AutoCloner

Multiple sequence alignment - TraesCS1A01G220700

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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	TraesCS1A01G220700	chr1A	100.000	3664	0	0	1	3664	389822405	389818742	0.000000e+00	6767.0
1	TraesCS1A01G220700	chr1A	86.195	297	23	6	63	350	56982849	56983136	4.600000e-79	305.0
2	TraesCS1A01G220700	chr3A	94.176	2112	61	21	1	2080	128563667	128565748	0.000000e+00	3162.0
3	TraesCS1A01G220700	chr3A	96.976	1554	40	6	2082	3632	128565847	128567396	0.000000e+00	2603.0
4	TraesCS1A01G220700	chr1B	94.668	1519	66	8	565	2079	419984797	419986304	0.000000e+00	2342.0
5	TraesCS1A01G220700	chr1B	88.833	1594	110	29	2074	3664	419986336	419987864	0.000000e+00	1895.0
6	TraesCS1A01G220700	chr1B	82.079	558	31	24	16	553	419984208	419984716	2.630000e-111	412.0
7	TraesCS1A01G220700	chr1B	90.385	104	7	1	2092	2195	533757878	533757778	2.300000e-27	134.0
8	TraesCS1A01G220700	chr1B	88.462	104	6	3	2092	2195	640477641	640477544	1.790000e-23	121.0
9	TraesCS1A01G220700	chr1D	94.609	1521	64	10	565	2079	309973579	309972071	0.000000e+00	2338.0
10	TraesCS1A01G220700	chr1D	91.476	1619	97	23	2074	3664	309972039	309970434	0.000000e+00	2187.0
11	TraesCS1A01G220700	chr1D	83.554	529	22	20	63	553	309974149	309973648	5.620000e-118	435.0
12	TraesCS1A01G220700	chr4A	88.176	296	17	8	64	350	362910403	362910689	1.630000e-88	337.0
13	TraesCS1A01G220700	chr3B	86.869	297	21	5	63	350	727664742	727664455	2.120000e-82	316.0
14	TraesCS1A01G220700	chr3B	85.669	314	20	10	45	350	511678847	511679143	1.280000e-79	307.0
15	TraesCS1A01G220700	chr6A	86.532	297	22	8	63	350	214069018	214069305	9.880000e-81	311.0
16	TraesCS1A01G220700	chr2A	86.195	297	23	7	63	350	165942552	165942265	4.600000e-79	305.0
17	TraesCS1A01G220700	chr2D	87.097	93	4	1	63	147	633473431	633473523	8.370000e-17	99.0
18	TraesCS1A01G220700	chr2D	86.585	82	3	1	63	136	633467100	633467019	2.340000e-12	84.2
19	TraesCS1A01G220700	chr7D	100.000	28	0	0	323	350	41515296	41515323	7.000000e-03	52.8

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	TraesCS1A01G220700	chr1A	389818742	389822405	3663	True	6767.000000	6767	100.000000	1	3664	1	chr1A.!!$R1	3663
1	TraesCS1A01G220700	chr3A	128563667	128567396	3729	False	2882.500000	3162	95.576000	1	3632	2	chr3A.!!$F1	3631
2	TraesCS1A01G220700	chr1B	419984208	419987864	3656	False	1549.666667	2342	88.526667	16	3664	3	chr1B.!!$F1	3648
3	TraesCS1A01G220700	chr1D	309970434	309974149	3715	True	1653.333333	2338	89.879667	63	3664	3	chr1D.!!$R1	3601

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
953	1081	0.035630	CCACTGAGAAGAGCCAAGGG	60.036	60.0	0.00	0.00	0.00	3.95	F
