AutoCloner

Multiple sequence alignment - TraesCS3D01G178400

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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	TraesCS3D01G178400	chr3D	100.000	2525	0	0	1	2525	160523881	160526405	0.000000e+00	4663.0
1	TraesCS3D01G178400	chr3B	90.339	1915	109	36	174	2057	237097328	237099197	0.000000e+00	2442.0
2	TraesCS3D01G178400	chr3B	91.925	161	12	1	1	161	237097124	237097283	9.090000e-55	224.0
3	TraesCS3D01G178400	chr3B	84.524	84	12	1	174	257	819216512	819216594	5.790000e-12	82.4
4	TraesCS3D01G178400	chr3B	83.721	86	13	1	173	257	71649537	71649622	2.080000e-11	80.5
5	TraesCS3D01G178400	chr3A	97.788	1311	24	2	627	1937	186707608	186708913	0.000000e+00	2255.0
6	TraesCS3D01G178400	chr3A	96.604	589	15	2	1937	2525	186710951	186711534	0.000000e+00	972.0
7	TraesCS3D01G178400	chr3A	87.214	743	72	13	1793	2521	674434229	674434962	0.000000e+00	824.0
8	TraesCS3D01G178400	chr6D	88.227	739	70	14	1794	2525	312685343	312684615	0.000000e+00	867.0
9	TraesCS3D01G178400	chr6D	82.390	159	23	5	1	157	13176384	13176539	1.580000e-27	134.0
10	TraesCS3D01G178400	chr6D	83.133	83	14	0	174	256	428261351	428261433	2.690000e-10	76.8
11	TraesCS3D01G178400	chr6D	81.928	83	15	0	174	256	80150763	80150845	1.250000e-08	71.3
12	TraesCS3D01G178400	chr2A	87.736	742	71	16	1793	2525	734496691	734497421	0.000000e+00	848.0
13	TraesCS3D01G178400	chr2A	84.337	83	13	0	174	256	66767752	66767834	5.790000e-12	82.4
14	TraesCS3D01G178400	chr4B	86.757	740	77	17	1790	2523	31522564	31521840	0.000000e+00	804.0
15	TraesCS3D01G178400	chr4B	81.818	165	23	7	1	162	638160454	638160294	5.670000e-27	132.0
16	TraesCS3D01G178400	chr4B	85.333	75	5	5	191	259	514621140	514621214	3.480000e-09	73.1
17	TraesCS3D01G178400	chr2D	86.431	737	83	13	1796	2523	87364826	87365554	0.000000e+00	791.0
18	TraesCS3D01G178400	chr7A	86.531	735	78	17	1794	2523	17435291	17434573	0.000000e+00	789.0
19	TraesCS3D01G178400	chr7A	85.445	742	89	14	1794	2523	649083279	649084013	0.000000e+00	754.0
20	TraesCS3D01G178400	chr7A	82.143	84	15	0	174	257	102330049	102330132	3.480000e-09	73.1
21	TraesCS3D01G178400	chr2B	85.946	740	84	17	1794	2523	711713312	711712583	0.000000e+00	773.0
22	TraesCS3D01G178400	chr7B	76.015	271	48	6	1	256	380077143	380077411	9.480000e-25	124.0
23	TraesCS3D01G178400	chr7B	84.337	83	13	0	174	256	641259844	641259762	5.790000e-12	82.4
24	TraesCS3D01G178400	chr6A	81.203	133	22	3	26	157	522221644	522221514	1.240000e-18	104.0

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	TraesCS3D01G178400	chr3D	160523881	160526405	2524	False	4663.0	4663	100.000	1	2525	1	chr3D.!!$F1	2524
1	TraesCS3D01G178400	chr3B	237097124	237099197	2073	False	1333.0	2442	91.132	1	2057	2	chr3B.!!$F3	2056
2	TraesCS3D01G178400	chr3A	186707608	186711534	3926	False	1613.5	2255	97.196	627	2525	2	chr3A.!!$F2	1898
3	TraesCS3D01G178400	chr3A	674434229	674434962	733	False	824.0	824	87.214	1793	2521	1	chr3A.!!$F1	728
