AutoCloner

Multiple sequence alignment - TraesCS3B01G033000

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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	TraesCS3B01G033000	chr3B	100.000	3608	0	0	1	3608	16034816	16038423	0.000000e+00	6663
1	TraesCS3B01G033000	chr3B	96.042	2754	78	6	596	3341	25282146	25279416	0.000000e+00	4453
2	TraesCS3B01G033000	chr3B	81.567	1481	244	14	1057	2519	16055665	16057134	0.000000e+00	1195
3	TraesCS3B01G033000	chr3B	83.724	682	98	7	1047	1717	25259781	25259102	1.830000e-177	632
4	TraesCS3B01G033000	chr3B	97.945	292	5	1	3318	3608	25276577	25276286	4.160000e-139	505
5	TraesCS3B01G033000	chr3B	85.388	438	33	13	617	1046	25283712	25283298	3.330000e-115	425
6	TraesCS3B01G033000	chr3B	84.694	294	21	8	312	594	25282996	25282716	4.590000e-69	272
7	TraesCS3B01G033000	chr3D	95.542	3163	99	12	465	3608	11360906	11364045	0.000000e+00	5022
8	TraesCS3B01G033000	chr3D	85.170	1497	192	14	1045	2514	11772884	11771391	0.000000e+00	1507
9	TraesCS3B01G033000	chr3D	83.066	1494	222	17	1047	2514	11370249	11371737	0.000000e+00	1328
10	TraesCS3B01G033000	chr3D	87.660	235	26	2	206	438	11360675	11360908	1.650000e-68	270
11	TraesCS3B01G033000	chr3D	87.081	209	17	5	1	207	11360339	11360539	1.010000e-55	228
12	TraesCS3B01G033000	chr3A	96.183	2384	72	7	596	2971	25912061	25909689	0.000000e+00	3880
13	TraesCS3B01G033000	chr3A	95.261	633	26	4	2978	3608	25909651	25909021	0.000000e+00	1000
14	TraesCS3B01G033000	chr3A	84.319	389	34	8	215	593	25913012	25912641	4.430000e-94	355
15	TraesCS3B01G033000	chr3A	83.624	287	28	9	314	600	25913422	25913155	5.980000e-63	252
16	TraesCS3B01G033000	chr3A	82.500	280	26	7	321	590	19063998	19063732	1.300000e-54	224

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	TraesCS3B01G033000	chr3B	16034816	16038423	3607	False	6663.00	6663	100.000000	1	3608	1	chr3B.!!$F1	3607
1	TraesCS3B01G033000	chr3B	25276286	25283712	7426	True	1413.75	4453	91.017250	312	3608	4	chr3B.!!$R2	3296
2	TraesCS3B01G033000	chr3B	16055665	16057134	1469	False	1195.00	1195	81.567000	1057	2519	1	chr3B.!!$F2	1462
3	TraesCS3B01G033000	chr3B	25259102	25259781	679	True	632.00	632	83.724000	1047	1717	1	chr3B.!!$R1	670
4	TraesCS3B01G033000	chr3D	11360339	11364045	3706	False	1840.00	5022	90.094333	1	3608	3	chr3D.!!$F2	3607
5	TraesCS3B01G033000	chr3D	11771391	11772884	1493	True	1507.00	1507	85.170000	1045	2514	1	chr3D.!!$R1	1469
6	TraesCS3B01G033000	chr3D	11370249	11371737	1488	False	1328.00	1328	83.066000	1047	2514	1	chr3D.!!$F1	1467
