AutoCloner

Multiple sequence alignment - TraesCS2B01G135100

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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	TraesCS2B01G135100	chr2B	100.000	2805	0	0	1	2805	101490748	101487944	0.000000e+00	5180.0
1	TraesCS2B01G135100	chr2B	100.000	1904	0	0	3125	5028	101487624	101485721	0.000000e+00	3517.0
2	TraesCS2B01G135100	chr2B	94.646	523	25	2	4508	5028	599007947	599008468	0.000000e+00	808.0
3	TraesCS2B01G135100	chr2B	81.926	675	93	21	2072	2727	101488608	101487944	1.230000e-150	544.0
4	TraesCS2B01G135100	chr2B	81.926	675	93	21	2141	2805	101488677	101488022	1.230000e-150	544.0
5	TraesCS2B01G135100	chr2B	82.410	614	86	14	1406	2017	39195089	39194496	2.680000e-142	516.0
6	TraesCS2B01G135100	chr2B	75.000	624	115	32	2054	2649	101488554	101487944	3.010000e-62	250.0
7	TraesCS2B01G135100	chr2B	75.000	624	115	32	2195	2805	101488695	101488100	3.010000e-62	250.0
8	TraesCS2B01G135100	chr2B	77.458	417	80	13	2357	2766	101488353	101487944	2.340000e-58	237.0
9	TraesCS2B01G135100	chr2B	77.566	419	76	14	2396	2805	101488392	101487983	2.340000e-58	237.0
10	TraesCS2B01G135100	chr2B	96.591	88	3	0	118	205	101490587	101490500	4.060000e-31	147.0
11	TraesCS2B01G135100	chr2B	96.591	88	3	0	162	249	101490631	101490544	4.060000e-31	147.0
12	TraesCS2B01G135100	chr2B	78.095	210	41	5	2410	2618	39194472	39194267	1.470000e-25	128.0
13	TraesCS2B01G135100	chr2B	90.722	97	4	2	109	205	715814804	715814713	1.900000e-24	124.0
14	TraesCS2B01G135100	chr2B	88.542	96	5	3	162	256	715814795	715814705	1.480000e-20	111.0
15	TraesCS2B01G135100	chr2A	93.644	1479	89	3	1231	2705	65822385	65820908	0.000000e+00	2206.0
16	TraesCS2B01G135100	chr2A	92.569	1413	84	11	3125	4522	65820466	65819060	0.000000e+00	2008.0
17	TraesCS2B01G135100	chr2A	86.233	523	56	10	1406	1926	24300484	24300992	2.050000e-153	553.0
18	TraesCS2B01G135100	chr2A	77.710	655	116	21	2141	2783	65821544	65820908	1.710000e-99	374.0
19	TraesCS2B01G135100	chr2A	79.878	328	54	9	2357	2678	65821217	65820896	3.920000e-56	230.0
20	TraesCS2B01G135100	chr2A	82.403	233	31	8	2560	2784	65820515	65820285	1.430000e-45	195.0
21	TraesCS2B01G135100	chr2A	89.172	157	12	3	2086	2238	65821386	65821231	1.850000e-44	191.0
22	TraesCS2B01G135100	chr2A	85.632	174	19	3	2638	2805	65820515	65820342	1.440000e-40	178.0
23	TraesCS2B01G135100	chr2A	84.672	137	21	0	3125	3261	65821046	65820910	2.440000e-28	137.0
24	TraesCS2B01G135100	chr2A	90.526	95	6	1	2714	2805	65820517	65820423	6.840000e-24	122.0
