AutoCloner

Multiple sequence alignment - TraesCS7D01G140400

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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	TraesCS7D01G140400	chr7D	100.000	4810	0	0	789	5598	89725904	89730713	0.000000e+00	8883.0
1	TraesCS7D01G140400	chr7D	100.000	602	0	0	1	602	89725116	89725717	0.000000e+00	1112.0
2	TraesCS7D01G140400	chr7D	82.698	341	27	20	4829	5142	89599332	89598997	1.990000e-69	274.0
3	TraesCS7D01G140400	chr7A	94.659	4007	107	42	1652	5598	90660048	90664007	0.000000e+00	6115.0
4	TraesCS7D01G140400	chr7A	89.669	513	32	5	789	1280	90658945	90659457	7.910000e-178	634.0
5	TraesCS7D01G140400	chr7A	92.838	377	12	6	2795	3156	90665906	90666282	2.970000e-147	532.0
6	TraesCS7D01G140400	chr7A	92.580	283	15	4	1294	1570	90659614	90659896	8.740000e-108	401.0
7	TraesCS7D01G140400	chr7A	82.090	335	28	19	4835	5142	90617277	90616948	2.000000e-64	257.0
8	TraesCS7D01G140400	chr7A	87.931	58	5	2	465	520	664781811	664781868	3.620000e-07	67.6
9	TraesCS7D01G140400	chr7B	92.037	3893	193	59	1727	5525	40438795	40442664	0.000000e+00	5363.0
10	TraesCS7D01G140400	chr7B	91.995	787	44	7	793	1565	40437977	40438758	0.000000e+00	1086.0
11	TraesCS7D01G140400	chr7B	76.762	525	90	23	4941	5439	40557377	40557895	1.200000e-66	265.0
12	TraesCS7D01G140400	chr7B	82.111	341	28	18	4829	5141	40353408	40353073	1.550000e-65	261.0
13	TraesCS7D01G140400	chr7B	90.164	61	4	2	334	393	435004384	435004325	1.670000e-10	78.7
14	TraesCS7D01G140400	chr6B	94.203	69	3	1	1562	1629	14541074	14541142	2.760000e-18	104.0
15	TraesCS7D01G140400	chr6B	89.873	79	4	4	1562	1637	113298945	113298868	1.280000e-16	99.0
16	TraesCS7D01G140400	chr6B	88.060	67	8	0	391	457	269946958	269946892	4.650000e-11	80.5
17	TraesCS7D01G140400	chr5D	92.958	71	1	2	1562	1628	415263883	415263953	3.570000e-17	100.0
18	TraesCS7D01G140400	chr5A	91.892	74	3	3	1555	1627	547647539	547647468	3.570000e-17	100.0
19	TraesCS7D01G140400	chr5A	88.889	81	5	4	1562	1638	561531569	561531489	4.620000e-16	97.1
20	TraesCS7D01G140400	chr4D	92.857	70	3	2	1562	1629	382324441	382324510	3.570000e-17	100.0
21	TraesCS7D01G140400	chr1A	92.857	70	3	2	1562	1629	60284313	60284382	3.570000e-17	100.0
22	TraesCS7D01G140400	chr3A	89.024	82	5	2	1555	1632	684589736	684589817	1.280000e-16	99.0
23	TraesCS7D01G140400	chr3A	92.063	63	3	2	330	390	737237910	737237972	2.780000e-13	87.9
24	TraesCS7D01G140400	chr1B	91.429	70	2	2	1562	1627	491239723	491239654	5.970000e-15	93.5
25	TraesCS7D01G140400	chr1D	92.063	63	2	3	330	390	433503622	433503561	9.990000e-13	86.1
26	TraesCS7D01G140400	chr2A	85.915	71	10	0	391	461	673450849	673450779	6.010000e-10	76.8
27	TraesCS7D01G140400	chr4B	95.652	46	2	0	465	510	576168111	576168066	2.160000e-09	75.0
28	TraesCS7D01G140400	chr3D	94.000	50	2	1	465	514	384867212	384867260	2.160000e-09	75.0
29	TraesCS7D01G140400	chr3D	92.683	41	1	2	77	117	143670306	143670268	2.180000e-04	58.4
30	TraesCS7D01G140400	chr2B	92.000	50	4	0	465	514	568278339	568278388	2.800000e-08	71.3
31	TraesCS7D01G140400	chr3B	89.796	49	4	1	392	440	559876917	559876870	1.680000e-05	62.1
32	TraesCS7D01G140400	chr2D	100.000	31	0	0	77	107	459807213	459807243	2.180000e-04	58.4

