AutoCloner

Multiple sequence alignment - TraesCS5B01G396000

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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	TraesCS5B01G396000	chr5B	100.000	2546	0	0	1	2546	573123342	573120797	0.000000e+00	4702.0
1	TraesCS5B01G396000	chr5B	95.582	1992	78	6	562	2545	446193260	446191271	0.000000e+00	3182.0
2	TraesCS5B01G396000	chr5B	95.480	1991	81	5	563	2546	269389470	269391458	0.000000e+00	3169.0
3	TraesCS5B01G396000	chr5B	89.464	522	27	5	1	521	311390546	311391040	3.570000e-178	634.0
4	TraesCS5B01G396000	chr2B	95.525	1989	80	8	563	2546	543889475	543887491	0.000000e+00	3171.0
5	TraesCS5B01G396000	chr2B	95.525	1989	80	8	563	2546	544319646	544317662	0.000000e+00	3171.0
6	TraesCS5B01G396000	chr2B	95.384	1993	85	5	561	2546	596962063	596964055	0.000000e+00	3164.0
7	TraesCS5B01G396000	chr2B	95.255	2002	81	10	555	2546	602077194	602075197	0.000000e+00	3158.0
8	TraesCS5B01G396000	chr2B	95.325	385	17	1	1	385	364848586	364848203	6.020000e-171	610.0
9	TraesCS5B01G396000	chr2B	85.542	83	7	5	487	566	165813381	165813301	5.840000e-12	82.4
10	TraesCS5B01G396000	chr7B	95.298	1999	85	8	553	2546	718488487	718486493	0.000000e+00	3162.0
11	TraesCS5B01G396000	chr7B	90.000	70	5	2	513	581	741608902	741608834	3.490000e-14	89.8
12	TraesCS5B01G396000	chr7B	86.420	81	6	4	504	581	307268867	307268789	1.620000e-12	84.2
13	TraesCS5B01G396000	chr7B	84.884	86	8	4	518	599	476194793	476194877	5.840000e-12	82.4
14	TraesCS5B01G396000	chr1B	95.334	1993	86	5	558	2546	498442428	498440439	0.000000e+00	3158.0
15	TraesCS5B01G396000	chr1B	95.298	1999	77	14	558	2546	232740725	232742716	0.000000e+00	3155.0
16	TraesCS5B01G396000	chr1B	94.962	397	19	1	1	397	492855194	492855589	2.780000e-174	621.0
17	TraesCS5B01G396000	chr1B	91.176	68	2	3	502	566	39520422	39520488	3.490000e-14	89.8
18	TraesCS5B01G396000	chr3B	92.628	529	22	9	1	521	52798829	52799348	0.000000e+00	745.0
19	TraesCS5B01G396000	chr3B	91.919	297	16	1	1	297	570443610	570443898	2.360000e-110	409.0
20	TraesCS5B01G396000	chr3B	92.373	236	10	3	293	521	570453883	570454117	1.890000e-86	329.0
21	TraesCS5B01G396000	chr3B	95.000	60	2	1	508	566	533462083	533462142	2.700000e-15	93.5
22	TraesCS5B01G396000	chr6A	95.000	360	16	1	1	360	32557859	32557502	4.760000e-157	564.0
23	TraesCS5B01G396000	chr6A	94.444	360	19	1	1	360	32424071	32423713	1.030000e-153	553.0
24	TraesCS5B01G396000	chr6A	94.444	360	19	1	1	360	32531666	32531308	1.030000e-153	553.0
25	TraesCS5B01G396000	chr4D	95.092	326	7	2	201	518	69251015	69250691	2.920000e-139	505.0
26	TraesCS5B01G396000	chr6B	95.455	242	11	0	2	243	202604334	202604575	1.100000e-103	387.0
