AutoCloner

Multiple sequence alignment - TraesCS6D01G009900

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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	TraesCS6D01G009900	chr6D	100.000	4371	0	0	1	4371	3821884	3817514	0.000000e+00	8072
1	TraesCS6D01G009900	chr6D	84.094	679	61	28	2591	3261	2834643	2834004	2.890000e-171	612
2	TraesCS6D01G009900	chr6D	79.811	317	34	17	2097	2411	2834950	2834662	2.060000e-48	204
3	TraesCS6D01G009900	chr6A	95.924	3508	84	23	884	4371	3687771	3691239	0.000000e+00	5631
4	TraesCS6D01G009900	chr6A	88.814	885	60	8	3	851	3686888	3687769	0.000000e+00	1050
5	TraesCS6D01G009900	chr6A	88.557	201	18	3	3013	3213	1815843	1815648	5.650000e-59	239
6	TraesCS6D01G009900	chr6A	93.407	91	3	3	2706	2796	1816390	1816303	9.860000e-27	132
7	TraesCS6D01G009900	chr6B	93.646	2345	85	22	21	2341	9101231	9098927	0.000000e+00	3446
8	TraesCS6D01G009900	chr6B	94.112	2038	62	19	2369	4371	9098927	9096913	0.000000e+00	3046
9	TraesCS6D01G009900	chr6B	86.012	336	29	7	2556	2889	196481389	196481708	1.160000e-90	344
10	TraesCS6D01G009900	chr6B	85.714	336	30	10	2556	2889	375644334	375644015	5.410000e-89	339
11	TraesCS6D01G009900	chr6B	85.714	336	30	7	2556	2889	393068877	393069196	5.410000e-89	339
12	TraesCS6D01G009900	chr6B	84.667	150	19	3	3248	3397	680478	680623	3.520000e-31	147
13	TraesCS6D01G009900	chr4D	95.502	867	22	2	3505	4371	266757768	266756919	0.000000e+00	1369
14	TraesCS6D01G009900	chr5D	95.284	721	13	4	3653	4371	30064178	30063477	0.000000e+00	1123
15	TraesCS6D01G009900	chr1B	86.350	337	27	11	2556	2889	586552723	586553043	2.500000e-92	350
16	TraesCS6D01G009900	chr2B	85.398	226	17	8	2556	2781	706089537	706089746	2.050000e-53	220

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	TraesCS6D01G009900	chr6D	3817514	3821884	4370	True	8072.0	8072	100.0000	1	4371	1	chr6D.!!$R1	4370
1	TraesCS6D01G009900	chr6D	2834004	2834950	946	True	408.0	612	81.9525	2097	3261	2	chr6D.!!$R2	1164
2	TraesCS6D01G009900	chr6A	3686888	3691239	4351	False	3340.5	5631	92.3690	3	4371	2	chr6A.!!$F1	4368
3	TraesCS6D01G009900	chr6B	9096913	9101231	4318	True	3246.0	3446	93.8790	21	4371	2	chr6B.!!$R2	4350
4	TraesCS6D01G009900	chr4D	266756919	266757768	849	True	1369.0	1369	95.5020	3505	4371	1	chr4D.!!$R1	866
5	TraesCS6D01G009900	chr5D	30063477	30064178	701	True	1123.0	1123	95.2840	3653	4371	1	chr5D.!!$R1	718

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	Hairpin	End Stability	Orientation
340	360	0.543749	ATGTTAGGTGCTCCTCTGCC	59.456	55.0	11.38	43.94	4.85	F
1077	1118	0.534877	TTGCGGTGATGACAGTGCTT	60.535	50.0	0.00	0.00	3.91	F
