AutoCloner

Multiple sequence alignment - TraesCS3B01G542300

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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	TraesCS3B01G542300	chr3B	100.000	2702	0	0	1	2702	780300748	780298047	0.000000e+00	4990
1	TraesCS3B01G542300	chr3B	90.375	1465	110	11	471	1912	780339318	780337862	0.000000e+00	1895
2	TraesCS3B01G542300	chr3B	91.412	1374	86	15	562	1912	780324265	780322901	0.000000e+00	1855
3	TraesCS3B01G542300	chr3B	91.266	1374	89	11	562	1912	780314286	780312921	0.000000e+00	1844
4	TraesCS3B01G542300	chr3B	94.567	681	29	7	2026	2702	780332509	780331833	0.000000e+00	1046
5	TraesCS3B01G542300	chr3B	92.217	681	44	8	2026	2702	780308086	780307411	0.000000e+00	955
6	TraesCS3B01G542300	chr3B	89.461	427	22	10	1969	2391	780312767	780312360	3.990000e-143	518
7	TraesCS3B01G542300	chr3B	89.227	427	23	10	1969	2391	780337711	780337304	1.860000e-141	512
8	TraesCS3B01G542300	chr3B	88.551	428	26	10	1969	2391	780317373	780316964	5.200000e-137	497
9	TraesCS3B01G542300	chr3B	88.551	428	26	10	1969	2391	780322747	780322338	5.200000e-137	497
10	TraesCS3B01G542300	chr3B	88.551	428	26	10	1969	2391	780327352	780326943	5.200000e-137	497
11	TraesCS3B01G542300	chr3B	90.123	243	19	5	562	801	780327999	780327759	7.260000e-81	311
12	TraesCS3B01G542300	chr3D	94.151	1949	72	14	4	1914	583186288	583184344	0.000000e+00	2929
13	TraesCS3B01G542300	chr3D	94.045	1948	74	13	4	1914	583283166	583281224	0.000000e+00	2916
14	TraesCS3B01G542300	chr3D	92.229	1467	88	10	471	1914	583223263	583221800	0.000000e+00	2054
15	TraesCS3B01G542300	chr3D	91.327	784	56	7	1924	2701	583184246	583183469	0.000000e+00	1061
16	TraesCS3B01G542300	chr3D	92.438	648	16	10	4	620	583180296	583179651	0.000000e+00	894
17	TraesCS3B01G542300	chr3D	91.252	503	31	8	1924	2421	583281125	583280631	0.000000e+00	673
18	TraesCS3B01G542300	chr3D	89.062	512	41	11	1924	2427	583221703	583221199	2.950000e-174	621
19	TraesCS3B01G542300	chr3D	78.648	281	43	14	390	655	583276403	583276125	1.290000e-38	171
20	TraesCS3B01G542300	chrUn	93.478	1104	65	4	810	1912	352585812	352586909	0.000000e+00	1633
21	TraesCS3B01G542300	chrUn	88.551	428	26	10	1969	2391	352587063	352587472	5.200000e-137	497
22	TraesCS3B01G542300	chr6A	89.867	1125	92	14	797	1914	34273291	34272182	0.000000e+00	1426
23	TraesCS3B01G542300	chr6A	89.600	1125	97	12	797	1914	34278093	34276982	0.000000e+00	1411
24	TraesCS3B01G542300	chr6A	81.464	1462	182	48	442	1839	34280562	34279126	0.000000e+00	1116
25	TraesCS3B01G542300	chr6A	81.519	1396	184	33	442	1787	34282541	34281170	0.000000e+00	1081
26	TraesCS3B01G542300	chr6A	81.183	1403	174	50	500	1839	34393068	34391693	0.000000e+00	1046
27	TraesCS3B01G542300	chr6A	83.544	316	46	5	2390	2701	144093301	144092988	9.460000e-75	291
28	TraesCS3B01G542300	chr6B	81.839	1338	180	32	489	1787	62691238	62689925	0.000000e+00	1066
