AutoCloner

Multiple sequence alignment - TraesCS4B01G384100

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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	TraesCS4B01G384100	chr4B	100.000	2564	0	0	1	2564	663620616	663623179	0.000000e+00	4735.0
1	TraesCS4B01G384100	chr4B	95.385	910	31	4	672	1580	663520384	663521283	0.000000e+00	1437.0
2	TraesCS4B01G384100	chr4B	92.177	882	65	4	701	1580	662720777	662719898	0.000000e+00	1243.0
3	TraesCS4B01G384100	chr4B	91.904	877	66	4	702	1577	663462565	663463437	0.000000e+00	1221.0
4	TraesCS4B01G384100	chr4B	91.115	619	42	5	1	619	663519198	663519803	0.000000e+00	826.0
5	TraesCS4B01G384100	chr4B	98.000	100	2	0	445	544	663461366	663461465	9.430000e-40	174.0
6	TraesCS4B01G384100	chr4B	95.000	100	4	1	567	665	662721133	662721034	3.420000e-34	156.0
7	TraesCS4B01G384100	chr4B	95.000	100	3	2	567	665	663461548	663461646	3.420000e-34	156.0
8	TraesCS4B01G384100	chr4B	92.857	98	7	0	446	543	662721405	662721308	2.660000e-30	143.0
9	TraesCS4B01G384100	chr4B	94.872	39	2	0	527	565	662721198	662721160	7.660000e-06	62.1
10	TraesCS4B01G384100	chr6B	97.264	987	24	3	1581	2564	565075367	565076353	0.000000e+00	1670.0
11	TraesCS4B01G384100	chr6B	95.335	986	35	5	1580	2564	698030691	698029716	0.000000e+00	1555.0
12	TraesCS4B01G384100	chr1B	96.548	985	27	2	1580	2564	644320449	644321426	0.000000e+00	1624.0
13	TraesCS4B01G384100	chr2B	96.244	985	31	4	1581	2564	768140461	768139482	0.000000e+00	1609.0
14	TraesCS4B01G384100	chr2B	97.692	130	2	1	1582	1710	47447827	47447698	3.320000e-54	222.0
15	TraesCS4B01G384100	chrUn	95.943	986	28	5	1581	2564	41282509	41281534	0.000000e+00	1589.0
16	TraesCS4B01G384100	chr3A	95.745	987	32	4	1579	2564	672647169	672646192	0.000000e+00	1581.0
17	TraesCS4B01G384100	chr5B	95.635	985	33	4	1581	2564	659489124	659488149	0.000000e+00	1572.0
18	TraesCS4B01G384100	chr7B	95.090	998	29	5	1581	2564	747119316	747118325	0.000000e+00	1554.0
19	TraesCS4B01G384100	chr3B	94.500	1000	35	5	1579	2564	766374946	766373953	0.000000e+00	1524.0
20	TraesCS4B01G384100	chr3B	96.947	131	3	1	1581	1710	586844861	586844991	4.300000e-53	219.0

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	TraesCS4B01G384100	chr4B	663620616	663623179	2563	False	4735.000	4735	100.0000	1	2564	1	chr4B.!!$F1	2563
1	TraesCS4B01G384100	chr4B	663519198	663521283	2085	False	1131.500	1437	93.2500	1	1580	2	chr4B.!!$F3	1579
