AutoCloner

Multiple sequence alignment - TraesCS2B01G422100

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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	TraesCS2B01G422100	chr2B	100.000	2769	0	0	1	2769	607299720	607302488	0.000000e+00	5114.0
1	TraesCS2B01G422100	chr2B	96.795	1248	32	6	857	2096	798711697	798710450	0.000000e+00	2076.0
2	TraesCS2B01G422100	chr2B	94.282	857	48	1	1	857	607283170	607284025	0.000000e+00	1310.0
3	TraesCS2B01G422100	chr2B	88.077	671	79	1	2096	2766	77485402	77484733	0.000000e+00	795.0
4	TraesCS2B01G422100	chr2B	91.880	234	17	1	2535	2766	749206099	749205866	2.660000e-85	326.0
5	TraesCS2B01G422100	chr2B	90.909	66	6	0	2028	2093	672745258	672745323	3.800000e-14	89.8
6	TraesCS2B01G422100	chr7B	96.782	1243	34	4	857	2093	211694744	211695986	0.000000e+00	2069.0
7	TraesCS2B01G422100	chr7B	93.349	857	55	2	2	858	323840335	323839481	0.000000e+00	1266.0
8	TraesCS2B01G422100	chr7B	90.909	220	16	3	2549	2765	89427361	89427143	2.700000e-75	292.0
9	TraesCS2B01G422100	chr5B	96.044	1264	45	4	857	2115	123020541	123021804	0.000000e+00	2052.0
10	TraesCS2B01G422100	chr7A	96.290	1240	43	2	857	2093	6752608	6751369	0.000000e+00	2032.0
11	TraesCS2B01G422100	chr1B	96.219	1243	44	2	857	2096	394374695	394375937	0.000000e+00	2032.0
12	TraesCS2B01G422100	chr1B	96.216	1242	44	2	857	2096	388170505	388169265	0.000000e+00	2030.0
13	TraesCS2B01G422100	chr1B	94.399	857	47	1	1	857	6002400	6001545	0.000000e+00	1315.0
14	TraesCS2B01G422100	chr1B	93.590	858	53	2	1	857	335406870	335407726	0.000000e+00	1279.0
15	TraesCS2B01G422100	chr6B	95.803	1239	50	1	857	2093	717064465	717065703	0.000000e+00	1999.0
16	TraesCS2B01G422100	chr6B	92.727	220	14	1	2549	2766	695474543	695474762	1.600000e-82	316.0
17	TraesCS2B01G422100	chr1A	95.642	1239	50	2	857	2093	579647903	579649139	0.000000e+00	1986.0
18	TraesCS2B01G422100	chr3D	96.007	1202	40	5	857	2052	516529768	516528569	0.000000e+00	1947.0
19	TraesCS2B01G422100	chr3D	95.413	218	10	0	2549	2766	136564089	136563872	5.680000e-92	348.0
20	TraesCS2B01G422100	chr3D	84.083	289	31	1	2296	2584	583380029	583379756	5.880000e-67	265.0
21	TraesCS2B01G422100	chr5D	94.049	857	49	2	1	857	41872252	41873106	0.000000e+00	1299.0
22	TraesCS2B01G422100	chr4B	93.582	857	50	3	1	857	199185383	199184532	0.000000e+00	1273.0
23	TraesCS2B01G422100	chr4B	93.466	857	53	3	1	857	21512929	21513782	0.000000e+00	1269.0
24	TraesCS2B01G422100	chr4B	92.989	271	19	0	2494	2764	465458008	465457738	2.000000e-106	396.0
