AutoCloner

Multiple sequence alignment - TraesCS4D01G245900

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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	TraesCS4D01G245900	chr4D	100.000	2951	0	0	1	2951	414366607	414363657	0.000000e+00	5450.0
1	TraesCS4D01G245900	chr4D	97.151	2387	55	8	570	2951	414337658	414335280	0.000000e+00	4019.0
2	TraesCS4D01G245900	chr4D	91.007	1479	110	14	1021	2481	414359382	414357909	0.000000e+00	1973.0
3	TraesCS4D01G245900	chr4D	88.402	1095	108	9	872	1951	414328815	414327725	0.000000e+00	1301.0
4	TraesCS4D01G245900	chr4D	81.548	1008	158	19	1307	2311	414349728	414348746	0.000000e+00	806.0
5	TraesCS4D01G245900	chr4D	90.816	196	18	0	347	542	414337847	414337652	2.260000e-66	263.0
6	TraesCS4D01G245900	chr4D	81.138	334	39	10	397	715	414329348	414329024	2.270000e-61	246.0
7	TraesCS4D01G245900	chr4B	89.400	2283	184	36	347	2591	510563338	510561076	0.000000e+00	2822.0
8	TraesCS4D01G245900	chr4B	93.288	1907	94	16	347	2229	510482873	510480977	0.000000e+00	2782.0
9	TraesCS4D01G245900	chr4B	88.026	1094	112	9	872	1950	510435159	510434070	0.000000e+00	1277.0
10	TraesCS4D01G245900	chr4B	91.901	568	34	10	2268	2829	510480981	510480420	0.000000e+00	784.0
11	TraesCS4D01G245900	chr4B	79.806	1030	171	23	1318	2337	510530517	510529515	0.000000e+00	715.0
12	TraesCS4D01G245900	chr4B	85.811	296	38	4	1	293	510483174	510482880	7.940000e-81	311.0
13	TraesCS4D01G245900	chr4B	84.797	296	42	3	1	293	510563640	510563345	8.000000e-76	294.0
14	TraesCS4D01G245900	chr4B	81.963	377	39	11	397	756	510435660	510435296	2.880000e-75	292.0
15	TraesCS4D01G245900	chr4A	89.222	1503	119	26	1290	2783	49040332	49041800	0.000000e+00	1838.0
16	TraesCS4D01G245900	chr4A	89.658	1083	97	6	879	1951	49199669	49200746	0.000000e+00	1365.0
17	TraesCS4D01G245900	chr4A	89.168	997	72	15	211	1189	49039242	49040220	0.000000e+00	1210.0
18	TraesCS4D01G245900	chr4A	82.011	378	40	16	397	756	49199152	49199519	2.220000e-76	296.0
19	TraesCS4D01G245900	chr4A	100.000	34	0	0	1174	1207	49040297	49040330	2.460000e-06	63.9
20	TraesCS4D01G245900	chr3B	86.364	154	14	5	999	1147	203613070	203613221	8.460000e-36	161.0
21	TraesCS4D01G245900	chr2B	93.182	44	2	1	270	313	154238898	154238856	2.460000e-06	63.9

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	TraesCS4D01G245900	chr4D	414363657	414366607	2950	True	5450.000000	5450	100.000000	1	2951	1	chr4D.!!$R3	2950
