AutoCloner

Multiple sequence alignment - TraesCS4B01G326700

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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	TraesCS4B01G326700	chr4B	100.000	3182	0	0	1	3182	617439450	617436269	0.000000e+00	5877.0
1	TraesCS4B01G326700	chr5A	94.633	1677	79	4	915	2591	665767644	665765979	0.000000e+00	2588.0
2	TraesCS4B01G326700	chr5A	91.892	111	8	1	815	925	665768592	665768483	1.530000e-33	154.0
3	TraesCS4B01G326700	chr4D	96.315	1547	47	6	807	2352	484726717	484725180	0.000000e+00	2532.0
4	TraesCS4B01G326700	chr4D	86.069	524	62	7	261	774	484727539	484727017	1.290000e-153	553.0
5	TraesCS4B01G326700	chr4D	90.909	77	7	0	1	77	484734766	484734690	1.560000e-18	104.0
6	TraesCS4B01G326700	chr3A	92.061	592	42	3	2591	3182	658300266	658299680	0.000000e+00	828.0
7	TraesCS4B01G326700	chr3A	78.378	185	32	7	2410	2591	694532457	694532636	2.590000e-21	113.0
8	TraesCS4B01G326700	chr3D	89.527	592	49	5	2592	3182	349899821	349900400	0.000000e+00	737.0
9	TraesCS4B01G326700	chr1D	88.735	577	49	5	2609	3182	9386889	9387452	0.000000e+00	691.0
10	TraesCS4B01G326700	chr6B	85.185	594	62	10	2592	3182	130500670	130501240	1.270000e-163	586.0
11	TraesCS4B01G326700	chr7B	85.017	594	52	10	2592	3182	745108783	745108224	1.280000e-158	569.0
12	TraesCS4B01G326700	chr2A	86.826	501	62	4	2592	3090	70150801	70151299	9.970000e-155	556.0
13	TraesCS4B01G326700	chr2A	80.412	97	13	4	2363	2459	596382990	596382900	5.700000e-08	69.4
14	TraesCS4B01G326700	chr1A	86.310	504	66	3	2589	3090	65787759	65788261	2.160000e-151	545.0
15	TraesCS4B01G326700	chr1A	87.143	70	8	1	2407	2476	479785853	479785921	9.460000e-11	78.7
16	TraesCS4B01G326700	chr7A	85.882	510	65	5	2587	3090	70184580	70185088	1.300000e-148	536.0
17	TraesCS4B01G326700	chr7D	85.972	499	66	4	2591	3089	18093036	18092542	6.040000e-147	531.0
18	TraesCS4B01G326700	chr6D	84.381	525	54	12	2589	3109	450667394	450667894	1.030000e-134	490.0
19	TraesCS4B01G326700	chr6D	88.889	45	4	1	2544	2587	63734907	63734951	2.000000e-03	54.7
20	TraesCS4B01G326700	chr3B	89.080	348	35	2	2587	2931	823321312	823320965	2.270000e-116	429.0
21	TraesCS4B01G326700	chr2B	86.458	96	6	6	2403	2496	544039181	544039091	7.260000e-17	99.0
22	TraesCS4B01G326700	chr2B	86.458	96	6	6	2403	2496	544470634	544470544	7.260000e-17	99.0
23	TraesCS4B01G326700	chr1B	95.238	42	2	0	2545	2586	540362033	540361992	2.050000e-07	67.6
24	TraesCS4B01G326700	chr5D	83.607	61	6	4	2409	2469	530435102	530435046	2.000000e-03	54.7

