AutoCloner

Multiple sequence alignment - TraesCS5B01G112700

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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	TraesCS5B01G112700	chr5B	100.000	4882	0	0	1	4882	176794461	176789580	0.000000e+00	9016
1	TraesCS5B01G112700	chr5B	96.684	4885	148	12	1	4882	204616559	204611686	0.000000e+00	8111
2	TraesCS5B01G112700	chr5B	97.170	212	6	0	1	212	705484503	705484292	4.650000e-95	359
3	TraesCS5B01G112700	chr1B	96.826	4883	138	12	1	4880	177157907	177162775	0.000000e+00	8142
4	TraesCS5B01G112700	chr1B	96.378	4887	154	13	1	4882	192673202	192678070	0.000000e+00	8022
5	TraesCS5B01G112700	chr1B	95.739	704	30	0	221	924	411019001	411018298	0.000000e+00	1134
6	TraesCS5B01G112700	chr1B	90.802	511	37	8	4380	4882	180009123	180009631	0.000000e+00	675
7	TraesCS5B01G112700	chr6B	96.210	4670	157	14	222	4882	361272421	361267763	0.000000e+00	7625
8	TraesCS5B01G112700	chr6B	96.210	4670	143	16	221	4882	570079120	570083763	0.000000e+00	7613
9	TraesCS5B01G112700	chr6B	96.420	3855	130	4	221	4072	308976668	308980517	0.000000e+00	6348
10	TraesCS5B01G112700	chr6D	91.470	3728	228	45	753	4460	77327960	77331617	0.000000e+00	5040
11	TraesCS5B01G112700	chr6D	92.043	465	37	0	1684	2148	387786119	387786583	0.000000e+00	654
12	TraesCS5B01G112700	chr6D	83.692	558	65	14	2145	2681	10401596	10402148	2.030000e-138	503
13	TraesCS5B01G112700	chr6D	96.244	213	8	0	1	213	245566668	245566880	2.800000e-92	350
14	TraesCS5B01G112700	chr2D	92.855	3079	159	24	753	3819	244754331	244757360	0.000000e+00	4410
15	TraesCS5B01G112700	chr7B	96.819	1666	42	10	2804	4465	131515161	131513503	0.000000e+00	2772
16	TraesCS5B01G112700	chr7B	90.980	510	37	9	4380	4882	120492979	120493486	0.000000e+00	678
17	TraesCS5B01G112700	chr7B	90.643	513	36	10	4380	4882	521854872	521854362	0.000000e+00	671
18	TraesCS5B01G112700	chr7B	96.698	212	7	0	1	212	40673580	40673369	2.160000e-93	353
19	TraesCS5B01G112700	chr7B	96.698	212	7	0	1	212	559685893	559685682	2.160000e-93	353
20	TraesCS5B01G112700	chr2B	94.134	1773	51	13	2690	4457	407887555	407889279	0.000000e+00	2649
21	TraesCS5B01G112700	chr2B	97.170	1449	40	1	221	1669	407886103	407887550	0.000000e+00	2447
22	TraesCS5B01G112700	chr2B	95.729	1522	55	8	3367	4882	51455682	51454165	0.000000e+00	2442
23	TraesCS5B01G112700	chr2B	97.017	704	21	0	221	924	371366908	371366205	0.000000e+00	1184
24	TraesCS5B01G112700	chr1A	87.823	657	66	12	2586	3236	132246153	132245505	0.000000e+00	758
25	TraesCS5B01G112700	chr4D	84.820	527	40	22	2586	3096	273301499	273302001	1.220000e-135	494
