AutoCloner

Multiple sequence alignment - TraesCS2B01G042100

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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	TraesCS2B01G042100	chr2B	100.000	2552	0	0	1	2552	19078084	19075533	0.000000e+00	4713.0
1	TraesCS2B01G042100	chr2B	87.669	1111	125	6	602	1700	19101937	19100827	0.000000e+00	1282.0
2	TraesCS2B01G042100	chr2B	87.004	1108	129	7	610	1702	19084244	19083137	0.000000e+00	1234.0
3	TraesCS2B01G042100	chr2B	92.462	597	40	4	1	594	70846402	70845808	0.000000e+00	848.0
4	TraesCS2B01G042100	chr2B	82.632	927	155	4	594	1518	18949693	18948771	0.000000e+00	815.0
5	TraesCS2B01G042100	chr2B	89.362	94	10	0	1161	1254	18914837	18914930	4.460000e-23	119.0
6	TraesCS2B01G042100	chr2A	91.038	1484	122	5	597	2071	13068410	13066929	0.000000e+00	1993.0
7	TraesCS2B01G042100	chr2A	82.888	935	150	5	594	1518	13013849	13014783	0.000000e+00	832.0
8	TraesCS2B01G042100	chr2A	81.268	1057	167	15	594	1625	13038756	13037706	0.000000e+00	826.0
9	TraesCS2B01G042100	chr2A	81.084	941	157	9	594	1517	12991004	12991940	0.000000e+00	732.0
10	TraesCS2B01G042100	chr2A	92.702	507	21	5	2054	2552	13040318	13039820	0.000000e+00	717.0
11	TraesCS2B01G042100	chr2A	88.398	181	15	5	1706	1884	13082966	13082790	1.990000e-51	213.0
12	TraesCS2B01G042100	chr2D	92.185	1318	88	4	1241	2552	12583236	12581928	0.000000e+00	1849.0
13	TraesCS2B01G042100	chr2D	82.386	1056	161	10	594	1625	12580902	12579848	0.000000e+00	896.0
14	TraesCS2B01G042100	chr2D	87.019	624	75	3	597	1219	12583843	12583225	0.000000e+00	699.0
15	TraesCS2B01G042100	chr5B	77.744	328	39	12	276	603	510708242	510708535	1.210000e-38	171.0
16	TraesCS2B01G042100	chr4D	96.875	32	0	1	2147	2178	497953649	497953619	5.000000e-03	52.8

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	TraesCS2B01G042100	chr2B	19075533	19078084	2551	True	4713.0	4713	100.000000	1	2552	1	chr2B.!!$R2	2551
1	TraesCS2B01G042100	chr2B	19100827	19101937	1110	True	1282.0	1282	87.669000	602	1700	1	chr2B.!!$R4	1098
2	TraesCS2B01G042100	chr2B	19083137	19084244	1107	True	1234.0	1234	87.004000	610	1702	1	chr2B.!!$R3	1092
3	TraesCS2B01G042100	chr2B	70845808	70846402	594	True	848.0	848	92.462000	1	594	1	chr2B.!!$R5	593
4	TraesCS2B01G042100	chr2B	18948771	18949693	922	True	815.0	815	82.632000	594	1518	1	chr2B.!!$R1	924
5	TraesCS2B01G042100	chr2A	13066929	13068410	1481	True	1993.0	1993	91.038000	597	2071	1	chr2A.!!$R1	1474
6	TraesCS2B01G042100	chr2A	13013849	13014783	934	False	832.0	832	82.888000	594	1518	1	chr2A.!!$F2	924
