AutoCloner

Multiple sequence alignment - TraesCS5D01G159500

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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	TraesCS5D01G159500	chr5D	100.000	3000	0	0	1	3000	249088580	249085581	0.000000e+00	5541.0
1	TraesCS5D01G159500	chr5B	94.728	1195	35	19	513	1701	282012684	282011512	0.000000e+00	1832.0
2	TraesCS5D01G159500	chr5B	96.981	530	10	4	1	525	282013347	282012819	0.000000e+00	885.0
3	TraesCS5D01G159500	chr5B	92.206	603	16	13	1709	2283	282011339	282010740	0.000000e+00	824.0
4	TraesCS5D01G159500	chr5B	88.433	683	63	13	2321	3000	288322477	288323146	0.000000e+00	809.0
5	TraesCS5D01G159500	chr5A	94.229	1161	35	14	323	1462	331890543	331889394	0.000000e+00	1744.0
6	TraesCS5D01G159500	chr5A	93.408	804	30	13	1530	2322	331889259	331888468	0.000000e+00	1170.0
7	TraesCS5D01G159500	chr5A	89.683	252	22	2	1	248	331890795	331890544	4.830000e-83	318.0
8	TraesCS5D01G159500	chr5A	100.000	37	0	0	1480	1516	331889405	331889369	5.370000e-08	69.4
9	TraesCS5D01G159500	chr3B	89.458	683	57	13	2318	2997	2121987	2122657	0.000000e+00	848.0
10	TraesCS5D01G159500	chr3B	85.755	702	66	21	2319	3000	793374793	793374106	0.000000e+00	712.0
11	TraesCS5D01G159500	chr6B	85.036	695	79	13	2319	3000	585168305	585168987	0.000000e+00	684.0
12	TraesCS5D01G159500	chr6B	85.036	695	79	13	2319	3000	585211971	585212653	0.000000e+00	684.0
13	TraesCS5D01G159500	chr6B	85.036	695	79	13	2319	3000	585214869	585215551	0.000000e+00	684.0
14	TraesCS5D01G159500	chr6B	85.057	696	77	14	2319	3000	585260641	585261323	0.000000e+00	684.0
15	TraesCS5D01G159500	chr6B	84.892	695	80	13	2319	3000	585159614	585160296	0.000000e+00	678.0
16	TraesCS5D01G159500	chrUn	84.935	697	76	17	2319	3000	250184851	250185533	0.000000e+00	678.0
17	TraesCS5D01G159500	chr2B	89.177	231	25	0	1771	2001	758389858	758389628	3.780000e-74	289.0
18	TraesCS5D01G159500	chr2B	88.745	231	26	0	1771	2001	758147492	758147262	1.760000e-72	283.0
19	TraesCS5D01G159500	chr2D	87.500	232	29	0	1771	2002	585861020	585861251	4.930000e-68	268.0
20	TraesCS5D01G159500	chr2D	87.446	231	29	0	1771	2001	619426466	619426236	1.770000e-67	267.0
21	TraesCS5D01G159500	chr2D	86.580	231	31	0	1771	2001	619436523	619436293	3.840000e-64	255.0
22	TraesCS5D01G159500	chr2A	86.580	231	31	0	1771	2001	750581233	750581003	3.840000e-64	255.0
23	TraesCS5D01G159500	chr2A	86.580	231	31	0	1771	2001	750617278	750617048	3.840000e-64	255.0

