AutoCloner

Multiple sequence alignment - TraesCS5B01G088200

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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	TraesCS5B01G088200	chr5B	100.000	2480	0	0	1	2480	113328973	113326494	0.000000e+00	4580.0
1	TraesCS5B01G088200	chr5B	87.336	687	62	13	827	1509	113457012	113456347	0.000000e+00	763.0
2	TraesCS5B01G088200	chr5B	81.143	175	24	8	2296	2463	395712451	395712623	5.570000e-27	132.0
3	TraesCS5B01G088200	chr5D	93.267	2510	114	19	1	2480	104114137	104111653	0.000000e+00	3648.0
4	TraesCS5B01G088200	chr5D	86.211	834	79	22	827	1653	104143120	104142316	0.000000e+00	870.0
5	TraesCS5B01G088200	chr5D	78.218	202	41	3	152	351	554404161	554404361	2.590000e-25	126.0
6	TraesCS5B01G088200	chr5D	77.391	230	38	9	1961	2178	84391693	84391920	9.310000e-25	124.0
7	TraesCS5B01G088200	chr5D	76.522	230	40	9	1961	2178	84427730	84427957	2.020000e-21	113.0
8	TraesCS5B01G088200	chr5A	87.855	1375	94	23	974	2291	94310774	94312132	0.000000e+00	1546.0
9	TraesCS5B01G088200	chr5A	85.006	827	80	24	827	1643	94092227	94093019	0.000000e+00	800.0
10	TraesCS5B01G088200	chr5A	89.326	534	37	11	435	960	94309836	94310357	0.000000e+00	652.0
11	TraesCS5B01G088200	chr5A	79.890	363	51	16	1832	2178	570173310	570172954	1.900000e-61	246.0
12	TraesCS5B01G088200	chr6B	85.008	647	69	17	892	1513	17091780	17091137	1.250000e-177	632.0
13	TraesCS5B01G088200	chr6B	84.615	624	70	11	892	1504	16970489	16971097	4.570000e-167	597.0
14	TraesCS5B01G088200	chr6B	81.298	262	45	4	89	348	112879284	112879543	2.500000e-50	209.0
15	TraesCS5B01G088200	chr6A	84.535	666	63	22	1001	1643	10138117	10137469	7.530000e-175	623.0
16	TraesCS5B01G088200	chr6D	85.572	603	60	14	892	1480	9147074	9147663	7.590000e-170	606.0
17	TraesCS5B01G088200	chr3D	80.183	328	42	15	1867	2178	108431363	108431683	8.930000e-55	224.0
18	TraesCS5B01G088200	chr7A	77.681	345	56	14	1849	2178	443967879	443968217	9.050000e-45	191.0
19	TraesCS5B01G088200	chr7A	81.176	170	27	5	2315	2480	125106506	125106338	5.570000e-27	132.0
20	TraesCS5B01G088200	chr2B	78.214	280	44	13	1909	2178	870629	870901	1.970000e-36	163.0
21	TraesCS5B01G088200	chr2B	82.353	170	22	8	2316	2480	621664474	621664308	9.250000e-30	141.0
22	TraesCS5B01G088200	chr2B	78.037	214	29	13	2258	2458	583779901	583779693	4.330000e-23	119.0
23	TraesCS5B01G088200	chr3B	76.301	346	55	18	1849	2178	190163403	190163737	2.550000e-35	159.0
24	TraesCS5B01G088200	chr3B	76.866	268	53	9	88	351	8358498	8358236	2.570000e-30	143.0
25	TraesCS5B01G088200	chr3B	81.921	177	23	9	2309	2480	19741624	19741452	9.250000e-30	141.0
