AutoCloner

Multiple sequence alignment - TraesCS6B01G061700

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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	TraesCS6B01G061700	chr6B	100.000	3173	0	0	1	3173	41411380	41408208	0.000000e+00	5860.0
1	TraesCS6B01G061700	chr6B	78.174	1205	235	21	1053	2237	14311180	14312376	0.000000e+00	743.0
2	TraesCS6B01G061700	chr6B	77.089	1209	251	20	1045	2237	13934027	13932829	0.000000e+00	675.0
3	TraesCS6B01G061700	chr6B	75.376	1397	287	40	997	2350	32301892	32300510	3.480000e-174	621.0
4	TraesCS6B01G061700	chr6B	76.836	1144	224	35	1043	2164	54422214	54421090	9.730000e-170	606.0
5	TraesCS6B01G061700	chr6B	76.302	1114	242	19	997	2096	28747998	28746893	2.740000e-160	575.0
6	TraesCS6B01G061700	chr6B	76.302	1114	242	19	997	2096	28753364	28752259	2.740000e-160	575.0
7	TraesCS6B01G061700	chr6B	75.770	1201	241	32	994	2179	16267385	16268550	7.690000e-156	560.0
8	TraesCS6B01G061700	chrUn	96.200	1658	55	4	1523	3173	71528349	71530005	0.000000e+00	2706.0
9	TraesCS6B01G061700	chrUn	96.200	1658	55	4	1523	3173	245547697	245546041	0.000000e+00	2706.0
10	TraesCS6B01G061700	chrUn	96.200	1658	55	4	1523	3173	280860581	280858925	0.000000e+00	2706.0
11	TraesCS6B01G061700	chrUn	89.094	651	62	5	880	1521	300093612	300092962	0.000000e+00	800.0
12	TraesCS6B01G061700	chrUn	87.191	648	66	12	880	1521	71525893	71526529	0.000000e+00	721.0
13	TraesCS6B01G061700	chrUn	76.302	1114	242	19	997	2096	76387392	76386287	2.740000e-160	575.0
14	TraesCS6B01G061700	chrUn	91.262	206	12	4	880	1079	310991526	310991321	3.120000e-70	276.0
15	TraesCS6B01G061700	chr5B	94.417	824	40	6	61	880	606882268	606883089	0.000000e+00	1262.0
16	TraesCS6B01G061700	chr5B	77.102	1201	244	25	997	2179	556628242	556627055	0.000000e+00	665.0
17	TraesCS6B01G061700	chr5B	89.286	56	2	3	845	897	539435631	539435577	2.040000e-07	67.6
18	TraesCS6B01G061700	chr2B	93.373	830	39	9	61	880	23696936	23696113	0.000000e+00	1214.0
19	TraesCS6B01G061700	chr2B	77.561	1230	257	18	992	2212	709426177	709424958	0.000000e+00	725.0
20	TraesCS6B01G061700	chr2B	97.297	37	1	0	844	880	53715196	53715160	2.640000e-06	63.9
21	TraesCS6B01G061700	chr5A	87.654	729	58	18	61	767	488036618	488037336	0.000000e+00	819.0
22	TraesCS6B01G061700	chr1A	87.260	730	60	17	61	766	27205651	27204931	0.000000e+00	802.0
23	TraesCS6B01G061700	chr6D	78.502	1228	248	16	992	2212	8967576	8968794	0.000000e+00	791.0
24	TraesCS6B01G061700	chr6D	75.605	1488	302	44	974	2430	7885724	7887181	0.000000e+00	680.0
25	TraesCS6B01G061700	chr2A	86.320	731	66	18	61	767	306142710	306141990	0.000000e+00	765.0
26	TraesCS6B01G061700	chr7B	94.567	497	20	3	61	555	592751870	592751379	0.000000e+00	761.0
27	TraesCS6B01G061700	chr7B	92.447	331	23	2	549	878	592742857	592742528	3.700000e-129	472.0