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	TraesCS7D01G140400	chr7D	89725116	89730713	5597	False	4997.5	8883	100.0000	1	5598	2	chr7D.!!$F1	5597
1	TraesCS7D01G140400	chr7A	90658945	90666282	7337	False	1920.5	6115	92.4365	789	5598	4	chr7A.!!$F2	4809
2	TraesCS7D01G140400	chr7B	40437977	40442664	4687	False	3224.5	5363	92.0160	793	5525	2	chr7B.!!$F2	4732
3	TraesCS7D01G140400	chr7B	40557377	40557895	518	False	265.0	265	76.7620	4941	5439	1	chr7B.!!$F1	498

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
554	555	0.037975	GCAAATTGGTCAGCAGGTGG	60.038	55.000	0.00	0.00	0.00	4.61	F
1271	1293	1.068541	GTTTGAGCGGGTTTAGCTTGG	60.069	52.381	0.00	0.00	46.13	3.61	F
2511	2762	1.065854	CCTCCTTCAGGCTGGTAAGTG	60.066	57.143	15.73	6.41	34.56	3.16	F
3397	3665	1.069513	TGTCTGTGTCCCTGGTAAACG	59.930	52.381	0.00	0.00	0.00	3.60	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1705	1951	1.176619	GCCAACCGTTTAGGCTTGGT	61.177	55.000	14.94	45.17	3.67	R
3070	3336	2.435805	CTGCTCCAAGTTCTATAGGCCA	59.564	50.000	5.01	0.00	5.36	R
4107	4402	2.633509	GCTCCCTTTGCCTGCACAG	61.634	63.158	0.00	0.00	3.66	R
4924	5244	1.139455	TCCGACGAACCAACTCCTTTT	59.861	47.619	0.00	0.00	2.27	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
28	29	8.873215	AATACTCCTAGTTTCGTCATAACATG	57.127	34.615	0.00	0.00	0.00	3.21
29	30	6.282199	ACTCCTAGTTTCGTCATAACATGT	57.718	37.500	0.00	0.00	0.00	3.21
30	31	6.698380	ACTCCTAGTTTCGTCATAACATGTT	58.302	36.000	16.68	16.68	0.00	2.71
31	32	6.590292	ACTCCTAGTTTCGTCATAACATGTTG	59.410	38.462	21.42	6.25	0.00	3.33
32	33	6.693466	TCCTAGTTTCGTCATAACATGTTGA	58.307	36.000	21.42	8.79	0.00	3.18
33	34	6.811665	TCCTAGTTTCGTCATAACATGTTGAG	59.188	38.462	21.42	12.85	0.00	3.02
34	35	5.283060	AGTTTCGTCATAACATGTTGAGC	57.717	39.130	21.42	7.61	0.00	4.26
35	36	4.997395	AGTTTCGTCATAACATGTTGAGCT	59.003	37.500	21.42	8.33	0.00	4.09
36	37	5.470098	AGTTTCGTCATAACATGTTGAGCTT	59.530	36.000	21.42	0.00	0.00	3.74
37	38	5.940192	TTCGTCATAACATGTTGAGCTTT	57.060	34.783	21.42	0.00	0.00	3.51
38	39	5.940192	TCGTCATAACATGTTGAGCTTTT	57.060	34.783	21.42	0.00	0.00	2.27
39	40	5.688823	TCGTCATAACATGTTGAGCTTTTG	58.311	37.500	21.42	7.19	0.00	2.44
40	41	4.853196	CGTCATAACATGTTGAGCTTTTGG	59.147	41.667	21.42	0.56	0.00	3.28
41	42	5.562696	CGTCATAACATGTTGAGCTTTTGGT	60.563	40.000	21.42	0.00	0.00	3.67
42	43	5.858581	GTCATAACATGTTGAGCTTTTGGTC	59.141	40.000	21.42	0.00	46.33	4.02
75	76	9.543783	CCTAGTGGTTTGTTAATCTAATACTCC	57.456	37.037	0.00	0.00	0.00	3.85
78	79	8.265764	AGTGGTTTGTTAATCTAATACTCCTCC	58.734	37.037	0.00	0.00	0.00	4.30
79	80	8.044908	GTGGTTTGTTAATCTAATACTCCTCCA	58.955	37.037	0.00	0.00	0.00	3.86
80	81	8.607713	TGGTTTGTTAATCTAATACTCCTCCAA	58.392	33.333	0.00	0.00	0.00	3.53
81	82	9.457436	GGTTTGTTAATCTAATACTCCTCCAAA	57.543	33.333	0.00	0.00	0.00	3.28
91	92	9.542462	TCTAATACTCCTCCAAATTAATTGACG	57.458	33.333	0.39	0.00	41.85	4.35
92	93	4.965119	ACTCCTCCAAATTAATTGACGC	57.035	40.909	0.39	0.00	41.85	5.19
93	94	4.331968	ACTCCTCCAAATTAATTGACGCA	58.668	39.130	0.39	0.00	41.85	5.24
94	95	4.396166	ACTCCTCCAAATTAATTGACGCAG	59.604	41.667	0.39	0.00	41.85	5.18
95	96	3.128589	TCCTCCAAATTAATTGACGCAGC	59.871	43.478	0.39	0.00	41.85	5.25

