AutoCloner

Multiple sequence alignment - TraesCS2D01G465200

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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	TraesCS2D01G465200	chr2D	100.000	6632	0	0	1	6632	571175918	571182549	0.000000e+00	12248
1	TraesCS2D01G465200	chr2B	95.895	5433	150	29	549	5948	683034931	683040323	0.000000e+00	8730
2	TraesCS2D01G465200	chr2B	94.854	719	29	5	1	717	683034217	683034929	0.000000e+00	1116
3	TraesCS2D01G465200	chr2A	95.824	3424	102	19	1	3398	709841708	709845116	0.000000e+00	5493
4	TraesCS2D01G465200	chr2A	94.907	2592	81	22	3394	5949	709845217	709847793	0.000000e+00	4008
5	TraesCS2D01G465200	chr1B	88.545	1746	117	33	2452	4162	640617089	640615392	0.000000e+00	2039
6	TraesCS2D01G465200	chr1B	97.638	127	3	0	6292	6418	633732526	633732652	1.120000e-52	219
7	TraesCS2D01G465200	chr4A	89.132	1647	120	24	2554	4162	538718279	538716654	0.000000e+00	1995
8	TraesCS2D01G465200	chr1A	87.408	1763	132	35	2449	4162	556839909	556841630	0.000000e+00	1943
9	TraesCS2D01G465200	chr1D	89.214	1502	90	33	2700	4162	464439459	464440927	0.000000e+00	1810
10	TraesCS2D01G465200	chr5A	88.503	1470	107	26	2554	3976	412223558	412222104	0.000000e+00	1722
11	TraesCS2D01G465200	chr5A	86.911	1230	64	28	2727	3938	121723766	121722616	0.000000e+00	1290
12	TraesCS2D01G465200	chr5A	87.214	1181	64	25	2778	3938	80514793	80513680	0.000000e+00	1264
13	TraesCS2D01G465200	chr5A	88.679	159	12	6	4006	4162	412222104	412221950	8.780000e-44	189
14	TraesCS2D01G465200	chr5D	85.395	1609	163	34	3715	5294	248588447	248586882	0.000000e+00	1604
15	TraesCS2D01G465200	chr5D	89.283	1241	64	23	2727	3938	118206770	118205570	0.000000e+00	1491
16	TraesCS2D01G465200	chr5D	83.095	1609	193	40	3715	5294	15415725	15414167	0.000000e+00	1391
17	TraesCS2D01G465200	chr5D	87.480	1230	67	25	2727	3938	87544631	87543471	0.000000e+00	1338
18	TraesCS2D01G465200	chr5D	79.185	908	100	44	1393	2241	248590369	248589492	1.260000e-151	547
19	TraesCS2D01G465200	chr5D	97.638	127	3	0	6292	6418	449149307	449149181	1.120000e-52	219
20	TraesCS2D01G465200	chr5D	88.636	176	20	0	1181	1356	248601163	248600988	1.450000e-51	215
21	TraesCS2D01G465200	chr5B	88.961	1232	69	22	2732	3935	128672529	128673721	0.000000e+00	1459
22	TraesCS2D01G465200	chr5B	88.530	1238	73	29	2727	3935	117250214	117251411	0.000000e+00	1435
23	TraesCS2D01G465200	chr5B	94.366	71	3	1	6562	6631	127434306	127434236	2.530000e-19	108
24	TraesCS2D01G465200	chr6A	88.296	1068	76	20	2940	3976	125153192	125154241	0.000000e+00	1234
25	TraesCS2D01G465200	chr6A	91.218	353	20	6	2554	2897	125152854	125153204	2.800000e-128	470
26	TraesCS2D01G465200	chr6A	91.089	101	5	2	2554	2651	125152647	125152746	4.170000e-27	134
