AutoCloner

Multiple sequence alignment - TraesCS5D01G478200

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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	TraesCS5D01G478200	chr5D	100.000	2020	0	0	311	2330	517053429	517055448	0.000000e+00	3731.0
1	TraesCS5D01G478200	chr5D	84.875	562	60	14	949	1492	517155423	517155977	5.660000e-151	544.0
2	TraesCS5D01G478200	chr5D	81.768	543	49	20	416	945	517093803	517094308	2.160000e-110	409.0
3	TraesCS5D01G478200	chr5D	100.000	167	0	0	1	167	517053119	517053285	2.250000e-80	309.0
4	TraesCS5D01G478200	chr4D	95.385	845	33	3	1492	2330	130544082	130544926	0.000000e+00	1339.0
5	TraesCS5D01G478200	chr5A	91.038	848	63	7	1491	2330	687408242	687407400	0.000000e+00	1133.0
6	TraesCS5D01G478200	chr5A	84.123	844	105	18	1495	2330	378496134	378496956	0.000000e+00	789.0
7	TraesCS5D01G478200	chr5A	95.575	452	15	2	420	870	644297275	644297722	0.000000e+00	719.0
8	TraesCS5D01G478200	chr5A	86.549	565	49	14	950	1491	644297794	644298354	4.290000e-167	597.0
9	TraesCS5D01G478200	chr5A	87.611	113	10	4	1494	1603	42283439	42283550	6.760000e-26	128.0
10	TraesCS5D01G478200	chr5A	90.526	95	4	4	76	165	644218166	644218260	1.130000e-23	121.0
11	TraesCS5D01G478200	chr5A	83.486	109	9	6	312	416	644218270	644218373	2.470000e-15	93.5
12	TraesCS5D01G478200	chr5B	88.221	815	34	14	703	1492	649459107	649459884	0.000000e+00	917.0
13	TraesCS5D01G478200	chr5B	91.205	523	20	7	313	815	649458533	649459049	0.000000e+00	688.0
14	TraesCS5D01G478200	chr5B	85.366	615	50	11	908	1492	649490326	649490930	3.310000e-168	601.0
15	TraesCS5D01G478200	chr5B	83.775	302	30	7	416	708	649489848	649490139	3.820000e-68	268.0
16	TraesCS5D01G478200	chr5B	93.529	170	5	3	1	167	649458358	649458524	4.970000e-62	248.0
17	TraesCS5D01G478200	chr5B	92.929	99	1	2	703	795	649490177	649490275	3.120000e-29	139.0
18	TraesCS5D01G478200	chr6B	85.121	867	89	21	1492	2330	526712697	526713551	0.000000e+00	850.0
19	TraesCS5D01G478200	chr3A	84.870	846	106	14	1493	2330	34477104	34476273	0.000000e+00	833.0
20	TraesCS5D01G478200	chr1A	84.681	470	59	10	1863	2330	539705028	539704570	7.590000e-125	457.0
21	TraesCS5D01G478200	chrUn	80.000	235	42	4	2099	2330	76224659	76224891	3.980000e-38	169.0
22	TraesCS5D01G478200	chr3D	81.250	208	34	4	2099	2303	208582363	208582568	1.850000e-36	163.0
23	TraesCS5D01G478200	chr2D	80.769	208	35	4	2099	2303	37230823	37231028	8.620000e-35	158.0
