AutoCloner

Multiple sequence alignment - TraesCS2B01G140600

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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	TraesCS2B01G140600	chr2B	100.000	1855	0	0	971	2825	107118499	107116645	0.000000e+00	3426.0
1	TraesCS2B01G140600	chr2B	100.000	590	0	0	1	590	107119469	107118880	0.000000e+00	1090.0
2	TraesCS2B01G140600	chr2B	80.735	789	126	15	1606	2380	107525638	107526414	2.420000e-165	592.0
3	TraesCS2B01G140600	chr2B	92.245	245	19	0	131	375	672340567	672340323	5.790000e-92	348.0
4	TraesCS2B01G140600	chr2B	90.141	213	21	0	80	292	672340763	672340551	7.710000e-71	278.0
5	TraesCS2B01G140600	chr2B	81.933	238	30	8	2330	2564	107500216	107500443	3.720000e-44	189.0
6	TraesCS2B01G140600	chr2B	81.092	238	36	6	2339	2574	107526417	107526647	6.220000e-42	182.0
7	TraesCS2B01G140600	chr2B	79.638	221	44	1	974	1193	107525073	107525293	1.050000e-34	158.0
8	TraesCS2B01G140600	chr2B	85.443	158	4	2	441	590	672340062	672339916	2.270000e-31	147.0
9	TraesCS2B01G140600	chr2B	90.411	73	7	0	2633	2705	107526657	107526729	2.320000e-16	97.1
10	TraesCS2B01G140600	chr2D	94.011	1870	85	14	977	2825	70821638	70819775	0.000000e+00	2808.0
11	TraesCS2B01G140600	chr2D	81.449	787	123	12	1606	2380	71204578	71205353	8.590000e-175	623.0
12	TraesCS2B01G140600	chr2D	80.420	715	106	18	1681	2380	71258549	71259244	5.400000e-142	514.0
13	TraesCS2B01G140600	chr2D	80.252	714	109	16	1681	2380	71384705	71385400	2.510000e-140	508.0
14	TraesCS2B01G140600	chr2D	82.353	238	31	8	2339	2574	71205356	71205584	2.220000e-46	196.0
15	TraesCS2B01G140600	chr2D	84.184	196	24	6	2339	2531	71385403	71385594	1.730000e-42	183.0
16	TraesCS2B01G140600	chr2D	83.673	196	25	6	2339	2531	71259247	71259438	8.040000e-41	178.0
17	TraesCS2B01G140600	chr2D	80.090	221	43	1	974	1193	71204007	71204227	2.250000e-36	163.0
18	TraesCS2B01G140600	chr2A	94.086	1285	60	5	974	2253	70183997	70182724	0.000000e+00	1938.0
19	TraesCS2B01G140600	chr2A	95.510	490	21	1	2336	2825	70182725	70182237	0.000000e+00	782.0
20	TraesCS2B01G140600	chr2A	82.273	220	31	5	974	1189	70186672	70186887	1.730000e-42	183.0
21	TraesCS2B01G140600	chr2A	79.268	246	30	11	2330	2564	70188011	70188246	4.870000e-33	152.0
22	TraesCS2B01G140600	chr2A	84.127	126	18	2	60	185	718887735	718887612	1.370000e-23	121.0
23	TraesCS2B01G140600	chr4A	96.800	375	12	0	1	375	712881922	712882296	6.640000e-176	627.0
24	TraesCS2B01G140600	chr4A	99.213	127	1	0	441	567	712882496	712882622	2.190000e-56	230.0
25	TraesCS2B01G140600	chr4A	96.250	80	3	0	365	444	712882328	712882407	6.350000e-27	132.0
26	TraesCS2B01G140600	chr4B	96.533	375	13	0	1	375	139108927	139108553	3.090000e-174	621.0
