AutoCloner

Multiple sequence alignment - TraesCS6B01G234500

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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	TraesCS6B01G234500	chr6B	100.000	3999	0	0	1	3999	394456092	394460090	0.000000e+00	7385
1	TraesCS6B01G234500	chr6B	97.046	3250	83	9	1	3241	297455568	297458813	0.000000e+00	5457
2	TraesCS6B01G234500	chr1B	98.705	3244	37	5	1	3241	672571648	672568407	0.000000e+00	5753
3	TraesCS6B01G234500	chr4D	98.618	3255	31	5	1	3241	123317914	123321168	0.000000e+00	5749
4	TraesCS6B01G234500	chr7A	98.273	3243	48	6	1	3241	120858685	120855449	0.000000e+00	5672
5	TraesCS6B01G234500	chr7A	99.274	689	5	0	3311	3999	4935380	4934692	0.000000e+00	1245
6	TraesCS6B01G234500	chr7A	99.127	687	6	0	3311	3997	60103936	60103250	0.000000e+00	1236
7	TraesCS6B01G234500	chr3B	97.939	3251	50	7	1	3241	483383156	483386399	0.000000e+00	5616
8	TraesCS6B01G234500	chr3B	97.722	3249	64	4	1	3241	669798077	669794831	0.000000e+00	5581
9	TraesCS6B01G234500	chr3B	98.101	158	3	0	2894	3051	754172790	754172947	3.940000e-70	276
10	TraesCS6B01G234500	chr2D	96.690	3263	80	11	1	3241	604405575	604402319	0.000000e+00	5404
11	TraesCS6B01G234500	chr2D	96.637	3182	80	11	81	3241	604397272	604394097	0.000000e+00	5260
12	TraesCS6B01G234500	chr2D	99.129	689	6	0	3311	3999	53917358	53916670	0.000000e+00	1240
13	TraesCS6B01G234500	chr2D	99.129	689	6	0	3311	3999	637316531	637315843	0.000000e+00	1240
14	TraesCS6B01G234500	chr2D	98.839	689	8	0	3311	3999	17976901	17977589	0.000000e+00	1229
15	TraesCS6B01G234500	chr3A	98.799	2665	29	3	1	2662	633130469	633133133	0.000000e+00	4741
16	TraesCS6B01G234500	chrUn	99.129	689	6	0	3311	3999	233532734	233532046	0.000000e+00	1240
17	TraesCS6B01G234500	chrUn	98.984	689	7	0	3311	3999	257937166	257937854	0.000000e+00	1234
18	TraesCS6B01G234500	chr3D	98.694	689	9	0	3311	3999	145415908	145416596	0.000000e+00	1223
19	TraesCS6B01G234500	chr1A	98.694	689	9	0	3311	3999	94659288	94658600	0.000000e+00	1223

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	TraesCS6B01G234500	chr6B	394456092	394460090	3998	False	7385	7385	100.000	1	3999	1	chr6B.!!$F2	3998
1	TraesCS6B01G234500	chr6B	297455568	297458813	3245	False	5457	5457	97.046	1	3241	1	chr6B.!!$F1	3240
2	TraesCS6B01G234500	chr1B	672568407	672571648	3241	True	5753	5753	98.705	1	3241	1	chr1B.!!$R1	3240
3	TraesCS6B01G234500	chr4D	123317914	123321168	3254	False	5749	5749	98.618	1	3241	1	chr4D.!!$F1	3240
4	TraesCS6B01G234500	chr7A	120855449	120858685	3236	True	5672	5672	98.273	1	3241	1	chr7A.!!$R3	3240
5	TraesCS6B01G234500	chr7A	4934692	4935380	688	True	1245	1245	99.274	3311	3999	1	chr7A.!!$R1	688
