AutoCloner

Multiple sequence alignment - TraesCS3A01G465900

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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	TraesCS3A01G465900	chr3A	100.000	2711	0	0	1	2711	699975357	699978067	0.000000e+00	5007.0
1	TraesCS3A01G465900	chr3A	79.487	897	144	30	1190	2061	699983078	699983959	3.860000e-168	601.0
2	TraesCS3A01G465900	chr3A	79.656	349	63	8	1321	1665	699763754	699764098	7.500000e-61	244.0
3	TraesCS3A01G465900	chr3A	79.091	330	60	8	1332	1659	700108068	700108390	4.540000e-53	219.0
4	TraesCS3A01G465900	chr3A	79.923	259	36	11	1825	2078	699880171	699880418	2.770000e-40	176.0
5	TraesCS3A01G465900	chr3A	96.429	56	2	0	1	56	700210337	700210282	2.870000e-15	93.5
6	TraesCS3A01G465900	chr3B	95.170	1118	46	6	962	2078	753867738	753868848	0.000000e+00	1759.0
7	TraesCS3A01G465900	chr3B	78.586	990	166	38	1098	2061	753916769	753917738	1.780000e-171	612.0
8	TraesCS3A01G465900	chr3B	80.000	590	101	12	1246	1824	753995100	753995683	1.160000e-113	420.0
9	TraesCS3A01G465900	chr3B	74.306	1117	222	36	962	2059	754308512	754309582	1.940000e-111	412.0
10	TraesCS3A01G465900	chr3B	91.513	271	19	1	2282	2548	753871327	753871597	1.190000e-98	370.0
11	TraesCS3A01G465900	chr3B	77.872	592	113	16	1243	1824	752808929	752808346	4.290000e-93	351.0
12	TraesCS3A01G465900	chr3B	93.243	222	14	1	1	222	753867527	753867747	2.600000e-85	326.0
13	TraesCS3A01G465900	chr3B	91.837	196	16	0	2090	2285	753869193	753869388	9.560000e-70	274.0
14	TraesCS3A01G465900	chr3B	94.366	142	8	0	2570	2711	753871655	753871796	4.540000e-53	219.0
15	TraesCS3A01G465900	chr5A	98.523	745	9	2	220	962	706468683	706469427	0.000000e+00	1314.0
16	TraesCS3A01G465900	chr3D	79.079	999	173	26	1094	2077	565642447	565643424	0.000000e+00	654.0
17	TraesCS3A01G465900	chr3D	76.355	1070	196	37	962	2000	565831141	565832184	3.090000e-144	521.0
18	TraesCS3A01G465900	chr3D	77.989	527	104	12	1327	1846	565259409	565259930	1.210000e-83	320.0
19	TraesCS3A01G465900	chr3D	80.779	385	70	2	1512	1895	562418661	562418280	5.670000e-77	298.0
20	TraesCS3A01G465900	chr3D	76.766	538	110	13	1327	1856	565326412	565326942	1.230000e-73	287.0
21	TraesCS3A01G465900	chr3D	75.712	527	110	17	1243	1760	562468177	562467660	5.800000e-62	248.0
22	TraesCS3A01G465900	chr3D	79.931	289	35	8	2105	2370	565643957	565644245	9.910000e-45	191.0
23	TraesCS3A01G465900	chr3D	94.565	92	4	1	2479	2570	565644246	565644336	1.010000e-29	141.0
24	TraesCS3A01G465900	chr3D	78.857	175	32	5	219	390	221566340	221566512	2.210000e-21	113.0
25	TraesCS3A01G465900	chr4A	94.832	387	17	2	220	605	692333077	692332693	3.860000e-168	601.0
