AutoCloner

Multiple sequence alignment - TraesCS5D01G088500

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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	TraesCS5D01G088500	chr5D	100.000	3818	0	0	1	3818	94499032	94502849	0.000000e+00	7051
1	TraesCS5D01G088500	chr5D	86.957	138	16	1	1470	1605	443071187	443071050	1.840000e-33	154
2	TraesCS5D01G088500	chr5B	97.231	2925	73	6	808	3729	101845399	101848318	0.000000e+00	4946
3	TraesCS5D01G088500	chr5B	79.354	712	89	30	2945	3639	539315109	539314439	7.520000e-122	448
4	TraesCS5D01G088500	chr5B	93.478	276	17	1	426	701	418818584	418818310	3.550000e-110	409
5	TraesCS5D01G088500	chr5B	86.082	194	24	2	1470	1661	539315497	539315305	5.000000e-49	206
6	TraesCS5D01G088500	chr5B	90.066	151	5	1	1	151	101844921	101845061	1.810000e-43	187
7	TraesCS5D01G088500	chr5B	92.105	114	5	3	697	809	101845056	101845166	1.420000e-34	158
8	TraesCS5D01G088500	chr5B	94.521	73	3	1	3746	3818	101848305	101848376	1.120000e-20	111
9	TraesCS5D01G088500	chr5A	96.966	2933	79	8	801	3729	88988622	88991548	0.000000e+00	4915
10	TraesCS5D01G088500	chr5A	79.144	1122	138	46	2574	3676	559097917	559096873	0.000000e+00	688
11	TraesCS5D01G088500	chr5A	94.937	158	8	0	1	158	88988334	88988491	8.190000e-62	248
12	TraesCS5D01G088500	chr5A	86.154	195	24	2	1469	1661	559098108	559097915	1.390000e-49	207
13	TraesCS5D01G088500	chr5A	94.068	118	4	3	692	809	88988484	88988598	3.920000e-40	176
14	TraesCS5D01G088500	chr5A	95.890	73	2	1	3746	3818	88991535	88991606	2.410000e-22	117
15	TraesCS5D01G088500	chr6D	93.455	275	17	1	426	700	201882305	201882578	1.280000e-109	407
16	TraesCS5D01G088500	chr6D	93.116	276	18	1	426	701	464139389	464139115	1.650000e-108	403
17	TraesCS5D01G088500	chr6D	94.094	254	9	4	160	412	201882072	201882320	7.740000e-102	381
18	TraesCS5D01G088500	chr2A	93.704	270	16	1	426	695	738019843	738020111	1.650000e-108	403
19	TraesCS5D01G088500	chr2A	93.309	269	12	4	145	412	738019595	738019858	3.580000e-105	392
20	TraesCS5D01G088500	chr1A	93.091	275	18	1	426	700	511161552	511161825	5.940000e-108	401
21	TraesCS5D01G088500	chr1A	92.248	258	16	2	156	412	511161313	511161567	2.800000e-96	363
22	TraesCS5D01G088500	chr4D	95.294	255	7	3	160	412	395485048	395485299	2.140000e-107	399
23	TraesCS5D01G088500	chr4D	93.040	273	18	1	426	698	395485284	395485555	7.690000e-107	398
24	TraesCS5D01G088500	chr4D	91.288	264	13	5	151	412	365507944	365508199	6.070000e-93	351
25	TraesCS5D01G088500	chr6A	92.391	276	20	1	426	701	610528187	610527913	3.580000e-105	392
26	TraesCS5D01G088500	chr4B	92.115	279	20	2	426	703	821006	820729	3.580000e-105	392
27	TraesCS5D01G088500	chr2D	94.553	257	9	2	156	412	329897558	329897307	3.580000e-105	392
28	TraesCS5D01G088500	chr2D	90.217	276	18	6	142	412	632459614	632459885	6.070000e-93	351
