AutoCloner

Multiple sequence alignment - TraesCS2B01G486500

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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	TraesCS2B01G486500	chr2B	100.000	2375	0	0	1	2375	683132092	683134466	0.000000e+00	4386
1	TraesCS2B01G486500	chr2B	86.726	2019	231	23	1	2003	683057645	683059642	0.000000e+00	2209
2	TraesCS2B01G486500	chr2B	84.263	1919	265	20	1	1911	683071247	683073136	0.000000e+00	1836
3	TraesCS2B01G486500	chr2B	82.826	1677	255	24	1	1662	683046526	683048184	0.000000e+00	1471
4	TraesCS2B01G486500	chr2B	81.813	1732	274	30	1	1704	794690872	794689154	0.000000e+00	1415
5	TraesCS2B01G486500	chr2B	81.813	1732	274	30	1	1704	794799773	794798055	0.000000e+00	1415
6	TraesCS2B01G486500	chr2B	94.648	355	14	3	2022	2375	683059621	683059971	1.610000e-151	545
7	TraesCS2B01G486500	chr2B	83.544	237	22	10	2135	2366	683074300	683074524	3.090000e-49	206
8	TraesCS2B01G486500	chr2A	88.670	2383	247	19	1	2375	710191499	710193866	0.000000e+00	2883
9	TraesCS2B01G486500	chr2A	86.466	1559	185	19	160	1704	710246190	710247736	0.000000e+00	1687
10	TraesCS2B01G486500	chr2A	85.567	1455	200	8	1	1449	710096620	710098070	0.000000e+00	1515
11	TraesCS2B01G486500	chr2A	81.538	390	47	16	1990	2366	710045295	710045672	4.960000e-77	298
12	TraesCS2B01G486500	chr2D	82.421	1974	281	36	1	1957	571212557	571214481	0.000000e+00	1663
13	TraesCS2B01G486500	chr2D	84.400	1718	231	27	2	1704	571530632	571532327	0.000000e+00	1653
14	TraesCS2B01G486500	chr2D	83.004	1671	256	24	1	1662	571198736	571200387	0.000000e+00	1487
15	TraesCS2B01G486500	chr2D	80.670	388	50	17	1990	2366	571216486	571216859	6.470000e-71	278

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	TraesCS2B01G486500	chr2B	683132092	683134466	2374	False	4386.0	4386	100.0000	1	2375	1	chr2B.!!$F2	2374
1	TraesCS2B01G486500	chr2B	683046526	683048184	1658	False	1471.0	1471	82.8260	1	1662	1	chr2B.!!$F1	1661
2	TraesCS2B01G486500	chr2B	794689154	794690872	1718	True	1415.0	1415	81.8130	1	1704	1	chr2B.!!$R1	1703
3	TraesCS2B01G486500	chr2B	794798055	794799773	1718	True	1415.0	1415	81.8130	1	1704	1	chr2B.!!$R2	1703
4	TraesCS2B01G486500	chr2B	683057645	683059971	2326	False	1377.0	2209	90.6870	1	2375	2	chr2B.!!$F3	2374
5	TraesCS2B01G486500	chr2B	683071247	683074524	3277	False	1021.0	1836	83.9035	1	2366	2	chr2B.!!$F4	2365
6	TraesCS2B01G486500	chr2A	710191499	710193866	2367	False	2883.0	2883	88.6700	1	2375	1	chr2A.!!$F3	2374
