AutoCloner

Multiple sequence alignment - TraesCS2A01G527800

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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	TraesCS2A01G527800	chr2A	100.000	3887	0	0	1	3887	747145725	747141839	0.000000e+00	7179.0
1	TraesCS2A01G527800	chr2A	86.801	841	86	14	1	826	746978705	746977875	0.000000e+00	915.0
2	TraesCS2A01G527800	chr2A	84.919	557	74	3	942	1491	746977660	746977107	4.390000e-154	555.0
3	TraesCS2A01G527800	chr2A	100.000	30	0	0	3289	3318	746974798	746974769	5.430000e-04	56.5
4	TraesCS2A01G527800	chr2D	95.813	3917	120	18	4	3887	617074835	617070930	0.000000e+00	6285.0
5	TraesCS2A01G527800	chr2B	92.437	3266	199	28	4	3247	752831852	752828613	0.000000e+00	4619.0
6	TraesCS2A01G527800	chr3B	83.917	2257	304	40	965	3194	671747470	671745246	0.000000e+00	2102.0
7	TraesCS2A01G527800	chr3B	79.755	163	32	1	2916	3077	28337369	28337531	2.450000e-22	117.0
8	TraesCS2A01G527800	chr3B	90.196	51	5	0	2837	2887	28337275	28337325	2.510000e-07	67.6
9	TraesCS2A01G527800	chr5A	82.020	2297	328	58	960	3218	584507059	584509308	0.000000e+00	1875.0
10	TraesCS2A01G527800	chr5A	80.196	818	109	26	1	774	584490946	584491754	7.290000e-157	564.0
11	TraesCS2A01G527800	chr5B	87.418	1216	141	10	2011	3218	570935943	570937154	0.000000e+00	1387.0
12	TraesCS2A01G527800	chr5B	87.608	1154	126	13	2011	3159	571174101	571175242	0.000000e+00	1323.0
13	TraesCS2A01G527800	chr5B	80.576	834	114	27	1	795	570933641	570934465	2.000000e-167	599.0
14	TraesCS2A01G527800	chr5B	78.394	884	133	29	8	836	571121725	571122605	4.450000e-144	521.0
15	TraesCS2A01G527800	chr5B	75.265	1039	193	39	960	1969	570934758	570935761	1.660000e-118	436.0
16	TraesCS2A01G527800	chr5D	88.245	1157	127	6	2011	3160	464078504	464079658	0.000000e+00	1375.0
17	TraesCS2A01G527800	chr5D	81.991	1105	184	9	2050	3140	544697176	544696073	0.000000e+00	924.0
18	TraesCS2A01G527800	chr5D	81.582	771	101	25	106	836	464076392	464077161	2.000000e-167	599.0
19	TraesCS2A01G527800	chr5D	77.974	849	144	23	960	1789	464077315	464078139	3.490000e-135	492.0
20	TraesCS2A01G527800	chr1A	81.991	1105	184	9	2050	3140	569451281	569452384	0.000000e+00	924.0

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	TraesCS2A01G527800	chr2A	747141839	747145725	3886	True	7179.000000	7179	100.000000	1	3887	1	chr2A.!!$R1	3886
1	TraesCS2A01G527800	chr2A	746974769	746978705	3936	True	508.833333	915	90.573333	1	3318	3	chr2A.!!$R2	3317