29	TraesCS3B01G542300	chr6B	83.544	316	48	4	2390	2702	699840124	699840438	2.630000e-75	292
30	TraesCS3B01G542300	chr6B	84.053	301	43	5	2390	2687	699800512	699800810	4.400000e-73	285
31	TraesCS3B01G542300	chr6B	83.228	316	48	5	2390	2702	699880031	699880344	4.400000e-73	285
32	TraesCS3B01G542300	chr7B	84.026	313	44	5	2392	2702	63027992	63028300	2.030000e-76	296
33	TraesCS3B01G542300	chr1D	83.492	315	46	4	2391	2702	79995332	79995021	3.400000e-74	289

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	TraesCS3B01G542300	chr3B	780298047	780300748	2701	True	4990.0	4990	100.000000	1	2702	1	chr3B.!!$R1	2701
1	TraesCS3B01G542300	chr3B	780337304	780339318	2014	True	1203.5	1895	89.801000	471	2391	2	chr3B.!!$R5	1920
2	TraesCS3B01G542300	chr3B	780307411	780308086	675	True	955.0	955	92.217000	2026	2702	1	chr3B.!!$R2	676
3	TraesCS3B01G542300	chr3B	780312360	780317373	5013	True	953.0	1844	89.759333	562	2391	3	chr3B.!!$R3	1829
4	TraesCS3B01G542300	chr3B	780322338	780332509	10171	True	841.2	1855	90.640800	562	2702	5	chr3B.!!$R4	2140
5	TraesCS3B01G542300	chr3D	583280631	583283166	2535	True	1794.5	2916	92.648500	4	2421	2	chr3D.!!$R4	2417
6	TraesCS3B01G542300	chr3D	583179651	583186288	6637	True	1628.0	2929	92.638667	4	2701	3	chr3D.!!$R2	2697
7	TraesCS3B01G542300	chr3D	583221199	583223263	2064	True	1337.5	2054	90.645500	471	2427	2	chr3D.!!$R3	1956
8	TraesCS3B01G542300	chrUn	352585812	352587472	1660	False	1065.0	1633	91.014500	810	2391	2	chrUn.!!$F1	1581
9	TraesCS3B01G542300	chr6A	34272182	34282541	10359	True	1258.5	1426	85.612500	442	1914	4	chr6A.!!$R3	1472
10	TraesCS3B01G542300	chr6A	34391693	34393068	1375	True	1046.0	1046	81.183000	500	1839	1	chr6A.!!$R1	1339
11	TraesCS3B01G542300	chr6B	62689925	62691238	1313	True	1066.0	1066	81.839000	489	1787	1	chr6B.!!$R1	1298

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
680	4735	0.242825	CCGTCAGACTAAACCGAGCA	59.757	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2024	12793	0.107066	TCGACCTGGCGTGTCCTATA	60.107	55.0	9.66	0.0	35.26	1.31	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
354	356	6.018589	AGTACGACTAAAAGGTAACAGGAC	57.981	41.667	0.00	0.00	41.41	3.85
367	369	5.587443	AGGTAACAGGACTGTACAAAAACAC	59.413	40.000	5.25	0.00	44.13	3.32
396	404	7.801716	AAAACTAGACACACATCAAAAGCTA	57.198	32.000	0.00	0.00	0.00	3.32
408	416	6.425114	CACATCAAAAGCTAGTCTGTGTAGTT	59.575	38.462	0.00	0.00	0.00	2.24
409	417	6.992715	ACATCAAAAGCTAGTCTGTGTAGTTT	59.007	34.615	0.00	0.00	0.00	2.66
410	418	8.148351	ACATCAAAAGCTAGTCTGTGTAGTTTA	58.852	33.333	0.00	0.00	0.00	2.01
440	448	3.701205	AATGGTCATGCTACTCACACA	57.299	42.857	0.00	0.00	0.00	3.72
498	531	2.497138	TCTTGTGCAGTGGATCTTGTG	58.503	47.619	0.00	0.00	0.00	3.33
522	555	0.324552	TGGCCTAAACATGCCAGCAT	60.325	50.000	3.32	0.00	37.08	3.79
