AutoCloner

Multiple sequence alignment - TraesCS2D01G376700

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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	TraesCS2D01G376700	chr2D	100.000	4271	0	0	1	4271	481046685	481050955	0.000000e+00	7888.0
1	TraesCS2D01G376700	chr2A	97.258	3428	85	4	851	4271	623937340	623940765	0.000000e+00	5801.0
2	TraesCS2D01G376700	chr2B	97.245	3412	82	5	866	4271	564228568	564231973	0.000000e+00	5770.0
3	TraesCS2D01G376700	chr2B	89.804	716	53	7	1	711	564227193	564227893	0.000000e+00	900.0
4	TraesCS2D01G376700	chr2B	85.207	169	21	3	714	879	564227952	564228119	2.040000e-38	171.0
5	TraesCS2D01G376700	chr5B	80.462	563	88	18	161	712	424143907	424144458	1.110000e-110	411.0
6	TraesCS2D01G376700	chr5B	81.633	294	43	8	235	525	216866116	216866401	2.570000e-57	233.0
7	TraesCS2D01G376700	chr6A	82.803	471	64	11	161	619	121929201	121928736	5.140000e-109	405.0
8	TraesCS2D01G376700	chr6A	78.671	286	52	6	241	524	479887828	479887550	9.430000e-42	182.0
9	TraesCS2D01G376700	chr4D	75.536	560	118	15	162	711	26915083	26915633	1.520000e-64	257.0
10	TraesCS2D01G376700	chr4D	85.629	167	17	4	2	161	120075089	120074923	7.340000e-38	169.0
11	TraesCS2D01G376700	chr4D	91.304	46	3	1	190	235	300311271	300311227	1.280000e-05	62.1
12	TraesCS2D01G376700	chrUn	81.570	293	45	5	235	525	115095525	115095240	2.570000e-57	233.0
13	TraesCS2D01G376700	chrUn	76.623	308	62	6	300	598	361340655	361340349	1.230000e-35	161.0
14	TraesCS2D01G376700	chrUn	81.633	147	23	4	567	711	287538090	287537946	7.500000e-23	119.0
15	TraesCS2D01G376700	chrUn	81.633	147	23	4	567	711	287544211	287544067	7.500000e-23	119.0
16	TraesCS2D01G376700	chrUn	81.633	147	23	4	567	711	389434824	389434968	7.500000e-23	119.0
17	TraesCS2D01G376700	chr3D	77.692	390	59	14	224	608	234802089	234801723	3.350000e-51	213.0
18	TraesCS2D01G376700	chr3D	85.802	162	22	1	1	161	585009474	585009313	2.040000e-38	171.0
19	TraesCS2D01G376700	chr3D	81.416	113	19	1	600	710	572631545	572631433	1.640000e-14	91.6
20	TraesCS2D01G376700	chr5A	79.181	293	52	6	235	525	258118660	258118945	1.210000e-45	195.0
21	TraesCS2D01G376700	chr6D	81.333	225	32	7	163	385	339689412	339689196	1.580000e-39	174.0
22	TraesCS2D01G376700	chr4B	83.333	150	21	4	19	165	643762227	643762375	7.450000e-28	135.0
23	TraesCS2D01G376700	chr4B	79.137	139	23	4	460	593	387896887	387897024	1.640000e-14	91.6

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	TraesCS2D01G376700	chr2D	481046685	481050955	4270	False	7888.000000	7888	100.000	1	4271	1	chr2D.!!$F1	4270