1	TraesCS4D01G245900	chr4D	414335280	414337847	2567	True	2141.000000	4019	93.983500	347	2951	2	chr4D.!!$R5	2604
2	TraesCS4D01G245900	chr4D	414357909	414359382	1473	True	1973.000000	1973	91.007000	1021	2481	1	chr4D.!!$R2	1460
3	TraesCS4D01G245900	chr4D	414348746	414349728	982	True	806.000000	806	81.548000	1307	2311	1	chr4D.!!$R1	1004
4	TraesCS4D01G245900	chr4D	414327725	414329348	1623	True	773.500000	1301	84.770000	397	1951	2	chr4D.!!$R4	1554
5	TraesCS4D01G245900	chr4B	510561076	510563640	2564	True	1558.000000	2822	87.098500	1	2591	2	chr4B.!!$R4	2590
6	TraesCS4D01G245900	chr4B	510480420	510483174	2754	True	1292.333333	2782	90.333333	1	2829	3	chr4B.!!$R3	2828
7	TraesCS4D01G245900	chr4B	510434070	510435660	1590	True	784.500000	1277	84.994500	397	1950	2	chr4B.!!$R2	1553
8	TraesCS4D01G245900	chr4B	510529515	510530517	1002	True	715.000000	715	79.806000	1318	2337	1	chr4B.!!$R1	1019
9	TraesCS4D01G245900	chr4A	49039242	49041800	2558	False	1037.300000	1838	92.796667	211	2783	3	chr4A.!!$F1	2572
10	TraesCS4D01G245900	chr4A	49199152	49200746	1594	False	830.500000	1365	85.834500	397	1951	2	chr4A.!!$F2	1554

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
819	916	0.108615	CCGCCTCTTTCGTGATGACT	60.109	55.0	0.00	0.0	0.0	3.41	F
1288	1552	0.892358	CCTATACTCGGCGGGCTACA	60.892	60.0	6.72	0.0	0.0	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1774	2046	1.898574	GACCCATTGGCGCCCATAG	60.899	63.158	26.77	15.59	31.53	2.23	R
2903	3214	4.324471	TGCTCCTGCGCATTTCAT	57.676	50.000	12.24	0.00	43.34	2.57	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
21	22	1.814793	GCCTTCCTTGTGAGAGTTCC	58.185	55.000	0.00	0.00	0.00	3.62
43	44	2.703536	GGGTGAAAACCTTGGTCCATTT	59.296	45.455	0.00	0.00	0.00	2.32
46	47	2.035321	TGAAAACCTTGGTCCATTTCGC	59.965	45.455	9.91	0.00	33.74	4.70
47	48	1.698506	AAACCTTGGTCCATTTCGCA	58.301	45.000	0.00	0.00	0.00	5.10
48	49	1.923356	AACCTTGGTCCATTTCGCAT	58.077	45.000	0.00	0.00	0.00	4.73
63	64	3.813143	CATGACGCGGCAATGGCA	61.813	61.111	23.46	0.00	43.71	4.92
90	91	0.309612	GCGCCGTTTTTCCTCTTGAA	59.690	50.000	0.00	0.00	0.00	2.69
97	98	3.488553	CGTTTTTCCTCTTGAAGGCGTTT	60.489	43.478	0.00	0.00	45.78	3.60
99	100	3.982576	TTTCCTCTTGAAGGCGTTTTC	57.017	42.857	0.00	0.00	45.78	2.29
115	116	0.256464	TTTCGTGGAACCCAGGTGTT	59.744	50.000	5.71	0.00	39.97	3.32
124	125	0.326927	ACCCAGGTGTTATTGGTCGG	59.673	55.000	0.00	0.00	32.40	4.79
129	130	1.170442	GGTGTTATTGGTCGGGGTTG	58.830	55.000	0.00	0.00	0.00	3.77