2	TraesCS4B01G384100	chr4B	663461366	663463437	2071	False	517.000	1221	94.9680	445	1577	3	chr4B.!!$F2	1132
3	TraesCS4B01G384100	chr4B	662719898	662721405	1507	True	401.025	1243	93.7265	446	1580	4	chr4B.!!$R1	1134
4	TraesCS4B01G384100	chr6B	565075367	565076353	986	False	1670.000	1670	97.2640	1581	2564	1	chr6B.!!$F1	983
5	TraesCS4B01G384100	chr6B	698029716	698030691	975	True	1555.000	1555	95.3350	1580	2564	1	chr6B.!!$R1	984
6	TraesCS4B01G384100	chr1B	644320449	644321426	977	False	1624.000	1624	96.5480	1580	2564	1	chr1B.!!$F1	984
7	TraesCS4B01G384100	chr2B	768139482	768140461	979	True	1609.000	1609	96.2440	1581	2564	1	chr2B.!!$R2	983
8	TraesCS4B01G384100	chrUn	41281534	41282509	975	True	1589.000	1589	95.9430	1581	2564	1	chrUn.!!$R1	983
9	TraesCS4B01G384100	chr3A	672646192	672647169	977	True	1581.000	1581	95.7450	1579	2564	1	chr3A.!!$R1	985
10	TraesCS4B01G384100	chr5B	659488149	659489124	975	True	1572.000	1572	95.6350	1581	2564	1	chr5B.!!$R1	983
11	TraesCS4B01G384100	chr7B	747118325	747119316	991	True	1554.000	1554	95.0900	1581	2564	1	chr7B.!!$R1	983
12	TraesCS4B01G384100	chr3B	766373953	766374946	993	True	1524.000	1524	94.5000	1579	2564	1	chr3B.!!$R1	985

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
91	92	0.457851	GGAGACAGTAGCAGCGTCAT	59.542	55.0	1.61	0.0	31.92	3.06	F
410	411	0.619832	TTGAGGGCTGGAGATGCTCT	60.620	55.0	0.00	0.0	44.97	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1370	2722	0.041839	CAGCAGTTCGACAAGCACAC	60.042	55.0	5.15	0.0	0.00	3.82	R
2402	3791	0.393402	TCACCTGATGATGCCACTGC	60.393	55.0	0.00	0.0	32.43	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
55	56	3.680786	CGACCTCGACCACTGCCA	61.681	66.667	0.00	0.00	43.02	4.92
57	58	2.524394	ACCTCGACCACTGCCACT	60.524	61.111	0.00	0.00	0.00	4.00
58	59	2.047844	CCTCGACCACTGCCACTG	60.048	66.667	0.00	0.00	0.00	3.66
63	64	3.170672	ACCACTGCCACTGCCTCA	61.171	61.111	0.00	0.00	36.33	3.86
64	65	2.359602	CCACTGCCACTGCCTCAG	60.360	66.667	0.00	0.00	37.52	3.35
88	89	2.352032	GGGGAGACAGTAGCAGCGT	61.352	63.158	0.00	0.00	0.00	5.07
89	90	1.139947	GGGAGACAGTAGCAGCGTC	59.860	63.158	0.00	0.00	0.00	5.19
90	91	1.595993	GGGAGACAGTAGCAGCGTCA	61.596	60.000	1.61	0.00	31.92	4.35
91	92	0.457851	GGAGACAGTAGCAGCGTCAT	59.542	55.000	1.61	0.00	31.92	3.06
109	110	4.035102	GCCAAAGGAGGAGCCGGT	62.035	66.667	1.90	0.00	43.43	5.28
131	132	1.438562	GCGACGAGGAGGAGGAGTAC	61.439	65.000	0.00	0.00	0.00	2.73
