AutoCloner

Multiple sequence alignment - TraesCS6B01G120000

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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	TraesCS6B01G120000	chr6B	100.000	2638	0	0	1	2638	114879189	114881826	0.000000e+00	4872
1	TraesCS6B01G120000	chr6B	95.539	2645	103	7	1	2638	115059657	115062293	0.000000e+00	4217
2	TraesCS6B01G120000	chr6B	93.769	1637	86	3	761	2397	115525099	115526719	0.000000e+00	2444
3	TraesCS6B01G120000	chr6B	93.959	1407	83	2	1232	2638	115022557	115023961	0.000000e+00	2126
4	TraesCS6B01G120000	chr6B	93.908	476	28	1	761	1236	115013080	115013554	0.000000e+00	717
5	TraesCS6B01G120000	chr6B	86.738	656	69	9	2	641	115524419	115525072	0.000000e+00	713
6	TraesCS6B01G120000	chr6B	87.627	493	56	5	152	641	115012563	115013053	3.810000e-158	568
7	TraesCS6B01G120000	chr6B	84.306	497	58	13	1	480	115057827	115058320	3.980000e-128	468
8	TraesCS6B01G120000	chr6B	92.623	244	17	1	2395	2638	115535372	115535614	1.500000e-92	350
9	TraesCS6B01G120000	chr6B	72.713	623	126	34	1755	2345	71356563	71355953	4.520000e-38	169
10	TraesCS6B01G120000	chr6B	71.981	621	134	25	1755	2345	71496008	71495398	2.120000e-31	147
11	TraesCS6B01G120000	chr6D	94.572	1879	100	2	761	2638	46443079	46444956	0.000000e+00	2904
12	TraesCS6B01G120000	chr6D	82.625	1318	207	15	1096	2409	46778330	46779629	0.000000e+00	1146
13	TraesCS6B01G120000	chr6D	87.062	657	67	9	1	641	46442398	46443052	0.000000e+00	726
14	TraesCS6B01G120000	chr6D	78.910	422	67	19	642	1047	46777791	46778206	1.560000e-67	267
15	TraesCS6B01G120000	chr6D	75.414	362	76	12	1991	2345	10441397	10441752	2.100000e-36	163
16	TraesCS6B01G120000	chr3D	81.058	1531	257	23	1111	2617	567412542	567411021	0.000000e+00	1190
17	TraesCS6B01G120000	chr3D	81.040	1519	261	13	1120	2617	569895117	569896629	0.000000e+00	1184
18	TraesCS6B01G120000	chr3D	79.143	350	51	18	1	332	537598402	537598747	3.420000e-54	222
19	TraesCS6B01G120000	chr3A	80.342	234	29	11	735	953	702517995	702518226	7.560000e-36	161
20	TraesCS6B01G120000	chr4B	82.249	169	26	2	1214	1380	667677860	667678026	2.740000e-30	143

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	TraesCS6B01G120000	chr6B	114879189	114881826	2637	False	4872.0	4872	100.0000	1	2638	1	chr6B.!!$F1	2637
1	TraesCS6B01G120000	chr6B	115057827	115062293	4466	False	2342.5	4217	89.9225	1	2638	2	chr6B.!!$F5	2637
2	TraesCS6B01G120000	chr6B	115022557	115023961	1404	False	2126.0	2126	93.9590	1232	2638	1	chr6B.!!$F2	1406
3	TraesCS6B01G120000	chr6B	115524419	115526719	2300	False	1578.5	2444	90.2535	2	2397	2	chr6B.!!$F6	2395
4	TraesCS6B01G120000	chr6B	115012563	115013554	991	False	642.5	717	90.7675	152	1236	2	chr6B.!!$F4	1084