6	TraesCS6B01G234500	chr7A	60103250	60103936	686	True	1236	1236	99.127	3311	3997	1	chr7A.!!$R2	686
7	TraesCS6B01G234500	chr3B	483383156	483386399	3243	False	5616	5616	97.939	1	3241	1	chr3B.!!$F1	3240
8	TraesCS6B01G234500	chr3B	669794831	669798077	3246	True	5581	5581	97.722	1	3241	1	chr3B.!!$R1	3240
9	TraesCS6B01G234500	chr2D	604402319	604405575	3256	True	5404	5404	96.690	1	3241	1	chr2D.!!$R3	3240
10	TraesCS6B01G234500	chr2D	604394097	604397272	3175	True	5260	5260	96.637	81	3241	1	chr2D.!!$R2	3160
11	TraesCS6B01G234500	chr2D	53916670	53917358	688	True	1240	1240	99.129	3311	3999	1	chr2D.!!$R1	688
12	TraesCS6B01G234500	chr2D	637315843	637316531	688	True	1240	1240	99.129	3311	3999	1	chr2D.!!$R4	688
13	TraesCS6B01G234500	chr2D	17976901	17977589	688	False	1229	1229	98.839	3311	3999	1	chr2D.!!$F1	688
14	TraesCS6B01G234500	chr3A	633130469	633133133	2664	False	4741	4741	98.799	1	2662	1	chr3A.!!$F1	2661
15	TraesCS6B01G234500	chrUn	233532046	233532734	688	True	1240	1240	99.129	3311	3999	1	chrUn.!!$R1	688
16	TraesCS6B01G234500	chrUn	257937166	257937854	688	False	1234	1234	98.984	3311	3999	1	chrUn.!!$F1	688
17	TraesCS6B01G234500	chr3D	145415908	145416596	688	False	1223	1223	98.694	3311	3999	1	chr3D.!!$F1	688
18	TraesCS6B01G234500	chr1A	94658600	94659288	688	True	1223	1223	98.694	3311	3999	1	chr1A.!!$R1	688

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
85	86	1.838077	GTAGGTGGTACCAGCATTCCT	59.162	52.381	37.99	29.41	45.79	3.36	F
1519	1537	0.326595	TAGCATGCCAGAAACGGGAA	59.673	50.000	15.66	0.00	0.00	3.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1829	1847	1.677217	CCGAAGCAAAGAAGGAGGAGG	60.677	57.143	0.0	0.0	0.0	4.30	R
3297	3335	0.041535	TAGGGTCTGGCGAAGGGTTA	59.958	55.000	0.0	0.0	0.0	2.85	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
85	86	1.838077	GTAGGTGGTACCAGCATTCCT	59.162	52.381	37.99	29.41	45.79	3.36
695	700	4.508551	TGGCATGACTAATTGATGAGGT	57.491	40.909	0.00	0.00	0.00	3.85
898	911	4.545823	TTGTCATGGAAGTTCGTGAAAC	57.454	40.909	10.16	2.84	34.83	2.78
1364	1381	6.506538	AGATCCAGCCATTACTATCAAAGT	57.493	37.500	0.00	0.00	42.62	2.66
1519	1537	0.326595	TAGCATGCCAGAAACGGGAA	59.673	50.000	15.66	0.00	0.00	3.97
1634	1652	1.411246	GGTGTGGTGGAGCGATATACA	59.589	52.381	0.00	0.00	0.00	2.29
2124	2145	3.455910	TGGGAATTCGAGGTCTCATGAAT	59.544	43.478	0.00	0.00	32.69	2.57
2633	2662	6.604396	TGAGTATTCGGACTATAACAGTTCCA	59.396	38.462	0.00	0.00	37.72	3.53
2669	2698	8.495949	CACTCACTTTTGACAGTTATACGATTT	58.504	33.333	0.00	0.00	0.00	2.17
2820	2849	3.072915	TCCTCAGGTGTCAAATGTGATGT	59.927	43.478	0.00	0.00	35.80	3.06
3009	3047	1.142936	ACCAACTAAACCGGGGAAGT	58.857	50.000	6.32	2.22	0.00	3.01
