AutoCloner

Multiple sequence alignment - TraesCS5D01G129900

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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	TraesCS5D01G129900	chr5D	100.000	3052	0	0	1	3052	204861485	204864536	0.000000e+00	5637.0
1	TraesCS5D01G129900	chr5D	82.496	1194	179	16	1423	2612	204860746	204859579	0.000000e+00	1020.0
2	TraesCS5D01G129900	chr5D	100.000	300	0	0	3242	3541	204864726	204865025	3.990000e-154	555.0
3	TraesCS5D01G129900	chr5B	94.374	3075	120	24	1	3050	207590008	207586962	0.000000e+00	4671.0
4	TraesCS5D01G129900	chr5B	81.732	843	141	10	1771	2612	207601205	207602035	0.000000e+00	691.0
5	TraesCS5D01G129900	chr5B	96.552	174	4	2	3242	3414	207586905	207586733	1.610000e-73	287.0
6	TraesCS5D01G129900	chr5B	98.667	75	1	0	3467	3541	207586389	207586315	2.220000e-27	134.0
7	TraesCS5D01G129900	chr5B	80.734	109	18	3	226	331	207589851	207589743	8.150000e-12	82.4
8	TraesCS5D01G129900	chr5A	96.854	2352	63	4	693	3043	244429194	244431535	0.000000e+00	3923.0
9	TraesCS5D01G129900	chr5A	81.932	1273	192	19	1423	2676	244427447	244426194	0.000000e+00	1042.0
10	TraesCS5D01G129900	chr5A	86.338	710	92	5	1	708	244428181	244428887	0.000000e+00	769.0
11	TraesCS5D01G129900	chr5A	94.158	291	16	1	3244	3533	244431795	244432085	3.240000e-120	442.0
12	TraesCS5D01G129900	chr4A	90.972	288	26	0	1210	1497	572540542	572540829	4.290000e-104	388.0
13	TraesCS5D01G129900	chr4B	90.813	283	25	1	1216	1497	43760167	43759885	9.280000e-101	377.0
14	TraesCS5D01G129900	chr4B	89.381	113	5	4	2538	2649	420422150	420422044	6.170000e-28	135.0
15	TraesCS5D01G129900	chr4B	88.596	114	5	5	2538	2649	330794561	330794454	7.980000e-27	132.0
16	TraesCS5D01G129900	chr4D	93.151	219	14	1	1280	1497	30505711	30505493	1.590000e-83	320.0
17	TraesCS5D01G129900	chrUn	90.265	113	4	4	2538	2649	12578621	12578727	1.330000e-29	141.0
18	TraesCS5D01G129900	chrUn	94.444	36	2	0	59	94	275922197	275922162	4.940000e-04	56.5
19	TraesCS5D01G129900	chrUn	94.444	36	2	0	59	94	275929751	275929716	4.940000e-04	56.5
20	TraesCS5D01G129900	chrUn	94.444	36	2	0	59	94	287242686	287242721	4.940000e-04	56.5
21	TraesCS5D01G129900	chr1B	89.286	112	4	5	2538	2647	44188625	44188730	2.220000e-27	134.0
22	TraesCS5D01G129900	chr3D	80.000	90	15	3	1	88	369507162	369507250	2.950000e-06	63.9
23	TraesCS5D01G129900	chr6D	94.286	35	2	0	59	93	368767818	368767784	2.000000e-03	54.7

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	TraesCS5D01G129900	chr5D	204861485	204865025	3540	False	3096.000000	5637	100.00000	1	3541	2	chr5D.!!$F1	3540
1	TraesCS5D01G129900	chr5D	204859579	204860746	1167	True	1020.000000	1020	82.49600	1423	2612	1	chr5D.!!$R1	1189
2	TraesCS5D01G129900	chr5B	207586315	207590008	3693	True	1293.600000	4671	92.58175	1	3541	4	chr5B.!!$R1	3540
3	TraesCS5D01G129900	chr5B	207601205	207602035	830	False	691.000000	691	81.73200	1771	2612	1	chr5B.!!$F1	841