5	TraesCS6B01G120000	chr6D	46442398	46444956	2558	False	1815.0	2904	90.8170	1	2638	2	chr6D.!!$F2	2637
6	TraesCS6B01G120000	chr6D	46777791	46779629	1838	False	706.5	1146	80.7675	642	2409	2	chr6D.!!$F3	1767
7	TraesCS6B01G120000	chr3D	567411021	567412542	1521	True	1190.0	1190	81.0580	1111	2617	1	chr3D.!!$R1	1506
8	TraesCS6B01G120000	chr3D	569895117	569896629	1512	False	1184.0	1184	81.0400	1120	2617	1	chr3D.!!$F2	1497

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
250	266	0.104462	CCTACTCCATCCCCCATCCA	60.104	60.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2180	4169	1.273606	CCCACATAGACTAGGCATCGG	59.726	57.143	0.0	0.0	0.0	4.18	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
40	41	1.368374	CCTCTTTGAACCTACCCCCA	58.632	55.000	0.00	0.00	0.00	4.96
41	42	1.923148	CCTCTTTGAACCTACCCCCAT	59.077	52.381	0.00	0.00	0.00	4.00
43	44	3.621558	CTCTTTGAACCTACCCCCATTC	58.378	50.000	0.00	0.00	0.00	2.67
45	46	1.761711	TTGAACCTACCCCCATTCCA	58.238	50.000	0.00	0.00	0.00	3.53
74	75	0.178975	TTACCCACCTTTGCCACTGG	60.179	55.000	0.00	0.00	0.00	4.00
112	113	3.612251	GGACCGATCCGAGGAACA	58.388	61.111	0.00	0.00	34.48	3.18
116	131	0.611062	ACCGATCCGAGGAACACTCA	60.611	55.000	0.00	0.00	46.98	3.41
128	143	2.608261	GGAACACTCACCTCTTGTCTCG	60.608	54.545	0.00	0.00	0.00	4.04
137	152	2.237643	ACCTCTTGTCTCGCTCTCTCTA	59.762	50.000	0.00	0.00	0.00	2.43
140	155	2.013400	CTTGTCTCGCTCTCTCTAGCA	58.987	52.381	0.00	0.00	42.91	3.49
196	212	3.322466	CGCCCAGGTCCCTTGTCT	61.322	66.667	0.00	0.00	0.00	3.41
198	214	2.224159	GCCCAGGTCCCTTGTCTCA	61.224	63.158	0.00	0.00	0.00	3.27
234	250	2.448542	GCCTCCAGCCCCATCCTA	60.449	66.667	0.00	0.00	34.35	2.94
239	255	1.384502	CCAGCCCCATCCTACTCCA	60.385	63.158	0.00	0.00	0.00	3.86
250	266	0.104462	CCTACTCCATCCCCCATCCA	60.104	60.000	0.00	0.00	0.00	3.41
254	270	3.889692	CCATCCCCCATCCACCCG	61.890	72.222	0.00	0.00	0.00	5.28
259	275	2.746375	CCCCCATCCACCCGAAGAG	61.746	68.421	0.00	0.00	0.00	2.85
321	337	1.757118	CGCTACAAATCAGGGGAGAGA	59.243	52.381	0.00	0.00	0.00	3.10
332	348	2.593956	GGGAGAGAACCACCGGCTT	61.594	63.158	0.00	0.00	0.00	4.35
338	354	4.204028	AACCACCGGCTTGCCACT	62.204	61.111	12.45	0.00	0.00	4.00
340	356	2.137177	AACCACCGGCTTGCCACTAT	62.137	55.000	12.45	0.00	0.00	2.12
347	363	0.249911	GGCTTGCCACTATAGTCGGG	60.250	60.000	17.67	12.27	0.00	5.14
348	364	0.750850	GCTTGCCACTATAGTCGGGA	59.249	55.000	12.38	11.20	0.00	5.14
354	370	1.478837	CCACTATAGTCGGGAGCCTCA	60.479	57.143	1.26	0.00	0.00	3.86
382	398	0.752009	ATCTGCCGGACGAGCTTCTA	60.752	55.000	5.05	0.00	0.00	2.10
395	411	0.824759	GCTTCTACACCCATCCGAGT	59.175	55.000	0.00	0.00	0.00	4.18
416	432	4.408821	CCCACCGCAAGCTAGCCA	62.409	66.667	12.13	0.00	0.00	4.75