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	TraesCS5D01G159500	chr5D	249085581	249088580	2999	True	5541.000000	5541	100.000000	1	3000	1	chr5D.!!$R1	2999
1	TraesCS5D01G159500	chr5B	282010740	282013347	2607	True	1180.333333	1832	94.638333	1	2283	3	chr5B.!!$R1	2282
2	TraesCS5D01G159500	chr5B	288322477	288323146	669	False	809.000000	809	88.433000	2321	3000	1	chr5B.!!$F1	679
3	TraesCS5D01G159500	chr5A	331888468	331890795	2327	True	825.350000	1744	94.330000	1	2322	4	chr5A.!!$R1	2321
4	TraesCS5D01G159500	chr3B	2121987	2122657	670	False	848.000000	848	89.458000	2318	2997	1	chr3B.!!$F1	679
5	TraesCS5D01G159500	chr3B	793374106	793374793	687	True	712.000000	712	85.755000	2319	3000	1	chr3B.!!$R1	681
6	TraesCS5D01G159500	chr6B	585168305	585168987	682	False	684.000000	684	85.036000	2319	3000	1	chr6B.!!$F2	681
7	TraesCS5D01G159500	chr6B	585211971	585215551	3580	False	684.000000	684	85.036000	2319	3000	2	chr6B.!!$F4	681
8	TraesCS5D01G159500	chr6B	585260641	585261323	682	False	684.000000	684	85.057000	2319	3000	1	chr6B.!!$F3	681
9	TraesCS5D01G159500	chr6B	585159614	585160296	682	False	678.000000	678	84.892000	2319	3000	1	chr6B.!!$F1	681
10	TraesCS5D01G159500	chrUn	250184851	250185533	682	False	678.000000	678	84.935000	2319	3000	1	chrUn.!!$F1	681

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
997	1161	1.030488	AAGTCTTCCGATCGAGCCGA	61.03	55.0	18.66	1.59	41.13	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2374	2849	0.179108	GCCAATCTAGCGACGGTTCT	60.179	55.0	4.26	0.0	0.0	3.01	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
118	122	3.821033	GCTGCTAAAACCTTCAGGAGAAA	59.179	43.478	0.00	0.00	38.94	2.52
153	158	3.445857	GACTATCTTGTTGGTCGTAGGC	58.554	50.000	0.00	0.00	0.00	3.93
164	169	2.942376	TGGTCGTAGGCTGCATTATTTG	59.058	45.455	2.89	0.00	0.00	2.32
269	274	2.279741	CCATTCACCGATCGACAATGT	58.720	47.619	18.66	1.85	0.00	2.71
449	455	2.726821	ACACCACCATATCTGCTTTGG	58.273	47.619	0.00	0.00	36.56	3.28
450	456	1.406539	CACCACCATATCTGCTTTGGC	59.593	52.381	0.00	0.00	33.66	4.52
452	458	1.410648	CCACCATATCTGCTTTGGCCT	60.411	52.381	3.32	0.00	37.74	5.19
467	475	2.342650	GCCTTTTGCCTCCGCATCA	61.343	57.895	0.00	0.00	46.67	3.07
565	724	2.009681	AGGGAAAACAATGGTGTCCC	57.990	50.000	19.03	19.03	46.03	4.46
867	1031	3.486108	CGTATCGTATCCACTTCAAGCAC	59.514	47.826	0.00	0.00	0.00	4.40
927	1091	6.567050	CCATGCACATTTGAGCTTAATTAGT	58.433	36.000	0.00	0.00	32.76	2.24
936	1100	7.787725	TTTGAGCTTAATTAGTTAGCTAGCC	57.212	36.000	12.13	0.00	35.83	3.93
