AutoCloner

Multiple sequence alignment - TraesCS2D01G144900

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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	TraesCS2D01G144900	chr2D	100.000	7444	0	0	1	7444	86490580	86498023	0.000000e+00	13747.0
1	TraesCS2D01G144900	chr2A	94.730	3245	124	15	923	4157	86898711	86901918	0.000000e+00	5001.0
2	TraesCS2D01G144900	chr2A	92.231	3025	143	28	1722	4704	86962575	86965549	0.000000e+00	4200.0
3	TraesCS2D01G144900	chr2A	95.802	524	21	1	6922	7444	86966013	86966536	0.000000e+00	845.0
4	TraesCS2D01G144900	chr2A	87.238	478	42	9	6429	6900	86965562	86966026	1.840000e-145	527.0
5	TraesCS2D01G144900	chr2A	90.074	403	29	7	4307	4704	86904953	86905349	5.150000e-141	512.0
6	TraesCS2D01G144900	chr2A	84.488	303	31	7	6124	6424	16078795	16079083	1.220000e-72	285.0
7	TraesCS2D01G144900	chr2A	84.488	303	31	7	6124	6424	16090136	16090424	1.220000e-72	285.0
8	TraesCS2D01G144900	chr2A	88.148	135	8	2	6767	6900	86905436	86905563	3.600000e-33	154.0
9	TraesCS2D01G144900	chr2A	80.342	117	22	1	343	459	125222626	125222511	3.700000e-13	87.9
10	TraesCS2D01G144900	chr2B	91.196	2601	149	44	68	2646	139339743	139342285	0.000000e+00	3461.0
11	TraesCS2D01G144900	chr2B	91.974	2118	110	20	2605	4704	139342277	139344352	0.000000e+00	2915.0
12	TraesCS2D01G144900	chr2B	84.211	304	41	5	6424	6724	139344360	139344659	9.450000e-74	289.0
13	TraesCS2D01G144900	chr2B	83.713	307	34	8	7149	7444	139346764	139347065	7.360000e-70	276.0
14	TraesCS2D01G144900	chr2B	95.833	72	3	0	1	72	139245797	139245868	4.720000e-22	117.0
15	TraesCS2D01G144900	chr3D	94.423	520	23	3	6927	7444	611522579	611522064	0.000000e+00	795.0
16	TraesCS2D01G144900	chr3D	87.277	448	45	9	6427	6868	611523020	611522579	1.120000e-137	501.0
17	TraesCS2D01G144900	chr3D	91.611	298	18	3	4410	4704	611523324	611523031	8.990000e-109	405.0
18	TraesCS2D01G144900	chr3D	85.542	249	26	8	46	286	394193426	394193672	1.240000e-62	252.0
19	TraesCS2D01G144900	chr3B	84.874	476	49	11	6428	6900	456923760	456924215	6.810000e-125	459.0
20	TraesCS2D01G144900	chr3B	87.838	296	28	4	4410	4701	456923455	456923746	2.570000e-89	340.0
21	TraesCS2D01G144900	chr3B	100.000	28	0	0	348	375	807880728	807880701	1.300000e-02	52.8
22	TraesCS2D01G144900	chr5D	78.031	701	107	26	3605	4287	432029108	432029779	1.500000e-106	398.0
23	TraesCS2D01G144900	chr5D	85.281	231	25	5	56	279	380691871	380692099	5.810000e-56	230.0
24	TraesCS2D01G144900	chr5D	82.470	251	33	10	47	292	520711068	520710824	7.570000e-50	209.0
