AutoCloner

Multiple sequence alignment - TraesCS2B01G514700

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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	TraesCS2B01G514700	chr2B	100.000	2651	0	0	1	2651	709570258	709567608	0.000000e+00	4896
1	TraesCS2B01G514700	chr2B	79.960	1512	269	25	493	1991	54016667	54015177	0.000000e+00	1083
2	TraesCS2B01G514700	chr2B	79.894	1512	266	27	493	1991	54044019	54042533	0.000000e+00	1074
3	TraesCS2B01G514700	chr2B	79.009	1272	202	38	1231	2463	89491352	89492597	0.000000e+00	809
4	TraesCS2B01G514700	chr2B	75.459	1471	268	57	244	1658	89494358	89495791	4.820000e-177	630
5	TraesCS2B01G514700	chr2B	88.732	142	12	4	99	236	757065181	757065040	1.260000e-38	171
6	TraesCS2B01G514700	chr2B	91.781	73	6	0	35	107	89494285	89494357	4.670000e-18	102
7	TraesCS2B01G514700	chr6B	91.794	2693	172	22	1	2651	15398473	15395788	0.000000e+00	3703
8	TraesCS2B01G514700	chr6B	84.772	2167	256	32	493	2651	670592701	670590601	0.000000e+00	2106
9	TraesCS2B01G514700	chr6B	88.269	1040	68	15	41	1047	15606722	15605704	0.000000e+00	1195
10	TraesCS2B01G514700	chr6B	75.406	1171	263	24	493	1649	52568249	52567090	6.450000e-151	544
11	TraesCS2B01G514700	chr6B	80.992	605	88	14	2067	2651	16269017	16269614	3.110000e-124	455
12	TraesCS2B01G514700	chr6B	79.180	610	94	20	2070	2651	15233170	15232566	2.470000e-105	392
13	TraesCS2B01G514700	chr6B	80.938	320	45	11	2345	2651	16238726	16239042	3.410000e-59	239
14	TraesCS2B01G514700	chr6B	83.893	149	16	5	98	245	195271589	195271448	4.600000e-28	135
15	TraesCS2B01G514700	chr6A	89.310	2030	201	9	628	2651	9355315	9357334	0.000000e+00	2532
16	TraesCS2B01G514700	chr6A	85.022	1589	228	8	483	2065	9461440	9463024	0.000000e+00	1607
17	TraesCS2B01G514700	chr6A	75.430	1221	257	35	431	1626	30560634	30559432	1.070000e-153	553
18	TraesCS2B01G514700	chr5B	86.277	2055	234	28	626	2651	556795625	556793590	0.000000e+00	2189
19	TraesCS2B01G514700	chr5B	79.479	614	87	19	2070	2651	556624877	556624271	1.480000e-107	399
20	TraesCS2B01G514700	chr6D	84.372	2086	279	40	483	2548	33895036	33897094	0.000000e+00	2002
21	TraesCS2B01G514700	chr6D	93.689	919	56	2	949	1866	8568351	8567434	0.000000e+00	1375
22	TraesCS2B01G514700	chr6D	92.866	799	43	6	1862	2651	8567307	8566514	0.000000e+00	1147
23	TraesCS2B01G514700	chr6D	76.242	1208	244	38	472	1656	8894030	8895217	3.780000e-168	601
24	TraesCS2B01G514700	chr6D	75.000	1168	270	21	493	1649	8397158	8396002	1.090000e-143	520
25	TraesCS2B01G514700	chr6D	82.965	317	47	5	2075	2384	8916718	8917034	2.010000e-71	279
26	TraesCS2B01G514700	chr1B	84.171	1453	197	18	631	2065	662037456	662038893	0.000000e+00	1378