29	TraesCS5D01G088500	chr7D	92.391	276	15	2	426	701	168503207	168502938	4.630000e-104	388
30	TraesCS5D01G088500	chr7D	94.208	259	6	5	155	412	168503442	168503192	1.660000e-103	387
31	TraesCS5D01G088500	chr3D	93.411	258	11	3	156	412	87674638	87674386	1.000000e-100	377

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	TraesCS5D01G088500	chr5D	94499032	94502849	3817	False	7051.0	7051	100.00000	1	3818	1	chr5D.!!$F1	3817
1	TraesCS5D01G088500	chr5B	101844921	101848376	3455	False	1350.5	4946	93.48075	1	3818	4	chr5B.!!$F1	3817
2	TraesCS5D01G088500	chr5B	539314439	539315497	1058	True	327.0	448	82.71800	1470	3639	2	chr5B.!!$R2	2169
3	TraesCS5D01G088500	chr5A	88988334	88991606	3272	False	1364.0	4915	95.46525	1	3818	4	chr5A.!!$F1	3817
4	TraesCS5D01G088500	chr5A	559096873	559098108	1235	True	447.5	688	82.64900	1469	3676	2	chr5A.!!$R1	2207
5	TraesCS5D01G088500	chr6D	201882072	201882578	506	False	394.0	407	93.77450	160	700	2	chr6D.!!$F1	540
6	TraesCS5D01G088500	chr2A	738019595	738020111	516	False	397.5	403	93.50650	145	695	2	chr2A.!!$F1	550
7	TraesCS5D01G088500	chr1A	511161313	511161825	512	False	382.0	401	92.66950	156	700	2	chr1A.!!$F1	544
8	TraesCS5D01G088500	chr4D	395485048	395485555	507	False	398.5	399	94.16700	160	698	2	chr4D.!!$F2	538
9	TraesCS5D01G088500	chr7D	168502938	168503442	504	True	387.5	388	93.29950	155	701	2	chr7D.!!$R1	546

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
840	1100	0.104934	ACTGCCTATCCCGGGAGAAT	60.105	55.000	30.42	15.37	44.48	2.40	F
957	1217	4.278513	CAAACCACCGCCCCCTCA	62.279	66.667	0.00	0.00	0.00	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1647	1909	0.882927	GCACGGTGTTCCAGCTTACA	60.883	55.0	10.24	0.0	33.46	2.41	R
2923	3187	0.694771	TTGCAGGATTCACTGGAGCT	59.305	50.0	0.00	0.0	39.99	4.09	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
105	106	5.542779	CTTTTCGGTCTGCTAGGCTATATT	58.457	41.667	0.00	0.00	0.00	1.28
106	107	5.546621	TTTCGGTCTGCTAGGCTATATTT	57.453	39.130	0.00	0.00	0.00	1.40
107	108	5.546621	TTCGGTCTGCTAGGCTATATTTT	57.453	39.130	0.00	0.00	0.00	1.82
108	109	5.546621	TCGGTCTGCTAGGCTATATTTTT	57.453	39.130	0.00	0.00	0.00	1.94
203	224	7.528307	ACGCACGTTTTAACATTATTATGGAA	58.472	30.769	0.00	0.00	36.01	3.53
206	227	9.296400	GCACGTTTTAACATTATTATGGAATGT	57.704	29.630	0.00	0.00	46.89	2.71
412	437	6.443849	TGTGGGATGGAGAGAGTATAACTTTT	59.556	38.462	0.00	0.00	0.00	2.27
413	438	7.037586	TGTGGGATGGAGAGAGTATAACTTTTT	60.038	37.037	0.00	0.00	0.00	1.94
443	468	8.887717	TGAGTAACGAGAGAGTATAACTTTACC	58.112	37.037	0.00	0.00	0.00	2.85
508	533	0.963962	CTCAAACTGCAACATGGGCT	59.036	50.000	12.08	0.00	0.00	5.19
619	644	2.704572	CGAATCCCACTCTTTTCAGCT	58.295	47.619	0.00	0.00	0.00	4.24