26	TraesCS5B01G088200	chr3B	78.462	195	23	11	1992	2170	764049947	764049756	2.610000e-20	110.0
27	TraesCS5B01G088200	chr4A	86.111	144	15	5	2320	2460	651346380	651346239	1.540000e-32	150.0
28	TraesCS5B01G088200	chr2D	82.500	160	22	5	2304	2460	476279345	476279189	4.300000e-28	135.0
29	TraesCS5B01G088200	chrUn	81.935	155	23	4	2309	2460	331367271	331367423	2.590000e-25	126.0
30	TraesCS5B01G088200	chr2A	84.685	111	17	0	241	351	60002727	60002617	7.250000e-21	111.0
31	TraesCS5B01G088200	chr2A	79.851	134	19	7	222	351	43450373	43450244	9.450000e-15	91.6

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	TraesCS5B01G088200	chr5B	113326494	113328973	2479	True	4580	4580	100.0000	1	2480	1	chr5B.!!$R1	2479
1	TraesCS5B01G088200	chr5B	113456347	113457012	665	True	763	763	87.3360	827	1509	1	chr5B.!!$R2	682
2	TraesCS5B01G088200	chr5D	104111653	104114137	2484	True	3648	3648	93.2670	1	2480	1	chr5D.!!$R1	2479
3	TraesCS5B01G088200	chr5D	104142316	104143120	804	True	870	870	86.2110	827	1653	1	chr5D.!!$R2	826
4	TraesCS5B01G088200	chr5A	94309836	94312132	2296	False	1099	1546	88.5905	435	2291	2	chr5A.!!$F2	1856
5	TraesCS5B01G088200	chr5A	94092227	94093019	792	False	800	800	85.0060	827	1643	1	chr5A.!!$F1	816
6	TraesCS5B01G088200	chr6B	17091137	17091780	643	True	632	632	85.0080	892	1513	1	chr6B.!!$R1	621
7	TraesCS5B01G088200	chr6B	16970489	16971097	608	False	597	597	84.6150	892	1504	1	chr6B.!!$F1	612
8	TraesCS5B01G088200	chr6A	10137469	10138117	648	True	623	623	84.5350	1001	1643	1	chr6A.!!$R1	642
9	TraesCS5B01G088200	chr6D	9147074	9147663	589	False	606	606	85.5720	892	1480	1	chr6D.!!$F1	588

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
80	81	0.032813	CCCCATGGTCTCTGGCATTT	60.033	55.0	11.73	0.0	32.08	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1779	2310	0.732571	ACTGCCGAACACAACACAAG	59.267	50.0	0.0	0.0	0.0	3.16	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
49	50	0.110823	CCCGCGCGCATTAGTTAATC	60.111	55.000	32.61	0.00	0.00	1.75
62	63	0.817654	GTTAATCCAGGCCAGCAACC	59.182	55.000	5.01	0.00	0.00	3.77
77	78	2.204136	ACCCCATGGTCTCTGGCA	60.204	61.111	11.73	0.00	43.06	4.92
80	81	0.032813	CCCCATGGTCTCTGGCATTT	60.033	55.000	11.73	0.00	32.08	2.32
116	117	1.033746	ATGGCTCATGGCGTTTCAGG	61.034	55.000	0.00	0.00	42.94	3.86
129	130	3.535629	TTCAGGCCTGCCACGTCAG	62.536	63.158	28.91	0.46	38.92	3.51
140	141	1.951130	CACGTCAGCGAGCAACACT	60.951	57.895	0.00	0.00	42.00	3.55
179	180	3.626924	AGGGCTGGAACGCGTTCT	61.627	61.111	40.90	24.07	39.45	3.01