28	TraesCS6B01G061700	chr4B	84.321	759	82	18	58	801	158721910	158722646	0.000000e+00	708.0
29	TraesCS6B01G061700	chr2D	100.000	84	0	0	61	144	2036061	2036144	4.240000e-34	156.0
30	TraesCS6B01G061700	chr3B	96.364	55	1	1	58	111	703901334	703901280	4.360000e-14	89.8
31	TraesCS6B01G061700	chr4D	84.810	79	8	3	504	582	218125027	218125101	3.390000e-10	76.8
32	TraesCS6B01G061700	chr7A	97.297	37	1	0	844	880	226567338	226567302	2.640000e-06	63.9

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	TraesCS6B01G061700	chr6B	41408208	41411380	3172	True	5860.0	5860	100.0000	1	3173	1	chr6B.!!$R5	3172
1	TraesCS6B01G061700	chr6B	14311180	14312376	1196	False	743.0	743	78.1740	1053	2237	1	chr6B.!!$F1	1184
2	TraesCS6B01G061700	chr6B	13932829	13934027	1198	True	675.0	675	77.0890	1045	2237	1	chr6B.!!$R1	1192
3	TraesCS6B01G061700	chr6B	32300510	32301892	1382	True	621.0	621	75.3760	997	2350	1	chr6B.!!$R4	1353
4	TraesCS6B01G061700	chr6B	54421090	54422214	1124	True	606.0	606	76.8360	1043	2164	1	chr6B.!!$R6	1121
5	TraesCS6B01G061700	chr6B	28746893	28747998	1105	True	575.0	575	76.3020	997	2096	1	chr6B.!!$R2	1099
6	TraesCS6B01G061700	chr6B	28752259	28753364	1105	True	575.0	575	76.3020	997	2096	1	chr6B.!!$R3	1099
7	TraesCS6B01G061700	chr6B	16267385	16268550	1165	False	560.0	560	75.7700	994	2179	1	chr6B.!!$F2	1185
8	TraesCS6B01G061700	chrUn	245546041	245547697	1656	True	2706.0	2706	96.2000	1523	3173	1	chrUn.!!$R2	1650
9	TraesCS6B01G061700	chrUn	280858925	280860581	1656	True	2706.0	2706	96.2000	1523	3173	1	chrUn.!!$R3	1650
10	TraesCS6B01G061700	chrUn	71525893	71530005	4112	False	1713.5	2706	91.6955	880	3173	2	chrUn.!!$F1	2293
11	TraesCS6B01G061700	chrUn	300092962	300093612	650	True	800.0	800	89.0940	880	1521	1	chrUn.!!$R4	641
12	TraesCS6B01G061700	chrUn	76386287	76387392	1105	True	575.0	575	76.3020	997	2096	1	chrUn.!!$R1	1099
13	TraesCS6B01G061700	chr5B	606882268	606883089	821	False	1262.0	1262	94.4170	61	880	1	chr5B.!!$F1	819
14	TraesCS6B01G061700	chr5B	556627055	556628242	1187	True	665.0	665	77.1020	997	2179	1	chr5B.!!$R2	1182
15	TraesCS6B01G061700	chr2B	23696113	23696936	823	True	1214.0	1214	93.3730	61	880	1	chr2B.!!$R1	819
16	TraesCS6B01G061700	chr2B	709424958	709426177	1219	True	725.0	725	77.5610	992	2212	1	chr2B.!!$R3	1220
17	TraesCS6B01G061700	chr5A	488036618	488037336	718	False	819.0	819	87.6540	61	767	1	chr5A.!!$F1	706
18	TraesCS6B01G061700	chr1A	27204931	27205651	720	True	802.0	802	87.2600	61	766	1	chr1A.!!$R1	705
19	TraesCS6B01G061700	chr6D	8967576	8968794	1218	False	791.0	791	78.5020	992	2212	1	chr6D.!!$F2	1220
20	TraesCS6B01G061700	chr6D	7885724	7887181	1457	False	680.0	680	75.6050	974	2430	1	chr6D.!!$F1	1456
21	TraesCS6B01G061700	chr2A	306141990	306142710	720	True	765.0	765	86.3200	61	767	1	chr2A.!!$R1	706
22	TraesCS6B01G061700	chr4B	158721910	158722646	736	False	708.0	708	84.3210	58	801	1	chr4B.!!$F1	743

