AutoCloner

Multiple sequence alignment - TraesCS7A01G237300

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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	TraesCS7A01G237300	chr7A	100.000	2483	0	0	1	2483	211243769	211241287	0.000000e+00	4586.0
1	TraesCS7A01G237300	chr7D	98.404	2444	38	1	41	2483	381958759	381961202	0.000000e+00	4296.0
2	TraesCS7A01G237300	chr7D	98.322	2444	40	1	41	2483	382065080	382062637	0.000000e+00	4285.0
3	TraesCS7A01G237300	chr7D	98.200	2444	43	1	41	2483	626682833	626685276	0.000000e+00	4268.0
4	TraesCS7A01G237300	chr7D	100.000	41	0	0	1	41	203559515	203559555	2.650000e-10	76.8
5	TraesCS7A01G237300	chr6D	98.404	2444	38	1	41	2483	124532524	124530081	0.000000e+00	4296.0
6	TraesCS7A01G237300	chr6D	100.000	41	0	0	1	41	425965965	425966005	2.650000e-10	76.8
7	TraesCS7A01G237300	chr7B	98.323	2445	39	2	41	2483	644463846	644461402	0.000000e+00	4287.0
8	TraesCS7A01G237300	chr1D	98.322	2444	39	2	41	2483	141316733	141319175	0.000000e+00	4285.0
9	TraesCS7A01G237300	chr1D	100.000	41	0	0	1	41	185766294	185766254	2.650000e-10	76.8
10	TraesCS7A01G237300	chrUn	98.202	2447	40	3	41	2483	189407486	189405040	0.000000e+00	4272.0
11	TraesCS7A01G237300	chrUn	100.000	41	0	0	1	41	159843673	159843633	2.650000e-10	76.8
12	TraesCS7A01G237300	chrUn	100.000	41	0	0	1	41	189389358	189389318	2.650000e-10	76.8
13	TraesCS7A01G237300	chr3A	98.077	2444	46	1	41	2483	633107658	633105215	0.000000e+00	4252.0
14	TraesCS7A01G237300	chr1B	97.958	2448	45	3	41	2483	668808757	668811204	0.000000e+00	4239.0
15	TraesCS7A01G237300	chr5D	100.000	41	0	0	1	41	79869516	79869476	2.650000e-10	76.8
16	TraesCS7A01G237300	chr4D	100.000	41	0	0	1	41	123409721	123409681	2.650000e-10	76.8
17	TraesCS7A01G237300	chr4D	100.000	41	0	0	1	41	398385974	398385934	2.650000e-10	76.8
18	TraesCS7A01G237300	chr4D	100.000	41	0	0	1	41	483700613	483700573	2.650000e-10	76.8

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	TraesCS7A01G237300	chr7A	211241287	211243769	2482	True	4586	4586	100.000	1	2483	1	chr7A.!!$R1	2482
1	TraesCS7A01G237300	chr7D	381958759	381961202	2443	False	4296	4296	98.404	41	2483	1	chr7D.!!$F2	2442
2	TraesCS7A01G237300	chr7D	382062637	382065080	2443	True	4285	4285	98.322	41	2483	1	chr7D.!!$R1	2442
3	TraesCS7A01G237300	chr7D	626682833	626685276	2443	False	4268	4268	98.200	41	2483	1	chr7D.!!$F3	2442
4	TraesCS7A01G237300	chr6D	124530081	124532524	2443	True	4296	4296	98.404	41	2483	1	chr6D.!!$R1	2442
5	TraesCS7A01G237300	chr7B	644461402	644463846	2444	True	4287	4287	98.323	41	2483	1	chr7B.!!$R1	2442
6	TraesCS7A01G237300	chr1D	141316733	141319175	2442	False	4285	4285	98.322	41	2483	1	chr1D.!!$F1	2442
7	TraesCS7A01G237300	chrUn	189405040	189407486	2446	True	4272	4272	98.202	41	2483	1	chrUn.!!$R3	2442
8	TraesCS7A01G237300	chr3A	633105215	633107658	2443	True	4252	4252	98.077	41	2483	1	chr3A.!!$R1	2442
9	TraesCS7A01G237300	chr1B	668808757	668811204	2447	False	4239	4239	97.958	41	2483	1	chr1B.!!$F1	2442

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
87	88	0.771127	TAACCAGCCCAGCAAGAAGT	59.229	50.000	0.00	0.0	0.0	3.01	F