25	TraesCS2D01G144900	chr5D	84.184	196	30	1	6225	6419	493359834	493359639	9.860000e-44	189.0
26	TraesCS2D01G144900	chr1B	89.655	232	19	4	54	282	532058941	532058712	2.630000e-74	291.0
27	TraesCS2D01G144900	chr1B	84.188	234	30	4	55	287	37566262	37566035	3.500000e-53	220.0
28	TraesCS2D01G144900	chrUn	84.488	303	31	7	6124	6424	325670203	325670491	1.220000e-72	285.0
29	TraesCS2D01G144900	chrUn	84.488	303	31	7	6124	6424	325827636	325827924	1.220000e-72	285.0
30	TraesCS2D01G144900	chr6D	86.220	254	25	8	53	301	131608727	131608975	4.430000e-67	267.0
31	TraesCS2D01G144900	chr6D	81.667	180	20	3	5697	5863	14162315	14162136	3.620000e-28	137.0
32	TraesCS2D01G144900	chr5A	83.513	279	34	9	3661	3934	547073318	547073589	4.460000e-62	250.0
33	TraesCS2D01G144900	chr7B	85.022	227	29	5	55	279	446140405	446140628	7.520000e-55	226.0
34	TraesCS2D01G144900	chr7D	84.581	227	31	4	55	279	428711368	428711592	9.720000e-54	222.0
35	TraesCS2D01G144900	chr7D	83.817	241	27	8	48	279	509500062	509500299	1.260000e-52	219.0
36	TraesCS2D01G144900	chr7A	76.571	350	43	17	5529	5842	473887857	473888203	1.000000e-33	156.0
37	TraesCS2D01G144900	chr4B	85.000	120	15	3	338	456	526732921	526733038	1.310000e-22	119.0
38	TraesCS2D01G144900	chr6B	80.800	125	20	3	334	456	578667311	578667433	2.210000e-15	95.3
39	TraesCS2D01G144900	chr4A	92.308	52	2	2	328	378	37781648	37781598	1.040000e-08	73.1
40	TraesCS2D01G144900	chr6A	83.117	77	13	0	334	410	532820230	532820306	3.730000e-08	71.3

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	TraesCS2D01G144900	chr2D	86490580	86498023	7443	False	13747.000000	13747	100.000000	1	7444	1	chr2D.!!$F1	7443
1	TraesCS2D01G144900	chr2A	86898711	86905563	6852	False	1889.000000	5001	90.984000	923	6900	3	chr2A.!!$F3	5977
2	TraesCS2D01G144900	chr2A	86962575	86966536	3961	False	1857.333333	4200	91.757000	1722	7444	3	chr2A.!!$F4	5722
3	TraesCS2D01G144900	chr2B	139339743	139347065	7322	False	1735.250000	3461	87.773500	68	7444	4	chr2B.!!$F2	7376
4	TraesCS2D01G144900	chr3D	611522064	611523324	1260	True	567.000000	795	91.103667	4410	7444	3	chr3D.!!$R1	3034
5	TraesCS2D01G144900	chr3B	456923455	456924215	760	False	399.500000	459	86.356000	4410	6900	2	chr3B.!!$F1	2490
6	TraesCS2D01G144900	chr5D	432029108	432029779	671	False	398.000000	398	78.031000	3605	4287	1	chr5D.!!$F2	682

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
727	736	0.248498	GCGACGTCGATCTTGATGGA	60.248	55.000	39.74	0.0	43.02	3.41	F
779	788	1.003233	CACCCACTAACCTCCTCCAAC	59.997	57.143	0.00	0.0	0.00	3.77	F
2234	2254	0.537143	TTGCCAGCGGTTTCATGAGT	60.537	50.000	0.00	0.0	0.00	3.41	F
