AutoCloner

Multiple sequence alignment - TraesCS3B01G352000

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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	TraesCS3B01G352000	chr3B	100.000	3904	0	0	1	3904	561699847	561703750	0.000000e+00	7210
1	TraesCS3B01G352000	chr3B	88.805	2251	163	32	1687	3898	793141736	793143936	0.000000e+00	2678
2	TraesCS3B01G352000	chr3B	86.726	339	36	5	220	558	630160630	630160301	6.160000e-98	368
3	TraesCS3B01G352000	chr3B	85.522	297	20	15	3617	3904	449164742	449164460	4.940000e-74	289
4	TraesCS3B01G352000	chr3B	88.618	123	8	4	1246	1363	774716298	774716419	1.130000e-30	145
5	TraesCS3B01G352000	chr5A	96.856	3308	60	8	571	3844	403898475	403901772	0.000000e+00	5493
6	TraesCS3B01G352000	chr5A	98.305	413	6	1	1	412	403898061	403898473	0.000000e+00	723
7	TraesCS3B01G352000	chr5A	91.852	135	9	2	2655	2788	482027212	482027345	1.850000e-43	187
8	TraesCS3B01G352000	chr2A	96.767	3310	61	7	571	3844	306684342	306681043	0.000000e+00	5478
9	TraesCS3B01G352000	chr2A	96.948	2490	48	4	1373	3844	69257506	69259985	0.000000e+00	4152
10	TraesCS3B01G352000	chr2A	97.686	821	17	2	571	1389	69256670	69257490	0.000000e+00	1410
11	TraesCS3B01G352000	chr2A	98.305	413	6	1	1	412	306684756	306684344	0.000000e+00	723
12	TraesCS3B01G352000	chr2A	98.063	413	7	1	1	412	69256256	69256668	0.000000e+00	717
13	TraesCS3B01G352000	chr2A	84.865	740	79	17	1	722	26028060	26028784	0.000000e+00	715
14	TraesCS3B01G352000	chr2A	81.156	467	63	15	3430	3883	347871778	347872232	6.210000e-93	351
15	TraesCS3B01G352000	chr3A	96.522	2645	43	8	1238	3844	405833217	405830584	0.000000e+00	4329
16	TraesCS3B01G352000	chr3A	97.177	673	18	1	571	1242	405842440	405841768	0.000000e+00	1136
17	TraesCS3B01G352000	chr3A	98.305	413	6	1	1	412	405842854	405842442	0.000000e+00	723
18	TraesCS3B01G352000	chr3A	84.483	290	21	16	3617	3898	455227976	455227703	8.320000e-67	265
19	TraesCS3B01G352000	chr3A	91.111	135	9	3	2655	2788	672876261	672876393	3.100000e-41	180
20	TraesCS3B01G352000	chr3A	94.444	108	6	0	2028	2135	42045565	42045458	2.410000e-37	167
21	TraesCS3B01G352000	chr6A	95.791	2447	65	6	1	2410	602828940	602831385	0.000000e+00	3914
22	TraesCS3B01G352000	chrUn	96.321	1631	33	3	1632	3244	384178460	384180081	0.000000e+00	2654
23	TraesCS3B01G352000	chr2B	86.811	417	46	7	408	819	183534587	183534175	1.280000e-124	457
24	TraesCS3B01G352000	chr6B	86.190	420	49	7	405	819	599819311	599819726	2.770000e-121	446
25	TraesCS3B01G352000	chr6B	82.192	292	38	7	3617	3898	536849880	536849593	5.040000e-59	239
26	TraesCS3B01G352000	chr5B	86.124	418	47	9	408	819	672541311	672540899	1.290000e-119	440
27	TraesCS3B01G352000	chr5B	82.548	361	45	7	3520	3872	415054874	415055224	6.340000e-78	302
28	TraesCS3B01G352000	chr5B	85.965	228	24	7	1144	1363	533416995	533417222	1.810000e-58	237