27	TraesCS5B01G396000	chr1A	100.000	53	0	0	514	566	290054807	290054755	5.800000e-17	99.0
28	TraesCS5B01G396000	chr5A	93.548	62	2	2	506	566	589248612	589248672	9.700000e-15	91.6
29	TraesCS5B01G396000	chr3A	92.188	64	4	1	503	566	548063488	548063426	3.490000e-14	89.8

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	TraesCS5B01G396000	chr5B	573120797	573123342	2545	True	4702	4702	100.000	1	2546	1	chr5B.!!$R2	2545
1	TraesCS5B01G396000	chr5B	446191271	446193260	1989	True	3182	3182	95.582	562	2545	1	chr5B.!!$R1	1983
2	TraesCS5B01G396000	chr5B	269389470	269391458	1988	False	3169	3169	95.480	563	2546	1	chr5B.!!$F1	1983
3	TraesCS5B01G396000	chr2B	543887491	543889475	1984	True	3171	3171	95.525	563	2546	1	chr2B.!!$R3	1983
4	TraesCS5B01G396000	chr2B	544317662	544319646	1984	True	3171	3171	95.525	563	2546	1	chr2B.!!$R4	1983
5	TraesCS5B01G396000	chr2B	596962063	596964055	1992	False	3164	3164	95.384	561	2546	1	chr2B.!!$F1	1985
6	TraesCS5B01G396000	chr2B	602075197	602077194	1997	True	3158	3158	95.255	555	2546	1	chr2B.!!$R5	1991
7	TraesCS5B01G396000	chr7B	718486493	718488487	1994	True	3162	3162	95.298	553	2546	1	chr7B.!!$R2	1993
8	TraesCS5B01G396000	chr1B	498440439	498442428	1989	True	3158	3158	95.334	558	2546	1	chr1B.!!$R1	1988
9	TraesCS5B01G396000	chr1B	232740725	232742716	1991	False	3155	3155	95.298	558	2546	1	chr1B.!!$F2	1988
10	TraesCS5B01G396000	chr3B	52798829	52799348	519	False	745	745	92.628	1	521	1	chr3B.!!$F1	520

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
672	681	0.457853	GTGCGCACCGACTCATTCTA	60.458	55.0	30.12	0.0	0.0	2.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2143	2161	1.812686	CGGTCTTGGGTTCGAGTCCA	61.813	60.0	10.17	7.69	33.8	4.02	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
27	28	7.227049	ACAGGATACGACATTTTCCAAAAAT	57.773	32.000	0.00	0.00	46.39	1.82
30	31	7.432252	CAGGATACGACATTTTCCAAAAATAGC	59.568	37.037	0.00	0.00	46.39	2.97
34	35	6.099341	ACGACATTTTCCAAAAATAGCCATC	58.901	36.000	0.00	0.00	0.00	3.51
36	37	6.371595	ACATTTTCCAAAAATAGCCATCCA	57.628	33.333	0.00	0.00	0.00	3.41
37	38	6.408869	ACATTTTCCAAAAATAGCCATCCAG	58.591	36.000	0.00	0.00	0.00	3.86
38	39	5.419239	TTTTCCAAAAATAGCCATCCAGG	57.581	39.130	0.00	0.00	41.84	4.45
39	40	4.329638	TTCCAAAAATAGCCATCCAGGA	57.670	40.909	0.00	0.00	41.22	3.86
115	116	9.665264	AGTTAAGACAGAAAATTAAAGCGAAAG	57.335	29.630	0.00	0.00	0.00	2.62
120	121	8.233190	AGACAGAAAATTAAAGCGAAAGAGATG	58.767	33.333	0.00	0.00	0.00	2.90
347	356	2.758736	TACCCAATTTGCAATGCCAC	57.241	45.000	1.53	0.00	0.00	5.01
423	432	3.947910	ACTGAACCATGGCAAATTGAG	57.052	42.857	13.04	4.62	0.00	3.02
441	450	3.435275	TGAGAAGCTCACATAGTCCACT	58.565	45.455	0.00	0.00	35.39	4.00