143	144	1.339727	GGGGTTGGTGTAGTGCTTAGG	60.340	57.143	0.00	0.00	0.00	2.69
149	150	2.176889	GGTGTAGTGCTTAGGTCCTCA	58.823	52.381	0.00	0.00	0.00	3.86
159	160	5.360144	GTGCTTAGGTCCTCATGTACTCTTA	59.640	44.000	0.00	0.00	0.00	2.10
165	166	2.950309	TCCTCATGTACTCTTACTCGGC	59.050	50.000	0.00	0.00	0.00	5.54
168	169	0.384669	ATGTACTCTTACTCGGCGGC	59.615	55.000	7.21	0.00	0.00	6.53
175	176	1.266786	CTTACTCGGCGGCGTAATCG	61.267	60.000	31.06	16.62	40.37	3.34
180	181	2.732670	CGGCGGCGTAATCGTGTTT	61.733	57.895	24.74	0.00	39.49	2.83
185	186	1.458064	CGGCGTAATCGTGTTTTGACT	59.542	47.619	0.00	0.00	39.49	3.41
186	187	2.720590	CGGCGTAATCGTGTTTTGACTG	60.721	50.000	0.00	0.00	39.49	3.51
189	190	4.081761	GCGTAATCGTGTTTTGACTGATG	58.918	43.478	0.00	0.00	39.49	3.07
197	198	5.525745	TCGTGTTTTGACTGATGTATGTTGT	59.474	36.000	0.00	0.00	0.00	3.32
199	200	6.142817	GTGTTTTGACTGATGTATGTTGTCC	58.857	40.000	0.00	0.00	0.00	4.02
297	301	7.338449	GGTTTGTGCTTTATCTATAAAGTGGGA	59.662	37.037	18.85	5.85	46.78	4.37
298	302	7.859325	TTGTGCTTTATCTATAAAGTGGGAC	57.141	36.000	18.85	12.78	46.78	4.46
300	304	6.127281	TGTGCTTTATCTATAAAGTGGGACGA	60.127	38.462	18.85	5.21	46.78	4.20
301	305	6.759827	GTGCTTTATCTATAAAGTGGGACGAA	59.240	38.462	18.85	0.00	46.78	3.85
302	306	7.279313	GTGCTTTATCTATAAAGTGGGACGAAA	59.721	37.037	18.85	0.00	46.78	3.46
303	307	7.825270	TGCTTTATCTATAAAGTGGGACGAAAA	59.175	33.333	18.85	0.00	46.78	2.29
304	308	8.671028	GCTTTATCTATAAAGTGGGACGAAAAA	58.329	33.333	18.85	0.00	46.78	1.94
341	351	8.429237	AACCTAGCAGACATAAATCTAGCTAT	57.571	34.615	0.00	0.00	36.08	2.97
343	353	9.707957	ACCTAGCAGACATAAATCTAGCTATAT	57.292	33.333	0.00	0.00	36.08	0.86
410	422	9.905713	AGATCTGCCTTAACAATTCTATGTTTA	57.094	29.630	0.00	0.00	40.52	2.01
432	444	2.695359	TCAGGAACAAGCCATTACGTC	58.305	47.619	0.00	0.00	0.00	4.34
435	447	1.612199	GGAACAAGCCATTACGTCCCA	60.612	52.381	0.00	0.00	0.00	4.37
518	530	1.076705	GGGGAGGCACATTCTTCCC	60.077	63.158	2.67	2.67	42.45	3.97
519	531	1.452108	GGGAGGCACATTCTTCCCG	60.452	63.158	0.00	0.00	0.00	5.14
526	539	1.464997	GCACATTCTTCCCGAGACAAC	59.535	52.381	0.00	0.00	33.02	3.32
653	683	5.241506	CCATTTCTTCAGAAAGTGTTAGGCA	59.758	40.000	7.97	0.00	45.87	4.75
654	684	6.239008	CCATTTCTTCAGAAAGTGTTAGGCAA	60.239	38.462	7.97	0.00	45.87	4.52
655	685	6.767524	TTTCTTCAGAAAGTGTTAGGCAAA	57.232	33.333	0.00	0.00	38.94	3.68
656	686	6.959639	TTCTTCAGAAAGTGTTAGGCAAAT	57.040	33.333	0.00	0.00	33.95	2.32