25	TraesCS2B01G422100	chr2D	93.473	858	54	2	1	857	40775426	40776282	0.000000e+00	1273.0
26	TraesCS2B01G422100	chr2D	93.357	858	55	2	1	857	40754029	40754885	0.000000e+00	1267.0
27	TraesCS2B01G422100	chr4A	92.620	271	20	0	2494	2764	86304865	86305135	9.300000e-105	390.0
28	TraesCS2B01G422100	chrUn	85.791	373	38	1	2290	2662	68202136	68202493	5.600000e-102	381.0
29	TraesCS2B01G422100	chr4D	91.882	271	22	0	2494	2764	378749207	378748937	2.010000e-101	379.0
30	TraesCS2B01G422100	chr5A	86.861	274	34	2	2493	2766	66002202	66002473	3.460000e-79	305.0

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	TraesCS2B01G422100	chr2B	607299720	607302488	2768	False	5114	5114	100.000	1	2769	1	chr2B.!!$F2	2768
1	TraesCS2B01G422100	chr2B	798710450	798711697	1247	True	2076	2076	96.795	857	2096	1	chr2B.!!$R3	1239
2	TraesCS2B01G422100	chr2B	607283170	607284025	855	False	1310	1310	94.282	1	857	1	chr2B.!!$F1	856
3	TraesCS2B01G422100	chr2B	77484733	77485402	669	True	795	795	88.077	2096	2766	1	chr2B.!!$R1	670
4	TraesCS2B01G422100	chr7B	211694744	211695986	1242	False	2069	2069	96.782	857	2093	1	chr7B.!!$F1	1236
5	TraesCS2B01G422100	chr7B	323839481	323840335	854	True	1266	1266	93.349	2	858	1	chr7B.!!$R2	856
6	TraesCS2B01G422100	chr5B	123020541	123021804	1263	False	2052	2052	96.044	857	2115	1	chr5B.!!$F1	1258
7	TraesCS2B01G422100	chr7A	6751369	6752608	1239	True	2032	2032	96.290	857	2093	1	chr7A.!!$R1	1236
8	TraesCS2B01G422100	chr1B	394374695	394375937	1242	False	2032	2032	96.219	857	2096	1	chr1B.!!$F2	1239
9	TraesCS2B01G422100	chr1B	388169265	388170505	1240	True	2030	2030	96.216	857	2096	1	chr1B.!!$R2	1239
10	TraesCS2B01G422100	chr1B	6001545	6002400	855	True	1315	1315	94.399	1	857	1	chr1B.!!$R1	856
11	TraesCS2B01G422100	chr1B	335406870	335407726	856	False	1279	1279	93.590	1	857	1	chr1B.!!$F1	856
12	TraesCS2B01G422100	chr6B	717064465	717065703	1238	False	1999	1999	95.803	857	2093	1	chr6B.!!$F2	1236
13	TraesCS2B01G422100	chr1A	579647903	579649139	1236	False	1986	1986	95.642	857	2093	1	chr1A.!!$F1	1236
14	TraesCS2B01G422100	chr3D	516528569	516529768	1199	True	1947	1947	96.007	857	2052	1	chr3D.!!$R2	1195
15	TraesCS2B01G422100	chr5D	41872252	41873106	854	False	1299	1299	94.049	1	857	1	chr5D.!!$F1	856
16	TraesCS2B01G422100	chr4B	199184532	199185383	851	True	1273	1273	93.582	1	857	1	chr4B.!!$R1	856
17	TraesCS2B01G422100	chr4B	21512929	21513782	853	False	1269	1269	93.466	1	857	1	chr4B.!!$F1	856
18	TraesCS2B01G422100	chr2D	40775426	40776282	856	False	1273	1273	93.473	1	857	1	chr2D.!!$F2	856