582	4626	4.341235	GCCCACCAAGGAAAATACCTTATC	59.659	45.833	0.00	0.00	46.94	1.75
677	4732	0.599558	CCACCGTCAGACTAAACCGA	59.400	55.000	0.00	0.00	0.00	4.69
678	4733	1.402456	CCACCGTCAGACTAAACCGAG	60.402	57.143	0.00	0.00	0.00	4.63
680	4735	0.242825	CCGTCAGACTAAACCGAGCA	59.757	55.000	0.00	0.00	0.00	4.26
744	6777	1.556451	TGTGGTGACTCATCTCATGGG	59.444	52.381	0.00	0.00	36.61	4.00
768	6801	5.278266	GCAGTAGGCACAGAAAACAATGTAA	60.278	40.000	0.00	0.00	43.97	2.41
898	10852	7.545965	ACAGCTGTACACATCTTCTGTATAAAC	59.454	37.037	20.16	0.00	35.91	2.01
966	10921	1.337703	CTGCTTCTCCTCCTCTCATCG	59.662	57.143	0.00	0.00	0.00	3.84
972	10927	0.748367	TCCTCCTCTCATCGACCACG	60.748	60.000	0.00	0.00	41.26	4.94
1150	11105	0.322975	TCTCAGGAGTCTTGCAAGCC	59.677	55.000	21.99	16.62	0.00	4.35
1173	11128	5.278266	CCTCTACGATGGTCTTGAAGAGATC	60.278	48.000	0.00	0.00	36.61	2.75
1230	11185	0.324943	AGAGGAACGTGTTGGATGGG	59.675	55.000	0.00	0.00	0.00	4.00
1295	11250	0.243907	CAAGAGACCTTCGCCGAGAA	59.756	55.000	0.00	0.00	37.31	2.87
1321	11276	3.434739	GGTCATCATCCAAGAGCTCCAAT	60.435	47.826	10.93	0.00	0.00	3.16
1352	11307	2.054232	AAAGGAGATGATGCAGCTGG	57.946	50.000	17.12	0.00	26.98	4.85
1473	11431	5.453903	GCTATTGACCAAGGCAAGAGAGATA	60.454	44.000	8.94	0.00	36.87	1.98
1514	11472	2.600731	CACACTCCATCTCTTGTCGAC	58.399	52.381	9.11	9.11	0.00	4.20
1659	11617	4.096081	GCAGGAGATCTGTTCAGGAAATTG	59.904	45.833	0.00	0.00	45.08	2.32
1854	11836	6.290605	TGATCCATCTCAGATTTTGCGATAA	58.709	36.000	0.00	0.00	30.29	1.75
1914	11896	5.711506	TGCATGACAAGAGGAAATGTGTATT	59.288	36.000	0.00	0.00	0.00	1.89
2112	12898	4.247267	AGTTGCAAATGTTGTCCATCAG	57.753	40.909	0.00	0.00	31.75	2.90
2116	12902	4.143543	TGCAAATGTTGTCCATCAGAAGA	58.856	39.130	0.00	0.00	31.75	2.87
2227	13276	9.958180	TGTGATGGATAGATTAAGTGAAAAGAA	57.042	29.630	0.00	0.00	0.00	2.52
2348	13404	4.394300	GGGAGATGATTATTGGATTGAGCG	59.606	45.833	0.00	0.00	0.00	5.03
2365	13421	5.022282	TGAGCGTCATGGATTTATGAGAA	57.978	39.130	0.00	0.00	37.72	2.87
2416	13472	1.479323	TCGAAAAGGAGTATGACCCCG	59.521	52.381	0.00	0.00	0.00	5.73
2418	13474	0.255033	AAAAGGAGTATGACCCCGGC	59.745	55.000	0.00	0.00	0.00	6.13
2425	13484	0.034896	GTATGACCCCGGCCTGTATG	59.965	60.000	0.00	0.00	0.00	2.39
2439	13498	2.158711	CCTGTATGTGGGAGATGCATGT	60.159	50.000	2.46	0.00	0.00	3.21
2504	13563	2.754472	TCAATATGTCTGAATCCGCCG	58.246	47.619	0.00	0.00	0.00	6.46
2536	13595	2.959516	TGTGTCGCAACTTCTATCCAG	58.040	47.619	0.00	0.00	0.00	3.86
2563	13622	1.289160	AGGGATGCAGTAAGCCTGAA	58.711	50.000	0.00	0.00	44.49	3.02
2632	13691	1.337074	CCGAACCAAGCCACGTACTAA	60.337	52.381	0.00	0.00	0.00	2.24
2653	13712	3.810188	TGGGGCACAAACGGGTCA	61.810	61.111	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.935495	AGCCGTGTGGTGGTGCTG	62.935	66.667	0.00	0.00	37.67	4.41
13	14	2.857575	TATGCCAGACTGCACAGCCG	62.858	60.000	0.00	0.00	45.48	5.52
