AutoCloner

Multiple sequence alignment - TraesCS5A01G019700

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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	TraesCS5A01G019700	chr5A	100.000	4333	0	0	1	4333	15868507	15864175	0.000000e+00	8002.0
1	TraesCS5A01G019700	chr5D	96.161	4298	105	22	66	4333	22403036	22398769	0.000000e+00	6968.0
2	TraesCS5A01G019700	chr5D	88.906	1325	114	15	1742	3044	22435089	22433776	0.000000e+00	1602.0
3	TraesCS5A01G019700	chr5D	78.412	1033	118	53	681	1669	22436100	22435129	3.760000e-160	575.0
4	TraesCS5A01G019700	chr5D	88.728	346	35	3	3043	3385	22433712	22433368	1.860000e-113	420.0
5	TraesCS5A01G019700	chr5D	79.050	463	70	20	3444	3894	22433287	22432840	4.240000e-75	292.0
6	TraesCS5A01G019700	chr5D	83.399	253	25	10	72	316	22436360	22436117	7.300000e-53	219.0
7	TraesCS5A01G019700	chr5D	95.714	70	3	0	1	70	22403150	22403081	3.540000e-21	113.0
8	TraesCS5A01G019700	chr5B	93.654	1954	96	17	1750	3692	15560091	15558155	0.000000e+00	2896.0
9	TraesCS5A01G019700	chr5B	88.755	1325	117	13	1742	3044	16003500	16002186	0.000000e+00	1592.0
10	TraesCS5A01G019700	chr5B	94.080	946	33	10	793	1719	15561202	15560261	0.000000e+00	1415.0
11	TraesCS5A01G019700	chr5B	91.188	749	48	10	66	797	15562070	15561323	0.000000e+00	1002.0
12	TraesCS5A01G019700	chr5B	87.687	601	48	15	3745	4333	15558150	15557564	0.000000e+00	676.0
13	TraesCS5A01G019700	chr5B	87.863	379	35	6	3043	3415	16002122	16001749	6.650000e-118	435.0
14	TraesCS5A01G019700	chr5B	82.967	364	49	7	3444	3802	16001663	16001308	2.510000e-82	316.0
15	TraesCS5A01G019700	chr5B	93.846	65	2	2	1681	1744	370194705	370194768	3.570000e-16	97.1
16	TraesCS5A01G019700	chr5B	93.846	65	2	2	1681	1744	370239565	370239628	3.570000e-16	97.1
17	TraesCS5A01G019700	chr2B	82.331	532	55	11	1175	1677	178773942	178773421	4.010000e-115	425.0
18	TraesCS5A01G019700	chr2B	88.073	218	24	2	1744	1961	178773382	178773167	1.550000e-64	257.0
19	TraesCS5A01G019700	chr2B	86.000	150	16	3	3970	4118	162504372	162504517	5.800000e-34	156.0
20	TraesCS5A01G019700	chr2B	83.237	173	23	3	3958	4129	566624803	566624970	2.090000e-33	154.0
21	TraesCS5A01G019700	chr2B	94.737	57	2	1	1687	1743	321689847	321689902	2.150000e-13	87.9
22	TraesCS5A01G019700	chr7D	86.667	165	12	5	3968	4127	265692827	265692986	1.600000e-39	174.0
23	TraesCS5A01G019700	chr2D	84.940	166	19	3	3963	4127	410600665	410600825	3.470000e-36	163.0
24	TraesCS5A01G019700	chr1D	84.337	166	18	6	3963	4127	104291528	104291686	5.800000e-34	156.0