27	TraesCS2D01G465200	chr4D	86.718	1039	70	26	2554	3557	57874063	57875068	0.000000e+00	1092
28	TraesCS2D01G465200	chr4D	86.598	388	39	7	3777	4162	57875362	57875738	3.700000e-112	416
29	TraesCS2D01G465200	chr6B	88.115	833	57	24	2554	3357	153234260	153233441	0.000000e+00	952
30	TraesCS2D01G465200	chrUn	97.638	127	3	0	6292	6418	331842992	331843118	1.120000e-52	219
31	TraesCS2D01G465200	chrUn	97.638	127	3	0	6292	6418	351215045	351215171	1.120000e-52	219
32	TraesCS2D01G465200	chrUn	97.638	127	3	0	6292	6418	363863582	363863708	1.120000e-52	219
33	TraesCS2D01G465200	chrUn	97.638	127	3	0	6292	6418	392771493	392771619	1.120000e-52	219
34	TraesCS2D01G465200	chrUn	97.638	127	3	0	6292	6418	430358327	430358201	1.120000e-52	219
35	TraesCS2D01G465200	chrUn	97.638	127	3	0	6292	6418	449931634	449931760	1.120000e-52	219
36	TraesCS2D01G465200	chr6D	97.638	127	3	0	6292	6418	447587247	447587121	1.120000e-52	219

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	TraesCS2D01G465200	chr2D	571175918	571182549	6631	False	12248.000000	12248	100.0000	1	6632	1	chr2D.!!$F1	6631
1	TraesCS2D01G465200	chr2B	683034217	683040323	6106	False	4923.000000	8730	95.3745	1	5948	2	chr2B.!!$F1	5947
2	TraesCS2D01G465200	chr2A	709841708	709847793	6085	False	4750.500000	5493	95.3655	1	5949	2	chr2A.!!$F1	5948
3	TraesCS2D01G465200	chr1B	640615392	640617089	1697	True	2039.000000	2039	88.5450	2452	4162	1	chr1B.!!$R1	1710
4	TraesCS2D01G465200	chr4A	538716654	538718279	1625	True	1995.000000	1995	89.1320	2554	4162	1	chr4A.!!$R1	1608
5	TraesCS2D01G465200	chr1A	556839909	556841630	1721	False	1943.000000	1943	87.4080	2449	4162	1	chr1A.!!$F1	1713
6	TraesCS2D01G465200	chr1D	464439459	464440927	1468	False	1810.000000	1810	89.2140	2700	4162	1	chr1D.!!$F1	1462
7	TraesCS2D01G465200	chr5A	121722616	121723766	1150	True	1290.000000	1290	86.9110	2727	3938	1	chr5A.!!$R2	1211
8	TraesCS2D01G465200	chr5A	80513680	80514793	1113	True	1264.000000	1264	87.2140	2778	3938	1	chr5A.!!$R1	1160
9	TraesCS2D01G465200	chr5A	412221950	412223558	1608	True	955.500000	1722	88.5910	2554	4162	2	chr5A.!!$R3	1608
10	TraesCS2D01G465200	chr5D	118205570	118206770	1200	True	1491.000000	1491	89.2830	2727	3938	1	chr5D.!!$R3	1211
11	TraesCS2D01G465200	chr5D	15414167	15415725	1558	True	1391.000000	1391	83.0950	3715	5294	1	chr5D.!!$R1	1579
12	TraesCS2D01G465200	chr5D	87543471	87544631	1160	True	1338.000000	1338	87.4800	2727	3938	1	chr5D.!!$R2	1211
13	TraesCS2D01G465200	chr5D	248586882	248590369	3487	True	1075.500000	1604	82.2900	1393	5294	2	chr5D.!!$R6	3901
14	TraesCS2D01G465200	chr5B	128672529	128673721	1192	False	1459.000000	1459	88.9610	2732	3935	1	chr5B.!!$F2	1203
