AutoCloner

Multiple sequence alignment - TraesCS3D01G058500

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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	TraesCS3D01G058500	chr3D	100.000	2141	0	0	1	2141	25162032	25159892	0.000000e+00	3954.0
1	TraesCS3D01G058500	chr3D	81.569	803	78	29	589	1365	25190855	25190097	1.090000e-167	599.0
2	TraesCS3D01G058500	chr3D	79.752	484	57	22	771	1225	25151433	25150962	1.600000e-81	313.0
3	TraesCS3D01G058500	chr3D	80.838	334	35	12	1530	1834	25189792	25189459	3.550000e-58	235.0
4	TraesCS3D01G058500	chr3D	82.822	163	13	8	1992	2141	25189240	25189080	4.790000e-27	132.0
5	TraesCS3D01G058500	chr3D	86.000	100	8	2	1283	1382	25150939	25150846	3.760000e-18	102.0
6	TraesCS3D01G058500	chr3D	96.078	51	2	0	1436	1486	25190061	25190011	1.360000e-12	84.2
7	TraesCS3D01G058500	chr3A	90.338	1832	91	23	1	1802	34584255	34582480	0.000000e+00	2324.0
8	TraesCS3D01G058500	chr3A	81.227	799	70	40	589	1365	34593681	34592941	2.380000e-159	571.0
9	TraesCS3D01G058500	chr3A	81.881	436	33	25	992	1422	34580318	34579924	2.050000e-85	326.0
10	TraesCS3D01G058500	chr3A	92.727	220	6	3	1931	2141	34582362	34582144	2.060000e-80	309.0
11	TraesCS3D01G058500	chr3A	86.164	159	12	8	1992	2141	34592271	34592114	1.700000e-36	163.0
12	TraesCS3D01G058500	chr3A	81.818	198	15	9	579	757	34580603	34580408	1.710000e-31	147.0
13	TraesCS3D01G058500	chr3A	80.311	193	22	6	1397	1577	34592941	34592753	4.790000e-27	132.0
14	TraesCS3D01G058500	chr3A	79.286	140	13	11	2002	2132	34539840	34539708	1.360000e-12	84.2
15	TraesCS3D01G058500	chr3B	93.189	1292	54	10	561	1831	42707798	42706520	0.000000e+00	1868.0
16	TraesCS3D01G058500	chr3B	90.133	527	39	9	1	518	42708314	42707792	0.000000e+00	673.0
17	TraesCS3D01G058500	chr3B	80.106	754	92	32	612	1342	42715053	42714335	1.900000e-140	508.0
18	TraesCS3D01G058500	chr3B	92.787	305	10	5	1845	2138	42706472	42706169	4.220000e-117	431.0
19	TraesCS3D01G058500	chr3B	79.753	647	63	40	852	1487	42701263	42700674	7.110000e-110	407.0
20	TraesCS3D01G058500	chr3B	77.733	494	49	31	1397	1834	42714317	42713829	1.640000e-61	246.0
21	TraesCS3D01G058500	chr3B	89.726	146	13	2	1280	1424	42689924	42689780	3.630000e-43	185.0
22	TraesCS3D01G058500	chr3B	86.957	161	9	7	1992	2141	42713612	42713453	1.020000e-38	171.0