342	343	4.893601	TTGCACGTCCGGTCGCAA	62.894	61.111	21.02	17.62	39.02	4.85
385	386	1.571215	AAAATTCGACACGGCCGGTC	61.571	55.000	31.76	28.92	0.00	4.79
392	393	2.590575	CACGGCCGGTCACTGTTT	60.591	61.111	31.76	0.57	0.00	2.83
410	411	0.619832	TTGAGGGCTGGAGATGCTCT	60.620	55.000	0.00	0.00	44.97	4.09
412	413	1.132913	TGAGGGCTGGAGATGCTCTAT	60.133	52.381	0.00	0.00	41.95	1.98
419	420	3.865302	GCTGGAGATGCTCTATGTCATGG	60.865	52.174	0.00	0.00	30.90	3.66
423	424	2.643304	AGATGCTCTATGTCATGGGCAT	59.357	45.455	18.43	18.43	42.05	4.40
445	446	9.221775	GGCATAATAAGTTGTAGAATTTGTTCG	57.778	33.333	0.00	0.00	0.00	3.95
448	449	3.806316	AGTTGTAGAATTTGTTCGCGG	57.194	42.857	6.13	0.00	0.00	6.46
487	488	1.276421	CGAGGCCATATCTTACCCAGG	59.724	57.143	5.01	0.00	0.00	4.45
530	657	1.030457	CCCGTCCTTCGCACTAGTAT	58.970	55.000	0.00	0.00	38.35	2.12
588	740	5.813672	TGTACGGCTAGCAATTAAAAGTAGG	59.186	40.000	18.24	0.00	0.00	3.18
604	756	4.851639	AGTAGGAAGAAAGATGCACCAT	57.148	40.909	0.00	0.00	0.00	3.55
605	757	5.184892	AGTAGGAAGAAAGATGCACCATT	57.815	39.130	0.00	0.00	0.00	3.16
681	1365	5.189180	AGACAGAGATTAATTTGTCTGGGC	58.811	41.667	20.93	14.55	46.12	5.36
756	2105	1.909302	TGGAGAAGGCTCGAAGGAAAT	59.091	47.619	0.00	0.00	42.25	2.17
811	2160	2.091885	TGGCCCCTCCTATGAAATTGTC	60.092	50.000	0.00	0.00	35.26	3.18
820	2169	6.604795	CCTCCTATGAAATTGTCAAACCAGAT	59.395	38.462	0.00	0.00	40.50	2.90
883	2235	1.144913	AGTTAGCTTTGTTGGCCTCCA	59.855	47.619	3.32	0.00	0.00	3.86
890	2242	3.367395	GCTTTGTTGGCCTCCACTAATTC	60.367	47.826	3.32	0.00	30.78	2.17
898	2250	5.437060	TGGCCTCCACTAATTCAAATCTAC	58.563	41.667	3.32	0.00	0.00	2.59
959	2311	3.439293	CCTGCACACACGTCTATAAGAG	58.561	50.000	0.00	0.00	0.00	2.85
970	2322	4.142790	CGTCTATAAGAGCCCTTAGGACA	58.857	47.826	17.40	0.00	39.16	4.02
1004	2356	1.337703	GCACACAACACACATCATGGT	59.662	47.619	0.00	0.00	0.00	3.55
1159	2511	1.526686	GATGCCATCCATCGCCACA	60.527	57.895	0.00	0.00	40.84	4.17
1192	2544	1.317613	GTTGTCTGACATTGCCACCA	58.682	50.000	11.86	0.00	0.00	4.17
1231	2583	0.974383	CAAGTACTCCCACCTCCGTT	59.026	55.000	0.00	0.00	0.00	4.44
1245	2597	4.465512	CGTTGGCTCATGCACGCC	62.466	66.667	14.71	14.71	46.46	5.68
1269	2621	1.658717	CGCTACCGGCATCTTCTCG	60.659	63.158	0.00	0.00	41.91	4.04
1356	2708	2.548178	CGAGAGCATGTGCAACCTT	58.452	52.632	7.83	0.00	45.16	3.50
1370	2722	0.609131	AACCTTTCTCCCATGGTGCG	60.609	55.000	11.73	0.00	32.53	5.34
1428	2780	4.083537	TGCAGCATAAAAGAGTGGTTTACG	60.084	41.667	0.00	0.00	0.00	3.18
