AutoCloner

Multiple sequence alignment - TraesCS5B01G315000

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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	TraesCS5B01G315000	chr5B	100.000	3605	0	0	1	3605	496991160	496994764	0.000000e+00	6658
1	TraesCS5B01G315000	chr5B	89.712	729	72	3	1	727	42247595	42246868	0.000000e+00	928
2	TraesCS5B01G315000	chr5D	96.328	2560	61	7	1044	3602	412608524	412611051	0.000000e+00	4176
3	TraesCS5B01G315000	chr5A	96.606	2269	76	1	721	2988	524719566	524721834	0.000000e+00	3762
4	TraesCS5B01G315000	chr5A	93.822	259	10	4	3178	3436	524721830	524722082	5.650000e-103	385
5	TraesCS5B01G315000	chr5A	94.595	185	9	1	3419	3602	524723996	524724180	5.890000e-73	285
6	TraesCS5B01G315000	chr6D	91.644	730	59	2	1	728	445915224	445914495	0.000000e+00	1009
7	TraesCS5B01G315000	chr6D	87.500	640	61	5	1736	2372	2702448	2701825	0.000000e+00	721
8	TraesCS5B01G315000	chr2B	91.644	730	55	3	1	728	799450332	799449607	0.000000e+00	1005
9	TraesCS5B01G315000	chr7B	91.298	724	61	2	4	725	211785682	211784959	0.000000e+00	987
10	TraesCS5B01G315000	chr7B	89.684	727	72	3	1	725	58647448	58648173	0.000000e+00	924
11	TraesCS5B01G315000	chr7B	89.409	727	75	2	1	725	560537391	560538117	0.000000e+00	915
12	TraesCS5B01G315000	chr4D	90.574	732	64	3	3	729	4088292	4089023	0.000000e+00	965
13	TraesCS5B01G315000	chr2D	90.522	728	68	1	1	727	589511340	589512067	0.000000e+00	961
14	TraesCS5B01G315000	chr2D	89.821	727	69	5	1	725	56436264	56435541	0.000000e+00	928

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	TraesCS5B01G315000	chr5B	496991160	496994764	3604	False	6658.000000	6658	100.000000	1	3605	1	chr5B.!!$F1	3604
1	TraesCS5B01G315000	chr5B	42246868	42247595	727	True	928.000000	928	89.712000	1	727	1	chr5B.!!$R1	726
2	TraesCS5B01G315000	chr5D	412608524	412611051	2527	False	4176.000000	4176	96.328000	1044	3602	1	chr5D.!!$F1	2558
3	TraesCS5B01G315000	chr5A	524719566	524724180	4614	False	1477.333333	3762	95.007667	721	3602	3	chr5A.!!$F1	2881
4	TraesCS5B01G315000	chr6D	445914495	445915224	729	True	1009.000000	1009	91.644000	1	728	1	chr6D.!!$R2	727
5	TraesCS5B01G315000	chr6D	2701825	2702448	623	True	721.000000	721	87.500000	1736	2372	1	chr6D.!!$R1	636
6	TraesCS5B01G315000	chr2B	799449607	799450332	725	True	1005.000000	1005	91.644000	1	728	1	chr2B.!!$R1	727
7	TraesCS5B01G315000	chr7B	211784959	211785682	723	True	987.000000	987	91.298000	4	725	1	chr7B.!!$R1	721
8	TraesCS5B01G315000	chr7B	58647448	58648173	725	False	924.000000	924	89.684000	1	725	1	chr7B.!!$F1	724
9	TraesCS5B01G315000	chr7B	560537391	560538117	726	False	915.000000	915	89.409000	1	725	1	chr7B.!!$F2	724
10	TraesCS5B01G315000	chr4D	4088292	4089023	731	False	965.000000	965	90.574000	3	729	1	chr4D.!!$F1	726
11	TraesCS5B01G315000	chr2D	589511340	589512067	727	False	961.000000	961	90.522000	1	727	1	chr2D.!!$F1	726