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
782	811	1.229177	GGGGGTTGGTTTGGCTCAT	60.229	57.895	0.0	0.0	0.0	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2179	4058	1.002468	GCTGCACCACACACAAGTTAG	60.002	52.381	0.0	0.0	0.0	2.34	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
50	51	9.898152	TGACATATTTAATACCACATCACAGAA	57.102	29.630	0.00	0.00	0.00	3.02
57	58	9.733556	TTTAATACCACATCACAGAAATGTACT	57.266	29.630	0.00	0.00	35.62	2.73
58	59	7.849804	AATACCACATCACAGAAATGTACTC	57.150	36.000	0.00	0.00	35.62	2.59
59	60	4.245660	ACCACATCACAGAAATGTACTCG	58.754	43.478	0.00	0.00	35.62	4.18
254	259	5.607119	TCTTCTTTTCTGGCGATTGTTAC	57.393	39.130	0.00	0.00	0.00	2.50
295	311	7.165485	TCACACACTTTGTAGGCAATATAACT	58.835	34.615	0.00	0.00	35.67	2.24
693	722	5.077134	AGGAGCATTTTTCCATTAGTTGC	57.923	39.130	0.00	0.00	37.18	4.17
715	744	6.973843	TGCATGAATTGGATTCTATAGTTGC	58.026	36.000	0.00	0.00	39.96	4.17
733	762	1.251251	GCTGGTTGCACTCTCCATTT	58.749	50.000	0.00	0.00	42.31	2.32
782	811	1.229177	GGGGGTTGGTTTGGCTCAT	60.229	57.895	0.00	0.00	0.00	2.90
818	851	6.851222	TTGTTTTTGCAAGACTTGTTTCAA	57.149	29.167	16.39	9.39	0.00	2.69
899	932	9.955208	AACTAGTTAGGGTTAAAAACAAAATCG	57.045	29.630	6.26	0.00	0.00	3.34
900	933	9.123902	ACTAGTTAGGGTTAAAAACAAAATCGT	57.876	29.630	0.00	0.00	0.00	3.73
911	944	4.795970	AACAAAATCGTCACTCTGTGTC	57.204	40.909	0.00	0.00	34.79	3.67
926	959	2.360475	GTCCAACTCAGCCCAGCC	60.360	66.667	0.00	0.00	0.00	4.85
942	975	4.845580	CCCAGCCTAGTGCAGCCG	62.846	72.222	6.07	0.00	44.83	5.52
943	976	3.774528	CCAGCCTAGTGCAGCCGA	61.775	66.667	6.07	0.00	44.83	5.54
945	978	3.465403	AGCCTAGTGCAGCCGAGG	61.465	66.667	6.07	5.89	44.83	4.63
1244	1301	3.441290	CGTCCTCGCCTTCCTCGT	61.441	66.667	0.00	0.00	0.00	4.18
1248	1305	4.194720	CTCGCCTTCCTCGTCGGG	62.195	72.222	0.00	0.00	0.00	5.14
1308	1365	4.597507	TCCAAGAATCCCAAGTTACTCTGT	59.402	41.667	0.00	0.00	0.00	3.41
1401	1458	2.740055	CGCTTTGCCTCGCTCAGT	60.740	61.111	0.00	0.00	0.00	3.41
1496	1553	4.851179	CCTCCGGGCGGTAAAGGC	62.851	72.222	0.00	0.00	36.47	4.35
1552	3427	1.429148	GGTCAAGCCTAATGTCGCGG	61.429	60.000	6.13	0.00	0.00	6.46
1573	3448	2.842462	TGCGGGAGTGCGGGATAT	60.842	61.111	0.00	0.00	37.81	1.63
1592	3467	1.229975	TGTGCTGGCGACATTGTCTG	61.230	55.000	14.54	9.22	41.51	3.51
1627	3502	2.569404	GTGAAGAGGATTCTGACCACCT	59.431	50.000	0.00	0.00	32.79	4.00
1906	3781	2.349580	GGTTTAGAACCGGCGTACATTC	59.650	50.000	6.01	4.27	42.62	2.67
1966	3845	1.113517	GCTCAGACCCCGCTACCATA	61.114	60.000	0.00	0.00	0.00	2.74
2062	3941	6.607198	TGAGAAGGTTTTCATGGAAAAGTTCT	59.393	34.615	18.39	18.39	42.41	3.01
2179	4058	3.220674	AGAAGGGGCTATGAGAATTGC	57.779	47.619	0.00	0.00	0.00	3.56
2198	4077	1.002468	GCTAACTTGTGTGTGGTGCAG	60.002	52.381	0.00	0.00	0.00	4.41