27	TraesCS2B01G514700	chr1B	81.370	1621	255	29	458	2059	662152992	662154584	0.000000e+00	1277
28	TraesCS2B01G514700	chr5D	82.998	447	51	12	2213	2637	499863241	499862798	5.350000e-102	381
29	TraesCS2B01G514700	chr1D	71.682	1183	282	35	493	1644	490417862	490419022	2.010000e-71	279
30	TraesCS2B01G514700	chr1D	71.719	739	167	26	576	1299	490008465	490007754	4.540000e-38	169
31	TraesCS2B01G514700	chr1A	91.241	137	9	2	103	236	409855167	409855031	1.620000e-42	183
32	TraesCS2B01G514700	chr3B	88.971	136	13	2	102	236	752683074	752682940	1.630000e-37	167
33	TraesCS2B01G514700	chr3B	86.111	144	18	2	94	236	815372774	815372916	1.270000e-33	154
34	TraesCS2B01G514700	chr7D	88.148	135	12	2	103	236	58821311	58821180	9.820000e-35	158
35	TraesCS2B01G514700	chr2A	87.681	138	13	4	103	236	418618398	418618261	9.820000e-35	158

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	TraesCS2B01G514700	chr2B	709567608	709570258	2650	True	4896.000000	4896	100.0000	1	2651	1	chr2B.!!$R3	2650
1	TraesCS2B01G514700	chr2B	54015177	54016667	1490	True	1083.000000	1083	79.9600	493	1991	1	chr2B.!!$R1	1498
2	TraesCS2B01G514700	chr2B	54042533	54044019	1486	True	1074.000000	1074	79.8940	493	1991	1	chr2B.!!$R2	1498
3	TraesCS2B01G514700	chr2B	89491352	89495791	4439	False	513.666667	809	82.0830	35	2463	3	chr2B.!!$F1	2428
4	TraesCS2B01G514700	chr6B	15395788	15398473	2685	True	3703.000000	3703	91.7940	1	2651	1	chr6B.!!$R2	2650
5	TraesCS2B01G514700	chr6B	670590601	670592701	2100	True	2106.000000	2106	84.7720	493	2651	1	chr6B.!!$R6	2158
6	TraesCS2B01G514700	chr6B	15605704	15606722	1018	True	1195.000000	1195	88.2690	41	1047	1	chr6B.!!$R3	1006
7	TraesCS2B01G514700	chr6B	52567090	52568249	1159	True	544.000000	544	75.4060	493	1649	1	chr6B.!!$R4	1156
8	TraesCS2B01G514700	chr6B	16269017	16269614	597	False	455.000000	455	80.9920	2067	2651	1	chr6B.!!$F2	584
9	TraesCS2B01G514700	chr6B	15232566	15233170	604	True	392.000000	392	79.1800	2070	2651	1	chr6B.!!$R1	581
10	TraesCS2B01G514700	chr6A	9355315	9357334	2019	False	2532.000000	2532	89.3100	628	2651	1	chr6A.!!$F1	2023
11	TraesCS2B01G514700	chr6A	9461440	9463024	1584	False	1607.000000	1607	85.0220	483	2065	1	chr6A.!!$F2	1582
12	TraesCS2B01G514700	chr6A	30559432	30560634	1202	True	553.000000	553	75.4300	431	1626	1	chr6A.!!$R1	1195
13	TraesCS2B01G514700	chr5B	556793590	556795625	2035	True	2189.000000	2189	86.2770	626	2651	1	chr5B.!!$R2	2025
14	TraesCS2B01G514700	chr5B	556624271	556624877	606	True	399.000000	399	79.4790	2070	2651	1	chr5B.!!$R1	581
15	TraesCS2B01G514700	chr6D	33895036	33897094	2058	False	2002.000000	2002	84.3720	483	2548	1	chr6D.!!$F3	2065
16	TraesCS2B01G514700	chr6D	8566514	8568351	1837	True	1261.000000	1375	93.2775	949	2651	2	chr6D.!!$R2	1702