7	TraesCS2B01G486500	chr2A	710246190	710247736	1546	False	1687.0	1687	86.4660	160	1704	1	chr2A.!!$F4	1544
8	TraesCS2B01G486500	chr2A	710096620	710098070	1450	False	1515.0	1515	85.5670	1	1449	1	chr2A.!!$F2	1448
9	TraesCS2B01G486500	chr2D	571530632	571532327	1695	False	1653.0	1653	84.4000	2	1704	1	chr2D.!!$F2	1702
10	TraesCS2B01G486500	chr2D	571198736	571200387	1651	False	1487.0	1487	83.0040	1	1662	1	chr2D.!!$F1	1661
11	TraesCS2B01G486500	chr2D	571212557	571216859	4302	False	970.5	1663	81.5455	1	2366	2	chr2D.!!$F3	2365

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
269	276	0.251073	TTACGGGGCTAGTCCTTTGC	59.749	55.0	14.34	0.0	34.39	3.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1782	3328	0.394899	GGAGCCACTGCCAAAGCTAT	60.395	55.0	0.0	0.0	40.8	2.97	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
33	34	2.912956	TCCCTTGAGGAGTTGCTGTTAT	59.087	45.455	0.00	0.00	40.93	1.89
113	114	1.202806	AGCAGTTTGGCTTCAGCAGTA	60.203	47.619	0.30	0.00	42.71	2.74
122	123	3.084786	GGCTTCAGCAGTAATGACCTTT	58.915	45.455	0.30	0.00	44.36	3.11
155	162	6.389091	TGAACATGAATTGAAACTGCCATAC	58.611	36.000	0.00	0.00	0.00	2.39
165	172	5.428253	TGAAACTGCCATACAATCTCCTAC	58.572	41.667	0.00	0.00	0.00	3.18
196	203	6.475504	TCAAGAAGTTATGGATTCAGCTGAA	58.524	36.000	30.23	30.23	38.56	3.02
218	225	2.182827	CTGGATCTGGAGTTCTGTGGA	58.817	52.381	0.00	0.00	0.00	4.02
256	263	2.892784	GGATTCACCTCTCTTACGGG	57.107	55.000	0.00	0.00	35.41	5.28
269	276	0.251073	TTACGGGGCTAGTCCTTTGC	59.749	55.000	14.34	0.00	34.39	3.68
270	277	0.905809	TACGGGGCTAGTCCTTTGCA	60.906	55.000	14.34	0.00	34.39	4.08
326	333	6.537301	GTGAAACGAAAGATGATGGTACCATA	59.463	38.462	27.42	15.53	36.70	2.74
360	370	2.038952	CTCCCACCATCACTTGAAGACA	59.961	50.000	0.00	0.00	0.00	3.41
363	373	3.192001	CCCACCATCACTTGAAGACATTG	59.808	47.826	0.00	0.00	0.00	2.82
383	393	1.904287	CTATCGGTCCTCTCCCAGAG	58.096	60.000	0.00	0.00	41.96	3.35
419	429	0.987294	CTCCTCAAGGCCTTCTCCAA	59.013	55.000	17.29	0.00	34.44	3.53
422	432	1.074566	CCTCAAGGCCTTCTCCAACTT	59.925	52.381	17.29	0.00	0.00	2.66
454	464	5.197682	AGTCTACGTAATAGCCCATGTTC	57.802	43.478	0.00	0.00	0.00	3.18
559	575	0.252467	CAGTTCCTCACCTCCCTCCT	60.252	60.000	0.00	0.00	0.00	3.69
585	601	4.279420	GCTTGAATATTGAGATGAACCCCC	59.721	45.833	0.00	0.00	0.00	5.40
647	663	3.592059	ACATGGCAGCAATCAAATTCAC	58.408	40.909	0.00	0.00	0.00	3.18
699	715	3.695606	GGGCTCTCACGGACAGCA	61.696	66.667	4.22	0.00	0.00	4.41