7	TraesCS3B01G033000	chr3A	25909021	25913422	4401	True	1371.75	3880	89.846750	215	3608	4	chr3A.!!$R2	3393

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
459	874	0.105760	AGCAACCCACCCATGTTTCA	60.106	50.0	0.00	0.00	0.00	2.69	F
547	973	0.550914	TTGGGTTCAGCAACTCACCT	59.449	50.0	0.00	0.00	43.09	4.00	F
891	1902	2.435372	ATTTAGATTGGCCAGCGGAA	57.565	45.0	5.11	3.62	0.00	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1372	2393	2.050144	GGGAGTGGCAAGATATGAGGA	58.950	52.381	0.00	3.71	R
2353	3393	3.609798	CCTTAGGACGAAGGGAGGA	57.390	57.895	42.12	3.71	R
2828	3868	1.605710	CTCAACTGGAACAAGTGGCAG	59.394	52.381	38.70	4.85	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
71	73	4.446371	ACTAATGCATGCTAGTTGAGACC	58.554	43.478	20.33	0.00	0.00	3.85
72	74	1.945387	ATGCATGCTAGTTGAGACCG	58.055	50.000	20.33	0.00	0.00	4.79
115	117	1.089920	CAGTGGAATGCTGCTACACC	58.910	55.000	0.00	0.19	32.71	4.16
131	133	4.142381	GCTACACCCCAGCTAAAAATTCAG	60.142	45.833	0.00	0.00	36.07	3.02
140	142	6.218746	CCAGCTAAAAATTCAGAGCAACTTT	58.781	36.000	7.82	0.00	37.40	2.66
145	147	8.487970	GCTAAAAATTCAGAGCAACTTTTTACC	58.512	33.333	0.00	0.00	34.96	2.85
176	178	9.456147	AGTATGTGGTAGAGATCTATATGTGTC	57.544	37.037	0.00	0.00	0.00	3.67
210	213	2.915869	TCAGGTACTTCAAGGGATGGT	58.084	47.619	0.00	0.00	34.60	3.55
212	215	3.263425	TCAGGTACTTCAAGGGATGGTTC	59.737	47.826	0.00	0.00	34.60	3.62
213	216	3.009033	CAGGTACTTCAAGGGATGGTTCA	59.991	47.826	0.00	0.00	34.60	3.18
214	217	3.852578	AGGTACTTCAAGGGATGGTTCAT	59.147	43.478	0.00	0.00	27.25	2.57
216	219	2.450476	ACTTCAAGGGATGGTTCATGC	58.550	47.619	0.00	0.00	0.00	4.06
217	220	2.042162	ACTTCAAGGGATGGTTCATGCT	59.958	45.455	0.00	0.00	32.77	3.79
250	663	3.691118	GCAAGCCATGTAGAGTGATTTCA	59.309	43.478	0.00	0.00	0.00	2.69
298	713	6.263168	AGAAAGTTTGTGATTTGGAGTACCTG	59.737	38.462	0.00	0.00	37.04	4.00
308	723	0.896940	GGAGTACCTGTCGGTGGTCA	60.897	60.000	0.00	0.00	45.18	4.02
309	724	1.183549	GAGTACCTGTCGGTGGTCAT	58.816	55.000	0.00	0.00	45.18	3.06
400	815	5.630121	TGAACACCAGAATTCCAACAGTAT	58.370	37.500	0.65	0.00	0.00	2.12
427	842	1.538047	TGAGAATTTGAGGGCAGCAC	58.462	50.000	0.00	0.00	0.00	4.40
443	858	3.126073	CAGCACAGCGATTCTATAAGCA	58.874	45.455	0.00	0.00	0.00	3.91
444	859	3.557185	CAGCACAGCGATTCTATAAGCAA	59.443	43.478	0.00	0.00	0.00	3.91
446	861	3.303395	GCACAGCGATTCTATAAGCAACC	60.303	47.826	0.00	0.00	0.00	3.77
447	862	3.248602	CACAGCGATTCTATAAGCAACCC	59.751	47.826	0.00	0.00	0.00	4.11