2306	2553	0.257328	TTGGAGGTGCACTGTCCAAA	59.743	50.0	33.72	23.55	45.38	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2332	2579	4.032703	AGCATATGATGTTTGTTTCGGC	57.967	40.909	6.97	0.00	0.0	5.54	R
3250	3504	2.738743	TCATGGGCCAGAAATTTCCTC	58.261	47.619	13.78	4.24	0.0	3.71	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
127	140	3.467374	AGATCGAAGCAAAGGAGATCC	57.533	47.619	0.00	0.00	38.67	3.36
216	234	3.490526	CACCGCACCTGAAAATTGAAAAG	59.509	43.478	0.00	0.00	0.00	2.27
220	240	4.445385	CGCACCTGAAAATTGAAAAGGAAG	59.555	41.667	0.00	0.00	0.00	3.46
270	294	6.506500	AGCATGAGTAGAATTCAAACAAGG	57.493	37.500	8.44	1.97	0.00	3.61
272	296	6.491403	AGCATGAGTAGAATTCAAACAAGGTT	59.509	34.615	8.44	0.00	0.00	3.50
277	301	6.681777	AGTAGAATTCAAACAAGGTTGATGC	58.318	36.000	8.44	0.00	37.36	3.91
279	303	5.291971	AGAATTCAAACAAGGTTGATGCAC	58.708	37.500	8.44	0.00	37.36	4.57
280	304	4.942761	ATTCAAACAAGGTTGATGCACT	57.057	36.364	0.79	0.00	37.36	4.40
281	305	3.713858	TCAAACAAGGTTGATGCACTG	57.286	42.857	0.00	0.00	32.56	3.66
282	306	2.361757	TCAAACAAGGTTGATGCACTGG	59.638	45.455	0.00	0.00	32.56	4.00
283	307	2.361757	CAAACAAGGTTGATGCACTGGA	59.638	45.455	0.00	0.00	0.00	3.86
284	308	2.592102	ACAAGGTTGATGCACTGGAT	57.408	45.000	0.00	0.00	0.00	3.41
285	309	2.165167	ACAAGGTTGATGCACTGGATG	58.835	47.619	0.00	0.00	0.00	3.51
286	310	1.475280	CAAGGTTGATGCACTGGATGG	59.525	52.381	0.00	0.00	0.00	3.51
288	312	1.567649	AGGTTGATGCACTGGATGGAT	59.432	47.619	0.00	0.00	43.10	3.41
289	313	2.779430	AGGTTGATGCACTGGATGGATA	59.221	45.455	0.00	0.00	39.93	2.59
290	314	2.880890	GGTTGATGCACTGGATGGATAC	59.119	50.000	0.00	0.00	39.93	2.24
291	315	2.531522	TGATGCACTGGATGGATACG	57.468	50.000	0.00	0.00	39.93	3.06
292	316	1.070601	TGATGCACTGGATGGATACGG	59.929	52.381	0.00	0.00	39.93	4.02
293	317	0.250467	ATGCACTGGATGGATACGGC	60.250	55.000	0.00	0.00	37.65	5.68
294	318	1.956170	GCACTGGATGGATACGGCG	60.956	63.158	4.80	4.80	42.51	6.46
295	319	1.956170	CACTGGATGGATACGGCGC	60.956	63.158	6.90	0.00	42.51	6.53
296	320	2.421314	CTGGATGGATACGGCGCA	59.579	61.111	10.83	0.00	42.51	6.09
297	321	1.956170	CTGGATGGATACGGCGCAC	60.956	63.158	10.83	0.00	42.51	5.34
474	531	1.605451	CCGGGAAAACAGGGGGTTC	60.605	63.158	0.00	0.00	39.29	3.62
948	1076	0.398318	ACCAACCACTGAGAAGAGCC	59.602	55.000	0.00	0.00	0.00	4.70
953	1081	0.035630	CCACTGAGAAGAGCCAAGGG	60.036	60.000	0.00	0.00	0.00	3.95
1122	1256	0.755698	TCGAGCCCATGGAGTACCTC	60.756	60.000	15.22	9.42	37.04	3.85
1187	1321	0.459411	GTCGGAGGCAAGAAGAGCTC	60.459	60.000	5.27	5.27	0.00	4.09
1297	1431	0.450583	CGTAAGCGAGCAGTCCACTA	59.549	55.000	0.00	0.00	41.33	2.74
1330	1466	2.223782	CCATCCTTTCTCTGCTCTCTCG	60.224	54.545	0.00	0.00	0.00	4.04
1348	1484	6.697395	TCTCTCGTTTCTGAATGTTTCCATA	58.303	36.000	0.00	0.00	0.00	2.74
1373	1509	0.677731	TCTGGCCATTTTCGAGCAGG	60.678	55.000	5.51	0.00	0.00	4.85