24	TraesCS5D01G478200	chr1D	80.000	215	37	5	2099	2309	246078453	246078665	1.110000e-33	154.0
25	TraesCS5D01G478200	chr3B	88.235	51	4	2	2002	2051	237493124	237493075	2.500000e-05	60.2

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	TraesCS5D01G478200	chr5D	517053119	517055448	2329	False	2020.000000	3731	100.000000	1	2330	2	chr5D.!!$F3	2329
1	TraesCS5D01G478200	chr5D	517155423	517155977	554	False	544.000000	544	84.875000	949	1492	1	chr5D.!!$F2	543
2	TraesCS5D01G478200	chr5D	517093803	517094308	505	False	409.000000	409	81.768000	416	945	1	chr5D.!!$F1	529
3	TraesCS5D01G478200	chr4D	130544082	130544926	844	False	1339.000000	1339	95.385000	1492	2330	1	chr4D.!!$F1	838
4	TraesCS5D01G478200	chr5A	687407400	687408242	842	True	1133.000000	1133	91.038000	1491	2330	1	chr5A.!!$R1	839
5	TraesCS5D01G478200	chr5A	378496134	378496956	822	False	789.000000	789	84.123000	1495	2330	1	chr5A.!!$F2	835
6	TraesCS5D01G478200	chr5A	644297275	644298354	1079	False	658.000000	719	91.062000	420	1491	2	chr5A.!!$F4	1071
7	TraesCS5D01G478200	chr5B	649458358	649459884	1526	False	617.666667	917	90.985000	1	1492	3	chr5B.!!$F1	1491
8	TraesCS5D01G478200	chr5B	649489848	649490930	1082	False	336.000000	601	87.356667	416	1492	3	chr5B.!!$F2	1076
9	TraesCS5D01G478200	chr6B	526712697	526713551	854	False	850.000000	850	85.121000	1492	2330	1	chr6B.!!$F1	838
10	TraesCS5D01G478200	chr3A	34476273	34477104	831	True	833.000000	833	84.870000	1493	2330	1	chr3A.!!$R1	837

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
979	1224	1.884235	ACAGCAAAGCACAGGACTAC	58.116	50.0	0.0	0.0	0.0	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1794	2071	2.583441	CGCCAGTTCCAGAGACCCA	61.583	63.158	0.0	0.0	0.0	4.51	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
55	56	7.232534	ACCTAACATTGTTGCCATTTTTCTCTA	59.767	33.333	12.30	0.00	0.00	2.43
414	418	2.821366	CAGGCGTGTGATGAGGGC	60.821	66.667	0.00	0.00	0.00	5.19
442	447	5.452078	TCTTTCATTTCCATGTGTCCAAC	57.548	39.130	0.00	0.00	0.00	3.77
620	629	2.003301	GCTTCCATTCGAGTCCAAGAC	58.997	52.381	0.80	0.00	0.00	3.01
811	1024	5.008019	CCCAATATTAGTGTCACATGCAGAC	59.992	44.000	5.62	10.97	36.55	3.51
875	1088	3.181505	TGCTTACACACGGAAACAAACAG	60.182	43.478	0.00	0.00	0.00	3.16
922	1139	2.278245	AGTCTCCAACCCCAATCATCA	58.722	47.619	0.00	0.00	0.00	3.07
968	1213	4.756642	TGGATCTCAGTACAAACAGCAAAG	59.243	41.667	0.00	0.00	0.00	2.77
979	1224	1.884235	ACAGCAAAGCACAGGACTAC	58.116	50.000	0.00	0.00	0.00	2.73
