AutoCloner

Multiple sequence alignment - TraesCS2D01G020300

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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	TraesCS2D01G020300	chr2D	100.000	3491	0	0	1	3491	9641976	9645466	0.000000e+00	6447.0
1	TraesCS2D01G020300	chr2D	79.449	1995	313	52	581	2533	9880180	9878241	0.000000e+00	1323.0
2	TraesCS2D01G020300	chr2D	82.418	1547	232	18	912	2438	8659700	8661226	0.000000e+00	1314.0
3	TraesCS2D01G020300	chr2D	79.921	1763	261	51	931	2662	9588218	9589918	0.000000e+00	1208.0
4	TraesCS2D01G020300	chr2D	80.365	1533	266	21	998	2521	19587012	19588518	0.000000e+00	1131.0
5	TraesCS2D01G020300	chr2D	80.051	1579	264	28	985	2547	9371499	9373042	0.000000e+00	1123.0
6	TraesCS2D01G020300	chr2D	81.569	510	68	10	1999	2506	9523803	9524288	7.020000e-107	398.0
7	TraesCS2D01G020300	chr2D	79.717	212	29	10	438	640	8480716	8480510	1.310000e-29	141.0
8	TraesCS2D01G020300	chr2B	89.856	3322	201	56	246	3486	11454978	11451712	0.000000e+00	4143.0
9	TraesCS2D01G020300	chr2B	92.022	2720	134	26	844	3491	12966279	12968987	0.000000e+00	3744.0
10	TraesCS2D01G020300	chr2B	81.842	1553	225	30	998	2533	138993293	138991781	0.000000e+00	1253.0
11	TraesCS2D01G020300	chr2B	81.121	1552	247	30	998	2533	768807004	768805483	0.000000e+00	1201.0
12	TraesCS2D01G020300	chr2B	80.774	1550	255	25	998	2533	768929424	768927904	0.000000e+00	1171.0
13	TraesCS2D01G020300	chr2B	80.364	1594	254	36	998	2565	12422311	12423871	0.000000e+00	1155.0
14	TraesCS2D01G020300	chr2B	79.587	1695	280	33	934	2608	11539734	11538086	0.000000e+00	1153.0
15	TraesCS2D01G020300	chr2B	78.539	1780	302	44	779	2533	13131758	13130034	0.000000e+00	1098.0
16	TraesCS2D01G020300	chr2B	81.818	209	33	4	438	644	11228474	11228269	1.670000e-38	171.0
17	TraesCS2D01G020300	chr2B	78.205	234	35	7	895	1125	4759876	4759656	6.080000e-28	135.0
18	TraesCS2D01G020300	chr2B	89.474	57	2	2	2450	2503	11221863	11221808	6.250000e-08	69.4
19	TraesCS2D01G020300	chr2A	93.550	2744	106	27	1	2734	8726344	8729026	0.000000e+00	4021.0
20	TraesCS2D01G020300	chr2A	79.940	1989	315	42	581	2533	9394707	9396647	0.000000e+00	1386.0
21	TraesCS2D01G020300	chr2A	79.889	1989	316	42	581	2533	9847184	9849124	0.000000e+00	1380.0
22	TraesCS2D01G020300	chr2A	81.265	1628	250	30	913	2517	7727305	7728900	0.000000e+00	1266.0
23	TraesCS2D01G020300	chr2A	80.032	1237	206	25	1214	2440	8683202	8684407	0.000000e+00	878.0
24	TraesCS2D01G020300	chr2A	79.323	1330	206	37	1378	2691	7514372	7513096	0.000000e+00	869.0
25	TraesCS2D01G020300	chr2A	97.395	499	12	1	2754	3251	8729098	8729596	0.000000e+00	848.0
26	TraesCS2D01G020300	chr2A	98.765	243	3	0	3249	3491	8729635	8729877	1.920000e-117	433.0
27	TraesCS2D01G020300	chr5B	80.040	1483	225	32	884	2348	485911595	485910166	0.000000e+00	1033.0