381	383	4.512944	ACACAGACTAGCTTTTGATGTGTG	59.487	41.667	17.95	13.72	45.71	3.82
388	390	9.856488	TCTATAAACTACACAGACTAGCTTTTG	57.144	33.333	0.00	0.00	0.00	2.44
410	418	8.819845	TGAGTAGCATGACCATTTGATATCTAT	58.180	33.333	3.98	0.00	0.00	1.98
473	506	3.341823	AGATCCACTGCACAAGATTCAC	58.658	45.455	0.00	0.00	0.00	3.18
498	531	1.800681	GCATGTTTAGGCCACGGAC	59.199	57.895	5.01	0.00	0.00	4.79
582	4626	5.062558	GCATTTAGCTGTAACATGCCTTTTG	59.937	40.000	0.00	0.00	41.15	2.44
677	4732	4.992951	GCAAGAACCAATGAAAAAGATGCT	59.007	37.500	0.00	0.00	0.00	3.79
678	4733	4.992951	AGCAAGAACCAATGAAAAAGATGC	59.007	37.500	0.00	0.00	0.00	3.91
680	4735	4.992951	GCAGCAAGAACCAATGAAAAAGAT	59.007	37.500	0.00	0.00	0.00	2.40
744	6777	3.004734	ACATTGTTTTCTGTGCCTACTGC	59.995	43.478	0.00	0.00	41.77	4.40
768	6801	8.507249	GCAACACTAAAGTCTTCTCATGTTTAT	58.493	33.333	0.00	0.00	0.00	1.40
966	10921	1.828832	CTTATCGCTGTCTCGTGGTC	58.171	55.000	0.00	0.00	0.00	4.02
1150	11105	5.298026	TGATCTCTTCAAGACCATCGTAGAG	59.702	44.000	0.00	0.00	36.92	2.43
1219	11174	0.918983	TCCATCTCCCCATCCAACAC	59.081	55.000	0.00	0.00	0.00	3.32
1321	11276	5.762179	TCATCTCCTTTTCTTAGAGCCAA	57.238	39.130	0.00	0.00	0.00	4.52
1352	11307	2.777832	AGACTGGATCTTGGCTTGAC	57.222	50.000	0.00	0.00	31.62	3.18
1473	11431	2.170187	GGACTCCAACAGAGAGATGCAT	59.830	50.000	0.00	0.00	46.50	3.96
1514	11472	2.223611	TGCTTTGGCATTTCAATTTGCG	59.776	40.909	0.00	0.00	44.28	4.85
1659	11617	4.344359	AAGAGAAACTCTGTTCTGGACC	57.656	45.455	1.97	0.00	40.28	4.46
1752	11713	2.783828	ACTGTATCAAGATCGGCTCG	57.216	50.000	0.00	0.00	0.00	5.03
1813	11794	5.901552	TGGATCAAAACTTTGGTCTTTGTC	58.098	37.500	13.64	0.14	45.36	3.18
1854	11836	4.870021	AGCCCCAAGAGACTTTATCAAT	57.130	40.909	0.00	0.00	0.00	2.57
1863	11845	2.026822	TCATCAGAAAGCCCCAAGAGAC	60.027	50.000	0.00	0.00	0.00	3.36
1968	12649	8.289939	AGATTGTGTGCTAATCAAGAATCATT	57.710	30.769	0.00	0.00	37.08	2.57
2007	12776	8.202811	GTGTCCTATATATGCATGATCAGTGAT	58.797	37.037	10.16	4.98	0.00	3.06
2024	12793	0.107066	TCGACCTGGCGTGTCCTATA	60.107	55.000	9.66	0.00	35.26	1.31
2163	13050	8.652810	ATTTTATCAGCAATGCAAACTTATCC	57.347	30.769	8.35	0.00	0.00	2.59
2282	13336	3.689347	TGCAGAAGAAACCAGCATACAT	58.311	40.909	0.00	0.00	0.00	2.29
2416	13472	0.536006	GCATCTCCCACATACAGGCC	60.536	60.000	0.00	0.00	0.00	5.19
2418	13474	2.158711	ACATGCATCTCCCACATACAGG	60.159	50.000	0.00	0.00	0.00	4.00
2425	13484	0.181114	TGGCTACATGCATCTCCCAC	59.819	55.000	0.00	0.00	45.15	4.61
2504	13563	3.876300	GACACATGTCGCCAGGAC	58.124	61.111	0.00	0.00	46.27	3.85
2528	13587	4.202398	GCATCCCTTCATCAACTGGATAGA	60.202	45.833	0.00	0.00	34.12	1.98
2536	13595	3.065925	GCTTACTGCATCCCTTCATCAAC	59.934	47.826	0.00	0.00	42.31	3.18
2563	13622	1.006758	TGAGAGGTCTGGGTATTCGGT	59.993	52.381	0.00	0.00	0.00	4.69
2653	13712	1.893786	GACCCATGAGAGTGCGTCT	59.106	57.895	0.00	0.00	38.71	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.