Showing 1 to 25 of 393 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	9.961265	CATGTTATGACGAAACTAGGAGTATTA	57.039	33.333	0.00	0.00	0.00	0.98
3	4	8.475639	ACATGTTATGACGAAACTAGGAGTATT	58.524	33.333	0.00	0.00	0.00	1.89
4	5	8.008513	ACATGTTATGACGAAACTAGGAGTAT	57.991	34.615	0.00	0.00	0.00	2.12
5	6	7.400599	ACATGTTATGACGAAACTAGGAGTA	57.599	36.000	0.00	0.00	0.00	2.59
6	7	6.282199	ACATGTTATGACGAAACTAGGAGT	57.718	37.500	0.00	0.00	0.00	3.85
7	8	6.811665	TCAACATGTTATGACGAAACTAGGAG	59.188	38.462	11.53	0.00	0.00	3.69
8	9	6.693466	TCAACATGTTATGACGAAACTAGGA	58.307	36.000	11.53	0.00	0.00	2.94
9	10	6.455646	GCTCAACATGTTATGACGAAACTAGG	60.456	42.308	11.53	0.00	0.00	3.02
10	11	6.311445	AGCTCAACATGTTATGACGAAACTAG	59.689	38.462	11.53	0.00	0.00	2.57
11	12	6.163476	AGCTCAACATGTTATGACGAAACTA	58.837	36.000	11.53	0.00	0.00	2.24
12	13	4.997395	AGCTCAACATGTTATGACGAAACT	59.003	37.500	11.53	2.07	0.00	2.66
13	14	5.283060	AGCTCAACATGTTATGACGAAAC	57.717	39.130	11.53	0.00	0.00	2.78
14	15	5.940192	AAGCTCAACATGTTATGACGAAA	57.060	34.783	11.53	0.00	0.00	3.46
15	16	5.940192	AAAGCTCAACATGTTATGACGAA	57.060	34.783	11.53	0.00	0.00	3.85
16	17	5.334802	CCAAAAGCTCAACATGTTATGACGA	60.335	40.000	11.53	3.04	0.00	4.20
17	18	4.853196	CCAAAAGCTCAACATGTTATGACG	59.147	41.667	11.53	0.00	0.00	4.35
18	19	5.772521	ACCAAAAGCTCAACATGTTATGAC	58.227	37.500	11.53	1.45	0.00	3.06
19	20	5.534278	TGACCAAAAGCTCAACATGTTATGA	59.466	36.000	11.53	5.36	0.00	2.15
20	21	5.771469	TGACCAAAAGCTCAACATGTTATG	58.229	37.500	11.53	8.11	0.00	1.90
21	22	6.594788	ATGACCAAAAGCTCAACATGTTAT	57.405	33.333	11.53	0.00	0.00	1.89
22	23	7.446931	TCTTATGACCAAAAGCTCAACATGTTA	59.553	33.333	11.53	0.00	0.00	2.41
23	24	4.942761	ATGACCAAAAGCTCAACATGTT	57.057	36.364	4.92	4.92	0.00	2.71
24	25	5.769662	TCTTATGACCAAAAGCTCAACATGT	59.230	36.000	0.00	0.00	0.00	3.21
25	26	6.088824	GTCTTATGACCAAAAGCTCAACATG	58.911	40.000	0.00	0.00	37.24	3.21
26	27	6.259550	GTCTTATGACCAAAAGCTCAACAT	57.740	37.500	0.00	0.00	37.24	2.71

Showing 1 to 25 of 407 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.