AutoCloner

Multiple sequence alignment - TraesCS7B01G173300

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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	TraesCS7B01G173300	chr7B	100.000	2330	0	0	1	2330	244718535	244716206	0.000000e+00	4303.0
1	TraesCS7B01G173300	chr7B	96.980	1523	31	6	809	2330	244694240	244692732	0.000000e+00	2543.0
2	TraesCS7B01G173300	chr7B	96.726	1527	45	4	807	2329	244646456	244644931	0.000000e+00	2538.0
3	TraesCS7B01G173300	chr7B	95.500	1200	54	0	809	2008	244652842	244651643	0.000000e+00	1917.0
4	TraesCS7B01G173300	chr7B	79.372	223	30	12	2081	2297	244651628	244651416	2.410000e-30	143.0
5	TraesCS7B01G173300	chr7B	84.466	103	13	3	132	234	114411661	114411760	5.300000e-17	99.0
6	TraesCS7B01G173300	chr7D	98.120	1862	34	1	470	2330	264372456	264370595	0.000000e+00	3243.0
7	TraesCS7B01G173300	chr7D	97.380	1527	35	3	809	2330	264362248	264360722	0.000000e+00	2593.0
8	TraesCS7B01G173300	chr7D	95.983	1444	55	3	812	2254	264340179	264338738	0.000000e+00	2342.0
9	TraesCS7B01G173300	chr7D	92.885	1518	87	17	809	2315	264327409	264325902	0.000000e+00	2185.0
10	TraesCS7B01G173300	chr7D	96.450	338	11	1	1	337	264376715	264376378	7.270000e-155	556.0
11	TraesCS7B01G173300	chr7D	95.833	144	5	1	341	483	264376413	264376270	5.010000e-57	231.0
12	TraesCS7B01G173300	chr7A	92.072	1501	93	23	809	2287	287890975	287889479	0.000000e+00	2089.0
13	TraesCS7B01G173300	chr7A	95.143	700	32	2	806	1504	287863347	287862649	0.000000e+00	1103.0
14	TraesCS7B01G173300	chr1D	89.423	104	6	4	133	235	19304454	19304553	2.430000e-25	126.0
15	TraesCS7B01G173300	chr4B	87.379	103	7	4	132	234	534405914	534405818	1.890000e-21	113.0
16	TraesCS7B01G173300	chr3A	86.364	88	8	4	154	240	705229915	705229831	2.470000e-15	93.5
17	TraesCS7B01G173300	chr3A	87.654	81	8	2	154	234	713220919	713220997	2.470000e-15	93.5
18	TraesCS7B01G173300	chr6A	83.673	98	13	3	133	230	524309624	524309530	3.190000e-14	89.8
19	TraesCS7B01G173300	chrUn	87.013	77	9	1	158	234	124835823	124835898	4.130000e-13	86.1
20	TraesCS7B01G173300	chr1A	85.915	71	5	4	153	222	373822514	373822448	1.160000e-08	71.3

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	TraesCS7B01G173300	chr7B	244716206	244718535	2329	True	4303.000000	4303	100.000	1	2330	1	chr7B.!!$R3	2329
1	TraesCS7B01G173300	chr7B	244692732	244694240	1508	True	2543.000000	2543	96.980	809	2330	1	chr7B.!!$R2	1521
2	TraesCS7B01G173300	chr7B	244644931	244646456	1525	True	2538.000000	2538	96.726	807	2329	1	chr7B.!!$R1	1522
3	TraesCS7B01G173300	chr7B	244651416	244652842	1426	True	1030.000000	1917	87.436	809	2297	2	chr7B.!!$R4	1488
4	TraesCS7B01G173300	chr7D	264360722	264362248	1526	True	2593.000000	2593	97.380	809	2330	1	chr7D.!!$R3	1521
5	TraesCS7B01G173300	chr7D	264338738	264340179	1441	True	2342.000000	2342	95.983	812	2254	1	chr7D.!!$R2	1442
6	TraesCS7B01G173300	chr7D	264325902	264327409	1507	True	2185.000000	2185	92.885	809	2315	1	chr7D.!!$R1	1506