7	TraesCS2B01G042100	chr2A	13037706	13040318	2612	True	771.5	826	86.985000	594	2552	2	chr2A.!!$R3	1958
8	TraesCS2B01G042100	chr2A	12991004	12991940	936	False	732.0	732	81.084000	594	1517	1	chr2A.!!$F1	923
9	TraesCS2B01G042100	chr2D	12579848	12583843	3995	True	1148.0	1849	87.196667	594	2552	3	chr2D.!!$R1	1958

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
594	598	0.600557	CCGGCAGCAAACATTTACCA	59.399	50.0	0.0	0.0	0.0	3.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1645	2655	0.112025	TGATGACATGGCCACAACCA	59.888	50.0	8.16	4.23	45.82	3.67	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
108	109	5.491982	GGTCCCAGTAAATATGATAGCCTG	58.508	45.833	0.00	0.00	0.00	4.85
147	148	1.299014	CGCCAAGACGCAGCAAAAA	60.299	52.632	0.00	0.00	0.00	1.94
153	154	1.953559	AGACGCAGCAAAAAGTCTCA	58.046	45.000	0.00	0.00	39.49	3.27
199	201	3.119463	CGCTTGTAGCAAAAATTGTTCGG	59.881	43.478	0.00	0.00	42.58	4.30
233	235	2.357836	CACCAGCCCCAGCAGAAT	59.642	61.111	0.00	0.00	43.56	2.40
290	293	1.985684	GCCAGTCGCAGCAAAAATTAC	59.014	47.619	0.00	0.00	37.47	1.89
292	295	1.643810	CAGTCGCAGCAAAAATTACGC	59.356	47.619	0.00	0.00	0.00	4.42
303	306	2.713863	AAATTACGCCCGTCCCATAA	57.286	45.000	0.00	0.00	0.00	1.90
338	341	5.053145	CCTGGTTGTAGCTCTATGTCAATC	58.947	45.833	0.00	0.00	0.00	2.67
376	379	1.466360	GCTGTCCATGACAATTGCGAC	60.466	52.381	5.05	4.55	42.26	5.19
397	400	6.297353	CGACGAAAGAAGACAGAATAAAACC	58.703	40.000	0.00	0.00	0.00	3.27
423	426	4.001652	GTGGAAAACTAGTAGACAAGGCC	58.998	47.826	3.59	0.00	0.00	5.19
428	431	0.745468	CTAGTAGACAAGGCCGGGAC	59.255	60.000	2.18	0.00	0.00	4.46
450	454	4.072839	CAGAGGTAAGTGGGGAAGAAAAC	58.927	47.826	0.00	0.00	0.00	2.43
460	464	1.702491	GGAAGAAAACCGATCGGGCG	61.702	60.000	35.87	13.56	40.62	6.13
594	598	0.600557	CCGGCAGCAAACATTTACCA	59.399	50.000	0.00	0.00	0.00	3.25
595	599	1.000283	CCGGCAGCAAACATTTACCAA	60.000	47.619	0.00	0.00	0.00	3.67
599	1570	4.506758	GGCAGCAAACATTTACCAATGAT	58.493	39.130	1.97	0.00	42.35	2.45
727	1701	5.026121	TCCTCCTCAACTTCATGATACACT	58.974	41.667	0.00	0.00	0.00	3.55
777	1751	5.622007	CGCCATCATTGTTAACACCTTTGAT	60.622	40.000	8.07	11.32	0.00	2.57
831	1805	2.431997	TCCATCCTTCCTATGCCCATT	58.568	47.619	0.00	0.00	0.00	3.16
874	1869	1.315981	CCTCACCGAGCAGCTAGTCA	61.316	60.000	0.00	0.00	0.00	3.41
878	1873	1.134995	CACCGAGCAGCTAGTCAATGA	60.135	52.381	0.00	0.00	0.00	2.57
914	1909	1.202758	CGCAATATGCCCCAACCTCTA	60.203	52.381	0.00	0.00	41.12	2.43
927	1922	4.456535	CCAACCTCTAGAGAGAAGATCGA	58.543	47.826	21.76	0.00	44.74	3.59
995	1990	3.674997	ACGTCAACTTTGGTAGCATCAT	58.325	40.909	0.00	0.00	0.00	2.45