2414	2434	0.459489	TGTTCTTGGTGCTTGTTGGC	59.541	50.000	0.00	0.0	0.00	4.52	F
4088	4202	0.390735	ACCGCCGTCGATTTTAGCTT	60.391	50.000	0.00	0.0	38.10	3.74	F
4743	7768	0.105401	TGGTGATACGGCCCAGGATA	60.105	55.000	0.00	0.0	0.00	2.59	F
4943	7968	0.029834	GGCATGCGTGGAATCACATC	59.970	55.000	12.44	0.0	43.79	3.06	F
4944	7969	0.029834	GCATGCGTGGAATCACATCC	59.970	55.000	8.27	0.0	43.79	3.51	F
6292	9317	0.032813	ATGTTTCCAGGGGCAGGATG	60.033	55.000	0.00	0.0	40.87	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2097	2117	0.450583	TCATACACCGACTCGTCAGC	59.549	55.000	0.00	0.0	0.00	4.26	R
2414	2434	0.606401	ACTCCAACACAATCAGGGCG	60.606	55.000	0.00	0.0	0.00	6.13	R
4017	4128	1.269936	ACCCGTATTATGTAGGCACGC	60.270	52.381	0.00	0.0	0.00	5.34	R
4325	7071	2.296190	CCGCAGCTGTCCTACATACATA	59.704	50.000	16.64	0.0	0.00	2.29	R
4924	7949	0.029834	GATGTGATTCCACGCATGCC	59.970	55.000	13.15	0.0	46.06	4.40	R
6273	9298	0.032813	CATCCTGCCCCTGGAAACAT	60.033	55.000	0.00	0.0	41.51	2.71	R
6386	9411	0.034670	GCTCCAGCCTTTCAGGTGAT	60.035	55.000	0.00	0.0	37.80	3.06	R
6388	9413	1.073722	TGCTCCAGCCTTTCAGGTG	59.926	57.895	0.00	0.0	41.18	4.00	R
7316	12073	0.745845	CTTATGAGGCCGCAGCTGTT	60.746	55.000	16.31	0.0	39.73	3.16	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
20	21	3.878086	GATGAAGACAAACAACAGCGA	57.122	42.857	0.00	0.00	0.00	4.93
21	22	3.803555	GATGAAGACAAACAACAGCGAG	58.196	45.455	0.00	0.00	0.00	5.03
22	23	2.627945	TGAAGACAAACAACAGCGAGT	58.372	42.857	0.00	0.00	0.00	4.18
23	24	3.787785	TGAAGACAAACAACAGCGAGTA	58.212	40.909	0.00	0.00	0.00	2.59
24	25	3.802139	TGAAGACAAACAACAGCGAGTAG	59.198	43.478	0.00	0.00	0.00	2.57
25	26	3.454371	AGACAAACAACAGCGAGTAGT	57.546	42.857	0.00	0.00	0.00	2.73
26	27	3.381949	AGACAAACAACAGCGAGTAGTC	58.618	45.455	0.00	0.00	0.00	2.59
36	37	2.969157	CGAGTAGTCGCGTAGGAGA	58.031	57.895	7.09	0.00	39.88	3.71
37	38	0.576328	CGAGTAGTCGCGTAGGAGAC	59.424	60.000	7.09	10.83	42.54	3.36
38	39	1.649664	GAGTAGTCGCGTAGGAGACA	58.350	55.000	19.23	5.08	44.37	3.41
39	40	1.327156	GAGTAGTCGCGTAGGAGACAC	59.673	57.143	19.23	14.65	44.37	3.67
40	41	1.066286	AGTAGTCGCGTAGGAGACACT	60.066	52.381	19.23	16.22	44.37	3.55
41	42	1.327156	GTAGTCGCGTAGGAGACACTC	59.673	57.143	19.23	7.18	44.37	3.51
52	53	3.441500	GGAGACACTCCCCAAAAATCT	57.558	47.619	6.54	0.00	44.36	2.40
53	54	4.569719	GGAGACACTCCCCAAAAATCTA	57.430	45.455	6.54	0.00	44.36	1.98
54	55	4.518249	GGAGACACTCCCCAAAAATCTAG	58.482	47.826	6.54	0.00	44.36	2.43
55	56	4.518249	GAGACACTCCCCAAAAATCTAGG	58.482	47.826	0.00	0.00	0.00	3.02
