AutoCloner

Multiple sequence alignment - TraesCS3D01G014400

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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	TraesCS3D01G014400	chr3D	100.000	2478	0	0	1	2478	4998082	5000559	0.000000e+00	4577.0
1	TraesCS3D01G014400	chr3D	97.998	1299	6	1	1200	2478	4960152	4961450	0.000000e+00	2237.0
2	TraesCS3D01G014400	chr3D	93.448	992	31	5	196	1184	4954581	4955541	0.000000e+00	1441.0
3	TraesCS3D01G014400	chr3D	90.634	363	25	6	1200	1554	9632565	9632204	8.020000e-130	473.0
4	TraesCS3D01G014400	chr3D	96.970	33	1	0	1732	1764	9632200	9632168	3.440000e-04	56.5
5	TraesCS3D01G014400	chrUn	81.509	1087	122	31	163	1184	285725631	285724559	0.000000e+00	821.0
6	TraesCS3D01G014400	chrUn	100.000	406	0	0	1218	1623	478122795	478123200	0.000000e+00	750.0
7	TraesCS3D01G014400	chrUn	85.328	518	43	9	168	659	208767896	208767386	2.840000e-139	505.0
8	TraesCS3D01G014400	chrUn	86.551	461	53	8	728	1184	208767108	208766653	1.320000e-137	499.0
9	TraesCS3D01G014400	chrUn	89.600	375	23	10	1200	1559	284403568	284403941	1.740000e-126	462.0
10	TraesCS3D01G014400	chrUn	89.600	375	23	10	1200	1559	284410102	284410475	1.740000e-126	462.0
11	TraesCS3D01G014400	chrUn	89.600	375	23	10	1200	1559	302993727	302994100	1.740000e-126	462.0
12	TraesCS3D01G014400	chrUn	86.016	379	37	7	3	365	208768245	208767867	2.310000e-105	392.0
13	TraesCS3D01G014400	chrUn	79.167	528	86	17	677	1184	35298920	35298397	6.560000e-91	344.0
14	TraesCS3D01G014400	chrUn	79.167	528	86	17	677	1184	229348760	229348237	6.560000e-91	344.0
15	TraesCS3D01G014400	chrUn	84.324	185	22	5	1951	2128	319857331	319857515	9.110000e-40	174.0
16	TraesCS3D01G014400	chrUn	84.324	185	22	5	1951	2128	331092811	331092627	9.110000e-40	174.0
17	TraesCS3D01G014400	chrUn	85.455	110	12	4	1696	1803	35292546	35292439	7.240000e-21	111.0
18	TraesCS3D01G014400	chrUn	85.455	110	12	4	1696	1803	229342386	229342279	7.240000e-21	111.0
19	TraesCS3D01G014400	chrUn	89.062	64	7	0	1698	1761	257888349	257888412	2.040000e-11	80.5
20	TraesCS3D01G014400	chr3A	89.091	605	53	8	584	1184	10880410	10881005	0.000000e+00	739.0
21	TraesCS3D01G014400	chr3A	90.867	427	23	7	1200	1617	10885363	10885782	2.150000e-155	558.0
22	TraesCS3D01G014400	chr3A	86.187	514	44	5	3	489	10879858	10880371	4.690000e-147	531.0
23	TraesCS3D01G014400	chr3A	89.189	370	27	8	1200	1561	10696996	10697360	1.350000e-122	449.0
24	TraesCS3D01G014400	chr3A	94.000	100	6	0	2375	2474	10885884	10885983	4.270000e-33	152.0
25	TraesCS3D01G014400	chr3A	96.970	33	1	0	1732	1764	10689859	10689891	3.440000e-04	56.5
26	TraesCS3D01G014400	chr3B	89.646	367	29	5	1200	1558	13814322	13813957	2.250000e-125	459.0
27	TraesCS3D01G014400	chr3B	97.573	206	5	0	1	206	13819188	13818983	1.090000e-93	353.0
28	TraesCS3D01G014400	chr4A	84.328	134	16	2	1572	1701	17481520	17481388	2.590000e-25	126.0