1158	1159	1.066573	CCAAGAGCTCCGTCAATCTGT	60.067	52.381	10.93	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1286	1287	1.962321	TAATGCGCCGCTTGACCCTA	61.962	55.000	11.67	0.0	0.0	3.53	R
2349	2357	2.192263	GGGTCCTCAGTCTGAATCCTT	58.808	52.381	3.67	0.0	0.0	3.36	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	9.822185	ATGTATTTCCTTTATGAAATTTGGCTC	57.178	29.630	0.00	0.00	41.05	4.70
36	37	8.811017	TGTATTTCCTTTATGAAATTTGGCTCA	58.189	29.630	0.00	0.00	41.05	4.26
37	38	9.087424	GTATTTCCTTTATGAAATTTGGCTCAC	57.913	33.333	0.00	0.00	41.05	3.51
38	39	5.659440	TCCTTTATGAAATTTGGCTCACC	57.341	39.130	0.00	0.00	0.00	4.02
39	40	4.466015	TCCTTTATGAAATTTGGCTCACCC	59.534	41.667	0.00	0.00	33.59	4.61
87	88	0.771127	TAACCAGCCCAGCAAGAAGT	59.229	50.000	0.00	0.00	0.00	3.01
158	159	1.734465	GTGACATAGGTGCACAAGAGC	59.266	52.381	20.43	0.00	34.58	4.09
284	285	3.963129	ACCGCCATAAAAATCTTCCTCA	58.037	40.909	0.00	0.00	0.00	3.86
312	313	3.427098	CGTCTGTAGCGGAACTATGAACA	60.427	47.826	0.00	0.00	32.15	3.18
387	388	7.011857	GGAAGAGTCAAAATATTCAGAAGCGAT	59.988	37.037	0.00	0.00	0.00	4.58
457	458	4.202524	TGGCTAATACCCGAGGCATAAAAT	60.203	41.667	0.00	0.00	42.73	1.82
460	461	5.935789	GCTAATACCCGAGGCATAAAATACA	59.064	40.000	0.00	0.00	0.00	2.29
479	480	2.574369	ACACATTTTCTACGGGATCCCA	59.426	45.455	30.42	11.27	35.37	4.37
577	578	4.766891	ACCGACATGTCAAGATCCAAATTT	59.233	37.500	24.93	0.00	0.00	1.82
639	640	1.228154	GGCGGTCCAACAAAGAGGT	60.228	57.895	0.00	0.00	0.00	3.85
795	796	3.446161	TGCTACGCAACAATAGAGTAGGT	59.554	43.478	0.00	0.00	34.76	3.08
812	813	2.673341	TGCGCCGCCCACAAAATA	60.673	55.556	6.63	0.00	0.00	1.40
854	855	4.093011	AGCGAGCTTCTTATATGGGATCT	58.907	43.478	0.00	0.00	0.00	2.75
894	895	2.229792	AGCAGCGTTCCATTCTTTTCA	58.770	42.857	0.00	0.00	0.00	2.69
948	949	2.696187	TGCCACAATCCCATTCATCATG	59.304	45.455	0.00	0.00	0.00	3.07
1052	1053	6.071165	GGATCTTGTGGAACTGGATTTGATTT	60.071	38.462	0.00	0.00	38.04	2.17
1158	1159	1.066573	CCAAGAGCTCCGTCAATCTGT	60.067	52.381	10.93	0.00	0.00	3.41
1398	1399	0.104620	AGGGAGTGTACAACTGGGGT	60.105	55.000	0.00	0.00	40.07	4.95
1600	1603	4.302067	ACCCTCATGATTAGACCATGTCT	58.698	43.478	0.00	1.94	45.54	3.41
2349	2357	2.371841	ACTGTTGGTCCAATGCTAGTGA	59.628	45.455	7.77	0.00	0.00	3.41
2417	2425	4.899502	TGAAGGATTGAAAGAGGACTGAC	58.100	43.478	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	9.822185	GAGCCAAATTTCATAAAGGAAATACAT	57.178	29.630	3.30	0.00	44.47	2.29
10	11	8.811017	TGAGCCAAATTTCATAAAGGAAATACA	58.189	29.630	3.30	0.00	44.47	2.29
11	12	9.087424	GTGAGCCAAATTTCATAAAGGAAATAC	57.913	33.333	3.30	0.00	44.47	1.89
12	13	8.257306	GGTGAGCCAAATTTCATAAAGGAAATA	58.743	33.333	3.30	0.00	39.23	1.40
13	14	7.105588	GGTGAGCCAAATTTCATAAAGGAAAT	58.894	34.615	0.00	0.00	40.47	2.17
14	15	6.463360	GGTGAGCCAAATTTCATAAAGGAAA	58.537	36.000	0.00	0.00	36.64	3.13
15	16	5.046663	GGGTGAGCCAAATTTCATAAAGGAA	60.047	40.000	0.00	0.00	36.17	3.36
16	17	4.466015	GGGTGAGCCAAATTTCATAAAGGA	59.534	41.667	0.00	0.00	36.17	3.36
17	18	4.222588	TGGGTGAGCCAAATTTCATAAAGG	59.777	41.667	0.00	0.00	36.17	3.11
18	19	5.404466	TGGGTGAGCCAAATTTCATAAAG	57.596	39.130	0.00	0.00	36.17	1.85