2297	4204	2.061028	GCTTGTTACATGCTGGTTTGC	58.939	47.619	14.71	0.00	32.80	3.68
2514	4433	6.861065	TTTCTACTTTCAGTTAGTTGCTGG	57.139	37.500	0.00	0.00	34.89	4.85
2601	4520	7.066781	CCCTGGAATTGGTAAAAGTGGTATAT	58.933	38.462	0.00	0.00	0.00	0.86
2673	4592	6.667558	TCAGATCAGAGTTATGCTCATCAT	57.332	37.500	0.00	0.00	46.47	2.45
2724	4643	2.035066	AGTTCACAATCTGCCAACTTGC	59.965	45.455	0.00	0.00	0.00	4.01
2755	4674	4.163268	TCAGATTGGATTTCGTGGGTATGA	59.837	41.667	0.00	0.00	0.00	2.15
2758	4677	3.704800	TGGATTTCGTGGGTATGACAA	57.295	42.857	0.00	0.00	0.00	3.18
2759	4678	4.229304	TGGATTTCGTGGGTATGACAAT	57.771	40.909	0.00	0.00	0.00	2.71
2860	4779	5.334569	CCACCGTGTCCACAAATTAGTTAAG	60.335	44.000	0.00	0.00	0.00	1.85
2950	4869	8.929260	TTGAGAGCATTTACATTCATGGATAT	57.071	30.769	0.00	0.00	0.00	1.63

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	9.898152	TTCTGTGATGTGGTATTAAATATGTCA	57.102	29.630	0.00	0.00	0.00	3.58
31	32	9.733556	AGTACATTTCTGTGATGTGGTATTAAA	57.266	29.630	0.00	0.00	38.17	1.52
32	33	9.378551	GAGTACATTTCTGTGATGTGGTATTAA	57.621	33.333	0.00	0.00	38.17	1.40
33	34	7.704899	CGAGTACATTTCTGTGATGTGGTATTA	59.295	37.037	0.00	0.00	38.17	0.98
34	35	6.535150	CGAGTACATTTCTGTGATGTGGTATT	59.465	38.462	0.00	0.00	38.17	1.89
35	36	6.042777	CGAGTACATTTCTGTGATGTGGTAT	58.957	40.000	0.00	0.00	38.17	2.73
36	37	5.047590	ACGAGTACATTTCTGTGATGTGGTA	60.048	40.000	0.00	0.00	38.17	3.25
37	38	4.245660	CGAGTACATTTCTGTGATGTGGT	58.754	43.478	0.00	0.00	38.17	4.16
38	39	4.091945	CACGAGTACATTTCTGTGATGTGG	59.908	45.833	0.00	0.00	38.17	4.17
39	40	4.434725	GCACGAGTACATTTCTGTGATGTG	60.435	45.833	0.00	0.00	38.17	3.21
40	41	3.679980	GCACGAGTACATTTCTGTGATGT	59.320	43.478	0.00	0.00	40.59	3.06
41	42	3.928992	AGCACGAGTACATTTCTGTGATG	59.071	43.478	0.00	0.00	36.79	3.07
42	43	4.193826	AGCACGAGTACATTTCTGTGAT	57.806	40.909	0.00	0.00	36.79	3.06
43	44	3.660501	AGCACGAGTACATTTCTGTGA	57.339	42.857	0.00	0.00	36.79	3.58
44	45	5.839262	TTTAGCACGAGTACATTTCTGTG	57.161	39.130	0.00	0.00	36.79	3.66
45	46	5.163854	GCATTTAGCACGAGTACATTTCTGT	60.164	40.000	0.00	0.00	44.79	3.41
46	47	5.258622	GCATTTAGCACGAGTACATTTCTG	58.741	41.667	0.00	0.00	44.79	3.02
47	48	5.470845	GCATTTAGCACGAGTACATTTCT	57.529	39.130	0.00	0.00	44.79	2.52
254	259	4.445718	GTGTGTGATAAGACATCGGCATAG	59.554	45.833	0.00	0.00	0.00	2.23
295	311	5.000591	TGCGATGAAAAGATAAGTTGGTCA	58.999	37.500	0.00	0.00	0.00	4.02
313	329	2.290260	TGGTTGGTTCTTCATCTGCGAT	60.290	45.455	0.00	0.00	0.00	4.58
492	512	9.053840	CAAGAATGCAGACATCTCTATAAACAT	57.946	33.333	0.00	0.00	34.62	2.71
616	643	1.203063	GGAGCCCCCACTTTCTTCTTT	60.203	52.381	0.00	0.00	34.14	2.52
618	645	0.476611	AGGAGCCCCCACTTTCTTCT	60.477	55.000	0.00	0.00	37.41	2.85
619	646	1.286248	TAGGAGCCCCCACTTTCTTC	58.714	55.000	0.00	0.00	37.41	2.87
644	672	6.389906	AGAATTAATGAAAAACTTGGCTCCG	58.610	36.000	0.00	0.00	0.00	4.63