4	TraesCS5D01G129900	chr5A	244428181	244432085	3904	False	1711.333333	3923	92.45000	1	3533	3	chr5A.!!$F1	3532
5	TraesCS5D01G129900	chr5A	244426194	244427447	1253	True	1042.000000	1042	81.93200	1423	2676	1	chr5A.!!$R1	1253

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
743	1091	0.034186	TGGTATGCCTTGCCTTGGAG	60.034	55.0	0.16	0.00	35.27	3.86	F
852	1202	0.239347	CTTTTGCTGCAGTCGGGAAG	59.761	55.0	16.64	8.96	30.44	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2498	2849	0.748367	TCTCTACGATGAGCGGTGCT	60.748	55.000	0.0	0.0	46.49	4.40	R
2657	3028	2.880268	CAGAACTGGTTTGATCACTGCA	59.120	45.455	0.0	0.0	0.00	4.41	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
35	36	1.803334	TGTGTCCTTGTTACCATCGC	58.197	50.000	0.00	0.00	0.00	4.58
64	66	0.979709	GTTAGTTCGGGGGCCCTACT	60.980	60.000	24.38	23.39	34.53	2.57
101	103	4.189188	CTCCGTCACTACCCGCCG	62.189	72.222	0.00	0.00	0.00	6.46
197	199	0.757188	CGCCACCAGTATCTCCTCCT	60.757	60.000	0.00	0.00	0.00	3.69
200	202	1.062886	CCACCAGTATCTCCTCCTCCA	60.063	57.143	0.00	0.00	0.00	3.86
207	209	0.626382	ATCTCCTCCTCCACGAGTCA	59.374	55.000	0.00	0.00	0.00	3.41
211	213	0.898320	CCTCCTCCACGAGTCACAAT	59.102	55.000	0.00	0.00	0.00	2.71
219	221	0.836400	ACGAGTCACAATCCCCACCT	60.836	55.000	0.00	0.00	0.00	4.00
221	223	1.280457	GAGTCACAATCCCCACCTCT	58.720	55.000	0.00	0.00	0.00	3.69
319	321	4.329545	GGGTTGCTCCTCGCCACA	62.330	66.667	0.00	0.00	36.07	4.17
373	375	5.456907	GGATAAGGAAAGGAGAGGGGAAATC	60.457	48.000	0.00	0.00	0.00	2.17
375	377	1.838077	GGAAAGGAGAGGGGAAATCGA	59.162	52.381	0.00	0.00	0.00	3.59
399	401	1.447140	TCGTGCGTAATGAGTGGGC	60.447	57.895	0.00	0.00	0.00	5.36
400	402	1.447838	CGTGCGTAATGAGTGGGCT	60.448	57.895	0.00	0.00	0.00	5.19
403	405	0.673333	TGCGTAATGAGTGGGCTGTG	60.673	55.000	0.00	0.00	0.00	3.66
422	424	1.202604	TGTTCCCGCCGAGGATATTTC	60.203	52.381	0.00	0.00	45.00	2.17
423	425	0.395312	TTCCCGCCGAGGATATTTCC	59.605	55.000	0.00	0.00	45.00	3.13
481	483	3.785505	GCCTGCATTAAGATTCGTGTTCG	60.786	47.826	0.00	0.00	38.55	3.95
484	486	3.369756	TGCATTAAGATTCGTGTTCGGAC	59.630	43.478	0.00	0.00	37.69	4.79
503	524	2.366833	GGTAGCCGAAGCGTTACAC	58.633	57.895	0.00	0.00	46.67	2.90
504	525	0.108945	GGTAGCCGAAGCGTTACACT	60.109	55.000	0.00	0.00	46.67	3.55
513	534	0.603569	AGCGTTACACTGGGAGACTG	59.396	55.000	0.00	0.00	0.00	3.51
523	544	5.880901	ACACTGGGAGACTGTAAATTTGAT	58.119	37.500	0.00	0.00	0.00	2.57
524	545	7.016153	ACACTGGGAGACTGTAAATTTGATA	57.984	36.000	0.00	0.00	0.00	2.15
556	577	9.619316	TTTATACTGTTTCCGAAAATCAATGTG	57.381	29.630	0.00	0.00	0.00	3.21
610	631	0.694771	ATCTCACTCTGCTTGCCCAA	59.305	50.000	0.00	0.00	0.00	4.12
650	676	4.400529	AAACATTTCCTTTCGCCTTTGT	57.599	36.364	0.00	0.00	0.00	2.83
651	677	5.523438	AAACATTTCCTTTCGCCTTTGTA	57.477	34.783	0.00	0.00	0.00	2.41
652	678	4.766404	ACATTTCCTTTCGCCTTTGTAG	57.234	40.909	0.00	0.00	0.00	2.74
673	699	2.567615	GCTTCACTCCCTTAGAACTCCA	59.432	50.000	0.00	0.00	0.00	3.86