719	735	3.434739	GCATCCAATCCCATCTTCTGTCT	60.435	47.826	0.00	0.00	0.00	3.41
804	820	0.901114	ATGCTGCATGGCACTGGAAA	60.901	50.000	15.44	0.00	45.36	3.13
826	842	1.200020	GTTGGAAATTGGAGACTGCGG	59.800	52.381	0.00	0.00	0.00	5.69
846	862	0.755079	CTCCCTTGCATCCATCGAGA	59.245	55.000	0.00	0.00	0.00	4.04
852	868	1.044790	TGCATCCATCGAGAGCCTCA	61.045	55.000	0.00	0.00	0.00	3.86
859	875	2.266554	CATCGAGAGCCTCAAGTTCAC	58.733	52.381	0.00	0.00	0.00	3.18
887	903	7.391833	AGAAACCTGACATCCTTGAAAGTATTC	59.608	37.037	0.00	0.00	36.04	1.75
930	946	0.592637	TTTGGAGCTTGTGTCGCATG	59.407	50.000	0.00	0.00	0.00	4.06
932	948	0.950555	TGGAGCTTGTGTCGCATGAC	60.951	55.000	0.00	0.00	45.71	3.06
934	950	1.959899	GAGCTTGTGTCGCATGACCG	61.960	60.000	0.00	0.00	44.86	4.79
945	961	1.457643	CATGACCGAGGGGCCTCTA	60.458	63.158	4.16	0.00	40.69	2.43
962	978	4.690261	GCCTCTAAGATCTGGTCTGGACTA	60.690	50.000	0.00	0.00	37.23	2.59
1144	1166	6.610830	ACCTCCCTTCAAGAACTTAAATTCA	58.389	36.000	0.00	0.00	0.00	2.57
1167	1189	1.471287	TGGTACACGAATCTCCTGTCG	59.529	52.381	0.00	0.00	42.91	4.35
1219	1241	6.444704	TCCCTTGAGAGGTTATCTATCAGTT	58.555	40.000	0.00	0.00	43.59	3.16
1225	1247	7.323420	TGAGAGGTTATCTATCAGTTGTTGTG	58.677	38.462	0.00	0.00	38.64	3.33
1306	1328	2.182827	TCAGTTGCAGTGAGGAGCTAT	58.817	47.619	0.00	0.00	0.00	2.97
1310	1332	0.107993	TGCAGTGAGGAGCTATGCAC	60.108	55.000	0.00	4.62	41.65	4.57
1357	1380	6.753913	AGAAGCTAAGGGTCATGATTGATA	57.246	37.500	0.00	0.00	33.56	2.15
1401	1425	6.153000	CACCAGTGTCTACTTCTAAGGTACAT	59.847	42.308	0.00	0.00	34.07	2.29
1423	1448	2.588464	TCGGGGCATTTTTCCTACAA	57.412	45.000	0.00	0.00	0.00	2.41
1455	1480	0.035881	TGCTCACCCTCTTTCTGCTG	59.964	55.000	0.00	0.00	0.00	4.41
1458	1483	2.697654	CTCACCCTCTTTCTGCTGAAG	58.302	52.381	6.13	2.05	33.28	3.02
1511	3017	6.201044	CACCCGAGATGTTGTACATATTTCTC	59.799	42.308	0.00	6.04	39.27	2.87
1567	3105	0.825840	TTCACCCCTTTGGCTTTCCG	60.826	55.000	0.00	0.00	37.83	4.30
1802	3348	2.803155	TAGCTTTGGCAGTGGCTCCG	62.803	60.000	18.53	6.76	41.70	4.63
1865	3419	7.654022	TTTCTGGTTAACTGATGAAAAGGTT	57.346	32.000	5.42	0.00	0.00	3.50
1866	3420	6.877611	TCTGGTTAACTGATGAAAAGGTTC	57.122	37.500	5.42	0.00	0.00	3.62
1868	3422	6.831353	TCTGGTTAACTGATGAAAAGGTTCAA	59.169	34.615	5.42	0.00	46.66	2.69
1869	3423	7.013274	TCTGGTTAACTGATGAAAAGGTTCAAG	59.987	37.037	5.42	0.00	46.66	3.02
1870	3424	6.605594	TGGTTAACTGATGAAAAGGTTCAAGT	59.394	34.615	5.42	0.00	46.66	3.16