25	TraesCS2B01G135100	chr2A	90.385	52	4	1	1006	1056	65822431	65822380	3.250000e-07	67.6
26	TraesCS2B01G135100	chr2D	88.039	1555	134	34	1229	2769	68924247	68922731	0.000000e+00	1794.0
27	TraesCS2B01G135100	chr2D	87.915	1415	117	27	3125	4522	68922369	68920992	0.000000e+00	1616.0
28	TraesCS2B01G135100	chr2D	83.968	630	84	14	2072	2691	68923353	68922731	5.610000e-164	588.0
29	TraesCS2B01G135100	chr2D	92.857	364	23	2	2367	2730	68923091	68922731	4.460000e-145	525.0
30	TraesCS2B01G135100	chr2D	85.141	498	59	7	1406	1903	22503109	22503591	3.500000e-136	496.0
31	TraesCS2B01G135100	chr2D	78.214	560	95	22	2072	2613	68923281	68922731	2.900000e-87	333.0
32	TraesCS2B01G135100	chr2D	74.342	608	115	31	3127	3715	68922406	68921821	2.360000e-53	220.0
33	TraesCS2B01G135100	chr2D	92.593	108	2	2	6	107	68924788	68924681	3.140000e-32	150.0
34	TraesCS2B01G135100	chr2D	94.845	97	4	1	109	205	189528070	189527975	3.140000e-32	150.0
35	TraesCS2B01G135100	chr2D	93.333	90	5	1	162	251	189528061	189527973	1.140000e-26	132.0
36	TraesCS2B01G135100	chr2D	76.923	234	43	5	2438	2664	68922420	68922191	6.840000e-24	122.0
37	TraesCS2B01G135100	chr2D	79.141	163	29	5	2410	2571	22503723	22503881	1.910000e-19	108.0
38	TraesCS2B01G135100	chr2D	81.967	122	19	2	938	1056	68924361	68924240	3.200000e-17	100.0
39	TraesCS2B01G135100	chr7B	95.174	518	23	2	4511	5028	505120358	505119843	0.000000e+00	817.0
40	TraesCS2B01G135100	chr7B	89.552	134	12	2	110	243	593417959	593418090	8.660000e-38	169.0
41	TraesCS2B01G135100	chr7B	83.146	178	18	8	1058	1227	581402032	581402205	8.720000e-33	152.0
42	TraesCS2B01G135100	chr6B	95.294	510	23	1	4519	5028	624622556	624623064	0.000000e+00	808.0
43	TraesCS2B01G135100	chr6B	94.605	519	24	2	4514	5028	59224845	59224327	0.000000e+00	800.0
44	TraesCS2B01G135100	chr6B	94.605	519	23	4	4513	5028	570952668	570952152	0.000000e+00	798.0
45	TraesCS2B01G135100	chr6B	94.402	518	29	0	4511	5028	163261551	163262068	0.000000e+00	797.0
46	TraesCS2B01G135100	chr6B	78.746	287	37	13	560	827	417237054	417237335	2.410000e-38	171.0
47	TraesCS2B01G135100	chr3B	95.127	513	24	1	4516	5028	687839685	687839174	0.000000e+00	808.0
48	TraesCS2B01G135100	chr3B	95.108	511	25	0	4518	5028	701683495	701682985	0.000000e+00	806.0
49	TraesCS2B01G135100	chr3B	94.584	517	26	2	4513	5028	16419446	16419961	0.000000e+00	798.0
50	TraesCS2B01G135100	chr3B	91.667	96	2	2	104	198	93718545	93718455	1.470000e-25	128.0
51	TraesCS2B01G135100	chr3B	89.583	96	6	2	110	201	91426569	91426474	8.840000e-23	119.0
52	TraesCS2B01G135100	chr6D	77.045	379	60	16	472	830	11663276	11662905	5.140000e-45	193.0