23	TraesCS3D01G058500	chr3B	84.211	152	13	7	610	757	42701453	42701309	1.030000e-28	137.0
24	TraesCS3D01G058500	chr1D	91.603	131	8	1	997	1127	453284769	453284896	6.070000e-41	178.0
25	TraesCS3D01G058500	chr1B	83.516	91	9	3	2051	2141	623993629	623993713	1.760000e-11	80.5
26	TraesCS3D01G058500	chr1B	86.076	79	5	3	2051	2129	624020541	624020613	1.760000e-11	80.5

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	TraesCS3D01G058500	chr3D	25159892	25162032	2140	True	3954.000000	3954	100.000000	1	2141	1	chr3D.!!$R1	2140
1	TraesCS3D01G058500	chr3D	25189080	25190855	1775	True	262.550000	599	85.326750	589	2141	4	chr3D.!!$R3	1552
2	TraesCS3D01G058500	chr3D	25150846	25151433	587	True	207.500000	313	82.876000	771	1382	2	chr3D.!!$R2	611
3	TraesCS3D01G058500	chr3A	34579924	34584255	4331	True	776.500000	2324	86.691000	1	2141	4	chr3A.!!$R2	2140
4	TraesCS3D01G058500	chr3A	34592114	34593681	1567	True	288.666667	571	82.567333	589	2141	3	chr3A.!!$R3	1552
5	TraesCS3D01G058500	chr3B	42706169	42708314	2145	True	990.666667	1868	92.036333	1	2138	3	chr3B.!!$R3	2137
6	TraesCS3D01G058500	chr3B	42713453	42715053	1600	True	308.333333	508	81.598667	612	2141	3	chr3B.!!$R4	1529
7	TraesCS3D01G058500	chr3B	42700674	42701453	779	True	272.000000	407	81.982000	610	1487	2	chr3B.!!$R2	877

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
494	506	0.036164	ACTAGAATTGCCCACACGCA	59.964	50.0	0.0	0.0	36.85	5.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1679	2036	0.39606	TTTTGCCCTGAAATGGTGGC	59.604	50.0	0.0	0.0	44.27	5.01	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
38	39	4.758251	CATGCACCGGAGACCGCA	62.758	66.667	9.46	9.18	46.86	5.69
51	52	3.041940	CCGCAGACGTGGTTGTCC	61.042	66.667	0.00	0.00	39.77	4.02
52	53	3.403057	CGCAGACGTGGTTGTCCG	61.403	66.667	0.00	0.00	39.77	4.79
77	78	1.735376	GATTGCGCTCCCGAGTCCTA	61.735	60.000	9.73	0.00	36.29	2.94
129	130	1.380302	CCAGTGGTCCCTCCTTTGG	59.620	63.158	0.00	0.00	37.07	3.28
135	136	0.544697	GGTCCCTCCTTTGGCGATTA	59.455	55.000	0.00	0.00	0.00	1.75
201	211	3.745723	GGGGGAGAAAGCAAGACAA	57.254	52.632	0.00	0.00	0.00	3.18
217	227	1.630878	GACAAAGGTGAGGTGGGAGAT	59.369	52.381	0.00	0.00	0.00	2.75
219	229	1.352352	CAAAGGTGAGGTGGGAGATGT	59.648	52.381	0.00	0.00	0.00	3.06
235	245	5.705441	GGGAGATGTGTGAAATGAAACAGTA	59.295	40.000	0.00	0.00	0.00	2.74
272	282	0.860533	GTAACAGTTGTAACCGCGCA	59.139	50.000	8.75	0.00	0.00	6.09