29	TraesCS3D01G014400	chr2A	86.765	68	9	0	1600	1667	706570517	706570584	2.640000e-10	76.8

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	TraesCS3D01G014400	chr3D	4998082	5000559	2477	False	4577.000000	4577	100.0000	1	2478	1	chr3D.!!$F3	2477
1	TraesCS3D01G014400	chr3D	4960152	4961450	1298	False	2237.000000	2237	97.9980	1200	2478	1	chr3D.!!$F2	1278
2	TraesCS3D01G014400	chr3D	4954581	4955541	960	False	1441.000000	1441	93.4480	196	1184	1	chr3D.!!$F1	988
3	TraesCS3D01G014400	chrUn	285724559	285725631	1072	True	821.000000	821	81.5090	163	1184	1	chrUn.!!$R5	1021
4	TraesCS3D01G014400	chrUn	208766653	208768245	1592	True	465.333333	505	85.9650	3	1184	3	chrUn.!!$R7	1181
5	TraesCS3D01G014400	chrUn	35298397	35298920	523	True	344.000000	344	79.1670	677	1184	1	chrUn.!!$R2	507
6	TraesCS3D01G014400	chrUn	229348237	229348760	523	True	344.000000	344	79.1670	677	1184	1	chrUn.!!$R4	507
7	TraesCS3D01G014400	chr3A	10879858	10881005	1147	False	635.000000	739	87.6390	3	1184	2	chr3A.!!$F3	1181
8	TraesCS3D01G014400	chr3A	10885363	10885983	620	False	355.000000	558	92.4335	1200	2474	2	chr3A.!!$F4	1274

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
132	134	0.318762	ACGGTGAGAGTTTCTGAGCC	59.681	55.000	0.0	0.0	0.00	4.70	F
986	1465	1.683011	GCCCCTGCTTGCAGAAGAATA	60.683	52.381	22.5	0.0	33.53	1.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1006	1498	0.920763	TGGAAGATGGGGCTGATGGT	60.921	55.0	0.0	0.0	0.0	3.55	R
1834	2368	7.054491	ACTCTACATGCTTTTGAATTTGGTT	57.946	32.0	0.0	0.0	0.0	3.67	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
42	43	5.009110	GCTTTTGAATAGCTAATCCAGGGAC	59.991	44.000	6.35	0.00	35.74	4.46
61	63	1.347817	CTGGTCGCGCTTCTCTTGAC	61.348	60.000	5.56	3.01	0.00	3.18
77	79	1.352083	TGACCCAGGAGAGTTTCAGG	58.648	55.000	0.00	0.00	0.00	3.86
80	82	1.301293	CCAGGAGAGTTTCAGGCCC	59.699	63.158	0.00	0.00	0.00	5.80
91	93	3.153919	GTTTCAGGCCCAAAGTATCACA	58.846	45.455	0.00	0.00	0.00	3.58
102	104	6.017109	GCCCAAAGTATCACATATACTTGGTG	60.017	42.308	10.32	6.81	42.19	4.17
113	115	7.445707	TCACATATACTTGGTGCTTTTGTGTAA	59.554	33.333	0.00	0.00	34.90	2.41
114	116	7.537306	CACATATACTTGGTGCTTTTGTGTAAC	59.463	37.037	0.00	0.00	37.35	2.50
132	134	0.318762	ACGGTGAGAGTTTCTGAGCC	59.681	55.000	0.00	0.00	0.00	4.70
149	151	5.652014	TCTGAGCCGGTTTAAATGAATGATT	59.348	36.000	1.90	0.00	0.00	2.57
248	449	2.213499	CTGTGGTGGTGTTCTCAGTTC	58.787	52.381	0.00	0.00	0.00	3.01
699	1005	4.747810	ACACTTTAGCAATTAAGCATGGC	58.252	39.130	0.00	0.00	36.85	4.40
703	1011	6.639686	CACTTTAGCAATTAAGCATGGCTATG	59.360	38.462	5.55	5.55	43.07	2.23
828	1299	4.877378	CTTGGTACAGGTACAACTGGTA	57.123	45.455	11.35	0.00	42.39	3.25
956	1435	8.245491	CAGATCACAGATAGTAGGAATCATCTG	58.755	40.741	8.49	8.49	46.37	2.90
975	1454	4.133373	ATCGGCATGCCCCTGCTT	62.133	61.111	30.79	6.53	41.95	3.91