26	TraesCS3A01G465900	chr4A	80.674	564	98	8	1246	1800	611378785	611378224	6.940000e-116	427.0
27	TraesCS3A01G465900	chr4A	93.970	199	12	0	764	962	692332692	692332494	4.390000e-78	302.0
28	TraesCS3A01G465900	chr4A	78.689	183	35	4	220	401	540300869	540300690	4.740000e-23	119.0
29	TraesCS3A01G465900	chrUn	78.347	859	146	23	962	1800	48324187	48323349	1.110000e-143	520.0
30	TraesCS3A01G465900	chrUn	79.902	612	92	18	1383	1976	39287690	39288288	1.160000e-113	420.0
31	TraesCS3A01G465900	chr2B	80.347	173	28	6	221	390	161015658	161015489	2.830000e-25	126.0

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	TraesCS3A01G465900	chr3A	699975357	699978067	2710	False	5007.000000	5007	100.0000	1	2711	1	chr3A.!!$F3	2710
1	TraesCS3A01G465900	chr3A	699983078	699983959	881	False	601.000000	601	79.4870	1190	2061	1	chr3A.!!$F4	871
2	TraesCS3A01G465900	chr3B	753916769	753917738	969	False	612.000000	612	78.5860	1098	2061	1	chr3B.!!$F1	963
3	TraesCS3A01G465900	chr3B	753867527	753871796	4269	False	589.600000	1759	93.2258	1	2711	5	chr3B.!!$F4	2710
4	TraesCS3A01G465900	chr3B	753995100	753995683	583	False	420.000000	420	80.0000	1246	1824	1	chr3B.!!$F2	578
5	TraesCS3A01G465900	chr3B	754308512	754309582	1070	False	412.000000	412	74.3060	962	2059	1	chr3B.!!$F3	1097
6	TraesCS3A01G465900	chr3B	752808346	752808929	583	True	351.000000	351	77.8720	1243	1824	1	chr3B.!!$R1	581
7	TraesCS3A01G465900	chr5A	706468683	706469427	744	False	1314.000000	1314	98.5230	220	962	1	chr5A.!!$F1	742
8	TraesCS3A01G465900	chr3D	565831141	565832184	1043	False	521.000000	521	76.3550	962	2000	1	chr3D.!!$F4	1038
9	TraesCS3A01G465900	chr3D	565642447	565644336	1889	False	328.666667	654	84.5250	1094	2570	3	chr3D.!!$F5	1476
10	TraesCS3A01G465900	chr3D	565259409	565259930	521	False	320.000000	320	77.9890	1327	1846	1	chr3D.!!$F2	519
11	TraesCS3A01G465900	chr3D	565326412	565326942	530	False	287.000000	287	76.7660	1327	1856	1	chr3D.!!$F3	529
12	TraesCS3A01G465900	chr3D	562467660	562468177	517	True	248.000000	248	75.7120	1243	1760	1	chr3D.!!$R2	517
13	TraesCS3A01G465900	chr4A	692332494	692333077	583	True	451.500000	601	94.4010	220	962	2	chr4A.!!$R3	742
14	TraesCS3A01G465900	chr4A	611378224	611378785	561	True	427.000000	427	80.6740	1246	1800	1	chr4A.!!$R2	554
15	TraesCS3A01G465900	chrUn	48323349	48324187	838	True	520.000000	520	78.3470	962	1800	1	chrUn.!!$R1	838
16	TraesCS3A01G465900	chrUn	39287690	39288288	598	False	420.000000	420	79.9020	1383	1976	1	chrUn.!!$F1	593

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