19	TraesCS2B01G422100	chr2D	40754029	40754885	856	False	1267	1267	93.357	1	857	1	chr2D.!!$F1	856

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
419	422	0.758734	GTTGCTTTGCTCCCCCTTTT	59.241	50.0	0.0	0.0	0.0	2.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2089	2106	0.48822	TGTGGTAGGTGGGGTACAGA	59.512	55.0	0.0	0.0	0.0	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
419	422	0.758734	GTTGCTTTGCTCCCCCTTTT	59.241	50.000	0.00	0.00	0.00	2.27
550	553	1.302033	CAGGCCGCTGACAAAGACT	60.302	57.895	0.00	0.00	0.00	3.24
651	655	9.691362	CTTATGGCAACTTGTTTAACTTATGTT	57.309	29.630	0.00	0.00	37.60	2.71
682	686	1.609208	ATTGTTGCTTCCGCTGACTT	58.391	45.000	0.00	0.00	36.97	3.01
818	823	8.274322	TCCCTGATCTTAATCATACACATTTGT	58.726	33.333	0.00	0.00	41.05	2.83
907	912	4.217118	GTGATGCTCAATCTTTGGTCAGTT	59.783	41.667	0.00	0.00	36.15	3.16
1102	1107	9.618890	TTCAAGCTAGTATTGAGATAGCAAAAT	57.381	29.630	10.96	0.00	43.49	1.82
1213	1218	6.929049	TCAAGACGAAGAAATACAGTTGTCAT	59.071	34.615	0.00	0.00	0.00	3.06
1362	1368	7.443302	AAATCTGAAGTCCTTGGATGATAGA	57.557	36.000	0.00	0.00	0.00	1.98
1445	1451	8.799367	TGATGTTGATCTTCATGATTTTGTCTT	58.201	29.630	0.00	0.00	35.14	3.01
1511	1517	2.348059	CAGCGCTTGAGATTCTTCAGTC	59.652	50.000	7.50	0.00	0.00	3.51
1573	1579	5.163301	GCCTATTGGATCCTCTTAACAGTGA	60.163	44.000	14.23	0.00	34.57	3.41
1574	1580	6.465035	GCCTATTGGATCCTCTTAACAGTGAT	60.465	42.308	14.23	0.00	34.57	3.06
2040	2057	6.337185	TGTCTTAGGACTTAGGACATAGGA	57.663	41.667	6.54	0.00	41.74	2.94
2049	2066	1.898863	AGGACATAGGAGCCCATGTT	58.101	50.000	2.19	0.00	35.55	2.71
2116	2133	1.066143	CCCACCTACCACACACATCTC	60.066	57.143	0.00	0.00	0.00	2.75
2117	2134	1.623311	CCACCTACCACACACATCTCA	59.377	52.381	0.00	0.00	0.00	3.27
2118	2135	2.612972	CCACCTACCACACACATCTCAC	60.613	54.545	0.00	0.00	0.00	3.51
2119	2136	2.037121	CACCTACCACACACATCTCACA	59.963	50.000	0.00	0.00	0.00	3.58
2127	2144	1.446099	CACATCTCACACGGTCGGG	60.446	63.158	0.00	0.00	0.00	5.14
2164	2181	3.626924	AGCCAACGTCGCCTCCTT	61.627	61.111	4.10	0.00	0.00	3.36
2171	2188	4.856607	GTCGCCTCCTTCTCGCCG	62.857	72.222	0.00	0.00	0.00	6.46
2209	2226	1.984570	CCTCCGCAACCTCCTCTCA	60.985	63.158	0.00	0.00	0.00	3.27
2222	2239	4.779733	TCTCACCCTCCCCTCGCC	62.780	72.222	0.00	0.00	0.00	5.54
2249	2266	3.535962	GCAGCCTAGCTCGAGCCT	61.536	66.667	32.94	20.03	43.38	4.58
2325	2342	2.154074	ACACCTCCTTCCCCGCTTT	61.154	57.895	0.00	0.00	0.00	3.51
2326	2343	1.074951	CACCTCCTTCCCCGCTTTT	59.925	57.895	0.00	0.00	0.00	2.27
2327	2344	0.539669	CACCTCCTTCCCCGCTTTTT	60.540	55.000	0.00	0.00	0.00	1.94