680	706	5.239525	CACTCCCTTAGAACTCCAAGTTTTG	59.760	44.000	0.00	0.00	38.80	2.44
741	1089	0.323725	AGTGGTATGCCTTGCCTTGG	60.324	55.000	0.16	0.00	35.27	3.61
743	1091	0.034186	TGGTATGCCTTGCCTTGGAG	60.034	55.000	0.16	0.00	35.27	3.86
772	1122	5.268068	ATGTACAGTGTGGACACGTTTCAG	61.268	45.833	5.88	0.00	45.23	3.02
852	1202	0.239347	CTTTTGCTGCAGTCGGGAAG	59.761	55.000	16.64	8.96	30.44	3.46
956	1306	2.808543	GGCAGATCGTCTTTTGTCTGTT	59.191	45.455	0.00	0.00	40.08	3.16
1038	1388	1.104577	GCGAGGGAGGAGAGGTACAG	61.105	65.000	0.00	0.00	0.00	2.74
1104	1454	5.455849	CGATCTACATCTTTAACACGGTGAG	59.544	44.000	16.29	1.41	0.00	3.51
1116	1466	4.803098	ACACGGTGAGCTAAAGATAGTT	57.197	40.909	16.29	0.00	0.00	2.24
1512	1862	0.876342	CGATAAGCCGCCCAAGAGAC	60.876	60.000	0.00	0.00	0.00	3.36
2601	2954	6.778108	TCCTTTTTACTTCGTTTGTTCAGAC	58.222	36.000	0.00	0.00	0.00	3.51
2715	3086	2.907042	AGGTGGAGGATTTTCGAGTTCT	59.093	45.455	0.00	0.00	0.00	3.01
2829	3201	3.012518	AGATGTGCATAGTTTGGCAGAC	58.987	45.455	0.00	0.00	41.35	3.51
2979	3351	0.667993	AAGGCACAAACATGTCACCG	59.332	50.000	0.00	0.00	0.00	4.94
3033	3405	2.187424	GCTGCTGCTCTCCCTGAG	59.813	66.667	8.53	0.00	45.33	3.35
3050	3616	4.114794	CCTGAGTTTTTCTTTTGGCACAG	58.885	43.478	0.00	0.00	42.39	3.66
3277	3844	0.995675	CCCCCAAGGTGGAGATGGAT	60.996	60.000	0.00	0.00	40.96	3.41
3326	3893	3.581024	TCTGCATCAGCCAAAAATGTC	57.419	42.857	0.00	0.00	41.13	3.06
3328	3895	4.334552	TCTGCATCAGCCAAAAATGTCTA	58.665	39.130	0.00	0.00	41.13	2.59
3458	4025	6.207691	TGTGGCTTTCTTTTTATATCAGGC	57.792	37.500	0.00	0.00	0.00	4.85
3462	4029	5.529800	GGCTTTCTTTTTATATCAGGCCGTA	59.470	40.000	0.00	0.00	0.00	4.02
3507	4365	1.956477	AGAACTGGGTGTTTCATGCAC	59.044	47.619	0.00	0.00	39.30	4.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	1.630148	CCGAACTAACGCTCTTGAGG	58.370	55.000	0.00	0.00	0.00	3.86
45	46	0.979709	AGTAGGGCCCCCGAACTAAC	60.980	60.000	21.43	4.08	41.95	2.34
64	66	1.111277	TCAAATCCGGCAGATCTCGA	58.889	50.000	5.45	0.00	32.47	4.04
145	147	1.826054	CACCAACAACCCTCGGCAA	60.826	57.895	0.00	0.00	0.00	4.52
197	199	0.834261	TGGGGATTGTGACTCGTGGA	60.834	55.000	0.00	0.00	0.00	4.02
200	202	0.836400	AGGTGGGGATTGTGACTCGT	60.836	55.000	0.00	0.00	0.00	4.18
207	209	0.987294	CAGTCAGAGGTGGGGATTGT	59.013	55.000	0.00	0.00	0.00	2.71
211	213	2.951813	ACCAGTCAGAGGTGGGGA	59.048	61.111	4.09	0.00	38.13	4.81
219	221	2.146724	CCCACCACCACCAGTCAGA	61.147	63.158	0.00	0.00	0.00	3.27
221	223	3.174987	CCCCACCACCACCAGTCA	61.175	66.667	0.00	0.00	0.00	3.41
375	377	0.734942	CTCATTACGCACGACCGGTT	60.735	55.000	9.42	0.00	0.00	4.44
399	401	1.672854	TATCCTCGGCGGGAACACAG	61.673	60.000	9.18	0.00	39.02	3.66
400	402	1.046472	ATATCCTCGGCGGGAACACA	61.046	55.000	9.18	1.45	39.02	3.72
403	405	1.509703	GAAATATCCTCGGCGGGAAC	58.490	55.000	9.18	1.50	39.02	3.62
422	424	1.144057	AATCTGCCCGTTCGCTAGG	59.856	57.895	0.00	0.00	0.00	3.02
423	425	0.460284	ACAATCTGCCCGTTCGCTAG	60.460	55.000	0.00	0.00	0.00	3.42