785	789	0.254462	CCTCCCTCCCTCTTTCTTGC	59.746	60.0	0.0	0.0	0.0	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2203	2898	0.739462	CGAAATGGTCTAGCGCCACA	60.739	55.0	2.29	0.0	39.03	4.17	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
31	32	2.046604	GTGTTCCCCTACGGCCAC	60.047	66.667	2.24	0.00	0.00	5.01
74	75	2.432300	ATCATCCCCGTCGACCACC	61.432	63.158	10.58	0.00	0.00	4.61
75	76	4.508128	CATCCCCGTCGACCACCG	62.508	72.222	10.58	0.00	40.25	4.94
121	122	2.401195	GCGCGACTTGATCAAGCC	59.599	61.111	30.95	21.75	41.99	4.35
208	209	2.259618	CACTTCGTCATCTGTAACCCG	58.740	52.381	0.00	0.00	0.00	5.28
211	212	1.876714	CGTCATCTGTAACCCGGCG	60.877	63.158	0.00	0.00	0.00	6.46
212	213	1.514087	GTCATCTGTAACCCGGCGA	59.486	57.895	9.30	0.00	0.00	5.54
213	214	0.804933	GTCATCTGTAACCCGGCGAC	60.805	60.000	9.30	0.00	0.00	5.19
214	215	1.520787	CATCTGTAACCCGGCGACC	60.521	63.158	9.30	0.00	0.00	4.79
215	216	2.728435	ATCTGTAACCCGGCGACCC	61.728	63.158	9.30	0.00	0.00	4.46
467	469	3.186613	GCCGTAGTCCAAACTCTTCTTTG	59.813	47.826	0.00	0.00	36.92	2.77
725	727	0.466124	GGGAATAGCAACGGAGCTCT	59.534	55.000	14.64	0.00	45.26	4.09
785	789	0.254462	CCTCCCTCCCTCTTTCTTGC	59.746	60.000	0.00	0.00	0.00	4.01
1063	1067	1.219124	CTACTGATGTGCCCGTGCT	59.781	57.895	0.00	0.00	38.71	4.40
1064	1068	1.079197	TACTGATGTGCCCGTGCTG	60.079	57.895	0.00	0.00	38.71	4.41
1078	1082	1.666888	CGTGCTGGTTTTTGGCTCATC	60.667	52.381	0.00	0.00	0.00	2.92
1096	1100	4.546674	TCATCAAGTGATAGCTGGGAGTA	58.453	43.478	0.00	0.00	32.63	2.59
1162	1169	3.561120	AACATCGGGCCGGAGCAAA	62.561	57.895	27.98	5.47	42.56	3.68
1192	1205	3.117625	ACTGATATCCGACACCAGGTCTA	60.118	47.826	0.00	0.00	44.68	2.59
1242	1258	0.322008	GGGTGCAGGAGAAGGTCAAG	60.322	60.000	0.00	0.00	0.00	3.02
1311	1327	1.210155	GCATGTTCCTGTTCGTGGC	59.790	57.895	0.00	0.00	0.00	5.01
1477	1502	1.131638	GGAGATCAGGGCATGGTGTA	58.868	55.000	0.00	0.00	0.00	2.90
1875	1941	8.279103	GCTGTTACAAGCTGTATGAAATCTATC	58.721	37.037	0.00	0.00	40.20	2.08
1923	1991	5.751243	AAGGGATTATTATGCGTGTCAAC	57.249	39.130	0.00	0.00	0.00	3.18
1981	2063	1.134521	TGTGCTAACTAATCTGCCCCG	60.135	52.381	0.00	0.00	0.00	5.73
2035	2119	3.517296	TGGTTTTGTATGAAGGCCTCA	57.483	42.857	5.23	6.53	38.81	3.86
2052	2136	4.466726	GGCCTCAAGGAGTCTTCTTAGTAA	59.533	45.833	0.00	0.00	37.39	2.24
2095	2730	9.303116	AGCAATCTAGCTAGCTAGTTAGAAATA	57.697	33.333	36.13	23.79	45.15	1.40
2203	2898	6.604396	TGAGCCATGTTCATTTTCATCTGTAT	59.396	34.615	0.00	0.00	0.00	2.29
2223	2938	0.739813	GTGGCGCTAGACCATTTCGT	60.740	55.000	7.64	0.00	39.95	3.85
2224	2939	0.459585	TGGCGCTAGACCATTTCGTC	60.460	55.000	7.64	0.00	30.29	4.20
2243	2958	3.685058	GTCTGCCGATAATTGAAAGCAC	58.315	45.455	0.00	0.00	0.00	4.40