507	2342	6.471233	TGTCTTGCTAGCATGTCTTAGTAT	57.529	37.500	25.00	0.00	0.00	2.12
663	2498	5.102953	ACTTTACATGATTAGCAGGCTGA	57.897	39.130	20.86	0.00	0.00	4.26
730	2565	7.401246	AGATCTCAGCTCTCCACTTAATTTTT	58.599	34.615	0.00	0.00	0.00	1.94
809	2654	2.678934	CCTCTCCGTCCCCGACAA	60.679	66.667	0.00	0.00	35.63	3.18
875	2723	9.898576	TCTCCTCCATCTCCTAGAAATAATTTA	57.101	33.333	0.00	0.00	0.00	1.40
974	2844	4.787280	AGGGAGGAGAGCGGGTGG	62.787	72.222	0.00	0.00	0.00	4.61
1226	3196	1.079819	CGTGTCCAAGGTGCTCGAT	60.080	57.895	0.00	0.00	0.00	3.59
1247	3217	5.923114	CGATGACGATAACCTTCTCATTGAT	59.077	40.000	0.00	0.00	42.66	2.57
1315	3285	2.907634	TGTCTGCAAACGTTGGTTCTA	58.092	42.857	0.00	0.00	34.62	2.10
1534	3522	6.016213	TGACATCATCTTCACCAAAACATG	57.984	37.500	0.00	0.00	0.00	3.21
1547	3535	5.349817	CACCAAAACATGTAACAACTGCAAA	59.650	36.000	0.00	0.00	0.00	3.68
1635	3623	1.349026	CTCCATTCCCATGCTACGGAT	59.651	52.381	0.00	0.00	0.00	4.18
1637	3625	1.072173	CCATTCCCATGCTACGGATGA	59.928	52.381	0.00	0.00	0.00	2.92
1660	3648	4.708421	ACAGGACGGCTATTTCTACAAGTA	59.292	41.667	0.00	0.00	0.00	2.24
1686	3674	8.365647	ACTGTAAACTCCTATTCGAAGAAGAAA	58.634	33.333	3.35	0.00	45.90	2.52
1997	3985	5.012664	ACGGGCATATGATAATTCTGGTGTA	59.987	40.000	6.97	0.00	0.00	2.90
2180	4169	4.948847	AGTTTGTTTTCTTGAAGATGGGC	58.051	39.130	0.00	0.00	0.00	5.36
2298	4287	0.179034	GATGATCTGGCCTCCCACAC	60.179	60.000	3.32	0.00	35.79	3.82
2531	4521	2.551459	GTTTGCTGCTGAACTGTGATCT	59.449	45.455	0.00	0.00	0.00	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.679837	CAAAGAGGCACGCATCATAAGT	59.320	45.455	6.45	0.00	0.00	2.24
11	12	1.470098	GTTCAAAGAGGCACGCATCAT	59.530	47.619	6.45	0.00	0.00	2.45
14	15	0.250901	AGGTTCAAAGAGGCACGCAT	60.251	50.000	0.00	0.00	0.00	4.73
61	62	4.850193	CCATCCAGTGGCAAAGGT	57.150	55.556	3.51	0.00	42.12	3.50
88	89	2.520982	CGGATCGGTCCTGGCCTA	60.521	66.667	14.05	0.00	42.73	3.93
106	107	2.630580	GAGACAAGAGGTGAGTGTTCCT	59.369	50.000	0.00	0.00	36.70	3.36
109	110	1.269831	GCGAGACAAGAGGTGAGTGTT	60.270	52.381	0.00	0.00	0.00	3.32
112	113	0.885196	GAGCGAGACAAGAGGTGAGT	59.115	55.000	0.00	0.00	0.00	3.41
116	131	1.004277	AGAGAGAGCGAGACAAGAGGT	59.996	52.381	0.00	0.00	0.00	3.85
128	143	4.376146	CAACCCTAATTGCTAGAGAGAGC	58.624	47.826	0.00	0.00	43.16	4.09
181	197	1.986413	CTGAGACAAGGGACCTGGG	59.014	63.158	0.00	0.00	0.00	4.45
184	200	2.286523	CGGCTGAGACAAGGGACCT	61.287	63.158	0.00	0.00	0.00	3.85
224	240	1.492993	GGGATGGAGTAGGATGGGGC	61.493	65.000	0.00	0.00	0.00	5.80
234	250	1.697754	GGTGGATGGGGGATGGAGT	60.698	63.158	0.00	0.00	0.00	3.85
239	255	2.043772	TTCGGGTGGATGGGGGAT	59.956	61.111	0.00	0.00	0.00	3.85
254	270	1.813192	CGGAGTGGAGAGCCTCTTC	59.187	63.158	0.00	0.00	38.10	2.87