2332	2349	1.908299	CTTCCCCGCTTTTTGCCCT	60.908	57.895	0.00	0.00	38.78	5.19
2357	2374	3.787001	CCTTCCTCCCCACTCGCC	61.787	72.222	0.00	0.00	0.00	5.54
2358	2375	3.003173	CTTCCTCCCCACTCGCCA	61.003	66.667	0.00	0.00	0.00	5.69
2363	2380	4.316823	TCCCCACTCGCCACCTCT	62.317	66.667	0.00	0.00	0.00	3.69
2374	2391	4.838486	CACCTCTCGCGACCGCTC	62.838	72.222	3.71	0.00	39.32	5.03
2435	2452	3.670629	CTCGGGAGGGAGCTCCAGT	62.671	68.421	33.29	20.43	45.06	4.00
2499	2516	1.101635	CCTACTCCTGGATCGCGTCA	61.102	60.000	5.77	2.55	0.00	4.35
2502	2519	1.323271	ACTCCTGGATCGCGTCATGT	61.323	55.000	5.77	1.14	0.00	3.21
2503	2520	0.179100	CTCCTGGATCGCGTCATGTT	60.179	55.000	5.77	0.00	0.00	2.71
2518	2535	0.608856	ATGTTGCGCCTTGATGGACA	60.609	50.000	4.18	0.00	38.35	4.02
2533	2550	2.524394	ACACCACCTCGTCCTGCT	60.524	61.111	0.00	0.00	0.00	4.24
2540	2557	1.451567	CCTCGTCCTGCTCGTCCTA	60.452	63.158	0.00	0.00	0.00	2.94
2543	2560	0.393944	TCGTCCTGCTCGTCCTACAT	60.394	55.000	0.00	0.00	0.00	2.29
2545	2562	0.818296	GTCCTGCTCGTCCTACATGT	59.182	55.000	2.69	2.69	0.00	3.21
2547	2564	0.532573	CCTGCTCGTCCTACATGTGT	59.467	55.000	9.11	0.00	0.00	3.72
2556	2573	0.462581	CCTACATGTGTCGCAGCCAT	60.463	55.000	9.11	0.00	0.00	4.40
2664	2681	2.720758	CTCCTTGACGCGCTTGTCG	61.721	63.158	5.73	0.00	41.87	4.35
2709	2726	2.437343	GCCGAAGAAGAGCACGACG	61.437	63.158	0.00	0.00	0.00	5.12
2766	2783	1.218763	CAAGCTGCATCTCCATCTCG	58.781	55.000	1.02	0.00	0.00	4.04
2767	2784	1.117994	AAGCTGCATCTCCATCTCGA	58.882	50.000	1.02	0.00	0.00	4.04
2768	2785	0.675083	AGCTGCATCTCCATCTCGAG	59.325	55.000	5.93	5.93	0.00	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
265	268	2.819019	GGGGTAGCTAGTCCTATCGAAC	59.181	54.545	11.53	0.00	0.00	3.95
419	422	5.885912	CGGGAAGAAGATGATAAAGGGAAAA	59.114	40.000	0.00	0.00	0.00	2.29
432	435	1.447643	CGGCATCCGGGAAGAAGAT	59.552	57.895	0.00	0.00	44.15	2.40
550	553	4.735537	TGGGATCCTCCTAAACTACTCCTA	59.264	45.833	12.58	0.00	36.57	2.94
651	655	5.580691	CGGAAGCAACAATATCTGAGTACAA	59.419	40.000	0.00	0.00	0.00	2.41
682	686	6.019881	CGAATACAAGTGCTCGATCATAAACA	60.020	38.462	0.00	0.00	33.13	2.83
721	725	5.439721	ACAAGCATCATATTACAAGCCAGA	58.560	37.500	0.00	0.00	0.00	3.86
775	780	1.269998	GGGACTCACGGGAAGATATCG	59.730	57.143	0.00	0.00	0.00	2.92
818	823	5.415221	TCAATCGTACACTAATCATGCACA	58.585	37.500	0.00	0.00	0.00	4.57
1102	1107	4.710313	TGTCCATATCAGATGCAATGGA	57.290	40.909	10.80	10.80	44.32	3.41
1362	1368	2.884639	AGCGCAACATTCCTGTAGTTTT	59.115	40.909	11.47	0.00	33.36	2.43
1445	1451	7.277396	AGTTACCTGCAACACTTTTAACTCTA	58.723	34.615	0.00	0.00	0.00	2.43