193	194	2.357034	TTCTTGCTCGGCGTGTCC	60.357	61.111	6.85	0.00	0.00	4.02
194	195	3.876589	TTCTTGCTCGGCGTGTCCC	62.877	63.158	6.85	0.00	0.00	4.46
240	241	1.429148	GGCGTTTCTATGTCGGGCAG	61.429	60.000	0.00	0.00	0.00	4.85
246	247	0.892755	TCTATGTCGGGCAGAAACGT	59.107	50.000	0.00	0.00	0.00	3.99
249	250	2.355481	GTCGGGCAGAAACGTCGT	60.355	61.111	0.00	0.00	0.00	4.34
253	254	2.280592	GGCAGAAACGTCGTGGGT	60.281	61.111	0.00	0.00	0.00	4.51
256	257	1.433837	GCAGAAACGTCGTGGGTTGT	61.434	55.000	0.00	0.00	0.00	3.32
258	259	0.812412	AGAAACGTCGTGGGTTGTGG	60.812	55.000	0.00	0.00	0.00	4.17
268	269	0.752009	TGGGTTGTGGCGTTGCTAAA	60.752	50.000	0.00	0.00	0.00	1.85
271	272	1.335496	GGTTGTGGCGTTGCTAAAAGA	59.665	47.619	0.00	0.00	0.00	2.52
274	275	2.294074	TGTGGCGTTGCTAAAAGAGTT	58.706	42.857	0.00	0.00	0.00	3.01
277	278	3.744426	GTGGCGTTGCTAAAAGAGTTAGA	59.256	43.478	0.00	0.00	0.00	2.10
295	296	7.976734	AGAGTTAGATCGTGAAATACTTTCCTG	59.023	37.037	0.00	0.00	38.90	3.86
303	304	5.164080	CGTGAAATACTTTCCTGTCGAGTTC	60.164	44.000	0.00	0.00	38.90	3.01
310	311	1.865865	TCCTGTCGAGTTCAGTTTGC	58.134	50.000	1.40	0.00	0.00	3.68
321	322	3.059597	AGTTCAGTTTGCGACAAAGATCG	60.060	43.478	5.45	0.00	45.09	3.69
329	330	2.776694	CGACAAAGATCGCTGACAAG	57.223	50.000	4.33	0.00	34.90	3.16
330	331	1.391485	CGACAAAGATCGCTGACAAGG	59.609	52.381	4.33	0.00	34.90	3.61
331	332	1.129437	GACAAAGATCGCTGACAAGGC	59.871	52.381	4.33	0.00	0.00	4.35
332	333	0.449388	CAAAGATCGCTGACAAGGCC	59.551	55.000	0.00	0.00	0.00	5.19
406	407	6.640907	GCATAGTTTTTCAGTTCGTTTTCCAT	59.359	34.615	0.00	0.00	0.00	3.41
560	578	4.035909	CACGTACTACCCAAAGCAAAAGTT	59.964	41.667	0.00	0.00	0.00	2.66
570	589	5.511202	CCCAAAGCAAAAGTTACCATGTGAT	60.511	40.000	0.00	0.00	0.00	3.06
571	590	6.295011	CCCAAAGCAAAAGTTACCATGTGATA	60.295	38.462	0.00	0.00	0.00	2.15
572	591	6.808212	CCAAAGCAAAAGTTACCATGTGATAG	59.192	38.462	0.00	0.00	0.00	2.08
644	664	1.334149	GCAGACACGAAACAGGCTTTC	60.334	52.381	0.00	0.00	0.00	2.62
676	696	0.173708	CCACTGGCTACGAGAGAACC	59.826	60.000	0.00	0.00	0.00	3.62
740	760	2.502080	CGACAGTCGACACGGCTC	60.502	66.667	18.63	3.34	40.90	4.70
741	761	2.643272	GACAGTCGACACGGCTCA	59.357	61.111	19.50	0.00	40.90	4.26
883	903	2.024941	CCTCCCAAAGCCCTAATGAAGT	60.025	50.000	0.00	0.00	0.00	3.01
981	1417	0.179000	CTCCCTGGTCATAGCACCAC	59.821	60.000	0.00	0.00	41.84	4.16
1011	1459	2.823829	GCTAACAATGGCGGCCTCG	61.824	63.158	21.46	10.76	39.81	4.63
1050	1504	4.056125	CTCGTGGCTCTGTCCGCA	62.056	66.667	0.00	0.00	36.44	5.69
1500	1966	2.743718	GATCCATCCATCGCCCGT	59.256	61.111	0.00	0.00	0.00	5.28