27	TraesCS2B01G140600	chr4B	98.750	80	1	0	365	444	139108521	139108442	2.930000e-30	143.0
28	TraesCS2B01G140600	chr3B	96.533	375	13	0	1	375	51952682	51953056	3.090000e-174	621.0
29	TraesCS2B01G140600	chr3B	94.118	153	9	0	223	375	612294783	612294935	1.690000e-57	233.0
30	TraesCS2B01G140600	chr3B	96.552	87	2	1	365	451	51953088	51953173	2.930000e-30	143.0
31	TraesCS2B01G140600	chr3B	97.826	46	1	0	169	214	612294436	612294481	2.330000e-11	80.5
32	TraesCS2B01G140600	chr7D	93.007	143	9	1	60	202	55445564	55445705	1.030000e-49	207.0
33	TraesCS2B01G140600	chr7D	100.000	57	0	0	215	271	55446146	55446202	3.850000e-19	106.0
34	TraesCS2B01G140600	chr1D	98.113	106	2	0	270	375	258554286	258554181	4.810000e-43	185.0
35	TraesCS2B01G140600	chr1D	96.429	56	1	1	390	444	258554001	258553946	1.080000e-14	91.6
36	TraesCS2B01G140600	chr1B	98.113	106	2	0	270	375	354239608	354239713	4.810000e-43	185.0
37	TraesCS2B01G140600	chr1B	94.643	56	2	1	390	444	354239893	354239948	5.010000e-13	86.1
38	TraesCS2B01G140600	chrUn	91.729	133	10	1	70	202	38166958	38166827	1.730000e-42	183.0
39	TraesCS2B01G140600	chr1A	97.170	106	3	0	270	375	342434016	342434121	2.240000e-41	180.0
40	TraesCS2B01G140600	chr1A	94.643	56	2	1	390	444	342434301	342434356	5.010000e-13	86.1
41	TraesCS2B01G140600	chr6A	88.722	133	14	1	70	202	536911287	536911418	8.100000e-36	161.0

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	TraesCS2B01G140600	chr2B	107116645	107119469	2824	True	2258.000000	3426	100.000000	1	2825	2	chr2B.!!$R1	2824
1	TraesCS2B01G140600	chr2B	672339916	672340763	847	True	257.666667	348	89.276333	80	590	3	chr2B.!!$R2	510
2	TraesCS2B01G140600	chr2B	107525073	107526729	1656	False	257.275000	592	82.969000	974	2705	4	chr2B.!!$F2	1731
3	TraesCS2B01G140600	chr2D	70819775	70821638	1863	True	2808.000000	2808	94.011000	977	2825	1	chr2D.!!$R1	1848
4	TraesCS2B01G140600	chr2D	71258549	71259438	889	False	346.000000	514	82.046500	1681	2531	2	chr2D.!!$F2	850
5	TraesCS2B01G140600	chr2D	71384705	71385594	889	False	345.500000	508	82.218000	1681	2531	2	chr2D.!!$F3	850
6	TraesCS2B01G140600	chr2D	71204007	71205584	1577	False	327.333333	623	81.297333	974	2574	3	chr2D.!!$F1	1600
7	TraesCS2B01G140600	chr2A	70182237	70183997	1760	True	1360.000000	1938	94.798000	974	2825	2	chr2A.!!$R2	1851
8	TraesCS2B01G140600	chr4A	712881922	712882622	700	False	329.666667	627	97.421000	1	567	3	chr4A.!!$F1	566

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