4	TraesCS3D01G178400	chr6D	312684615	312685343	728	True	867.0	867	88.227	1794	2525	1	chr6D.!!$R1	731
5	TraesCS3D01G178400	chr2A	734496691	734497421	730	False	848.0	848	87.736	1793	2525	1	chr2A.!!$F2	732
6	TraesCS3D01G178400	chr4B	31521840	31522564	724	True	804.0	804	86.757	1790	2523	1	chr4B.!!$R1	733
7	TraesCS3D01G178400	chr2D	87364826	87365554	728	False	791.0	791	86.431	1796	2523	1	chr2D.!!$F1	727
8	TraesCS3D01G178400	chr7A	17434573	17435291	718	True	789.0	789	86.531	1794	2523	1	chr7A.!!$R1	729
9	TraesCS3D01G178400	chr7A	649083279	649084013	734	False	754.0	754	85.445	1794	2523	1	chr7A.!!$F2	729
10	TraesCS3D01G178400	chr2B	711712583	711713312	729	True	773.0	773	85.946	1794	2523	1	chr2B.!!$R1	729

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
32	33	0.37861	CGCTCTGATGACGCTAGACA	59.621	55.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2034	4166	6.317893	TCTGTAGTGCGTTCAGATTATAGACA	59.682	38.462	0.0	0.0	34.0	3.41	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
19	20	2.031516	CACCTCCACAAGCGCTCTG	61.032	63.158	12.06	14.10	0.00	3.35
32	33	0.378610	CGCTCTGATGACGCTAGACA	59.621	55.000	0.00	0.00	0.00	3.41
39	40	2.159240	TGATGACGCTAGACACATCACC	60.159	50.000	16.43	0.00	42.31	4.02
45	46	2.205074	GCTAGACACATCACCGGAATG	58.795	52.381	9.46	14.29	0.00	2.67
82	83	5.951747	TGAGAACCTTATTCCATTTTCAGGG	59.048	40.000	0.00	0.00	0.00	4.45
108	109	1.593196	CACCGCCTTGTCTTCTCAAA	58.407	50.000	0.00	0.00	0.00	2.69
135	136	6.206498	GGACACAAATCCTAAACAAACTCAC	58.794	40.000	0.00	0.00	35.68	3.51
141	142	8.931775	ACAAATCCTAAACAAACTCACAAAAAC	58.068	29.630	0.00	0.00	0.00	2.43
153	154	7.749539	AACTCACAAAAACATCTAAAAACGG	57.250	32.000	0.00	0.00	0.00	4.44
161	162	6.575162	AAACATCTAAAAACGGAGCAAGAT	57.425	33.333	0.00	0.00	0.00	2.40
162	163	6.575162	AACATCTAAAAACGGAGCAAGATT	57.425	33.333	0.00	0.00	0.00	2.40
163	164	7.681939	AACATCTAAAAACGGAGCAAGATTA	57.318	32.000	0.00	0.00	0.00	1.75
164	165	7.308782	ACATCTAAAAACGGAGCAAGATTAG	57.691	36.000	0.00	0.00	0.00	1.73
165	166	6.316390	ACATCTAAAAACGGAGCAAGATTAGG	59.684	38.462	0.00	0.00	0.00	2.69
166	167	5.183228	TCTAAAAACGGAGCAAGATTAGGG	58.817	41.667	0.00	0.00	0.00	3.53
167	168	3.434940	AAAACGGAGCAAGATTAGGGT	57.565	42.857	0.00	0.00	0.00	4.34
169	170	1.867363	ACGGAGCAAGATTAGGGTCT	58.133	50.000	0.00	0.00	0.00	3.85
200	233	3.063197	ATCGGAGAGGAGACGGGCT	62.063	63.158	0.00	0.00	43.63	5.19
205	238	3.827898	GAGGAGACGGGCTGACGG	61.828	72.222	0.00	0.00	38.39	4.79
235	268	0.702316	GGGAGGCAAAGGAACCCTAA	59.298	55.000	0.00	0.00	37.75	2.69
272	322	2.125552	CGGCGGATGTCTTGCTGA	60.126	61.111	0.00	0.00	37.16	4.26
287	337	1.938657	GCTGAGCACGAGCAGGTCTA	61.939	60.000	7.77	0.00	45.49	2.59
294	344	0.396417	ACGAGCAGGTCTAGCTGGAT	60.396	55.000	2.00	0.00	43.58	3.41
300	350	2.366916	GCAGGTCTAGCTGGATGTATGT	59.633	50.000	2.00	0.00	0.00	2.29
301	351	3.181461	GCAGGTCTAGCTGGATGTATGTT	60.181	47.826	2.00	0.00	0.00	2.71