29	TraesCS3B01G352000	chr5B	90.116	172	15	2	1373	1542	505361030	505361201	5.080000e-54	222
30	TraesCS3B01G352000	chr6D	82.655	467	60	11	3430	3887	425060481	425060935	1.020000e-105	394
31	TraesCS3B01G352000	chr4A	88.474	321	37	0	2024	2344	222106844	222107164	4.730000e-104	388
32	TraesCS3B01G352000	chr4B	86.127	346	38	6	214	558	241184998	241185334	7.970000e-97	364
33	TraesCS3B01G352000	chr4B	82.935	293	34	9	3617	3898	305510803	305510516	2.330000e-62	250
34	TraesCS3B01G352000	chr2D	87.075	294	35	2	138	429	117801407	117801699	2.910000e-86	329
35	TraesCS3B01G352000	chr3D	86.242	298	36	5	527	819	550355729	550356026	6.290000e-83	318
36	TraesCS3B01G352000	chr3D	83.590	195	16	8	2937	3130	266665125	266665304	6.710000e-38	169
37	TraesCS3B01G352000	chr7B	85.567	291	19	15	3617	3898	353328535	353328811	2.300000e-72	283
38	TraesCS3B01G352000	chr1B	90.964	166	14	1	1376	1540	562727229	562727064	5.080000e-54	222
39	TraesCS3B01G352000	chr1B	87.903	124	9	3	1246	1363	562727811	562727688	1.460000e-29	141
40	TraesCS3B01G352000	chr7A	94.262	122	7	0	2655	2776	731392157	731392036	1.850000e-43	187
41	TraesCS3B01G352000	chr7A	88.618	123	9	3	1246	1363	121783571	121783693	1.130000e-30	145
42	TraesCS3B01G352000	chr1A	91.852	135	9	2	2655	2788	371923309	371923176	1.850000e-43	187
43	TraesCS3B01G352000	chr4D	94.286	70	4	0	1148	1217	459921306	459921237	1.480000e-19	108

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	TraesCS3B01G352000	chr3B	561699847	561703750	3903	False	7210.0	7210	100.000000	1	3904	1	chr3B.!!$F1	3903
1	TraesCS3B01G352000	chr3B	793141736	793143936	2200	False	2678.0	2678	88.805000	1687	3898	1	chr3B.!!$F3	2211
2	TraesCS3B01G352000	chr5A	403898061	403901772	3711	False	3108.0	5493	97.580500	1	3844	2	chr5A.!!$F2	3843
3	TraesCS3B01G352000	chr2A	306681043	306684756	3713	True	3100.5	5478	97.536000	1	3844	2	chr2A.!!$R1	3843
4	TraesCS3B01G352000	chr2A	69256256	69259985	3729	False	2093.0	4152	97.565667	1	3844	3	chr2A.!!$F3	3843
5	TraesCS3B01G352000	chr2A	26028060	26028784	724	False	715.0	715	84.865000	1	722	1	chr2A.!!$F1	721
6	TraesCS3B01G352000	chr3A	405830584	405833217	2633	True	4329.0	4329	96.522000	1238	3844	1	chr3A.!!$R2	2606
7	TraesCS3B01G352000	chr3A	405841768	405842854	1086	True	929.5	1136	97.741000	1	1242	2	chr3A.!!$R4	1241
8	TraesCS3B01G352000	chr6A	602828940	602831385	2445	False	3914.0	3914	95.791000	1	2410	1	chr6A.!!$F1	2409
9	TraesCS3B01G352000	chrUn	384178460	384180081	1621	False	2654.0	2654	96.321000	1632	3244	1	chrUn.!!$F1	1612

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	Hairpin	End Stability	Orientation
112	113	2.639347	TCAGGTTGCAAATCTCCAGAGA	59.361	45.455	0.00	32.67	3.10	F
455	463	3.685139	ACATGGACGACAGTGATTTCT	57.315	42.857	0.00	0.00	2.52	F