1035	2030	3.134127	GTGGAGTTCGCATGGGGC	61.134	66.667	10.21	3.70	39.90	5.80
1036	2031	3.329889	TGGAGTTCGCATGGGGCT	61.330	61.111	10.21	8.54	41.67	5.19
1075	2070	1.276421	ACTTCTTGTGGATCGTGAGGG	59.724	52.381	0.00	0.00	0.00	4.30
1101	2097	1.449601	CGTAAAGGGTGATGGCGCT	60.450	57.895	7.64	0.00	0.00	5.92
1129	2125	2.491022	CCCGAGTTCCTAGAGGCGG	61.491	68.421	5.61	5.61	37.03	6.13
1146	2142	2.612493	GGCCAAGGGAAGGTGCCTA	61.612	63.158	0.00	0.00	37.13	3.93
1149	2145	0.253327	CCAAGGGAAGGTGCCTACTC	59.747	60.000	0.00	0.00	37.13	2.59
1151	2147	0.544595	AAGGGAAGGTGCCTACTCGT	60.545	55.000	0.00	0.00	37.13	4.18
1161	2157	1.878656	GCCTACTCGTGAGCTGGTGT	61.879	60.000	0.00	0.00	0.00	4.16
1167	2163	0.392706	TCGTGAGCTGGTGTGAACAT	59.607	50.000	0.00	0.00	0.00	2.71
1212	2208	1.077716	GGGTGCCTTCCTTACGCAT	60.078	57.895	0.00	0.00	34.51	4.73
1308	2304	0.606944	AAACCAATTCCCGCTACGCA	60.607	50.000	0.00	0.00	0.00	5.24
1340	2336	3.014085	GCGTTGGGATGGAGGTCGA	62.014	63.158	0.00	0.00	0.00	4.20
1418	2414	2.178106	GAGAGGTAGGGAGGGAGATGAA	59.822	54.545	0.00	0.00	0.00	2.57
1476	2472	3.429372	AACCGCAAAGCCTGGTGGA	62.429	57.895	0.00	0.00	38.07	4.02
1544	2540	2.488153	GTGCAGGTAAGAATGTTGGGTC	59.512	50.000	0.00	0.00	0.00	4.46
1546	2542	2.356135	CAGGTAAGAATGTTGGGTCGG	58.644	52.381	0.00	0.00	0.00	4.79
1562	2566	1.672363	GTCGGATTGAGATGCATGCAA	59.328	47.619	26.68	8.17	0.00	4.08
1632	2642	8.499406	ACTGGTTGTCCAATAAGGCTATATTTA	58.501	33.333	0.00	0.00	43.81	1.40
1670	2680	0.038599	TGGCCATGTCATCAGCTTGT	59.961	50.000	0.00	0.00	0.00	3.16
1719	2729	9.912634	CTGGTTTTATTCTCATATGTTTGTGTT	57.087	29.630	1.90	0.00	0.00	3.32
1907	2917	3.742433	AAGGATATCAGAGTTGGCTCG	57.258	47.619	4.83	0.00	46.03	5.03
2007	3017	4.962362	AGAACTGGAACAAAAATCACCCTT	59.038	37.500	0.00	0.00	38.70	3.95
2050	3060	4.039245	CGAATTCTAGGGTGGATTAGCAGA	59.961	45.833	3.52	0.00	0.00	4.26
2163	3173	7.681939	ATCCTACGTTCAAGAGCAATTTTAA	57.318	32.000	0.00	0.00	0.00	1.52
2178	3188	5.393461	GCAATTTTAACATGGTCCCTCTCAG	60.393	44.000	0.00	0.00	0.00	3.35
2250	3260	8.854614	AGAACATATGCTAAAGTTTCTTGACT	57.145	30.769	1.58	0.00	0.00	3.41
2259	3269	8.506437	TGCTAAAGTTTCTTGACTGATAACATG	58.494	33.333	0.00	0.00	0.00	3.21
2302	3312	9.906660	GAGAATGTTTTATTGTAATGTTGTGGA	57.093	29.630	0.00	0.00	0.00	4.02
2348	3358	6.403866	TCATATTATTTGTGTGGGCCATTC	57.596	37.500	10.70	6.74	0.00	2.67
2350	3360	2.917713	TATTTGTGTGGGCCATTCCT	57.082	45.000	10.70	0.00	34.39	3.36
2351	3361	2.028561	ATTTGTGTGGGCCATTCCTT	57.971	45.000	10.70	0.00	34.39	3.36
2352	3362	2.685106	TTTGTGTGGGCCATTCCTTA	57.315	45.000	10.70	0.00	34.39	2.69
