AutoCloner

Multiple sequence alignment - TraesCS2B01G621500

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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	TraesCS2B01G621500	chr2B	100.000	4190	0	0	1	4190	795855679	795859868	0.000000e+00	7738
1	TraesCS2B01G621500	chr2B	95.730	4215	117	17	1	4190	50583487	50579311	0.000000e+00	6728
2	TraesCS2B01G621500	chr7B	95.254	4214	161	16	1	4190	685613133	685617331	0.000000e+00	6637
3	TraesCS2B01G621500	chr7B	91.223	376	12	7	1354	1728	467424387	467424032	3.760000e-135	492
4	TraesCS2B01G621500	chr6D	92.906	1748	81	19	1	1725	322695264	322696991	0.000000e+00	2501
5	TraesCS2B01G621500	chr6D	92.894	1745	81	22	6	1728	384198948	384197225	0.000000e+00	2495
6	TraesCS2B01G621500	chr6D	96.671	1382	40	4	2811	4190	322698295	322699672	0.000000e+00	2292
7	TraesCS2B01G621500	chr6D	96.527	1382	41	5	2811	4190	384195944	384194568	0.000000e+00	2279
8	TraesCS2B01G621500	chr6D	95.918	1078	37	4	1741	2816	384197112	384196040	0.000000e+00	1740
9	TraesCS2B01G621500	chr6D	94.940	1087	38	4	1741	2810	322697107	322698193	0.000000e+00	1687
10	TraesCS2B01G621500	chrUn	92.206	1745	87	21	6	1728	102602576	102600859	0.000000e+00	2423
11	TraesCS2B01G621500	chrUn	92.048	1748	88	28	1	1724	162674040	162675760	0.000000e+00	2410
12	TraesCS2B01G621500	chrUn	96.237	1382	46	4	2811	4190	102599560	102598183	0.000000e+00	2259
13	TraesCS2B01G621500	chrUn	94.053	1093	46	8	1741	2816	102600746	102599656	0.000000e+00	1640
14	TraesCS2B01G621500	chrUn	94.112	1087	41	7	1741	2810	162681542	162682622	0.000000e+00	1631
15	TraesCS2B01G621500	chr3D	92.005	1726	89	16	12	1725	596626039	596627727	0.000000e+00	2377
16	TraesCS2B01G621500	chr3D	96.237	1382	43	5	2811	4190	596629028	596630402	0.000000e+00	2255
17	TraesCS2B01G621500	chr3D	94.475	1086	43	5	1741	2810	596627843	596628927	0.000000e+00	1657
18	TraesCS2B01G621500	chr1D	91.517	1674	74	28	1	1650	353178397	353180026	0.000000e+00	2242
19	TraesCS2B01G621500	chr1D	94.567	1086	40	9	1741	2810	353180198	353181280	0.000000e+00	1661
20	TraesCS2B01G621500	chr1B	95.876	1382	52	3	2811	4190	39265505	39266883	0.000000e+00	2231
21	TraesCS2B01G621500	chr7A	94.935	1382	56	7	2811	4190	175945294	175943925	0.000000e+00	2152
22	TraesCS2B01G621500	chr3B	94.702	1378	64	6	2814	4189	87708599	87707229	0.000000e+00	2132
23	TraesCS2B01G621500	chr2A	90.916	1365	102	13	1	1351	722107047	722105691	0.000000e+00	1814
24	TraesCS2B01G621500	chr4B	93.664	1089	52	5	1744	2816	608367758	608366671	0.000000e+00	1613
25	TraesCS2B01G621500	chr4B	88.499	1026	58	21	724	1728	608368860	608367874	0.000000e+00	1186
26	TraesCS2B01G621500	chr2D	95.152	330	14	2	2489	2816	614385460	614385131	1.730000e-143	520
27	TraesCS2B01G621500	chr7D	90.426	376	27	6	1354	1728	449457459	449457092	1.750000e-133	486