28	TraesCS2D01G020300	chr5B	87.931	116	11	2	2444	2559	485909903	485909791	2.190000e-27	134.0

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	TraesCS2D01G020300	chr2D	9641976	9645466	3490	False	6447.000000	6447	100.0000	1	3491	1	chr2D.!!$F5	3490
1	TraesCS2D01G020300	chr2D	9878241	9880180	1939	True	1323.000000	1323	79.4490	581	2533	1	chr2D.!!$R2	1952
2	TraesCS2D01G020300	chr2D	8659700	8661226	1526	False	1314.000000	1314	82.4180	912	2438	1	chr2D.!!$F1	1526
3	TraesCS2D01G020300	chr2D	9588218	9589918	1700	False	1208.000000	1208	79.9210	931	2662	1	chr2D.!!$F4	1731
4	TraesCS2D01G020300	chr2D	19587012	19588518	1506	False	1131.000000	1131	80.3650	998	2521	1	chr2D.!!$F6	1523
5	TraesCS2D01G020300	chr2D	9371499	9373042	1543	False	1123.000000	1123	80.0510	985	2547	1	chr2D.!!$F2	1562
6	TraesCS2D01G020300	chr2B	11451712	11454978	3266	True	4143.000000	4143	89.8560	246	3486	1	chr2B.!!$R4	3240
7	TraesCS2D01G020300	chr2B	12966279	12968987	2708	False	3744.000000	3744	92.0220	844	3491	1	chr2B.!!$F2	2647
8	TraesCS2D01G020300	chr2B	138991781	138993293	1512	True	1253.000000	1253	81.8420	998	2533	1	chr2B.!!$R7	1535
9	TraesCS2D01G020300	chr2B	768805483	768807004	1521	True	1201.000000	1201	81.1210	998	2533	1	chr2B.!!$R8	1535
10	TraesCS2D01G020300	chr2B	768927904	768929424	1520	True	1171.000000	1171	80.7740	998	2533	1	chr2B.!!$R9	1535
11	TraesCS2D01G020300	chr2B	12422311	12423871	1560	False	1155.000000	1155	80.3640	998	2565	1	chr2B.!!$F1	1567
12	TraesCS2D01G020300	chr2B	11538086	11539734	1648	True	1153.000000	1153	79.5870	934	2608	1	chr2B.!!$R5	1674
13	TraesCS2D01G020300	chr2B	13130034	13131758	1724	True	1098.000000	1098	78.5390	779	2533	1	chr2B.!!$R6	1754
14	TraesCS2D01G020300	chr2A	8726344	8729877	3533	False	1767.333333	4021	96.5700	1	3491	3	chr2A.!!$F5	3490
15	TraesCS2D01G020300	chr2A	9394707	9396647	1940	False	1386.000000	1386	79.9400	581	2533	1	chr2A.!!$F3	1952
16	TraesCS2D01G020300	chr2A	9847184	9849124	1940	False	1380.000000	1380	79.8890	581	2533	1	chr2A.!!$F4	1952
17	TraesCS2D01G020300	chr2A	7727305	7728900	1595	False	1266.000000	1266	81.2650	913	2517	1	chr2A.!!$F1	1604
18	TraesCS2D01G020300	chr2A	8683202	8684407	1205	False	878.000000	878	80.0320	1214	2440	1	chr2A.!!$F2	1226
19	TraesCS2D01G020300	chr2A	7513096	7514372	1276	True	869.000000	869	79.3230	1378	2691	1	chr2A.!!$R1	1313
20	TraesCS2D01G020300	chr5B	485909791	485911595	1804	True	583.500000	1033	83.9855	884	2559	2	chr5B.!!$R1	1675

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
473	476	0.174162	GCATGGAGTTGTGATTGCCC	59.826	55.0	0.00	0.0	0.00	5.36	F
1400	1470	0.037160	ATGCGCCATGAGCCATATGA	59.963	50.0	4.18	0.0	38.78	2.15	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2411	2682	2.423185	CCTTCATATGTTTCCGCAGCAA	59.577	45.455	1.9	0.0	0.0	3.91	R