476	485	4.081406	ACATGACAAATAGCAAGGCTCAA	58.919	39.130	0.00	0.00	40.44	3.02
502	511	5.543790	TGGCCACATAGTCTCATACACATAT	59.456	40.000	0.00	0.00	0.00	1.78
527	536	7.296628	AGTTTAAATGGCAAATAGTGTTGGA	57.703	32.000	0.00	0.00	0.00	3.53
528	537	7.731054	AGTTTAAATGGCAAATAGTGTTGGAA	58.269	30.769	0.00	0.00	0.00	3.53
529	538	8.207545	AGTTTAAATGGCAAATAGTGTTGGAAA	58.792	29.630	0.00	0.00	0.00	3.13
530	539	8.998377	GTTTAAATGGCAAATAGTGTTGGAAAT	58.002	29.630	0.00	0.00	0.00	2.17
533	542	8.721019	AAATGGCAAATAGTGTTGGAAATATG	57.279	30.769	0.00	0.00	0.00	1.78
534	543	5.659463	TGGCAAATAGTGTTGGAAATATGC	58.341	37.500	0.00	0.00	0.00	3.14
535	544	5.049828	GGCAAATAGTGTTGGAAATATGCC	58.950	41.667	0.00	0.00	42.26	4.40
536	545	5.049828	GCAAATAGTGTTGGAAATATGCCC	58.950	41.667	0.00	0.00	0.00	5.36
537	546	5.163416	GCAAATAGTGTTGGAAATATGCCCT	60.163	40.000	0.00	0.00	0.00	5.19
538	547	6.040391	GCAAATAGTGTTGGAAATATGCCCTA	59.960	38.462	0.00	0.00	0.00	3.53
539	548	7.651808	CAAATAGTGTTGGAAATATGCCCTAG	58.348	38.462	0.00	0.00	0.00	3.02
540	549	6.763715	ATAGTGTTGGAAATATGCCCTAGA	57.236	37.500	0.00	0.00	0.00	2.43
541	550	5.041191	AGTGTTGGAAATATGCCCTAGAG	57.959	43.478	0.00	0.00	0.00	2.43
542	551	4.137543	GTGTTGGAAATATGCCCTAGAGG	58.862	47.826	0.00	0.00	39.47	3.69
672	681	0.457853	GTGCGCACCGACTCATTCTA	60.458	55.000	30.12	0.00	0.00	2.10
811	820	1.407258	GAGAGCCGTTGAGCATAGAGT	59.593	52.381	0.00	0.00	34.23	3.24
858	867	4.760047	GACAGCGGCGGTGACCAT	62.760	66.667	41.06	22.06	34.87	3.55
875	884	3.295273	TGGCGACAGAGAGCACGT	61.295	61.111	0.00	0.00	35.01	4.49
966	977	3.774528	CTAGCTGTGGAGGGCGCA	61.775	66.667	10.83	0.00	0.00	6.09
981	992	2.175621	CGCAGCGGCATTGAGATCA	61.176	57.895	7.00	0.00	41.24	2.92
993	1004	1.248101	TGAGATCACGTTCGGCTCCA	61.248	55.000	0.00	0.00	0.00	3.86
1018	1029	0.392193	CATGTCTTCCGCAAGCTCCT	60.392	55.000	0.00	0.00	0.00	3.69
1043	1054	4.519437	CTCGCGGATGCAGAGCCA	62.519	66.667	6.13	0.00	42.97	4.75
1048	1059	4.479993	GGATGCAGAGCCAGGCGT	62.480	66.667	5.55	0.00	0.00	5.68
1059	1070	1.003355	CCAGGCGTGTGTGGAGATT	60.003	57.895	5.57	0.00	35.67	2.40
1063	1074	0.535335	GGCGTGTGTGGAGATTCCTA	59.465	55.000	0.00	0.00	37.46	2.94
1127	1140	1.597027	CACACACCGAGGAACCACC	60.597	63.158	0.00	0.00	39.35	4.61
1234	1247	4.250464	GGTTGATCTGTTCCGTGTTCATA	58.750	43.478	0.00	0.00	0.00	2.15
1270	1283	3.513912	TCTTTCTTTGGGTCGATGCTCTA	59.486	43.478	0.00	0.00	0.00	2.43
1280	1293	2.619177	GTCGATGCTCTAGCCAAGACTA	59.381	50.000	0.00	0.00	41.18	2.59
1310	1323	2.556144	ACTGCAAGAAGAGCATGACA	57.444	45.000	0.00	0.00	41.82	3.58
1425	1439	4.397417	GCTGTTGAGCTTAGGATGTTGAAT	59.603	41.667	0.00	0.00	42.52	2.57
1507	1521	5.103898	TGGGCATTTGTAGGTATGGTAATCA	60.104	40.000	0.00	0.00	0.00	2.57