334	345	1.291132	GCGAACTGGCTAGAATCACC	58.709	55.000	3.17	0.00	0.00	4.02
456	468	3.196254	CCTAAACCCTCACTAGCGGTTTA	59.804	47.826	16.84	16.84	41.98	2.01
458	470	2.226962	ACCCTCACTAGCGGTTTAGA	57.773	50.000	0.00	0.00	0.00	2.10
494	506	0.036164	ACTAGAATTGCCCACACGCA	59.964	50.000	0.00	0.00	36.85	5.24
495	507	1.340017	ACTAGAATTGCCCACACGCAT	60.340	47.619	0.00	0.00	38.87	4.73
522	534	1.812571	CCACCTTAGTTGTGCCATCAC	59.187	52.381	0.00	0.00	43.40	3.06
524	536	0.447801	CCTTAGTTGTGCCATCACGC	59.552	55.000	0.00	0.00	46.01	5.34
528	540	3.364441	TTGTGCCATCACGCTGCC	61.364	61.111	0.00	0.00	46.01	4.85
564	576	1.501337	CGCAACAGTGAGAGCTTGCA	61.501	55.000	13.77	0.00	39.19	4.08
587	599	1.090052	GCACCTCCACCATTAGTCGC	61.090	60.000	0.00	0.00	0.00	5.19
774	795	2.438434	GGTGCCCCCAACATCTCG	60.438	66.667	0.00	0.00	0.00	4.04
839	863	4.523083	TGCCAGAGTAGTTTGTCTTTTGT	58.477	39.130	0.00	0.00	0.00	2.83
840	864	4.335315	TGCCAGAGTAGTTTGTCTTTTGTG	59.665	41.667	0.00	0.00	0.00	3.33
841	865	4.789802	GCCAGAGTAGTTTGTCTTTTGTGC	60.790	45.833	0.00	0.00	0.00	4.57
842	866	4.261197	CCAGAGTAGTTTGTCTTTTGTGCC	60.261	45.833	0.00	0.00	0.00	5.01
843	867	4.335315	CAGAGTAGTTTGTCTTTTGTGCCA	59.665	41.667	0.00	0.00	0.00	4.92
844	868	5.009010	CAGAGTAGTTTGTCTTTTGTGCCAT	59.991	40.000	0.00	0.00	0.00	4.40
845	869	5.594317	AGAGTAGTTTGTCTTTTGTGCCATT	59.406	36.000	0.00	0.00	0.00	3.16
966	1021	1.818642	CCTTTCTTCCAGCTCACCAG	58.181	55.000	0.00	0.00	0.00	4.00
1278	1372	3.251571	AGATTTCGCTGACGGTTAGTTC	58.748	45.455	1.71	0.00	40.63	3.01
1310	1405	2.073252	TTTGTGTGGTGCCATGGTTA	57.927	45.000	14.67	0.00	0.00	2.85
1312	1407	3.441500	TTGTGTGGTGCCATGGTTATA	57.558	42.857	14.67	0.00	0.00	0.98
1417	1514	6.936900	TCAGTAATGGAAGGTTCTCAGAAAAG	59.063	38.462	0.00	0.00	0.00	2.27
1476	1576	5.008415	AGCAAAAGATTATCTCTTGGCATCG	59.992	40.000	9.92	0.00	43.60	3.84
1500	1622	6.560711	GTCCAATTGTACCATAATTGTGACC	58.439	40.000	17.07	0.00	41.60	4.02
1517	1639	2.028658	TGACCTGTGAGTCTCTGATTGC	60.029	50.000	0.65	0.00	37.66	3.56
1518	1640	2.233431	GACCTGTGAGTCTCTGATTGCT	59.767	50.000	0.65	0.00	33.79	3.91
1519	1641	3.435275	ACCTGTGAGTCTCTGATTGCTA	58.565	45.455	0.65	0.00	0.00	3.49
1520	1642	3.834813	ACCTGTGAGTCTCTGATTGCTAA	59.165	43.478	0.65	0.00	0.00	3.09
1521	1643	4.180057	CCTGTGAGTCTCTGATTGCTAAC	58.820	47.826	0.65	0.00	0.00	2.34