2267	2982	0.322975	GCCTTGTCTCAAGCAGAGGA	59.677	55.000	6.38	0.00	44.81	3.71
2268	2983	1.065564	GCCTTGTCTCAAGCAGAGGAT	60.066	52.381	6.38	0.00	44.81	3.24
2273	2988	2.167281	TGTCTCAAGCAGAGGATAGCAC	59.833	50.000	6.38	0.00	44.81	4.40
2312	4969	5.452356	GCAATGCCATTATAGAAGCAGGTTT	60.452	40.000	0.00	0.00	38.89	3.27
2387	5044	2.632377	TCGTCCTTGAATCTTCATGGC	58.368	47.619	16.24	11.79	46.47	4.40
2398	5055	6.540083	TGAATCTTCATGGCATCTGATGTAT	58.460	36.000	18.19	10.70	31.01	2.29
2399	5056	7.002276	TGAATCTTCATGGCATCTGATGTATT	58.998	34.615	18.19	6.47	31.01	1.89
2401	5058	6.628919	TCTTCATGGCATCTGATGTATTTG	57.371	37.500	18.19	11.18	0.00	2.32
2433	5094	6.651225	GCCAAATAGAAGTTGTTCTCTACAGT	59.349	38.462	0.00	0.00	42.40	3.55
2441	5102	8.351461	AGAAGTTGTTCTCTACAGTTACAGTAC	58.649	37.037	0.00	0.00	38.84	2.73
2453	5114	4.020573	CAGTTACAGTACTGATGTTCCCCA	60.021	45.833	29.30	0.00	46.72	4.96
2455	5116	2.621070	ACAGTACTGATGTTCCCCACT	58.379	47.619	29.30	0.00	0.00	4.00
2463	5124	4.583489	ACTGATGTTCCCCACTATAGTACG	59.417	45.833	4.74	0.00	0.00	3.67
2525	5186	0.036732	GTGAGGTGATGCCAGACCAA	59.963	55.000	0.00	0.00	40.61	3.67
2606	5303	1.291877	ATTCAGTTCTGCCACGACGC	61.292	55.000	0.00	0.00	0.00	5.19
2615	5312	1.741770	GCCACGACGCTTCTTCCAT	60.742	57.895	0.00	0.00	0.00	3.41
2620	5317	3.186909	CACGACGCTTCTTCCATATCAA	58.813	45.455	0.00	0.00	0.00	2.57
2624	5321	1.528586	CGCTTCTTCCATATCAAGGCG	59.471	52.381	0.00	0.00	0.00	5.52
2656	5353	7.848539	GCGCATCTAGAATTTCTTTAGAAGAAC	59.151	37.037	0.30	0.00	46.53	3.01
2688	5385	6.038271	CACTTCCCCTTAACTAATATGTGCAC	59.962	42.308	10.75	10.75	0.00	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	0.470833	ATGATGTCTAGGGAGGCGCT	60.471	55.000	7.64	0.00	0.00	5.92
44	45	0.980423	GGGATGATGTCTAGGGAGGC	59.020	60.000	0.00	0.00	0.00	4.70
121	122	2.471818	TCGAGACGATAGAAGTCGGAG	58.528	52.381	0.00	0.00	45.49	4.63
208	209	3.834799	CCCTACTGACGGGTCGCC	61.835	72.222	0.00	0.00	36.91	5.54
214	215	1.910580	ATGCCCAACCCTACTGACGG	61.911	60.000	0.00	0.00	0.00	4.79
215	216	0.828022	TATGCCCAACCCTACTGACG	59.172	55.000	0.00	0.00	0.00	4.35
216	217	3.577805	AATATGCCCAACCCTACTGAC	57.422	47.619	0.00	0.00	0.00	3.51
217	218	4.288626	GGATAATATGCCCAACCCTACTGA	59.711	45.833	0.00	0.00	0.00	3.41
218	219	4.589908	GGATAATATGCCCAACCCTACTG	58.410	47.826	0.00	0.00	0.00	2.74
467	469	1.585214	GTTGTATACGTGCGGCTGTAC	59.415	52.381	3.28	3.28	0.00	2.90
725	727	1.406341	GGTATGGTCGCTGGCTACAAA	60.406	52.381	0.09	0.00	0.00	2.83
756	758	1.541672	GGAGGGAGGGAGAGAGAGG	59.458	68.421	0.00	0.00	0.00	3.69
785	789	1.249407	GAGTAGGGCCGATCTACAGG	58.751	60.000	16.94	0.00	39.48	4.00
915	919	3.411808	CGATCGGTTCGGTTTCTCA	57.588	52.632	7.38	0.00	44.28	3.27