1871	3425	7.776030	TGGTTAACTGATGAAAAGGTTCAAGTA	59.224	33.333	5.42	0.00	46.66	2.24
1872	3426	8.793592	GGTTAACTGATGAAAAGGTTCAAGTAT	58.206	33.333	5.42	0.00	46.66	2.12
1988	3544	1.890876	TTTGCGGGGGATATCAATCG	58.109	50.000	4.83	5.84	32.44	3.34
2009	3565	4.113354	CGATGTTGTTAACTAGGCTCTCC	58.887	47.826	7.22	0.00	0.00	3.71
2158	3769	5.174395	ACTTGACTGTTCAGCATATGAGAC	58.826	41.667	6.97	0.00	39.68	3.36
2231	4800	4.644498	TCTGTCTCATGATGCAGTTTCAA	58.356	39.130	19.59	4.59	0.00	2.69
2280	5369	7.005709	ACTAGGTTTGTTGCTGAAGTATACT	57.994	36.000	0.00	0.00	0.00	2.12
2281	5370	8.130671	ACTAGGTTTGTTGCTGAAGTATACTA	57.869	34.615	5.65	0.00	0.00	1.82
2282	5371	8.033626	ACTAGGTTTGTTGCTGAAGTATACTAC	58.966	37.037	5.65	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	1.366319	ACAGCAACTCCTCAAGGGAT	58.634	50.000	0.00	0.00	44.15	3.85
33	34	7.506114	AGAAACTTTATCTGTGGACAGTTACA	58.494	34.615	6.68	0.00	44.12	2.41
113	114	3.173953	TCATCTTGGGCAAAGGTCATT	57.826	42.857	0.88	0.00	36.46	2.57
122	123	4.087907	TCAATTCATGTTCATCTTGGGCA	58.912	39.130	0.00	0.00	0.00	5.36
155	162	5.568685	TCTTGAGAGAACGTAGGAGATTG	57.431	43.478	0.00	0.00	0.00	2.67
165	172	6.813649	TGAATCCATAACTTCTTGAGAGAACG	59.186	38.462	0.00	0.00	36.99	3.95
196	203	1.905215	CACAGAACTCCAGATCCAGGT	59.095	52.381	2.06	0.00	0.00	4.00
218	225	4.931027	TCCTGTGAAGTCTCTACTACCT	57.069	45.455	0.00	0.00	33.75	3.08
256	263	0.523519	GCAACTGCAAAGGACTAGCC	59.476	55.000	0.00	0.00	41.59	3.93
269	276	2.203538	ACCAGCTTGGGGCAACTG	60.204	61.111	7.06	0.00	43.37	3.16
270	277	2.116125	GACCAGCTTGGGGCAACT	59.884	61.111	7.06	0.00	43.37	3.16
326	333	1.272147	GGTGGGAGCAATCCAACTTCT	60.272	52.381	1.96	0.00	38.86	2.85
360	370	1.343069	GGGAGAGGACCGATAGCAAT	58.657	55.000	0.00	0.00	0.00	3.56
363	373	0.178987	TCTGGGAGAGGACCGATAGC	60.179	60.000	0.00	0.00	0.00	2.97
422	432	9.586435	GGGCTATTACGTAGACTTAACTTTTTA	57.414	33.333	0.00	0.00	38.59	1.52
454	464	2.001812	ATGCAGCTGTACAGACTTCG	57.998	50.000	27.08	12.26	0.00	3.79
559	575	6.772716	GGGGTTCATCTCAATATTCAAGCTTA	59.227	38.462	0.00	0.00	0.00	3.09
585	601	0.035725	TCCCATGCAGAAGACAGCTG	60.036	55.000	13.48	13.48	36.47	4.24
629	645	2.028839	CAGGTGAATTTGATTGCTGCCA	60.029	45.455	0.00	0.00	0.00	4.92
647	663	1.280133	TCAAGTGATGGAGGAAGCAGG	59.720	52.381	0.00	0.00	0.00	4.85
699	715	4.789807	CAAGACAGAAGATGGGATTGGAT	58.210	43.478	0.00	0.00	0.00	3.41
793	809	2.151502	TTCCAACTTTTCCAGTGCCA	57.848	45.000	0.00	0.00	35.12	4.92
