AutoCloner

Multiple sequence alignment - TraesCS1D01G397100

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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	TraesCS1D01G397100	chr1D	100.000	3404	0	0	1	3404	464862657	464866060	0.000000e+00	6287
1	TraesCS1D01G397100	chr1B	92.839	2332	100	20	409	2707	641630830	641633127	0.000000e+00	3319
2	TraesCS1D01G397100	chr1B	93.275	342	17	2	1	336	641630335	641630676	1.820000e-137	499
3	TraesCS1D01G397100	chr1B	93.469	245	10	4	2944	3184	641633123	641633365	3.230000e-95	359
4	TraesCS1D01G397100	chr1B	90.991	222	18	2	3181	3401	641633446	641633666	7.140000e-77	298
5	TraesCS1D01G397100	chr1A	92.298	2337	93	43	888	3184	557154262	557156551	0.000000e+00	3238
6	TraesCS1D01G397100	chr1A	89.182	758	54	14	3	744	557153378	557154123	0.000000e+00	920
7	TraesCS1D01G397100	chr1A	90.991	222	15	4	3181	3401	557156632	557156849	9.240000e-76	294
8	TraesCS1D01G397100	chr1A	84.416	231	23	5	3187	3404	425068253	425068023	7.400000e-52	215
9	TraesCS1D01G397100	chr1A	83.772	228	24	4	3187	3401	406654940	406655167	1.600000e-48	204
10	TraesCS1D01G397100	chr3B	88.755	1992	129	42	923	2853	657945721	657947678	0.000000e+00	2350
11	TraesCS1D01G397100	chr3B	84.454	238	22	8	3181	3404	777722116	777721880	1.590000e-53	220
12	TraesCS1D01G397100	chr3B	84.483	232	23	3	3186	3404	789488956	789488725	2.060000e-52	217
13	TraesCS1D01G397100	chr3B	89.474	114	9	1	1	114	648406428	648406318	1.270000e-29	141
14	TraesCS1D01G397100	chr5D	90.665	782	73	0	1014	1795	271481224	271480443	0.000000e+00	1040
15	TraesCS1D01G397100	chr5D	89.515	763	79	1	1033	1795	271475985	271475224	0.000000e+00	965
16	TraesCS1D01G397100	chr5D	89.488	761	80	0	1035	1795	271465567	271464807	0.000000e+00	963
17	TraesCS1D01G397100	chr5D	89.384	763	81	0	1033	1795	271470785	271470023	0.000000e+00	961
18	TraesCS1D01G397100	chr5D	87.838	296	30	6	1	295	271708162	271708452	3.250000e-90	342
19	TraesCS1D01G397100	chr5A	87.500	416	51	1	1380	1795	361365010	361364596	2.380000e-131	479
20	TraesCS1D01G397100	chr5A	77.243	769	113	38	1	744	361447508	361446777	8.850000e-106	394
21	TraesCS1D01G397100	chr5A	81.989	372	60	4	916	1285	361365363	361364997	3.300000e-80	309
22	TraesCS1D01G397100	chr5B	89.860	286	24	5	1	286	307881259	307880979	2.500000e-96	363
23	TraesCS1D01G397100	chr5B	85.714	238	19	7	3181	3404	101902516	101902280	1.580000e-58	237
24	TraesCS1D01G397100	chrUn	82.105	285	39	3	1015	1299	31027386	31027114	2.040000e-57	233