657	687	8.458573	TTTCTTCAGAAAGTGTTAGGCAAATA	57.541	30.769	0.00	0.00	38.94	1.40
658	688	7.435068	TCTTCAGAAAGTGTTAGGCAAATAC	57.565	36.000	0.00	0.00	33.95	1.89
659	689	5.856126	TCAGAAAGTGTTAGGCAAATACG	57.144	39.130	0.00	0.00	34.59	3.06
660	690	4.693566	TCAGAAAGTGTTAGGCAAATACGG	59.306	41.667	0.00	0.00	34.59	4.02
700	777	8.329203	AGCTGTTGTTATAAGGAAGAAGAAAG	57.671	34.615	0.00	0.00	0.00	2.62
730	807	1.556564	GTGTCTGCGCGTACATACAT	58.443	50.000	16.38	0.00	30.55	2.29
732	809	2.347452	GTGTCTGCGCGTACATACATTT	59.653	45.455	16.38	0.00	30.55	2.32
819	916	0.108615	CCGCCTCTTTCGTGATGACT	60.109	55.000	0.00	0.00	0.00	3.41
834	931	1.079057	GACTTTGCCGAGTCCCTCC	60.079	63.158	5.50	0.00	40.10	4.30
918	1059	6.908825	TGATACAAGAACAAACACATAAGCC	58.091	36.000	0.00	0.00	0.00	4.35
924	1070	3.347958	ACAAACACATAAGCCACAACG	57.652	42.857	0.00	0.00	0.00	4.10
968	1124	3.487042	CGTACAGATAGACAAGTCGGTGG	60.487	52.174	0.00	0.00	34.09	4.61
1288	1552	0.892358	CCTATACTCGGCGGGCTACA	60.892	60.000	6.72	0.00	0.00	2.74
1405	1669	1.523154	GATGTTCTGCAAACCCGGCA	61.523	55.000	0.00	0.00	39.32	5.69
1774	2046	5.407407	TGTCAAGACCTCTAATTCAGACC	57.593	43.478	0.00	0.00	0.00	3.85
1775	2047	5.087323	TGTCAAGACCTCTAATTCAGACCT	58.913	41.667	0.00	0.00	0.00	3.85
2012	2288	4.071961	TGTGAGCATACCATCATACACC	57.928	45.455	0.00	0.00	0.00	4.16
2123	2400	2.027192	GTCACCCTCATGTAGCTCCAAA	60.027	50.000	0.00	0.00	0.00	3.28
2865	3175	5.887754	TGGCCTAGTTTTTCCTCATAAACT	58.112	37.500	3.32	0.00	44.38	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	1.071857	AGGTTTTCACCCGGAACTCTC	59.928	52.381	0.73	0.00	45.63	3.20
21	22	0.466555	TGGACCAAGGTTTTCACCCG	60.467	55.000	0.00	0.00	45.63	5.28
46	47	3.339539	TTGCCATTGCCGCGTCATG	62.340	57.895	4.92	3.81	36.33	3.07
47	48	3.061231	TTGCCATTGCCGCGTCAT	61.061	55.556	4.92	0.00	36.33	3.06
48	49	4.036804	GTTGCCATTGCCGCGTCA	62.037	61.111	4.92	0.00	36.33	4.35
66	67	1.344226	GAGGAAAAACGGCGCAATGC	61.344	55.000	10.83	0.00	45.38	3.56
90	91	1.895231	GGGTTCCACGAAAACGCCT	60.895	57.895	0.00	0.00	34.51	5.52
97	98	1.129917	TAACACCTGGGTTCCACGAA	58.870	50.000	0.00	0.00	32.29	3.85
99	100	1.810151	CAATAACACCTGGGTTCCACG	59.190	52.381	0.00	0.00	32.29	4.94
115	116	1.555992	CTACACCAACCCCGACCAATA	59.444	52.381	0.00	0.00	0.00	1.90
124	125	1.350019	ACCTAAGCACTACACCAACCC	59.650	52.381	0.00	0.00	0.00	4.11
129	130	2.176889	TGAGGACCTAAGCACTACACC	58.823	52.381	0.00	0.00	0.00	4.16