986	1465	1.683011	GCCCCTGCTTGCAGAAGAATA	60.683	52.381	22.50	0.00	33.53	1.75
1027	1519	0.549950	CATCAGCCCCATCTTCCAGT	59.450	55.000	0.00	0.00	0.00	4.00
1041	1533	6.071447	CCATCTTCCAGTATCTCTATCACCTG	60.071	46.154	0.00	0.00	0.00	4.00
1102	1624	5.303333	TGGAACCCCAATTCTTAAAACTGTC	59.697	40.000	0.00	0.00	40.09	3.51
1129	1651	6.013725	TGGTGTTCTCAGTTTCCTATGTGTAT	60.014	38.462	0.00	0.00	0.00	2.29
1132	1654	7.063544	GTGTTCTCAGTTTCCTATGTGTATGAC	59.936	40.741	0.00	0.00	0.00	3.06
1136	1658	6.460781	TCAGTTTCCTATGTGTATGACGTTT	58.539	36.000	0.00	0.00	0.00	3.60
1137	1659	6.932400	TCAGTTTCCTATGTGTATGACGTTTT	59.068	34.615	0.00	0.00	0.00	2.43
1138	1660	7.442969	TCAGTTTCCTATGTGTATGACGTTTTT	59.557	33.333	0.00	0.00	0.00	1.94
1139	1661	7.533900	CAGTTTCCTATGTGTATGACGTTTTTG	59.466	37.037	0.00	0.00	0.00	2.44
1140	1662	7.227910	AGTTTCCTATGTGTATGACGTTTTTGT	59.772	33.333	0.00	0.00	0.00	2.83
1141	1663	7.499321	TTCCTATGTGTATGACGTTTTTGTT	57.501	32.000	0.00	0.00	0.00	2.83
1142	1664	8.604640	TTCCTATGTGTATGACGTTTTTGTTA	57.395	30.769	0.00	0.00	0.00	2.41
1144	1666	8.661257	TCCTATGTGTATGACGTTTTTGTTATG	58.339	33.333	0.00	0.00	0.00	1.90
1151	1676	7.644551	TGTATGACGTTTTTGTTATGTTTGTCC	59.355	33.333	0.00	0.00	0.00	4.02
1184	1709	8.877779	TGATGGTTCATTTTTGTTAAGTTTGTG	58.122	29.630	0.00	0.00	0.00	3.33
1185	1710	7.066374	TGGTTCATTTTTGTTAAGTTTGTGC	57.934	32.000	0.00	0.00	0.00	4.57
1186	1711	6.092807	TGGTTCATTTTTGTTAAGTTTGTGCC	59.907	34.615	0.00	0.00	0.00	5.01
1187	1712	6.092807	GGTTCATTTTTGTTAAGTTTGTGCCA	59.907	34.615	0.00	0.00	0.00	4.92
1188	1713	7.361286	GGTTCATTTTTGTTAAGTTTGTGCCAA	60.361	33.333	0.00	0.00	0.00	4.52
1189	1714	7.066374	TCATTTTTGTTAAGTTTGTGCCAAC	57.934	32.000	0.00	0.00	0.00	3.77
1190	1715	6.876257	TCATTTTTGTTAAGTTTGTGCCAACT	59.124	30.769	0.00	0.00	0.00	3.16
1191	1716	6.473397	TTTTTGTTAAGTTTGTGCCAACTG	57.527	33.333	0.00	0.00	0.00	3.16
1192	1717	3.157932	TGTTAAGTTTGTGCCAACTGC	57.842	42.857	0.00	0.00	41.77	4.40
1216	1741	4.799473	CGCCGACTGCATGCAACG	62.799	66.667	28.22	28.22	41.33	4.10
1758	2292	9.967451	TGTAATATTTTTGTGGATTAGTGGAGA	57.033	29.630	0.00	0.00	0.00	3.71
1834	2368	9.225436	TGTTTGATAGTGACATGTATTAGCAAA	57.775	29.630	16.62	16.62	30.12	3.68
1961	2515	4.351192	CAACCACTAGTTTGTGTTGCTTC	58.649	43.478	0.00	0.00	36.18	3.86
1980	2534	5.184864	TGCTTCCAGTTTCAACTTTCAAAGA	59.815	36.000	3.49	0.00	37.08	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	1.080501	TCAAGAGAAGCGCGACCAG	60.081	57.895	12.10	0.00	0.00	4.00
50	52	1.206849	CTCTCCTGGGTCAAGAGAAGC	59.793	57.143	4.54	0.00	39.09	3.86
61	63	1.301293	GGCCTGAAACTCTCCTGGG	59.699	63.158	0.00	0.00	0.00	4.45
77	79	6.017109	CACCAAGTATATGTGATACTTTGGGC	60.017	42.308	19.09	0.00	41.40	5.36
80	82	7.792374	AGCACCAAGTATATGTGATACTTTG	57.208	36.000	7.14	7.00	41.40	2.77
91	93	6.128117	CCGTTACACAAAAGCACCAAGTATAT	60.128	38.462	0.00	0.00	0.00	0.86
