AutoCloner

Multiple sequence alignment - TraesCS2A01G047100

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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	TraesCS2A01G047100	chr2A	100.000	3256	0	0	1	3256	18346059	18349314	0.000000e+00	6013.0
1	TraesCS2A01G047100	chr2A	90.387	1966	113	45	329	2272	18353357	18355268	0.000000e+00	2514.0
2	TraesCS2A01G047100	chr2A	95.996	999	17	2	2270	3256	20564452	20565439	0.000000e+00	1602.0
3	TraesCS2A01G047100	chr2A	89.347	291	31	0	2959	3249	645094503	645094213	1.850000e-97	366.0
4	TraesCS2A01G047100	chr2B	90.140	2292	147	47	1	2265	28719163	28721402	0.000000e+00	2907.0
5	TraesCS2A01G047100	chr2D	90.604	1756	90	37	547	2256	16486008	16487734	0.000000e+00	2259.0
6	TraesCS2A01G047100	chr2D	85.501	469	43	19	1	457	16484534	16484989	1.770000e-127	466.0
7	TraesCS2A01G047100	chr2D	97.222	36	1	0	248	283	16484741	16484776	9.750000e-06	62.1
8	TraesCS2A01G047100	chr1A	92.300	987	47	6	2270	3256	72242757	72243714	0.000000e+00	1375.0
9	TraesCS2A01G047100	chr4B	89.298	299	31	1	2959	3256	549199430	549199132	1.100000e-99	374.0
10	TraesCS2A01G047100	chr6D	91.829	257	11	3	2271	2527	454959635	454959881	1.860000e-92	350.0
11	TraesCS2A01G047100	chr6A	88.652	282	32	0	2969	3250	1825310	1825591	8.650000e-91	344.0
12	TraesCS2A01G047100	chr6A	89.796	147	14	1	3111	3256	604399584	604399438	1.540000e-43	187.0
13	TraesCS2A01G047100	chr6A	97.778	45	1	0	2959	3003	174112370	174112414	9.690000e-11	78.7
14	TraesCS2A01G047100	chr3D	89.796	147	14	1	3111	3256	603529610	603529756	1.540000e-43	187.0
15	TraesCS2A01G047100	chr7D	89.116	147	15	1	3111	3256	100497486	100497340	7.180000e-42	182.0
16	TraesCS2A01G047100	chr7D	83.060	183	25	6	1419	1598	538603044	538603223	9.350000e-36	161.0
17	TraesCS2A01G047100	chr7D	82.514	183	26	6	1419	1598	538332923	538332744	4.350000e-34	156.0
18	TraesCS2A01G047100	chr7D	94.118	51	3	0	2959	3009	111563929	111563979	9.690000e-11	78.7
19	TraesCS2A01G047100	chr1D	89.116	147	15	1	3111	3256	91482872	91483018	7.180000e-42	182.0
20	TraesCS2A01G047100	chr7B	82.873	181	25	6	1419	1596	580885295	580885118	1.210000e-34	158.0
21	TraesCS2A01G047100	chr7B	82.514	183	26	6	1419	1598	580969931	580969752	4.350000e-34	156.0
22	TraesCS2A01G047100	chr7A	82.609	184	26	6	1419	1599	619633659	619633479	1.210000e-34	158.0
23	TraesCS2A01G047100	chr7A	82.609	184	26	6	1419	1599	619907539	619907719	1.210000e-34	158.0
24	TraesCS2A01G047100	chr3A	94.118	51	3	0	2959	3009	590366310	590366360	9.690000e-11	78.7

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	TraesCS2A01G047100	chr2A	18346059	18349314	3255	False	6013.000000	6013	100.000	1	3256	1	chr2A.!!$F1	3255
