AutoCloner

Multiple sequence alignment - TraesCS7B01G060200

Loading Multiple Alignment...

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	TraesCS7B01G060200	chr7B	100.000	3077	0	0	1	3077	62698148	62695072	0.000000e+00	5683
1	TraesCS7B01G060200	chr7B	91.768	328	14	6	934	1260	62705613	62705298	7.830000e-121	444
2	TraesCS7B01G060200	chr7B	91.983	237	14	4	711	946	62706881	62706649	8.230000e-86	327
3	TraesCS7B01G060200	chr7D	94.561	2390	83	25	710	3077	104576590	104574226	0.000000e+00	3650
4	TraesCS7B01G060200	chr7A	93.503	2155	92	16	940	3077	108818513	108816390	0.000000e+00	3160
5	TraesCS7B01G060200	chr7A	90.672	268	17	5	2	262	348963	348697	1.760000e-92	350
6	TraesCS7B01G060200	chr7A	90.795	239	17	4	709	945	108819104	108818869	6.400000e-82	315
7	TraesCS7B01G060200	chr7A	86.512	215	21	6	711	925	108822053	108821847	2.390000e-56	230
8	TraesCS7B01G060200	chr4A	98.204	724	11	2	1	724	140987693	140988414	0.000000e+00	1264
9	TraesCS7B01G060200	chr6A	97.187	711	20	0	1	711	279946964	279947674	0.000000e+00	1203
10	TraesCS7B01G060200	chr6A	95.696	395	16	1	315	709	93340977	93340584	4.330000e-178	634
11	TraesCS7B01G060200	chr2A	97.038	709	20	1	1	709	247008832	247009539	0.000000e+00	1192
12	TraesCS7B01G060200	chr5A	96.897	709	22	0	1	709	666047494	666048202	0.000000e+00	1188
13	TraesCS7B01G060200	chr5A	93.709	461	26	3	262	722	79469141	79468684	0.000000e+00	688
14	TraesCS7B01G060200	chr3A	94.621	725	23	1	1	709	560685462	560686186	0.000000e+00	1109
15	TraesCS7B01G060200	chr3A	95.332	407	17	2	312	718	714153910	714154314	0.000000e+00	645
16	TraesCS7B01G060200	chr3A	90.421	261	23	2	2	262	471288618	471288876	2.940000e-90	342
17	TraesCS7B01G060200	chr2D	94.248	452	21	4	262	710	353545042	353544593	0.000000e+00	686
18	TraesCS7B01G060200	chr4B	96.212	396	14	1	315	710	624156668	624156274	0.000000e+00	647
19	TraesCS7B01G060200	chr1A	92.337	261	18	2	2	262	496141343	496141601	1.350000e-98	370
20	TraesCS7B01G060200	chr1A	90.805	261	23	1	2	262	552326795	552326536	6.310000e-92	348

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	TraesCS7B01G060200	chr7B	62695072	62698148	3076	True	5683.0	5683	100.0000	1	3077	1	chr7B.!!$R1	3076
1	TraesCS7B01G060200	chr7B	62705298	62706881	1583	True	385.5	444	91.8755	711	1260	2	chr7B.!!$R2	549
2	TraesCS7B01G060200	chr7D	104574226	104576590	2364	True	3650.0	3650	94.5610	710	3077	1	chr7D.!!$R1	2367
3	TraesCS7B01G060200	chr7A	108816390	108822053	5663	True	1235.0	3160	90.2700	709	3077	3	chr7A.!!$R2	2368