2	TraesCS2A01G527800	chr2D	617070930	617074835	3905	True	6285.000000	6285	95.813000	4	3887	1	chr2D.!!$R1	3883
3	TraesCS2A01G527800	chr2B	752828613	752831852	3239	True	4619.000000	4619	92.437000	4	3247	1	chr2B.!!$R1	3243
4	TraesCS2A01G527800	chr3B	671745246	671747470	2224	True	2102.000000	2102	83.917000	965	3194	1	chr3B.!!$R1	2229
5	TraesCS2A01G527800	chr5A	584507059	584509308	2249	False	1875.000000	1875	82.020000	960	3218	1	chr5A.!!$F2	2258
6	TraesCS2A01G527800	chr5A	584490946	584491754	808	False	564.000000	564	80.196000	1	774	1	chr5A.!!$F1	773
7	TraesCS2A01G527800	chr5B	571174101	571175242	1141	False	1323.000000	1323	87.608000	2011	3159	1	chr5B.!!$F2	1148
8	TraesCS2A01G527800	chr5B	570933641	570937154	3513	False	807.333333	1387	81.086333	1	3218	3	chr5B.!!$F3	3217
9	TraesCS2A01G527800	chr5B	571121725	571122605	880	False	521.000000	521	78.394000	8	836	1	chr5B.!!$F1	828
10	TraesCS2A01G527800	chr5D	544696073	544697176	1103	True	924.000000	924	81.991000	2050	3140	1	chr5D.!!$R1	1090
11	TraesCS2A01G527800	chr5D	464076392	464079658	3266	False	822.000000	1375	82.600333	106	3160	3	chr5D.!!$F1	3054
12	TraesCS2A01G527800	chr1A	569451281	569452384	1103	False	924.000000	924	81.991000	2050	3140	1	chr1A.!!$F1	1090

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
356	391	1.033746	CATCTTTGCTGCACCGGGAT	61.034	55.000	6.32	1.01	0.0	3.85	F
1116	1405	1.555075	TGCTCTCCTTTCTATTGCGGT	59.445	47.619	0.00	0.00	0.0	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1170	1459	0.454600	GCTCGTATGACGGAGAACCA	59.545	55.000	0.00	0.0	42.81	3.67	R
3026	4028	1.604308	CAACTGCAGGCCATCCACA	60.604	57.895	19.93	0.0	33.74	4.17	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
51	52	1.118965	TGGCGTGAACTCCCTTGAGA	61.119	55.000	0.00	0.00	41.42	3.27
85	86	2.316108	TCCAGTTCTGCTGTAGTGTGA	58.684	47.619	4.73	0.29	43.55	3.58
120	124	1.302192	GCAGCCGGTGGTGAACTTA	60.302	57.895	1.90	0.00	42.66	2.24
122	126	1.821216	CAGCCGGTGGTGAACTTATT	58.179	50.000	1.90	0.00	42.66	1.40
199	204	2.645802	GGCACCGGTGTAATTTATGGA	58.354	47.619	33.92	0.00	0.00	3.41
264	269	2.191375	GGCCTGAGCATGCTAGCA	59.809	61.111	28.09	21.85	42.56	3.49
356	391	1.033746	CATCTTTGCTGCACCGGGAT	61.034	55.000	6.32	1.01	0.00	3.85
398	433	3.499406	TGGTCATCCCAAGCTGCT	58.501	55.556	0.00	0.00	41.50	4.24
583	633	3.258622	CCTGAGTAAGAACTTCCTCCGTT	59.741	47.826	5.06	0.00	35.56	4.44
622	674	5.937111	ACCTCCTGTATGTTGTTTTGTAGT	58.063	37.500	0.00	0.00	0.00	2.73