649	674	1.202580	AGCACACGAATGGCTAGGATC	60.203	52.381	0.00	0.00	35.82	3.36
663	688	0.248565	AGGATCGATGATCATGCCCG	59.751	55.000	14.30	10.89	40.50	6.13
669	694	1.462283	CGATGATCATGCCCGATTCAC	59.538	52.381	14.30	0.00	0.00	3.18
670	695	1.808945	GATGATCATGCCCGATTCACC	59.191	52.381	14.30	0.00	0.00	4.02
673	698	0.466189	ATCATGCCCGATTCACCACC	60.466	55.000	0.00	0.00	0.00	4.61
674	699	1.077501	CATGCCCGATTCACCACCT	60.078	57.895	0.00	0.00	0.00	4.00
675	700	0.680921	CATGCCCGATTCACCACCTT	60.681	55.000	0.00	0.00	0.00	3.50
676	701	0.394352	ATGCCCGATTCACCACCTTC	60.394	55.000	0.00	0.00	0.00	3.46
677	702	1.749258	GCCCGATTCACCACCTTCC	60.749	63.158	0.00	0.00	0.00	3.46
678	703	1.991230	CCCGATTCACCACCTTCCT	59.009	57.895	0.00	0.00	0.00	3.36
809	835	1.212935	CCTGTTTGGCCAGCTATACCT	59.787	52.381	5.11	0.00	0.00	3.08
811	837	2.684881	CTGTTTGGCCAGCTATACCTTG	59.315	50.000	5.11	0.00	0.00	3.61
840	1100	0.104934	ACTGCCTATCCCGGGAGAAT	60.105	55.000	30.42	15.37	44.48	2.40
957	1217	4.278513	CAAACCACCGCCCCCTCA	62.279	66.667	0.00	0.00	0.00	3.86
1647	1909	0.616111	AGATGCCGGAGAAGGACACT	60.616	55.000	5.05	0.00	0.00	3.55
2085	2347	2.159128	TGACATGTTTTGCAAGTGTGGG	60.159	45.455	0.00	0.51	0.00	4.61
2109	2371	2.286833	CGTAAACCGGGCTGATTATGTG	59.713	50.000	6.32	0.00	0.00	3.21
2210	2472	0.890996	AAGGCGCTGGACTTCTTTGG	60.891	55.000	7.64	0.00	36.54	3.28
2244	2506	2.124695	GGGTTCCGTCCTGATGCC	60.125	66.667	0.00	0.00	0.00	4.40
2739	3001	3.137544	ACTCAGACTCGGACCAGATATCT	59.862	47.826	0.00	0.00	0.00	1.98
2853	3115	4.580167	GGGTATGCTAAATTGCTCATGTCA	59.420	41.667	0.00	0.00	0.00	3.58
2900	3164	1.154035	GGTGTTAGCATTGCACGGC	60.154	57.895	11.91	0.54	34.25	5.68
2923	3187	3.378112	GCAATCTATGTAAGCAAGCACCA	59.622	43.478	0.00	0.00	0.00	4.17
2961	3251	3.439476	GCAATCAAGAAGATGCTGTGACT	59.561	43.478	0.00	0.00	36.96	3.41
2989	3279	2.170607	AGAATTACCCACGATGGACTGG	59.829	50.000	5.71	0.00	40.96	4.00
3090	3380	5.142061	TGTTAAGACGAAAGCTGGTGATA	57.858	39.130	0.00	0.00	0.00	2.15
3174	3471	6.998802	AGTACTTCTAGTGCTTCACTTCATT	58.001	36.000	4.70	0.00	42.59	2.57
3180	3477	5.827797	TCTAGTGCTTCACTTCATTTGGTTT	59.172	36.000	4.70	0.00	42.59	3.27
3309	3614	7.264947	CAGAAAGTGGTTATGTTGGAAAAGTT	58.735	34.615	0.00	0.00	0.00	2.66
3324	3629	7.259290	TGGAAAAGTTGAATAGTTGAGTGTC	57.741	36.000	0.00	0.00	0.00	3.67
3417	3725	7.926555	ACAATCTTCGTAATATTCAGATTCGGT	59.073	33.333	0.00	0.00	32.91	4.69
3432	3740	8.365399	TCAGATTCGGTTATTAAGCTTGTATG	57.635	34.615	9.86	0.00	0.00	2.39
3570	3881	6.406370	TCTTGTTTCTCTGTCTTCTGTCAAA	58.594	36.000	0.00	0.00	0.00	2.69
3581	3892	9.342308	TCTGTCTTCTGTCAAATTTTAACTCAT	57.658	29.630	0.00	0.00	0.00	2.90
3722	4039	9.921637	GTGGAATGTTTGGAACTTCAATAATTA	57.078	29.630	0.00	0.00	0.00	1.40
3728	4045	9.959749	TGTTTGGAACTTCAATAATTAGTTCAC	57.040	29.630	16.19	9.03	45.97	3.18