2536	2583	0.173255	CACATGGCCCCACGAATTTC	59.827	55.0	0.00	0.00	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1917	1962	0.038251	CAGACGCTAGTGTTCCTGCA	60.038	55.000	10.89	0.00	4.41	R
2576	2639	2.226437	CCTGAACCATTCTTTGTGTCGG	59.774	50.000	0.00	0.00	4.79	R
3432	3503	1.073474	ATGGGCCAGGGCAGATAGA	60.073	57.895	16.36	44.11	1.98	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
89	91	1.147376	TAGTGTTGCCTGCGTTGGT	59.853	52.632	0.00	0.00	0.00	3.67
180	182	5.132502	TGATCCTTGTTCTCTTTTGCTTGA	58.867	37.500	0.00	0.00	0.00	3.02
244	246	7.039270	GGTCTTTAGATCAGAGAACTTTCCTC	58.961	42.308	0.00	0.00	0.00	3.71
246	248	5.584253	TTAGATCAGAGAACTTTCCTCGG	57.416	43.478	0.00	0.00	35.88	4.63
248	250	3.445805	AGATCAGAGAACTTTCCTCGGAC	59.554	47.826	0.00	0.00	37.60	4.79
274	276	5.278561	GCCTATCTTAGAGTATGTGCGAACT	60.279	44.000	0.00	0.00	0.00	3.01
306	308	2.890945	GCCAGTCATAAGTTTGTTGGGT	59.109	45.455	0.00	0.00	0.00	4.51
340	360	0.543749	ATGTTAGGTGCTCCTCTGCC	59.456	55.000	11.38	0.00	43.94	4.85
344	364	4.792804	GGTGCTCCTCTGCCCTGC	62.793	72.222	0.00	0.00	0.00	4.85
347	367	2.354343	GCTCCTCTGCCCTGCTTT	59.646	61.111	0.00	0.00	0.00	3.51
372	392	5.880332	TGAGAACCCTTGTATGCTTATGTTC	59.120	40.000	0.00	0.00	32.98	3.18
378	398	6.128007	ACCCTTGTATGCTTATGTTCGAAAAG	60.128	38.462	0.00	1.05	0.00	2.27
379	399	6.258160	CCTTGTATGCTTATGTTCGAAAAGG	58.742	40.000	0.00	0.66	0.00	3.11
412	436	4.160329	TGTTCAGAGTCCAATCTACCTGT	58.840	43.478	0.00	0.00	0.00	4.00
460	484	7.608153	TGCTAGTTGTGTTCTAGTTAGCAATA	58.392	34.615	1.21	0.00	37.69	1.90
497	538	3.439129	GGAACATACAAACTGGTAGTGCC	59.561	47.826	0.00	0.00	37.90	5.01
559	600	4.749310	AGTGCTTCCTCTGCCGCG	62.749	66.667	0.00	0.00	0.00	6.46
810	851	8.293699	TCTCTCACATATAAAGCTAGTGACAA	57.706	34.615	0.00	0.00	35.57	3.18
812	853	7.492524	TCTCACATATAAAGCTAGTGACAAGG	58.507	38.462	0.00	0.00	35.57	3.61
814	855	5.817296	CACATATAAAGCTAGTGACAAGGCA	59.183	40.000	0.00	0.00	32.14	4.75
972	1013	2.104111	CACCACCTAAGACCAGTGACAA	59.896	50.000	0.00	0.00	33.21	3.18
975	1016	3.261897	CCACCTAAGACCAGTGACAAGAT	59.738	47.826	0.00	0.00	33.21	2.40
1077	1118	0.534877	TTGCGGTGATGACAGTGCTT	60.535	50.000	0.00	0.00	0.00	3.91
1878	1923	4.022589	TGAAACTAGTTACACAGGTCGGAG	60.023	45.833	8.92	0.00	0.00	4.63
1917	1962	2.125106	GCGGGTCTGGCGAAGATT	60.125	61.111	0.00	0.00	37.23	2.40
2250	2295	3.612247	TTGGCTGCTCCGAGGAAGC	62.612	63.158	7.17	7.17	37.80	3.86
2313	2359	2.678190	GCTCAGATACCACCAACCTGTC	60.678	54.545	0.00	0.00	0.00	3.51
2320	2366	2.586425	ACCACCAACCTGTCAAGAATG	58.414	47.619	0.00	0.00	0.00	2.67
2500	2546	6.627087	AGGAGACCTTACAATTCTTCATGA	57.373	37.500	0.00	0.00	0.00	3.07
2532	2579	1.602323	GAACACATGGCCCCACGAA	60.602	57.895	0.00	0.00	0.00	3.85
2535	2582	0.541764	ACACATGGCCCCACGAATTT	60.542	50.000	0.00	0.00	0.00	1.82