623	675	7.069877	ACCTCCTGTATGTTGTTTTGTAGTA	57.930	36.000	0.00	0.00	0.00	1.82
624	676	7.159372	ACCTCCTGTATGTTGTTTTGTAGTAG	58.841	38.462	0.00	0.00	0.00	2.57
625	677	6.092259	CCTCCTGTATGTTGTTTTGTAGTAGC	59.908	42.308	0.00	0.00	0.00	3.58
711	783	4.323028	CCTGACACTGACATGTATCAACCT	60.323	45.833	0.00	0.00	31.24	3.50
748	820	3.262915	AGAAGCATATACCAGCATCCCTC	59.737	47.826	0.00	0.00	0.00	4.30
871	1059	2.100197	CTGACCGGGTCATTCTACAGA	58.900	52.381	28.85	4.17	41.94	3.41
905	1105	7.547697	TCCATCATCCCTTGTATATTTCGTA	57.452	36.000	0.00	0.00	0.00	3.43
929	1129	6.607004	TTTGTTTTCACCCTTGTTTCCTTA	57.393	33.333	0.00	0.00	0.00	2.69
996	1273	9.424319	GAACAAGAGATAAACAGTTGACTATCA	57.576	33.333	6.34	0.00	0.00	2.15
1109	1398	5.405063	AGGTATACCTGCTCTCCTTTCTA	57.595	43.478	24.01	0.00	46.55	2.10
1116	1405	1.555075	TGCTCTCCTTTCTATTGCGGT	59.445	47.619	0.00	0.00	0.00	5.68
1170	1459	1.852157	AAGGCGATCCATGGTGGTGT	61.852	55.000	12.58	0.00	39.03	4.16
1191	1480	1.134560	GGTTCTCCGTCATACGAGCTT	59.865	52.381	0.15	0.00	46.05	3.74
1194	1483	1.945394	TCTCCGTCATACGAGCTTACC	59.055	52.381	0.15	0.00	46.05	2.85
1308	1597	1.901591	CCAACTTGGACATGAGCAGT	58.098	50.000	0.92	0.00	40.96	4.40
1768	2216	6.737254	ACATACATTCCTTACTTTTCCACG	57.263	37.500	0.00	0.00	0.00	4.94
1812	2267	0.394352	GCCCTGGGTATTCAGTGGTG	60.394	60.000	15.56	0.00	33.14	4.17
1821	2276	4.142004	GGGTATTCAGTGGTGTATCTCGTT	60.142	45.833	0.00	0.00	0.00	3.85
2098	2717	2.041081	CCCCTGGTGGTATTGTTCTTCA	59.959	50.000	0.00	0.00	0.00	3.02
2103	2722	5.431765	CTGGTGGTATTGTTCTTCATAGCT	58.568	41.667	0.00	0.00	0.00	3.32
2284	3256	4.704833	GCGTTCTGCTCCCAGGCA	62.705	66.667	0.00	0.00	41.73	4.75
2290	3262	1.203441	TCTGCTCCCAGGCAATGTCT	61.203	55.000	0.00	0.00	41.94	3.41
2397	3369	0.315886	ACGTCAATGTGGTGCGTCTA	59.684	50.000	0.00	0.00	29.42	2.59
2429	3401	0.042731	TCGGAGGAAATGAGGAGGGT	59.957	55.000	0.00	0.00	0.00	4.34
2435	3407	1.475930	GGAAATGAGGAGGGTGCTAGC	60.476	57.143	8.10	8.10	0.00	3.42
2835	3816	4.424711	GGAATGCTGACCCGGGCA	62.425	66.667	24.08	18.89	42.80	5.36
2939	3941	3.265221	AGATGCATGAGTTGGAGAGGAAA	59.735	43.478	2.46	0.00	0.00	3.13
2991	3993	4.194720	AGTCTCACGATCGGCCGC	62.195	66.667	23.51	6.46	0.00	6.53
3023	4025	5.451103	CGAAGTCATAGAGATGCTTGAAGGA	60.451	44.000	0.00	0.00	32.81	3.36
3026	4028	4.100808	GTCATAGAGATGCTTGAAGGAGGT	59.899	45.833	0.00	0.00	32.62	3.85
3098	4103	1.272872	ACCCCTGTAGCGGAGTCTTAA	60.273	52.381	0.00	0.00	0.00	1.85
3252	4260	6.604735	AAGAATGTGAATTATCTACCGTGC	57.395	37.500	0.00	0.00	0.00	5.34