2631	2924	0.957395	CAGGTGCTGGTTTGCTCGAT	60.957	55.000	0.0	0.0	0.0	3.59	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
22	23	0.538287	ACAAGGAGGTTGCAAGAGCC	60.538	55.000	0.00	0.77	40.15	4.70
28	29	2.338785	GGTTGCAAGAGCCCTCTGC	61.339	63.158	0.00	5.83	40.36	4.26
61	62	4.996434	GCTGCACTGGCTGGACGT	62.996	66.667	0.00	0.00	41.91	4.34
154	155	6.936335	TCTCAGTCAGTAAATTTCAGAATGCA	59.064	34.615	0.00	0.00	34.76	3.96
180	182	4.654915	TGCTTTGGTCATTTCTCTCATCA	58.345	39.130	0.00	0.00	0.00	3.07
219	221	4.561213	GCAAATATACAGGGCGACAAAAAC	59.439	41.667	0.00	0.00	0.00	2.43
221	223	5.968528	AATATACAGGGCGACAAAAACAA	57.031	34.783	0.00	0.00	0.00	2.83
224	226	3.535280	ACAGGGCGACAAAAACAATTT	57.465	38.095	0.00	0.00	0.00	1.82
228	230	4.511082	CAGGGCGACAAAAACAATTTCATT	59.489	37.500	0.00	0.00	0.00	2.57
276	278	9.581099	TTTTCCTATTTCCATTTTCGCTATTTC	57.419	29.630	0.00	0.00	0.00	2.17
473	476	0.174162	GCATGGAGTTGTGATTGCCC	59.826	55.000	0.00	0.00	0.00	5.36
499	502	2.420022	CACTGACCAAGATAAAAGGGCG	59.580	50.000	0.00	0.00	31.18	6.13
504	507	1.135402	CCAAGATAAAAGGGCGCACAC	60.135	52.381	14.57	0.00	0.00	3.82
519	522	0.606401	CACACCGTTGCCTTCCTGAT	60.606	55.000	0.00	0.00	0.00	2.90
543	548	2.394563	GCGCTCTGCTTTCTCCACC	61.395	63.158	0.00	0.00	41.73	4.61
745	762	1.333258	GCTTGTCGTTCTCACACTTGC	60.333	52.381	0.00	0.00	0.00	4.01
754	790	5.805486	TCGTTCTCACACTTGCAGATATAAC	59.195	40.000	0.00	0.00	0.00	1.89
755	791	5.807520	CGTTCTCACACTTGCAGATATAACT	59.192	40.000	0.00	0.00	0.00	2.24
756	792	6.237675	CGTTCTCACACTTGCAGATATAACTG	60.238	42.308	5.67	5.67	40.43	3.16
757	793	6.286240	TCTCACACTTGCAGATATAACTGT	57.714	37.500	11.23	0.00	39.73	3.55
758	794	7.404671	TCTCACACTTGCAGATATAACTGTA	57.595	36.000	11.23	4.41	39.73	2.74
759	795	7.484140	TCTCACACTTGCAGATATAACTGTAG	58.516	38.462	11.23	10.84	39.73	2.74
760	796	7.339466	TCTCACACTTGCAGATATAACTGTAGA	59.661	37.037	11.23	0.69	39.73	2.59
761	797	7.836842	TCACACTTGCAGATATAACTGTAGAA	58.163	34.615	11.23	2.62	39.73	2.10
762	798	8.311109	TCACACTTGCAGATATAACTGTAGAAA	58.689	33.333	11.23	2.04	39.73	2.52
763	799	8.598924	CACACTTGCAGATATAACTGTAGAAAG	58.401	37.037	11.23	11.44	39.73	2.62
764	800	8.314751	ACACTTGCAGATATAACTGTAGAAAGT	58.685	33.333	11.23	11.93	39.73	2.66
765	801	8.598924	CACTTGCAGATATAACTGTAGAAAGTG	58.401	37.037	21.08	21.08	38.70	3.16
766	802	8.314751	ACTTGCAGATATAACTGTAGAAAGTGT	58.685	33.333	11.23	0.00	39.73	3.55
767	803	8.703604	TTGCAGATATAACTGTAGAAAGTGTC	57.296	34.615	11.23	0.00	39.73	3.67
768	804	7.265673	TGCAGATATAACTGTAGAAAGTGTCC	58.734	38.462	11.23	0.00	39.73	4.02
769	805	7.093509	TGCAGATATAACTGTAGAAAGTGTCCA	60.094	37.037	11.23	0.00	39.73	4.02
770	806	7.764443	GCAGATATAACTGTAGAAAGTGTCCAA	59.236	37.037	11.23	0.00	39.73	3.53