4	TraesCS7B01G060200	chr4A	140987693	140988414	721	False	1264.0	1264	98.2040	1	724	1	chr4A.!!$F1	723
5	TraesCS7B01G060200	chr6A	279946964	279947674	710	False	1203.0	1203	97.1870	1	711	1	chr6A.!!$F1	710
6	TraesCS7B01G060200	chr2A	247008832	247009539	707	False	1192.0	1192	97.0380	1	709	1	chr2A.!!$F1	708
7	TraesCS7B01G060200	chr5A	666047494	666048202	708	False	1188.0	1188	96.8970	1	709	1	chr5A.!!$F1	708
8	TraesCS7B01G060200	chr3A	560685462	560686186	724	False	1109.0	1109	94.6210	1	709	1	chr3A.!!$F2	708

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
938	3906	0.243907	CACCTCGTGACCTGGTACTG	59.756	60.0	0.0	0.0	35.23	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2906	7325	0.321653	CTTCTAGTGCAAGGCCGGTT	60.322	55.0	1.9	0.0	0.0	4.44	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
211	212	1.880819	TACTCGGTGTTCCTTCGCCC	61.881	60.000	0.00	0.00	34.83	6.13
446	463	3.106054	CATTGGTTCAAATCCCATCCCA	58.894	45.455	0.00	0.00	0.00	4.37
461	478	6.129179	TCCCATCCCATTCTTCATTACTTTC	58.871	40.000	0.00	0.00	0.00	2.62
591	608	7.400599	GTATGGATACGACTGGGTATAATGA	57.599	40.000	0.00	0.00	42.51	2.57
756	773	7.015195	TGCATGATAAAGTGGCATAGAGTACTA	59.985	37.037	0.00	0.00	0.00	1.82
759	776	6.778069	TGATAAAGTGGCATAGAGTACTAGCT	59.222	38.462	0.00	0.00	31.78	3.32
899	3867	0.463654	TGGCAAACGACAGAACAGCT	60.464	50.000	0.00	0.00	0.00	4.24
909	3877	0.801251	CAGAACAGCTTAGCAGTGCC	59.199	55.000	12.58	0.72	0.00	5.01
938	3906	0.243907	CACCTCGTGACCTGGTACTG	59.756	60.000	0.00	0.00	35.23	2.74
1002	5392	1.577328	AACGCCAAGGTCGAGCAATG	61.577	55.000	18.15	14.60	0.00	2.82
1003	5393	2.034879	CGCCAAGGTCGAGCAATGT	61.035	57.895	18.15	0.00	0.00	2.71
1004	5394	1.796796	GCCAAGGTCGAGCAATGTC	59.203	57.895	18.15	1.40	0.00	3.06
1027	5417	1.345176	CCGTCGTACTCGTCGTACC	59.655	63.158	10.58	0.59	44.52	3.34
1239	5638	1.153208	GGACCAGCTCAGCATCCTG	60.153	63.158	0.00	0.00	40.54	3.86
1659	6067	2.264480	CTGCCGTTCATGGACCGA	59.736	61.111	0.00	0.00	0.00	4.69
1660	6068	1.375396	CTGCCGTTCATGGACCGAA	60.375	57.895	0.00	0.00	0.00	4.30
1661	6069	0.953471	CTGCCGTTCATGGACCGAAA	60.953	55.000	0.00	0.00	0.00	3.46
1726	6134	2.678580	TCGTCCAGTGGATCGCCA	60.679	61.111	16.67	3.57	43.47	5.69
1762	6170	0.323957	GAGGAAGGCCAAAGGTACGT	59.676	55.000	5.01	0.00	36.29	3.57
1763	6171	1.551883	GAGGAAGGCCAAAGGTACGTA	59.448	52.381	5.01	0.00	36.29	3.57
1764	6172	1.277273	AGGAAGGCCAAAGGTACGTAC	59.723	52.381	17.56	17.56	36.29	3.67