17	TraesCS2B01G514700	chr6D	8894030	8895217	1187	False	601.000000	601	76.2420	472	1656	1	chr6D.!!$F1	1184
18	TraesCS2B01G514700	chr6D	8396002	8397158	1156	True	520.000000	520	75.0000	493	1649	1	chr6D.!!$R1	1156
19	TraesCS2B01G514700	chr1B	662037456	662038893	1437	False	1378.000000	1378	84.1710	631	2065	1	chr1B.!!$F1	1434
20	TraesCS2B01G514700	chr1B	662152992	662154584	1592	False	1277.000000	1277	81.3700	458	2059	1	chr1B.!!$F2	1601
21	TraesCS2B01G514700	chr1D	490417862	490419022	1160	False	279.000000	279	71.6820	493	1644	1	chr1D.!!$F1	1151

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
574	3529	0.031111	CCCCATCTCCCACCTGAGTA	60.031	60.0	0.0	0.0	33.93	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2039	5164	0.546598	ACCTAGATTTGGGAAGGGCG	59.453	55.0	0.0	0.0	33.16	6.13	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
24	25	0.039256	CAACACATCAAACTGGCCGG	60.039	55.000	11.02	11.02	0.00	6.13
32	33	2.580601	AAACTGGCCGGTCGTAGCT	61.581	57.895	20.00	0.00	0.00	3.32
151	3052	8.986991	AGTCTTTGTAGAGATTCCACTATGAAT	58.013	33.333	0.00	0.00	37.66	2.57
169	3076	9.836864	ACTATGAATCATGCATTTAGAGTGTAA	57.163	29.630	5.91	0.00	32.72	2.41
209	3116	8.148351	GCTCTGTATGTGGTCCATAGTAAAATA	58.852	37.037	0.00	0.00	36.71	1.40
245	3152	9.804758	ACTTATATTTAGGAACGACTGAAGAAG	57.195	33.333	0.00	0.00	0.00	2.85
250	3157	7.852971	TTTAGGAACGACTGAAGAAGAAAAA	57.147	32.000	0.00	0.00	0.00	1.94
407	3315	2.046292	CTTTGGGTTGGGTTGAACCAT	58.954	47.619	17.27	0.00	46.42	3.55
456	3378	1.601248	CTCTTTCCCCCATTCCCTCT	58.399	55.000	0.00	0.00	0.00	3.69
491	3434	1.915266	CAGGCTCCACTCTCCACCA	60.915	63.158	0.00	0.00	0.00	4.17
573	3528	1.307343	CCCCATCTCCCACCTGAGT	60.307	63.158	0.00	0.00	33.93	3.41
574	3529	0.031111	CCCCATCTCCCACCTGAGTA	60.031	60.000	0.00	0.00	33.93	2.59
659	3620	2.270205	CTTCACCTGCGGCCTCAT	59.730	61.111	0.00	0.00	0.00	2.90
690	3652	2.034066	CTCAAGGCCTCCCGCAAA	59.966	61.111	5.23	0.00	40.31	3.68
713	3676	0.178846	TCCCACCTCAAATCCCCAGA	60.179	55.000	0.00	0.00	0.00	3.86
718	3681	4.387891	CCCACCTCAAATCCCCAGATAATT	60.388	45.833	0.00	0.00	30.42	1.40
725	3688	5.072741	CAAATCCCCAGATAATTCCGATGT	58.927	41.667	0.00	0.00	30.42	3.06
764	3727	1.997874	GCCTGGGTCTCTCCACCAT	60.998	63.158	0.00	0.00	38.32	3.55
833	3796	4.704103	TGAGAGGACCCTGGCGCT	62.704	66.667	7.64	0.00	0.00	5.92
920	3884	1.523758	GCCGCCAATTCCATAGTAGG	58.476	55.000	0.00	0.00	0.00	3.18
1176	4152	1.885887	GCTCAAAACATAGGTGTGCCA	59.114	47.619	0.00	0.00	38.92	4.92
1185	4161	1.687297	TAGGTGTGCCACGTGGTTCA	61.687	55.000	33.92	27.67	34.83	3.18
1204	4180	2.434185	GGATGTTCAGGCACGCGA	60.434	61.111	15.93	0.00	0.00	5.87
1408	4396	1.327303	ACCGGTGCACATTGTTCAAT	58.673	45.000	20.43	0.00	0.00	2.57