771	807	9.307121	CAGATATAACTGTAGAAAGTGTCCAAG	57.693	37.037	1.93	0.00	33.73	3.61
772	808	8.478877	AGATATAACTGTAGAAAGTGTCCAAGG	58.521	37.037	0.00	0.00	0.00	3.61
773	809	4.772886	AACTGTAGAAAGTGTCCAAGGT	57.227	40.909	0.00	0.00	0.00	3.50
774	810	4.772886	ACTGTAGAAAGTGTCCAAGGTT	57.227	40.909	0.00	0.00	0.00	3.50
868	909	0.238289	GTTGGCATGTCCTTGTCACG	59.762	55.000	0.00	0.00	29.27	4.35
1400	1470	0.037160	ATGCGCCATGAGCCATATGA	59.963	50.000	4.18	0.00	38.78	2.15
1429	1499	5.305585	TGGAAAGATTAGAAGTCGCTGTTT	58.694	37.500	0.00	0.00	0.00	2.83
1672	1754	1.234615	ATGTGGCGACGAAAGGGTTG	61.235	55.000	0.00	0.00	0.00	3.77
1673	1755	1.890510	GTGGCGACGAAAGGGTTGT	60.891	57.895	0.00	0.00	0.00	3.32
2134	2223	3.537580	TGCGTATTGAACAAGGGGATAC	58.462	45.455	0.00	0.00	0.00	2.24
2341	2430	4.480115	TCCTAGTGTCAGACCAGAAGAAA	58.520	43.478	0.00	0.00	0.00	2.52
2411	2682	9.896645	ATCATTCACTCATTATGTTACAAGTCT	57.103	29.630	0.00	0.00	0.00	3.24
2717	3012	4.880164	ACTGGGCTATTCTCAGTAAGGTA	58.120	43.478	0.00	0.00	39.63	3.08
2733	3063	9.032624	TCAGTAAGGTAGCTTACAGTTAAAGAT	57.967	33.333	34.42	16.16	41.01	2.40
2744	3074	9.974750	GCTTACAGTTAAAGATAAGCTTAAGTG	57.025	33.333	10.85	10.10	43.96	3.16
2863	3218	1.153745	GTCGGTGAGGCTAGTGCAG	60.154	63.158	0.00	0.00	41.91	4.41
2884	3248	2.352715	GCAGCCCTTAATTCAACACCAC	60.353	50.000	0.00	0.00	0.00	4.16
2924	3295	9.146984	TGTGGTTTCTTATGAATACTAAAGACG	57.853	33.333	0.00	0.00	31.56	4.18
3093	3467	9.236498	TGTGGGCAAATGTATCCCTATATATAT	57.764	33.333	0.00	0.00	40.69	0.86
3198	3579	5.655090	TGGTAAATTCCTTTTTAGCTAGCCC	59.345	40.000	12.13	0.00	39.27	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	0.035176	GTTGTAACCGGGGTGCTACA	59.965	55.000	6.32	2.44	0.00	2.74
154	155	5.258841	TGAGAGAAATGACCAAAGCATCAT	58.741	37.500	0.00	0.00	37.14	2.45
219	221	7.159437	TGACTTGTTTGCGTAAATGAAATTG	57.841	32.000	0.99	0.00	36.10	2.32
221	223	7.945033	AATGACTTGTTTGCGTAAATGAAAT	57.055	28.000	0.99	0.00	0.00	2.17
224	226	7.197071	AGTAATGACTTGTTTGCGTAAATGA	57.803	32.000	0.99	0.00	28.61	2.57
228	230	9.601971	GAAAATAGTAATGACTTGTTTGCGTAA	57.398	29.630	0.00	0.00	37.10	3.18
276	278	1.078426	GACCTGATGTTGACCCCCG	60.078	63.158	0.00	0.00	0.00	5.73
473	476	5.587844	CCCTTTTATCTTGGTCAGTGATGAG	59.412	44.000	0.00	0.00	0.00	2.90
499	502	2.594592	AGGAAGGCAACGGTGTGC	60.595	61.111	0.66	0.15	44.14	4.57
504	507	0.036010	ACTCATCAGGAAGGCAACGG	60.036	55.000	0.00	0.00	46.39	4.44
718	735	1.138069	TGAGAACGACAAGCCAACTGA	59.862	47.619	0.00	0.00	0.00	3.41
745	762	9.307121	CTTGGACACTTTCTACAGTTATATCTG	57.693	37.037	8.92	8.92	40.80	2.90
754	790	5.238583	CCTAACCTTGGACACTTTCTACAG	58.761	45.833	0.00	0.00	0.00	2.74
755	791	4.504340	GCCTAACCTTGGACACTTTCTACA	60.504	45.833	0.00	0.00	0.00	2.74