7	TraesCS7B01G173300	chr7D	264370595	264376715	6120	True	1343.333333	3243	96.801	1	2330	3	chr7D.!!$R4	2329
8	TraesCS7B01G173300	chr7A	287889479	287890975	1496	True	2089.000000	2089	92.072	809	2287	1	chr7A.!!$R2	1478
9	TraesCS7B01G173300	chr7A	287862649	287863347	698	True	1103.000000	1103	95.143	806	1504	1	chr7A.!!$R1	698

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
974	4806	0.244994	ACGGTGCAAGAGTAGCAGAG	59.755	55.0	0.0	0.0	43.63	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2160	6019	1.331214	CAACACTCCAAGTTGGCCAT	58.669	50.0	17.68	1.74	41.92	4.4	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
49	50	5.106555	ACACATAGCATGCTTTCTACACAAC	60.107	40.000	28.02	0.00	0.00	3.32
117	118	8.034313	TGGAGTTATGATTCTATAGCCTTTGT	57.966	34.615	0.00	0.00	0.00	2.83
191	193	5.876651	ATGTAGCATCAAGAGGATACACA	57.123	39.130	13.92	0.00	44.78	3.72
270	272	7.229506	CCAAGATTACAGTTTTCCTTCTGAAGT	59.770	37.037	15.72	0.00	33.63	3.01
274	276	5.819825	ACAGTTTTCCTTCTGAAGTTGTC	57.180	39.130	15.72	3.44	33.63	3.18
286	288	7.095439	CCTTCTGAAGTTGTCTTAAAGCTACAG	60.095	40.741	15.72	0.00	33.64	2.74
287	289	6.817184	TCTGAAGTTGTCTTAAAGCTACAGT	58.183	36.000	0.00	0.00	33.64	3.55
317	319	6.418819	CAGTGGAAAAGTTGATTTAGTGCAAG	59.581	38.462	0.00	0.00	0.00	4.01
338	340	3.661944	GGATATGTCCAGACTCTGCATG	58.338	50.000	3.16	0.00	44.42	4.06
339	341	3.556633	GGATATGTCCAGACTCTGCATGG	60.557	52.174	3.16	0.00	44.42	3.66
340	342	1.576577	ATGTCCAGACTCTGCATGGA	58.423	50.000	1.73	1.73	40.80	3.41
341	343	0.900421	TGTCCAGACTCTGCATGGAG	59.100	55.000	8.12	8.12	43.61	3.86
343	345	1.277557	GTCCAGACTCTGCATGGAGTT	59.722	52.381	14.43	2.40	45.32	3.01
344	346	1.277273	TCCAGACTCTGCATGGAGTTG	59.723	52.381	14.43	10.70	45.32	3.16
345	347	1.277273	CCAGACTCTGCATGGAGTTGA	59.723	52.381	14.43	0.00	45.32	3.18
346	348	2.093075	CCAGACTCTGCATGGAGTTGAT	60.093	50.000	14.43	0.00	45.32	2.57
347	349	3.607741	CAGACTCTGCATGGAGTTGATT	58.392	45.455	14.43	0.00	45.32	2.57
348	350	4.008330	CAGACTCTGCATGGAGTTGATTT	58.992	43.478	14.43	0.00	45.32	2.17
349	351	5.181009	CAGACTCTGCATGGAGTTGATTTA	58.819	41.667	14.43	0.00	45.32	1.40
350	352	5.293814	CAGACTCTGCATGGAGTTGATTTAG	59.706	44.000	14.43	4.79	45.32	1.85
351	353	5.046014	AGACTCTGCATGGAGTTGATTTAGT	60.046	40.000	14.43	8.08	45.32	2.24
352	354	4.940046	ACTCTGCATGGAGTTGATTTAGTG	59.060	41.667	14.43	0.00	43.14	2.74
353	355	3.691118	TCTGCATGGAGTTGATTTAGTGC	59.309	43.478	14.43	0.00	0.00	4.40
354	356	3.419943	TGCATGGAGTTGATTTAGTGCA	58.580	40.909	0.00	0.00	38.83	4.57
355	357	3.825585	TGCATGGAGTTGATTTAGTGCAA	59.174	39.130	0.00	0.00	38.27	4.08
356	358	4.082625	TGCATGGAGTTGATTTAGTGCAAG	60.083	41.667	0.00	0.00	38.27	4.01
357	359	4.676196	GCATGGAGTTGATTTAGTGCAAGG	60.676	45.833	0.00	0.00	0.00	3.61
358	360	4.365514	TGGAGTTGATTTAGTGCAAGGA	57.634	40.909	0.00	0.00	0.00	3.36
359	361	4.922206	TGGAGTTGATTTAGTGCAAGGAT	58.078	39.130	0.00	0.00	0.00	3.24