1412	4400	2.545532	CGGTGCACATTGTTCAATGGTT	60.546	45.455	20.43	6.64	34.56	3.67
1428	4416	5.133660	TCAATGGTTGGTAATACTAGGGCAT	59.866	40.000	0.00	0.00	0.00	4.40
1628	4616	1.466851	GCTTGCAAAGGGGAAGTGCT	61.467	55.000	0.00	0.00	46.35	4.40
1663	4651	6.543465	CAGATTCACATAAGCCAATAACAGGA	59.457	38.462	0.00	0.00	0.00	3.86
1682	4670	2.939103	GGATCTGATGTAACTGTGTGCC	59.061	50.000	0.00	0.00	0.00	5.01
1768	4757	7.459125	AGCTGATAATTTGATCCCTGGATACTA	59.541	37.037	0.00	0.00	34.60	1.82
1785	4774	9.996554	CTGGATACTAATATGTAATGTCACCAA	57.003	33.333	0.00	0.00	37.61	3.67
2039	5164	8.697507	AGTGGATAATTTGGGATAAATCTGAC	57.302	34.615	0.00	0.00	0.00	3.51
2163	5296	9.552114	CATAGAGATCTGTTTTTGCTTTAACTG	57.448	33.333	0.00	0.00	0.00	3.16
2205	5342	7.879160	ACTTAACCATTCAATTACGAAGGTGTA	59.121	33.333	0.00	0.00	31.21	2.90
2220	5357	5.479306	GAAGGTGTATGCAAGTGAGTTCTA	58.521	41.667	0.00	0.00	0.00	2.10
2226	5363	7.386848	GGTGTATGCAAGTGAGTTCTACTTTAA	59.613	37.037	0.00	0.00	36.29	1.52
2239	5376	7.051000	AGTTCTACTTTAATTGGATCAGAGGC	58.949	38.462	0.00	0.00	0.00	4.70
2247	5384	2.028420	TGGATCAGAGGCAACGATTG	57.972	50.000	0.00	0.00	46.39	2.67
2296	5441	0.962356	CTGGGCTGCAGGACGAAATT	60.962	55.000	17.12	0.00	0.00	1.82
2307	5452	1.664151	GGACGAAATTTACAGGGCTCG	59.336	52.381	0.00	0.00	0.00	5.03
2387	5537	3.633986	GGAGGAGGTTTGGCATCATTTAG	59.366	47.826	0.00	0.00	0.00	1.85
2516	5725	3.649981	AGGTGTATTATCCTGCTCTGCAT	59.350	43.478	0.00	0.00	38.13	3.96
2552	5792	6.596309	TTATGTGTTTATTGTGGATGGCAA	57.404	33.333	0.00	0.00	0.00	4.52
2589	5829	6.539173	AGTTCATTATTGTGTGTTGGTCCTA	58.461	36.000	0.00	0.00	0.00	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	3.740044	TTTTTATGCAGCAGCTACGAC	57.260	42.857	0.00	0.00	42.74	4.34
48	2948	6.985188	TTTAATGAGCGAAAGTCTGCTTAT	57.015	33.333	0.00	0.00	42.60	1.73
49	2949	6.985188	ATTTAATGAGCGAAAGTCTGCTTA	57.015	33.333	0.00	0.00	42.60	3.09
151	3052	8.565896	AGTGAATTTACACTCTAAATGCATGA	57.434	30.769	0.00	0.00	46.36	3.07
169	3076	7.310664	CACATACAGAGCAAAATGAGTGAATT	58.689	34.615	0.00	0.00	0.00	2.17
369	3277	2.847234	TGGCCCCACTCGTCAGTT	60.847	61.111	0.00	0.00	0.00	3.16
407	3315	4.318332	AGTGAAAAGATGAAGTGCGATGA	58.682	39.130	0.00	0.00	0.00	2.92
573	3528	3.606662	GCGGCGGAGATGAGGCTA	61.607	66.667	9.78	0.00	0.00	3.93
686	3648	3.118992	GGATTTGAGGTGGGAGATTTTGC	60.119	47.826	0.00	0.00	0.00	3.68
690	3652	1.570979	GGGGATTTGAGGTGGGAGATT	59.429	52.381	0.00	0.00	0.00	2.40
713	3676	3.889538	TGAGAGGACGACATCGGAATTAT	59.110	43.478	6.21	0.00	44.95	1.28
718	3681	1.676529	GAATGAGAGGACGACATCGGA	59.323	52.381	6.21	0.00	44.95	4.55
725	3688	1.384989	GGCGAGGAATGAGAGGACGA	61.385	60.000	0.00	0.00	0.00	4.20