1077	1333	4.821589	GCCTCCTCCTCGGCGTTG	62.822	72.222	6.85	0.75	36.45	4.10
1078	1334	3.068691	CCTCCTCCTCGGCGTTGA	61.069	66.667	6.85	3.72	0.00	3.18
1093	1349	3.459148	TTGAGGTCGCTGCTGCACA	62.459	57.895	16.29	4.66	39.64	4.57
1134	1390	4.753662	TACCTGGGTCTCGCGGCT	62.754	66.667	6.13	0.00	0.00	5.52
1157	1413	0.875728	CTAGCATCCGACTACTCCCG	59.124	60.000	0.00	0.00	0.00	5.14
1360	1627	1.134551	CAGCTTCCTTGTAGGCTCCTC	60.135	57.143	0.00	0.00	34.61	3.71
1365	1632	1.833630	TCCTTGTAGGCTCCTCATGTG	59.166	52.381	0.00	0.00	34.61	3.21
1404	1671	4.588899	TCATCGATGTTTGGGTCTGAATT	58.411	39.130	24.09	0.00	0.00	2.17
1503	1772	7.595875	CCGTCTTTTATTTATGGGAAACGTTTT	59.404	33.333	15.89	1.23	0.00	2.43
1509	1778	4.920640	TTATGGGAAACGTTTTGCTTCA	57.079	36.364	15.89	9.55	0.00	3.02
1587	1859	2.204136	AGCTCATCCCACCCACCA	60.204	61.111	0.00	0.00	0.00	4.17
1588	1860	1.620589	AGCTCATCCCACCCACCAT	60.621	57.895	0.00	0.00	0.00	3.55
1665	1937	1.839994	TCGCATCTCTCCTCCCAAATT	59.160	47.619	0.00	0.00	0.00	1.82
1794	2071	0.537188	GATCCATGGTCACAGACGGT	59.463	55.000	12.58	0.00	32.65	4.83
1806	2083	3.787394	GACGGTGGGTCTCTGGAA	58.213	61.111	0.00	0.00	42.62	3.53
1936	2234	3.826157	TCGGTGAAGAAAATTGCTGGAAT	59.174	39.130	0.00	0.00	0.00	3.01
1946	2244	3.498774	ATTGCTGGAATCGGCTATTCT	57.501	42.857	11.04	0.00	45.25	2.40
2056	2354	3.321497	GGCTACTAGATTTGCTGGATCG	58.679	50.000	0.00	0.00	0.00	3.69
2160	2458	0.882484	TGATTCGCTGCAACCGTTCA	60.882	50.000	0.00	8.00	0.00	3.18
2164	2462	0.040514	TCGCTGCAACCGTTCAATTG	60.041	50.000	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
310	314	0.318762	GAAGAGCAGTCGGTCCAAGT	59.681	55.000	0.00	0.00	40.69	3.16
311	315	0.390472	GGAAGAGCAGTCGGTCCAAG	60.390	60.000	0.00	0.00	40.69	3.61
345	349	5.888161	AGAACACAGAGGAACATCAGTTTTT	59.112	36.000	0.00	0.00	38.30	1.94
346	350	5.297776	CAGAACACAGAGGAACATCAGTTTT	59.702	40.000	0.00	0.00	38.30	2.43
347	351	4.818546	CAGAACACAGAGGAACATCAGTTT	59.181	41.667	0.00	0.00	38.30	2.66
348	352	4.141620	ACAGAACACAGAGGAACATCAGTT	60.142	41.667	0.00	0.00	41.64	3.16
349	353	3.389329	ACAGAACACAGAGGAACATCAGT	59.611	43.478	0.00	0.00	0.00	3.41
350	354	4.000331	ACAGAACACAGAGGAACATCAG	58.000	45.455	0.00	0.00	0.00	2.90
351	355	4.129380	CAACAGAACACAGAGGAACATCA	58.871	43.478	0.00	0.00	0.00	3.07
352	356	4.212214	GTCAACAGAACACAGAGGAACATC	59.788	45.833	0.00	0.00	0.00	3.06
353	357	4.130118	GTCAACAGAACACAGAGGAACAT	58.870	43.478	0.00	0.00	0.00	2.71
414	418	6.404074	GGACACATGGAAATGAAAGAGCTTAG	60.404	42.308	0.00	0.00	0.00	2.18