448	863	3.118408	ACAGCGATTCTATAAGCAACCCA	60.118	43.478	0.00	0.00	0.00	4.51
449	864	3.248602	CAGCGATTCTATAAGCAACCCAC	59.751	47.826	0.00	0.00	0.00	4.61
450	865	2.548480	GCGATTCTATAAGCAACCCACC	59.452	50.000	0.00	0.00	0.00	4.61
451	866	3.139077	CGATTCTATAAGCAACCCACCC	58.861	50.000	0.00	0.00	0.00	4.61
452	867	3.433031	CGATTCTATAAGCAACCCACCCA	60.433	47.826	0.00	0.00	0.00	4.51
453	868	4.729868	GATTCTATAAGCAACCCACCCAT	58.270	43.478	0.00	0.00	0.00	4.00
454	869	3.576078	TCTATAAGCAACCCACCCATG	57.424	47.619	0.00	0.00	0.00	3.66
455	870	2.849943	TCTATAAGCAACCCACCCATGT	59.150	45.455	0.00	0.00	0.00	3.21
456	871	2.621556	ATAAGCAACCCACCCATGTT	57.378	45.000	0.00	0.00	0.00	2.71
457	872	2.390225	TAAGCAACCCACCCATGTTT	57.610	45.000	0.00	0.00	0.00	2.83
458	873	1.047801	AAGCAACCCACCCATGTTTC	58.952	50.000	0.00	0.00	0.00	2.78
459	874	0.105760	AGCAACCCACCCATGTTTCA	60.106	50.000	0.00	0.00	0.00	2.69
547	973	0.550914	TTGGGTTCAGCAACTCACCT	59.449	50.000	0.00	0.00	43.09	4.00
733	1744	5.744666	AAAAGCAACACGTTGTACTATGT	57.255	34.783	11.33	0.00	42.31	2.29
734	1745	6.847956	AAAAGCAACACGTTGTACTATGTA	57.152	33.333	11.33	0.00	42.31	2.29
735	1746	6.462073	AAAGCAACACGTTGTACTATGTAG	57.538	37.500	11.33	0.91	42.31	2.74
736	1747	5.381174	AGCAACACGTTGTACTATGTAGA	57.619	39.130	11.33	0.00	42.31	2.59
737	1748	5.159209	AGCAACACGTTGTACTATGTAGAC	58.841	41.667	11.33	0.00	42.31	2.59
738	1749	5.048224	AGCAACACGTTGTACTATGTAGACT	60.048	40.000	11.33	0.00	42.31	3.24
824	1835	4.104738	TCCTAAGATCCCACCATGGATTTC	59.895	45.833	21.47	7.71	45.25	2.17
891	1902	2.435372	ATTTAGATTGGCCAGCGGAA	57.565	45.000	5.11	3.62	0.00	4.30
962	1974	9.862371	CATCTATCTCAACCACACCTTATATAC	57.138	37.037	0.00	0.00	0.00	1.47
1277	2295	3.525537	TGCAACTGAAGATGCTAGCTAC	58.474	45.455	17.23	9.79	43.18	3.58
1317	2335	4.350368	TCATGCACTAGACACCTTCAAA	57.650	40.909	0.00	0.00	0.00	2.69
1353	2374	3.011369	TCAGAGAGGGCACTAAGGAAGTA	59.989	47.826	0.00	0.00	35.76	2.24
2353	3393	7.151694	AGGATTGGAGAGATCATTGAGAATT	57.848	36.000	0.00	0.00	0.00	2.17
2828	3868	4.782019	TTGCAATTCACACCAGATAACC	57.218	40.909	0.00	0.00	0.00	2.85
3169	4240	3.508840	GCGATCAACAAGGCCGGG	61.509	66.667	2.18	0.00	0.00	5.73
3170	4241	3.508840	CGATCAACAAGGCCGGGC	61.509	66.667	22.67	22.67	0.00	6.13
3263	4334	6.054860	ACAATGGCTTATGTCAGTCTTAGT	57.945	37.500	0.00	0.00	0.00	2.24
3264	4335	6.476378	ACAATGGCTTATGTCAGTCTTAGTT	58.524	36.000	0.00	0.00	0.00	2.24
3291	4362	2.694628	AGAAAATGCAGCAAAGGTGTGA	59.305	40.909	0.00	0.00	33.19	3.58