693	722	7.230108	ACCAGCAACTATAGAATCCAATTCATG	59.770	37.037	6.78	0.00	41.71	3.07
715	744	2.624838	ACAAAATGGAGAGTGCAACCAG	59.375	45.455	0.00	0.00	37.80	4.00
724	753	5.122396	GTGCTACCTTGTACAAAATGGAGAG	59.878	44.000	16.89	13.70	0.00	3.20
733	762	6.263392	TGCAAAAATAGTGCTACCTTGTACAA	59.737	34.615	8.28	8.28	42.69	2.41
782	811	9.814899	TCTTGCAAAAACAAATCTCTATTTTGA	57.185	25.926	12.05	0.00	41.26	2.69
830	863	7.521529	CACGTCTCAAACATTTATGACTTCAT	58.478	34.615	0.00	0.00	40.22	2.57
835	868	4.081761	CGCACGTCTCAAACATTTATGAC	58.918	43.478	0.00	0.00	0.00	3.06
864	897	5.373812	AACCCTAACTAGTTAGCATGCAT	57.626	39.130	29.72	13.65	40.79	3.96
899	932	2.748605	CTGAGTTGGACACAGAGTGAC	58.251	52.381	3.88	0.00	38.79	3.67
900	933	1.069204	GCTGAGTTGGACACAGAGTGA	59.931	52.381	9.24	0.00	38.79	3.41
911	944	3.933048	CTGGGCTGGGCTGAGTTGG	62.933	68.421	0.00	0.00	0.00	3.77
942	975	1.546029	GTGAAGATTTGGGTTGGCCTC	59.454	52.381	3.32	0.00	34.45	4.70
943	976	1.632589	GTGAAGATTTGGGTTGGCCT	58.367	50.000	3.32	0.00	34.45	5.19
945	978	1.200020	CTCGTGAAGATTTGGGTTGGC	59.800	52.381	0.00	0.00	0.00	4.52
951	984	2.275318	GAGAGGCTCGTGAAGATTTGG	58.725	52.381	9.22	0.00	0.00	3.28
953	986	1.208293	GGGAGAGGCTCGTGAAGATTT	59.792	52.381	9.22	0.00	0.00	2.17
1248	1305	4.847444	GCCCTGGAGAAGCCGAGC	62.847	72.222	0.00	0.00	40.66	5.03
1308	1365	1.069090	GGTTGTGTCCACTCTCGCA	59.931	57.895	0.00	0.00	0.00	5.10
1360	1417	4.421479	CTCCGGACGCGACAAGCT	62.421	66.667	15.93	0.00	45.59	3.74
1496	1553	2.424246	GACGAGAGAAGGTAGGAGTTGG	59.576	54.545	0.00	0.00	0.00	3.77
1573	3448	1.071299	AGACAATGTCGCCAGCACA	59.929	52.632	7.83	0.00	37.67	4.57
1592	3467	1.003839	TTCACACGGATGAGCACCC	60.004	57.895	0.00	0.00	0.00	4.61
2062	3941	3.466836	CAGCTTCGTTATGAGGGCATAA	58.533	45.455	0.00	0.00	42.96	1.90
2179	4058	1.002468	GCTGCACCACACACAAGTTAG	60.002	52.381	0.00	0.00	0.00	2.34
2198	4077	3.565902	ACCAGCTAGAGTGAAAACTTTGC	59.434	43.478	0.00	0.00	0.00	3.68
2497	4416	3.273919	GCACCAGCAACTAACTGAAAG	57.726	47.619	0.00	0.00	41.58	2.62
2514	4433	6.484818	AATACCAAAATTCTTGCAATGCAC	57.515	33.333	7.72	0.00	38.71	4.57
2655	4574	6.823497	TGATGAATGATGAGCATAACTCTGA	58.177	36.000	0.00	0.00	46.41	3.27
2673	4592	6.839124	ATGAACCTTTTGCTGTATGATGAA	57.161	33.333	0.00	0.00	0.00	2.57
2724	4643	3.492383	CGAAATCCAATCTGAGATGGTCG	59.508	47.826	0.00	9.52	37.94	4.79
2755	4674	2.812011	GCTTTCCTGGTTGTCGTATTGT	59.188	45.455	0.00	0.00	0.00	2.71
2758	4677	3.767673	TCTAGCTTTCCTGGTTGTCGTAT	59.232	43.478	0.00	0.00	0.00	3.06
2759	4678	3.159472	TCTAGCTTTCCTGGTTGTCGTA	58.841	45.455	0.00	0.00	0.00	3.43
2860	4779	6.744112	TGTGAAATACATTGTTGGAGAAACC	58.256	36.000	0.00	0.00	34.35	3.27
2950	4869	4.157472	TCCACGCAGAAAAATATTGATGCA	59.843	37.500	12.24	0.00	32.90	3.96
3124	5046	4.470462	CAGAAGTTGTAGATGTGCAAAGC	58.530	43.478	0.00	0.00	29.18	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.