1550	2903	2.665185	GTCGCCGACAGCAACCTT	60.665	61.111	13.23	0.00	44.04	3.50
1728	3109	3.256704	ACACCCTCCCTCAATCTTAACA	58.743	45.455	0.00	0.00	0.00	2.41
1811	3192	2.499289	AGAGGCTTCGTGAAGATGTCAT	59.501	45.455	13.60	0.00	40.79	3.06
1890	3271	6.089551	CGTTCTCGAACAAAGTGATAGTCAAT	59.910	38.462	10.10	0.00	41.20	2.57
1907	3288	9.249457	GATAGTCAATCTCAATATGTTTCGTCA	57.751	33.333	0.00	0.00	0.00	4.35
1951	3332	6.578944	AGACGACAAATATGTAGCACCAATA	58.421	36.000	0.00	0.00	40.74	1.90
2272	3661	2.820197	AGTGAGACAGACATAACGCAGA	59.180	45.455	0.00	0.00	0.00	4.26
2311	3700	0.036010	AATGAGAAGTCCTGGGTGCG	60.036	55.000	0.00	0.00	0.00	5.34
2322	3711	0.320374	CTGGGTGCGTGGAGAAACTA	59.680	55.000	0.00	0.00	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	2.359230	GAGGCAGTGGCAGTGGTC	60.359	66.667	22.98	7.84	43.71	4.02
63	64	2.575455	CTACTGTCTCCCCCTCGGCT	62.575	65.000	0.00	0.00	0.00	5.52
64	65	2.043248	TACTGTCTCCCCCTCGGC	60.043	66.667	0.00	0.00	0.00	5.54
68	69	1.687493	GCTGCTACTGTCTCCCCCT	60.687	63.158	0.00	0.00	0.00	4.79
76	77	1.448540	GGCATGACGCTGCTACTGT	60.449	57.895	0.00	0.00	41.95	3.55
88	89	1.304282	GGCTCCTCCTTTGGCATGA	59.696	57.895	0.00	0.00	0.00	3.07
89	90	2.117156	CGGCTCCTCCTTTGGCATG	61.117	63.158	0.00	0.00	0.00	4.06
90	91	2.273449	CGGCTCCTCCTTTGGCAT	59.727	61.111	0.00	0.00	0.00	4.40
91	92	4.033776	CCGGCTCCTCCTTTGGCA	62.034	66.667	0.00	0.00	0.00	4.92
109	110	2.438614	CCTCCTCCTCGTCGCTCA	60.439	66.667	0.00	0.00	0.00	4.26
143	144	1.095807	GCAAGCCGAAGTGGGGATAC	61.096	60.000	0.00	0.00	38.63	2.24
148	149	0.734889	CTATTGCAAGCCGAAGTGGG	59.265	55.000	4.94	0.00	38.63	4.61
354	355	0.731174	CGAATTTTTCGCCGTTGGGG	60.731	55.000	0.00	0.00	46.97	4.96
368	369	2.433664	GACCGGCCGTGTCGAATT	60.434	61.111	26.12	0.00	29.41	2.17
385	386	0.397941	TCTCCAGCCCTCAAACAGTG	59.602	55.000	0.00	0.00	0.00	3.66
388	389	0.322816	GCATCTCCAGCCCTCAAACA	60.323	55.000	0.00	0.00	0.00	2.83
392	393	3.639445	GAGCATCTCCAGCCCTCA	58.361	61.111	0.00	0.00	0.00	3.86
410	411	8.655901	TCTACAACTTATTATGCCCATGACATA	58.344	33.333	0.00	0.00	0.00	2.29
412	413	6.894682	TCTACAACTTATTATGCCCATGACA	58.105	36.000	0.00	0.00	0.00	3.58
419	420	9.221775	CGAACAAATTCTACAACTTATTATGCC	57.778	33.333	0.00	0.00	32.12	4.40
423	424	7.118101	ACCGCGAACAAATTCTACAACTTATTA	59.882	33.333	8.23	0.00	32.12	0.98
445	446	2.573609	ATAACGCCTGGACTCACCGC	62.574	60.000	0.00	0.00	42.61	5.68
448	449	1.641577	GTGATAACGCCTGGACTCAC	58.358	55.000	0.00	0.00	0.00	3.51