1	TraesCS2D01G376700	chr2A	623937340	623940765	3425	False	5801.000000	5801	97.258	851	4271	1	chr2A.!!$F1	3420
2	TraesCS2D01G376700	chr2B	564227193	564231973	4780	False	2280.333333	5770	90.752	1	4271	3	chr2B.!!$F1	4270
3	TraesCS2D01G376700	chr5B	424143907	424144458	551	False	411.000000	411	80.462	161	712	1	chr5B.!!$F2	551
4	TraesCS2D01G376700	chr4D	26915083	26915633	550	False	257.000000	257	75.536	162	711	1	chr4D.!!$F1	549

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	Hairpin	End Stability	Orientation
332	338	0.037232	GTGAAGGCGAGCTGGTACTT	60.037	55.000	0.00	0.00	2.24	F
346	352	0.108281	GTACTTCTCCTTGGTCGCCC	60.108	60.000	0.00	0.00	6.13	F
1575	2106	0.685097	TGTACTCCAAGAGCGGCTTT	59.315	50.000	2.97	33.60	3.51	F
1872	2403	1.067416	GAGCGACATGTATGCCCGA	59.933	57.895	16.57	31.67	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2119	2650	0.041090	ACATCCCCATCCAAACCCAC	59.959	55.000	0.00	0.00	0.00	4.61	R
2391	2922	1.167851	ATGCATGGACCTGTTTCACG	58.832	50.000	0.00	0.00	0.00	4.35	R
2782	3313	1.014564	GTTAGTCTCCCAGCACGTGC	61.015	60.000	32.79	32.79	42.49	5.34	R
3316	3847	3.181445	ACAAAGACCAAGTGCCATACAGA	60.181	43.478	0.00	0.00	0.00	3.41	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
70	72	6.857964	CAGAAGTTGCAAAATAAATCGTCAGT	59.142	34.615	0.00	0.00	0.00	3.41
73	75	6.314784	AGTTGCAAAATAAATCGTCAGTAGC	58.685	36.000	0.00	0.00	0.00	3.58
74	76	6.149474	AGTTGCAAAATAAATCGTCAGTAGCT	59.851	34.615	0.00	0.00	0.00	3.32
76	78	7.234187	TGCAAAATAAATCGTCAGTAGCTAG	57.766	36.000	0.00	0.00	0.00	3.42
77	79	6.257849	TGCAAAATAAATCGTCAGTAGCTAGG	59.742	38.462	0.00	0.00	0.00	3.02
78	80	6.292919	GCAAAATAAATCGTCAGTAGCTAGGG	60.293	42.308	0.00	0.00	0.00	3.53
79	81	5.470047	AATAAATCGTCAGTAGCTAGGGG	57.530	43.478	0.00	0.00	0.00	4.79
80	82	1.041437	AATCGTCAGTAGCTAGGGGC	58.959	55.000	0.00	0.00	42.19	5.80
81	83	0.106167	ATCGTCAGTAGCTAGGGGCA	60.106	55.000	0.00	0.00	44.79	5.36
82	84	1.035932	TCGTCAGTAGCTAGGGGCAC	61.036	60.000	0.00	0.00	44.79	5.01
83	85	1.437986	GTCAGTAGCTAGGGGCACG	59.562	63.158	0.00	0.00	44.79	5.34
122	124	4.680237	CGAGCAAGGCGGTGGACA	62.680	66.667	0.00	0.00	0.00	4.02
136	138	1.734465	GTGGACAGAGCCAAGAAATCG	59.266	52.381	0.00	0.00	40.20	3.34
148	150	1.263356	AGAAATCGACCGGTTGAGGA	58.737	50.000	27.99	14.68	34.73	3.71
153	155	2.133281	TCGACCGGTTGAGGAGAATA	57.867	50.000	21.16	0.00	34.73	1.75
217	219	3.425359	CGCTGGAAGTTCATCACACATTC	60.425	47.826	5.01	0.00	35.30	2.67
218	220	3.503363	GCTGGAAGTTCATCACACATTCA	59.497	43.478	5.01	0.00	35.30	2.57
332	338	0.037232	GTGAAGGCGAGCTGGTACTT	60.037	55.000	0.00	0.00	0.00	2.24