1522	1644	3.838120	TGTGAGTCTCTGATTGCTAACG	58.162	45.455	0.65	0.00	0.00	3.18
1523	1645	2.600867	GTGAGTCTCTGATTGCTAACGC	59.399	50.000	0.65	0.00	0.00	4.84
1524	1646	2.197577	GAGTCTCTGATTGCTAACGCC	58.802	52.381	0.00	0.00	34.43	5.68
1525	1647	1.550524	AGTCTCTGATTGCTAACGCCA	59.449	47.619	0.00	0.00	34.43	5.69
1526	1648	2.169352	AGTCTCTGATTGCTAACGCCAT	59.831	45.455	0.00	0.00	34.43	4.40
1527	1649	3.384789	AGTCTCTGATTGCTAACGCCATA	59.615	43.478	0.00	0.00	34.43	2.74
1528	1650	3.491267	GTCTCTGATTGCTAACGCCATAC	59.509	47.826	0.00	0.00	34.43	2.39
1529	1651	3.132111	TCTCTGATTGCTAACGCCATACA	59.868	43.478	0.00	0.00	34.43	2.29
1530	1652	4.060900	CTCTGATTGCTAACGCCATACAT	58.939	43.478	0.00	0.00	34.43	2.29
1531	1653	3.809279	TCTGATTGCTAACGCCATACATG	59.191	43.478	0.00	0.00	34.43	3.21
1659	2016	4.288626	AGTTACTCAGGAAATTGGCACCTA	59.711	41.667	0.00	0.00	32.35	3.08
1660	2017	3.806949	ACTCAGGAAATTGGCACCTAA	57.193	42.857	0.00	0.00	32.35	2.69
1661	2018	4.322057	ACTCAGGAAATTGGCACCTAAT	57.678	40.909	0.00	0.00	32.35	1.73
1679	2036	8.360390	GCACCTAATTAATATTTCAGGGAAAGG	58.640	37.037	0.00	0.00	34.92	3.11
1680	2037	8.360390	CACCTAATTAATATTTCAGGGAAAGGC	58.640	37.037	0.00	0.00	34.92	4.35
1683	2053	6.731292	ATTAATATTTCAGGGAAAGGCCAC	57.269	37.500	5.01	0.00	38.95	5.01
1790	2162	6.156949	AGACTCATTTTATCTTCTGCCCAGTA	59.843	38.462	0.00	0.00	0.00	2.74
1831	2203	0.321671	TCTACACACAGCTCCTTGCC	59.678	55.000	0.00	0.00	44.23	4.52
1832	2204	0.035317	CTACACACAGCTCCTTGCCA	59.965	55.000	0.00	0.00	44.23	4.92
1833	2205	0.692476	TACACACAGCTCCTTGCCAT	59.308	50.000	0.00	0.00	44.23	4.40
1836	2208	0.403271	ACACAGCTCCTTGCCATCTT	59.597	50.000	0.00	0.00	44.23	2.40
1838	2210	1.201647	CACAGCTCCTTGCCATCTTTG	59.798	52.381	0.00	0.00	44.23	2.77
1839	2211	1.202976	ACAGCTCCTTGCCATCTTTGT	60.203	47.619	0.00	0.00	44.23	2.83
1840	2212	1.891150	CAGCTCCTTGCCATCTTTGTT	59.109	47.619	0.00	0.00	44.23	2.83
1841	2213	2.094854	CAGCTCCTTGCCATCTTTGTTC	60.095	50.000	0.00	0.00	44.23	3.18
1843	2262	2.094854	GCTCCTTGCCATCTTTGTTCTG	60.095	50.000	0.00	0.00	35.15	3.02
1861	2280	8.833231	TTGTTCTGAGTTTGTCTAGGAAATAG	57.167	34.615	0.00	0.00	0.00	1.73
1985	2411	2.032620	CTGGGTATACTCGCCTCAACT	58.967	52.381	2.25	0.00	0.00	3.16
1994	2453	2.300152	ACTCGCCTCAACTTGAATCTCA	59.700	45.455	0.00	0.00	0.00	3.27
2092	2562	1.373570	GAGGCTGCGTAAGAAATGCT	58.626	50.000	0.00	0.00	41.03	3.79