53	TraesCS2B01G135100	chr6D	79.661	177	26	8	647	818	269122009	269122180	8.840000e-23	119.0
54	TraesCS2B01G135100	chr6D	88.764	89	7	1	162	250	312136265	312136350	6.880000e-19	106.0
55	TraesCS2B01G135100	chr4A	77.419	341	46	19	475	790	597177202	597176868	1.860000e-39	174.0
56	TraesCS2B01G135100	chr4A	90.625	96	5	2	110	205	278325735	278325826	1.900000e-24	124.0
57	TraesCS2B01G135100	chr4A	89.888	89	5	1	162	250	278325743	278325827	1.480000e-20	111.0
58	TraesCS2B01G135100	chr7A	83.417	199	20	8	1045	1231	163381952	163382149	6.690000e-39	172.0
59	TraesCS2B01G135100	chr6A	77.660	282	37	16	558	818	383475879	383476155	1.130000e-31	148.0
60	TraesCS2B01G135100	chr4B	75.434	346	63	15	472	801	10834750	10835089	1.130000e-31	148.0
61	TraesCS2B01G135100	chr4B	79.397	199	32	5	573	762	10946853	10947051	1.140000e-26	132.0
62	TraesCS2B01G135100	chr5B	76.452	310	50	10	474	762	314290044	314290351	4.060000e-31	147.0
63	TraesCS2B01G135100	chr5A	75.065	385	61	16	473	827	337827734	337828113	4.060000e-31	147.0
64	TraesCS2B01G135100	chr3D	75.316	316	59	13	1420	1733	555454737	555454439	3.160000e-27	134.0
65	TraesCS2B01G135100	chr1A	91.111	90	7	1	162	250	276575254	276575165	2.460000e-23	121.0
66	TraesCS2B01G135100	chr1D	88.542	96	6	2	110	205	494045180	494045090	1.480000e-20	111.0
67	TraesCS2B01G135100	chr1B	87.629	97	7	2	110	201	675092970	675093066	1.910000e-19	108.0

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	TraesCS2B01G135100	chr2B	101485721	101490748	5027	True	1105.300000	5180	86.205800	1	5028	10	chr2B.!!$R2	5027
1	TraesCS2B01G135100	chr2B	599007947	599008468	521	False	808.000000	808	94.646000	4508	5028	1	chr2B.!!$F1	520
2	TraesCS2B01G135100	chr2B	39194267	39195089	822	True	322.000000	516	80.252500	1406	2618	2	chr2B.!!$R1	1212
3	TraesCS2B01G135100	chr2A	65819060	65822431	3371	True	570.860000	2206	86.659100	1006	4522	10	chr2A.!!$R1	3516
4	TraesCS2B01G135100	chr2A	24300484	24300992	508	False	553.000000	553	86.233000	1406	1926	1	chr2A.!!$F1	520
5	TraesCS2B01G135100	chr2D	68920992	68924788	3796	True	605.333333	1794	84.090889	6	4522	9	chr2D.!!$R1	4516
6	TraesCS2B01G135100	chr2D	22503109	22503881	772	False	302.000000	496	82.141000	1406	2571	2	chr2D.!!$F1	1165
7	TraesCS2B01G135100	chr7B	505119843	505120358	515	True	817.000000	817	95.174000	4511	5028	1	chr7B.!!$R1	517
8	TraesCS2B01G135100	chr6B	624622556	624623064	508	False	808.000000	808	95.294000	4519	5028	1	chr6B.!!$F3	509
9	TraesCS2B01G135100	chr6B	59224327	59224845	518	True	800.000000	800	94.605000	4514	5028	1	chr6B.!!$R1	514