2536	2583	0.173255	CACATGGCCCCACGAATTTC	59.827	55.000	0.00	0.00	0.00	2.17
2537	2584	0.970427	ACATGGCCCCACGAATTTCC	60.970	55.000	0.00	0.00	0.00	3.13
2538	2585	1.752694	ATGGCCCCACGAATTTCCG	60.753	57.895	0.00	0.00	0.00	4.30
3011	3081	6.873997	TGATCCAGATATCGTTGTACACTTT	58.126	36.000	0.00	0.00	0.00	2.66
3137	3207	6.923012	ACAATTGACATATTGCTAAGTTGCA	58.077	32.000	13.59	0.00	38.74	4.08
3172	3242	3.190327	GGCCAAACAACAACTTTGCTTTT	59.810	39.130	0.00	0.00	0.00	2.27
3432	3503	6.493166	TCAAGAATGACCCTAAATGTTCCAT	58.507	36.000	0.00	0.00	0.00	3.41
3500	3571	9.500785	TTGAATAAGTCAGTGTCATATTTGTGA	57.499	29.630	0.61	0.00	37.61	3.58
3913	4002	0.034476	CTGCAGTCTCAGTGCTTCCA	59.966	55.000	5.25	0.00	44.61	3.53
4028	4120	4.320690	CGTTTGCACTACCAATTTGATTCG	59.679	41.667	0.00	0.00	0.00	3.34
4220	4313	7.290948	TGAGTAGCATTGCAGGGCTATATATAT	59.709	37.037	20.05	0.00	43.78	0.86
4221	4314	8.727100	AGTAGCATTGCAGGGCTATATATATA	57.273	34.615	20.05	2.49	43.78	0.86
4222	4315	9.331466	AGTAGCATTGCAGGGCTATATATATAT	57.669	33.333	20.05	10.10	43.78	0.86
4309	4402	2.753029	GGTGCAGGAGTGGAAGCT	59.247	61.111	0.00	0.00	0.00	3.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	4.749245	AAGCCAAAACGATAGAACAGTG	57.251	40.909	0.00	0.00	41.38	3.66
89	91	5.900865	AAAGTGGTTTTACAAACGGAAGA	57.099	34.783	0.00	0.00	0.00	2.87
180	182	0.606401	CTCACATGGCGTCCCTGTTT	60.606	55.000	0.00	0.00	0.00	2.83
244	246	4.762765	ACATACTCTAAGATAGGCTGTCCG	59.237	45.833	7.72	0.00	37.47	4.79
246	248	5.465935	GCACATACTCTAAGATAGGCTGTC	58.534	45.833	2.62	2.62	0.00	3.51
248	250	4.216472	TCGCACATACTCTAAGATAGGCTG	59.784	45.833	0.00	0.00	0.00	4.85
274	276	6.463995	ACTTATGACTGGCTCAAAACAAAA	57.536	33.333	0.00	0.00	30.60	2.44
306	308	6.267014	GCACCTAACATCCTAATCCAGTAGTA	59.733	42.308	0.00	0.00	0.00	1.82
340	360	2.310538	ACAAGGGTTCTCAAAAGCAGG	58.689	47.619	0.00	0.00	0.00	4.85
344	364	5.712152	AAGCATACAAGGGTTCTCAAAAG	57.288	39.130	0.00	0.00	0.00	2.27
347	367	5.815581	ACATAAGCATACAAGGGTTCTCAA	58.184	37.500	0.00	0.00	0.00	3.02
372	392	5.116180	TGAACATACAGATAGGCCTTTTCG	58.884	41.667	12.58	7.98	0.00	3.46
378	398	4.262249	GGACTCTGAACATACAGATAGGCC	60.262	50.000	0.00	0.00	44.32	5.19
379	399	4.342378	TGGACTCTGAACATACAGATAGGC	59.658	45.833	0.00	0.00	44.32	3.93
412	436	0.037326	GGAGAGGATGTGTCGCAACA	60.037	55.000	0.00	0.00	0.00	3.33
460	484	1.160137	GTTCCAACGAAGAGCTGCAT	58.840	50.000	1.02	0.00	0.00	3.96
497	538	0.934496	TGCCGTGTTGAAGAAGAACG	59.066	50.000	0.00	0.00	0.00	3.95
559	600	5.694006	CAGATCACCTACTAGCTTTATGTGC	59.306	44.000	0.00	0.00	0.00	4.57
778	819	6.824553	AGCTTTATATGTGAGAGAGCAATGA	58.175	36.000	0.00	0.00	0.00	2.57