25	TraesCS5A01G019700	chr1D	94.737	57	2	1	1687	1743	351255328	351255383	2.150000e-13	87.9
26	TraesCS5A01G019700	chr6B	83.626	171	21	4	3959	4127	345218545	345218710	2.090000e-33	154.0
27	TraesCS5A01G019700	chr3B	83.432	169	19	2	3964	4127	158707492	158707656	9.710000e-32	148.0
28	TraesCS5A01G019700	chr3A	94.030	67	3	1	1681	1747	67912179	67912114	2.760000e-17	100.0
29	TraesCS5A01G019700	chr4A	95.082	61	1	2	1687	1746	6936559	6936618	1.280000e-15	95.3
30	TraesCS5A01G019700	chr6A	94.737	57	2	1	1687	1743	573510818	573510873	2.150000e-13	87.9

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	TraesCS5A01G019700	chr5A	15864175	15868507	4332	True	8002.00	8002	100.000000	1	4333	1	chr5A.!!$R1	4332
1	TraesCS5A01G019700	chr5D	22398769	22403150	4381	True	3540.50	6968	95.937500	1	4333	2	chr5D.!!$R1	4332
2	TraesCS5A01G019700	chr5D	22432840	22436360	3520	True	621.60	1602	83.699000	72	3894	5	chr5D.!!$R2	3822
3	TraesCS5A01G019700	chr5B	15557564	15562070	4506	True	1497.25	2896	91.652250	66	4333	4	chr5B.!!$R1	4267
4	TraesCS5A01G019700	chr5B	16001308	16003500	2192	True	781.00	1592	86.528333	1742	3802	3	chr5B.!!$R2	2060
5	TraesCS5A01G019700	chr2B	178773167	178773942	775	True	341.00	425	85.202000	1175	1961	2	chr2B.!!$R1	786

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	End Stability	Orientation
906	1118	0.476771	TCACCTCTTCCCCCAACAAC	59.523	55.0	3.32	F
907	1119	0.478507	CACCTCTTCCCCCAACAACT	59.521	55.0	3.16	F
908	1120	0.771755	ACCTCTTCCCCCAACAACTC	59.228	55.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
2422	2831	0.771127	TACTTTTGCAGGCCAGAGGT	59.229	50.0	5.01	3.85	R
3123	3625	0.749454	GCAGATCGGTGGCTTGGAAT	60.749	55.0	0.00	3.01	R
3338	3846	5.700832	CAGTTGCTACATGTCCTAGTTTTCA	59.299	40.0	0.00	2.69	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
63	64	2.328099	GCAACTGTTCCAGGCTCCG	61.328	63.158	0.00	0.00	35.51	4.63
133	183	6.492772	AGTGATCATCAGATATGTAGCAGTCA	59.507	38.462	0.00	0.00	33.72	3.41
190	247	2.028130	TGAACAAAATCGTGGTTGGCT	58.972	42.857	0.00	0.00	0.00	4.75
195	252	2.396590	AAATCGTGGTTGGCTATCGT	57.603	45.000	0.00	0.00	0.00	3.73
203	260	2.427812	TGGTTGGCTATCGTTATCGTGA	59.572	45.455	0.00	0.00	38.33	4.35
293	353	8.855110	TCCAAATTTGACATGTTAGTATGTTGT	58.145	29.630	19.86	0.00	41.15	3.32
296	356	9.474920	AAATTTGACATGTTAGTATGTTGTTGG	57.525	29.630	0.00	0.00	41.15	3.77
391	451	1.197036	GACCGCATCATCATCAGCATG	59.803	52.381	0.00	0.00	37.54	4.06
487	547	1.966451	CCCGGTTGCTCGCTTCTTT	60.966	57.895	0.00	0.00	0.00	2.52