3275	4285	8.825745	GTGCTTCTTTTGAATGTTATCCAAAAA	58.174	29.630	0.00	0.00	38.70	1.94
3376	4451	7.187824	AGGTACAGCAGAGAATATCAAAGAA	57.812	36.000	0.00	0.00	0.00	2.52
3424	4499	3.014085	TTGGCGAGGACCCGATGAC	62.014	63.158	6.56	0.00	0.00	3.06
3437	4512	2.352225	CCCGATGACGCCAAATGAAAAA	60.352	45.455	0.00	0.00	38.29	1.94
3463	4538	3.169355	TCTGATGATGTCGACCACATG	57.831	47.619	22.71	13.10	46.53	3.21
3670	4745	0.235665	ACACGAGCGACATTTGCAAG	59.764	50.000	0.00	0.00	33.85	4.01
3836	4911	3.409026	AGAGGAGTGCAACCTGTTTAG	57.591	47.619	16.86	0.00	37.80	1.85
3838	4913	3.067833	GAGGAGTGCAACCTGTTTAGAC	58.932	50.000	16.86	0.00	37.80	2.59
3852	4927	3.201266	TGTTTAGACACCTCCTGTTTGGT	59.799	43.478	0.00	0.00	36.96	3.67
3876	4951	6.923508	GTGCTTAAATGTTGCTCCTAAAACTT	59.076	34.615	0.00	0.00	0.00	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	2.887151	ACTGGAATGCTTGTAGGCTT	57.113	45.000	0.00	0.00	0.00	4.35
85	86	1.070758	CTGCTGACCACCACTGTACTT	59.929	52.381	0.00	0.00	0.00	2.24
120	124	8.841300	CACAATGATTCAGAATCTCATCTCAAT	58.159	33.333	21.44	4.08	38.72	2.57
122	126	6.260271	GCACAATGATTCAGAATCTCATCTCA	59.740	38.462	21.44	4.03	38.72	3.27
199	204	0.542467	TGGCCCATGCAATGTCAACT	60.542	50.000	0.00	0.00	44.81	3.16
292	324	2.223340	CGGCTTGATTCCAGCAATACAC	60.223	50.000	11.44	0.00	0.00	2.90
356	391	0.756294	TCTTCAGAAACTGTCCGCCA	59.244	50.000	0.00	0.00	32.61	5.69
398	433	0.320683	CCGACATGACCACAGCTTCA	60.321	55.000	0.00	0.00	0.00	3.02
583	633	1.669760	GGTTTGCACCGATCCACGA	60.670	57.895	0.00	0.00	45.77	4.35
622	674	1.763968	ACGATGCAGTCACCTAGCTA	58.236	50.000	0.00	0.00	0.00	3.32
623	675	0.898320	AACGATGCAGTCACCTAGCT	59.102	50.000	0.00	0.00	0.00	3.32
624	676	1.002366	CAACGATGCAGTCACCTAGC	58.998	55.000	0.00	0.00	0.00	3.42
625	677	2.370281	ACAACGATGCAGTCACCTAG	57.630	50.000	0.00	0.00	0.00	3.02
711	783	1.815408	GCTTCTGTGACTTGGCAAGGA	60.815	52.381	29.26	14.62	0.00	3.36
748	820	5.403512	TCCTCCTGGTTAGTATAATCAGGG	58.596	45.833	22.59	15.30	43.66	4.45
795	873	4.571984	TGTCATCATAAAGAGGATGTTGCG	59.428	41.667	0.00	0.00	43.04	4.85
871	1059	9.887862	ATACAAGGGATGATGGAATAAAAGAAT	57.112	29.630	0.00	0.00	0.00	2.40
905	1105	5.692115	AGGAAACAAGGGTGAAAACAAAT	57.308	34.783	0.00	0.00	0.00	2.32
996	1273	1.348008	ACCACCATGGAGGCATCGAT	61.348	55.000	26.47	4.54	40.96	3.59
1093	1382	2.419297	CGCAATAGAAAGGAGAGCAGGT	60.419	50.000	0.00	0.00	0.00	4.00
1099	1388	3.706594	AGATGACCGCAATAGAAAGGAGA	59.293	43.478	0.00	0.00	0.00	3.71