26	TraesCS5B01G112700	chr4D	97.642	212	5	0	1	212	37438037	37438248	9.990000e-97	364
27	TraesCS5B01G112700	chr1D	97.129	209	6	0	4	212	396366974	396366766	2.160000e-93	353

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	TraesCS5B01G112700	chr5B	176789580	176794461	4881	True	9016	9016	100.000	1	4882	1	chr5B.!!$R1	4881
1	TraesCS5B01G112700	chr5B	204611686	204616559	4873	True	8111	8111	96.684	1	4882	1	chr5B.!!$R2	4881
2	TraesCS5B01G112700	chr1B	177157907	177162775	4868	False	8142	8142	96.826	1	4880	1	chr1B.!!$F1	4879
3	TraesCS5B01G112700	chr1B	192673202	192678070	4868	False	8022	8022	96.378	1	4882	1	chr1B.!!$F3	4881
4	TraesCS5B01G112700	chr1B	411018298	411019001	703	True	1134	1134	95.739	221	924	1	chr1B.!!$R1	703
5	TraesCS5B01G112700	chr1B	180009123	180009631	508	False	675	675	90.802	4380	4882	1	chr1B.!!$F2	502
6	TraesCS5B01G112700	chr6B	361267763	361272421	4658	True	7625	7625	96.210	222	4882	1	chr6B.!!$R1	4660
7	TraesCS5B01G112700	chr6B	570079120	570083763	4643	False	7613	7613	96.210	221	4882	1	chr6B.!!$F2	4661
8	TraesCS5B01G112700	chr6B	308976668	308980517	3849	False	6348	6348	96.420	221	4072	1	chr6B.!!$F1	3851
9	TraesCS5B01G112700	chr6D	77327960	77331617	3657	False	5040	5040	91.470	753	4460	1	chr6D.!!$F2	3707
10	TraesCS5B01G112700	chr6D	10401596	10402148	552	False	503	503	83.692	2145	2681	1	chr6D.!!$F1	536
11	TraesCS5B01G112700	chr2D	244754331	244757360	3029	False	4410	4410	92.855	753	3819	1	chr2D.!!$F1	3066
12	TraesCS5B01G112700	chr7B	131513503	131515161	1658	True	2772	2772	96.819	2804	4465	1	chr7B.!!$R2	1661
13	TraesCS5B01G112700	chr7B	120492979	120493486	507	False	678	678	90.980	4380	4882	1	chr7B.!!$F1	502
14	TraesCS5B01G112700	chr7B	521854362	521854872	510	True	671	671	90.643	4380	4882	1	chr7B.!!$R3	502
15	TraesCS5B01G112700	chr2B	407886103	407889279	3176	False	2548	2649	95.652	221	4457	2	chr2B.!!$F1	4236
16	TraesCS5B01G112700	chr2B	51454165	51455682	1517	True	2442	2442	95.729	3367	4882	1	chr2B.!!$R1	1515
17	TraesCS5B01G112700	chr2B	371366205	371366908	703	True	1184	1184	97.017	221	924	1	chr2B.!!$R2	703
18	TraesCS5B01G112700	chr1A	132245505	132246153	648	True	758	758	87.823	2586	3236	1	chr1A.!!$R1	650
19	TraesCS5B01G112700	chr4D	273301499	273302001	502	False	494	494	84.820	2586	3096	1	chr4D.!!$F2	510

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
713	715	5.880332	CAGTACAACTATTATTGGGTGTGCT	59.120	40.000	4.36	4.36	33.63	4.40	F
1404	1415	0.323629	TCCGGTCTGAACATTGGGAC	59.676	55.000	0.00	0.00	0.00	4.46	F