1758	1846	4.283467	TGCGCAGTGGATTACCTAGAATAT	59.717	41.667	5.66	37.04	1.28	F
2263	2381	2.666272	TATCTTGGTTGGGCACACAA	57.334	45.000	0.00	0.00	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1851	1958	0.322008	CACCAGGAAGAAGCAGGTCC	60.322	60.000	0.00	0.00	4.46	R
2263	2381	1.985116	GCTCCTCGGACCAAGGTCT	60.985	63.158	18.03	44.04	3.85	R
2861	2980	4.689705	GCCCATGAATTCCTCACCTGATAA	60.690	45.833	2.27	36.69	1.75	R
3872	3999	1.399440	CAAATGACGCAGAGACCCATG	59.601	52.381	0.00	0.00	3.66	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
49	50	3.515502	TGAAACTATGCCTACAGAGCTGT	59.484	43.478	8.35	8.35	46.87	4.40
112	113	2.639347	TCAGGTTGCAAATCTCCAGAGA	59.361	45.455	0.00	0.00	32.67	3.10
306	307	8.750515	TCATTTCCATGTGCAGAAATAGATTA	57.249	30.769	10.33	0.00	39.97	1.75
444	452	7.173735	AGTCACATATTACGTATACATGGACGA	59.826	37.037	19.73	3.34	41.60	4.20
455	463	3.685139	ACATGGACGACAGTGATTTCT	57.315	42.857	0.00	0.00	0.00	2.52
618	626	8.762481	TGCTTCCTATACTACACTCTTGATTA	57.238	34.615	0.00	0.00	0.00	1.75
746	764	5.064707	CCCTGACATAAATTCGTTTCGTGAT	59.935	40.000	0.00	0.00	0.00	3.06
784	802	4.588899	TCACTATTTTGTGTGCCTGCTAT	58.411	39.130	0.00	0.00	38.90	2.97
853	871	6.930667	TTTCTTACTTTTGTAGTGGGTGAC	57.069	37.500	0.00	0.00	37.73	3.67
1022	1040	5.962031	TCATGGTGTTGGTAGGTAAGTCTAT	59.038	40.000	0.00	0.00	0.00	1.98
1031	1049	8.435982	GTTGGTAGGTAAGTCTATACTCCTCTA	58.564	40.741	0.00	0.00	33.25	2.43
1559	1629	9.369904	CTTTACCCTCATATCAAACAAAAATGG	57.630	33.333	0.00	0.00	0.00	3.16
1715	1803	5.527582	CACAACTGAACTTACTTAAGCAGGT	59.472	40.000	1.29	0.00	36.79	4.00
1758	1846	4.283467	TGCGCAGTGGATTACCTAGAATAT	59.717	41.667	5.66	0.00	37.04	1.28
1848	1955	6.069440	TGAGAGGATGAATGGTTTAGTTGGAT	60.069	38.462	0.00	0.00	0.00	3.41
1851	1958	6.055588	AGGATGAATGGTTTAGTTGGATACG	58.944	40.000	0.00	0.00	42.51	3.06
1883	1990	6.425210	TCTTCCTGGTGATATCCATTGTAG	57.575	41.667	0.00	0.00	36.84	2.74
2143	2261	6.681729	TGTTCCTGTAGAATTACCAGTTCT	57.318	37.500	0.00	0.00	39.19	3.01
2263	2381	2.666272	TATCTTGGTTGGGCACACAA	57.334	45.000	0.00	0.00	0.00	3.33
2324	2442	7.525688	TTGTCTAGATACAAGCTGAAATTCG	57.474	36.000	0.00	0.00	34.50	3.34
2328	2446	4.832248	AGATACAAGCTGAAATTCGGTCA	58.168	39.130	3.54	0.00	0.00	4.02
2329	2447	5.245531	AGATACAAGCTGAAATTCGGTCAA	58.754	37.500	3.54	0.00	0.00	3.18
2542	2660	7.819900	GTGGTTTGAGACTGATACTGATACTTT	59.180	37.037	0.00	0.00	0.00	2.66
2627	2745	3.069729	GCCGTGATGGGTTTCTAGAGTAT	59.930	47.826	0.00	0.00	38.63	2.12
3025	3144	0.114364	TCACAGCTAGGAGTGGTGGA	59.886	55.000	2.42	0.00	37.25	4.02
3026	3145	0.534412	CACAGCTAGGAGTGGTGGAG	59.466	60.000	0.00	0.00	37.25	3.86
3027	3146	0.115349	ACAGCTAGGAGTGGTGGAGT	59.885	55.000	0.00	0.00	37.25	3.85
3028	3147	0.534412	CAGCTAGGAGTGGTGGAGTG	59.466	60.000	0.00	0.00	0.00	3.51