25	TraesCS1D01G397100	chrUn	84.483	232	23	3	3186	3404	41735689	41735458	2.060000e-52	217
26	TraesCS1D01G397100	chrUn	84.716	229	22	3	3186	3401	373663388	373663616	2.060000e-52	217
27	TraesCS1D01G397100	chr3D	85.294	238	20	7	3181	3404	209469063	209468827	7.350000e-57	231
28	TraesCS1D01G397100	chr6B	85.043	234	20	7	3181	3400	92348636	92348404	1.230000e-54	224
29	TraesCS1D01G397100	chr4B	84.279	229	20	9	3188	3401	604114437	604114664	3.440000e-50	209
30	TraesCS1D01G397100	chr2D	88.298	94	10	1	1507	1599	648365784	648365877	9.990000e-21	111

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	TraesCS1D01G397100	chr1D	464862657	464866060	3403	False	6287.00	6287	100.000000	1	3404	1	chr1D.!!$F1	3403
1	TraesCS1D01G397100	chr1B	641630335	641633666	3331	False	1118.75	3319	92.643500	1	3401	4	chr1B.!!$F1	3400
2	TraesCS1D01G397100	chr1A	557153378	557156849	3471	False	1484.00	3238	90.823667	3	3401	3	chr1A.!!$F2	3398
3	TraesCS1D01G397100	chr3B	657945721	657947678	1957	False	2350.00	2350	88.755000	923	2853	1	chr3B.!!$F1	1930
4	TraesCS1D01G397100	chr5D	271480443	271481224	781	True	1040.00	1040	90.665000	1014	1795	1	chr5D.!!$R4	781
5	TraesCS1D01G397100	chr5D	271475224	271475985	761	True	965.00	965	89.515000	1033	1795	1	chr5D.!!$R3	762
6	TraesCS1D01G397100	chr5D	271464807	271465567	760	True	963.00	963	89.488000	1035	1795	1	chr5D.!!$R1	760
7	TraesCS1D01G397100	chr5D	271470023	271470785	762	True	961.00	961	89.384000	1033	1795	1	chr5D.!!$R2	762
8	TraesCS1D01G397100	chr5A	361364596	361365363	767	True	394.00	479	84.744500	916	1795	2	chr5A.!!$R2	879
9	TraesCS1D01G397100	chr5A	361446777	361447508	731	True	394.00	394	77.243000	1	744	1	chr5A.!!$R1	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
957	1107	0.047176	TCCTCCTCCTCCTCTCCTCT	59.953	60.0	0.0	0.0	0.00	3.69	F
1994	2172	0.551131	ATGGAAGAAGCCCCAGAGGT	60.551	55.0	0.0	0.0	38.26	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2152	2333	0.040067	GCTTCCTTGGTTTCACGCTG	60.040	55.000	0.0	0.0	0.0	5.18	R
3029	3313	1.796617	GCGAGGCATTTCATTGAGCAC	60.797	52.381	0.0	0.0	0.0	4.40	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
170	176	2.742589	CCCCTACGAGAAAAACAAGAGC	59.257	50.000	0.00	0.00	0.00	4.09
172	178	2.412089	CCTACGAGAAAAACAAGAGCGG	59.588	50.000	0.00	0.00	0.00	5.52
309	316	2.039974	TTATGCAGCGGCTGGTGTG	61.040	57.895	29.44	6.96	45.36	3.82
329	336	4.637091	TGTGTGATCTATGATGCCAAGTTG	59.363	41.667	0.00	0.00	0.00	3.16
361	368	0.108804	ATGACGGGTAACACGCTGAG	60.109	55.000	0.00	0.00	39.74	3.35