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	TraesCS2B01G621500	chr2B	795855679	795859868	4189	False	7738.000000	7738	100.000000	1	4190	1	chr2B.!!$F1	4189
1	TraesCS2B01G621500	chr2B	50579311	50583487	4176	True	6728.000000	6728	95.730000	1	4190	1	chr2B.!!$R1	4189
2	TraesCS2B01G621500	chr7B	685613133	685617331	4198	False	6637.000000	6637	95.254000	1	4190	1	chr7B.!!$F1	4189
3	TraesCS2B01G621500	chr6D	384194568	384198948	4380	True	2171.333333	2495	95.113000	6	4190	3	chr6D.!!$R1	4184
4	TraesCS2B01G621500	chr6D	322695264	322699672	4408	False	2160.000000	2501	94.839000	1	4190	3	chr6D.!!$F1	4189
5	TraesCS2B01G621500	chrUn	162674040	162675760	1720	False	2410.000000	2410	92.048000	1	1724	1	chrUn.!!$F1	1723
6	TraesCS2B01G621500	chrUn	102598183	102602576	4393	True	2107.333333	2423	94.165333	6	4190	3	chrUn.!!$R1	4184
7	TraesCS2B01G621500	chrUn	162681542	162682622	1080	False	1631.000000	1631	94.112000	1741	2810	1	chrUn.!!$F2	1069
8	TraesCS2B01G621500	chr3D	596626039	596630402	4363	False	2096.333333	2377	94.239000	12	4190	3	chr3D.!!$F1	4178
9	TraesCS2B01G621500	chr1D	353178397	353181280	2883	False	1951.500000	2242	93.042000	1	2810	2	chr1D.!!$F1	2809
10	TraesCS2B01G621500	chr1B	39265505	39266883	1378	False	2231.000000	2231	95.876000	2811	4190	1	chr1B.!!$F1	1379
11	TraesCS2B01G621500	chr7A	175943925	175945294	1369	True	2152.000000	2152	94.935000	2811	4190	1	chr7A.!!$R1	1379
12	TraesCS2B01G621500	chr3B	87707229	87708599	1370	True	2132.000000	2132	94.702000	2814	4189	1	chr3B.!!$R1	1375
13	TraesCS2B01G621500	chr2A	722105691	722107047	1356	True	1814.000000	1814	90.916000	1	1351	1	chr2A.!!$R1	1350
14	TraesCS2B01G621500	chr4B	608366671	608368860	2189	True	1399.500000	1613	91.081500	724	2816	2	chr4B.!!$R1	2092

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
604	618	0.035317	TGCTGCGTTCTGATTGGACT	59.965	50.0	0.00	0.0	0.00	3.85	F
2340	2533	0.107897	TATTGATGGTGCGCCGACTT	60.108	50.0	12.58	0.0	37.67	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2528	2750	0.380378	TGCAAACTGGAAGACGTTGC	59.620	50.000	0.0	0.0	44.18	4.17	R
3456	3782	1.202290	GCAATGCCCAATCCTTACACG	60.202	52.381	0.0	0.0	0.00	4.49	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
62	65	1.641577	CGTTCCTAGCTAGTGGTTGC	58.358	55.000	19.31	3.09	0.00	4.17
72	75	2.819608	GCTAGTGGTTGCATCTTGGAAA	59.180	45.455	0.00	0.00	26.96	3.13
73	76	3.255642	GCTAGTGGTTGCATCTTGGAAAA	59.744	43.478	0.00	0.00	26.96	2.29
74	77	3.733443	AGTGGTTGCATCTTGGAAAAC	57.267	42.857	0.00	0.00	26.96	2.43
181	186	5.079689	ACAGTTCAAATTTGACCCGTTTT	57.920	34.783	20.35	0.00	36.83	2.43
191	196	1.314730	GACCCGTTTTCCAGCTGAAA	58.685	50.000	17.39	11.04	41.18	2.69
197	202	1.595794	GTTTTCCAGCTGAAACGACGA	59.404	47.619	17.39	0.00	42.56	4.20