15	TraesCS2D01G465200	chr5B	117250214	117251411	1197	False	1435.000000	1435	88.5300	2727	3935	1	chr5B.!!$F1	1208
16	TraesCS2D01G465200	chr6A	125152647	125154241	1594	False	612.666667	1234	90.2010	2554	3976	3	chr6A.!!$F1	1422
17	TraesCS2D01G465200	chr4D	57874063	57875738	1675	False	754.000000	1092	86.6580	2554	4162	2	chr4D.!!$F1	1608
18	TraesCS2D01G465200	chr6B	153233441	153234260	819	True	952.000000	952	88.1150	2554	3357	1	chr6B.!!$R1	803

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	Hairpin	End Stability	Orientation
985	1179	0.323178	CATCTCCTTGTGCAGGGCTT	60.323	55.000	0.00	44.12	4.35	F
1905	2122	1.722034	AACAGGAGTCCAGCTCTGAA	58.278	50.000	12.86	43.62	3.02	F
2318	2676	1.412343	TGAGCTGTGTCTTGTGTGCTA	59.588	47.619	0.00	0.00	3.49	F
3317	4706	2.490903	CAGTTCAATCTTCCAAGGCTGG	59.509	50.000	0.00	45.08	4.85	F
4094	5781	0.951558	ATCGGTGTCAGTGGCAAAAC	59.048	50.000	0.00	0.00	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1914	2131	0.388294	CATCATCGGAGCTGCTCTCA	59.612	55.000	27.09	15.25	43.70	3.27	R
3033	4339	1.804151	TGGCAAGTGCAAGAATACGTC	59.196	47.619	5.52	0.00	44.36	4.34	R
4094	5781	4.124851	ACTATACTTCGTTCTGCTTGGG	57.875	45.455	0.00	0.00	0.00	4.12	R
4665	6356	0.689745	ACCCGCTGCCAGGAGTAATA	60.690	55.000	10.11	0.00	0.00	0.98	R
6051	7786	0.109179	TTTCGCAACATGAGCCATGC	60.109	50.000	13.19	1.01	44.80	4.06	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
130	132	1.142262	GGTTTACAGACACACCCCAGT	59.858	52.381	0.00	0.00	0.00	4.00
132	134	3.396560	GTTTACAGACACACCCCAGTAC	58.603	50.000	0.00	0.00	0.00	2.73
134	136	2.688902	ACAGACACACCCCAGTACTA	57.311	50.000	0.00	0.00	0.00	1.82
135	137	2.966915	ACAGACACACCCCAGTACTAA	58.033	47.619	0.00	0.00	0.00	2.24
136	138	3.517612	ACAGACACACCCCAGTACTAAT	58.482	45.455	0.00	0.00	0.00	1.73
137	139	3.514309	ACAGACACACCCCAGTACTAATC	59.486	47.826	0.00	0.00	0.00	1.75
194	197	2.732016	GGGGCCACGAAAAACACC	59.268	61.111	4.39	0.00	0.00	4.16
235	238	5.266242	AGAAACGCAAAAATCGCATATCTC	58.734	37.500	0.00	0.00	0.00	2.75
386	389	4.097361	GTTCCTCCCCGCCTCCAC	62.097	72.222	0.00	0.00	0.00	4.02
387	390	4.649705	TTCCTCCCCGCCTCCACA	62.650	66.667	0.00	0.00	0.00	4.17
465	472	4.717629	TCGCTGTTCCGTGCTCCG	62.718	66.667	0.00	0.00	0.00	4.63
484	491	4.228097	CGCGTCGATCGTACCCGT	62.228	66.667	15.94	0.00	42.13	5.28
717	894	4.057432	ACAAAATCCTTTGCAATTGTCGG	58.943	39.130	7.40	3.03	44.96	4.79
752	929	1.271597	GCCCGAGATATGCCCTGATTT	60.272	52.381	0.00	0.00	0.00	2.17
767	944	4.889409	CCCTGATTTTGCTTAGCCATAGAA	59.111	41.667	0.29	0.00	0.00	2.10
811	997	1.734465	GCTGCTTCGTTATGCTGTTCT	59.266	47.619	0.00	0.00	0.00	3.01
870	1056	5.590259	CCCATGATTCGATGAAAACTTACCT	59.410	40.000	0.00	0.00	0.00	3.08