1063	1067	3.295093	TCACTTGATGAGCCAAAAACCA	58.705	40.909	0.00	0.00	31.91	3.67
1064	1068	4.525912	ATCACTTGATGAGCCAAAAACC	57.474	40.909	0.00	0.00	41.91	3.27
1078	1082	5.344743	TCTTTACTCCCAGCTATCACTTG	57.655	43.478	0.00	0.00	0.00	3.16
1096	1100	5.220416	GCGATAAAACGTAGCAGTCATCTTT	60.220	40.000	0.00	0.00	35.59	2.52
1162	1169	4.049186	GTGTCGGATATCAGTTTATGCGT	58.951	43.478	4.83	0.00	42.08	5.24
1192	1205	3.181455	TGCAATCTACCACGGAATAGCAT	60.181	43.478	0.00	0.00	0.00	3.79
1242	1258	8.572828	TGTCAAACACAATTATCATGTTGTTC	57.427	30.769	0.00	0.00	36.48	3.18
1311	1327	0.035881	ACAGGTCATCACCAGTGCAG	59.964	55.000	0.00	0.00	46.68	4.41
1362	1381	7.665145	TCAATGATTGTCCATGTGTCTCTAAAA	59.335	33.333	4.93	0.00	0.00	1.52
1477	1502	5.180868	GCTCGCATAATTCATCATCCTTTCT	59.819	40.000	0.00	0.00	0.00	2.52
1665	1709	4.261801	CAACATAACCCTCTAGTGTTGGG	58.738	47.826	10.68	10.31	43.45	4.12
1875	1941	4.566004	TCCGAAAGAGTATTGACACAAGG	58.434	43.478	0.00	0.00	0.00	3.61
2064	2148	9.221933	CTAACTAGCTAGCTAGATTGCTAACTA	57.778	37.037	43.93	22.04	46.56	2.24
2172	2867	2.812836	ATGAACATGGCTCATGGACA	57.187	45.000	16.39	14.92	45.16	4.02
2173	2868	4.082081	TGAAAATGAACATGGCTCATGGAC	60.082	41.667	16.39	11.17	45.16	4.02
2203	2898	0.739462	CGAAATGGTCTAGCGCCACA	60.739	55.000	2.29	0.00	39.03	4.17
2223	2938	3.342719	TGTGCTTTCAATTATCGGCAGA	58.657	40.909	0.00	0.00	0.00	4.26
2224	2939	3.763097	TGTGCTTTCAATTATCGGCAG	57.237	42.857	0.00	0.00	0.00	4.85
2243	2958	2.555325	TCTGCTTGAGACAAGGCAATTG	59.445	45.455	12.36	0.00	45.01	2.32
2267	2982	3.688414	GCCCACTTAATTCCTGGTGCTAT	60.688	47.826	0.00	0.00	0.00	2.97
2268	2983	2.356741	GCCCACTTAATTCCTGGTGCTA	60.357	50.000	0.00	0.00	0.00	3.49
2273	2988	2.159057	GCATTGCCCACTTAATTCCTGG	60.159	50.000	0.00	0.00	0.00	4.45
2299	4956	6.241645	AGTTGAGCTTTAAACCTGCTTCTAT	58.758	36.000	2.35	0.00	37.16	1.98
2308	4965	5.690997	AGCAACTAGTTGAGCTTTAAACC	57.309	39.130	34.43	15.21	42.93	3.27
2387	5044	4.516698	GGCCAGTACCAAATACATCAGATG	59.483	45.833	9.03	9.03	36.09	2.90
2401	5058	4.332828	ACAACTTCTATTTGGCCAGTACC	58.667	43.478	5.11	0.00	0.00	3.34
2433	5094	4.164981	AGTGGGGAACATCAGTACTGTAA	58.835	43.478	21.99	4.68	0.00	2.41
2441	5102	4.825634	TCGTACTATAGTGGGGAACATCAG	59.174	45.833	15.90	0.00	0.00	2.90
2525	5186	4.145052	GGGAGAAATCTGTTCACAACCTT	58.855	43.478	0.00	0.00	0.00	3.50
2606	5303	3.310774	CACACGCCTTGATATGGAAGAAG	59.689	47.826	0.00	0.00	0.00	2.85
2615	5312	2.125310	CGCCCACACGCCTTGATA	60.125	61.111	0.00	0.00	0.00	2.15
2624	5321	1.668419	AATTCTAGATGCGCCCACAC	58.332	50.000	4.18	0.00	0.00	3.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.