3029	3148	0.616111	AGCTAGGAGTGGTGGAGTGG	60.616	60.000	0.00	0.00	0.00	4.00
3030	3149	0.905337	GCTAGGAGTGGTGGAGTGGT	60.905	60.000	0.00	0.00	0.00	4.16
3031	3150	0.898320	CTAGGAGTGGTGGAGTGGTG	59.102	60.000	0.00	0.00	0.00	4.17
3032	3151	0.485543	TAGGAGTGGTGGAGTGGTGA	59.514	55.000	0.00	0.00	0.00	4.02
3233	3352	7.718314	ACTGATGATGTAATGTGTTATCTGCAT	59.282	33.333	0.00	0.00	0.00	3.96
3835	3962	5.922544	GCTTGCTCAAACATGAAGTTATTGT	59.077	36.000	0.00	0.00	40.26	2.71
3872	3999	3.791993	TCAACGCGTACATGGTTTTAC	57.208	42.857	14.46	0.00	0.00	2.01
3886	4013	2.423577	GTTTTACATGGGTCTCTGCGT	58.576	47.619	0.00	0.00	0.00	5.24
3903	4030	1.290203	CGTCATTTGGCGCATCTAGT	58.710	50.000	10.83	0.00	35.94	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
112	113	9.732130	GCAAGAGTGAAAGAAGGGATATAATAT	57.268	33.333	0.00	0.00	0.00	1.28
306	307	8.225603	ACGGAATCTATAACAAAGCATGATTT	57.774	30.769	2.39	2.39	0.00	2.17
618	626	8.511604	AAAATATCGAGGACATGAACAGAAAT	57.488	30.769	0.00	0.00	0.00	2.17
746	764	9.173021	CAAAATAGTGATGTGTGGAATTACCTA	57.827	33.333	0.00	0.00	39.86	3.08
784	802	4.047822	CGATTAACAAGCCAAGCAAACAA	58.952	39.130	0.00	0.00	0.00	2.83
853	871	0.037303	TGCTTGGGCTCCTTTCTCAG	59.963	55.000	0.00	0.00	39.59	3.35
998	1016	4.164981	AGACTTACCTACCAACACCATGA	58.835	43.478	0.00	0.00	0.00	3.07
1559	1629	2.977405	AGTTCAGTTGCAATCGAAGC	57.023	45.000	0.59	6.29	0.00	3.86
1715	1803	5.866092	GCGCAGACAAGATATCATCTATCAA	59.134	40.000	0.30	0.00	39.08	2.57
1848	1955	0.895530	CAGGAAGAAGCAGGTCCGTA	59.104	55.000	0.00	0.00	36.49	4.02
1851	1958	0.322008	CACCAGGAAGAAGCAGGTCC	60.322	60.000	0.00	0.00	0.00	4.46
1883	1990	5.804979	AGCACATTATATCGCCAACAAAAAC	59.195	36.000	0.00	0.00	0.00	2.43
1976	2083	6.032956	ACGGTGTGAGTGATATTGAGTTAA	57.967	37.500	0.00	0.00	0.00	2.01
1986	2093	8.038944	ACAATAAAGTTATACGGTGTGAGTGAT	58.961	33.333	0.00	0.00	0.00	3.06
1988	2095	7.591006	ACAATAAAGTTATACGGTGTGAGTG	57.409	36.000	0.00	0.00	0.00	3.51
1997	2104	9.901724	CTCAAGCAACTACAATAAAGTTATACG	57.098	33.333	0.00	0.00	35.44	3.06
2143	2261	5.782893	AAAGCACATAAAACCTGTAAGCA	57.217	34.783	0.00	0.00	0.00	3.91
2263	2381	1.985116	GCTCCTCGGACCAAGGTCT	60.985	63.158	18.03	0.00	44.04	3.85
2861	2980	4.689705	GCCCATGAATTCCTCACCTGATAA	60.690	45.833	2.27	0.00	36.69	1.75
3025	3144	4.777896	ACAGTTATATGTCCACTCACCACT	59.222	41.667	0.00	0.00	0.00	4.00
3026	3145	5.086104	ACAGTTATATGTCCACTCACCAC	57.914	43.478	0.00	0.00	0.00	4.16
3027	3146	5.339008	GACAGTTATATGTCCACTCACCA	57.661	43.478	0.00	0.00	43.12	4.17
3861	3988	4.335416	CAGAGACCCATGTAAAACCATGT	58.665	43.478	0.00	0.00	40.50	3.21
3872	3999	1.399440	CAAATGACGCAGAGACCCATG	59.601	52.381	0.00	0.00	0.00	3.66
3875	4002	1.648467	GCCAAATGACGCAGAGACCC	61.648	60.000	0.00	0.00	0.00	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.