3051	3089	2.209809	TGAGGGAAGGGGGAAGCA	59.790	61.111	0.00	0.00	0.00	3.91
3241	3279	5.054780	CGAAGCTTAACGCACTATAACAG	57.945	43.478	0.00	0.00	42.61	3.16
3242	3280	4.548346	CGAAGCTTAACGCACTATAACAGC	60.548	45.833	0.00	0.00	42.61	4.40
3243	3281	4.124851	AGCTTAACGCACTATAACAGCT	57.875	40.909	0.00	0.00	42.61	4.24
3244	3282	4.504858	AGCTTAACGCACTATAACAGCTT	58.495	39.130	0.00	0.00	42.61	3.74
3245	3283	4.330074	AGCTTAACGCACTATAACAGCTTG	59.670	41.667	0.00	0.00	42.61	4.01
3246	3284	4.578601	CTTAACGCACTATAACAGCTTGC	58.421	43.478	0.00	0.00	0.00	4.01
3247	3285	2.386661	ACGCACTATAACAGCTTGCT	57.613	45.000	3.07	0.00	0.00	3.91
3248	3286	2.271800	ACGCACTATAACAGCTTGCTC	58.728	47.619	3.07	0.00	0.00	4.26
3249	3287	2.270923	CGCACTATAACAGCTTGCTCA	58.729	47.619	3.07	0.00	0.00	4.26
3250	3288	2.868583	CGCACTATAACAGCTTGCTCAT	59.131	45.455	3.07	0.00	0.00	2.90
3251	3289	3.310774	CGCACTATAACAGCTTGCTCATT	59.689	43.478	3.07	0.00	0.00	2.57
3252	3290	4.507756	CGCACTATAACAGCTTGCTCATTA	59.492	41.667	3.07	0.00	0.00	1.90
3253	3291	5.332883	CGCACTATAACAGCTTGCTCATTAG	60.333	44.000	3.07	0.00	0.00	1.73
3268	3306	5.993106	CTCATTAGCAACCTAGTTTAGCC	57.007	43.478	0.00	0.00	0.00	3.93
3269	3307	5.428253	CTCATTAGCAACCTAGTTTAGCCA	58.572	41.667	0.00	0.00	0.00	4.75
3270	3308	5.811190	TCATTAGCAACCTAGTTTAGCCAA	58.189	37.500	0.00	0.00	0.00	4.52
3271	3309	5.880332	TCATTAGCAACCTAGTTTAGCCAAG	59.120	40.000	0.00	0.00	0.00	3.61
3272	3310	5.492855	TTAGCAACCTAGTTTAGCCAAGA	57.507	39.130	0.00	0.00	0.00	3.02
3273	3311	4.367039	AGCAACCTAGTTTAGCCAAGAA	57.633	40.909	0.00	0.00	0.00	2.52
3274	3312	4.923415	AGCAACCTAGTTTAGCCAAGAAT	58.077	39.130	0.00	0.00	0.00	2.40
3275	3313	4.702131	AGCAACCTAGTTTAGCCAAGAATG	59.298	41.667	0.00	0.00	0.00	2.67
3276	3314	4.700213	GCAACCTAGTTTAGCCAAGAATGA	59.300	41.667	0.00	0.00	0.00	2.57
3277	3315	5.358160	GCAACCTAGTTTAGCCAAGAATGAT	59.642	40.000	0.00	0.00	0.00	2.45
3278	3316	6.458888	GCAACCTAGTTTAGCCAAGAATGATC	60.459	42.308	0.00	0.00	0.00	2.92
3279	3317	6.313519	ACCTAGTTTAGCCAAGAATGATCA	57.686	37.500	0.00	0.00	0.00	2.92
3280	3318	6.116126	ACCTAGTTTAGCCAAGAATGATCAC	58.884	40.000	0.00	0.00	0.00	3.06
3281	3319	5.529060	CCTAGTTTAGCCAAGAATGATCACC	59.471	44.000	0.00	0.00	0.00	4.02
3282	3320	5.184892	AGTTTAGCCAAGAATGATCACCT	57.815	39.130	0.00	0.00	0.00	4.00
3283	3321	5.574188	AGTTTAGCCAAGAATGATCACCTT	58.426	37.500	0.00	1.61	0.00	3.50
3284	3322	5.416952	AGTTTAGCCAAGAATGATCACCTTG	59.583	40.000	23.01	23.01	37.58	3.61
3285	3323	3.726557	AGCCAAGAATGATCACCTTGA	57.273	42.857	27.94	0.00	39.55	3.02
3286	3324	4.246712	AGCCAAGAATGATCACCTTGAT	57.753	40.909	27.94	18.54	40.34	2.57
3287	3325	4.607239	AGCCAAGAATGATCACCTTGATT	58.393	39.130	27.94	18.00	37.20	2.57
