AutoCloner

Multiple sequence alignment - TraesCS7B01G173800

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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	TraesCS7B01G173800	chr7B	100.000	3957	0	0	1	3957	244886426	244882470	0.000000e+00	7308.0
1	TraesCS7B01G173800	chr7D	94.252	3027	150	12	194	3209	550635824	550638837	0.000000e+00	4604.0
2	TraesCS7B01G173800	chr7D	95.745	94	4	0	1	94	264677009	264676916	6.850000e-33	152.0
3	TraesCS7B01G173800	chr5D	93.987	3027	150	16	193	3209	350369588	350366584	0.000000e+00	4553.0
4	TraesCS7B01G173800	chr5D	93.787	3026	167	10	193	3209	41771427	41768414	0.000000e+00	4527.0
5	TraesCS7B01G173800	chr5D	93.313	3021	175	16	193	3203	320660538	320663541	0.000000e+00	4434.0
6	TraesCS7B01G173800	chr5D	93.188	3024	182	12	193	3204	530733136	530736147	0.000000e+00	4421.0
7	TraesCS7B01G173800	chr5B	93.591	3027	177	9	193	3209	184288881	184291900	0.000000e+00	4499.0
8	TraesCS7B01G173800	chr5B	76.489	638	119	16	3338	3950	515181648	515182279	6.380000e-83	318.0
9	TraesCS7B01G173800	chr6B	93.311	3035	186	7	190	3212	521149809	521146780	0.000000e+00	4464.0
10	TraesCS7B01G173800	chr6B	93.111	3034	187	10	193	3214	197818492	197815469	0.000000e+00	4425.0
11	TraesCS7B01G173800	chr4B	93.583	2992	172	10	193	3173	446326669	446329651	0.000000e+00	4444.0
12	TraesCS7B01G173800	chr4B	77.021	631	121	22	3337	3950	72974914	72974291	1.360000e-89	340.0
13	TraesCS7B01G173800	chr3D	76.992	778	129	29	3206	3950	404975093	404974333	2.220000e-107	399.0
14	TraesCS7B01G173800	chr3D	77.508	618	121	14	3339	3954	183679336	183679937	4.860000e-94	355.0
15	TraesCS7B01G173800	chr2A	79.599	549	99	9	3206	3744	711666069	711665524	8.020000e-102	381.0
16	TraesCS7B01G173800	chr4A	78.369	564	102	14	3399	3950	477876464	477877019	8.140000e-92	348.0
17	TraesCS7B01G173800	chr6D	79.701	468	91	4	3378	3844	310554842	310555306	6.340000e-88	335.0
18	TraesCS7B01G173800	chr6D	79.808	416	80	4	3371	3783	110985036	110984622	2.310000e-77	300.0
19	TraesCS7B01G173800	chr6A	79.826	461	84	9	3378	3833	199986632	199986176	1.060000e-85	327.0
20	TraesCS7B01G173800	chr6A	79.176	437	88	3	3355	3789	450106519	450106084	2.310000e-77	300.0
21	TraesCS7B01G173800	chr3B	81.047	401	74	2	3355	3753	173113860	173114260	6.380000e-83	318.0
22	TraesCS7B01G173800	chr2B	80.630	413	67	11	3345	3753	88410231	88409828	1.380000e-79	307.0
23	TraesCS7B01G173800	chr2B	87.755	49	6	0	3882	3930	646067585	646067633	1.540000e-04	58.4
24	TraesCS7B01G173800	chr7A	90.291	103	4	2	1	100	288867892	288867793	3.210000e-26	130.0
25	TraesCS7B01G173800	chr4D	86.667	60	7	1	3891	3949	170675914	170675855	9.180000e-07	65.8

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	TraesCS7B01G173800	chr7B	244882470	244886426	3956	True	7308	7308	100.000	1	3957	1	chr7B.!!$R1	3956
1	TraesCS7B01G173800	chr7D	550635824	550638837	3013	False	4604	4604	94.252	194	3209	1	chr7D.!!$F1	3015
2	TraesCS7B01G173800	chr5D	350366584	350369588	3004	True	4553	4553	93.987	193	3209	1	chr5D.!!$R2	3016
3	TraesCS7B01G173800	chr5D	41768414	41771427	3013	True	4527	4527	93.787	193	3209	1	chr5D.!!$R1	3016
4	TraesCS7B01G173800	chr5D	320660538	320663541	3003	False	4434	4434	93.313	193	3203	1	chr5D.!!$F1	3010
5	TraesCS7B01G173800	chr5D	530733136	530736147	3011	False	4421	4421	93.188	193	3204	1	chr5D.!!$F2	3011
6	TraesCS7B01G173800	chr5B	184288881	184291900	3019	False	4499	4499	93.591	193	3209	1	chr5B.!!$F1	3016
7	TraesCS7B01G173800	chr5B	515181648	515182279	631	False	318	318	76.489	3338	3950	1	chr5B.!!$F2	612
8	TraesCS7B01G173800	chr6B	521146780	521149809	3029	True	4464	4464	93.311	190	3212	1	chr6B.!!$R2	3022
9	TraesCS7B01G173800	chr6B	197815469	197818492	3023	True	4425	4425	93.111	193	3214	1	chr6B.!!$R1	3021
10	TraesCS7B01G173800	chr4B	446326669	446329651	2982	False	4444	4444	93.583	193	3173	1	chr4B.!!$F1	2980
11	TraesCS7B01G173800	chr4B	72974291	72974914	623	True	340	340	77.021	3337	3950	1	chr4B.!!$R1	613
12	TraesCS7B01G173800	chr3D	404974333	404975093	760	True	399	399	76.992	3206	3950	1	chr3D.!!$R1	744
13	TraesCS7B01G173800	chr3D	183679336	183679937	601	False	355	355	77.508	3339	3954	1	chr3D.!!$F1	615
14	TraesCS7B01G173800	chr2A	711665524	711666069	545	True	381	381	79.599	3206	3744	1	chr2A.!!$R1	538
15	TraesCS7B01G173800	chr4A	477876464	477877019	555	False	348	348	78.369	3399	3950	1	chr4A.!!$F1	551