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	TraesCS4B01G326700	chr4B	617436269	617439450	3181	True	5877.0	5877	100.0000	1	3182	1	chr4B.!!$R1	3181
1	TraesCS4B01G326700	chr5A	665765979	665768592	2613	True	1371.0	2588	93.2625	815	2591	2	chr5A.!!$R1	1776
2	TraesCS4B01G326700	chr4D	484725180	484727539	2359	True	1542.5	2532	91.1920	261	2352	2	chr4D.!!$R2	2091
3	TraesCS4B01G326700	chr3A	658299680	658300266	586	True	828.0	828	92.0610	2591	3182	1	chr3A.!!$R1	591
4	TraesCS4B01G326700	chr3D	349899821	349900400	579	False	737.0	737	89.5270	2592	3182	1	chr3D.!!$F1	590
5	TraesCS4B01G326700	chr1D	9386889	9387452	563	False	691.0	691	88.7350	2609	3182	1	chr1D.!!$F1	573
6	TraesCS4B01G326700	chr6B	130500670	130501240	570	False	586.0	586	85.1850	2592	3182	1	chr6B.!!$F1	590
7	TraesCS4B01G326700	chr7B	745108224	745108783	559	True	569.0	569	85.0170	2592	3182	1	chr7B.!!$R1	590
8	TraesCS4B01G326700	chr1A	65787759	65788261	502	False	545.0	545	86.3100	2589	3090	1	chr1A.!!$F1	501
9	TraesCS4B01G326700	chr7A	70184580	70185088	508	False	536.0	536	85.8820	2587	3090	1	chr7A.!!$F1	503
10	TraesCS4B01G326700	chr6D	450667394	450667894	500	False	490.0	490	84.3810	2589	3109	1	chr6D.!!$F2	520

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
179	180	0.028637	GCATCGCCTCTTTAGCAAGC	59.971	55.0	0.0	0.0	0.00	4.01	F
263	264	0.109643	TGCTGCAATGACGAATGCAC	60.110	50.0	0.0	0.0	46.87	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2103	3229	1.446966	GAACTCCTGCACGAGCTCC	60.447	63.158	8.47	0.0	42.74	4.70	R
2213	3339	0.450482	CATCGACACGACAAAACCGC	60.450	55.000	0.00	0.0	39.18	5.68	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
19	20	2.516227	TCTCAGTCCATCTCGTCCTT	57.484	50.000	0.00	0.00	0.00	3.36
20	21	2.370349	TCTCAGTCCATCTCGTCCTTC	58.630	52.381	0.00	0.00	0.00	3.46
21	22	1.407258	CTCAGTCCATCTCGTCCTTCC	59.593	57.143	0.00	0.00	0.00	3.46
22	23	0.461961	CAGTCCATCTCGTCCTTCCC	59.538	60.000	0.00	0.00	0.00	3.97
23	24	0.041238	AGTCCATCTCGTCCTTCCCA	59.959	55.000	0.00	0.00	0.00	4.37
24	25	0.902531	GTCCATCTCGTCCTTCCCAA	59.097	55.000	0.00	0.00	0.00	4.12
25	26	0.902531	TCCATCTCGTCCTTCCCAAC	59.097	55.000	0.00	0.00	0.00	3.77
26	27	0.613260	CCATCTCGTCCTTCCCAACA	59.387	55.000	0.00	0.00	0.00	3.33
27	28	1.406069	CCATCTCGTCCTTCCCAACAG	60.406	57.143	0.00	0.00	0.00	3.16
28	29	1.550524	CATCTCGTCCTTCCCAACAGA	59.449	52.381	0.00	0.00	0.00	3.41
29	30	1.938585	TCTCGTCCTTCCCAACAGAT	58.061	50.000	0.00	0.00	0.00	2.90
30	31	1.550524	TCTCGTCCTTCCCAACAGATG	59.449	52.381	0.00	0.00	0.00	2.90
31	32	1.276421	CTCGTCCTTCCCAACAGATGT	59.724	52.381	0.00	0.00	0.00	3.06
32	33	1.697432	TCGTCCTTCCCAACAGATGTT	59.303	47.619	0.00	0.00	39.12	2.71
33	34	2.901192	TCGTCCTTCCCAACAGATGTTA	59.099	45.455	0.00	0.00	36.32	2.41
34	35	3.517901	TCGTCCTTCCCAACAGATGTTAT	59.482	43.478	0.00	0.00	36.32	1.89
35	36	3.623060	CGTCCTTCCCAACAGATGTTATG	59.377	47.826	0.00	0.00	36.32	1.90
36	37	4.622933	CGTCCTTCCCAACAGATGTTATGA	60.623	45.833	0.00	0.00	36.32	2.15
37	38	4.878397	GTCCTTCCCAACAGATGTTATGAG	59.122	45.833	0.00	0.00	36.32	2.90
38	39	3.629398	CCTTCCCAACAGATGTTATGAGC	59.371	47.826	0.00	0.00	36.32	4.26
39	40	4.521146	CTTCCCAACAGATGTTATGAGCT	58.479	43.478	0.00	0.00	36.32	4.09
40	41	4.142609	TCCCAACAGATGTTATGAGCTC	57.857	45.455	6.82	6.82	36.32	4.09
41	42	3.519107	TCCCAACAGATGTTATGAGCTCA	59.481	43.478	20.79	20.79	36.32	4.26
42	43	3.624861	CCCAACAGATGTTATGAGCTCAC	59.375	47.826	20.97	7.27	36.32	3.51
43	44	3.624861	CCAACAGATGTTATGAGCTCACC	59.375	47.826	20.97	10.69	36.32	4.02