143	144	3.243134	GCCGAGTAAGAGTACATGAGGAC	60.243	52.174	0.00	0.00	32.12	3.85
149	150	0.384669	GCCGCCGAGTAAGAGTACAT	59.615	55.000	0.00	0.00	32.12	2.29
159	160	3.818787	ACGATTACGCCGCCGAGT	61.819	61.111	0.00	0.00	43.96	4.18
165	166	1.458064	AGTCAAAACACGATTACGCCG	59.542	47.619	0.00	0.00	43.96	6.46
168	169	5.264060	ACATCAGTCAAAACACGATTACG	57.736	39.130	0.00	0.00	45.75	3.18
175	176	6.142817	GGACAACATACATCAGTCAAAACAC	58.857	40.000	0.00	0.00	0.00	3.32
180	181	4.265904	ACGGACAACATACATCAGTCAA	57.734	40.909	0.00	0.00	0.00	3.18
248	252	6.071221	ACCATAAATATACGGCCAGACGATTA	60.071	38.462	2.24	0.00	37.61	1.75
249	253	5.175859	CCATAAATATACGGCCAGACGATT	58.824	41.667	2.24	0.00	37.61	3.34
255	259	5.757886	CACAAACCATAAATATACGGCCAG	58.242	41.667	2.24	0.00	0.00	4.85
335	345	2.232941	GCAAGGGTGCGGTATATAGCTA	59.767	50.000	10.08	0.00	41.93	3.32
390	402	9.736023	CCTGAATAAACATAGAATTGTTAAGGC	57.264	33.333	0.00	0.00	38.85	4.35
410	422	3.686016	ACGTAATGGCTTGTTCCTGAAT	58.314	40.909	0.00	0.00	0.00	2.57
518	530	2.805353	CTGCGTCCCGTTGTCTCG	60.805	66.667	0.00	0.00	0.00	4.04
519	531	3.112709	GCTGCGTCCCGTTGTCTC	61.113	66.667	0.00	0.00	0.00	3.36
526	539	2.960129	GGTATTCGCTGCGTCCCG	60.960	66.667	22.48	0.00	0.00	5.14
659	689	3.798202	ACAGCTCTTCATCGGTATTTCC	58.202	45.455	0.00	0.00	0.00	3.13
660	690	4.631813	ACAACAGCTCTTCATCGGTATTTC	59.368	41.667	0.00	0.00	0.00	2.17
798	888	1.218047	CATCACGAAAGAGGCGGGA	59.782	57.895	0.00	0.00	46.12	5.14
918	1059	2.121564	CTGGGAAGCTGTGCGTTGTG	62.122	60.000	0.00	0.00	0.00	3.33
924	1070	1.375098	GCTGATCTGGGAAGCTGTGC	61.375	60.000	1.46	0.00	34.05	4.57
968	1124	3.576550	TGGATGCCCTTGAAAACTAAACC	59.423	43.478	0.00	0.00	0.00	3.27
997	1159	3.071837	TGGAGCCGACGCCATGTA	61.072	61.111	0.00	0.00	41.32	2.29
1260	1524	1.067516	GCCGAGTATAGGTTGCCGTAA	59.932	52.381	0.00	0.00	31.21	3.18
1405	1669	0.460284	GCCGTGATTGTCACCGAGAT	60.460	55.000	4.65	0.00	44.20	2.75
1774	2046	1.898574	GACCCATTGGCGCCCATAG	60.899	63.158	26.77	15.59	31.53	2.23
1775	2047	2.194597	GACCCATTGGCGCCCATA	59.805	61.111	26.77	10.04	31.53	2.74
2012	2288	2.024414	GAAATTCCAACCATCCCTCCG	58.976	52.381	0.00	0.00	0.00	4.63
2123	2400	9.059260	ACAATAAGTTAAACACGTACAAGGAAT	57.941	29.630	0.00	0.00	0.00	3.01
2889	3200	7.706159	TGCGCATTTCATGTAGATAGAAAAAT	58.294	30.769	5.66	0.00	35.20	1.82
2903	3214	4.324471	TGCTCCTGCGCATTTCAT	57.676	50.000	12.24	0.00	43.34	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.