497	557	3.242739	TGCTCGCTTCTTTGAACTTGAAC	60.243	43.478	0.00	0.00	0.00	3.18
513	575	3.268103	AACAAATCGCCCGGCCTCT	62.268	57.895	3.10	0.00	0.00	3.69
592	661	3.067461	CACACATTTCTTTTCCGGTTCCA	59.933	43.478	0.00	0.00	0.00	3.53
626	703	8.912988	TCTATCATTTAAAATTCTCGCCCAAAT	58.087	29.630	0.00	0.00	0.00	2.32
717	794	9.295825	TGAGAATAATTAGTTGCTTTCTTTGGA	57.704	29.630	0.00	0.00	0.00	3.53
745	825	9.905713	TGCCATTCTTTAGAAGTAGTTCAATAT	57.094	29.630	12.77	0.00	37.48	1.28
784	864	4.560856	TTGCCAAACGTGCACGGC	62.561	61.111	39.21	31.62	44.95	5.68
901	1113	2.124996	CCCTCACCTCTTCCCCCA	59.875	66.667	0.00	0.00	0.00	4.96
903	1115	1.685820	CCTCACCTCTTCCCCCAAC	59.314	63.158	0.00	0.00	0.00	3.77
904	1116	1.133809	CCTCACCTCTTCCCCCAACA	61.134	60.000	0.00	0.00	0.00	3.33
906	1118	0.476771	TCACCTCTTCCCCCAACAAC	59.523	55.000	0.00	0.00	0.00	3.32
907	1119	0.478507	CACCTCTTCCCCCAACAACT	59.521	55.000	0.00	0.00	0.00	3.16
908	1120	0.771755	ACCTCTTCCCCCAACAACTC	59.228	55.000	0.00	0.00	0.00	3.01
910	1122	1.068121	CTCTTCCCCCAACAACTCCT	58.932	55.000	0.00	0.00	0.00	3.69
942	1169	9.638176	ATCTCTCTAGCCAATAATTGATTGTTT	57.362	29.630	0.00	0.00	43.09	2.83
1005	1232	6.841229	TCTTTCTCTATAGCTTTCAGATGGGA	59.159	38.462	0.00	0.00	0.00	4.37
1023	1250	2.671619	GGCACCTTTACGGCAGCA	60.672	61.111	0.00	0.00	38.48	4.41
1062	1292	1.065126	GTTCTAGTCATGGCTGGCCTT	60.065	52.381	10.89	3.63	36.94	4.35
1065	1295	2.041620	TCTAGTCATGGCTGGCCTTTTT	59.958	45.455	10.89	0.00	36.94	1.94
1144	1374	3.372349	CCCTCATCAGGTCACCATGATTT	60.372	47.826	0.00	0.00	38.30	2.17
1199	1429	1.550524	TCAGATAGGCGACAAGTGCTT	59.449	47.619	0.00	0.00	0.00	3.91
1332	1576	4.940654	AGAGCTTGCTTAATTCTTCCAGTC	59.059	41.667	0.00	0.00	0.00	3.51
1350	1594	4.446051	CCAGTCGTTTGTCTCTTCTTCTTC	59.554	45.833	0.00	0.00	0.00	2.87
1669	1937	6.194796	TGGCCTAATTTTCTCTCAAAATCG	57.805	37.500	3.32	0.00	0.00	3.34
1769	2175	9.110502	CTTCTCAAAATACCCAGTTAGGATTAC	57.889	37.037	0.00	0.00	41.22	1.89
1782	2188	8.047310	CCAGTTAGGATTACAGGACTTGTTTAT	58.953	37.037	0.00	0.00	39.59	1.40
2367	2776	4.006989	CCAACCCATCTGAAATCGTTACA	58.993	43.478	0.00	0.00	0.00	2.41
2422	2831	2.063266	GCCTGACGAACGTGTTCAATA	58.937	47.619	12.76	0.00	39.46	1.90
3197	3699	3.368571	GGCTTGCCAGGTGAGTGC	61.369	66.667	6.79	0.00	0.00	4.40
3260	3762	5.221048	GCCTCTTGTTGTCTTTGTTATGTGT	60.221	40.000	0.00	0.00	0.00	3.72
3276	3778	7.337938	TGTTATGTGTATCATGACATGACCTT	58.662	34.615	20.21	7.70	44.34	3.50
3338	3846	2.770802	AGTATGCTCTGCCTGAATCTGT	59.229	45.455	0.00	0.00	0.00	3.41