2353	3363	2.685106	TTGTGTGGGCCATTCCTTAA	57.315	45.000	10.70	0.00	34.39	1.85
2385	3395	2.177394	TCAGCATTTTAGCGTGGTGA	57.823	45.000	3.43	3.43	46.83	4.02
2387	3397	2.483877	TCAGCATTTTAGCGTGGTGAAG	59.516	45.455	4.95	0.00	46.26	3.02
2403	3413	4.515191	TGGTGAAGAAAAGAATGGAAGACG	59.485	41.667	0.00	0.00	0.00	4.18
2408	3418	2.789409	AAAGAATGGAAGACGGAGGG	57.211	50.000	0.00	0.00	0.00	4.30
2413	3423	1.903877	ATGGAAGACGGAGGGCACTG	61.904	60.000	0.00	0.00	0.00	3.66
2494	3510	8.170730	ACTTATTGTGGGGAGAGTTAGATTTTT	58.829	33.333	0.00	0.00	0.00	1.94
2522	3538	9.638239	TCACAAAAACAAATAGCAAATATCTCC	57.362	29.630	0.00	0.00	0.00	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
80	81	0.395312	ATATTTACTGGGACCGGCGG	59.605	55.000	27.06	27.06	0.00	6.13
147	148	2.435805	TCTTGCTTGGACAACTGAGACT	59.564	45.455	0.00	0.00	0.00	3.24
199	201	2.258755	GGTGTGATTATTTTGTGGCGC	58.741	47.619	0.00	0.00	0.00	6.53
233	235	7.225734	TGTGTTTTTCTCAATAATGACGAGTCA	59.774	33.333	8.48	8.48	44.59	3.41
303	306	0.661020	CAACCAGGCGAGTCGTTTTT	59.339	50.000	15.08	0.00	0.00	1.94
309	312	0.458716	GAGCTACAACCAGGCGAGTC	60.459	60.000	0.00	0.00	0.00	3.36
317	320	4.441495	CCGATTGACATAGAGCTACAACCA	60.441	45.833	0.00	0.00	0.00	3.67
376	379	6.554334	TGGGTTTTATTCTGTCTTCTTTCG	57.446	37.500	0.00	0.00	0.00	3.46
397	400	5.701290	CCTTGTCTACTAGTTTTCCACTTGG	59.299	44.000	0.00	0.00	36.88	3.61
423	426	1.614241	CCCCACTTACCTCTGTCCCG	61.614	65.000	0.00	0.00	0.00	5.14
428	431	4.072839	GTTTTCTTCCCCACTTACCTCTG	58.927	47.826	0.00	0.00	0.00	3.35
529	533	3.454574	GTGCGCAACGTACGATCA	58.545	55.556	24.41	8.73	32.53	2.92
594	598	5.163248	TGTGTCCATATACCCGTTCATCATT	60.163	40.000	0.00	0.00	0.00	2.57
595	599	4.346709	TGTGTCCATATACCCGTTCATCAT	59.653	41.667	0.00	0.00	0.00	2.45
599	1570	2.168936	GGTGTGTCCATATACCCGTTCA	59.831	50.000	0.00	0.00	35.97	3.18
708	1682	5.911752	AGCTAGTGTATCATGAAGTTGAGG	58.088	41.667	0.00	0.00	0.00	3.86
727	1701	1.828660	GGCCCGACTGCTCTAGCTA	60.829	63.158	3.26	0.00	42.66	3.32
777	1751	2.575993	GCCTTCTGCTCGAGCTCA	59.424	61.111	35.27	20.40	42.66	4.26
831	1805	1.615165	TAAGCGGGCCGATGGTGTAA	61.615	55.000	33.44	2.51	0.00	2.41
892	1887	1.756561	GGTTGGGGCATATTGCGGT	60.757	57.895	0.00	0.00	46.21	5.68
897	1892	3.906846	CTCTCTAGAGGTTGGGGCATATT	59.093	47.826	19.67	0.00	38.48	1.28
914	1909	2.158475	AGGCAGGATCGATCTTCTCTCT	60.158	50.000	23.96	9.35	0.00	3.10
995	1990	1.545428	GCTCTTGGTTGGACATGGTGA	60.545	52.381	0.00	0.00	0.00	4.02
1075	2070	3.458189	CATCACCCTTTACGAGGTCATC	58.542	50.000	0.00	0.00	44.71	2.92
1101	2097	3.240134	GAACTCGGGAGGCAGCACA	62.240	63.158	0.00	0.00	0.00	4.57