1981	1994	0.691078	ATATGTCCAGCACCGTCCCT	60.691	55.000	0.00	0.00	0.00	4.20	F
2019	2032	1.211969	CCGACGGTCGAGTTCATGT	59.788	57.895	30.33	0.00	43.74	3.21	F
2660	2693	1.427368	TGGTGGCTGTAAAGGGTCATT	59.573	47.619	0.00	0.00	0.00	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2019	2032	1.579932	GTCGTGGACTGCTTCTCGA	59.420	57.895	0.00	0.00	0.00	4.04	R
3294	3346	1.651631	GCACAACGTTTCACACCAAAC	59.348	47.619	0.00	0.00	33.57	2.93	R
3394	3447	3.005155	AGGAGAGCATTTGAAACAAGTGC	59.995	43.478	19.06	19.06	36.11	4.40	R
3789	3907	4.035558	CACTGTGCTGATGTGTTTGTACTT	59.964	41.667	0.00	0.00	0.00	2.24	R
4525	4658	5.593679	TTTTTATTCCAAACGGACCACAA	57.406	34.783	0.00	0.00	30.04	3.33	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
114	115	8.321005	GTGCAAGTTTGAAAATTCTGTAAGTTC	58.679	33.333	0.00	0.00	33.76	3.01
152	153	7.388460	AGAAAAATTGATGAGTCACCATCTC	57.612	36.000	0.00	0.00	42.49	2.75
713	715	5.880332	CAGTACAACTATTATTGGGTGTGCT	59.120	40.000	4.36	4.36	33.63	4.40
910	921	9.265901	GTACATCATTATCTTACAGTGCAGATT	57.734	33.333	10.02	0.00	31.89	2.40
1378	1389	5.358298	AACTTTTAGATCACAAACCGCTC	57.642	39.130	0.00	0.00	0.00	5.03
1404	1415	0.323629	TCCGGTCTGAACATTGGGAC	59.676	55.000	0.00	0.00	0.00	4.46
1981	1994	0.691078	ATATGTCCAGCACCGTCCCT	60.691	55.000	0.00	0.00	0.00	4.20
2019	2032	1.211969	CCGACGGTCGAGTTCATGT	59.788	57.895	30.33	0.00	43.74	3.21
2041	2054	2.022129	GAAGCAGTCCACGACCGTG	61.022	63.158	14.89	14.89	45.02	4.94
2402	2433	6.987992	TCGTTGTTAATTAGTGACCAGAACTT	59.012	34.615	0.00	0.00	0.00	2.66
2637	2670	4.729868	AGGGTGTAAGTGCAGAAGAAAAT	58.270	39.130	0.00	0.00	0.00	1.82
2660	2693	1.427368	TGGTGGCTGTAAAGGGTCATT	59.573	47.619	0.00	0.00	0.00	2.57
2670	2703	7.099120	GCTGTAAAGGGTCATTGATTGAAAAT	58.901	34.615	0.00	0.00	35.70	1.82
3117	3165	5.606348	AGAGGATTGTCGAATCTAAAGCT	57.394	39.130	0.00	0.00	38.48	3.74
3184	3235	6.531948	GTGCTCCTACAGTAGTGTTCTAATTG	59.468	42.308	8.85	0.00	38.19	2.32
3294	3346	9.046296	AGTGTGTGACTGAAAGAAACTAAATAG	57.954	33.333	0.00	0.00	37.43	1.73
3394	3447	1.472376	GCAGGAAGTTCGAGATGGGAG	60.472	57.143	0.00	0.00	0.00	4.30
3530	3584	7.774134	TGCTAATCAATTGTCTGCATGTAATT	58.226	30.769	5.13	0.00	0.00	1.40
3753	3871	8.576442	CCTGTTAGAACCAAATAGTGTTTGAAT	58.424	33.333	13.40	2.29	0.00	2.57
3789	3907	4.458989	GTGCTCTCACATATTTGTTTGGGA	59.541	41.667	0.00	0.00	42.66	4.37
4416	4548	5.348724	CAGTATGTGAAAACACGCTCAGTAT	59.651	40.000	0.00	0.00	0.00	2.12
4537	4671	5.968254	ACAAGTTAAAATTGTGGTCCGTTT	58.032	33.333	6.53	0.00	39.36	3.60
4799	4944	7.934120	AGAGCAAAGTCTAGTTACTGAAAACAT	59.066	33.333	0.00	0.00	0.00	2.71