1	TraesCS2A01G047100	chr2A	18353357	18355268	1911	False	2514.000000	2514	90.387	329	2272	1	chr2A.!!$F2	1943
2	TraesCS2A01G047100	chr2A	20564452	20565439	987	False	1602.000000	1602	95.996	2270	3256	1	chr2A.!!$F3	986
3	TraesCS2A01G047100	chr2B	28719163	28721402	2239	False	2907.000000	2907	90.140	1	2265	1	chr2B.!!$F1	2264
4	TraesCS2A01G047100	chr2D	16484534	16487734	3200	False	929.033333	2259	91.109	1	2256	3	chr2D.!!$F1	2255
5	TraesCS2A01G047100	chr1A	72242757	72243714	957	False	1375.000000	1375	92.300	2270	3256	1	chr1A.!!$F1	986

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
228	235	0.308993	GACAGCTGAACAACACCTGC	59.691	55.0	23.35	0.0	36.10	4.85	F
424	473	0.524862	CAAGAGCGCAGGAGCATTTT	59.475	50.0	11.47	0.0	42.27	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1379	2434	0.594602	GTCAGCATCTGCAGCACAAA	59.405	50.000	9.47	0.00	45.16	2.83	R
2359	3430	2.648454	GCTCTAGCGGGCTCTAGC	59.352	66.667	10.27	10.27	36.77	3.42	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
30	31	2.091541	TGGATGTCGGCCTTTTGAATC	58.908	47.619	0.00	0.00	0.00	2.52
32	33	2.369394	GATGTCGGCCTTTTGAATCCT	58.631	47.619	0.00	0.00	0.00	3.24
72	74	1.131126	TCTACACGCTTGGTAGTACGC	59.869	52.381	0.00	0.00	39.36	4.42
150	152	1.170919	TCTAGCCGGTGCGATCTACC	61.171	60.000	1.90	6.06	44.33	3.18
185	187	7.094805	TGCCTGTTTGACTTTAGATCATGTTAC	60.095	37.037	0.00	0.00	0.00	2.50
228	235	0.308993	GACAGCTGAACAACACCTGC	59.691	55.000	23.35	0.00	36.10	4.85
229	236	1.280746	CAGCTGAACAACACCTGCG	59.719	57.895	8.42	0.00	33.34	5.18
230	237	1.153168	AGCTGAACAACACCTGCGT	60.153	52.632	0.00	0.00	33.34	5.24
231	238	0.748005	AGCTGAACAACACCTGCGTT	60.748	50.000	0.00	0.00	33.34	4.84
235	242	1.301423	GAACAACACCTGCGTTGGTA	58.699	50.000	8.51	0.00	46.65	3.25
236	243	1.671845	GAACAACACCTGCGTTGGTAA	59.328	47.619	8.51	0.00	46.65	2.85
237	244	2.093106	AACAACACCTGCGTTGGTAAA	58.907	42.857	8.51	0.00	44.88	2.01
238	245	2.691011	AACAACACCTGCGTTGGTAAAT	59.309	40.909	8.51	0.00	44.88	1.40
239	246	2.660490	CAACACCTGCGTTGGTAAATG	58.340	47.619	1.37	0.00	42.10	2.32
240	247	1.975660	ACACCTGCGTTGGTAAATGT	58.024	45.000	1.37	0.00	38.45	2.71
241	248	1.877443	ACACCTGCGTTGGTAAATGTC	59.123	47.619	1.37	0.00	38.45	3.06
242	249	2.151202	CACCTGCGTTGGTAAATGTCT	58.849	47.619	1.37	0.00	38.45	3.41
243	250	3.244284	ACACCTGCGTTGGTAAATGTCTA	60.244	43.478	1.37	0.00	38.45	2.59
244	251	3.938963	CACCTGCGTTGGTAAATGTCTAT	59.061	43.478	1.37	0.00	38.45	1.98
245	252	4.034048	CACCTGCGTTGGTAAATGTCTATC	59.966	45.833	1.37	0.00	38.45	2.08
246	253	4.081087	ACCTGCGTTGGTAAATGTCTATCT	60.081	41.667	0.00	0.00	38.79	1.98
247	254	5.128171	ACCTGCGTTGGTAAATGTCTATCTA	59.872	40.000	0.00	0.00	38.79	1.98
248	255	5.462398	CCTGCGTTGGTAAATGTCTATCTAC	59.538	44.000	0.00	0.00	0.00	2.59