341	347	1.903183	GAGCTGGTACTTCTCCTTGGT	59.097	52.381	0.00	0.00	0.00	3.67
346	352	0.108281	GTACTTCTCCTTGGTCGCCC	60.108	60.000	0.00	0.00	0.00	6.13
396	404	1.672854	CCGTGACCCTCATTCGCCTA	61.673	60.000	0.00	0.00	0.00	3.93
438	446	2.019337	GGAAACGCTTTGTGGTCGT	58.981	52.632	0.00	0.00	38.15	4.34
451	459	1.550976	GTGGTCGTCCAAAGGAGATCT	59.449	52.381	2.02	0.00	46.15	2.75
452	460	2.028020	GTGGTCGTCCAAAGGAGATCTT	60.028	50.000	2.02	0.00	46.15	2.40
484	492	2.284625	TCCATCCACGCCCTCTGT	60.285	61.111	0.00	0.00	0.00	3.41
561	571	3.411517	CGGGGGTGGATGGAGCTT	61.412	66.667	0.00	0.00	0.00	3.74
562	572	2.983879	CGGGGGTGGATGGAGCTTT	61.984	63.158	0.00	0.00	0.00	3.51
722	789	4.464951	GGGTGGATTTGGTTAACCCTAAAG	59.535	45.833	21.97	0.00	45.93	1.85
768	836	3.450893	CGGAGCCGAGTCTTTTTAAAC	57.549	47.619	2.00	0.00	42.83	2.01
770	838	2.159037	GGAGCCGAGTCTTTTTAAACGG	59.841	50.000	7.99	7.99	42.63	4.44
771	839	3.062042	GAGCCGAGTCTTTTTAAACGGA	58.938	45.455	14.73	1.82	42.40	4.69
777	847	5.107568	CCGAGTCTTTTTAAACGGAGTCTTC	60.108	44.000	16.08	4.62	45.00	2.87
782	852	9.557061	AGTCTTTTTAAACGGAGTCTTCTTTAT	57.443	29.630	0.00	0.00	45.00	1.40
795	865	9.474920	GGAGTCTTCTTTATATGATCTGTTCAG	57.525	37.037	0.00	0.00	37.89	3.02
797	867	8.986991	AGTCTTCTTTATATGATCTGTTCAGGT	58.013	33.333	0.00	0.00	37.89	4.00
798	868	9.606631	GTCTTCTTTATATGATCTGTTCAGGTT	57.393	33.333	0.00	0.00	37.89	3.50
845	915	3.057033	CGATCGGAATTATAAGGACGGGT	60.057	47.826	7.38	0.00	0.00	5.28
846	916	4.156556	CGATCGGAATTATAAGGACGGGTA	59.843	45.833	7.38	0.00	0.00	3.69
875	945	4.462132	TGCTAGAGATGCTCTGATGATACC	59.538	45.833	7.19	0.00	41.37	2.73
948	1479	7.308589	CGTCTCCAAACATTTTACCAATCTCTT	60.309	37.037	0.00	0.00	0.00	2.85
1341	1872	4.521146	CTGTCTCTTGGGCATCTGTTATT	58.479	43.478	0.00	0.00	0.00	1.40
1515	2046	5.358090	CATGCACAGTCTATGAAGTCTGAT	58.642	41.667	6.64	0.00	40.17	2.90
1554	2085	2.661537	CAGAACGCGCTGGTCACA	60.662	61.111	17.21	0.00	32.26	3.58
1575	2106	0.685097	TGTACTCCAAGAGCGGCTTT	59.315	50.000	2.97	0.00	33.60	3.51
1587	2118	1.606313	CGGCTTTGTTGGGGATGGT	60.606	57.895	0.00	0.00	0.00	3.55
1772	2303	2.840753	GGGCTTGTGGGGTTCTGGA	61.841	63.158	0.00	0.00	0.00	3.86
1789	2320	3.973973	TCTGGATAGTTTGGAGTATGGGG	59.026	47.826	0.00	0.00	0.00	4.96
1872	2403	1.067416	GAGCGACATGTATGCCCGA	59.933	57.895	16.57	0.00	31.67	5.14
2113	2644	4.383552	GCAGATTGATCCACTCCTACTTGT	60.384	45.833	0.00	0.00	0.00	3.16
2119	2650	5.551233	TGATCCACTCCTACTTGTTCAAAG	58.449	41.667	0.00	0.00	0.00	2.77
2267	2798	4.633126	CAGCATTCTTACTGCATGTGTACT	59.367	41.667	0.00	0.00	42.15	2.73
2391	2922	3.439129	CCGAGTTGGGTTACCTTGAAATC	59.561	47.826	0.00	0.58	37.76	2.17