198	203	1.214367	TTTCCAGCTGAAACGACGAC	58.786	50.000	17.39	0.00	38.04	4.34
604	618	0.035317	TGCTGCGTTCTGATTGGACT	59.965	50.000	0.00	0.00	0.00	3.85
608	622	3.525537	CTGCGTTCTGATTGGACTATGT	58.474	45.455	0.00	0.00	0.00	2.29
639	653	0.676466	GGATCACGCATCAACCACCA	60.676	55.000	0.00	0.00	32.33	4.17
640	654	0.447801	GATCACGCATCAACCACCAC	59.552	55.000	0.00	0.00	0.00	4.16
641	655	0.960364	ATCACGCATCAACCACCACC	60.960	55.000	0.00	0.00	0.00	4.61
645	659	1.599518	GCATCAACCACCACCGTCA	60.600	57.895	0.00	0.00	0.00	4.35
927	942	2.122167	GCGACCGAGGACCAGAGAT	61.122	63.158	0.00	0.00	0.00	2.75
1392	1461	4.772100	ACATATTTTTCCTGGACCCTGTTG	59.228	41.667	0.00	0.00	0.00	3.33
1393	1462	1.408969	TTTTTCCTGGACCCTGTTGC	58.591	50.000	0.00	0.00	0.00	4.17
1394	1463	0.821711	TTTTCCTGGACCCTGTTGCG	60.822	55.000	0.00	0.00	0.00	4.85
1395	1464	1.990160	TTTCCTGGACCCTGTTGCGT	61.990	55.000	0.00	0.00	0.00	5.24
1396	1465	2.358737	CCTGGACCCTGTTGCGTC	60.359	66.667	0.00	0.00	0.00	5.19
1397	1466	2.738521	CTGGACCCTGTTGCGTCG	60.739	66.667	0.00	0.00	0.00	5.12
1398	1467	3.220999	CTGGACCCTGTTGCGTCGA	62.221	63.158	0.00	0.00	0.00	4.20
1400	1469	2.338984	GACCCTGTTGCGTCGAGT	59.661	61.111	0.00	0.00	0.00	4.18
1406	1475	0.229753	CTGTTGCGTCGAGTGTTGAC	59.770	55.000	0.00	0.00	0.00	3.18
1407	1476	0.458716	TGTTGCGTCGAGTGTTGACA	60.459	50.000	0.00	0.00	36.11	3.58
1431	1500	2.111043	ACACCAGTGGCAGGTTCG	59.889	61.111	9.78	0.00	37.23	3.95
1627	1696	1.490574	ATCTGACAGCCCCTGTACTC	58.509	55.000	0.00	0.00	45.44	2.59
2262	2455	4.799949	GCACCTCGTCGTGTGTAATTATTA	59.200	41.667	15.46	0.00	36.08	0.98
2333	2526	6.852853	GTGATTGAGTATTTATTGATGGTGCG	59.147	38.462	0.00	0.00	0.00	5.34
2340	2533	0.107897	TATTGATGGTGCGCCGACTT	60.108	50.000	12.58	0.00	37.67	3.01
2528	2750	0.908180	AGGGACCCCTCAAGGTAACG	60.908	60.000	7.00	0.00	44.43	3.18
2566	2789	3.573538	TGCACTTTGCTCACCAACAATAT	59.426	39.130	0.00	0.00	45.31	1.28
2699	2923	1.136329	AAGGTGGAGCAGGACATGGT	61.136	55.000	0.00	0.00	44.02	3.55
2965	3290	8.747471	TGTAGTGGCAAAATTCATGAAATCATA	58.253	29.630	13.09	0.00	34.26	2.15
3264	3590	5.290493	TCTTGTTGTGGTTCATGTAGTCT	57.710	39.130	0.00	0.00	0.00	3.24
3277	3603	8.818057	GGTTCATGTAGTCTTGTATGTGTTATC	58.182	37.037	0.00	0.00	0.00	1.75
3354	3680	2.754552	GGCAGGATGTATGCACAAAGAA	59.245	45.455	0.00	0.00	45.68	2.52
3360	3686	7.262772	CAGGATGTATGCACAAAGAATGATTT	58.737	34.615	0.00	0.00	38.42	2.17
3456	3782	7.581476	ACTTGCATATTTACGCCATTATACAC	58.419	34.615	0.00	0.00	0.00	2.90
3961	4287	2.025767	TTGCCACAATTTGCAGCGGT	62.026	50.000	0.00	0.00	38.95	5.68
4167	4494	5.215252	TCTCTGTCTCCTTACTGTTTTGG	57.785	43.478	0.00	0.00	0.00	3.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	40	2.159226	CCACTAGCTAGGAACGGTCAAG	60.159	54.545	24.35	0.00	0.00	3.02
38	41	1.822990	CCACTAGCTAGGAACGGTCAA	59.177	52.381	24.35	0.00	0.00	3.18