249	256	5.968254	TGCGTTGGTAAATGTCTATCTACA	58.032	37.500	0.00	0.00	0.00	2.74
250	257	6.040247	TGCGTTGGTAAATGTCTATCTACAG	58.960	40.000	0.00	0.00	31.70	2.74
251	258	5.050972	GCGTTGGTAAATGTCTATCTACAGC	60.051	44.000	0.00	0.00	31.70	4.40
252	259	6.273825	CGTTGGTAAATGTCTATCTACAGCT	58.726	40.000	0.00	0.00	31.70	4.24
253	260	6.199154	CGTTGGTAAATGTCTATCTACAGCTG	59.801	42.308	13.48	13.48	31.70	4.24
254	261	7.265673	GTTGGTAAATGTCTATCTACAGCTGA	58.734	38.462	23.35	2.95	31.70	4.26
255	262	7.418337	TGGTAAATGTCTATCTACAGCTGAA	57.582	36.000	23.35	5.64	31.70	3.02
256	263	7.265673	TGGTAAATGTCTATCTACAGCTGAAC	58.734	38.462	23.35	6.99	31.70	3.18
257	264	7.093509	TGGTAAATGTCTATCTACAGCTGAACA	60.094	37.037	23.35	12.14	31.70	3.18
258	265	7.764443	GGTAAATGTCTATCTACAGCTGAACAA	59.236	37.037	23.35	2.83	31.70	2.83
259	266	7.602517	AAATGTCTATCTACAGCTGAACAAC	57.397	36.000	23.35	9.23	31.70	3.32
260	267	5.722021	TGTCTATCTACAGCTGAACAACA	57.278	39.130	23.35	11.66	0.00	3.33
261	268	5.470368	TGTCTATCTACAGCTGAACAACAC	58.530	41.667	23.35	8.86	0.00	3.32
262	269	4.865365	GTCTATCTACAGCTGAACAACACC	59.135	45.833	23.35	0.00	0.00	4.16
263	270	4.772624	TCTATCTACAGCTGAACAACACCT	59.227	41.667	23.35	0.00	0.00	4.00
264	271	3.111853	TCTACAGCTGAACAACACCTG	57.888	47.619	23.35	0.00	37.97	4.00
293	320	4.701956	AAATGCCTATCCTTCACAAACG	57.298	40.909	0.00	0.00	0.00	3.60
307	334	2.979813	CACAAACGGTATGCTGCTTTTC	59.020	45.455	0.00	0.00	0.00	2.29
424	473	0.524862	CAAGAGCGCAGGAGCATTTT	59.475	50.000	11.47	0.00	42.27	1.82
481	1474	7.797038	TCTAAGCGTATATAGTGTGTCAAGA	57.203	36.000	0.00	0.00	0.00	3.02
501	1494	2.165030	GAGTCAACAAGGCATCATTGGG	59.835	50.000	0.00	0.00	31.76	4.12
518	1511	9.458727	CATCATTGGGCAGATACTAATCTTTAT	57.541	33.333	0.00	0.00	40.65	1.40
544	1551	8.214364	TGTGTATGCCTTATGGTTGAATATACA	58.786	33.333	0.00	0.00	35.27	2.29
545	1552	9.231297	GTGTATGCCTTATGGTTGAATATACAT	57.769	33.333	0.00	0.00	32.97	2.29
549	1556	6.426633	TGCCTTATGGTTGAATATACATGTCG	59.573	38.462	0.00	0.00	35.27	4.35
573	1580	9.790389	TCGAGTTTTGAGTAGATCTAGAAATTC	57.210	33.333	1.64	7.66	0.00	2.17
586	1593	5.479306	TCTAGAAATTCGACCCACAAGAAG	58.521	41.667	0.00	0.00	0.00	2.85
598	1606	4.104102	ACCCACAAGAAGTCCACAATAAGA	59.896	41.667	0.00	0.00	0.00	2.10
622	1630	3.610911	CCTAAAACCCTCTCCATGTCAC	58.389	50.000	0.00	0.00	0.00	3.67
721	1734	6.270000	CCCACATCCCATAATAGAACTACTCA	59.730	42.308	0.00	0.00	0.00	3.41
834	1847	6.017605	CCAGCCAATCACATCTAGTTCATTAC	60.018	42.308	0.00	0.00	0.00	1.89
893	1911	2.286184	CGTTTGTACTTCACACACTGGC	60.286	50.000	0.00	0.00	35.97	4.85
916	1934	1.349026	CCCACTAGCCCATTCGATCAT	59.651	52.381	0.00	0.00	0.00	2.45
917	1935	2.224621	CCCACTAGCCCATTCGATCATT	60.225	50.000	0.00	0.00	0.00	2.57