360	362	4.701651	TGGAGTTGATTTAGTGCAAGGATG	59.298	41.667	0.00	0.00	0.00	3.51
361	363	4.702131	GGAGTTGATTTAGTGCAAGGATGT	59.298	41.667	0.00	0.00	0.00	3.06
362	364	5.392380	GGAGTTGATTTAGTGCAAGGATGTG	60.392	44.000	0.00	0.00	0.00	3.21
363	365	5.072741	AGTTGATTTAGTGCAAGGATGTGT	58.927	37.500	0.00	0.00	0.00	3.72
364	366	5.182001	AGTTGATTTAGTGCAAGGATGTGTC	59.818	40.000	0.00	0.00	0.00	3.67
365	367	4.009675	TGATTTAGTGCAAGGATGTGTCC	58.990	43.478	0.00	0.00	45.45	4.02
374	376	3.450028	GGATGTGTCCAGACTCTGC	57.550	57.895	0.00	0.00	44.42	4.26
375	377	0.610174	GGATGTGTCCAGACTCTGCA	59.390	55.000	0.00	0.00	44.42	4.41
539	4369	7.206981	AGAAGGTTTGATGTTGAATACACAG	57.793	36.000	0.00	0.00	40.19	3.66
563	4393	5.691754	GGTAAATGCATTTATTAGCCAGTGC	59.308	40.000	29.36	15.12	35.02	4.40
581	4411	4.386652	CAGTGCAAAATTTACATGGCTGAC	59.613	41.667	0.00	0.00	0.00	3.51
668	4498	4.006319	GAGAAGGAAGAAACTCCCATGTG	58.994	47.826	0.00	0.00	35.95	3.21
712	4542	2.615912	GAGAAACTACCATGGCTCATGC	59.384	50.000	13.04	0.00	40.20	4.06
729	4559	6.018262	GGCTCATGCGTAACTTATTTCATGTA	60.018	38.462	0.00	0.00	40.82	2.29
894	4724	9.817809	TTTCTGTATGGAGTATTCTGTACATTC	57.182	33.333	0.00	0.00	0.00	2.67
974	4806	0.244994	ACGGTGCAAGAGTAGCAGAG	59.755	55.000	0.00	0.00	43.63	3.35
1230	5062	0.636647	TGGTGATCTCCCTAGCCTCA	59.363	55.000	11.24	0.00	0.00	3.86
1336	5168	0.974010	TAGGCGGGTGTAAGACTGGG	60.974	60.000	0.00	0.00	0.00	4.45
1541	5373	1.674962	GCACAGGATCTCTTCAATGGC	59.325	52.381	0.00	0.00	0.00	4.40
1560	5392	1.134965	GCGCTGTAGATGTCTCCAAGT	60.135	52.381	0.00	0.00	0.00	3.16
1664	5496	1.902508	CTTGGTGTGAGGCCTAGAAGA	59.097	52.381	4.42	0.00	31.96	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	8.106462	TCCATGTCTCCTCAACAATTTAATACA	58.894	33.333	0.00	0.00	0.00	2.29
92	93	8.034313	ACAAAGGCTATAGAATCATAACTCCA	57.966	34.615	3.21	0.00	0.00	3.86
191	193	1.473965	CGGGTGTAAGCTCATCATGCT	60.474	52.381	0.00	0.00	43.32	3.79
240	242	8.290325	CAGAAGGAAAACTGTAATCTTGGTTAC	58.710	37.037	0.00	0.00	35.60	2.50
270	272	6.156748	TGAGACACTGTAGCTTTAAGACAA	57.843	37.500	0.00	0.00	0.00	3.18
274	276	4.926238	CCACTGAGACACTGTAGCTTTAAG	59.074	45.833	0.00	0.00	0.00	1.85
286	288	5.757850	AATCAACTTTTCCACTGAGACAC	57.242	39.130	0.00	0.00	0.00	3.67
287	289	7.012327	CACTAAATCAACTTTTCCACTGAGACA	59.988	37.037	0.00	0.00	0.00	3.41
317	319	3.556633	CCATGCAGAGTCTGGACATATCC	60.557	52.174	21.54	2.94	46.48	2.59
337	339	4.365514	TCCTTGCACTAAATCAACTCCA	57.634	40.909	0.00	0.00	0.00	3.86
338	340	4.702131	ACATCCTTGCACTAAATCAACTCC	59.298	41.667	0.00	0.00	0.00	3.85
339	341	5.182001	ACACATCCTTGCACTAAATCAACTC	59.818	40.000	0.00	0.00	0.00	3.01
340	342	5.072741	ACACATCCTTGCACTAAATCAACT	58.927	37.500	0.00	0.00	0.00	3.16
341	343	5.376854	ACACATCCTTGCACTAAATCAAC	57.623	39.130	0.00	0.00	0.00	3.18
342	344	4.458989	GGACACATCCTTGCACTAAATCAA	59.541	41.667	0.00	0.00	42.45	2.57
343	345	4.009675	GGACACATCCTTGCACTAAATCA	58.990	43.478	0.00	0.00	42.45	2.57
344	346	4.009675	TGGACACATCCTTGCACTAAATC	58.990	43.478	0.00	0.00	46.43	2.17