12	TraesCS5B01G315000	chr2D	56435541	56436264	723	True	928.000000	928	89.821000	1	725	1	chr2D.!!$R1	724

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
41	42	0.872388	GCCATTTCGTCGAACACCTT	59.128	50.000	7.29	0.00	0.00	3.50	F
1030	1041	0.543174	ACCACTCGGCCTCTCTCTTT	60.543	55.000	0.00	0.00	34.57	2.52	F
2016	2030	1.477295	CATGAGCTGCTCTCTCTCACA	59.523	52.381	28.04	8.44	42.38	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2016	2030	1.081641	CGTGGTACGCTTGTCGACT	60.082	57.895	17.92	41.67	4.18	R
2396	2410	0.029834	GGCACCATCGTCATCAATGC	59.970	55.000	0.00	0.00	3.56	R
3265	3280	0.749649	CGCATAGCTCTCAACTCCCT	59.250	55.000	0.00	0.00	4.20	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
41	42	0.872388	GCCATTTCGTCGAACACCTT	59.128	50.000	7.29	0.00	0.00	3.50
66	67	4.324991	GGGGGAGCGACACCGTTT	62.325	66.667	0.00	0.00	44.45	3.60
385	390	2.962827	GCGACCTCGACAGTGACGA	61.963	63.158	16.43	16.43	43.02	4.20
422	427	1.822990	GTCCATGTTAGTGAGGGACGA	59.177	52.381	0.00	0.00	38.71	4.20
528	538	3.880846	GCCAAATCTCGCTGCGGG	61.881	66.667	23.03	20.33	0.00	6.13
557	567	2.718073	GCTCGGGTCGGCCTTCTAA	61.718	63.158	5.77	0.00	34.45	2.10
745	756	6.016360	GCTCTAATAAGATCTCTCTGCTCACA	60.016	42.308	0.00	0.00	0.00	3.58
746	757	7.309377	GCTCTAATAAGATCTCTCTGCTCACAT	60.309	40.741	0.00	0.00	0.00	3.21
749	760	6.921486	ATAAGATCTCTCTGCTCACATGAT	57.079	37.500	0.00	0.00	0.00	2.45
787	798	7.039363	TCCACTGTTTACCCATTATTTCTTTGG	60.039	37.037	0.00	0.00	0.00	3.28
827	838	6.716628	CCATAATATGGTTGCAAGTATCCACT	59.283	38.462	11.07	2.44	45.54	4.00
829	840	9.453572	CATAATATGGTTGCAAGTATCCACTAT	57.546	33.333	8.55	6.01	33.48	2.12
830	841	7.750229	AATATGGTTGCAAGTATCCACTATG	57.250	36.000	8.55	0.00	33.48	2.23
856	867	8.063630	GTGTGAGAAAACTTGCCAATAAATTTG	58.936	33.333	0.00	0.00	0.00	2.32
915	926	7.112122	TGATAGTTCAACTGGTTAGAATGCAT	58.888	34.615	0.00	0.00	0.00	3.96
933	944	0.890683	ATTGGCCAGCGGAAAGAAAG	59.109	50.000	5.11	0.00	0.00	2.62
936	947	0.958822	GGCCAGCGGAAAGAAAGAAA	59.041	50.000	0.00	0.00	0.00	2.52
937	948	1.546029	GGCCAGCGGAAAGAAAGAAAT	59.454	47.619	0.00	0.00	0.00	2.17
1030	1041	0.543174	ACCACTCGGCCTCTCTCTTT	60.543	55.000	0.00	0.00	34.57	2.52
1034	1045	1.662438	CTCGGCCTCTCTCTTTCGCT	61.662	60.000	0.00	0.00	0.00	4.93
1224	1235	1.592669	CGACGGCATCATGGAGGTC	60.593	63.158	0.00	0.00	0.00	3.85
1674	1685	1.526917	CATCCTGTCCAATCCCGCC	60.527	63.158	0.00	0.00	0.00	6.13
1728	1739	3.083997	GTGCCCTCCCCTGACGAT	61.084	66.667	0.00	0.00	0.00	3.73
2016	2030	1.477295	CATGAGCTGCTCTCTCTCACA	59.523	52.381	28.04	8.44	42.38	3.58
2099	2113	6.798959	CCAAAGAAGATTAAAGAGTTCTTGCG	59.201	38.462	0.00	0.00	38.84	4.85
2118	2132	5.401531	TGCGTAAGTATCAGGGGATATTC	57.598	43.478	0.00	0.00	38.24	1.75
2396	2410	1.986882	AAGAGGAAAGTTGGTGCTGG	58.013	50.000	0.00	0.00	0.00	4.85