10	TraesCS2B01G135100	chr6B	570952152	570952668	516	True	798.000000	798	94.605000	4513	5028	1	chr6B.!!$R2	515
11	TraesCS2B01G135100	chr6B	163261551	163262068	517	False	797.000000	797	94.402000	4511	5028	1	chr6B.!!$F1	517
12	TraesCS2B01G135100	chr3B	687839174	687839685	511	True	808.000000	808	95.127000	4516	5028	1	chr3B.!!$R3	512
13	TraesCS2B01G135100	chr3B	701682985	701683495	510	True	806.000000	806	95.108000	4518	5028	1	chr3B.!!$R4	510
14	TraesCS2B01G135100	chr3B	16419446	16419961	515	False	798.000000	798	94.584000	4513	5028	1	chr3B.!!$F1	515

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
828	836	0.034896	TTTTCACTCTCGGGCTCACC	59.965	55.0	0.00	0.00	0.00	4.02	F
1144	1211	0.040646	GGTTTTTAGGGGAGGGTGGG	59.959	60.0	0.00	0.00	0.00	4.61	F
1145	1212	0.040646	GTTTTTAGGGGAGGGTGGGG	59.959	60.0	0.00	0.00	0.00	4.96	F
2597	2737	0.872881	CAGAAACCGGTCGAACGTGT	60.873	55.0	23.08	16.23	0.00	4.49	F
3352	3838	1.049289	ACCTTCTGGATACGAGGCCC	61.049	60.0	0.00	0.00	42.51	5.80	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2239	2376	1.002087	GCTCCCGTACCCATAAGGATG	59.998	57.143	0.0	0.0	39.89	3.51	R
2522	2662	1.450312	GGAGAAGGTGGCATGGACG	60.450	63.158	0.0	0.0	0.00	4.79	R
2760	2900	1.741401	TTTCTGAGACGGCGGCATG	60.741	57.895	18.3	4.1	0.00	4.06	R
3987	4523	0.188342	ACCCAGTCATGCCAAACCTT	59.812	50.000	0.0	0.0	0.00	3.50	R
4812	5367	0.108329	CCCACCGACGTATTCAGCTT	60.108	55.000	0.0	0.0	0.00	3.74	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	End Stability
107	114	5.852282	AATTCACAAGGCGGCTATTATTT	57.148	34.783	13.71	0.00	1.40
108	115	4.630894	TTCACAAGGCGGCTATTATTTG	57.369	40.909	13.71	8.39	2.32
109	116	3.616219	TCACAAGGCGGCTATTATTTGT	58.384	40.909	13.71	9.15	2.83
113	120	4.814771	ACAAGGCGGCTATTATTTGTACTC	59.185	41.667	13.71	0.00	2.59
114	121	4.004196	AGGCGGCTATTATTTGTACTCC	57.996	45.455	11.03	0.00	3.85
116	123	3.244457	GGCGGCTATTATTTGTACTCCCT	60.244	47.826	0.00	0.00	4.20
117	124	3.995048	GCGGCTATTATTTGTACTCCCTC	59.005	47.826	0.00	0.00	4.30
120	127	4.040095	GGCTATTATTTGTACTCCCTCCGT	59.960	45.833	0.00	0.00	4.69
121	128	5.228665	GCTATTATTTGTACTCCCTCCGTC	58.771	45.833	0.00	0.00	4.79
122	129	4.684484	ATTATTTGTACTCCCTCCGTCC	57.316	45.455	0.00	0.00	4.79
123	130	1.201424	ATTTGTACTCCCTCCGTCCC	58.799	55.000	0.00	0.00	4.46
124	131	0.178926	TTTGTACTCCCTCCGTCCCA	60.179	55.000	0.00	0.00	4.37
125	132	0.178926	TTGTACTCCCTCCGTCCCAA	60.179	55.000	0.00	0.00	4.12
126	133	0.178926	TGTACTCCCTCCGTCCCAAA	60.179	55.000	0.00	0.00	3.28
127	134	0.535797	GTACTCCCTCCGTCCCAAAG	59.464	60.000	0.00	0.00	2.77