884	1070	7.973388	TGAAAACTTACCTTGAGAAATTGTGTG	59.027	33.333	0.00	0.00	0.00	3.82
981	1175	1.751927	GCCCATCTCCTTGTGCAGG	60.752	63.158	0.00	0.00	45.64	4.85
985	1179	0.323178	CATCTCCTTGTGCAGGGCTT	60.323	55.000	0.00	0.00	44.12	4.35
1005	1199	6.374613	GGGCTTAGAAAATACATACTATGGGC	59.625	42.308	1.11	0.00	33.60	5.36
1031	1225	2.487934	GAGCAAGAAGTCTGCTGTTGA	58.512	47.619	1.36	0.00	39.21	3.18
1084	1278	5.773176	GGTGGAAAATCTGGAAAGAAAGGTA	59.227	40.000	0.00	0.00	0.00	3.08
1157	1351	3.508402	TGTGGCGTAACTCTTGTGATCTA	59.492	43.478	0.00	0.00	0.00	1.98
1203	1397	2.106566	AGATGACATCGAGAAGGCTGT	58.893	47.619	9.77	0.00	0.00	4.40

Showing 1 to 25 of 473 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	104	3.307480	GGTGTGTCTGTAAACCTGCCTAT	60.307	47.826	0.00	0.00	0.00	2.57
110	112	1.142262	ACTGGGGTGTGTCTGTAAACC	59.858	52.381	0.00	0.00	0.00	3.27
132	134	9.003658	GGTGTGATATTGGAAATAGTGGATTAG	57.996	37.037	0.00	0.00	0.00	1.73
134	136	6.777580	GGGTGTGATATTGGAAATAGTGGATT	59.222	38.462	0.00	0.00	0.00	3.01
135	137	6.306987	GGGTGTGATATTGGAAATAGTGGAT	58.693	40.000	0.00	0.00	0.00	3.41
136	138	5.398581	GGGGTGTGATATTGGAAATAGTGGA	60.399	44.000	0.00	0.00	0.00	4.02
137	139	4.827284	GGGGTGTGATATTGGAAATAGTGG	59.173	45.833	0.00	0.00	0.00	4.00
177	179	1.677637	TTGGTGTTTTTCGTGGCCCC	61.678	55.000	0.00	0.00	0.00	5.80
184	186	1.208259	GCCTGCTTTGGTGTTTTTCG	58.792	50.000	0.00	0.00	0.00	3.46
194	197	1.589716	CTTTCCCCTCGCCTGCTTTG	61.590	60.000	0.00	0.00	0.00	2.77
484	491	0.389817	CCGAAGTTCACCGATCAGCA	60.390	55.000	3.32	0.00	0.00	4.41
717	894	2.111251	GGCTGAATCCTACCCGCC	59.889	66.667	0.00	0.00	0.00	6.13
775	952	1.737363	GCAGCACAGGACTAGTACTGC	60.737	57.143	31.33	21.01	45.43	4.40
776	953	1.821753	AGCAGCACAGGACTAGTACTG	59.178	52.381	30.08	30.08	46.90	2.74
777	954	2.223803	AGCAGCACAGGACTAGTACT	57.776	50.000	0.17	0.17	0.00	2.73
778	955	2.732597	CGAAGCAGCACAGGACTAGTAC	60.733	54.545	0.00	0.00	0.00	2.73
779	956	1.472878	CGAAGCAGCACAGGACTAGTA	59.527	52.381	0.00	0.00	0.00	1.82
781	958	0.244994	ACGAAGCAGCACAGGACTAG	59.755	55.000	0.00	0.00	0.00	2.57
811	997	4.968259	ACCAGCAACTAGACATAAACACA	58.032	39.130	0.00	0.00	0.00	3.72
870	1056	2.543445	CGCAAGCCACACAATTTCTCAA	60.543	45.455	0.00	0.00	0.00	3.02
884	1070	3.764885	AACAATTCATCTACGCAAGCC	57.235	42.857	0.00	0.00	45.62	4.35
981	1175	6.940298	TGCCCATAGTATGTATTTTCTAAGCC	59.060	38.462	9.28	0.00	0.00	4.35
985	1179	7.870954	CGACTTGCCCATAGTATGTATTTTCTA	59.129	37.037	9.28	0.00	0.00	2.10
1005	1199	1.458827	GCAGACTTCTTGCTCGACTTG	59.541	52.381	0.00	0.00	0.00	3.16
1061	1255	5.791336	ACCTTTCTTTCCAGATTTTCCAC	57.209	39.130	0.00	0.00	0.00	4.02

Showing 1 to 25 of 474 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.