426	428	0.304705	CATACAATCTGCCCGTTCGC	59.695	55.000	0.00	0.00	0.00	4.70
428	430	1.593006	CGTCATACAATCTGCCCGTTC	59.407	52.381	0.00	0.00	0.00	3.95
484	486	3.720984	AGTGTAACGCTTCGGCTACCG	62.721	57.143	0.00	0.00	46.51	4.02
536	557	5.119931	TCCACATTGATTTTCGGAAACAG	57.880	39.130	1.96	0.00	0.00	3.16
542	563	7.031226	AGTTGATATCCACATTGATTTTCGG	57.969	36.000	9.43	0.00	0.00	4.30
556	577	2.104792	TGCAGCCCAGTAGTTGATATCC	59.895	50.000	0.00	0.00	0.00	2.59
610	631	4.254492	GTTTACGAGCCTCTTTGATCCTT	58.746	43.478	0.00	0.00	0.00	3.36
650	676	4.024670	GGAGTTCTAAGGGAGTGAAGCTA	58.975	47.826	0.00	0.00	0.00	3.32
651	677	2.835156	GGAGTTCTAAGGGAGTGAAGCT	59.165	50.000	0.00	0.00	0.00	3.74
652	678	2.567615	TGGAGTTCTAAGGGAGTGAAGC	59.432	50.000	0.00	0.00	0.00	3.86
673	699	8.150945	TCAGAAGATAGAGCTAACACAAAACTT	58.849	33.333	0.00	0.00	0.00	2.66
680	706	9.810545	AATAAACTCAGAAGATAGAGCTAACAC	57.189	33.333	0.00	0.00	35.28	3.32
741	1089	6.563381	CGTGTCCACACTGTACATTTTTACTC	60.563	42.308	8.19	0.00	44.34	2.59
743	1091	5.006941	ACGTGTCCACACTGTACATTTTTAC	59.993	40.000	8.19	0.00	44.34	2.01
772	1122	1.064060	CCGCTATTTGCTTACCTGCAC	59.936	52.381	0.00	0.00	43.20	4.57
788	1138	0.107214	CCAACCATACATCCACCGCT	60.107	55.000	0.00	0.00	0.00	5.52
852	1202	1.999051	CCACGCTGCGACTGAATAC	59.001	57.895	30.47	0.00	0.00	1.89
956	1306	0.179702	GGCAGCAGATGACAGGATGA	59.820	55.000	0.00	0.00	39.69	2.92
1038	1388	6.522946	AGGTAAAGAAAGATAAGCCGATACC	58.477	40.000	0.00	0.00	0.00	2.73
1246	1596	2.202492	CGAGGACGAACAGGAGCG	60.202	66.667	0.00	0.00	42.66	5.03
1247	1597	2.507324	GCGAGGACGAACAGGAGC	60.507	66.667	0.00	0.00	42.66	4.70
1512	1862	3.978272	GTGCAGGCACCTCTTCAG	58.022	61.111	13.28	0.00	40.79	3.02
1604	1954	2.165030	CGTCCCGTTCTTACTGTACCAT	59.835	50.000	0.00	0.00	0.00	3.55
1881	2231	2.224793	GCAACCTCCCTTTCTTGTACCT	60.225	50.000	0.00	0.00	0.00	3.08
2498	2849	0.748367	TCTCTACGATGAGCGGTGCT	60.748	55.000	0.00	0.00	46.49	4.40
2601	2954	6.161381	AGCTTAAAATTTCCAAGCATCAGTG	58.839	36.000	26.65	0.00	45.63	3.66
2655	3026	3.316308	AGAACTGGTTTGATCACTGCAAC	59.684	43.478	0.00	0.00	0.00	4.17
2657	3028	2.880268	CAGAACTGGTTTGATCACTGCA	59.120	45.455	0.00	0.00	0.00	4.41
2747	3119	6.183360	CCCACTAATTTTCCATTGGAGTCATC	60.183	42.308	5.36	0.00	31.21	2.92
2829	3201	4.473199	CATCTTGCCAAATATCTGATGCG	58.527	43.478	0.00	0.00	0.00	4.73
2979	3351	2.167075	AGCATGCAGAATGTAAAAGGCC	59.833	45.455	21.98	0.00	38.65	5.19
3277	3844	7.509546	GGAATGACAGATTAACCCAGATTAGA	58.490	38.462	0.00	0.00	0.00	2.10
3429	3996	3.557228	AAAAAGAAAGCCACAATGCCA	57.443	38.095	0.00	0.00	0.00	4.92
3430	3997	7.041107	TGATATAAAAAGAAAGCCACAATGCC	58.959	34.615	0.00	0.00	0.00	4.40
3458	4025	6.513393	GCTCAAGAATCAAACCCATAATACGG	60.513	42.308	0.00	0.00	0.00	4.02
3462	4029	5.163478	GCAGCTCAAGAATCAAACCCATAAT	60.163	40.000	0.00	0.00	0.00	1.28
3507	4365	4.201950	CCAAGTCCATTCTTTAATCCGCAG	60.202	45.833	0.00	0.00	0.00	5.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.