1129	2125	1.378646	GTAGGCACCTTCCCTTGGC	60.379	63.158	0.00	0.00	38.55	4.52
1146	2142	0.249489	GTTCACACCAGCTCACGAGT	60.249	55.000	0.00	0.00	0.00	4.18
1149	2145	0.514255	CATGTTCACACCAGCTCACG	59.486	55.000	0.00	0.00	0.00	4.35
1151	2147	1.271001	CCTCATGTTCACACCAGCTCA	60.271	52.381	0.00	0.00	0.00	4.26
1161	2157	1.672030	CAGCACCGCCTCATGTTCA	60.672	57.895	0.00	0.00	0.00	3.18
1167	2163	4.019312	TGATGCAGCACCGCCTCA	62.019	61.111	0.00	0.00	34.67	3.86
1212	2208	1.375396	CATCGAGTTCCACCCGCAA	60.375	57.895	0.00	0.00	0.00	4.85
1231	2227	2.853542	TGCACTGAGCCCCTCCAA	60.854	61.111	0.00	0.00	44.83	3.53
1355	2351	4.361971	TCGCCTCGACCACCTCCT	62.362	66.667	0.00	0.00	0.00	3.69
1465	2461	1.705997	AACGACCTTCCACCAGGCTT	61.706	55.000	0.00	0.00	37.47	4.35
1467	2463	1.966451	CAACGACCTTCCACCAGGC	60.966	63.158	0.00	0.00	37.47	4.85
1527	2523	2.262637	TCCGACCCAACATTCTTACCT	58.737	47.619	0.00	0.00	0.00	3.08
1544	2540	2.855660	TTTGCATGCATCTCAATCCG	57.144	45.000	23.37	0.00	0.00	4.18
1546	2542	4.316205	TGGATTTGCATGCATCTCAATC	57.684	40.909	24.94	24.94	0.00	2.67
1587	2591	4.096984	CCAGTCCATGCAGAAACTAATTCC	59.903	45.833	0.00	0.00	38.94	3.01
1632	2642	3.938334	GCCACAACCAAAACAAACAAGAT	59.062	39.130	0.00	0.00	0.00	2.40
1645	2655	0.112025	TGATGACATGGCCACAACCA	59.888	50.000	8.16	4.23	45.82	3.67
1765	2775	9.230122	TCATGCATCCACGTATCATATTTATTT	57.770	29.630	0.00	0.00	0.00	1.40
1825	2835	4.164843	ACCATCAAACACACCACTAAGT	57.835	40.909	0.00	0.00	0.00	2.24
1880	2890	9.561069	GAGCCAACTCTGATATCCTTTTATTTA	57.439	33.333	0.00	0.00	40.03	1.40
1893	2903	1.786937	AGGATCGAGCCAACTCTGAT	58.213	50.000	23.83	0.00	41.09	2.90
1907	2917	4.250464	TGTCCACAATACAACGAAGGATC	58.750	43.478	0.00	0.00	0.00	3.36
2103	3113	8.827832	TGGAATTTCATCCTTTAGTTCATCAT	57.172	30.769	0.00	0.00	40.35	2.45
2135	3145	8.958119	AAATTGCTCTTGAACGTAGGATATAA	57.042	30.769	0.00	0.00	0.00	0.98
2151	3161	4.677182	AGGGACCATGTTAAAATTGCTCT	58.323	39.130	0.00	0.00	0.00	4.09
2163	3173	0.835941	GATGCTGAGAGGGACCATGT	59.164	55.000	0.00	0.00	0.00	3.21
2353	3363	8.721478	CGCTAAAATGCTGATATACAACCTAAT	58.279	33.333	0.00	0.00	0.00	1.73
2385	3395	4.327680	CCTCCGTCTTCCATTCTTTTCTT	58.672	43.478	0.00	0.00	0.00	2.52
2387	3397	3.010420	CCCTCCGTCTTCCATTCTTTTC	58.990	50.000	0.00	0.00	0.00	2.29
2459	3469	7.393515	ACTCTCCCCACAATAAGTATTTTTGTC	59.606	37.037	0.00	0.00	44.95	3.18
2463	3473	8.832735	TCTAACTCTCCCCACAATAAGTATTTT	58.167	33.333	0.00	0.00	0.00	1.82
2515	3531	8.821686	TTTATTGGATGTGTGTTTGGAGATAT	57.178	30.769	0.00	0.00	0.00	1.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.