283	299	2.282745	GCAGGGGCAGCAGAAGTT	60.283	61.111	0.00	0.00	40.72	2.66
305	321	2.040412	GTGGTTCTCTCCCCTGATTTGT	59.960	50.000	0.00	0.00	0.00	2.83
321	337	2.137177	ATAGTGGCAAGCCGGTGGTT	62.137	55.000	1.90	0.00	39.42	3.67
332	348	1.113517	GGCTCCCGACTATAGTGGCA	61.114	60.000	10.90	0.00	0.00	4.92
338	354	2.526432	GGATTGAGGCTCCCGACTATA	58.474	52.381	12.86	0.00	0.00	1.31
340	356	0.759436	GGGATTGAGGCTCCCGACTA	60.759	60.000	12.86	0.00	42.94	2.59
366	382	1.974875	TGTAGAAGCTCGTCCGGCA	60.975	57.895	0.00	0.00	0.00	5.69
368	384	1.139095	GGTGTAGAAGCTCGTCCGG	59.861	63.158	0.00	0.00	0.00	5.14
382	398	2.351276	GGCAACTCGGATGGGTGT	59.649	61.111	0.00	0.00	0.00	4.16
415	431	6.867662	AAACATTCAGAAGTACCTTCAGTG	57.132	37.500	6.74	0.00	42.37	3.66
416	432	7.990886	TGTAAAACATTCAGAAGTACCTTCAGT	59.009	33.333	6.74	0.00	42.37	3.41
472	490	6.514947	TGCTAGCAAGACAACAATTTTGAAT	58.485	32.000	16.84	0.00	0.00	2.57
507	2342	9.439461	AGCTATCAATGGCCTCATATAGTAATA	57.561	33.333	3.32	0.00	34.49	0.98
663	2498	1.887198	CTGAGGACCAGTACGAGTGTT	59.113	52.381	0.00	0.00	38.10	3.32
730	2565	2.554142	CGCTGTTATGCTGGAGATTGA	58.446	47.619	0.00	0.00	0.00	2.57
809	2654	5.640147	TCCTGACCTCAAATATTTGGTTGT	58.360	37.500	24.40	18.69	38.66	3.32
974	2844	6.657541	CACCTATCTACCTCCTCTTATCTCAC	59.342	46.154	0.00	0.00	0.00	3.51
1063	2933	6.978674	TCACAAAGTTAAGGAGAGAGAAGA	57.021	37.500	0.00	0.00	0.00	2.87
1226	3196	7.233553	AGGATATCAATGAGAAGGTTATCGTCA	59.766	37.037	4.83	0.00	0.00	4.35
1247	3217	3.308976	GGTAGCCGATTAGGAGGAGGATA	60.309	52.174	0.00	0.00	45.00	2.59
1315	3285	1.530771	GCAGGGTCAGAGGCATGAT	59.469	57.895	0.00	0.00	0.00	2.45
1534	3522	4.607955	GGGTTCTTCTTTGCAGTTGTTAC	58.392	43.478	0.00	0.00	0.00	2.50
1547	3535	6.688073	ATATGTATTGATCCGGGTTCTTCT	57.312	37.500	0.00	0.00	0.00	2.85
1635	3623	3.093814	TGTAGAAATAGCCGTCCTGTCA	58.906	45.455	0.00	0.00	0.00	3.58
1637	3625	3.514309	ACTTGTAGAAATAGCCGTCCTGT	59.486	43.478	0.00	0.00	0.00	4.00
1660	3648	7.463961	TCTTCTTCGAATAGGAGTTTACAGT	57.536	36.000	0.00	0.00	0.00	3.55
1704	3692	1.961277	GTTCACCCCGCACACAGAG	60.961	63.158	0.00	0.00	0.00	3.35
1748	3736	6.582437	TCTTGCAACATATACACATACACG	57.418	37.500	0.00	0.00	0.00	4.49
1876	3864	4.008074	TCCAACACAAGAGATTCACTCC	57.992	45.455	0.00	0.00	45.96	3.85
1884	3872	3.565482	GCTGTCAAATCCAACACAAGAGA	59.435	43.478	0.00	0.00	0.00	3.10
1885	3873	3.304928	GGCTGTCAAATCCAACACAAGAG	60.305	47.826	0.00	0.00	0.00	2.85
1970	3958	5.188434	CCAGAATTATCATATGCCCGTGAT	58.812	41.667	0.00	0.00	38.53	3.06
1997	3985	5.380043	AGCCCGTTCAAATGAATGAGATAT	58.620	37.500	15.24	0.00	42.18	1.63
2180	4169	1.273606	CCCACATAGACTAGGCATCGG	59.726	57.143	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.