2583	3114	2.230660	GGCTATGCCCAATCTGGTTAC	58.769	52.381	0.00	0.00	44.06	2.50
2782	3313	5.179929	TGTTCATGTGTCATTGACTTGCTAG	59.820	40.000	17.26	0.00	33.15	3.42
3207	3738	5.414454	TGTTCCAAAGCTACCATGTCAATAC	59.586	40.000	0.00	0.00	0.00	1.89
3254	3785	6.594547	AGTGATTTGTCAGATGAAGACATGAG	59.405	38.462	0.00	0.00	44.66	2.90
3324	3855	3.632145	GCCAACCTACCAAATCTGTATGG	59.368	47.826	0.00	0.00	42.60	2.74
3395	3926	1.345415	CAGCAGGCCATTGGTTTCTTT	59.655	47.619	5.01	0.00	0.00	2.52
3396	3927	2.049372	AGCAGGCCATTGGTTTCTTTT	58.951	42.857	5.01	0.00	0.00	2.27
3444	3975	2.945668	AGTTTGTGACCAGAAGCTGTTC	59.054	45.455	0.00	0.00	0.00	3.18
3553	4084	6.591834	TGAAAGAGCTACTAAAGTGATCTTGC	59.408	38.462	11.23	10.42	34.56	4.01
3600	4131	7.652909	AGTTAAATGTGTTTGAATGACCACATG	59.347	33.333	5.02	0.00	45.19	3.21
3701	4237	6.497259	ACCAGTCTCTTTTAATCTACCACTGA	59.503	38.462	0.00	0.00	32.18	3.41
3858	4394	5.935945	TGAATTCACAAGGGAGTAACAGAA	58.064	37.500	3.38	0.00	0.00	3.02
3910	4446	8.141268	GGTGGACTGTTCAAAAATTCAATAGAA	58.859	33.333	0.00	0.00	38.31	2.10
3942	4478	7.363268	CCTCATTATTTTCCTCAGAAGGTTTGG	60.363	40.741	0.00	0.00	43.82	3.28
4038	4576	9.185680	GTGTTTACATCATAGGGTTAAGGATTT	57.814	33.333	0.00	0.00	0.00	2.17
4105	4643	9.078990	TGATCATGTATTCAGTAGGTAAGTAGG	57.921	37.037	0.00	0.00	0.00	3.18
4210	4748	2.159240	GGCTTTGCCCTGCAGTAAATAC	60.159	50.000	13.81	6.49	44.06	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	3.152341	CCATGTTGCAGAAGTTTCTCCT	58.848	45.455	0.00	0.00	34.74	3.69
65	67	1.321074	ACGTGCCCCTAGCTACTGAC	61.321	60.000	0.00	0.00	44.23	3.51
70	72	2.412323	CGTGACGTGCCCCTAGCTA	61.412	63.158	0.00	0.00	44.23	3.32
81	83	3.134879	ATGTGTCCCACGTGACGT	58.865	55.556	19.30	4.10	42.36	4.34
122	124	0.108138	CCGGTCGATTTCTTGGCTCT	60.108	55.000	0.00	0.00	0.00	4.09
136	138	3.889520	AACTATTCTCCTCAACCGGTC	57.110	47.619	8.04	0.00	0.00	4.79
430	438	1.275291	GATCTCCTTTGGACGACCACA	59.725	52.381	5.99	0.00	46.80	4.17
438	446	2.481969	CGCATCGAAGATCTCCTTTGGA	60.482	50.000	0.00	0.00	45.12	3.53
470	478	3.023949	GCAGACAGAGGGCGTGGAT	62.024	63.158	0.00	0.00	0.00	3.41
484	492	4.069232	CTCTCCCGCAACGGCAGA	62.069	66.667	0.00	0.00	41.94	4.26
545	553	1.076705	GAAAGCTCCATCCACCCCC	60.077	63.158	0.00	0.00	0.00	5.40
550	558	1.852157	AAGGCCGAAAGCTCCATCCA	61.852	55.000	0.00	0.00	43.05	3.41
561	571	2.355363	CACGACGACAAGGCCGAA	60.355	61.111	0.00	0.00	0.00	4.30
669	680	1.442520	CGTTTTCCATGCGCACAGG	60.443	57.895	14.90	19.08	0.00	4.00
735	803	1.356938	GGCTCCGCCGCTATATTTAC	58.643	55.000	0.00	0.00	39.62	2.01
747	815	1.435577	TTAAAAAGACTCGGCTCCGC	58.564	50.000	2.96	0.00	39.59	5.54