1109	1398	1.740380	CGTCTTGGAGATGACCGCAAT	60.740	52.381	0.00	0.00	33.07	3.56
1116	1405	1.924731	ACTGGACGTCTTGGAGATGA	58.075	50.000	16.46	0.00	34.89	2.92
1170	1459	0.454600	GCTCGTATGACGGAGAACCA	59.545	55.000	0.00	0.00	42.81	3.67
1191	1480	1.810031	GCATTGCTATCGGTGCAGGTA	60.810	52.381	0.16	0.00	41.71	3.08
1194	1483	1.528586	GTAGCATTGCTATCGGTGCAG	59.471	52.381	20.63	0.00	43.30	4.41
1308	1597	2.427245	GCGAGGAAGAGGGCAGCTA	61.427	63.158	0.00	0.00	0.00	3.32
1405	1697	3.492313	GCGAACAATTCACAAAGCTAGG	58.508	45.455	0.00	0.00	0.00	3.02
1583	2015	8.843262	CCAGAATTTCATGACTTGCATTATCTA	58.157	33.333	0.00	0.00	34.15	1.98
1584	2016	7.341256	ACCAGAATTTCATGACTTGCATTATCT	59.659	33.333	0.00	0.00	34.15	1.98
1724	2165	6.214191	TGTATTTTCCAAAACAGAAGCACA	57.786	33.333	0.00	0.00	0.00	4.57
2098	2717	6.170506	TCGTTTTCCAGTATTTGTGAGCTAT	58.829	36.000	0.00	0.00	0.00	2.97
2103	2722	4.963373	TCCTCGTTTTCCAGTATTTGTGA	58.037	39.130	0.00	0.00	0.00	3.58
2284	3256	4.508551	TCTTGATGGCCACATAGACATT	57.491	40.909	8.16	0.00	37.47	2.71
2290	3262	3.647590	TCTAGCATCTTGATGGCCACATA	59.352	43.478	8.16	0.00	37.47	2.29
2397	3369	2.282958	TCCGAGCAGAACCCGACT	60.283	61.111	0.00	0.00	0.00	4.18
2429	3401	2.753452	GGCATATACTCGTAGGCTAGCA	59.247	50.000	18.24	0.00	0.00	3.49
2435	3407	2.168521	CCATGGGGCATATACTCGTAGG	59.831	54.545	2.85	0.00	0.00	3.18
2814	3794	2.190578	CGGGTCAGCATTCCTCCC	59.809	66.667	0.00	0.00	35.22	4.30
2939	3941	2.934801	GCAAAGCCCAACAACACAAAGT	60.935	45.455	0.00	0.00	0.00	2.66
2991	3993	2.550180	TCTCTATGACTTCGCTCATCGG	59.450	50.000	0.00	0.00	39.05	4.18
3023	4025	3.259314	TGCAGGCCATCCACACCT	61.259	61.111	5.01	0.00	33.74	4.00
3026	4028	1.604308	CAACTGCAGGCCATCCACA	60.604	57.895	19.93	0.00	33.74	4.17
3275	4285	9.599866	TGAAACTTTACACTCGATATGATTGAT	57.400	29.630	3.96	0.00	31.99	2.57
3415	4490	0.322098	TTCATTTGGCGTCATCGGGT	60.322	50.000	0.00	0.00	37.56	5.28
3438	4513	5.003160	TGTGGTCGACATCATCAGATTTTT	58.997	37.500	18.91	0.00	30.20	1.94
3439	4514	4.578871	TGTGGTCGACATCATCAGATTTT	58.421	39.130	18.91	0.00	30.20	1.82
3463	4538	7.268199	TCATAATGTGCCATGAAGAAAGATC	57.732	36.000	0.00	0.00	0.00	2.75
3491	4566	5.530915	CCATGGAGAGTGTAAGTTGTTTTCA	59.469	40.000	5.56	0.00	0.00	2.69
3492	4567	5.048713	CCCATGGAGAGTGTAAGTTGTTTTC	60.049	44.000	15.22	0.00	0.00	2.29
3670	4745	1.196354	GCTCACTGATCCATTATGCGC	59.804	52.381	0.00	0.00	0.00	6.09
3852	4927	6.648879	AGTTTTAGGAGCAACATTTAAGCA	57.351	33.333	0.00	0.00	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.