302	352	4.684485	GCAGGTCTAGCTGGATGTATGTTT	60.684	45.833	2.00	0.00	0.00	2.83
303	353	5.431765	CAGGTCTAGCTGGATGTATGTTTT	58.568	41.667	2.00	0.00	0.00	2.43
304	354	5.882557	CAGGTCTAGCTGGATGTATGTTTTT	59.117	40.000	2.00	0.00	0.00	1.94
352	402	4.261994	GGATGGCAGTTTTAAAGTTCAGCA	60.262	41.667	0.00	0.00	0.00	4.41
355	405	5.288804	TGGCAGTTTTAAAGTTCAGCATTC	58.711	37.500	0.00	0.00	0.00	2.67
357	407	5.509670	GGCAGTTTTAAAGTTCAGCATTCCT	60.510	40.000	0.00	0.00	0.00	3.36
500	552	5.538053	TGGCAATTAAGGTCTTTGTTGATGA	59.462	36.000	10.07	0.00	0.00	2.92
536	588	2.919772	AAATGGACCTAAACAGGGGG	57.080	50.000	0.00	0.00	0.00	5.40
539	591	2.599757	GGACCTAAACAGGGGGCGT	61.600	63.158	0.00	0.00	0.00	5.68
545	597	0.826062	TAAACAGGGGGCGTACTAGC	59.174	55.000	0.00	0.00	0.00	3.42
547	599	3.912907	CAGGGGGCGTACTAGCGG	61.913	72.222	0.00	0.00	38.18	5.52
582	634	2.475339	TGGCATGCCCCAGATATTTT	57.525	45.000	33.44	0.00	34.56	1.82
583	635	2.761809	TGGCATGCCCCAGATATTTTT	58.238	42.857	33.44	0.00	34.56	1.94
584	636	3.921104	TGGCATGCCCCAGATATTTTTA	58.079	40.909	33.44	7.40	34.56	1.52
585	637	4.491675	TGGCATGCCCCAGATATTTTTAT	58.508	39.130	33.44	0.00	34.56	1.40
586	638	4.283978	TGGCATGCCCCAGATATTTTTATG	59.716	41.667	33.44	0.00	34.56	1.90
587	639	4.284234	GGCATGCCCCAGATATTTTTATGT	59.716	41.667	27.24	0.00	0.00	2.29
588	640	5.221702	GGCATGCCCCAGATATTTTTATGTT	60.222	40.000	27.24	0.00	0.00	2.71
589	641	5.928264	GCATGCCCCAGATATTTTTATGTTC	59.072	40.000	6.36	0.00	0.00	3.18
590	642	6.239402	GCATGCCCCAGATATTTTTATGTTCT	60.239	38.462	6.36	0.00	0.00	3.01
591	643	7.687592	GCATGCCCCAGATATTTTTATGTTCTT	60.688	37.037	6.36	0.00	0.00	2.52
592	644	7.346751	TGCCCCAGATATTTTTATGTTCTTC	57.653	36.000	0.00	0.00	0.00	2.87
593	645	6.323739	TGCCCCAGATATTTTTATGTTCTTCC	59.676	38.462	0.00	0.00	0.00	3.46
594	646	6.239317	GCCCCAGATATTTTTATGTTCTTCCC	60.239	42.308	0.00	0.00	0.00	3.97
595	647	6.267699	CCCCAGATATTTTTATGTTCTTCCCC	59.732	42.308	0.00	0.00	0.00	4.81
596	648	7.069344	CCCAGATATTTTTATGTTCTTCCCCT	58.931	38.462	0.00	0.00	0.00	4.79
597	649	8.224720	CCCAGATATTTTTATGTTCTTCCCCTA	58.775	37.037	0.00	0.00	0.00	3.53
694	746	4.040445	TCGCTCAAAAACCAAGGAAAAG	57.960	40.909	0.00	0.00	0.00	2.27
741	793	5.736338	TCGTCGTGTGTTAAAAATGGTAAC	58.264	37.500	0.00	0.00	33.00	2.50
863	915	1.994779	CCACCCGTGTCACGTATTTAC	59.005	52.381	23.01	0.00	40.58	2.01
864	916	1.994779	CACCCGTGTCACGTATTTACC	59.005	52.381	23.01	0.00	40.58	2.85
865	917	1.066929	ACCCGTGTCACGTATTTACCC	60.067	52.381	23.01	0.00	40.58	3.69
1607	1671	0.107703	CCTGACCTTGATTGCCGCTA	60.108	55.000	0.00	0.00	0.00	4.26
2034	4166	2.038033	ACATCAGCCAAAGCAAAAGCAT	59.962	40.909	0.00	0.00	43.56	3.79
2327	4462	7.373493	CAAATTTTCCAGATCAAAGCAGTAGT	58.627	34.615	0.00	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	1.133216	TGTGTCTAGCGTCATCAGAGC	59.867	52.381	0.00	0.00	0.00	4.09
19	20	2.464865	GGTGATGTGTCTAGCGTCATC	58.535	52.381	11.29	11.29	37.68	2.92
26	27	2.483714	CCCATTCCGGTGATGTGTCTAG	60.484	54.545	15.86	0.00	0.00	2.43