442	447	2.256461	GCCACCAGAAGCAAAGCG	59.744	61.111	0.00	0.00	0.00	4.68
470	475	6.475727	TCTTATTTTAGGATTGAACGCTCTCG	59.524	38.462	0.00	0.00	42.43	4.04
472	477	8.738645	ATTCTTATTTTAGGATTGAACGCTCT	57.261	30.769	0.00	0.00	0.00	4.09
568	577	2.023414	AACGGCGGACTGACTGACAA	62.023	55.000	13.24	0.00	32.09	3.18
702	863	1.198408	CACACAGCACATCACATGGAC	59.802	52.381	0.00	0.00	33.60	4.02
811	1024	0.861837	GTTGACTGTTGACTCCAGCG	59.138	55.000	0.00	0.00	33.09	5.18
893	1106	1.420138	GGGTTGGAGACTTGGAGAACA	59.580	52.381	0.00	0.00	0.00	3.18
894	1107	1.271434	GGGGTTGGAGACTTGGAGAAC	60.271	57.143	0.00	0.00	0.00	3.01
896	1109	0.104672	TGGGGTTGGAGACTTGGAGA	60.105	55.000	0.00	0.00	0.00	3.71
898	1111	1.354368	GATTGGGGTTGGAGACTTGGA	59.646	52.381	0.00	0.00	0.00	3.53
903	1116	2.806945	TGATGATTGGGGTTGGAGAC	57.193	50.000	0.00	0.00	0.00	3.36
904	1117	3.075882	ACTTTGATGATTGGGGTTGGAGA	59.924	43.478	0.00	0.00	0.00	3.71
922	1139	6.319658	CCATGTCCATTTATAGTGAGCACTTT	59.680	38.462	8.60	3.70	42.54	2.66
968	1213	2.498078	AGAAGCTTAGGTAGTCCTGTGC	59.502	50.000	0.00	1.92	44.81	4.57
979	1224	4.021102	TGGTCCTGAAAAGAAGCTTAGG	57.979	45.455	0.00	0.91	0.00	2.69
981	1226	4.042809	TCCATGGTCCTGAAAAGAAGCTTA	59.957	41.667	12.58	0.00	0.00	3.09
1021	1277	1.645710	TCTTCCCCGAAGCTCTTCTT	58.354	50.000	7.88	0.00	39.29	2.52
1077	1333	3.117171	CTGTGCAGCAGCGACCTC	61.117	66.667	0.00	0.00	46.23	3.85
1093	1349	3.142838	GCATCGTTGGGCCATGCT	61.143	61.111	19.92	0.00	39.92	3.79
1114	1370	3.141488	CGCGAGACCCAGGTAGCT	61.141	66.667	0.00	0.00	0.00	3.32
1134	1390	0.851469	AGTAGTCGGATGCTAGGGGA	59.149	55.000	0.00	0.00	0.00	4.81
1180	1436	2.613506	CGCCGGTTGGTTTCAGGTC	61.614	63.158	1.90	0.00	37.67	3.85
1360	1627	1.198713	ACTGGAGGTAGAGGCACATG	58.801	55.000	0.00	0.00	0.00	3.21
1365	1632	3.057174	CGATGATTACTGGAGGTAGAGGC	60.057	52.174	0.00	0.00	0.00	4.70
1665	1937	4.386761	GGAGGAATTTCATGGAGGATTGGA	60.387	45.833	0.00	0.00	0.00	3.53
1794	2071	2.583441	CGCCAGTTCCAGAGACCCA	61.583	63.158	0.00	0.00	0.00	4.51
1806	2083	3.052082	GCACAGCACATCGCCAGT	61.052	61.111	0.00	0.00	44.04	4.00
1936	2234	5.521010	CGGTTGTAACAAATAGAATAGCCGA	59.479	40.000	0.00	0.00	30.21	5.54
1946	2244	8.447833	GTCTTGAATCATCGGTTGTAACAAATA	58.552	33.333	0.00	0.00	0.00	1.40
2160	2458	7.330208	GCTCTGAATGAATGTAGCAAAACAATT	59.670	33.333	0.00	0.00	32.02	2.32
2164	2462	5.098211	GGCTCTGAATGAATGTAGCAAAAC	58.902	41.667	0.00	0.00	0.00	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.