810	3773	1.500474	CCAGGGTCCTCTCAATGCTA	58.500	55.000	0.00	0.00	0.00	3.49
814	3777	3.036429	GCGCCAGGGTCCTCTCAAT	62.036	63.158	0.00	0.00	0.00	2.57
833	3796	1.082300	GTGAGCTCGACGACAACGA	60.082	57.895	9.64	0.00	42.66	3.85
913	3877	1.147191	TGGAGACGATGGGCCTACTAT	59.853	52.381	4.53	0.00	0.00	2.12
920	3884	1.142748	CAGACTGGAGACGATGGGC	59.857	63.158	0.00	0.00	0.00	5.36
1118	4094	1.758592	ACACGCATGGGGTTAGTGT	59.241	52.632	14.94	5.95	40.69	3.55
1122	4098	1.298340	CTGGACACGCATGGGGTTA	59.702	57.895	14.94	2.87	0.00	2.85
1176	4152	2.494059	CTGAACATCCTTGAACCACGT	58.506	47.619	0.00	0.00	0.00	4.49
1185	4161	2.034879	CGCGTGCCTGAACATCCTT	61.035	57.895	0.00	0.00	0.00	3.36
1408	4396	4.041198	GCTATGCCCTAGTATTACCAACCA	59.959	45.833	0.00	0.00	0.00	3.67
1628	4616	7.828717	TGGCTTATGTGAATCTGAAATTAGTGA	59.171	33.333	0.00	0.00	0.00	3.41
1663	4651	2.621338	CGGCACACAGTTACATCAGAT	58.379	47.619	0.00	0.00	0.00	2.90
1695	4683	4.410228	ACCCAGCATCTAACAGACATACAT	59.590	41.667	0.00	0.00	0.00	2.29
1768	4757	7.056006	TCTGCTGATTGGTGACATTACATATT	58.944	34.615	0.00	0.00	42.32	1.28
1785	4774	3.265221	TCCATGGTTTCTTCTCTGCTGAT	59.735	43.478	12.58	0.00	0.00	2.90
1857	4848	6.127703	GCCTGATCTCACACTTACTTAGTACA	60.128	42.308	0.00	0.00	34.56	2.90
1935	5057	4.721776	AGACCTTACCTTGGCTCATTATCA	59.278	41.667	0.00	0.00	0.00	2.15
2039	5164	0.546598	ACCTAGATTTGGGAAGGGCG	59.453	55.000	0.00	0.00	33.16	6.13
2130	5257	7.446625	AGCAAAAACAGATCTCTATGAGTTTGT	59.553	33.333	7.21	0.49	31.95	2.83
2185	5318	5.065859	TGCATACACCTTCGTAATTGAATGG	59.934	40.000	0.00	0.00	0.00	3.16
2193	5326	4.242475	CTCACTTGCATACACCTTCGTAA	58.758	43.478	0.00	0.00	0.00	3.18
2196	5329	2.688507	ACTCACTTGCATACACCTTCG	58.311	47.619	0.00	0.00	0.00	3.79
2205	5342	7.665559	TCCAATTAAAGTAGAACTCACTTGCAT	59.334	33.333	0.00	0.00	36.38	3.96
2220	5357	4.396166	CGTTGCCTCTGATCCAATTAAAGT	59.604	41.667	0.00	0.00	0.00	2.66
2226	5363	2.947652	CAATCGTTGCCTCTGATCCAAT	59.052	45.455	0.00	0.00	0.00	3.16
2239	5376	1.439353	CCGATGGCTCCCAATCGTTG	61.439	60.000	4.57	0.00	36.95	4.10
2247	5384	1.611673	CCAATATGACCGATGGCTCCC	60.612	57.143	0.00	0.00	0.00	4.30
2296	5441	1.264749	ACCAGATGCGAGCCCTGTAA	61.265	55.000	11.56	0.00	0.00	2.41
2307	5452	5.605534	TCTCTTTAGCAGATAACCAGATGC	58.394	41.667	0.00	0.00	38.97	3.91
2387	5537	9.330063	ACACACCTAAGTTTACTTACTTAAACC	57.670	33.333	0.00	0.00	41.17	3.27
2447	5601	1.740025	GCGGCAAGTGCTTCTCTATTT	59.260	47.619	2.85	0.00	41.70	1.40
2451	5605	1.375268	GAGCGGCAAGTGCTTCTCT	60.375	57.895	1.45	0.00	44.18	3.10
2516	5725	9.761504	CAATAAACACATAATTTATGGCCATCA	57.238	29.630	24.80	9.00	40.47	3.07
2580	5820	5.949952	ACAAAGAATTACCCATAGGACCAAC	59.050	40.000	0.00	0.00	36.73	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.