Showing 1 to 25 of 297 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	2.370349	GAAGGACGAGATGGACTGAGA	58.630	52.381	0.00	0.00	0.00	3.27
2	3	1.475403	GGAAGGACGAGATGGACTGA	58.525	55.000	0.00	0.00	0.00	3.41
4	5	0.041238	TGGGAAGGACGAGATGGACT	59.959	55.000	0.00	0.00	0.00	3.85
5	6	0.902531	TTGGGAAGGACGAGATGGAC	59.097	55.000	0.00	0.00	0.00	4.02
7	8	0.613260	TGTTGGGAAGGACGAGATGG	59.387	55.000	0.00	0.00	0.00	3.51
9	10	1.938585	TCTGTTGGGAAGGACGAGAT	58.061	50.000	0.00	0.00	0.00	2.75
10	11	1.550524	CATCTGTTGGGAAGGACGAGA	59.449	52.381	0.00	0.00	0.00	4.04
11	12	1.276421	ACATCTGTTGGGAAGGACGAG	59.724	52.381	0.00	0.00	0.00	4.18
14	15	4.843728	TCATAACATCTGTTGGGAAGGAC	58.156	43.478	5.84	0.00	38.90	3.85
16	17	3.629398	GCTCATAACATCTGTTGGGAAGG	59.371	47.826	5.84	0.00	38.90	3.46
17	18	4.521146	AGCTCATAACATCTGTTGGGAAG	58.479	43.478	5.84	0.47	38.90	3.46
18	19	4.019411	TGAGCTCATAACATCTGTTGGGAA	60.019	41.667	13.74	0.00	38.90	3.97
19	20	3.519107	TGAGCTCATAACATCTGTTGGGA	59.481	43.478	13.74	2.83	38.90	4.37
20	21	3.624861	GTGAGCTCATAACATCTGTTGGG	59.375	47.826	21.47	0.00	38.90	4.12
21	22	3.624861	GGTGAGCTCATAACATCTGTTGG	59.375	47.826	21.47	0.00	38.90	3.77
22	23	4.093998	GTGGTGAGCTCATAACATCTGTTG	59.906	45.833	21.47	0.00	38.90	3.33
23	24	4.256920	GTGGTGAGCTCATAACATCTGTT	58.743	43.478	21.47	0.69	41.73	3.16
24	25	3.369892	GGTGGTGAGCTCATAACATCTGT	60.370	47.826	21.47	0.00	0.00	3.41
25	26	3.201290	GGTGGTGAGCTCATAACATCTG	58.799	50.000	21.47	0.00	0.00	2.90
26	27	2.840038	TGGTGGTGAGCTCATAACATCT	59.160	45.455	21.47	0.00	0.00	2.90
27	28	2.939103	GTGGTGGTGAGCTCATAACATC	59.061	50.000	21.47	18.93	0.00	3.06
28	29	2.305635	TGTGGTGGTGAGCTCATAACAT	59.694	45.455	21.47	0.00	0.00	2.71
29	30	1.696884	TGTGGTGGTGAGCTCATAACA	59.303	47.619	21.47	17.81	0.00	2.41
30	31	2.076863	GTGTGGTGGTGAGCTCATAAC	58.923	52.381	21.47	19.74	0.00	1.89
31	32	1.696884	TGTGTGGTGGTGAGCTCATAA	59.303	47.619	21.47	8.53	0.00	1.90

Showing 1 to 25 of 329 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.