2103	2577	4.963953	CGTAAGAAATGCTTTTATCCTGCG	59.036	41.667	0.00	0.00	38.05	5.18
2121	2599	0.322098	CGACCCCACTTGCCATGTAA	60.322	55.000	0.00	0.00	0.00	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	2.029073	CAACCACGTCTGCGGTCT	59.971	61.111	0.00	0.00	43.45	3.85
37	38	2.357034	CCCGGACAACCACGTCTG	60.357	66.667	0.73	0.00	41.21	3.51
38	39	3.622826	CCCCGGACAACCACGTCT	61.623	66.667	0.73	0.00	36.12	4.18
51	52	2.897350	GGAGCGCAATCTTCCCCG	60.897	66.667	11.47	0.00	0.00	5.73
52	53	2.517166	GGGAGCGCAATCTTCCCC	60.517	66.667	18.60	8.95	34.65	4.81
77	78	5.542635	TGACTACAAGGTGGATGACTAACTT	59.457	40.000	0.00	0.00	34.93	2.66
135	136	3.081409	ATGGTAGCGGCGGGACTT	61.081	61.111	9.78	0.00	0.00	3.01
188	189	3.217626	CCTCACCTTTGTCTTGCTTTCT	58.782	45.455	0.00	0.00	0.00	2.52
189	190	2.952310	ACCTCACCTTTGTCTTGCTTTC	59.048	45.455	0.00	0.00	0.00	2.62
190	191	2.689983	CACCTCACCTTTGTCTTGCTTT	59.310	45.455	0.00	0.00	0.00	3.51
199	200	1.352352	ACATCTCCCACCTCACCTTTG	59.648	52.381	0.00	0.00	0.00	2.77
201	211	0.987294	CACATCTCCCACCTCACCTT	59.013	55.000	0.00	0.00	0.00	3.50
217	227	5.008613	GGAAGCTACTGTTTCATTTCACACA	59.991	40.000	0.00	0.00	35.50	3.72
219	229	4.213270	CGGAAGCTACTGTTTCATTTCACA	59.787	41.667	0.00	0.00	35.50	3.58
235	245	0.466555	ACCTAGCTCGATCGGAAGCT	60.467	55.000	27.80	27.80	40.96	3.74
494	506	4.705023	GGCACAACTAAGGTGGTCAAATAT	59.295	41.667	0.00	0.00	36.76	1.28
495	507	4.076394	GGCACAACTAAGGTGGTCAAATA	58.924	43.478	0.00	0.00	36.76	1.40
541	553	1.958205	GCTCTCACTGTTGCGCACT	60.958	57.895	11.12	0.00	0.00	4.40
549	561	1.072159	GGGTGCAAGCTCTCACTGT	59.928	57.895	15.19	0.00	33.91	3.55
564	576	1.910580	CTAATGGTGGAGGTGCGGGT	61.911	60.000	0.00	0.00	0.00	5.28
774	795	8.943002	TCCTACTTGCAAGTATAAAAAGCTTAC	58.057	33.333	33.45	0.00	40.46	2.34
907	935	2.547211	CACTGCTGCTATACTGGATTGC	59.453	50.000	0.00	0.00	36.88	3.56
966	1021	0.036875	AAGGTGGTGGTTGAGCTAGC	59.963	55.000	6.62	6.62	0.00	3.42
1278	1372	3.181491	ACCACACAAAACTTCAACATCCG	60.181	43.478	0.00	0.00	0.00	4.18
1310	1405	1.553248	TGCCGTTGCAGGACTTAGTAT	59.447	47.619	0.00	0.00	44.23	2.12
1312	1407	1.752198	TGCCGTTGCAGGACTTAGT	59.248	52.632	0.00	0.00	44.23	2.24
1500	1622	3.856521	CGTTAGCAATCAGAGACTCACAG	59.143	47.826	5.02	0.00	0.00	3.66
1522	1644	1.202290	CCAAAAGGACGCATGTATGGC	60.202	52.381	0.00	0.00	0.00	4.40