1554	2050	5.450592	TGAATAATGTTGCAGCTGTTTCA	57.549	34.783	16.64	11.90	0.00	2.69
1584	2094	1.063469	GTTGTGTGTTCCAACGAGGTG	59.937	52.381	0.00	0.00	39.02	4.00
1779	2310	2.159327	AGCTGGATTTGCTTTGTTGC	57.841	45.000	0.00	0.00	37.52	4.17
1819	2350	3.744940	TTGAGCTGGATTTGGGAGAAT	57.255	42.857	0.00	0.00	0.00	2.40
2010	2553	6.360370	AACCTCAGTGCTTCTAAATAGTGA	57.640	37.500	0.00	0.00	0.00	3.41
2217	2770	3.757493	CCCATAGGACAGTACGTAGATCC	59.243	52.174	10.43	10.43	33.47	3.36
2267	2820	6.211584	AGGCCTATATGTCGTGAAATCACTAT	59.788	38.462	1.29	5.43	44.34	2.12
2323	2877	3.197265	TCTGTGATGTGTGTCACTTGTG	58.803	45.455	4.27	0.00	46.70	3.33
2329	2883	1.884067	TGTGTGTCACTTGTGGCAACA	60.884	47.619	9.74	12.67	38.92	3.33
2416	2972	0.869730	AATTCCGAACCGTTTCACCG	59.130	50.000	0.00	0.00	0.00	4.94
2427	2983	2.292292	CCGTTTCACCGTTGGATTTCTT	59.708	45.455	0.00	0.00	0.00	2.52
2453	3009	6.699204	GCATCAAGATCTTCGAAACTAGATCA	59.301	38.462	21.20	6.68	45.90	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	2.549754	CTGGCCTGGATTAACTAATGCG	59.450	50.000	3.32	0.00	36.90	4.73
43	44	0.817654	GGTTGCTGGCCTGGATTAAC	59.182	55.000	12.06	3.89	0.00	2.01
49	50	4.387343	ATGGGGTTGCTGGCCTGG	62.387	66.667	12.06	1.66	0.00	4.45
62	63	1.341285	TGAAATGCCAGAGACCATGGG	60.341	52.381	18.09	0.00	38.33	4.00
77	78	1.589716	GGCGTTGCTGAGGCTGAAAT	61.590	55.000	0.00	0.00	39.10	2.17
80	81	3.258228	ATGGCGTTGCTGAGGCTGA	62.258	57.895	0.00	0.00	39.10	4.26
150	151	4.640690	AGCCCTGGTCCACGGTCT	62.641	66.667	8.52	4.02	0.00	3.85
169	170	2.470286	CCGAGCAAGAACGCGTTC	59.530	61.111	38.00	38.00	39.78	3.95
176	177	2.357034	GGACACGCCGAGCAAGAA	60.357	61.111	0.00	0.00	0.00	2.52
177	178	4.373116	GGGACACGCCGAGCAAGA	62.373	66.667	0.00	0.00	37.63	3.02
179	180	4.680237	CAGGGACACGCCGAGCAA	62.680	66.667	0.00	0.00	37.63	3.91
240	241	1.644913	CCACAACCCACGACGTTTC	59.355	57.895	0.00	0.00	0.00	2.78
246	247	2.897846	CAACGCCACAACCCACGA	60.898	61.111	0.00	0.00	0.00	4.35
249	250	0.752009	TTTAGCAACGCCACAACCCA	60.752	50.000	0.00	0.00	0.00	4.51
253	254	2.294074	ACTCTTTTAGCAACGCCACAA	58.706	42.857	0.00	0.00	0.00	3.33
256	257	3.997762	TCTAACTCTTTTAGCAACGCCA	58.002	40.909	0.00	0.00	0.00	5.69
258	259	4.326548	ACGATCTAACTCTTTTAGCAACGC	59.673	41.667	0.00	0.00	0.00	4.84
295	296	1.205657	TGTCGCAAACTGAACTCGAC	58.794	50.000	6.18	6.18	46.58	4.20
310	311	1.391485	CCTTGTCAGCGATCTTTGTCG	59.609	52.381	0.00	0.00	44.14	4.35
321	322	0.536006	ACTGTTCTGGCCTTGTCAGC	60.536	55.000	3.32	0.00	34.96	4.26
324	325	2.191128	ATCACTGTTCTGGCCTTGTC	57.809	50.000	3.32	0.00	0.00	3.18