1481	1487	2.703416	TCTCAAGCGCTGACATCAAAT	58.297	42.857	12.58	0.00	0.00	2.32
1511	1517	6.992123	TGGATAGCAATCTACAACCATAACAG	59.008	38.462	0.00	0.00	32.29	3.16
1573	1579	5.349061	TCAGCTGATGATACAGTCACAAT	57.651	39.130	13.74	0.00	40.28	2.71
1574	1580	4.806640	TCAGCTGATGATACAGTCACAA	57.193	40.909	13.74	0.00	40.28	3.33
1585	1591	5.862845	AGAGAAACTTCTTTCAGCTGATGA	58.137	37.500	19.04	15.85	38.67	2.92
1587	1593	8.093659	GTTTAGAGAAACTTCTTTCAGCTGAT	57.906	34.615	19.04	0.00	41.55	2.90
1801	1810	8.265165	ACCTCAAATAAGAACGAAATTAGACC	57.735	34.615	0.00	0.00	0.00	3.85
2040	2057	0.670546	CGAACTCGACAACATGGGCT	60.671	55.000	0.00	0.00	43.02	5.19
2089	2106	0.488220	TGTGGTAGGTGGGGTACAGA	59.512	55.000	0.00	0.00	0.00	3.41
2152	2169	4.117661	GCGAGAAGGAGGCGACGT	62.118	66.667	0.00	0.00	0.00	4.34
2158	2175	4.856607	GCGACGGCGAGAAGGAGG	62.857	72.222	18.90	0.00	40.82	4.30
2190	2207	2.685380	AGAGGAGGTTGCGGAGGG	60.685	66.667	0.00	0.00	0.00	4.30
2198	2215	1.081277	GGGAGGGTGAGAGGAGGTT	59.919	63.158	0.00	0.00	0.00	3.50
2199	2216	2.781406	GGGAGGGTGAGAGGAGGT	59.219	66.667	0.00	0.00	0.00	3.85
2231	2248	3.842923	GGCTCGAGCTAGGCTGCA	61.843	66.667	34.46	0.00	39.88	4.41
2238	2255	3.518998	GGCGACAGGCTCGAGCTA	61.519	66.667	34.46	0.00	46.14	3.32
2300	2317	2.741092	GAAGGAGGTGTGGCGACA	59.259	61.111	0.00	0.00	38.70	4.35
2309	2326	0.539669	CAAAAAGCGGGGAAGGAGGT	60.540	55.000	0.00	0.00	0.00	3.85
2394	2411	4.208686	GTCCGCTAGGTCGCCTGG	62.209	72.222	8.44	6.75	39.05	4.45
2414	2431	2.043852	GAGCTCCCTCCCGAGACA	60.044	66.667	0.87	0.00	31.68	3.41
2423	2440	1.684049	CGAGGAACTGGAGCTCCCT	60.684	63.158	29.95	18.73	41.55	4.20
2477	2494	3.043419	CGATCCAGGAGTAGGGCG	58.957	66.667	0.00	0.00	0.00	6.13
2483	2500	1.323271	ACATGACGCGATCCAGGAGT	61.323	55.000	15.93	5.50	0.00	3.85
2499	2516	0.608856	TGTCCATCAAGGCGCAACAT	60.609	50.000	10.83	0.00	37.29	2.71
2502	2519	1.971167	GGTGTCCATCAAGGCGCAA	60.971	57.895	10.83	0.00	37.29	4.85
2503	2520	2.359850	GGTGTCCATCAAGGCGCA	60.360	61.111	10.83	0.00	37.29	6.09
2518	2535	3.374402	CGAGCAGGACGAGGTGGT	61.374	66.667	0.00	0.00	0.00	4.16
2533	2550	0.170339	CTGCGACACATGTAGGACGA	59.830	55.000	11.12	0.00	0.00	4.20
2540	2557	2.693762	GCATGGCTGCGACACATGT	61.694	57.895	14.94	0.00	42.89	3.21
2640	2657	2.103143	CGCGTCAAGGAGCTCGAT	59.897	61.111	7.83	0.00	0.00	3.59
2675	2692	2.908940	GCAAGTGGTGGCAGCTGT	60.909	61.111	18.53	1.68	0.00	4.40
2748	2765	1.068895	CTCGAGATGGAGATGCAGCTT	59.931	52.381	5.67	0.00	36.08	3.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.