1510	1524	6.490040	GGCATTTGTAGGTATGGTAATCACAT	59.510	38.462	0.00	0.00	0.00	3.21
1680	1695	8.482852	AAAAGGAGAAGAAATGAGGAATTCAA	57.517	30.769	7.93	0.00	39.77	2.69
2026	2042	1.550130	TTAGGGCTGCGCTGGTAACT	61.550	55.000	27.01	3.65	37.61	2.24
2028	2044	2.358737	GGCTGCGCTGGTAACTGT	60.359	61.111	16.47	0.00	37.92	3.55
2181	2199	0.589708	GCGTGGGTTAGTGGTGTTTC	59.410	55.000	0.00	0.00	0.00	2.78
2230	2248	1.909700	GGCAAGAGTTTGACATGGGA	58.090	50.000	0.00	0.00	42.21	4.37
2504	2533	8.884124	TTTGAATAAAACAGAGGGATTCTCAT	57.116	30.769	0.00	0.00	44.81	2.90
2535	2564	7.338196	TCTTTTGAATGACAACCACAAGTTCTA	59.662	33.333	6.36	0.00	36.18	2.10
2540	2569	2.731976	GACAACCACAAGTTCTAGAGCG	59.268	50.000	0.47	0.00	36.18	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	6.371595	TGGATGGCTATTTTTGGAAAATGT	57.628	33.333	8.48	0.00	0.00	2.71
27	28	0.685097	GCCGTATTCCTGGATGGCTA	59.315	55.000	17.46	0.00	43.30	3.93
30	31	0.319900	CTCGCCGTATTCCTGGATGG	60.320	60.000	0.00	0.00	37.10	3.51
34	35	5.769484	ATATATACTCGCCGTATTCCTGG	57.231	43.478	3.15	0.00	39.48	4.45
143	144	1.598701	GAGACACCAAATGGGGCAGC	61.599	60.000	0.45	0.00	44.30	5.25
260	262	6.585695	TGTGGGACGGAATATATCTTCTAC	57.414	41.667	1.36	0.00	0.00	2.59
261	263	7.792364	ATTGTGGGACGGAATATATCTTCTA	57.208	36.000	1.36	0.00	0.00	2.10
262	264	6.688073	ATTGTGGGACGGAATATATCTTCT	57.312	37.500	1.36	0.00	0.00	2.85
263	265	8.311836	TCTTATTGTGGGACGGAATATATCTTC	58.688	37.037	0.00	0.00	0.00	2.87
264	266	8.202461	TCTTATTGTGGGACGGAATATATCTT	57.798	34.615	0.00	0.00	0.00	2.40
265	267	7.792364	TCTTATTGTGGGACGGAATATATCT	57.208	36.000	0.00	0.00	0.00	1.98
266	268	7.876068	TGTTCTTATTGTGGGACGGAATATATC	59.124	37.037	0.00	0.00	0.00	1.63
267	269	7.660208	GTGTTCTTATTGTGGGACGGAATATAT	59.340	37.037	0.00	0.00	0.00	0.86
275	277	3.126858	CCATGTGTTCTTATTGTGGGACG	59.873	47.826	0.00	0.00	0.00	4.79
309	311	5.056480	GGGTAAGCAAAGCAAACATCTTTT	58.944	37.500	0.00	0.00	31.94	2.27
310	312	4.100808	TGGGTAAGCAAAGCAAACATCTTT	59.899	37.500	0.00	0.00	34.37	2.52
405	414	3.306225	GCTTCTCAATTTGCCATGGTTCA	60.306	43.478	14.67	0.00	0.00	3.18
406	415	3.056322	AGCTTCTCAATTTGCCATGGTTC	60.056	43.478	14.67	0.00	0.00	3.62
423	432	5.126384	ACTCTTAGTGGACTATGTGAGCTTC	59.874	44.000	0.00	0.00	30.76	3.86
441	450	9.587772	GCTATTTGTCATGTTCTTAGACTCTTA	57.412	33.333	0.00	0.00	33.56	2.10
476	485	4.164030	TGTGTATGAGACTATGTGGCCATT	59.836	41.667	9.72	1.78	32.29	3.16
502	511	8.410673	TCCAACACTATTTGCCATTTAAACTA	57.589	30.769	0.00	0.00	0.00	2.24
507	516	9.814899	CATATTTCCAACACTATTTGCCATTTA	57.185	29.630	0.00	0.00	0.00	1.40
521	530	4.437682	CCTCTAGGGCATATTTCCAACA	57.562	45.455	0.00	0.00	0.00	3.33
560	569	9.150028	GGGCAAAAGGATAATTAACCCTAATAA	57.850	33.333	8.09	0.00	31.84	1.40