997	1161	1.030488	AAGTCTTCCGATCGAGCCGA	61.030	55.000	18.66	1.59	41.13	5.54
1430	1612	7.800380	CGAGCTAATCATTAATCAACCATTCAC	59.200	37.037	0.00	0.00	0.00	3.18
1457	1640	8.885494	TTTTTCATGTCAACCCTAATTTCTTG	57.115	30.769	0.00	0.00	0.00	3.02
1458	1641	7.595819	TTTCATGTCAACCCTAATTTCTTGT	57.404	32.000	0.00	0.00	0.00	3.16
1459	1642	8.698973	TTTCATGTCAACCCTAATTTCTTGTA	57.301	30.769	0.00	0.00	0.00	2.41
1460	1643	8.877864	TTCATGTCAACCCTAATTTCTTGTAT	57.122	30.769	0.00	0.00	0.00	2.29
1461	1644	8.506168	TCATGTCAACCCTAATTTCTTGTATC	57.494	34.615	0.00	0.00	0.00	2.24
1462	1645	8.328758	TCATGTCAACCCTAATTTCTTGTATCT	58.671	33.333	0.00	0.00	0.00	1.98
1463	1646	7.921786	TGTCAACCCTAATTTCTTGTATCTG	57.078	36.000	0.00	0.00	0.00	2.90
1464	1647	7.685481	TGTCAACCCTAATTTCTTGTATCTGA	58.315	34.615	0.00	0.00	0.00	3.27
1465	1648	7.824289	TGTCAACCCTAATTTCTTGTATCTGAG	59.176	37.037	0.00	0.00	0.00	3.35
1466	1649	7.824779	GTCAACCCTAATTTCTTGTATCTGAGT	59.175	37.037	0.00	0.00	0.00	3.41
1467	1650	8.383175	TCAACCCTAATTTCTTGTATCTGAGTT	58.617	33.333	0.00	0.00	0.00	3.01
1468	1651	9.014297	CAACCCTAATTTCTTGTATCTGAGTTT	57.986	33.333	0.00	0.00	0.00	2.66
1469	1652	8.794335	ACCCTAATTTCTTGTATCTGAGTTTC	57.206	34.615	0.00	0.00	0.00	2.78
1470	1653	8.383175	ACCCTAATTTCTTGTATCTGAGTTTCA	58.617	33.333	0.00	0.00	0.00	2.69
1471	1654	9.231297	CCCTAATTTCTTGTATCTGAGTTTCAA	57.769	33.333	0.00	0.00	0.00	2.69
1595	1874	2.495669	TGATGTCAGTCATGGTAAGCGA	59.504	45.455	0.00	0.00	36.83	4.93
1701	1980	1.135053	TGCATGTGGATTTCGCATTGG	60.135	47.619	0.00	0.00	43.43	3.16
1711	2155	5.527214	TGGATTTCGCATTGGACTATTGTAG	59.473	40.000	0.00	0.00	0.00	2.74
1757	2206	7.095102	TGTGTTAAGTTTTCTTATTACTCCGCC	60.095	37.037	0.00	0.00	41.33	6.13
2075	2525	5.163343	CCGGTCTGACCTAATTATTGAAGGA	60.163	44.000	23.49	0.00	35.66	3.36
2091	2549	6.866010	TTGAAGGATATGACATACACATGC	57.134	37.500	0.00	0.00	35.39	4.06
2307	2779	0.798776	ATCTCCTTGCACGCGAAAAG	59.201	50.000	15.93	12.96	0.00	2.27
2433	2910	1.305802	AGTCATAGGCCCACGGTCA	60.306	57.895	0.00	0.00	0.00	4.02
2544	3027	6.567769	AAACGTAAAAACATGCAAGAACTG	57.432	33.333	0.00	0.00	0.00	3.16
2597	3097	2.717485	GCCGCCGTCGTCTACATA	59.283	61.111	0.00	0.00	0.00	2.29
2636	3136	4.409218	GTGTAGTCGCCGCCGTCA	62.409	66.667	0.00	0.00	35.54	4.35
2680	3189	4.385405	GACGTCCCTGCTGCAGCT	62.385	66.667	36.61	17.15	42.66	4.24
2738	3247	4.824515	CCGACCTCGCCCTCCTCT	62.825	72.222	0.00	0.00	38.18	3.69
2742	3251	2.363018	CCTCGCCCTCCTCTGTCA	60.363	66.667	0.00	0.00	0.00	3.58