382	528	0.106967	GGCCATGTCCCTCTTCTTCC	60.107	60.0	0.0	0.0	0.0	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2140	2534	1.199789	TGATTGGTCAAACAGCGATGC	59.8	47.619	0.0	0.0	0.0	3.91	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	2.178890	GCTCTCTCTTGCATGCCCG	61.179	63.158	16.68	6.08	0.00	6.13
232	378	4.988598	CCACCTTGTCAGCGCGGT	62.989	66.667	4.23	4.23	0.00	5.68
375	521	1.524621	CATGACGGCCATGTCCCTC	60.525	63.158	2.24	0.00	45.83	4.30
377	523	1.274703	ATGACGGCCATGTCCCTCTT	61.275	55.000	2.24	0.00	38.11	2.85
378	524	1.153349	GACGGCCATGTCCCTCTTC	60.153	63.158	2.24	0.00	32.61	2.87
380	526	1.201429	ACGGCCATGTCCCTCTTCTT	61.201	55.000	2.24	0.00	0.00	2.52
382	528	0.106967	GGCCATGTCCCTCTTCTTCC	60.107	60.000	0.00	0.00	0.00	3.46
383	529	0.462759	GCCATGTCCCTCTTCTTCCG	60.463	60.000	0.00	0.00	0.00	4.30
384	530	0.179000	CCATGTCCCTCTTCTTCCGG	59.821	60.000	0.00	0.00	0.00	5.14
385	531	1.195115	CATGTCCCTCTTCTTCCGGA	58.805	55.000	0.00	0.00	0.00	5.14
386	532	1.137872	CATGTCCCTCTTCTTCCGGAG	59.862	57.143	3.34	0.00	0.00	4.63
449	595	2.499205	CGCTCTTGCCGGGATGTA	59.501	61.111	2.18	0.00	35.36	2.29
450	596	1.883084	CGCTCTTGCCGGGATGTAC	60.883	63.158	2.18	0.00	35.36	2.90
451	597	1.523938	GCTCTTGCCGGGATGTACC	60.524	63.158	2.18	0.00	38.08	3.34
452	598	1.972660	GCTCTTGCCGGGATGTACCT	61.973	60.000	2.18	0.00	38.98	3.08
453	599	0.179073	CTCTTGCCGGGATGTACCTG	60.179	60.000	2.18	0.00	44.27	4.00
459	605	2.900273	GGGATGTACCTGAGCGCA	59.100	61.111	11.47	0.00	38.98	6.09
460	606	1.521681	GGGATGTACCTGAGCGCAC	60.522	63.158	11.47	3.13	38.98	5.34
461	607	1.521681	GGATGTACCTGAGCGCACC	60.522	63.158	11.47	0.50	35.41	5.01
462	608	1.521681	GATGTACCTGAGCGCACCC	60.522	63.158	11.47	0.00	0.00	4.61
463	609	3.371097	ATGTACCTGAGCGCACCCG	62.371	63.158	11.47	0.00	37.57	5.28
464	610	4.814294	GTACCTGAGCGCACCCGG	62.814	72.222	11.47	9.53	34.32	5.73
533	679	3.732849	GTGGGGCTTGGGAGGGAG	61.733	72.222	0.00	0.00	0.00	4.30
536	682	4.760220	GGGCTTGGGAGGGAGGGA	62.760	72.222	0.00	0.00	0.00	4.20
537	683	3.093172	GGCTTGGGAGGGAGGGAG	61.093	72.222	0.00	0.00	0.00	4.30
538	684	2.041265	GCTTGGGAGGGAGGGAGA	59.959	66.667	0.00	0.00	0.00	3.71
539	685	2.069430	GCTTGGGAGGGAGGGAGAG	61.069	68.421	0.00	0.00	0.00	3.20
540	686	2.041265	TTGGGAGGGAGGGAGAGC	59.959	66.667	0.00	0.00	0.00	4.09
541	687	3.984186	TTGGGAGGGAGGGAGAGCG	62.984	68.421	0.00	0.00	0.00	5.03
1106	1253	1.451387	GGATCGTTTGGGTCGGCAT	60.451	57.895	0.00	0.00	0.00	4.40
1170	1323	4.368543	GTCGAGGGTTCCGCCGTT	62.369	66.667	0.00	0.00	38.44	4.44
1519	1772	8.981724	TTAAGTGCATATAATATGACCTCGTC	57.018	34.615	0.00	0.00	0.00	4.20
1589	1843	1.003718	AGCCCCCGAAAACTCTTCG	60.004	57.895	0.00	0.00	41.21	3.79
1816	2187	2.527624	TGCTGAGGCAGTGGAGGT	60.528	61.111	0.00	0.00	44.28	3.85