1523	1645	1.405105	CCCAAAAGGACGCATGTATGG	59.595	52.381	0.00	0.00	38.24	2.74
1524	1646	1.405105	CCCCAAAAGGACGCATGTATG	59.595	52.381	0.00	0.00	38.24	2.39
1525	1647	1.005450	ACCCCAAAAGGACGCATGTAT	59.995	47.619	0.00	0.00	38.24	2.29
1526	1648	0.402504	ACCCCAAAAGGACGCATGTA	59.597	50.000	0.00	0.00	38.24	2.29
1527	1649	1.152830	ACCCCAAAAGGACGCATGT	59.847	52.632	0.00	0.00	38.24	3.21
1528	1650	1.178534	ACACCCCAAAAGGACGCATG	61.179	55.000	0.00	0.00	38.24	4.06
1529	1651	0.469144	AACACCCCAAAAGGACGCAT	60.469	50.000	0.00	0.00	38.24	4.73
1530	1652	1.076632	AACACCCCAAAAGGACGCA	60.077	52.632	0.00	0.00	38.24	5.24
1531	1653	0.822121	AGAACACCCCAAAAGGACGC	60.822	55.000	0.00	0.00	38.24	5.19
1659	2016	6.099701	GGTGGCCTTTCCCTGAAATATTAATT	59.900	38.462	3.32	0.00	30.85	1.40
1660	2017	5.602561	GGTGGCCTTTCCCTGAAATATTAAT	59.397	40.000	3.32	0.00	30.85	1.40
1661	2018	4.959839	GGTGGCCTTTCCCTGAAATATTAA	59.040	41.667	3.32	0.00	30.85	1.40
1679	2036	0.396060	TTTTGCCCTGAAATGGTGGC	59.604	50.000	0.00	0.00	44.27	5.01
1680	2037	3.421919	AATTTTGCCCTGAAATGGTGG	57.578	42.857	0.00	0.00	0.00	4.61
1683	2053	4.820716	TGTTCAAATTTTGCCCTGAAATGG	59.179	37.500	4.19	0.00	30.03	3.16
1790	2162	0.668706	GTCGCTCAGTGTGTCTGCAT	60.669	55.000	0.00	0.00	43.32	3.96
1831	2203	6.931281	TCCTAGACAAACTCAGAACAAAGATG	59.069	38.462	0.00	0.00	0.00	2.90
1832	2204	7.067496	TCCTAGACAAACTCAGAACAAAGAT	57.933	36.000	0.00	0.00	0.00	2.40
1833	2205	6.479972	TCCTAGACAAACTCAGAACAAAGA	57.520	37.500	0.00	0.00	0.00	2.52
1836	2208	7.387948	GCTATTTCCTAGACAAACTCAGAACAA	59.612	37.037	0.00	0.00	0.00	2.83
1838	2210	6.314152	GGCTATTTCCTAGACAAACTCAGAAC	59.686	42.308	0.00	0.00	35.31	3.01
1839	2211	6.013725	TGGCTATTTCCTAGACAAACTCAGAA	60.014	38.462	0.00	0.00	42.77	3.02
1840	2212	5.483937	TGGCTATTTCCTAGACAAACTCAGA	59.516	40.000	0.00	0.00	42.77	3.27
1841	2213	5.734720	TGGCTATTTCCTAGACAAACTCAG	58.265	41.667	0.00	0.00	42.77	3.35
1843	2262	4.572795	GCTGGCTATTTCCTAGACAAACTC	59.427	45.833	0.00	0.00	45.08	3.01
1985	2411	3.795688	AAGTGCCTCCTTGAGATTCAA	57.204	42.857	0.00	0.00	34.79	2.69
1994	2453	2.177016	ACTAAACCCAAAGTGCCTCCTT	59.823	45.455	0.00	0.00	0.00	3.36
2092	2562	0.988832	AGTGGGGTCGCAGGATAAAA	59.011	50.000	0.00	0.00	0.00	1.52
2103	2577	2.143876	ATTACATGGCAAGTGGGGTC	57.856	50.000	5.49	0.00	0.00	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.