102	104	2.870411	ACTCTCACCGTTACACAAAAGC	59.130	45.455	0.00	0.00	0.00	3.51
113	115	0.318762	GGCTCAGAAACTCTCACCGT	59.681	55.000	0.00	0.00	0.00	4.83
114	116	0.734253	CGGCTCAGAAACTCTCACCG	60.734	60.000	0.00	0.00	30.36	4.94
132	134	8.208718	TCCTACAGAATCATTCATTTAAACCG	57.791	34.615	0.00	0.00	0.00	4.44
149	151	4.669866	TCAGGGTTCTAGTTCCTACAGA	57.330	45.455	0.00	0.00	0.00	3.41
248	449	2.943033	CCAGGAACGCTTACAAATAGGG	59.057	50.000	0.00	0.00	0.00	3.53
496	735	9.357652	TGCTGCTGATATTATTTGTTTTCTTTC	57.642	29.630	0.00	0.00	0.00	2.62
828	1299	5.365895	ACTTAACTCACTGGAACCTGTAGTT	59.634	40.000	18.53	18.53	43.07	2.24
836	1307	4.065088	TGATGCACTTAACTCACTGGAAC	58.935	43.478	0.00	0.00	0.00	3.62
1006	1498	0.920763	TGGAAGATGGGGCTGATGGT	60.921	55.000	0.00	0.00	0.00	3.55
1027	1519	4.745351	ACATGAGCCAGGTGATAGAGATA	58.255	43.478	0.00	0.00	0.00	1.98
1041	1533	9.542462	TTACATAATTTAGTGTAGACATGAGCC	57.458	33.333	0.00	0.00	32.87	4.70
1102	1624	2.240493	AGGAAACTGAGAACACCACG	57.760	50.000	0.00	0.00	41.13	4.94
1129	1651	6.197364	AGGACAAACATAACAAAAACGTCA	57.803	33.333	0.00	0.00	0.00	4.35
1132	1654	7.274686	ACAGAAAGGACAAACATAACAAAAACG	59.725	33.333	0.00	0.00	0.00	3.60
1136	1658	7.397892	TCACAGAAAGGACAAACATAACAAA	57.602	32.000	0.00	0.00	0.00	2.83
1137	1659	7.424803	CATCACAGAAAGGACAAACATAACAA	58.575	34.615	0.00	0.00	0.00	2.83
1138	1660	6.016360	CCATCACAGAAAGGACAAACATAACA	60.016	38.462	0.00	0.00	0.00	2.41
1139	1661	6.016276	ACCATCACAGAAAGGACAAACATAAC	60.016	38.462	0.00	0.00	0.00	1.89
1140	1662	6.068010	ACCATCACAGAAAGGACAAACATAA	58.932	36.000	0.00	0.00	0.00	1.90
1141	1663	5.630121	ACCATCACAGAAAGGACAAACATA	58.370	37.500	0.00	0.00	0.00	2.29
1142	1664	4.473444	ACCATCACAGAAAGGACAAACAT	58.527	39.130	0.00	0.00	0.00	2.71
1144	1666	4.338118	TGAACCATCACAGAAAGGACAAAC	59.662	41.667	0.00	0.00	0.00	2.93
1151	1676	7.775397	AACAAAAATGAACCATCACAGAAAG	57.225	32.000	0.00	0.00	38.69	2.62
1184	1709	3.107661	GCGTTGCATGCAGTTGGC	61.108	61.111	21.50	17.77	45.13	4.52
1185	1710	2.431260	GGCGTTGCATGCAGTTGG	60.431	61.111	21.50	12.13	0.00	3.77
1186	1711	2.801996	CGGCGTTGCATGCAGTTG	60.802	61.111	21.50	15.16	0.00	3.16
1187	1712	2.977456	TCGGCGTTGCATGCAGTT	60.977	55.556	21.50	0.00	0.00	3.16
1188	1713	3.726517	GTCGGCGTTGCATGCAGT	61.727	61.111	21.50	0.00	0.00	4.40
1189	1714	3.425713	AGTCGGCGTTGCATGCAG	61.426	61.111	21.50	11.65	0.00	4.41
1190	1715	3.725459	CAGTCGGCGTTGCATGCA	61.725	61.111	18.46	18.46	0.00	3.96
1623	2157	8.958175	AACTTGATTCGCGTTTAATAAAATGA	57.042	26.923	5.77	0.00	34.10	2.57
1834	2368	7.054491	ACTCTACATGCTTTTGAATTTGGTT	57.946	32.000	0.00	0.00	0.00	3.67
1961	2515	7.707104	AGTATGTCTTTGAAAGTTGAAACTGG	58.293	34.615	4.68	0.00	39.66	4.00
1980	2534	7.169982	GCTCGTATCTAAATGCTGAAAGTATGT	59.830	37.037	0.00	0.00	38.77	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.