377	384	2.301346	CTGAGGGAGCACAAAGTTGTT	58.699	47.619	0.00	0.00	39.91	2.83
383	390	0.175531	AGCACAAAGTTGTTGGCCAC	59.824	50.000	3.88	0.75	39.91	5.01
407	414	6.482308	ACCGCCAGATATCTAAATGTAACAAC	59.518	38.462	4.54	0.00	0.00	3.32
582	678	1.268539	GCACAAGTCAACCAAGGTTCG	60.269	52.381	0.51	0.00	36.00	3.95
604	709	2.487762	GGCATTTCATCGAACAGGTCAA	59.512	45.455	0.00	0.00	0.00	3.18
632	741	3.005050	CGCCCAATGTCATGCATAGATTT	59.995	43.478	0.00	0.00	36.67	2.17
655	764	1.933853	CGAAATTTAGGACGCCAGGAG	59.066	52.381	0.00	0.00	0.00	3.69
656	765	2.418197	CGAAATTTAGGACGCCAGGAGA	60.418	50.000	0.00	0.00	0.00	3.71
657	766	2.990066	AATTTAGGACGCCAGGAGAG	57.010	50.000	0.00	0.00	0.00	3.20
658	767	1.123928	ATTTAGGACGCCAGGAGAGG	58.876	55.000	0.00	0.00	0.00	3.69
681	790	2.766263	AGGAGACACTCACAAGTCACAA	59.234	45.455	0.00	0.00	37.23	3.33
785	918	0.177836	GAGGAAGGAGAGGAAGCAGC	59.822	60.000	0.00	0.00	0.00	5.25
786	919	1.153469	GGAAGGAGAGGAAGCAGCG	60.153	63.158	0.00	0.00	0.00	5.18
788	921	0.739112	GAAGGAGAGGAAGCAGCGTG	60.739	60.000	0.00	0.00	0.00	5.34
794	927	4.373116	GGAAGCAGCGTGGGACGA	62.373	66.667	0.00	0.00	46.05	4.20
807	940	2.743928	GACGAGCTGGCCCAGTTG	60.744	66.667	13.35	5.06	33.43	3.16
809	942	2.281761	CGAGCTGGCCCAGTTGTT	60.282	61.111	13.35	0.00	33.43	2.83
810	943	1.003839	CGAGCTGGCCCAGTTGTTA	60.004	57.895	13.35	0.00	33.43	2.41
811	944	0.392998	CGAGCTGGCCCAGTTGTTAT	60.393	55.000	13.35	0.00	33.43	1.89
812	945	1.839424	GAGCTGGCCCAGTTGTTATT	58.161	50.000	13.35	0.00	33.43	1.40
814	947	2.562738	GAGCTGGCCCAGTTGTTATTTT	59.437	45.455	13.35	0.00	33.43	1.82
815	948	2.972021	AGCTGGCCCAGTTGTTATTTTT	59.028	40.909	13.35	0.00	33.43	1.94
957	1107	0.047176	TCCTCCTCCTCCTCTCCTCT	59.953	60.000	0.00	0.00	0.00	3.69
1994	2172	0.551131	ATGGAAGAAGCCCCAGAGGT	60.551	55.000	0.00	0.00	38.26	3.85
2152	2333	5.410132	GCAGAAAAGAAGGGTAAGAAGAGTC	59.590	44.000	0.00	0.00	0.00	3.36
2161	2342	3.554337	GGGTAAGAAGAGTCAGCGTGAAA	60.554	47.826	0.00	0.00	0.00	2.69
2355	2578	2.183679	GAAGAGAAGAAGAGCAGGGGA	58.816	52.381	0.00	0.00	0.00	4.81
2400	2647	0.343372	AGAGATCCAGGGCAAGGGTA	59.657	55.000	0.00	0.00	0.00	3.69
2607	2857	2.851195	CTGAGTGTAATATGGGGGTGC	58.149	52.381	0.00	0.00	0.00	5.01
2732	2994	4.039004	TCTGGTATGCAACAATTTTGTGCT	59.961	37.500	14.44	6.97	41.31	4.40
2750	3012	8.747538	TTTGTGCTAGTCTGATACTACTATGA	57.252	34.615	0.00	0.00	39.80	2.15
2826	3088	8.123639	TGATTCTGGATAGCAGGTATACTAAC	57.876	38.462	2.25	0.00	0.00	2.34