345	347	4.012374	CTGGACACATCCTTGCACTAAAT	58.988	43.478	0.00	0.00	46.43	1.40
346	348	3.072330	TCTGGACACATCCTTGCACTAAA	59.928	43.478	0.00	0.00	46.43	1.85
347	349	2.637382	TCTGGACACATCCTTGCACTAA	59.363	45.455	0.00	0.00	46.43	2.24
348	350	2.028112	GTCTGGACACATCCTTGCACTA	60.028	50.000	0.00	0.00	46.43	2.74
349	351	1.059098	TCTGGACACATCCTTGCACT	58.941	50.000	0.00	0.00	46.43	4.40
350	352	1.160137	GTCTGGACACATCCTTGCAC	58.840	55.000	0.00	0.00	46.43	4.57
351	353	1.002430	GAGTCTGGACACATCCTTGCA	59.998	52.381	3.51	0.00	46.43	4.08
352	354	1.277557	AGAGTCTGGACACATCCTTGC	59.722	52.381	0.00	0.00	46.43	4.01
353	355	2.934364	GCAGAGTCTGGACACATCCTTG	60.934	54.545	21.54	0.00	46.43	3.61
354	356	1.277557	GCAGAGTCTGGACACATCCTT	59.722	52.381	21.54	0.00	46.43	3.36
355	357	0.901124	GCAGAGTCTGGACACATCCT	59.099	55.000	21.54	0.00	46.43	3.24
356	358	0.610174	TGCAGAGTCTGGACACATCC	59.390	55.000	21.54	2.94	46.48	3.51
357	359	2.072298	GTTGCAGAGTCTGGACACATC	58.928	52.381	21.54	6.55	30.08	3.06
358	360	1.271054	GGTTGCAGAGTCTGGACACAT	60.271	52.381	21.54	0.00	30.08	3.21
359	361	0.106708	GGTTGCAGAGTCTGGACACA	59.893	55.000	21.54	8.09	30.08	3.72
360	362	0.106708	TGGTTGCAGAGTCTGGACAC	59.893	55.000	21.54	17.24	30.08	3.67
361	363	1.059098	ATGGTTGCAGAGTCTGGACA	58.941	50.000	21.54	14.01	30.08	4.02
362	364	1.446907	CATGGTTGCAGAGTCTGGAC	58.553	55.000	21.54	12.77	30.08	4.02
363	365	3.942351	CATGGTTGCAGAGTCTGGA	57.058	52.632	21.54	16.58	31.21	3.86
374	376	0.171903	GTTGGCTAGCTGCATGGTTG	59.828	55.000	15.72	0.00	45.15	3.77
375	377	0.038744	AGTTGGCTAGCTGCATGGTT	59.961	50.000	15.72	0.00	45.15	3.67
539	4369	5.691754	GCACTGGCTAATAAATGCATTTACC	59.308	40.000	29.32	24.84	34.62	2.85
563	4393	4.806640	AGGGTCAGCCATGTAAATTTTG	57.193	40.909	0.00	0.00	36.17	2.44
581	4411	3.421844	ACTAGCAGCCAACTTTTAAGGG	58.578	45.455	0.00	0.00	0.00	3.95
631	4461	8.899427	TCTTCCTTCTCTTAATTCTATGCATG	57.101	34.615	10.16	0.00	0.00	4.06
668	4498	7.444487	TCTCCCTTTTCTTAACTTTAAGCAGTC	59.556	37.037	4.15	0.00	39.90	3.51
729	4559	4.690748	CACGGTTCAAGATGTAGAATGTGT	59.309	41.667	0.00	0.00	32.78	3.72
894	4724	9.684448	CTTTCTCAGTGTGTGTATATATGTAGG	57.316	37.037	0.00	0.00	0.00	3.18
974	4806	8.172352	TCTTAGCTCATAGATACTCTTCAACC	57.828	38.462	0.00	0.00	0.00	3.77
1230	5062	0.326264	GGATGGTCAGGCTGTTGAGT	59.674	55.000	15.27	0.00	0.00	3.41
1336	5168	1.261619	CACCGCTGTTCAAGTCAAGAC	59.738	52.381	0.00	0.00	0.00	3.01
1541	5373	2.425312	AGACTTGGAGACATCTACAGCG	59.575	50.000	0.00	0.00	38.22	5.18
1560	5392	5.523588	ACTATCTCTGATGGTTTGAGGAGA	58.476	41.667	0.00	0.00	34.91	3.71
1664	5496	9.113838	CTTGCCATATTAGATCAGTTAGTTTGT	57.886	33.333	0.00	0.00	0.00	2.83
1682	5514	2.886523	GCAACAGATATGGCTTGCCATA	59.113	45.455	29.35	29.35	37.13	2.74
1852	5684	2.547211	GGAGATGAGTTGGCATGATTCG	59.453	50.000	0.00	0.00	0.00	3.34
2160	6019	1.331214	CAACACTCCAAGTTGGCCAT	58.669	50.000	17.68	1.74	41.92	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.