918	1936	3.480470	CCACTAGCCCATTCGATCATTT	58.520	45.455	0.00	0.00	0.00	2.32
970	1999	0.933097	CAGCACACACACTCACTCAC	59.067	55.000	0.00	0.00	0.00	3.51
997	2027	5.491323	AAGAAACCACTAGAAGGAGAAGG	57.509	43.478	11.98	0.00	0.00	3.46
1089	2119	0.988832	TTTCCCCGGTAGCAAGTGAT	59.011	50.000	0.00	0.00	0.00	3.06
1170	2200	0.822121	GCCAAACCGTTTCCCTGTCT	60.822	55.000	0.00	0.00	0.00	3.41
1379	2434	4.098894	TCCTCGGGTTAACCATTAGTTCT	58.901	43.478	25.71	0.00	40.05	3.01
1501	2562	0.034477	ACATTTACGCCAGGGGAAGG	60.034	55.000	11.28	0.00	0.00	3.46
2278	3349	9.492973	GTAGGAGTGGTTAATTAACACTACAAA	57.507	33.333	27.10	18.93	37.92	2.83
2369	3440	4.899239	CAAGCCCGCTAGAGCCCG	62.899	72.222	0.00	0.00	37.91	6.13
2723	3806	1.147824	CATTCTGGCTGGATCCGCT	59.852	57.895	22.14	5.36	0.00	5.52
3009	4092	4.347453	GGCTTGCACTGCAACCCG	62.347	66.667	12.59	4.85	43.99	5.28
3025	4108	2.356135	ACCCGTGCATCATCTACAAAC	58.644	47.619	0.00	0.00	0.00	2.93
3056	4139	3.963374	TGAGCACTTATATCTCTGCCTGT	59.037	43.478	0.00	0.00	0.00	4.00
3116	4199	2.936919	TGTGGTCATTGAGCTGAACT	57.063	45.000	16.19	0.00	33.84	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	3.504906	ACATTCAAGAAGATGCACACAGG	59.495	43.478	0.00	0.00	0.00	4.00
32	33	4.392047	AGACATTCAAGAAGATGCACACA	58.608	39.130	0.00	0.00	0.00	3.72
72	74	4.096003	ATTCCCCACCGTCCAGCG	62.096	66.667	0.00	0.00	40.95	5.18
228	235	6.199154	CAGCTGTAGATAGACATTTACCAACG	59.801	42.308	5.25	0.00	0.00	4.10
229	236	7.265673	TCAGCTGTAGATAGACATTTACCAAC	58.734	38.462	14.67	0.00	0.00	3.77
230	237	7.418337	TCAGCTGTAGATAGACATTTACCAA	57.582	36.000	14.67	0.00	0.00	3.67
231	238	7.093509	TGTTCAGCTGTAGATAGACATTTACCA	60.094	37.037	14.67	0.00	0.00	3.25
232	239	7.265673	TGTTCAGCTGTAGATAGACATTTACC	58.734	38.462	14.67	0.00	0.00	2.85
233	240	8.596380	GTTGTTCAGCTGTAGATAGACATTTAC	58.404	37.037	14.67	1.59	0.00	2.01
234	241	8.311109	TGTTGTTCAGCTGTAGATAGACATTTA	58.689	33.333	14.67	0.00	0.00	1.40
235	242	7.118390	GTGTTGTTCAGCTGTAGATAGACATTT	59.882	37.037	14.67	0.00	0.00	2.32
236	243	6.591834	GTGTTGTTCAGCTGTAGATAGACATT	59.408	38.462	14.67	0.00	0.00	2.71
237	244	6.102663	GTGTTGTTCAGCTGTAGATAGACAT	58.897	40.000	14.67	0.00	0.00	3.06
238	245	5.470368	GTGTTGTTCAGCTGTAGATAGACA	58.530	41.667	14.67	8.04	0.00	3.41
239	246	4.865365	GGTGTTGTTCAGCTGTAGATAGAC	59.135	45.833	14.67	5.61	40.87	2.59
240	247	5.073311	GGTGTTGTTCAGCTGTAGATAGA	57.927	43.478	14.67	0.00	40.87	1.98
250	257	1.603678	CCAATGCAGGTGTTGTTCAGC	60.604	52.381	0.00	0.00	43.96	4.26
251	258	1.682854	ACCAATGCAGGTGTTGTTCAG	59.317	47.619	0.00	0.00	41.30	3.02
252	259	1.774110	ACCAATGCAGGTGTTGTTCA	58.226	45.000	0.00	0.00	41.30	3.18
253	260	4.314740	TTTACCAATGCAGGTGTTGTTC	57.685	40.909	7.87	0.00	43.14	3.18