2827	3089	7.950684	TGATTCTGGATAGCAGGTATACTAACT	59.049	37.037	2.25	0.54	0.00	2.24
2828	3090	9.463902	GATTCTGGATAGCAGGTATACTAACTA	57.536	37.037	2.25	2.75	0.00	2.24
2829	3091	9.824216	ATTCTGGATAGCAGGTATACTAACTAA	57.176	33.333	2.25	0.00	0.00	2.24
2910	3194	6.640907	GTGACCAAAGAATGATTTACCAACAC	59.359	38.462	0.00	0.00	0.00	3.32
2963	3247	6.623486	TGAATAACACAGGATTCATGCTTTG	58.377	36.000	0.00	0.00	37.19	2.77
3029	3313	3.209410	GTGCTGGACTTTCATATCCCTG	58.791	50.000	0.00	0.00	33.69	4.45
3035	3319	3.118261	GGACTTTCATATCCCTGTGCTCA	60.118	47.826	0.00	0.00	0.00	4.26
3184	3473	1.555075	CCCAGAGAAGAACGGATTCCA	59.445	52.381	3.09	0.00	35.18	3.53
3207	3580	5.344743	TGTTCTCTGAAGTCTGAACACTT	57.655	39.130	5.60	0.00	42.25	3.16
3257	3630	9.807649	ATGGTTCTAATGCATTTTCATCTTAAC	57.192	29.630	18.75	9.92	0.00	2.01
3280	3653	6.809869	ACTGCTTCTTGCTTCAGTTTTAAAT	58.190	32.000	0.00	0.00	43.37	1.40
3281	3654	7.267857	ACTGCTTCTTGCTTCAGTTTTAAATT	58.732	30.769	0.00	0.00	43.37	1.82
3368	3741	6.296720	CCTTGTCTCTCCCTTCTTCCTTAAAT	60.297	42.308	0.00	0.00	0.00	1.40
3371	3744	6.044404	TGTCTCTCCCTTCTTCCTTAAATTGT	59.956	38.462	0.00	0.00	0.00	2.71
3402	3775	9.450807	AGATTTTCTGAATTGTTTGTAGTTTCG	57.549	29.630	0.00	0.00	0.00	3.46
3403	3776	9.445786	GATTTTCTGAATTGTTTGTAGTTTCGA	57.554	29.630	0.00	0.00	0.00	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
134	140	3.869246	CGTAGGGGTGTAATGTTTAGCAG	59.131	47.826	0.00	0.00	0.00	4.24
170	176	1.005394	ACCTGGTAAGTTGCGACCG	60.005	57.895	0.00	0.00	38.69	4.79
172	178	1.623973	GCGACCTGGTAAGTTGCGAC	61.624	60.000	0.00	0.00	35.04	5.19
309	316	4.036027	CACCAACTTGGCATCATAGATCAC	59.964	45.833	7.81	0.00	42.67	3.06
329	336	0.393077	CCGTCATCTACCCCATCACC	59.607	60.000	0.00	0.00	0.00	4.02
361	368	0.249447	GCCAACAACTTTGTGCTCCC	60.249	55.000	0.00	0.00	41.31	4.30
383	390	6.481976	TGTTGTTACATTTAGATATCTGGCGG	59.518	38.462	15.79	5.28	0.00	6.13
407	414	4.456280	TGTAGTAGGTTCATGCTCACTG	57.544	45.455	0.00	0.00	0.00	3.66
435	528	2.501261	TCTCCTATGCAATGCTCATGC	58.499	47.619	6.82	2.57	44.08	4.06
468	561	2.357517	GTGCAGGTGAGGACGTGG	60.358	66.667	0.00	0.00	38.23	4.94
514	607	2.125552	TGAGCTCCGGCATCAACG	60.126	61.111	12.15	0.00	41.70	4.10
582	678	1.401905	GACCTGTTCGATGAAATGCCC	59.598	52.381	0.00	0.00	0.00	5.36
632	741	2.419021	CCTGGCGTCCTAAATTTCGGTA	60.419	50.000	8.48	0.00	0.00	4.02
655	764	1.548269	CTTGTGAGTGTCTCCTCCCTC	59.452	57.143	0.00	0.00	0.00	4.30
656	765	1.133009	ACTTGTGAGTGTCTCCTCCCT	60.133	52.381	0.00	0.00	33.99	4.20