3596	7535	3.380637	GCTGTGCTGATCAATTCATTCCT	59.619	43.478	0.00	0.00	32.72	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	38	5.065218	GCATGCATTAGTTGTAGCACTACTT	59.935	40.000	14.21	0.00	40.14	2.24
38	40	4.572389	AGCATGCATTAGTTGTAGCACTAC	59.428	41.667	21.98	0.70	40.14	2.73
71	73	4.686091	TGCACAGACAATTCTTTAGACTCG	59.314	41.667	0.00	0.00	0.00	4.18
72	74	5.390356	GCTGCACAGACAATTCTTTAGACTC	60.390	44.000	0.81	0.00	0.00	3.36
108	110	3.761752	TGAATTTTTAGCTGGGGTGTAGC	59.238	43.478	0.00	0.00	41.43	3.58
110	112	5.249780	TCTGAATTTTTAGCTGGGGTGTA	57.750	39.130	0.00	0.00	0.00	2.90
111	113	4.082125	CTCTGAATTTTTAGCTGGGGTGT	58.918	43.478	0.00	0.00	0.00	4.16
112	114	3.119352	GCTCTGAATTTTTAGCTGGGGTG	60.119	47.826	0.00	0.00	32.18	4.61
115	117	4.219288	AGTTGCTCTGAATTTTTAGCTGGG	59.781	41.667	0.00	0.00	35.95	4.45
131	133	8.015658	CACATACTAGTTGGTAAAAAGTTGCTC	58.984	37.037	0.00	0.00	0.00	4.26
140	142	8.834004	ATCTCTACCACATACTAGTTGGTAAA	57.166	34.615	20.37	10.84	35.08	2.01
191	194	3.009033	TGAACCATCCCTTGAAGTACCTG	59.991	47.826	0.00	0.00	0.00	4.00
196	199	2.042162	AGCATGAACCATCCCTTGAAGT	59.958	45.455	0.00	0.00	0.00	3.01
217	220	3.221771	ACATGGCTTGCTTGTAGAACAA	58.778	40.909	0.00	0.00	36.54	2.83
272	687	6.486993	AGGTACTCCAAATCACAAACTTTCTC	59.513	38.462	0.00	0.00	35.89	2.87
298	713	1.571919	GTAGATGCATGACCACCGAC	58.428	55.000	2.46	0.00	0.00	4.79
308	723	3.181437	TGCATGGAATCTGGTAGATGCAT	60.181	43.478	0.00	0.00	40.83	3.96
309	724	2.173143	TGCATGGAATCTGGTAGATGCA	59.827	45.455	0.00	0.00	42.84	3.96
400	815	3.623203	GCCCTCAAATTCTCATGGACAGA	60.623	47.826	0.00	0.00	0.00	3.41
427	842	3.248602	GTGGGTTGCTTATAGAATCGCTG	59.751	47.826	0.00	0.00	0.00	5.18
443	858	0.560688	ACCTGAAACATGGGTGGGTT	59.439	50.000	0.00	0.00	31.48	4.11
444	859	0.178964	CACCTGAAACATGGGTGGGT	60.179	55.000	9.53	2.77	44.63	4.51
448	863	1.271926	GGTAGCACCTGAAACATGGGT	60.272	52.381	0.00	0.00	34.73	4.51
449	864	1.271871	TGGTAGCACCTGAAACATGGG	60.272	52.381	0.00	0.00	39.58	4.00
450	865	2.198827	TGGTAGCACCTGAAACATGG	57.801	50.000	0.00	0.00	39.58	3.66
451	866	3.346315	TGATGGTAGCACCTGAAACATG	58.654	45.455	0.00	0.00	39.58	3.21
452	867	3.719268	TGATGGTAGCACCTGAAACAT	57.281	42.857	0.00	0.00	39.58	2.71
453	868	3.008923	TCATGATGGTAGCACCTGAAACA	59.991	43.478	0.00	0.00	39.58	2.83
454	869	3.609853	TCATGATGGTAGCACCTGAAAC	58.390	45.455	0.00	0.00	39.58	2.78
455	870	3.998913	TCATGATGGTAGCACCTGAAA	57.001	42.857	0.00	0.00	39.58	2.69
456	871	3.200605	ACATCATGATGGTAGCACCTGAA	59.799	43.478	33.31	0.00	42.91	3.02