2796	3305	4.335647	CAACGGGCCTGGTGCTCT	62.336	66.667	18.78	0.00	38.81	4.09
2856	3365	1.580059	AGTCCTCCTTCGCCCATTTA	58.420	50.000	0.00	0.00	0.00	1.40
2907	3416	3.575351	GACGTGCTCCGGCTTCACT	62.575	63.158	15.19	5.92	43.06	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	95	0.442699	GAAGGTTTTAGCAGCGTCCG	59.557	55.000	0.00	0.00	0.00	4.79
118	122	5.186021	ACAAGATAGTCCAACTCGAAGTGAT	59.814	40.000	0.00	0.00	0.00	3.06
153	158	3.181493	GCTCCTGTGTCCAAATAATGCAG	60.181	47.826	0.00	0.00	0.00	4.41
164	169	3.567478	AATCTTATGGCTCCTGTGTCC	57.433	47.619	0.00	0.00	0.00	4.02
269	274	9.884636	TTTCTAATGACTACTATGCTAAGCAAA	57.115	29.630	0.00	0.00	43.62	3.68
467	475	6.869913	TCGTATTGGATTCTTCACGTAAAGTT	59.130	34.615	0.00	0.00	0.00	2.66
565	724	2.324014	TACCCCAGCAGCAATAGCCG	62.324	60.000	0.00	0.00	43.56	5.52
867	1031	5.236263	TGCATTGGTGAGCTACGTATTTATG	59.764	40.000	0.00	0.00	0.00	1.90
927	1091	5.065988	CGCAAGGAAAATAAAGGCTAGCTAA	59.934	40.000	15.72	0.00	0.00	3.09
997	1161	1.583495	TTCCTCGACGTGCTCATCGT	61.583	55.000	4.08	0.66	44.27	3.73
1477	1660	9.346005	TGATGCATCAACTGATACAAGAAATAT	57.654	29.630	26.87	0.00	32.14	1.28
1478	1661	8.735692	TGATGCATCAACTGATACAAGAAATA	57.264	30.769	26.87	0.00	32.14	1.40
1479	1662	7.634671	TGATGCATCAACTGATACAAGAAAT	57.365	32.000	26.87	0.00	32.14	2.17
1480	1663	7.337436	TGATGATGCATCAACTGATACAAGAAA	59.663	33.333	31.79	7.23	46.17	2.52
1595	1874	5.009010	CCATATTAATTTCTGCCAAGTCGCT	59.991	40.000	0.00	0.00	0.00	4.93
1729	2178	8.767085	CGGAGTAATAAGAAAACTTAACACACA	58.233	33.333	0.00	0.00	0.00	3.72
1730	2179	7.743400	GCGGAGTAATAAGAAAACTTAACACAC	59.257	37.037	0.00	0.00	0.00	3.82
1757	2206	2.155732	CAGTTCCTGACACGTTTGATCG	59.844	50.000	0.00	0.00	32.44	3.69
2024	2474	1.944676	GTCGATGATGGACGACGGC	60.945	63.158	0.00	0.00	46.39	5.68
2075	2525	4.875536	ACGTTGTGCATGTGTATGTCATAT	59.124	37.500	0.00	0.00	36.65	1.78
2091	2549	6.200097	TGCATGCATACTTATACTACGTTGTG	59.800	38.462	18.46	0.00	0.00	3.33
2360	2835	2.856988	TTCTCCCCCAGGCCGTTT	60.857	61.111	0.00	0.00	0.00	3.60
2374	2849	0.179108	GCCAATCTAGCGACGGTTCT	60.179	55.000	4.26	0.00	0.00	3.01
2381	2856	2.443394	CCAGGGGCCAATCTAGCGA	61.443	63.158	4.39	0.00	0.00	4.93
2565	3058	1.650314	GCGGCGGCTAGGCTTTTTAA	61.650	55.000	15.11	0.00	44.22	1.52
2597	3097	0.533032	GCTTCTACAGGCTTCTCGGT	59.467	55.000	0.00	0.00	0.00	4.69
2724	3233	2.363147	GACAGAGGAGGGCGAGGT	60.363	66.667	0.00	0.00	0.00	3.85
2856	3365	2.963371	GACGACGAGTCTGGCCTT	59.037	61.111	3.32	0.00	46.13	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.