4807	4952	8.436200	GTCTAGTTACTGAAAACATGCTTAGTG	58.564	37.037	0.00	0.00	0.00	2.74
4827	4973	1.608542	GCAAACCCATGCAAGCATCAA	60.609	47.619	4.24	0.00	45.70	2.57
4830	4976	4.699637	CAAACCCATGCAAGCATCAATAT	58.300	39.130	4.24	0.00	33.90	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
152	153	6.261603	TGCTGCAGAGAACATGAATATAAAGG	59.738	38.462	20.43	0.00	0.00	3.11
358	359	1.623163	GAGGAGCTTATAGAGGCGGT	58.377	55.000	0.00	0.00	0.00	5.68
668	670	6.407202	ACTGAGATGGTCAACTAATTGTACC	58.593	40.000	0.00	0.00	36.93	3.34
713	715	9.649167	GTTACCTTAGACTTGCATCTAGTTTTA	57.351	33.333	0.00	0.00	32.78	1.52
756	758	6.740411	TGTACCGGTTTACACATTAATTCC	57.260	37.500	15.04	0.00	0.00	3.01
958	969	8.847196	TCTGTAGAAATTCTGTATATAGCGTGT	58.153	33.333	5.64	0.00	0.00	4.49
1378	1389	5.050490	CCAATGTTCAGACCGGAATACTAG	58.950	45.833	9.46	0.00	0.00	2.57
1404	1415	5.149973	TGTCATGATCAAAATGGGTTTGG	57.850	39.130	0.00	0.00	45.73	3.28
2019	2032	1.579932	GTCGTGGACTGCTTCTCGA	59.420	57.895	0.00	0.00	0.00	4.04
2270	2289	6.903883	TCAGTATATTTTTCTTCGCTGGTC	57.096	37.500	0.00	0.00	0.00	4.02
2402	2433	7.842982	TGCACTAGTATAATCCAAAGTACACA	58.157	34.615	0.00	0.00	0.00	3.72
2637	2670	2.645297	TGACCCTTTACAGCCACCAATA	59.355	45.455	0.00	0.00	0.00	1.90
2660	2693	9.906660	GTGGTGAACTTATAACATTTTCAATCA	57.093	29.630	0.00	0.00	0.00	2.57
2670	2703	4.022935	AGACGTCGTGGTGAACTTATAACA	60.023	41.667	10.46	0.00	0.00	2.41
3021	3069	3.958798	TCACTCACCTTACCCTATAGCAC	59.041	47.826	0.00	0.00	0.00	4.40
3184	3235	3.573967	TCCCTTCTCATTGTTCTTTTGCC	59.426	43.478	0.00	0.00	0.00	4.52
3294	3346	1.651631	GCACAACGTTTCACACCAAAC	59.348	47.619	0.00	0.00	33.57	2.93
3302	3354	3.181501	CCAGAGAAAAGCACAACGTTTCA	60.182	43.478	0.00	0.00	45.75	2.69
3394	3447	3.005155	AGGAGAGCATTTGAAACAAGTGC	59.995	43.478	19.06	19.06	36.11	4.40
3530	3584	5.590530	ATGCAACAAACACCTACTTTTCA	57.409	34.783	0.00	0.00	0.00	2.69
3789	3907	4.035558	CACTGTGCTGATGTGTTTGTACTT	59.964	41.667	0.00	0.00	0.00	2.24
4096	4219	6.603095	AGCACTCGAACTGATAATTGTTTTC	58.397	36.000	0.00	0.00	0.00	2.29
4217	4345	6.889198	TCTCAAATTCCATAGAAGAACCGAT	58.111	36.000	0.00	0.00	34.86	4.18
4454	4587	9.630098	TTTGTAGAACGGACGAATATATATTCC	57.370	33.333	23.67	13.68	39.04	3.01
4525	4658	5.593679	TTTTTATTCCAAACGGACCACAA	57.406	34.783	0.00	0.00	30.04	3.33
4807	4952	0.037139	TGATGCTTGCATGGGTTTGC	60.037	50.000	13.18	0.00	43.07	3.68
4827	4973	6.961042	TGGTTCCGAAAAAGGGTACTTATAT	58.039	36.000	0.00	0.00	35.41	0.86
4830	4976	4.703379	TGGTTCCGAAAAAGGGTACTTA	57.297	40.909	0.00	0.00	35.41	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.