32	33	1.506028	AACCCCCATTCCGGTGATGT	61.506	55.000	15.86	0.00	30.96	3.06
39	40	1.152963	CTGCCTAACCCCCATTCCG	60.153	63.158	0.00	0.00	0.00	4.30
45	46	0.035343	GTTCTCACTGCCTAACCCCC	60.035	60.000	0.00	0.00	0.00	5.40
87	88	2.032681	AGAAGACAAGGCGGTGGC	59.967	61.111	0.00	0.00	38.90	5.01
97	98	3.904800	TGTGTCCTGTTTGAGAAGACA	57.095	42.857	0.00	0.00	35.20	3.41
135	136	6.695278	TCTTGCTCCGTTTTTAGATGTTTTTG	59.305	34.615	0.00	0.00	0.00	2.44
141	142	6.238484	CCCTAATCTTGCTCCGTTTTTAGATG	60.238	42.308	0.00	0.00	0.00	2.90
153	154	1.539280	GCGGAGACCCTAATCTTGCTC	60.539	57.143	0.00	0.00	31.33	4.26
161	162	1.232216	CCCTAGGCGGAGACCCTAA	59.768	63.158	2.05	0.00	31.70	2.69
162	163	2.932736	CCCTAGGCGGAGACCCTA	59.067	66.667	2.05	0.00	31.70	3.53
163	164	4.862823	GCCCTAGGCGGAGACCCT	62.863	72.222	2.05	0.00	39.62	4.34
212	245	0.895559	GGTTCCTTTGCCTCCCACAG	60.896	60.000	0.00	0.00	0.00	3.66
218	251	1.004862	AGCTTAGGGTTCCTTTGCCTC	59.995	52.381	0.00	0.00	34.61	4.70
220	253	1.924731	AAGCTTAGGGTTCCTTTGCC	58.075	50.000	0.00	0.00	34.61	4.52
224	257	4.141018	TCCAAGAAAAGCTTAGGGTTCCTT	60.141	41.667	0.00	0.00	34.31	3.36
235	268	2.720915	GCCTCATCTCCAAGAAAAGCT	58.279	47.619	0.00	0.00	0.00	3.74
272	322	1.680651	AGCTAGACCTGCTCGTGCT	60.681	57.895	11.19	0.00	40.48	4.40
318	368	8.871629	TTAAAACTGCCATCCTCTACATAAAA	57.128	30.769	0.00	0.00	0.00	1.52
324	374	6.430000	TGAACTTTAAAACTGCCATCCTCTAC	59.570	38.462	0.00	0.00	0.00	2.59
476	528	5.538053	TCATCAACAAAGACCTTAATTGCCA	59.462	36.000	0.00	0.00	0.00	4.92
509	561	7.452189	CCCCTGTTTAGGTCCATTTAACTTTTA	59.548	37.037	0.00	0.00	42.96	1.52
536	588	4.281947	GGGCTCCCGCTAGTACGC	62.282	72.222	0.00	0.00	36.09	4.42
559	611	2.347691	TATCTGGGGCATGCCAGCTG	62.348	60.000	36.56	22.40	37.98	4.24
560	612	1.432852	ATATCTGGGGCATGCCAGCT	61.433	55.000	36.56	20.50	37.98	4.24
562	614	2.005370	AAATATCTGGGGCATGCCAG	57.995	50.000	36.56	26.09	37.98	4.85
563	615	2.475339	AAAATATCTGGGGCATGCCA	57.525	45.000	36.56	18.14	37.98	4.92
564	616	4.284234	ACATAAAAATATCTGGGGCATGCC	59.716	41.667	29.47	29.47	0.00	4.40
565	617	5.473066	ACATAAAAATATCTGGGGCATGC	57.527	39.130	9.90	9.90	0.00	4.06
566	618	7.294017	AGAACATAAAAATATCTGGGGCATG	57.706	36.000	0.00	0.00	0.00	4.06
567	619	7.015584	GGAAGAACATAAAAATATCTGGGGCAT	59.984	37.037	0.00	0.00	0.00	4.40
568	620	6.323739	GGAAGAACATAAAAATATCTGGGGCA	59.676	38.462	0.00	0.00	0.00	5.36
569	621	6.239317	GGGAAGAACATAAAAATATCTGGGGC	60.239	42.308	0.00	0.00	0.00	5.80
674	726	4.040445	TCTTTTCCTTGGTTTTTGAGCG	57.960	40.909	0.00	0.00	0.00	5.03
694	746	1.048601	TGGACGCTGGGAATAGGATC	58.951	55.000	0.00	0.00	0.00	3.36
882	934	2.806009	GGCTGGGGTTTTGCTGCAA	61.806	57.895	11.69	11.69	0.00	4.08
2034	4166	6.317893	TCTGTAGTGCGTTCAGATTATAGACA	59.682	38.462	0.00	0.00	34.00	3.41
2327	4462	5.104109	AGGGCTATTGTTTCTATTGGTGCTA	60.104	40.000	0.00	0.00	0.00	3.49
2495	4632	6.431198	TTTTGTGACTTTTGTAGTGTCTCC	57.569	37.500	0.00	0.00	37.17	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.