457	872	2.773661	ACATCATGATGGTAGCACCTGA	59.226	45.455	33.31	0.94	42.91	3.86
458	873	3.204306	ACATCATGATGGTAGCACCTG	57.796	47.619	33.31	11.65	42.91	4.00
459	874	3.200605	TCAACATCATGATGGTAGCACCT	59.799	43.478	33.31	12.16	42.91	4.00
533	948	5.717178	AGAATAGACTAGGTGAGTTGCTGAA	59.283	40.000	0.00	0.00	39.06	3.02
535	950	5.105554	ACAGAATAGACTAGGTGAGTTGCTG	60.106	44.000	0.00	0.00	39.06	4.41
536	951	5.020132	ACAGAATAGACTAGGTGAGTTGCT	58.980	41.667	0.00	0.00	39.06	3.91
537	952	5.331876	ACAGAATAGACTAGGTGAGTTGC	57.668	43.478	0.00	0.00	39.06	4.17
547	973	5.181245	GCAAAGTGGCAAACAGAATAGACTA	59.819	40.000	0.00	0.00	0.00	2.59
611	1614	1.344065	ACCTGATGGTTGTCCGTACA	58.656	50.000	0.00	0.00	46.05	2.90
722	1733	8.266392	ACAGTCTACAGTCTACATAGTACAAC	57.734	38.462	0.00	0.00	0.00	3.32
732	1743	5.411977	TGCAAGTCTACAGTCTACAGTCTAC	59.588	44.000	0.00	0.00	0.00	2.59
733	1744	5.557866	TGCAAGTCTACAGTCTACAGTCTA	58.442	41.667	0.00	0.00	0.00	2.59
734	1745	4.399219	TGCAAGTCTACAGTCTACAGTCT	58.601	43.478	0.00	0.00	0.00	3.24
735	1746	4.728534	CTGCAAGTCTACAGTCTACAGTC	58.271	47.826	0.00	0.00	0.00	3.51
736	1747	3.057174	GCTGCAAGTCTACAGTCTACAGT	60.057	47.826	0.00	0.00	36.26	3.55
737	1748	3.192422	AGCTGCAAGTCTACAGTCTACAG	59.808	47.826	1.02	0.00	36.26	2.74
738	1749	3.157881	AGCTGCAAGTCTACAGTCTACA	58.842	45.455	1.02	0.00	36.26	2.74
824	1835	0.320771	GTGGAGGTAGTGCACACCAG	60.321	60.000	28.54	0.00	46.49	4.00
962	1974	3.444034	TGTAGAGATCAGGTTTCGAGGTG	59.556	47.826	0.00	0.00	0.00	4.00
1184	2202	2.374184	TCTGAGCTCTTAGCAGGAGTC	58.626	52.381	16.19	0.00	45.56	3.36
1317	2335	4.521146	CCTCTCTGATTAGTTGGTTGCAT	58.479	43.478	0.00	0.00	0.00	3.96
1372	2393	2.050144	GGGAGTGGCAAGATATGAGGA	58.950	52.381	0.00	0.00	0.00	3.71
2353	3393	3.609798	CCTTAGGACGAAGGGAGGA	57.390	57.895	0.00	0.00	42.12	3.71
2828	3868	1.605710	CTCAACTGGAACAAGTGGCAG	59.394	52.381	0.00	0.00	38.70	4.85
3169	4240	1.515304	GCGTCAAGACTCTCCTCGC	60.515	63.158	0.00	0.00	35.86	5.03
3170	4241	1.137825	GGCGTCAAGACTCTCCTCG	59.862	63.158	0.00	0.00	0.00	4.63
3263	4334	6.867816	CACCTTTGCTGCATTTTCTGTAATAA	59.132	34.615	1.84	0.00	0.00	1.40
3264	4335	6.015519	ACACCTTTGCTGCATTTTCTGTAATA	60.016	34.615	1.84	0.00	0.00	0.98
3291	4362	6.071952	CCATACTTGGAACATTAGTTTGCTGT	60.072	38.462	0.00	0.00	46.92	4.40
3336	7273	6.205270	GGTTCAAAGGAATTTCGTACCTTGTA	59.795	38.462	0.00	0.00	42.25	2.41
3337	7274	5.009310	GGTTCAAAGGAATTTCGTACCTTGT	59.991	40.000	0.00	0.00	42.25	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.