326	327	2.095567	CGAAATCACTGTTCTGGCCTTG	60.096	50.000	3.32	0.00	0.00	3.61
327	328	2.154462	CGAAATCACTGTTCTGGCCTT	58.846	47.619	3.32	0.00	0.00	4.35
328	329	1.611673	CCGAAATCACTGTTCTGGCCT	60.612	52.381	3.32	0.00	0.00	5.19
329	330	0.804989	CCGAAATCACTGTTCTGGCC	59.195	55.000	0.00	0.00	0.00	5.36
330	331	0.169009	GCCGAAATCACTGTTCTGGC	59.831	55.000	0.00	0.00	37.44	4.85
331	332	0.804989	GGCCGAAATCACTGTTCTGG	59.195	55.000	0.00	0.00	0.00	3.86
332	333	0.443869	CGGCCGAAATCACTGTTCTG	59.556	55.000	24.07	0.00	0.00	3.02
361	362	1.595993	GGAGCGACACAGGTAGAGCA	61.596	60.000	0.00	0.00	0.00	4.26
415	416	9.778993	CAGAAATCACACCATTAGATTTAGTTG	57.221	33.333	0.00	0.00	40.83	3.16
560	578	5.595542	GTGGTACTGGTACTATCACATGGTA	59.404	44.000	10.19	0.00	36.36	3.25
570	589	2.568509	GCTTTGGGTGGTACTGGTACTA	59.431	50.000	10.19	2.24	36.36	1.82
571	590	1.350019	GCTTTGGGTGGTACTGGTACT	59.650	52.381	10.19	0.00	36.36	2.73
572	591	1.072648	TGCTTTGGGTGGTACTGGTAC	59.927	52.381	2.58	2.58	35.40	3.34
672	692	0.872388	ATGTTTCCTCGCGTTGGTTC	59.128	50.000	17.35	11.01	0.00	3.62
676	696	3.226347	GAGAAAATGTTTCCTCGCGTTG	58.774	45.455	5.77	0.00	0.00	4.10
763	783	0.719465	CATTGTTACCACGACGAGGC	59.281	55.000	11.51	0.00	0.00	4.70
801	821	3.008330	AGTCACGTAGTACTAGCTGTGG	58.992	50.000	20.96	9.59	41.61	4.17
809	829	3.131223	TCGCTACCTAGTCACGTAGTACT	59.869	47.826	0.00	0.00	41.61	2.73
810	830	3.448686	TCGCTACCTAGTCACGTAGTAC	58.551	50.000	0.00	0.00	41.61	2.73
811	831	3.801114	TCGCTACCTAGTCACGTAGTA	57.199	47.619	0.00	0.00	41.61	1.82
816	836	4.451435	TCTGATATTCGCTACCTAGTCACG	59.549	45.833	0.00	0.00	0.00	4.35
883	903	3.328637	GGGGGTATTTATAGGCGGAGAAA	59.671	47.826	0.00	0.00	0.00	2.52
1500	1966	2.786495	GGTGCGGCAGCTAGCTAGA	61.786	63.158	25.15	0.00	45.42	2.43
1554	2050	4.787551	TGGAACACACAACAGATTAACCT	58.212	39.130	0.00	0.00	0.00	3.50
1584	2094	1.133790	ACGACGGTACAATCTACTGGC	59.866	52.381	0.00	0.00	0.00	4.85
1779	2310	0.732571	ACTGCCGAACACAACACAAG	59.267	50.000	0.00	0.00	0.00	3.16
1819	2350	3.620488	GGGTTCATATTCAGGAAGTGCA	58.380	45.455	0.00	0.00	0.00	4.57
2010	2553	5.816258	TGTGCAAAACAAATGTGTCATGAAT	59.184	32.000	0.00	0.00	36.80	2.57
2296	2850	4.591202	GTGACACACATCACAGAAAGTTG	58.409	43.478	0.00	0.00	46.89	3.16
2370	2926	7.096353	CGGTCGCACGATTCTAAAGATAAAATA	60.096	37.037	0.00	0.00	35.47	1.40
2380	2936	2.572191	ATTCGGTCGCACGATTCTAA	57.428	45.000	0.00	0.00	43.11	2.10
2427	2983	5.965922	TCTAGTTTCGAAGATCTTGATGCA	58.034	37.500	14.00	0.00	35.04	3.96
2453	3009	7.945033	AAAATTGTGAAAGCGATTAACATGT	57.055	28.000	0.00	0.00	32.22	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.