128	135	0.115745	TACTCCCTCCGTCCCAAAGT	59.884	55.000	0.00	0.00	2.66
129	136	0.767060	ACTCCCTCCGTCCCAAAGTT	60.767	55.000	0.00	0.00	2.66
130	137	0.036294	CTCCCTCCGTCCCAAAGTTC	60.036	60.000	0.00	0.00	3.01
131	138	0.473117	TCCCTCCGTCCCAAAGTTCT	60.473	55.000	0.00	0.00	3.01
132	139	0.400594	CCCTCCGTCCCAAAGTTCTT	59.599	55.000	0.00	0.00	2.52
133	140	1.523758	CCTCCGTCCCAAAGTTCTTG	58.476	55.000	0.00	0.00	3.02
134	141	1.202770	CCTCCGTCCCAAAGTTCTTGT	60.203	52.381	0.00	0.00	3.16
135	142	2.143925	CTCCGTCCCAAAGTTCTTGTC	58.856	52.381	0.00	0.00	3.18
136	143	1.766496	TCCGTCCCAAAGTTCTTGTCT	59.234	47.619	0.00	0.00	3.41
137	144	2.171870	TCCGTCCCAAAGTTCTTGTCTT	59.828	45.455	0.00	0.00	3.01

Showing 1 to 25 of 529 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
0	1	6.551601	AGAGTAGTGGTGGGAGATATACTTTG	59.448	42.308	0.00	2.77
1	2	6.551601	CAGAGTAGTGGTGGGAGATATACTTT	59.448	42.308	0.00	2.66
2	3	6.071984	CAGAGTAGTGGTGGGAGATATACTT	58.928	44.000	0.00	2.24
3	4	5.458362	CCAGAGTAGTGGTGGGAGATATACT	60.458	48.000	32.32	2.12
38	42	8.201242	TGCACCTCATACATATAATAACCTCA	57.799	34.615	0.00	3.86
75	82	4.226761	CGCCTTGTGAATTTTGGACTTAC	58.773	43.478	0.00	2.34
107	114	0.178926	TTTGGGACGGAGGGAGTACA	60.179	55.000	0.00	2.90
108	115	0.535797	CTTTGGGACGGAGGGAGTAC	59.464	60.000	0.00	2.73
109	116	0.115745	ACTTTGGGACGGAGGGAGTA	59.884	55.000	0.00	2.59
113	120	0.400594	AAGAACTTTGGGACGGAGGG	59.599	55.000	0.00	4.30
114	121	1.202770	ACAAGAACTTTGGGACGGAGG	60.203	52.381	0.00	4.30
116	123	1.766496	AGACAAGAACTTTGGGACGGA	59.234	47.619	0.00	4.69
117	124	2.256117	AGACAAGAACTTTGGGACGG	57.744	50.000	0.00	4.79
120	127	7.060421	ACAAATCTAAGACAAGAACTTTGGGA	58.940	34.615	33.04	4.37
121	128	7.229506	AGACAAATCTAAGACAAGAACTTTGGG	59.770	37.037	33.04	4.12
122	129	8.159344	AGACAAATCTAAGACAAGAACTTTGG	57.841	34.615	33.04	3.28
129	136	8.622157	CCGTATCTAGACAAATCTAAGACAAGA	58.378	37.037	36.98	3.02
130	137	8.622157	TCCGTATCTAGACAAATCTAAGACAAG	58.378	37.037	36.98	3.16
131	138	8.515695	TCCGTATCTAGACAAATCTAAGACAA	57.484	34.615	36.98	3.18
132	139	8.515695	TTCCGTATCTAGACAAATCTAAGACA	57.484	34.615	36.98	3.41
133	140	8.623030	ACTTCCGTATCTAGACAAATCTAAGAC	58.377	37.037	36.98	3.01
134	141	8.749026	ACTTCCGTATCTAGACAAATCTAAGA	57.251	34.615	36.98	2.10
135	142	9.881529	GTACTTCCGTATCTAGACAAATCTAAG	57.118	37.037	36.98	2.18
136	143	8.844244	GGTACTTCCGTATCTAGACAAATCTAA	58.156	37.037	36.98	2.10
137	144	8.388484	GGTACTTCCGTATCTAGACAAATCTA	57.612	38.462	36.29	1.98

Showing 1 to 25 of 546 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.