1888	2266	2.166459	TCTCTGTTCTCCTATTGGCGTG	59.834	50.000	0.00	0.00	0.00	5.34
1898	2276	7.004555	TCTCCTATTGGCGTGACATTATATT	57.995	36.000	0.00	0.00	0.00	1.28
1899	2277	7.097192	TCTCCTATTGGCGTGACATTATATTC	58.903	38.462	0.00	0.00	0.00	1.75
2042	2426	4.555348	TCCAAACCATTTTGTCGTACAC	57.445	40.909	0.00	0.00	40.61	2.90
2140	2534	6.202188	AGTTAACAGTGATCTTGTTTGGTACG	59.798	38.462	17.33	0.00	0.00	3.67
2142	2536	2.805671	CAGTGATCTTGTTTGGTACGCA	59.194	45.455	0.00	0.00	0.00	5.24
2172	2566	5.651612	TTGACCAATCAGATCCATATGGT	57.348	39.130	21.28	8.97	43.50	3.55
2200	2594	5.925509	TCATTAGTGGAAACCTAGTATGCC	58.074	41.667	0.00	0.00	0.00	4.40
2240	2634	3.609853	TCCCATGCTTATTATGATCGGC	58.390	45.455	0.00	0.00	0.00	5.54
2260	2661	3.448660	GGCCAGCTTTGAATTTATCCACT	59.551	43.478	0.00	0.00	0.00	4.00
2292	2695	4.388577	AAGTGGTAGGCCTCAAATTTCT	57.611	40.909	9.68	0.00	35.27	2.52
2309	2712	0.472352	TCTAAGGGTTGGGTCGTGGT	60.472	55.000	0.00	0.00	0.00	4.16
2310	2713	1.203162	TCTAAGGGTTGGGTCGTGGTA	60.203	52.381	0.00	0.00	0.00	3.25
2358	2761	8.641499	TCTTGTTATTTAACTGCCTTTGTTTG	57.359	30.769	2.45	0.00	37.12	2.93
2531	2978	5.347342	TGACATTTTTGTCGAAGTGCATTT	58.653	33.333	0.00	0.00	41.43	2.32
2760	3207	2.816087	CACTGTTGGGGAGTCAATTCAG	59.184	50.000	0.00	0.00	31.29	3.02
2769	3216	5.073144	TGGGGAGTCAATTCAGTAAAGACTT	59.927	40.000	0.00	0.00	39.47	3.01
2773	3220	7.660208	GGGAGTCAATTCAGTAAAGACTTAACA	59.340	37.037	0.00	0.00	39.47	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	3.137637	GAGAGCAGAGGAGCGAGGC	62.138	68.421	0.00	0.00	40.15	4.70
327	473	2.668632	GAGTTCGACCCCATGGCA	59.331	61.111	6.09	0.00	33.59	4.92
375	521	2.269241	GGCACCCTCCGGAAGAAG	59.731	66.667	5.23	0.00	0.00	2.85
431	577	3.733344	TACATCCCGGCAAGAGCGC	62.733	63.158	0.00	0.00	43.41	5.92
432	578	1.883084	GTACATCCCGGCAAGAGCG	60.883	63.158	0.00	0.00	43.41	5.03
433	579	1.523938	GGTACATCCCGGCAAGAGC	60.524	63.158	0.00	0.00	41.10	4.09
434	580	0.179073	CAGGTACATCCCGGCAAGAG	60.179	60.000	0.00	0.00	36.75	2.85
435	581	0.616395	TCAGGTACATCCCGGCAAGA	60.616	55.000	0.00	0.00	36.75	3.02
436	582	0.179073	CTCAGGTACATCCCGGCAAG	60.179	60.000	0.00	0.00	36.75	4.01
437	583	1.904771	CTCAGGTACATCCCGGCAA	59.095	57.895	0.00	0.00	36.75	4.52
438	584	2.731571	GCTCAGGTACATCCCGGCA	61.732	63.158	0.00	0.00	36.75	5.69
439	585	2.109181	GCTCAGGTACATCCCGGC	59.891	66.667	0.00	0.00	36.75	6.13
440	586	2.417516	CGCTCAGGTACATCCCGG	59.582	66.667	0.00	0.00	36.75	5.73
441	587	2.279517	GCGCTCAGGTACATCCCG	60.280	66.667	0.00	0.00	36.75	5.14
442	588	1.521681	GTGCGCTCAGGTACATCCC	60.522	63.158	9.73	0.00	36.75	3.85
443	589	1.521681	GGTGCGCTCAGGTACATCC	60.522	63.158	9.73	0.00	0.00	3.51