748	816	2.159881	CGTTTAAAAAGACTCGGCTCCG	60.160	50.000	1.14	1.14	41.35	4.63
765	833	8.478877	ACAGATCATATAAAGAAGACTCCGTTT	58.521	33.333	0.00	0.00	0.00	3.60
766	834	8.012957	ACAGATCATATAAAGAAGACTCCGTT	57.987	34.615	0.00	0.00	0.00	4.44
767	835	7.589958	ACAGATCATATAAAGAAGACTCCGT	57.410	36.000	0.00	0.00	0.00	4.69
768	836	8.138074	TGAACAGATCATATAAAGAAGACTCCG	58.862	37.037	0.00	0.00	31.50	4.63
770	838	9.474920	CCTGAACAGATCATATAAAGAAGACTC	57.525	37.037	3.19	0.00	37.44	3.36
771	839	8.986991	ACCTGAACAGATCATATAAAGAAGACT	58.013	33.333	3.19	0.00	37.44	3.24
1275	1806	4.021925	ACCAAGCGGGCAGAGTCC	62.022	66.667	0.00	0.00	42.05	3.85
1288	1819	0.589223	GGCATTTCGTCGAACACCAA	59.411	50.000	7.29	0.00	0.00	3.67
1501	2032	7.067615	GTCACTTCCAGTATCAGACTTCATAGA	59.932	40.741	0.00	0.00	35.64	1.98
1515	2046	4.065088	GCACAATCAAGTCACTTCCAGTA	58.935	43.478	0.00	0.00	0.00	2.74
1533	2064	4.908687	ACCAGCGCGTTCTGCACA	62.909	61.111	8.43	0.00	46.97	4.57
1548	2079	3.003480	GCTCTTGGAGTACATTGTGACC	58.997	50.000	0.00	1.13	31.39	4.02
1554	2085	0.905357	AGCCGCTCTTGGAGTACATT	59.095	50.000	0.00	0.00	31.39	2.71
1575	2106	0.608035	GCGAGAAACCATCCCCAACA	60.608	55.000	0.00	0.00	0.00	3.33
1772	2303	3.392616	CTGCTCCCCATACTCCAAACTAT	59.607	47.826	0.00	0.00	0.00	2.12
1789	2320	4.270566	CACAGACAAGCTATGAATCTGCTC	59.729	45.833	10.75	0.00	36.23	4.26
1872	2403	2.157738	GCAGACTCCAACTTCTTGCAT	58.842	47.619	0.00	0.00	0.00	3.96
1971	2502	4.896482	AGTACCATAGCCTCACTAAGAAGG	59.104	45.833	0.00	0.00	33.57	3.46
2113	2644	2.324541	CCCATCCAAACCCACTTTGAA	58.675	47.619	0.00	0.00	41.81	2.69
2119	2650	0.041090	ACATCCCCATCCAAACCCAC	59.959	55.000	0.00	0.00	0.00	4.61
2391	2922	1.167851	ATGCATGGACCTGTTTCACG	58.832	50.000	0.00	0.00	0.00	4.35
2583	3114	2.712057	AATCAAGTGCTTTCCTTGCG	57.288	45.000	0.00	0.00	39.30	4.85
2782	3313	1.014564	GTTAGTCTCCCAGCACGTGC	61.015	60.000	32.79	32.79	42.49	5.34
3249	3780	7.219322	TGACTCAACCATATTCCATACTCATG	58.781	38.462	0.00	0.00	0.00	3.07
3254	3785	5.930135	ACCTGACTCAACCATATTCCATAC	58.070	41.667	0.00	0.00	0.00	2.39
3316	3847	3.181445	ACAAAGACCAAGTGCCATACAGA	60.181	43.478	0.00	0.00	0.00	3.41
3444	3975	4.467438	ACATATGGAAGCCAAAGGAAAAGG	59.533	41.667	7.80	0.00	36.95	3.11
3488	4019	4.497291	AGGTAGACTGTTCAAACAACCA	57.503	40.909	13.96	0.00	38.13	3.67
3910	4446	7.443302	TCTGAGGAAAATAATGAGGTGAGAT	57.557	36.000	0.00	0.00	0.00	2.75
3942	4478	3.067461	CCTGATAGACTGCTGGTGACTAC	59.933	52.174	0.00	0.00	0.00	2.73
4105	4643	8.454894	CAAAAGAAAGGAAGAATCTAACTAGGC	58.545	37.037	0.00	0.00	0.00	3.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.