561	570	8.516198	AGGGCAAAAGGATAATTAACCCTAATA	58.484	33.333	8.09	0.00	43.36	0.98
562	571	7.370238	AGGGCAAAAGGATAATTAACCCTAAT	58.630	34.615	8.09	0.44	43.36	1.73
563	572	6.747931	AGGGCAAAAGGATAATTAACCCTAA	58.252	36.000	8.09	0.00	43.36	2.69
564	573	6.349897	AGGGCAAAAGGATAATTAACCCTA	57.650	37.500	8.09	0.00	43.36	3.53
565	574	5.220872	AGGGCAAAAGGATAATTAACCCT	57.779	39.130	8.09	6.12	40.37	4.34
566	575	5.950544	AAGGGCAAAAGGATAATTAACCC	57.049	39.130	8.09	3.96	34.91	4.11
736	745	3.882888	CTGAATAAAATTGGGCGCCTCTA	59.117	43.478	28.56	13.87	0.00	2.43
744	753	4.173256	GCAACGGTCTGAATAAAATTGGG	58.827	43.478	0.00	0.00	0.00	4.12
789	798	2.100584	CTCTATGCTCAACGGCTCTCTT	59.899	50.000	0.00	0.00	0.00	2.85
811	820	2.443260	ATAGCACACACCCGCAACGA	62.443	55.000	0.00	0.00	0.00	3.85
858	867	3.268965	GACGTGCTCTCTGTCGCCA	62.269	63.158	0.00	0.00	0.00	5.69
939	950	1.679311	CACAGCTAGCTTCCCACCA	59.321	57.895	16.46	0.00	0.00	4.17
966	977	0.391661	AACGTGATCTCAATGCCGCT	60.392	50.000	0.00	0.00	0.00	5.52
981	992	2.048127	GAGCTTGGAGCCGAACGT	60.048	61.111	0.00	0.00	43.77	3.99
993	1004	0.036732	TTGCGGAAGACATGGAGCTT	59.963	50.000	0.00	0.00	0.00	3.74
1043	1054	1.194781	AGGAATCTCCACACACGCCT	61.195	55.000	0.00	0.00	39.61	5.52
1048	1059	4.023980	ACGAAGATAGGAATCTCCACACA	58.976	43.478	0.00	0.00	41.81	3.72
1059	1070	1.022735	GCGGACAGACGAAGATAGGA	58.977	55.000	0.00	0.00	35.47	2.94
1063	1074	2.341101	ACCGCGGACAGACGAAGAT	61.341	57.895	35.90	0.00	35.47	2.40
1127	1140	1.588404	GCACACGTAGAATGGACGATG	59.412	52.381	1.71	1.67	42.98	3.84
1234	1247	1.202976	AGAAAGAAGCATGCCACCTGT	60.203	47.619	15.66	3.88	0.00	4.00
1270	1283	6.261826	GCAGTTCATTTATCATAGTCTTGGCT	59.738	38.462	0.00	0.00	0.00	4.75
1280	1293	6.376299	TGCTCTTCTTGCAGTTCATTTATCAT	59.624	34.615	0.00	0.00	35.31	2.45
1310	1323	4.582760	CAGCATGCGCAACCATTT	57.417	50.000	17.11	0.00	42.27	2.32
1425	1439	6.681729	TCTTCAAGCTTCCTAACCTTCTTA	57.318	37.500	0.00	0.00	0.00	2.10
1510	1524	8.642432	TCCATACATTTTCAACATTACAACCAA	58.358	29.630	0.00	0.00	0.00	3.67
1680	1695	8.441312	ACTGCATTTCATTGATCAAAAGTTTT	57.559	26.923	13.09	0.00	0.00	2.43
2026	2042	2.906389	ACTCTTGCCATCTGTCCTAACA	59.094	45.455	0.00	0.00	0.00	2.41
2028	2044	4.041567	TCAAACTCTTGCCATCTGTCCTAA	59.958	41.667	0.00	0.00	32.14	2.69
2143	2161	1.812686	CGGTCTTGGGTTCGAGTCCA	61.813	60.000	10.17	7.69	33.80	4.02
2181	2199	2.358247	AGTTACCAACGCAGCCCG	60.358	61.111	0.00	0.00	44.21	6.13
2230	2248	7.789831	TCTCACTATGTATACATTCCTTCCCTT	59.210	37.037	22.90	0.00	37.76	3.95
2497	2526	5.890419	GTCATTCAAAAGAGGGGATGAGAAT	59.110	40.000	0.00	0.00	0.00	2.40
2504	2533	3.117322	TGGTTGTCATTCAAAAGAGGGGA	60.117	43.478	0.00	0.00	37.81	4.81

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.