62	65	8.652810	AGAAACATCAAAAGTTTTCCAAGATG	57.347	30.769	18.07	18.07	39.15	2.90
150	155	4.216257	TCAAATTTGAACTGTAGCTGCCTC	59.784	41.667	18.45	0.00	33.55	4.70
181	186	0.103390	TTGTCGTCGTTTCAGCTGGA	59.897	50.000	15.13	0.46	0.00	3.86
197	202	5.422012	ACCTCTGGTGAAAAAGACAAATTGT	59.578	36.000	0.00	0.00	32.98	2.71
198	203	5.906073	ACCTCTGGTGAAAAAGACAAATTG	58.094	37.500	0.00	0.00	32.98	2.32
608	622	0.939106	CGTGATCCGCGTGATATGCA	60.939	55.000	4.92	0.00	32.41	3.96
639	653	1.330655	ATCCGGAAGCATCTGACGGT	61.331	55.000	9.01	0.00	44.54	4.83
640	654	0.598680	GATCCGGAAGCATCTGACGG	60.599	60.000	9.01	0.00	45.52	4.79
641	655	0.598680	GGATCCGGAAGCATCTGACG	60.599	60.000	9.01	0.00	33.44	4.35
645	659	0.179073	CGTTGGATCCGGAAGCATCT	60.179	55.000	9.01	0.00	0.00	2.90
769	784	0.926720	AGGGAGAGTAGAGGGGCTCA	60.927	60.000	0.00	0.00	34.39	4.26
1392	1461	0.229753	CAACTGTCAACACTCGACGC	59.770	55.000	0.00	0.00	36.11	5.19
1393	1462	1.517276	GTCAACTGTCAACACTCGACG	59.483	52.381	0.00	0.00	36.11	5.12
1394	1463	2.281762	GTGTCAACTGTCAACACTCGAC	59.718	50.000	14.75	0.00	40.07	4.20
1395	1464	2.094442	TGTGTCAACTGTCAACACTCGA	60.094	45.455	19.77	0.00	42.89	4.04
1396	1465	2.029244	GTGTGTCAACTGTCAACACTCG	59.971	50.000	19.77	0.00	42.89	4.18
1397	1466	2.351726	GGTGTGTCAACTGTCAACACTC	59.648	50.000	19.77	17.01	42.89	3.51
1398	1467	2.290008	TGGTGTGTCAACTGTCAACACT	60.290	45.455	19.77	0.00	42.89	3.55
1400	1469	2.290008	ACTGGTGTGTCAACTGTCAACA	60.290	45.455	0.00	0.00	27.10	3.33
1406	1475	0.747644	TGCCACTGGTGTGTCAACTG	60.748	55.000	0.00	0.00	42.34	3.16
1407	1476	0.464373	CTGCCACTGGTGTGTCAACT	60.464	55.000	0.00	0.00	42.34	3.16
1431	1500	1.717937	CACTAGTTGGCGCTGATGC	59.282	57.895	7.64	0.00	0.00	3.91
1627	1696	7.031975	AGGATTAGTCTACGTTCGGTTAAAAG	58.968	38.462	0.00	0.00	0.00	2.27
2262	2455	1.446907	CGTAGGTCTCGTACACACCT	58.553	55.000	11.18	11.18	43.32	4.00
2333	2526	7.448748	AATGGGTAAATAATATGAAGTCGGC	57.551	36.000	0.00	0.00	0.00	5.54
2528	2750	0.380378	TGCAAACTGGAAGACGTTGC	59.620	50.000	0.00	0.00	44.18	4.17
2566	2789	4.944317	AGCATCTACCTATCGATCGATCAA	59.056	41.667	32.50	16.44	36.17	2.57
2833	3158	7.402862	AGAATACACTTTATTAGTTGGCAGGT	58.597	34.615	0.00	0.00	33.85	4.00
3300	3626	2.239400	GCCAAGTAAGCTCCCAAAAGT	58.761	47.619	0.00	0.00	0.00	2.66
3354	3680	9.331282	GTAGTATTTCTGACTAGCCAAAATCAT	57.669	33.333	0.00	0.00	30.08	2.45
3360	3686	6.852420	AGTGTAGTATTTCTGACTAGCCAA	57.148	37.500	0.00	0.00	30.08	4.52
3414	3740	6.599356	TGCAAGTTAGACCTAGATGTTACA	57.401	37.500	0.00	0.00	0.00	2.41
3442	3768	4.337836	TCCTTACACGTGTATAATGGCGTA	59.662	41.667	27.82	9.71	35.71	4.42
3456	3782	1.202290	GCAATGCCCAATCCTTACACG	60.202	52.381	0.00	0.00	0.00	4.49
4034	4360	5.419471	AGCAACAGTAGGTAGTAGAAGAAGG	59.581	44.000	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.