2398	2412	0.823356	GAGGAAAGTTGGTGCTGGCA	60.823	55.000	0.00	0.00	0.00	4.92
2399	2413	0.178953	AGGAAAGTTGGTGCTGGCAT	60.179	50.000	0.00	0.00	0.00	4.40
2403	2417	1.636148	AAGTTGGTGCTGGCATTGAT	58.364	45.000	0.00	0.00	0.00	2.57
2433	2447	0.106167	CCGATAGTGGGGAGGACTCA	60.106	60.000	1.32	0.00	0.00	3.41
2457	2471	5.419155	AGGAGTTGAATCACTCTACATCGAA	59.581	40.000	10.85	0.00	42.63	3.71
2478	2492	7.275183	TCGAATGAGGAACAGAATCATACAAT	58.725	34.615	0.00	0.00	33.40	2.71
2587	2601	4.186926	CACCATGGTGTAGTGATCTTGAG	58.813	47.826	32.94	5.73	40.91	3.02
2632	2646	5.684704	TGAGGTGAAAATTTGAGTGAGAGT	58.315	37.500	0.00	0.00	0.00	3.24
2654	2668	0.037975	TCGTCCTAAACTTGCGGACC	60.038	55.000	0.00	0.00	43.30	4.46
2849	2864	7.819500	TGGATCTATTTCATTCATTTCTCCCT	58.180	34.615	0.00	0.00	0.00	4.20
2939	2954	7.253950	GTTTTGCAACATACTGTAACCAAACAG	60.254	37.037	0.00	2.56	41.41	3.16
2964	2979	8.136165	AGTTGATACTGTAATCGGTTAGATGAC	58.864	37.037	0.00	0.00	40.50	3.06
3071	3086	1.037030	CCGTGGGAATGTGGGATTGG	61.037	60.000	0.00	0.00	0.00	3.16
3072	3087	0.034574	CGTGGGAATGTGGGATTGGA	60.035	55.000	0.00	0.00	0.00	3.53
3073	3088	1.410083	CGTGGGAATGTGGGATTGGAT	60.410	52.381	0.00	0.00	0.00	3.41
3074	3089	2.034124	GTGGGAATGTGGGATTGGATG	58.966	52.381	0.00	0.00	0.00	3.51
3075	3090	1.645391	TGGGAATGTGGGATTGGATGT	59.355	47.619	0.00	0.00	0.00	3.06
3076	3091	2.034124	GGGAATGTGGGATTGGATGTG	58.966	52.381	0.00	0.00	0.00	3.21
3125	3140	1.026182	CGTGCACATGGTGGCATAGT	61.026	55.000	18.64	0.00	42.75	2.12
3126	3141	0.452987	GTGCACATGGTGGCATAGTG	59.547	55.000	13.17	0.00	42.75	2.74
3180	3195	0.682209	ATCAGGGTTGCCACTCATGC	60.682	55.000	0.00	0.00	0.00	4.06
3265	3280	3.593096	TGAACACATGTTTTTGCAGCAA	58.407	36.364	2.83	2.83	38.56	3.91
3284	3299	0.749649	AGGGAGTTGAGAGCTATGCG	59.250	55.000	0.00	0.00	0.00	4.73
3356	3372	9.590088	CGTTGTAGGTTATCTTGTTAGTTTTTC	57.410	33.333	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
77	78	2.528127	TGGAAAGAGGTGCCCCGA	60.528	61.111	0.00	0.00	35.12	5.14
343	347	4.733725	TCCTTCCCCTCGGGTGGG	62.734	72.222	2.53	2.53	44.74	4.61
378	383	3.699894	CTGCTGCCCCTCGTCACT	61.700	66.667	0.00	0.00	0.00	3.41
409	414	2.693762	CGCGGTCGTCCCTCACTAA	61.694	63.158	0.00	0.00	0.00	2.24
410	415	3.129502	CGCGGTCGTCCCTCACTA	61.130	66.667	0.00	0.00	0.00	2.74
528	538	3.541713	CCCGAGCTCAGCCCCTAC	61.542	72.222	15.40	0.00	0.00	3.18
553	563	3.771216	ACCTCTAGTTTCACGGGTTAGA	58.229	45.455	0.00	0.00	0.00	2.10
557	567	1.346722	CCAACCTCTAGTTTCACGGGT	59.653	52.381	0.00	0.00	36.18	5.28
631	642	3.083349	CCTGCCCGATCAGACCCA	61.083	66.667	5.61	0.00	36.19	4.51
787	798	6.820656	CCATATTATGGTGATCTAGCTGAACC	59.179	42.308	13.70	0.00	45.54	3.62
827	838	7.517614	TTATTGGCAAGTTTTCTCACACATA	57.482	32.000	5.96	0.00	0.00	2.29
829	840	5.843673	TTATTGGCAAGTTTTCTCACACA	57.156	34.783	5.96	0.00	0.00	3.72