657	766	1.273886	GACTTGTGAGTGTCTCCTCCC	59.726	57.143	0.00	0.00	35.88	4.30
658	767	1.964223	TGACTTGTGAGTGTCTCCTCC	59.036	52.381	0.00	0.00	35.88	4.30
794	927	2.309136	AAATAACAACTGGGCCAGCT	57.691	45.000	33.04	19.67	34.37	4.24
822	955	2.267961	CTGGGCCAGGTCGTAACC	59.732	66.667	26.34	0.00	46.87	2.85
823	956	2.267961	CCTGGGCCAGGTCGTAAC	59.732	66.667	39.34	0.00	45.82	2.50
831	964	1.814527	GTCGTAGTACCTGGGCCAG	59.185	63.158	27.04	27.04	0.00	4.85
957	1107	4.683721	TTAGCGTGGCGGCGGAAA	62.684	61.111	9.78	0.00	38.18	3.13
1994	2172	3.816398	TCTTCCTCCTCTTCTCAGTCA	57.184	47.619	0.00	0.00	0.00	3.41
2152	2333	0.040067	GCTTCCTTGGTTTCACGCTG	60.040	55.000	0.00	0.00	0.00	5.18
2161	2342	0.396974	TTGTTGCTGGCTTCCTTGGT	60.397	50.000	0.00	0.00	0.00	3.67
2355	2578	8.868522	TCATCTTATCACCACTTGATTTCTTT	57.131	30.769	0.00	0.00	42.87	2.52
2400	2647	8.528044	TTCAGGAAAAACAAGTACAACCTTAT	57.472	30.769	0.00	0.00	0.00	1.73
2607	2857	0.753262	CTACTCCAGACATTCCCCCG	59.247	60.000	0.00	0.00	0.00	5.73
2616	2866	7.971183	AAAATCTGAAGAAACTACTCCAGAC	57.029	36.000	0.00	0.00	34.08	3.51
2732	2994	8.610035	CAACACGTTCATAGTAGTATCAGACTA	58.390	37.037	0.00	0.00	39.81	2.59
2750	3012	2.684001	TGAAGACAGACCAACACGTT	57.316	45.000	0.00	0.00	0.00	3.99
2826	3088	9.868277	AAGATGAGACTACAGAATTTCACTTAG	57.132	33.333	0.00	0.00	0.00	2.18
2828	3090	8.997323	CAAAGATGAGACTACAGAATTTCACTT	58.003	33.333	0.00	0.00	0.00	3.16
2829	3091	8.370940	TCAAAGATGAGACTACAGAATTTCACT	58.629	33.333	0.00	0.00	0.00	3.41
2837	3099	5.770162	TGACTGTCAAAGATGAGACTACAGA	59.230	40.000	8.27	0.00	35.88	3.41
2842	3104	5.999205	AGATGACTGTCAAAGATGAGACT	57.001	39.130	15.31	0.00	35.88	3.24
2843	3105	8.715191	AATAAGATGACTGTCAAAGATGAGAC	57.285	34.615	15.31	0.00	35.88	3.36
2870	3136	5.434182	TTGGTCACAGATGTTGGATCATA	57.566	39.130	0.00	0.00	0.00	2.15
3029	3313	1.796617	GCGAGGCATTTCATTGAGCAC	60.797	52.381	0.00	0.00	0.00	4.40
3035	3319	3.144506	CTCTATGGCGAGGCATTTCATT	58.855	45.455	17.11	0.00	0.00	2.57
3332	3705	7.169287	AGGGAGAGACAAGGTCTACTATTAT	57.831	40.000	0.00	0.00	43.53	1.28
3333	3706	6.593759	AGGGAGAGACAAGGTCTACTATTA	57.406	41.667	0.00	0.00	43.53	0.98
3336	3709	4.540906	AGAAGGGAGAGACAAGGTCTACTA	59.459	45.833	0.00	0.00	43.53	1.82
3337	3710	3.335484	AGAAGGGAGAGACAAGGTCTACT	59.665	47.826	0.00	0.00	43.53	2.57
3346	3719	6.044404	ACAATTTAAGGAAGAAGGGAGAGACA	59.956	38.462	0.00	0.00	0.00	3.41
3368	3741	9.734620	CAAACAATTCAGAAAATCTAGACACAA	57.265	29.630	0.00	0.00	0.00	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.