1765	6173	1.353076	GAAGGCCAAAGGTACGTACG	58.647	55.000	18.98	15.01	0.00	3.67
1788	6196	0.108585	TCCCTCTGCTTGTGAACCAC	59.891	55.000	0.00	0.00	34.56	4.16
1792	6203	1.261619	CTCTGCTTGTGAACCACGAAC	59.738	52.381	0.00	0.00	37.14	3.95
1808	6224	4.322049	CCACGAACTCCAGTAGAACATCTT	60.322	45.833	0.00	0.00	0.00	2.40
2039	6456	1.666553	CGCACTTCAACGCCACCTA	60.667	57.895	0.00	0.00	0.00	3.08
2084	6501	5.022787	AGAGGGGAGCTCATAGATTCATAC	58.977	45.833	17.19	0.00	0.00	2.39
2085	6502	4.100373	AGGGGAGCTCATAGATTCATACC	58.900	47.826	17.19	2.26	0.00	2.73
2086	6503	3.118956	GGGGAGCTCATAGATTCATACCG	60.119	52.174	17.19	0.00	0.00	4.02
2087	6504	3.511934	GGGAGCTCATAGATTCATACCGT	59.488	47.826	17.19	0.00	0.00	4.83
2088	6505	4.705507	GGGAGCTCATAGATTCATACCGTA	59.294	45.833	17.19	0.00	0.00	4.02
2089	6506	5.361285	GGGAGCTCATAGATTCATACCGTAT	59.639	44.000	17.19	0.00	0.00	3.06
2090	6507	6.269315	GGAGCTCATAGATTCATACCGTATG	58.731	44.000	17.19	11.73	37.52	2.39
2091	6508	6.127591	GGAGCTCATAGATTCATACCGTATGT	60.128	42.308	17.19	0.46	37.45	2.29
2092	6509	6.625362	AGCTCATAGATTCATACCGTATGTG	58.375	40.000	16.44	7.97	37.45	3.21
2093	6510	5.807520	GCTCATAGATTCATACCGTATGTGG	59.192	44.000	16.44	4.46	37.45	4.17
2094	6511	6.350194	GCTCATAGATTCATACCGTATGTGGA	60.350	42.308	16.44	6.49	37.45	4.02
2100	6517	3.367321	TCATACCGTATGTGGAAGACCA	58.633	45.455	16.44	0.00	38.14	4.02
2343	6762	3.327757	TGTACAGAATGAAACCAGAGGCT	59.672	43.478	0.00	0.00	39.69	4.58
2389	6808	2.028876	TCTACTCGCCATTTCGATCCA	58.971	47.619	0.00	0.00	37.87	3.41
2398	6817	3.443681	GCCATTTCGATCCAAGAAAGGAA	59.556	43.478	7.51	0.00	40.51	3.36
2403	6822	4.826274	TCGATCCAAGAAAGGAACTCAT	57.174	40.909	0.00	0.00	41.92	2.90
2420	6839	3.721172	ATCATCCCTGGGACGCCCT	62.721	63.158	19.82	0.00	45.70	5.19
2675	7094	2.334946	GCGGATGCAGCAAGGTGAA	61.335	57.895	3.51	0.00	42.15	3.18
2680	7099	1.337703	GATGCAGCAAGGTGAACACAA	59.662	47.619	0.00	0.00	0.00	3.33
2699	7118	4.855388	CACAACAGATATCTTGTGCAAAGC	59.145	41.667	19.60	0.00	40.51	3.51
2702	7121	5.710513	ACAGATATCTTGTGCAAAGCAAA	57.289	34.783	1.33	0.00	41.47	3.68
2706	7125	6.527023	CAGATATCTTGTGCAAAGCAAAGAAG	59.473	38.462	1.33	9.20	41.47	2.85
2726	7145	5.418209	AGAAGCGCTAGAGACCTTTTAACTA	59.582	40.000	12.05	0.00	0.00	2.24
2735	7154	2.574824	GACCTTTTAACTAGGGGCAGGA	59.425	50.000	7.53	0.00	37.09	3.86
2759	7178	5.479027	ACTCTTTCTAGACCTTCTTGACTCC	59.521	44.000	0.00	0.00	28.47	3.85