804	820	2.554032	CGCAGTCTCCAATTTCCAACTT	59.446	45.455	0.00	0.00	0.00	2.66
826	842	0.883814	CTCGATGGATGCAAGGGAGC	60.884	60.000	0.00	0.00	0.00	4.70
830	846	0.883814	GGCTCTCGATGGATGCAAGG	60.884	60.000	0.00	0.00	0.00	3.61
846	862	3.648545	AGGTTTCTAGTGAACTTGAGGCT	59.351	43.478	10.18	0.00	31.02	4.58
852	868	5.308237	AGGATGTCAGGTTTCTAGTGAACTT	59.692	40.000	10.18	2.46	31.02	2.66
859	875	6.234177	ACTTTCAAGGATGTCAGGTTTCTAG	58.766	40.000	0.00	0.00	0.00	2.43
930	946	0.470268	ATCTTAGAGGCCCCTCGGTC	60.470	60.000	0.00	0.00	46.90	4.79
932	948	0.178947	AGATCTTAGAGGCCCCTCGG	60.179	60.000	0.00	4.18	46.90	4.63
934	950	1.347062	CCAGATCTTAGAGGCCCCTC	58.653	60.000	0.00	6.20	43.03	4.30
967	983	5.366460	AGATGCGTCATCAATCTCAAGATT	58.634	37.500	17.94	0.00	44.93	2.40
968	984	4.958509	AGATGCGTCATCAATCTCAAGAT	58.041	39.130	17.94	0.00	42.72	2.40
1144	1166	2.897969	ACAGGAGATTCGTGTACCACTT	59.102	45.455	2.87	0.00	42.83	3.16
1167	1189	2.159324	GCTATGAAGGTTTGCAGGAAGC	60.159	50.000	0.00	0.00	45.96	3.86
1225	1247	1.375098	GGCAGCCTTGTGATGCTCTC	61.375	60.000	3.29	0.00	39.88	3.20
1261	1283	1.898472	CTGAAGGTGCCTGAGAGAAGA	59.102	52.381	0.00	0.00	0.00	2.87
1310	1332	2.547913	TGCTACAATTCTGCATTGCG	57.452	45.000	3.84	0.00	45.74	4.85
1401	1425	3.231818	TGTAGGAAAAATGCCCCGAAAA	58.768	40.909	0.00	0.00	0.00	2.29
1423	1448	6.485171	AGAGGGTGAGCATGTAAACTAATTT	58.515	36.000	0.00	0.00	0.00	1.82
1455	1480	5.752955	GTCTGCAGAGAGATGAATTACCTTC	59.247	44.000	18.89	0.00	0.00	3.46
1458	1483	5.049167	CAGTCTGCAGAGAGATGAATTACC	58.951	45.833	18.89	0.00	0.00	2.85
1782	3328	0.394899	GGAGCCACTGCCAAAGCTAT	60.395	55.000	0.00	0.00	40.80	2.97
1791	3337	3.277211	TACGTCACGGAGCCACTGC	62.277	63.158	0.35	0.00	37.95	4.40
1840	3386	7.654022	ACCTTTTCATCAGTTAACCAGAAAA	57.346	32.000	16.96	16.96	34.81	2.29
1893	3447	3.072915	TGGAACTGGACAAGATGTGATGT	59.927	43.478	0.00	0.00	0.00	3.06
1988	3544	4.113354	CGGAGAGCCTAGTTAACAACATC	58.887	47.826	8.61	0.00	0.00	3.06
2197	3810	6.850752	TCATGAGACAGATGGTAGTAAACA	57.149	37.500	0.00	0.00	0.00	2.83
2199	3812	6.127083	TGCATCATGAGACAGATGGTAGTAAA	60.127	38.462	0.09	0.00	41.43	2.01
2248	5337	4.686554	CAGCAACAAACCTAGTACTCACTC	59.313	45.833	0.00	0.00	36.14	3.51
2280	5369	6.940298	ACAAACCTAGAGCAAAATAGCAAGTA	59.060	34.615	0.00	0.00	36.85	2.24
2281	5370	5.770162	ACAAACCTAGAGCAAAATAGCAAGT	59.230	36.000	0.00	0.00	36.85	3.16
2282	5371	6.259550	ACAAACCTAGAGCAAAATAGCAAG	57.740	37.500	0.00	0.00	36.85	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.