444	590	1.521681	GGGTGCGCTCAGGTACATC	60.522	63.158	9.73	0.00	0.00	3.06
445	591	2.584608	GGGTGCGCTCAGGTACAT	59.415	61.111	9.73	0.00	0.00	2.29
446	592	4.063967	CGGGTGCGCTCAGGTACA	62.064	66.667	9.73	0.00	0.00	2.90
447	593	4.814294	CCGGGTGCGCTCAGGTAC	62.814	72.222	9.73	0.00	0.00	3.34
516	662	3.732849	CTCCCTCCCAAGCCCCAC	61.733	72.222	0.00	0.00	0.00	4.61
519	665	4.760220	TCCCTCCCTCCCAAGCCC	62.760	72.222	0.00	0.00	0.00	5.19
520	666	3.093172	CTCCCTCCCTCCCAAGCC	61.093	72.222	0.00	0.00	0.00	4.35
521	667	2.041265	TCTCCCTCCCTCCCAAGC	59.959	66.667	0.00	0.00	0.00	4.01
522	668	2.069430	GCTCTCCCTCCCTCCCAAG	61.069	68.421	0.00	0.00	0.00	3.61
523	669	2.041265	GCTCTCCCTCCCTCCCAA	59.959	66.667	0.00	0.00	0.00	4.12
524	670	4.465446	CGCTCTCCCTCCCTCCCA	62.465	72.222	0.00	0.00	0.00	4.37
971	1117	3.154473	CCTAGGCGCAGGTGGCTA	61.154	66.667	10.83	14.31	43.83	3.93
1296	1524	1.353694	AGGCACAGAGGAGCATTTTCT	59.646	47.619	0.00	0.00	31.64	2.52
1304	1532	2.951642	TGTTGAAAAAGGCACAGAGGAG	59.048	45.455	0.00	0.00	0.00	3.69
1557	1811	2.551071	CGGGGGCTCTTTGATATCCTTC	60.551	54.545	0.00	0.00	0.00	3.46
1589	1843	2.117156	ATCATCTGCGCAACCTGGC	61.117	57.895	13.05	0.00	0.00	4.85
1816	2187	7.323420	CACATCCACATAACTCTCTACTTCAA	58.677	38.462	0.00	0.00	0.00	2.69
1898	2276	9.138596	ACCAAAAACAGTAGGCTTATAAAAAGA	57.861	29.630	0.00	0.00	0.00	2.52
1899	2277	9.758651	AACCAAAAACAGTAGGCTTATAAAAAG	57.241	29.630	0.00	0.00	0.00	2.27
1920	2301	7.893302	AGTTATCAGGATTATTCACCAAACCAA	59.107	33.333	0.00	0.00	0.00	3.67
1922	2303	7.881775	AGTTATCAGGATTATTCACCAAACC	57.118	36.000	0.00	0.00	0.00	3.27
2042	2426	4.286291	ACTTTCTTGTAGGTCTAACTGGGG	59.714	45.833	0.00	0.00	0.00	4.96
2123	2515	3.483574	CGATGCGTACCAAACAAGATCAC	60.484	47.826	0.00	0.00	0.00	3.06
2140	2534	1.199789	TGATTGGTCAAACAGCGATGC	59.800	47.619	0.00	0.00	0.00	3.91
2142	2536	3.057969	TCTGATTGGTCAAACAGCGAT	57.942	42.857	13.77	0.00	39.93	4.58
2200	2594	3.944015	GGGAATGACTGAACATGGAGAAG	59.056	47.826	0.00	0.00	0.00	2.85
2240	2634	5.902613	TCAGTGGATAAATTCAAAGCTGG	57.097	39.130	0.00	0.00	0.00	4.85
2292	2695	1.955451	ATACCACGACCCAACCCTTA	58.045	50.000	0.00	0.00	0.00	2.69
2345	2748	2.757868	TGTAACAGCAAACAAAGGCAGT	59.242	40.909	0.00	0.00	0.00	4.40
2419	2866	5.057843	ACCATCATGGATTGCTTGAGTAT	57.942	39.130	11.90	0.00	40.96	2.12
2531	2978	7.094508	ACTACAACATTGACATGTGTTTTCA	57.905	32.000	1.15	0.00	43.34	2.69
2760	3207	9.269453	AGTGGTATTTCAGTGTTAAGTCTTTAC	57.731	33.333	0.00	0.00	0.00	2.01
2769	3216	6.693466	TCGATGAAGTGGTATTTCAGTGTTA	58.307	36.000	0.00	0.00	37.91	2.41
2773	3220	7.504924	TTTTTCGATGAAGTGGTATTTCAGT	57.495	32.000	0.00	0.00	37.91	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.