3457	4023	0.030235	GGTGGTTTTGGCTGACGTTC	59.970	55.000	0.00	0.00	0.00	3.95
3498	4065	1.069204	GCGGAGAACTGGAGATGCATA	59.931	52.381	0.00	0.00	0.00	3.14
3591	4165	3.533068	AGGATCCAGATTTCCCAAATCCA	59.467	43.478	15.82	0.00	46.65	3.41
3682	4257	6.368243	AGTGAACATGATTCATCGATATGCTC	59.632	38.462	0.00	0.00	32.76	4.26
3696	4271	1.588674	ATGCTCTACTCTCGGTCTCG	58.411	55.000	0.00	0.00	37.82	4.04
3884	4483	0.808453	GCATGTGCATTGCATGGGAC	60.808	55.000	15.49	1.77	41.91	4.46
3939	4551	7.568861	CGGTAGCAAGTCAGTTTGTAAAAGTAG	60.569	40.741	0.00	0.00	0.00	2.57
3966	4578	1.331214	ACTGTGGGCATTGGTCAAAG	58.669	50.000	0.00	0.00	0.00	2.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	5.486526	CCCTATCTGGAATGAAGATACAGC	58.513	45.833	0.00	0.00	38.35	4.40
126	176	5.709164	AGCTAAAGATGTGAAAATGACTGCT	59.291	36.000	0.00	0.00	0.00	4.24
133	183	8.887717	GTGATCACTAGCTAAAGATGTGAAAAT	58.112	33.333	18.83	1.81	40.37	1.82
168	225	2.738135	CCAACCACGATTTTGTTCACC	58.262	47.619	0.00	0.00	0.00	4.02
190	247	5.357878	ACCACCTTAACTCACGATAACGATA	59.642	40.000	0.00	0.00	42.66	2.92
195	252	5.018809	ACCTACCACCTTAACTCACGATAA	58.981	41.667	0.00	0.00	0.00	1.75
203	260	5.644188	TGTGTACTACCTACCACCTTAACT	58.356	41.667	0.00	0.00	0.00	2.24
293	353	5.973899	TTAATGAATTGTGTAGCAGCCAA	57.026	34.783	0.00	0.00	0.00	4.52
296	356	6.690098	CAGACATTAATGAATTGTGTAGCAGC	59.310	38.462	22.16	0.00	0.00	5.25
391	451	4.612264	TCCTCAGGTAGTTGTTTGTACC	57.388	45.455	0.00	0.00	39.31	3.34
403	463	6.472887	CCAAGACTTTGTTATTCCTCAGGTA	58.527	40.000	0.00	0.00	32.21	3.08
404	464	5.316987	CCAAGACTTTGTTATTCCTCAGGT	58.683	41.667	0.00	0.00	32.21	4.00
487	547	1.265635	CGGGCGATTTGTTCAAGTTCA	59.734	47.619	0.00	0.00	0.00	3.18
497	557	3.204827	CAGAGGCCGGGCGATTTG	61.205	66.667	23.81	15.16	0.00	2.32
513	575	3.755905	TGTTGTTCTTGTGTTCTTGCTCA	59.244	39.130	0.00	0.00	0.00	4.26
701	778	3.894427	TGGCATTCCAAAGAAAGCAACTA	59.106	39.130	5.52	0.00	46.16	2.24
717	794	8.635765	TTGAACTACTTCTAAAGAATGGCATT	57.364	30.769	13.54	13.54	33.01	3.56
745	825	7.862372	GGCAAATCGAATAAGATAAGATTGCAA	59.138	33.333	0.00	0.00	40.03	4.08
763	843	1.595982	CGTGCACGTTTGGCAAATCG	61.596	55.000	30.50	23.51	43.91	3.34
858	1063	7.337718	GTGATTGTTAGCATTGTCATACTACG	58.662	38.462	0.00	0.00	0.00	3.51
880	1092	1.229529	GGGAAGAGGTGAGGGGTGA	60.230	63.158	0.00	0.00	0.00	4.02
901	1113	6.546034	GCTAGAGAGATAGAGAAGGAGTTGTT	59.454	42.308	0.00	0.00	0.00	2.83
903	1115	5.473504	GGCTAGAGAGATAGAGAAGGAGTTG	59.526	48.000	0.00	0.00	0.00	3.16