3288	3326	5.759059	AGCCAAGAATGATCACCTTGATTA	58.241	37.500	27.94	0.00	37.20	1.75
3289	3327	5.826737	AGCCAAGAATGATCACCTTGATTAG	59.173	40.000	27.94	17.85	37.20	1.73
3290	3328	5.506982	GCCAAGAATGATCACCTTGATTAGC	60.507	44.000	27.94	21.53	37.20	3.09
3291	3329	5.009410	CCAAGAATGATCACCTTGATTAGCC	59.991	44.000	27.94	0.00	37.20	3.93
3292	3330	5.378230	AGAATGATCACCTTGATTAGCCA	57.622	39.130	0.00	0.00	37.20	4.75
3293	3331	5.759059	AGAATGATCACCTTGATTAGCCAA	58.241	37.500	0.00	0.00	37.20	4.52
3294	3332	5.826737	AGAATGATCACCTTGATTAGCCAAG	59.173	40.000	0.00	0.00	37.20	3.61
3302	3340	4.983671	CTTGATTAGCCAAGGTTAACCC	57.016	45.455	21.30	5.76	39.74	4.11
3960	3998	3.964031	TCAAACATAGGGTTGGCAAACTT	59.036	39.130	15.94	10.57	40.35	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	86	3.476552	GATTGGAATGCCCTATCGACAA	58.523	45.455	0.00	0.00	37.41	3.18
695	700	4.081972	ACCTCGTGAGTACTACTTAGTCGA	60.082	45.833	0.00	0.00	37.73	4.20
794	807	5.056894	ACTATACGCGTTTTCTGAAGAGT	57.943	39.130	20.78	7.30	0.00	3.24
898	911	6.639671	TTCCAACGAAAAACAAGAACATTG	57.360	33.333	0.00	0.00	0.00	2.82
1364	1381	6.181206	TCCGATACCATTGATGTCCAATAA	57.819	37.500	0.00	0.00	43.27	1.40
1519	1537	4.961099	GGTATAGGTCTAACCACCTCAACT	59.039	45.833	0.00	0.00	44.08	3.16
1829	1847	1.677217	CCGAAGCAAAGAAGGAGGAGG	60.677	57.143	0.00	0.00	0.00	4.30
2041	2062	7.338710	CCAATTTCTTGAGTCACCCTTATCTA	58.661	38.462	0.00	0.00	34.04	1.98
2633	2662	5.647658	TGTCAAAAGTGAGTGACTGTTCATT	59.352	36.000	0.00	0.00	43.73	2.57
2669	2698	4.476113	ACCCAATTCTGGATCATCTTCTGA	59.524	41.667	0.00	0.00	46.92	3.27
2820	2849	4.345859	AGATTTGAACGACCAGGTACAA	57.654	40.909	0.00	0.00	0.00	2.41
3009	3047	3.670359	CGAGAATTGCATTTCCGCTTCAA	60.670	43.478	15.83	0.00	0.00	2.69
3246	3284	5.428253	TGGCTAAACTAGGTTGCTAATGAG	58.572	41.667	2.38	0.00	0.00	2.90
3247	3285	5.429681	TGGCTAAACTAGGTTGCTAATGA	57.570	39.130	2.38	0.00	0.00	2.57
3248	3286	5.880332	TCTTGGCTAAACTAGGTTGCTAATG	59.120	40.000	2.38	4.40	0.00	1.90
3249	3287	6.062258	TCTTGGCTAAACTAGGTTGCTAAT	57.938	37.500	2.38	0.00	0.00	1.73
3250	3288	5.492855	TCTTGGCTAAACTAGGTTGCTAA	57.507	39.130	2.38	8.20	0.00	3.09
3251	3289	5.492855	TTCTTGGCTAAACTAGGTTGCTA	57.507	39.130	2.38	0.03	0.00	3.49
3252	3290	4.367039	TTCTTGGCTAAACTAGGTTGCT	57.633	40.909	2.38	0.00	0.00	3.91
3253	3291	4.700213	TCATTCTTGGCTAAACTAGGTTGC	59.300	41.667	2.38	4.88	0.00	4.17
3254	3292	6.599244	TGATCATTCTTGGCTAAACTAGGTTG	59.401	38.462	2.38	0.00	0.00	3.77
3255	3293	6.599638	GTGATCATTCTTGGCTAAACTAGGTT	59.400	38.462	0.00	0.00	0.00	3.50
3256	3294	6.116126	GTGATCATTCTTGGCTAAACTAGGT	58.884	40.000	0.00	0.00	0.00	3.08
3257	3295	5.529060	GGTGATCATTCTTGGCTAAACTAGG	59.471	44.000	0.00	0.00	0.00	3.02