810	851	2.368221	GAGAGAGCATTATCAGGTGCCT	59.632	50.000	0.00	0.00	42.20	4.75
812	853	3.129871	GTGAGAGAGCATTATCAGGTGC	58.870	50.000	0.00	0.00	41.57	5.01
814	855	4.652881	TGATGTGAGAGAGCATTATCAGGT	59.347	41.667	0.00	0.00	0.00	4.00
1041	1082	1.069090	AAAGAGCGTGTCGAAGGCA	59.931	52.632	12.45	0.00	43.93	4.75
1077	1118	0.737367	CATCGAGCGCCTTCTTCACA	60.737	55.000	2.29	0.00	0.00	3.58
1236	1277	4.469657	TGAGTTTCCAGGTGCTAAACATT	58.530	39.130	4.70	0.00	35.93	2.71
1291	1332	6.677431	GCTTTTCAGATAAACATGCAGAGGAG	60.677	42.308	0.00	0.00	0.00	3.69
1666	1711	5.449107	AGTGCCCTGTATACAGTTATACG	57.551	43.478	27.07	13.25	42.18	3.06
1878	1923	3.430098	CCTTGCTCCTCACATCTACTGTC	60.430	52.174	0.00	0.00	35.29	3.51
1917	1962	0.038251	CAGACGCTAGTGTTCCTGCA	60.038	55.000	10.89	0.00	0.00	4.41
2250	2295	4.685169	AAGAACGGTTGCAATCTGTATG	57.315	40.909	8.32	0.00	0.00	2.39
2500	2546	6.051717	GCCATGTGTTCATAACTATCAGAGT	58.948	40.000	0.00	0.00	33.87	3.24
2532	2579	9.191995	GAATTTACAATTCTTTGTGTCGGAAAT	57.808	29.630	1.76	0.00	45.56	2.17
2535	2582	7.012894	ACTGAATTTACAATTCTTTGTGTCGGA	59.987	33.333	9.93	0.00	45.56	4.55
2536	2583	7.138736	ACTGAATTTACAATTCTTTGTGTCGG	58.861	34.615	9.93	2.65	45.56	4.79
2537	2584	8.560576	AACTGAATTTACAATTCTTTGTGTCG	57.439	30.769	9.93	0.00	45.56	4.35
2576	2639	2.226437	CCTGAACCATTCTTTGTGTCGG	59.774	50.000	0.00	0.00	0.00	4.79
3011	3081	9.132923	CCTTGTAGGTGAGATAAGTCATAGTAA	57.867	37.037	0.00	0.00	0.00	2.24
3026	3096	6.269077	TGTCAATTCTTAGTCCTTGTAGGTGA	59.731	38.462	0.00	0.00	36.53	4.02
3027	3097	6.464222	TGTCAATTCTTAGTCCTTGTAGGTG	58.536	40.000	0.00	0.00	36.53	4.00
3137	3207	4.481368	TGTTTGGCCGATAGTTCTGTAT	57.519	40.909	0.00	0.00	0.00	2.29
3172	3242	5.992829	TGTTTTGCCGAAGTTCTATGTCTTA	59.007	36.000	0.56	0.00	0.00	2.10
3432	3503	1.073474	ATGGGCCAGGGCAGATAGA	60.073	57.895	16.36	0.00	44.11	1.98
3500	3571	5.536161	ACCAGAAAGTAAAGTGCACAATGAT	59.464	36.000	21.04	2.36	0.00	2.45
3913	4002	4.473444	TGCCAAGAAAGTGGAGAAAAGAT	58.527	39.130	0.00	0.00	41.65	2.40
4028	4120	9.712305	ATAAAATGGCATATCAGTAGACAGTAC	57.288	33.333	0.00	0.00	0.00	2.73
4084	4176	6.644248	TGCTACTCTTGTGACAACTTACTA	57.356	37.500	0.00	0.00	0.00	1.82
4231	4324	8.526978	ACGCTCATCAACTGTCTGATTATATAT	58.473	33.333	0.00	0.00	33.66	0.86
4232	4325	7.886338	ACGCTCATCAACTGTCTGATTATATA	58.114	34.615	3.71	0.00	33.66	0.86
4233	4326	6.753180	ACGCTCATCAACTGTCTGATTATAT	58.247	36.000	3.71	0.00	33.66	0.86
4234	4327	6.149129	ACGCTCATCAACTGTCTGATTATA	57.851	37.500	3.71	0.00	33.66	0.98
4249	4342	4.615949	ACAAGATGACTGATACGCTCATC	58.384	43.478	2.49	2.49	40.40	2.92
4309	4402	1.380246	GCCAGCATTCCCATCACCA	60.380	57.895	0.00	0.00	0.00	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.