2816	7235	1.289160	TGGCCTGGCTAGATTCACTT	58.711	50.000	19.68	0.00	0.00	3.16
2832	7251	0.540830	ACTTGCTCGAGACCTGGACT	60.541	55.000	18.75	0.00	0.00	3.85
2906	7325	2.413837	GTTGGCTTCGACTTTGCTCTA	58.586	47.619	0.00	0.00	0.00	2.43
2911	7330	1.993370	CTTCGACTTTGCTCTAACCGG	59.007	52.381	0.00	0.00	0.00	5.28
2933	7352	0.320374	TTGCACTAGAAGACCCACGG	59.680	55.000	0.00	0.00	0.00	4.94
2960	7379	0.104120	GTTTTGAACCCACACCCTGC	59.896	55.000	0.00	0.00	0.00	4.85
3016	7435	5.772521	ACACTGGTCATTATTTTCTTGCAC	58.227	37.500	0.00	0.00	0.00	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
211	212	5.048713	GCGTATTTCATTGATTAGAAGGGGG	60.049	44.000	0.00	0.00	0.00	5.40
329	330	5.062558	GTGCTATTTATTGAACACGTACCGT	59.937	40.000	0.00	0.00	42.36	4.83
461	478	8.991243	TGCAGAAAATCCTCAAATAAAATGAG	57.009	30.769	0.00	0.00	43.15	2.90
591	608	3.243434	CCTCGTTCATATACGGTGCTTCT	60.243	47.826	0.00	0.00	41.67	2.85
756	773	7.331791	AGATTCTCTTGGAAACGTTATTAGCT	58.668	34.615	0.00	0.00	37.49	3.32
759	776	6.755141	CGGAGATTCTCTTGGAAACGTTATTA	59.245	38.462	13.22	0.00	37.49	0.98
899	3867	2.224744	TGTGGAATTGAGGCACTGCTAA	60.225	45.455	0.00	0.00	41.55	3.09
938	3906	4.212004	CACATGGGCGCATACATATATAGC	59.788	45.833	16.74	0.00	0.00	2.97
984	5369	2.034879	CATTGCTCGACCTTGGCGT	61.035	57.895	0.00	0.00	34.61	5.68
985	5370	1.970917	GACATTGCTCGACCTTGGCG	61.971	60.000	0.00	0.00	34.09	5.69
986	5371	1.796796	GACATTGCTCGACCTTGGC	59.203	57.895	0.00	0.00	0.00	4.52
1231	5630	4.457496	CACGCCGACCAGGATGCT	62.457	66.667	0.00	0.00	45.00	3.79
1659	6067	2.358247	ATGAACGGCGGCGACTTT	60.358	55.556	38.93	22.14	0.00	2.66
1660	6068	3.118454	CATGAACGGCGGCGACTT	61.118	61.111	38.93	22.96	0.00	3.01
1690	6098	4.500116	GTCCCAGGAGAGCGCGTC	62.500	72.222	8.43	2.43	0.00	5.19
1726	6134	0.972983	CTCCTGACCATGTCGGAGGT	60.973	60.000	18.82	0.00	43.04	3.85
1762	6170	2.038975	AAGCAGAGGGAGGGCGTA	59.961	61.111	0.00	0.00	0.00	4.42
1763	6171	3.710722	CAAGCAGAGGGAGGGCGT	61.711	66.667	0.00	0.00	0.00	5.68
1764	6172	3.710722	ACAAGCAGAGGGAGGGCG	61.711	66.667	0.00	0.00	0.00	6.13
1765	6173	2.045536	CACAAGCAGAGGGAGGGC	60.046	66.667	0.00	0.00	0.00	5.19
1788	6196	5.470368	TGAAAGATGTTCTACTGGAGTTCG	58.530	41.667	0.00	0.00	0.00	3.95
1792	6203	6.401394	TGTGATGAAAGATGTTCTACTGGAG	58.599	40.000	0.00	0.00	0.00	3.86
1808	6224	4.271696	AGTTTCGAGGACATGTGATGAA	57.728	40.909	1.15	0.00	0.00	2.57
1848	6265	4.598257	GTGGTCACATCCTCCACG	57.402	61.111	0.00	0.00	41.37	4.94
2084	6501	3.880047	TTACTGGTCTTCCACATACGG	57.120	47.619	0.00	0.00	39.03	4.02