56	57	4.175962	AGACACTCCCCAAAAATCTAGGA	58.824	43.478	0.00	0.00	0.00	2.94
57	58	4.019231	AGACACTCCCCAAAAATCTAGGAC	60.019	45.833	0.00	0.00	0.00	3.85
58	59	3.010250	ACACTCCCCAAAAATCTAGGACC	59.990	47.826	0.00	0.00	0.00	4.46
59	60	2.581246	ACTCCCCAAAAATCTAGGACCC	59.419	50.000	0.00	0.00	0.00	4.46
60	61	2.853077	CTCCCCAAAAATCTAGGACCCT	59.147	50.000	0.00	0.00	0.00	4.34
61	62	2.580783	TCCCCAAAAATCTAGGACCCTG	59.419	50.000	0.00	0.00	0.00	4.45
62	63	2.580783	CCCCAAAAATCTAGGACCCTGA	59.419	50.000	0.00	0.00	0.00	3.86
63	64	3.205282	CCCCAAAAATCTAGGACCCTGAT	59.795	47.826	0.00	0.00	0.00	2.90

Showing 1 to 25 of 1,586 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.248602	ACTCGCTGTTGTTTGTCTTCATC	59.751	43.478	0.00	0.00	0.00	2.92
1	2	3.206150	ACTCGCTGTTGTTTGTCTTCAT	58.794	40.909	0.00	0.00	0.00	2.57
2	3	2.627945	ACTCGCTGTTGTTTGTCTTCA	58.372	42.857	0.00	0.00	0.00	3.02
4	5	3.793559	ACTACTCGCTGTTGTTTGTCTT	58.206	40.909	0.00	0.00	30.87	3.01
5	6	3.381949	GACTACTCGCTGTTGTTTGTCT	58.618	45.455	0.00	0.00	34.95	3.41
6	7	2.153247	CGACTACTCGCTGTTGTTTGTC	59.847	50.000	0.00	0.00	34.95	3.18
7	8	2.124903	CGACTACTCGCTGTTGTTTGT	58.875	47.619	0.00	0.00	34.95	2.83
8	9	2.837337	CGACTACTCGCTGTTGTTTG	57.163	50.000	0.00	0.00	34.95	2.93
18	19	0.576328	GTCTCCTACGCGACTACTCG	59.424	60.000	15.93	0.00	43.28	4.18
19	20	1.327156	GTGTCTCCTACGCGACTACTC	59.673	57.143	15.93	0.00	0.00	2.59
20	21	1.066286	AGTGTCTCCTACGCGACTACT	60.066	52.381	15.93	3.03	43.67	2.57
21	22	1.327156	GAGTGTCTCCTACGCGACTAC	59.673	57.143	15.93	2.34	43.67	2.73
22	23	1.649664	GAGTGTCTCCTACGCGACTA	58.350	55.000	15.93	0.00	43.67	2.59
23	24	1.025647	GGAGTGTCTCCTACGCGACT	61.026	60.000	15.93	1.89	46.41	4.18
24	25	1.428620	GGAGTGTCTCCTACGCGAC	59.571	63.158	15.93	0.00	46.41	5.19
25	26	3.900855	GGAGTGTCTCCTACGCGA	58.099	61.111	15.93	0.00	46.41	5.87
33	34	4.225267	TCCTAGATTTTTGGGGAGTGTCTC	59.775	45.833	0.00	0.00	0.00	3.36
34	35	4.019231	GTCCTAGATTTTTGGGGAGTGTCT	60.019	45.833	0.00	0.00	0.00	3.41
35	36	4.262617	GTCCTAGATTTTTGGGGAGTGTC	58.737	47.826	0.00	0.00	0.00	3.67
36	37	3.010250	GGTCCTAGATTTTTGGGGAGTGT	59.990	47.826	0.00	0.00	0.00	3.55
37	38	3.621558	GGTCCTAGATTTTTGGGGAGTG	58.378	50.000	0.00	0.00	0.00	3.51
38	39	2.581246	GGGTCCTAGATTTTTGGGGAGT	59.419	50.000	0.00	0.00	0.00	3.85
39	40	2.853077	AGGGTCCTAGATTTTTGGGGAG	59.147	50.000	0.00	0.00	0.00	4.30
40	41	2.580783	CAGGGTCCTAGATTTTTGGGGA	59.419	50.000	0.00	0.00	0.00	4.81
41	42	2.580783	TCAGGGTCCTAGATTTTTGGGG	59.419	50.000	0.00	0.00	0.00	4.96

Showing 1 to 25 of 1,571 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.