AGGGTTTTCCATTTGCCTTTCAT	59.348	39.130	42.91	2.57
22	23	3.044894	AGGGTTTTCCATTTGCCTTTCA	58.955	40.909	42.91	2.69
23	24	3.769739	AGGGTTTTCCATTTGCCTTTC	57.230	42.857	42.91	2.62
24	25	3.007940	GCTAGGGTTTTCCATTTGCCTTT	59.992	43.478	42.91	3.11

Showing 1 to 25 of 784 entries

Previous1 2 3 4 5…32Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.