756	792	4.001652	GCCTAACCTTGGACACTTTCTAC	58.998	47.826	0.00	0.00	0.00	2.59
757	793	3.649023	TGCCTAACCTTGGACACTTTCTA	59.351	43.478	0.00	0.00	0.00	2.10
758	794	2.441750	TGCCTAACCTTGGACACTTTCT	59.558	45.455	0.00	0.00	0.00	2.52
759	795	2.858745	TGCCTAACCTTGGACACTTTC	58.141	47.619	0.00	0.00	0.00	2.62
760	796	3.306472	TTGCCTAACCTTGGACACTTT	57.694	42.857	0.00	0.00	0.00	2.66
761	797	3.525800	ATTGCCTAACCTTGGACACTT	57.474	42.857	0.00	0.00	0.00	3.16
762	798	4.650972	TTATTGCCTAACCTTGGACACT	57.349	40.909	0.00	0.00	0.00	3.55
763	799	5.914898	AATTATTGCCTAACCTTGGACAC	57.085	39.130	0.00	0.00	0.00	3.67
764	800	8.058847	AGATTAATTATTGCCTAACCTTGGACA	58.941	33.333	0.00	0.00	0.00	4.02
765	801	8.352942	CAGATTAATTATTGCCTAACCTTGGAC	58.647	37.037	0.00	0.00	0.00	4.02
766	802	7.505585	CCAGATTAATTATTGCCTAACCTTGGA	59.494	37.037	0.00	0.00	0.00	3.53
767	803	7.505585	TCCAGATTAATTATTGCCTAACCTTGG	59.494	37.037	0.00	0.00	0.00	3.61
768	804	8.352942	GTCCAGATTAATTATTGCCTAACCTTG	58.647	37.037	0.00	0.00	0.00	3.61
769	805	7.505923	GGTCCAGATTAATTATTGCCTAACCTT	59.494	37.037	0.00	0.00	0.00	3.50
770	806	7.004691	GGTCCAGATTAATTATTGCCTAACCT	58.995	38.462	0.00	0.00	0.00	3.50
771	807	7.004691	AGGTCCAGATTAATTATTGCCTAACC	58.995	38.462	0.00	0.00	0.00	2.85
772	808	9.000486	GTAGGTCCAGATTAATTATTGCCTAAC	58.000	37.037	9.23	3.81	0.00	2.34
773	809	8.945193	AGTAGGTCCAGATTAATTATTGCCTAA	58.055	33.333	9.23	0.00	0.00	2.69
774	810	8.506196	AGTAGGTCCAGATTAATTATTGCCTA	57.494	34.615	0.00	0.00	0.00	3.93
868	909	1.451936	AGACAAGGGTGGCTGACAC	59.548	57.895	4.68	4.68	43.62	3.67
1400	1470	4.878397	CGACTTCTAATCTTTCCAAGGCAT	59.122	41.667	0.00	0.00	0.00	4.40
1429	1499	5.722263	CACAACAAATTCTGCCATATTGGA	58.278	37.500	0.00	0.00	40.96	3.53
1672	1754	4.537936	AAACAGAAGAGAAGCGTGAAAC	57.462	40.909	0.00	0.00	0.00	2.78
1673	1755	4.730613	GCAAAACAGAAGAGAAGCGTGAAA	60.731	41.667	0.00	0.00	0.00	2.69
2341	2430	6.418057	TTTCCATGCAATTAAGGTGAAGTT	57.582	33.333	0.00	0.00	0.00	2.66
2411	2682	2.423185	CCTTCATATGTTTCCGCAGCAA	59.577	45.455	1.90	0.00	0.00	3.91
2631	2924	0.957395	CAGGTGCTGGTTTGCTCGAT	60.957	55.000	0.00	0.00	0.00	3.59
2632	2925	1.597854	CAGGTGCTGGTTTGCTCGA	60.598	57.895	0.00	0.00	0.00	4.04
2633	2926	2.949106	CAGGTGCTGGTTTGCTCG	59.051	61.111	0.00	0.00	0.00	5.03
2664	2959	4.437390	GCCACTTTAGATGATGTTGTTCGG	60.437	45.833	0.00	0.00	0.00	4.30
2733	3063	1.821216	GCCCAGCACACTTAAGCTTA	58.179	50.000	0.86	0.86	39.50	3.09
2734	3064	1.237285	CGCCCAGCACACTTAAGCTT	61.237	55.000	3.48	3.48	39.50	3.74
2863	3218	1.892474	TGGTGTTGAATTAAGGGCTGC	59.108	47.619	0.00	0.00	0.00	5.25
2884	3248	2.918712	ACCACAGGTTGAGTGAGAAG	57.081	50.000	0.00	0.00	39.30	2.85
2924	3295	1.133869	GTCAACGGGCGTTATGTGC	59.866	57.895	0.00	0.00	36.46	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.