2085	6502	6.542852	CAAATTTACTGGTCTTCCACATACG	58.457	40.000	0.00	0.00	39.03	3.06
2086	6503	6.072175	TGCAAATTTACTGGTCTTCCACATAC	60.072	38.462	0.00	0.00	39.03	2.39
2087	6504	6.007076	TGCAAATTTACTGGTCTTCCACATA	58.993	36.000	0.00	0.00	39.03	2.29
2088	6505	4.832266	TGCAAATTTACTGGTCTTCCACAT	59.168	37.500	0.00	0.00	39.03	3.21
2089	6506	4.211125	TGCAAATTTACTGGTCTTCCACA	58.789	39.130	0.00	0.00	39.03	4.17
2090	6507	4.278419	ACTGCAAATTTACTGGTCTTCCAC	59.722	41.667	0.00	0.00	39.03	4.02
2091	6508	4.469657	ACTGCAAATTTACTGGTCTTCCA	58.530	39.130	0.00	0.00	42.05	3.53
2092	6509	4.518970	TGACTGCAAATTTACTGGTCTTCC	59.481	41.667	12.66	0.00	0.00	3.46
2093	6510	5.689383	TGACTGCAAATTTACTGGTCTTC	57.311	39.130	12.66	0.00	0.00	2.87
2094	6511	6.096846	AGTTTGACTGCAAATTTACTGGTCTT	59.903	34.615	12.66	0.00	45.01	3.01
2141	6560	4.326826	TGTGAAACTGCTGGATTTCTAGG	58.673	43.478	7.77	0.00	38.04	3.02
2380	6799	4.968259	TGAGTTCCTTTCTTGGATCGAAA	58.032	39.130	0.00	0.00	35.83	3.46
2389	6808	4.324874	CCAGGGATGATGAGTTCCTTTCTT	60.325	45.833	0.00	0.00	32.34	2.52
2398	6817	1.690219	GCGTCCCAGGGATGATGAGT	61.690	60.000	29.91	0.00	40.94	3.41
2420	6839	2.803155	AAGATCCAAGCAGCCGCGAA	62.803	55.000	8.23	0.00	45.49	4.70
2462	6881	1.883732	GACTAGCTGTCGGTGAGCA	59.116	57.895	0.00	0.00	39.05	4.26
2680	7099	5.474532	TCTTTGCTTTGCACAAGATATCTGT	59.525	36.000	5.86	4.11	38.71	3.41
2699	7118	2.663826	AGGTCTCTAGCGCTTCTTTG	57.336	50.000	18.68	1.93	0.00	2.77
2702	7121	4.221041	AGTTAAAAGGTCTCTAGCGCTTCT	59.779	41.667	18.68	1.00	0.00	2.85
2706	7125	4.361420	CCTAGTTAAAAGGTCTCTAGCGC	58.639	47.826	0.00	0.00	0.00	5.92
2726	7145	1.362932	TCTAGAAAGAGTCCTGCCCCT	59.637	52.381	0.00	0.00	0.00	4.79
2735	7154	5.479027	GGAGTCAAGAAGGTCTAGAAAGAGT	59.521	44.000	0.00	0.00	30.45	3.24
2759	7178	1.543429	GGTCCTGAACACAAGTCCAGG	60.543	57.143	0.00	0.00	45.63	4.45
2816	7235	1.536073	CCAAGTCCAGGTCTCGAGCA	61.536	60.000	7.81	0.00	0.00	4.26
2832	7251	1.410004	AGAAGCCGACGGATATCCAA	58.590	50.000	20.50	0.00	35.14	3.53
2906	7325	0.321653	CTTCTAGTGCAAGGCCGGTT	60.322	55.000	1.90	0.00	0.00	4.44
2911	7330	0.324943	TGGGTCTTCTAGTGCAAGGC	59.675	55.000	0.00	0.00	0.00	4.35
2933	7352	2.362717	TGTGGGTTCAAAACGGAAATCC	59.637	45.455	0.00	0.00	0.00	3.01
2960	7379	5.476945	ACAAGGATTAAAACAGGTGGCTAAG	59.523	40.000	0.00	0.00	0.00	2.18
3016	7435	6.506147	TCAACATCAATTGTTTGTTCAGAGG	58.494	36.000	19.61	12.25	46.51	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.