3729	4046	9.959749	GTTTGGAACTTCAATAATTAGTTCACA	57.040	29.630	16.19	10.62	45.97	3.58
3787	4104	5.152623	TCAGACTGGTCCATGTCTTTTAG	57.847	43.478	16.77	9.30	41.06	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	4.033776	CCTGGGCCGAGGAGCAAA	62.034	66.667	29.00	0.00	34.69	3.68
112	113	3.455543	ACAATCCAATAGGCCCAAAATGG	59.544	43.478	0.00	1.17	37.25	3.16
113	114	4.758773	ACAATCCAATAGGCCCAAAATG	57.241	40.909	0.00	0.00	33.74	2.32
114	115	5.488561	AGAAACAATCCAATAGGCCCAAAAT	59.511	36.000	0.00	0.00	33.74	1.82
242	264	7.546358	ACGATATTTTCATTTTGCCTTGATGA	58.454	30.769	0.00	0.00	0.00	2.92
243	265	7.760131	ACGATATTTTCATTTTGCCTTGATG	57.240	32.000	0.00	0.00	0.00	3.07
244	266	8.776376	AAACGATATTTTCATTTTGCCTTGAT	57.224	26.923	0.00	0.00	0.00	2.57
417	442	8.887717	GGTAAAGTTATACTCTCTCGTTACTCA	58.112	37.037	0.00	0.00	0.00	3.41
418	443	8.061268	CGGTAAAGTTATACTCTCTCGTTACTC	58.939	40.741	0.00	0.00	0.00	2.59
419	444	7.550906	ACGGTAAAGTTATACTCTCTCGTTACT	59.449	37.037	0.00	0.00	0.00	2.24
420	445	7.689299	ACGGTAAAGTTATACTCTCTCGTTAC	58.311	38.462	0.00	0.00	0.00	2.50
421	446	7.849804	ACGGTAAAGTTATACTCTCTCGTTA	57.150	36.000	0.00	0.00	0.00	3.18
422	447	6.749923	ACGGTAAAGTTATACTCTCTCGTT	57.250	37.500	0.00	0.00	0.00	3.85
423	448	9.717942	ATATACGGTAAAGTTATACTCTCTCGT	57.282	33.333	0.00	0.00	0.00	4.18
434	459	9.412460	TCAGAGAGGAAATATACGGTAAAGTTA	57.588	33.333	0.00	0.00	0.00	2.24
435	460	8.302515	TCAGAGAGGAAATATACGGTAAAGTT	57.697	34.615	0.00	0.00	0.00	2.66
436	461	7.893124	TCAGAGAGGAAATATACGGTAAAGT	57.107	36.000	0.00	0.00	0.00	2.66
437	462	9.595823	TTTTCAGAGAGGAAATATACGGTAAAG	57.404	33.333	0.00	0.00	36.71	1.85
438	463	9.374838	GTTTTCAGAGAGGAAATATACGGTAAA	57.625	33.333	0.00	0.00	36.71	2.01
439	464	8.533657	TGTTTTCAGAGAGGAAATATACGGTAA	58.466	33.333	0.00	0.00	36.71	2.85
440	465	8.070034	TGTTTTCAGAGAGGAAATATACGGTA	57.930	34.615	0.00	0.00	36.71	4.02
441	466	6.942976	TGTTTTCAGAGAGGAAATATACGGT	58.057	36.000	0.00	0.00	36.71	4.83
442	467	7.549488	AGTTGTTTTCAGAGAGGAAATATACGG	59.451	37.037	0.00	0.00	36.71	4.02
443	468	8.480643	AGTTGTTTTCAGAGAGGAAATATACG	57.519	34.615	0.00	0.00	36.71	3.06
508	533	4.665009	AGTGGCCCATATTGATTCCTCTTA	59.335	41.667	0.00	0.00	0.00	2.10
619	644	3.190327	CCATTCGTGTGCTAAATCCAACA	59.810	43.478	0.00	0.00	0.00	3.33
649	674	1.462283	GTGAATCGGGCATGATCATCG	59.538	52.381	4.86	7.09	0.00	3.84
663	688	4.762289	ATAGTGAGGAAGGTGGTGAATC	57.238	45.455	0.00	0.00	0.00	2.52
669	694	9.233649	CTATACTACTTATAGTGAGGAAGGTGG	57.766	40.741	0.00	0.00	41.92	4.61
780	806	3.128375	CCAAACAGGCCGTGCTTT	58.872	55.556	0.00	0.00	0.00	3.51
809	835	3.132289	GGATAGGCAGTGTGCTACTACAA	59.868	47.826	0.00	0.00	44.28	2.41
811	837	2.036089	GGGATAGGCAGTGTGCTACTAC	59.964	54.545	0.00	0.00	44.28	2.73
840	1100	1.754621	TGGGTCAGCGCCAAAAACA	60.755	52.632	2.29	0.00	0.00	2.83