830	841	7.713764	AATTTATTGGCAAGTTTTCTCACAC	57.286	32.000	5.96	0.00	0.00	3.82
856	867	5.288804	TGGCAGCTTTTGTTTTCATACTTC	58.711	37.500	0.00	0.00	0.00	3.01
915	926	0.179004	TCTTTCTTTCCGCTGGCCAA	60.179	50.000	7.01	0.00	0.00	4.52
933	944	6.458284	GCGACGCAATTTTCATGTTTTATTTC	59.542	34.615	16.42	0.00	0.00	2.17
936	947	4.030083	CGCGACGCAATTTTCATGTTTTAT	59.970	37.500	21.35	0.00	0.00	1.40
937	948	3.359286	CGCGACGCAATTTTCATGTTTTA	59.641	39.130	21.35	0.00	0.00	1.52
965	976	4.829518	TCGGATGCGCACGAGACG	62.830	66.667	14.90	13.47	34.67	4.18
987	998	3.121030	CGCGGGTGAAAGAGGCAG	61.121	66.667	0.00	0.00	0.00	4.85
1728	1739	4.608774	ACGGTGAGGTCGGGTGGA	62.609	66.667	0.00	0.00	0.00	4.02
2016	2030	1.081641	CGTGGTACGCTTGTCGACT	60.082	57.895	17.92	0.00	41.67	4.18
2118	2132	6.540189	CCTGGTTTCCTCTTGTTGATATGTAG	59.460	42.308	0.00	0.00	0.00	2.74
2396	2410	0.029834	GGCACCATCGTCATCAATGC	59.970	55.000	0.00	0.00	0.00	3.56
2398	2412	0.177836	TCGGCACCATCGTCATCAAT	59.822	50.000	0.00	0.00	0.00	2.57
2399	2413	0.177836	ATCGGCACCATCGTCATCAA	59.822	50.000	0.00	0.00	0.00	2.57
2403	2417	0.102300	CACTATCGGCACCATCGTCA	59.898	55.000	0.00	0.00	0.00	4.35
2433	2447	4.950475	TCGATGTAGAGTGATTCAACTCCT	59.050	41.667	10.65	0.00	46.51	3.69
2457	2471	7.281774	GTGTCATTGTATGATTCTGTTCCTCAT	59.718	37.037	0.00	0.00	42.04	2.90
2539	2553	7.627298	AGATGCTAGCATGATAAATCAATCC	57.373	36.000	34.16	14.61	40.69	3.01
2587	2601	9.906660	CCTCAGAATATAACACTCTCTTATCAC	57.093	37.037	0.00	0.00	0.00	3.06
2632	2646	1.614903	TCCGCAAGTTTAGGACGAGAA	59.385	47.619	0.00	0.00	0.00	2.87
2654	2668	5.770162	GGTGATAACTTCCCCAATTCATAGG	59.230	44.000	0.00	0.00	0.00	2.57
2849	2864	4.458295	TCCGTAACACAAACAGTTTTCCAA	59.542	37.500	0.00	0.00	0.00	3.53
2939	2954	7.381678	GGTCATCTAACCGATTACAGTATCAAC	59.618	40.741	0.00	0.00	29.62	3.18
2964	2979	8.882415	ATAGCATTTCTGATTTTATTTGCAGG	57.118	30.769	0.00	0.00	0.00	4.85
2995	3010	2.727123	TGAAGCCAAACAACAGAGGA	57.273	45.000	0.00	0.00	0.00	3.71
3071	3086	2.029649	ACAAAACATGGAGCAGCACATC	60.030	45.455	0.00	0.00	0.00	3.06
3072	3087	1.965643	ACAAAACATGGAGCAGCACAT	59.034	42.857	0.00	0.00	0.00	3.21
3073	3088	1.067364	CACAAAACATGGAGCAGCACA	59.933	47.619	0.00	0.00	0.00	4.57
3074	3089	1.067516	ACACAAAACATGGAGCAGCAC	59.932	47.619	0.00	0.00	0.00	4.40
3075	3090	1.067364	CACACAAAACATGGAGCAGCA	59.933	47.619	0.00	0.00	0.00	4.41
3076	3091	1.067516	ACACACAAAACATGGAGCAGC	59.932	47.619	0.00	0.00	0.00	5.25
3125	3140	1.066716	GCTGCCTGCATGAAAATTCCA	60.067	47.619	0.00	0.00	42.31	3.53
3126	3141	1.206371	AGCTGCCTGCATGAAAATTCC	59.794	47.619	0.00	0.00	45.94	3.01
3180	3195	0.955919	GTTTTCTGACGCCCCCTCAG	60.956	60.000	0.00	0.00	37.14	3.35
3265	3280	0.749649	CGCATAGCTCTCAACTCCCT	59.250	55.000	0.00	0.00	0.00	4.20
3356	3372	8.896744	ACATCATCACCACTGAATTACATTAAG	58.103	33.333	0.00	0.00	0.00	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.