19	20	5.815233	TTGGGTGAGCCAAATTTCATAAA	57.185	34.783	14.54	0.00	36.17	1.40
20	21	5.104982	GGATTGGGTGAGCCAAATTTCATAA	60.105	40.000	20.90	0.00	38.50	1.90
21	22	4.405358	GGATTGGGTGAGCCAAATTTCATA	59.595	41.667	20.90	0.00	38.50	2.15
22	23	3.198417	GGATTGGGTGAGCCAAATTTCAT	59.802	43.478	20.90	2.03	38.50	2.57
23	24	2.566724	GGATTGGGTGAGCCAAATTTCA	59.433	45.455	20.90	0.00	38.50	2.69
24	25	2.417243	CGGATTGGGTGAGCCAAATTTC	60.417	50.000	20.90	13.10	38.50	2.17
25	26	1.550072	CGGATTGGGTGAGCCAAATTT	59.450	47.619	20.90	3.68	38.50	1.82
26	27	1.185315	CGGATTGGGTGAGCCAAATT	58.815	50.000	20.90	4.51	38.50	1.82
27	28	0.684153	CCGGATTGGGTGAGCCAAAT	60.684	55.000	20.90	8.97	41.05	2.32
28	29	1.304052	CCGGATTGGGTGAGCCAAA	60.304	57.895	20.90	4.11	36.17	3.28
29	30	2.354729	CCGGATTGGGTGAGCCAA	59.645	61.111	19.31	19.31	36.17	4.52
30	31	4.424711	GCCGGATTGGGTGAGCCA	62.425	66.667	5.05	0.00	38.63	4.75
31	32	4.424711	TGCCGGATTGGGTGAGCC	62.425	66.667	5.05	0.00	38.63	4.70
32	33	2.825836	CTGCCGGATTGGGTGAGC	60.826	66.667	5.05	0.00	38.63	4.26
33	34	2.825836	GCTGCCGGATTGGGTGAG	60.826	66.667	5.05	0.00	38.63	3.51
34	35	4.424711	GGCTGCCGGATTGGGTGA	62.425	66.667	5.05	0.00	38.63	4.02
35	36	4.738998	TGGCTGCCGGATTGGGTG	62.739	66.667	14.98	0.00	38.63	4.61
36	37	4.431131	CTGGCTGCCGGATTGGGT	62.431	66.667	23.22	0.00	38.63	4.51
38	39	4.809496	AGCTGGCTGCCGGATTGG	62.809	66.667	31.08	9.14	44.23	3.16
39	40	3.515286	CAGCTGGCTGCCGGATTG	61.515	66.667	31.08	22.05	44.23	2.67
54	55	2.286872	CTGGTTATTCAGAGCCAGCAG	58.713	52.381	0.00	0.00	41.46	4.24
158	159	2.513065	GATGGTTGTGGCGCGAAGTG	62.513	60.000	12.10	0.00	43.41	3.16
284	285	2.950309	AGTTCCGCTACAGACGATACAT	59.050	45.455	0.00	0.00	0.00	2.29
312	313	1.403687	GGTCCGGATTGCTAGCTCCT	61.404	60.000	17.23	0.00	0.00	3.69
387	388	2.716424	ACCCCTTCTTCATTCTTGGACA	59.284	45.455	0.00	0.00	0.00	4.02
457	458	3.775866	TGGGATCCCGTAGAAAATGTGTA	59.224	43.478	26.03	0.00	39.42	2.90
460	461	4.310022	TTTGGGATCCCGTAGAAAATGT	57.690	40.909	26.03	0.00	39.42	2.71
479	480	2.123033	GGGGTGGCTGGTGGTTTT	60.123	61.111	0.00	0.00	0.00	2.43
577	578	1.075374	CCAGGACCAGGAACCAATTCA	59.925	52.381	0.00	0.00	36.46	2.57
639	640	5.104693	TGGAAAGAAAGACACCACTACTTCA	60.105	40.000	0.00	0.00	0.00	3.02
795	796	1.599606	AATATTTTGTGGGCGGCGCA	61.600	50.000	34.36	16.31	0.00	6.09
812	813	4.273480	CGCTCTTTACCCGATCATTCAAAT	59.727	41.667	0.00	0.00	0.00	2.32
854	855	2.125391	GCTCTGCTGGATGCGTCA	60.125	61.111	8.47	0.00	46.63	4.35
948	949	5.163550	GGGCTTTGGGTTATGTAGATCAAAC	60.164	44.000	0.00	0.00	0.00	2.93
1052	1053	2.311701	CGTACCGAACCGCTTGCAA	61.312	57.895	0.00	0.00	0.00	4.08
1286	1287	1.962321	TAATGCGCCGCTTGACCCTA	61.962	55.000	11.67	0.00	0.00	3.53
1347	1348	5.066593	AGAACCCTTGTTGATTCTGAACTC	58.933	41.667	0.00	0.00	33.97	3.01
1671	1676	3.211045	CTTTCCTTGGTCTTTCGTTCCA	58.789	45.455	0.00	0.00	0.00	3.53
1817	1822	8.480501	ACTAAGCATAAATTTGGAAATGAGCAT	58.519	29.630	0.00	0.00	0.00	3.79
2349	2357	2.192263	GGGTCCTCAGTCTGAATCCTT	58.808	52.381	3.67	0.00	0.00	3.36
2417	2425	2.240667	AGATCACAAATCAGAGGGGTGG	59.759	50.000	0.00	0.00	0.00	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.