254	261	4.630111	CATTTACCAATGCAGGTGTTGTT	58.370	39.130	7.87	0.00	43.14	2.83
255	262	4.255833	CATTTACCAATGCAGGTGTTGT	57.744	40.909	7.87	0.00	43.14	3.32
293	320	1.176527	TGCAGGAAAAGCAGCATACC	58.823	50.000	0.00	0.00	37.02	2.73
307	334	3.752796	CAATGGGAATTGCTGCAGG	57.247	52.632	17.12	0.00	0.00	4.85
424	473	7.148355	AGACACAGAAAACGTAAAAAGGAAA	57.852	32.000	0.00	0.00	0.00	3.13
481	1474	2.173519	CCCAATGATGCCTTGTTGACT	58.826	47.619	0.00	0.00	0.00	3.41
501	1494	8.660373	GGCATACACATAAAGATTAGTATCTGC	58.340	37.037	0.00	0.00	40.26	4.26
518	1511	8.214364	TGTATATTCAACCATAAGGCATACACA	58.786	33.333	0.00	0.00	39.06	3.72
544	1551	7.867305	TCTAGATCTACTCAAAACTCGACAT	57.133	36.000	0.00	0.00	0.00	3.06
545	1552	7.683437	TTCTAGATCTACTCAAAACTCGACA	57.317	36.000	0.00	0.00	0.00	4.35
549	1556	9.790389	TCGAATTTCTAGATCTACTCAAAACTC	57.210	33.333	0.00	0.00	0.00	3.01
573	1580	0.105964	TGTGGACTTCTTGTGGGTCG	59.894	55.000	0.00	0.00	0.00	4.79
586	1593	4.398358	GGTTTTAGGCCTCTTATTGTGGAC	59.602	45.833	9.68	0.00	37.60	4.02
598	1606	1.566231	CATGGAGAGGGTTTTAGGCCT	59.434	52.381	11.78	11.78	0.00	5.19
622	1630	1.134491	GGGAGTCGAGGGTTTATGGTG	60.134	57.143	0.00	0.00	0.00	4.17
733	1746	6.616947	TCAAGTGGGAATAATTAAGTTTGCG	58.383	36.000	0.00	0.00	0.00	4.85
834	1847	4.221926	TGTGTTGGATTCGTCAAACATG	57.778	40.909	2.06	0.00	0.00	3.21
893	1911	1.153168	CGAATGGGCTAGTGGGGTG	60.153	63.158	0.00	0.00	0.00	4.61
916	1934	7.842982	TGGTGTGCACTTATATAGACTACAAA	58.157	34.615	19.41	0.00	0.00	2.83
917	1935	7.412853	TGGTGTGCACTTATATAGACTACAA	57.587	36.000	19.41	0.00	0.00	2.41
918	1936	7.597288	ATGGTGTGCACTTATATAGACTACA	57.403	36.000	19.41	0.18	0.00	2.74
970	1999	6.525629	TCTCCTTCTAGTGGTTTCTTTCAAG	58.474	40.000	4.87	0.00	0.00	3.02
1089	2119	1.103803	GGTCGAGGCTGTCTGTCATA	58.896	55.000	0.00	0.00	0.00	2.15
1170	2200	3.429141	GTCGTCCAGCGGTCGAGA	61.429	66.667	14.49	0.00	42.88	4.04
1281	2311	6.892456	TCACTTCAGGATCACTTACATAGAGT	59.108	38.462	0.00	0.00	0.00	3.24
1354	2409	5.803237	ACTAATGGTTAACCCGAGGATAG	57.197	43.478	21.97	15.19	35.15	2.08
1379	2434	0.594602	GTCAGCATCTGCAGCACAAA	59.405	50.000	9.47	0.00	45.16	2.83
2359	3430	2.648454	GCTCTAGCGGGCTCTAGC	59.352	66.667	10.27	10.27	36.77	3.42
2369	3440	2.809010	GGTCAGTCGGGCTCTAGC	59.191	66.667	0.00	0.00	41.14	3.42
2723	3806	3.536917	CGCCATAGACCGGGAGCA	61.537	66.667	6.32	0.00	0.00	4.26
3009	4092	4.455533	TGAAGTGGTTTGTAGATGATGCAC	59.544	41.667	0.00	0.00	0.00	4.57
3025	4108	5.911752	AGATATAAGTGCTCACTGAAGTGG	58.088	41.667	10.45	3.12	45.65	4.00
3056	4139	1.381056	GGGCTCAGAGCAGAGGAGA	60.381	63.158	24.09	0.00	44.75	3.71
3116	4199	7.287061	CAATACCCTAACTAACCATGGATCAA	58.713	38.462	21.47	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.