1390	1526	1.823041	GGCAGATGCAAGGAGGAGC	60.823	63.158	7.19	0.00	44.36	4.70
1456	1592	4.717629	CACAAGGACGCGAGCCGA	62.718	66.667	15.93	0.00	41.02	5.54
1519	1655	2.977456	GTGCACGCCATGGTGTCA	60.977	61.111	28.06	23.22	40.08	3.58
1532	1668	3.220658	TGTCAGTGGTCCGCGTCA	61.221	61.111	4.92	0.00	0.00	4.35
2042	2188	1.538512	GTACAGACTACACAGCCGTGA	59.461	52.381	7.16	0.00	46.80	4.35
2079	2225	7.830697	ACATTCAGTCATGGATCAACATCTTTA	59.169	33.333	0.00	0.00	0.00	1.85
2080	2226	8.847196	CATTCAGTCATGGATCAACATCTTTAT	58.153	33.333	0.00	0.00	0.00	1.40
2142	2384	7.482169	AAGTATCTGTCTACATCAACAGGAA	57.518	36.000	2.96	0.00	42.52	3.36
2146	2388	4.220821	TCTGTCTACATCAACAGGAAGTCC	59.779	45.833	2.96	0.00	42.52	3.85
2306	2553	0.257328	TTGGAGGTGCACTGTCCAAA	59.743	50.000	33.72	23.55	45.38	3.28
2332	2579	3.397482	ACAAGAGTAAGTTCAGCAGCAG	58.603	45.455	0.00	0.00	0.00	4.24
2591	2838	1.374125	CTGGGTCGACGATGTGCAA	60.374	57.895	9.92	0.00	0.00	4.08
2669	2916	4.853924	AGTGAAAATGGGTTGATGTGTC	57.146	40.909	0.00	0.00	0.00	3.67
2693	2941	1.149627	TTTTCCCGGTGTGAGGTGG	59.850	57.895	0.00	0.00	0.00	4.61
2949	3202	0.331278	TGTATCCTGTGGGGGCAAAG	59.669	55.000	0.00	0.00	35.33	2.77
2982	3235	9.660180	CTAGTTAGCTTAGTTTTCTCTTCCATT	57.340	33.333	0.00	0.00	0.00	3.16
3250	3504	4.331992	CACTTGGAGCTACATCTGACAATG	59.668	45.833	0.00	0.00	0.00	2.82
3307	3561	4.534500	TCATGGTGACCCAACTAACTGTAT	59.466	41.667	0.00	0.00	46.04	2.29
3318	3572	6.659242	CCCAACTAACTGTATGTCCTTTCAAT	59.341	38.462	0.00	0.00	0.00	2.57
3661	3927	2.876945	CGAGGCCAGGGGATAGCTG	61.877	68.421	5.01	0.00	0.00	4.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
127	140	0.660595	GTACGTGAGGGCGATCGATG	60.661	60.000	21.57	5.29	35.59	3.84
216	234	1.271054	TGGCTCTCTGTTTCTGCTTCC	60.271	52.381	0.00	0.00	0.00	3.46
220	240	1.274728	TCTCTGGCTCTCTGTTTCTGC	59.725	52.381	0.00	0.00	0.00	4.26
270	294	2.545526	CGTATCCATCCAGTGCATCAAC	59.454	50.000	0.00	0.00	0.00	3.18
272	296	1.070601	CCGTATCCATCCAGTGCATCA	59.929	52.381	0.00	0.00	0.00	3.07
277	301	1.956170	GCGCCGTATCCATCCAGTG	60.956	63.158	0.00	0.00	0.00	3.66
279	303	1.956170	GTGCGCCGTATCCATCCAG	60.956	63.158	4.18	0.00	0.00	3.86
280	304	2.108157	GTGCGCCGTATCCATCCA	59.892	61.111	4.18	0.00	0.00	3.41
281	305	3.036084	CGTGCGCCGTATCCATCC	61.036	66.667	4.18	0.00	0.00	3.51
282	306	3.702555	GCGTGCGCCGTATCCATC	61.703	66.667	17.38	0.00	39.32	3.51
283	307	4.522689	TGCGTGCGCCGTATCCAT	62.523	61.111	14.16	0.00	41.09	3.41
296	320	4.269523	TTGGGCTCTTGGCTGCGT	62.270	61.111	0.00	0.00	41.46	5.24
297	321	3.437795	CTTGGGCTCTTGGCTGCG	61.438	66.667	0.00	0.00	41.46	5.18
298	322	2.034687	TCTTGGGCTCTTGGCTGC	59.965	61.111	0.00	0.00	41.46	5.25
299	323	1.676967	GGTCTTGGGCTCTTGGCTG	60.677	63.158	0.00	0.00	41.46	4.85
300	324	2.759795	GGTCTTGGGCTCTTGGCT	59.240	61.111	0.00	0.00	41.46	4.75