487	488	2.006772	CGTGGCTTGCCGTAATCTC	58.993	57.895	7.18	0.00	0.00	2.75
604	756	6.323203	AGCTAGTTCTAGTTCGTAACACAA	57.677	37.500	8.38	0.00	0.00	3.33
605	757	5.954296	AGCTAGTTCTAGTTCGTAACACA	57.046	39.130	8.38	0.00	0.00	3.72
665	982	3.541632	TCTCCGCCCAGACAAATTAATC	58.458	45.455	0.00	0.00	0.00	1.75
666	983	3.644966	TCTCCGCCCAGACAAATTAAT	57.355	42.857	0.00	0.00	0.00	1.40
667	984	3.644966	ATCTCCGCCCAGACAAATTAA	57.355	42.857	0.00	0.00	0.00	1.40
668	985	3.644966	AATCTCCGCCCAGACAAATTA	57.355	42.857	0.00	0.00	0.00	1.40
669	986	2.514458	AATCTCCGCCCAGACAAATT	57.486	45.000	0.00	0.00	0.00	1.82
670	987	3.644966	TTAATCTCCGCCCAGACAAAT	57.355	42.857	0.00	0.00	0.00	2.32
679	1363	2.229792	TGCATGGAATTAATCTCCGCC	58.770	47.619	0.00	0.00	35.55	6.13
681	1365	5.934043	TCTACATGCATGGAATTAATCTCCG	59.066	40.000	29.41	6.40	35.55	4.63
756	2105	1.993653	CTCTGCCATTGGTCTGGGA	59.006	57.895	4.26	0.00	36.75	4.37
847	2199	8.774586	CAAAGCTAACTCTGCTAAAAAGTTCTA	58.225	33.333	0.00	0.00	40.22	2.10
860	2212	2.485814	GAGGCCAACAAAGCTAACTCTG	59.514	50.000	5.01	0.00	0.00	3.35
898	2250	2.439553	TTAGTGGGGGCCAAAGCTGG	62.440	60.000	4.39	0.00	46.65	4.85
970	2322	0.752658	GTGTGCCAAAAGCTCCCTTT	59.247	50.000	0.00	0.00	42.93	3.11
1004	2356	4.462508	TTTTTGTGTTGCATTCCTGACA	57.537	36.364	0.00	0.00	0.00	3.58
1070	2422	0.250513	CAAGGAGTGGTGGTAGAGCC	59.749	60.000	0.00	0.00	37.90	4.70
1356	2708	1.302431	CACACGCACCATGGGAGAA	60.302	57.895	18.09	0.00	34.12	2.87
1370	2722	0.041839	CAGCAGTTCGACAAGCACAC	60.042	55.000	5.15	0.00	0.00	3.82
1550	2903	2.919772	TCAGGACTACCTCCATGACA	57.080	50.000	0.00	0.00	45.94	3.58
1728	3109	6.481434	ACTTAGTTTGTACTTCAGGTCACT	57.519	37.500	0.00	0.00	35.78	3.41
1811	3192	6.714278	TCATCTCATCAAAGGATCAACTTGA	58.286	36.000	0.00	0.38	0.00	3.02
1890	3271	5.072040	TGCTCTGACGAAACATATTGAGA	57.928	39.130	0.00	0.00	0.00	3.27
1907	3288	3.776969	TCTAATCCTGTGTTCCATGCTCT	59.223	43.478	0.00	0.00	0.00	4.09
1951	3332	4.389374	CTCCAGTACTTTGGTGTGACAAT	58.611	43.478	0.00	0.00	39.35	2.71
2152	3541	2.280186	GATGACCGGCGATCCACC	60.280	66.667	9.30	0.00	0.00	4.61
2272	3661	1.001974	TGGTCAGCTGTGAAGCGTATT	59.998	47.619	14.67	0.00	40.27	1.89
2311	3700	3.624410	ACCGTGTTTGTTAGTTTCTCCAC	59.376	43.478	0.00	0.00	0.00	4.02
2322	3711	1.169577	TGCAGTCAACCGTGTTTGTT	58.830	45.000	0.00	0.00	0.00	2.83
2402	3791	0.393402	TCACCTGATGATGCCACTGC	60.393	55.000	0.00	0.00	32.43	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.