3258	3296	6.352516	AGGTGATCATTCTTGGCTAAACTAG	58.647	40.000	0.00	0.00	0.00	2.57
3259	3297	6.313519	AGGTGATCATTCTTGGCTAAACTA	57.686	37.500	0.00	0.00	0.00	2.24
3260	3298	5.184892	AGGTGATCATTCTTGGCTAAACT	57.815	39.130	0.00	0.00	0.00	2.66
3261	3299	5.415701	TCAAGGTGATCATTCTTGGCTAAAC	59.584	40.000	26.94	3.20	38.59	2.01
3262	3300	5.569355	TCAAGGTGATCATTCTTGGCTAAA	58.431	37.500	26.94	14.18	38.59	1.85
3263	3301	5.178096	TCAAGGTGATCATTCTTGGCTAA	57.822	39.130	26.94	14.42	38.59	3.09
3264	3302	4.842531	TCAAGGTGATCATTCTTGGCTA	57.157	40.909	26.94	14.66	38.59	3.93
3265	3303	3.726557	TCAAGGTGATCATTCTTGGCT	57.273	42.857	26.94	4.41	38.59	4.75
3266	3304	4.996788	AATCAAGGTGATCATTCTTGGC	57.003	40.909	26.94	5.58	35.76	4.52
3267	3305	5.009410	GGCTAATCAAGGTGATCATTCTTGG	59.991	44.000	26.94	18.07	35.76	3.61
3268	3306	5.591472	TGGCTAATCAAGGTGATCATTCTTG	59.409	40.000	24.16	24.16	35.76	3.02
3269	3307	5.759059	TGGCTAATCAAGGTGATCATTCTT	58.241	37.500	0.00	3.52	35.76	2.52
3270	3308	5.378230	TGGCTAATCAAGGTGATCATTCT	57.622	39.130	0.00	0.00	35.76	2.40
3271	3309	6.069684	CTTGGCTAATCAAGGTGATCATTC	57.930	41.667	0.00	0.00	40.14	2.67
3281	3319	4.983671	GGGTTAACCTTGGCTAATCAAG	57.016	45.455	23.69	0.00	42.63	3.02
3294	3332	0.675837	GGTCTGGCGAAGGGTTAACC	60.676	60.000	16.85	16.85	40.67	2.85
3295	3333	0.675837	GGGTCTGGCGAAGGGTTAAC	60.676	60.000	0.00	0.00	0.00	2.01
3296	3334	0.838987	AGGGTCTGGCGAAGGGTTAA	60.839	55.000	0.00	0.00	0.00	2.01
3297	3335	0.041535	TAGGGTCTGGCGAAGGGTTA	59.958	55.000	0.00	0.00	0.00	2.85
3298	3336	1.229400	TAGGGTCTGGCGAAGGGTT	60.229	57.895	0.00	0.00	0.00	4.11
3299	3337	1.988406	GTAGGGTCTGGCGAAGGGT	60.988	63.158	0.00	0.00	0.00	4.34
3300	3338	1.265454	AAGTAGGGTCTGGCGAAGGG	61.265	60.000	0.00	0.00	0.00	3.95
3301	3339	0.613777	AAAGTAGGGTCTGGCGAAGG	59.386	55.000	0.00	0.00	0.00	3.46
3302	3340	1.405661	GGAAAGTAGGGTCTGGCGAAG	60.406	57.143	0.00	0.00	0.00	3.79
3303	3341	0.611714	GGAAAGTAGGGTCTGGCGAA	59.388	55.000	0.00	0.00	0.00	4.70
3304	3342	0.543410	TGGAAAGTAGGGTCTGGCGA	60.543	55.000	0.00	0.00	0.00	5.54
3305	3343	0.323629	TTGGAAAGTAGGGTCTGGCG	59.676	55.000	0.00	0.00	0.00	5.69
3306	3344	2.808906	ATTGGAAAGTAGGGTCTGGC	57.191	50.000	0.00	0.00	0.00	4.85
3307	3345	3.689649	CGAAATTGGAAAGTAGGGTCTGG	59.310	47.826	0.00	0.00	0.00	3.86
3308	3346	4.324267	ACGAAATTGGAAAGTAGGGTCTG	58.676	43.478	0.00	0.00	0.00	3.51
3309	3347	4.635699	ACGAAATTGGAAAGTAGGGTCT	57.364	40.909	0.00	0.00	0.00	3.85
3401	3439	5.279758	GGATAGGATAGTTCTTTCTGGGCTC	60.280	48.000	0.00	0.00	0.00	4.70
3778	3816	7.640313	TCTTCCTACTAGTGAAACCAGATCTA	58.360	38.462	5.39	0.00	37.80	1.98
3960	3998	2.586425	CCTTCTTTTCTGTGCCTTCCA	58.414	47.619	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.