301	325	2.543067	ATCGGTCTTGGGCTCTTGGC	62.543	60.000	0.00	0.00	40.90	4.52
302	326	0.745845	CATCGGTCTTGGGCTCTTGG	60.746	60.000	0.00	0.00	0.00	3.61
303	327	0.250234	TCATCGGTCTTGGGCTCTTG	59.750	55.000	0.00	0.00	0.00	3.02
304	328	0.984230	TTCATCGGTCTTGGGCTCTT	59.016	50.000	0.00	0.00	0.00	2.85
305	329	0.539051	CTTCATCGGTCTTGGGCTCT	59.461	55.000	0.00	0.00	0.00	4.09
306	330	1.092345	GCTTCATCGGTCTTGGGCTC	61.092	60.000	0.00	0.00	0.00	4.70
307	331	1.078143	GCTTCATCGGTCTTGGGCT	60.078	57.895	0.00	0.00	0.00	5.19
308	332	1.372087	CTGCTTCATCGGTCTTGGGC	61.372	60.000	0.00	0.00	0.00	5.36
474	531	0.942962	GATGCGATGCTTCCAAGAGG	59.057	55.000	0.00	0.00	0.00	3.69
891	1019	1.605710	GACGGTCGCCTACTTATAGCA	59.394	52.381	0.00	0.00	0.00	3.49
948	1076	0.107017	CCAGTGCACTATCCCCCTTG	60.107	60.000	21.20	4.38	0.00	3.61
987	1115	1.074775	GGCCATCAGTCCCACACAA	59.925	57.895	0.00	0.00	0.00	3.33
1122	1256	2.752238	ACGCTCCAGGACCTCGAG	60.752	66.667	11.54	11.54	0.00	4.04
1264	1398	1.468565	GCTTACGTGGTGTCGATAGCA	60.469	52.381	10.18	10.18	38.96	3.49
1297	1431	0.178861	AAGGATGGGAGTGAGTGGGT	60.179	55.000	0.00	0.00	0.00	4.51
1348	1484	2.489329	CTCGAAAATGGCCAGACAACAT	59.511	45.455	13.05	0.00	0.00	2.71
1373	1509	0.814812	GAGCTCCTCCTTGCATCTGC	60.815	60.000	0.87	0.00	42.50	4.26
1390	1526	2.028190	CCGGTAGCGCTGATGGAG	59.972	66.667	22.90	5.18	0.00	3.86
1401	1537	1.144057	GACTGATGGTGGCCGGTAG	59.856	63.158	1.90	0.00	0.00	3.18
1402	1538	2.363975	GGACTGATGGTGGCCGGTA	61.364	63.158	1.90	0.00	0.00	4.02
1404	1540	2.947938	GATGGACTGATGGTGGCCGG	62.948	65.000	0.00	0.00	0.00	6.13
1456	1592	1.153409	CTTGCTGCTCTGCCTCGAT	60.153	57.895	0.00	0.00	0.00	3.59
2042	2188	8.812513	TCCATGACTGAATGTTCTGAATATTT	57.187	30.769	12.68	0.00	0.00	1.40
2161	2403	7.458409	AATTTGATATTGTGCAGTCAGAGTT	57.542	32.000	0.00	0.00	0.00	3.01
2162	2404	8.743085	ATAATTTGATATTGTGCAGTCAGAGT	57.257	30.769	0.00	0.00	0.00	3.24
2306	2553	5.449177	GCTGCTGAACTTACTCTTGTTGTTT	60.449	40.000	0.00	0.00	0.00	2.83
2332	2579	4.032703	AGCATATGATGTTTGTTTCGGC	57.967	40.909	6.97	0.00	0.00	5.54
2963	3216	5.392487	GCTGGAATGGAAGAGAAAACTAAGC	60.392	44.000	0.00	0.00	0.00	3.09
2964	3217	5.707298	TGCTGGAATGGAAGAGAAAACTAAG	59.293	40.000	0.00	0.00	0.00	2.18
2982	3235	2.358957	GTGCACATGTAGAATGCTGGA	58.641	47.619	13.17	0.00	40.13	3.86
3250	3504	2.738743	TCATGGGCCAGAAATTTCCTC	58.261	47.619	13.78	4.24	0.00	3.71
3300	3554	5.079643	AGCCAATTGAAAGGACATACAGTT	58.920	37.500	7.12	0.00	0.00	3.16
3307	3561	4.661222	TGTCATAGCCAATTGAAAGGACA	58.339	39.130	7.12	11.70	0.00	4.02
3318	3572	3.221771	ACAACAGCTTTGTCATAGCCAA	58.778	40.909	11.19	0.00	39.47	4.52
3548	3814	3.874807	TTGCTTGCGCGCCTAGACA	62.875	57.895	30.77	21.91	39.65	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.