1647	1909	0.882927	GCACGGTGTTCCAGCTTACA	60.883	55.000	10.24	0.00	33.46	2.41
1839	2101	1.000955	GCCGAGACCATTATCGTCCAT	59.999	52.381	0.00	0.00	37.23	3.41
2022	2284	2.671682	GACCTCCCCAGTTGCCTC	59.328	66.667	0.00	0.00	0.00	4.70
2085	2347	1.303091	AATCAGCCCGGTTTACGCAC	61.303	55.000	0.00	0.00	42.52	5.34
2109	2371	6.348050	CCTTCTCAGCTATTTCAGTGTCAAAC	60.348	42.308	0.00	0.00	0.00	2.93
2210	2472	2.171003	ACCCTTGTAGCTTCATTTGGC	58.829	47.619	0.00	0.00	0.00	4.52
2244	2506	4.389664	AAGAACGTTGATCATTGTCACG	57.610	40.909	5.00	13.80	0.00	4.35
2739	3001	3.378512	ACTCAGCCTATCAACCATCTCA	58.621	45.455	0.00	0.00	0.00	3.27
2797	3059	1.068588	TCACTGCACAAGTAGCTCGTT	59.931	47.619	0.00	0.00	36.83	3.85
2799	3061	1.336332	ACTCACTGCACAAGTAGCTCG	60.336	52.381	0.00	0.00	36.83	5.03
2805	3067	2.292267	CAAAGGACTCACTGCACAAGT	58.708	47.619	0.00	0.00	40.93	3.16
2878	3142	1.739466	CGTGCAATGCTAACACCTCAT	59.261	47.619	6.82	0.00	0.00	2.90
2900	3164	3.546815	GGTGCTTGCTTACATAGATTGCG	60.547	47.826	0.00	0.00	0.00	4.85
2923	3187	0.694771	TTGCAGGATTCACTGGAGCT	59.305	50.000	0.00	0.00	39.99	4.09
2961	3251	4.509616	CATCGTGGGTAATTCTGTACCAA	58.490	43.478	3.93	0.00	44.73	3.67
3090	3380	3.864789	AGTGTTTTGTCAGTCCATCCT	57.135	42.857	0.00	0.00	0.00	3.24
3180	3477	4.520874	TCATGGCTTGTTTTGGTTTCGATA	59.479	37.500	0.00	0.00	0.00	2.92
3309	3614	6.016527	ACGACTGTAAGACACTCAACTATTCA	60.017	38.462	0.00	0.00	37.43	2.57
3324	3629	5.880054	AAAATGGGATGAACGACTGTAAG	57.120	39.130	0.00	0.00	42.29	2.34
3409	3717	7.441458	GGACATACAAGCTTAATAACCGAATCT	59.559	37.037	0.00	0.00	0.00	2.40
3432	3740	8.885722	TGAATGATTTATACGGTTTTGTAGGAC	58.114	33.333	0.00	0.00	0.00	3.85
3503	3811	7.212976	ACCTCATAACATAGCATGACACTAAG	58.787	38.462	0.00	0.00	0.00	2.18
3545	3854	5.595885	TGACAGAAGACAGAGAAACAAGAG	58.404	41.667	0.00	0.00	0.00	2.85
3581	3892	7.004555	TCAGGATTCTTTGTAGTCTTAGCAA	57.995	36.000	0.00	0.00	0.00	3.91
3745	4062	9.574516	AGTCTGAACTTGGTGAACTAATTTATT	57.425	29.630	0.00	0.00	28.74	1.40
3746	4063	9.003658	CAGTCTGAACTTGGTGAACTAATTTAT	57.996	33.333	0.00	0.00	31.71	1.40
3747	4064	7.444183	CCAGTCTGAACTTGGTGAACTAATTTA	59.556	37.037	0.00	0.00	31.71	1.40
3748	4065	6.263168	CCAGTCTGAACTTGGTGAACTAATTT	59.737	38.462	0.00	0.00	31.71	1.82
3749	4066	5.765182	CCAGTCTGAACTTGGTGAACTAATT	59.235	40.000	0.00	0.00	31.71	1.40
3750	4067	5.163195	ACCAGTCTGAACTTGGTGAACTAAT	60.163	40.000	0.00	0.00	36.31	1.73
3751	4068	4.163458	ACCAGTCTGAACTTGGTGAACTAA	59.837	41.667	0.00	0.00	36.31	2.24
3752	4069	3.709653	ACCAGTCTGAACTTGGTGAACTA	59.290	43.478	0.00	0.00	36.31	2.24
3753	4070	2.505819	ACCAGTCTGAACTTGGTGAACT	59.494	45.455	0.00	0.00	36.31	3.01
3787	4104	7.433425	GCCATTTCTTAGCATAACAATGACTTC	59.567	37.037	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.