904	1116	5.133660	TGGCTAGAGAGATAGAGAAGGAGTT	59.866	44.000	0.00	0.00	0.00	3.01
906	1118	5.241403	TGGCTAGAGAGATAGAGAAGGAG	57.759	47.826	0.00	0.00	0.00	3.69
907	1119	5.654901	TTGGCTAGAGAGATAGAGAAGGA	57.345	43.478	0.00	0.00	0.00	3.36
908	1120	8.593945	ATTATTGGCTAGAGAGATAGAGAAGG	57.406	38.462	0.00	0.00	0.00	3.46
910	1122	9.593565	TCAATTATTGGCTAGAGAGATAGAGAA	57.406	33.333	5.02	0.00	0.00	2.87
942	1169	3.603965	AAGGATAACACCAACCAACCA	57.396	42.857	0.00	0.00	0.00	3.67
1005	1232	2.359975	GCTGCCGTAAAGGTGCCT	60.360	61.111	0.00	0.00	43.70	4.75
1062	1292	1.143620	GGCAGTTGCAGCACCAAAA	59.856	52.632	2.55	0.00	44.36	2.44
1065	1295	1.833492	ATTGGCAGTTGCAGCACCA	60.833	52.632	10.63	10.63	44.36	4.17
1144	1374	4.588528	ACCCAAAGCTCAATTTTAGCAGAA	59.411	37.500	11.20	0.00	42.62	3.02
1199	1429	4.700365	CGCAGTCCGCACTCGTCA	62.700	66.667	0.00	0.00	42.60	4.35
1456	1724	1.271856	TCTGCCCGTCTCATTAACCA	58.728	50.000	0.00	0.00	0.00	3.67
1468	1736	1.066143	AGGTGAACTACAATCTGCCCG	60.066	52.381	0.00	0.00	0.00	6.13
1769	2175	6.070995	TGGGTACTGAGTATAAACAAGTCCTG	60.071	42.308	0.00	0.00	0.00	3.86
1782	2188	7.252612	TCATGATTTTCTTGGGTACTGAGTA	57.747	36.000	0.00	0.00	0.00	2.59
2367	2776	6.986817	CGTTAACATAGTCTTCCAGGATCAAT	59.013	38.462	6.39	0.00	0.00	2.57
2422	2831	0.771127	TACTTTTGCAGGCCAGAGGT	59.229	50.000	5.01	0.00	0.00	3.85
3123	3625	0.749454	GCAGATCGGTGGCTTGGAAT	60.749	55.000	0.00	0.00	0.00	3.01
3338	3846	5.700832	CAGTTGCTACATGTCCTAGTTTTCA	59.299	40.000	0.00	0.00	0.00	2.69
3457	4023	3.615496	GCTGCAGCAATTTCATAAAGGTG	59.385	43.478	33.36	0.00	41.59	4.00
3498	4065	5.946942	TCTTGAGACTAAATCATCAGGCT	57.053	39.130	0.00	0.00	30.85	4.58
3561	4135	5.221925	TGGGAAATCTGGATCCTAAGTATGC	60.222	44.000	14.23	0.38	35.95	3.14
3591	4165	4.801516	CGAAACCCGTCATTTTCAACTTTT	59.198	37.500	0.00	0.00	32.21	2.27
3682	4257	0.464870	TCTCCCGAGACCGAGAGTAG	59.535	60.000	0.00	0.00	40.82	2.57
3696	4271	2.237392	AGGCAGAACTACAATGTCTCCC	59.763	50.000	0.00	0.00	0.00	4.30
3817	4416	7.922505	TTGCAAAACACAGTAAATGTATGAC	57.077	32.000	0.00	0.00	41.41	3.06
3818	4417	9.539825	AATTTGCAAAACACAGTAAATGTATGA	57.460	25.926	17.19	0.00	41.41	2.15
3884	4483	0.110238	CAAACATGACTTGCCGTCCG	60.110	55.000	0.00	0.00	42.13	4.79
3939	4551	1.949525	CAATGCCCACAGTACTATGCC	59.050	52.381	0.00	0.00	0.00	4.40
3966	4578	6.063496	AGTTTGGAAAGGAGGGAGTATTAC	57.937	41.667	0.00	0.00	0.00	1.89
4240	4853	5.182190	TGCCTTTTTGTTTTTGAAAAGACCC	59.818	36.000	9.45	0.82	42.58	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.