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
154	155	0.035056	ATCTGGCCCTCAAAAGACCG	60.035	55.0	0.00	0.00	4.79	F
1541	1571	0.038166	CTGCCACCCAGGTGTACAAT	59.962	55.0	15.49	44.02	2.71	F
2239	2269	0.466189	CTCACAGGGTGTTGTGGCTT	60.466	55.0	6.33	46.55	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2115	2145	0.770166	TCCACCCTGGGTCATGACAA	60.770	55.0	26.47	13.47	38.32	3.18	R
2694	2741	0.030504	CAACGCCACTTGTGCATTGA	59.969	50.0	0.00	0.00	0.00	2.57	R
3340	3395	0.107897	TTTGCACTATCCGCCGATGT	60.108	50.0	0.00	0.00	0.00	3.06	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
20	21	3.079960	GATGTAAACGGAGATCGCTGA	57.920	47.619	12.67	0.00	43.89	4.26
21	22	3.444916	GATGTAAACGGAGATCGCTGAA	58.555	45.455	12.67	0.00	43.89	3.02
22	23	2.602878	TGTAAACGGAGATCGCTGAAC	58.397	47.619	12.67	7.58	43.89	3.18
23	24	1.582502	GTAAACGGAGATCGCTGAACG	59.417	52.381	12.67	1.78	43.89	3.95
24	25	0.736325	AAACGGAGATCGCTGAACGG	60.736	55.000	12.67	0.00	43.89	4.44
25	26	2.278857	CGGAGATCGCTGAACGGG	60.279	66.667	0.00	0.00	43.89	5.28
26	27	2.107141	GGAGATCGCTGAACGGGG	59.893	66.667	0.00	0.00	43.89	5.73
27	28	2.107141	GAGATCGCTGAACGGGGG	59.893	66.667	0.00	0.00	43.89	5.40
28	29	2.683933	AGATCGCTGAACGGGGGT	60.684	61.111	0.00	0.00	43.89	4.95
29	30	1.380785	AGATCGCTGAACGGGGGTA	60.381	57.895	0.00	0.00	43.89	3.69
30	31	1.227176	GATCGCTGAACGGGGGTAC	60.227	63.158	0.00	0.00	43.89	3.34
31	32	2.639883	GATCGCTGAACGGGGGTACC	62.640	65.000	2.17	2.17	46.24	3.34
42	43	3.892581	GGGTACCGCGGGTAGTCG	61.893	72.222	31.76	1.69	39.02	4.18
50	51	2.183555	CGGGTAGTCGCCTTCCAC	59.816	66.667	0.00	0.00	30.00	4.02
51	52	2.642254	CGGGTAGTCGCCTTCCACA	61.642	63.158	0.00	0.00	30.00	4.17
52	53	1.079336	GGGTAGTCGCCTTCCACAC	60.079	63.158	0.00	0.00	30.00	3.82
53	54	1.542187	GGGTAGTCGCCTTCCACACT	61.542	60.000	0.00	0.00	30.00	3.55
54	55	0.108756	GGTAGTCGCCTTCCACACTC	60.109	60.000	0.00	0.00	0.00	3.51
55	56	0.108756	GTAGTCGCCTTCCACACTCC	60.109	60.000	0.00	0.00	0.00	3.85
56	57	0.251653	TAGTCGCCTTCCACACTCCT	60.252	55.000	0.00	0.00	0.00	3.69
57	58	1.122019	AGTCGCCTTCCACACTCCTT	61.122	55.000	0.00	0.00	0.00	3.36
58	59	0.606604	GTCGCCTTCCACACTCCTTA	59.393	55.000	0.00	0.00	0.00	2.69
59	60	0.606604	TCGCCTTCCACACTCCTTAC	59.393	55.000	0.00	0.00	0.00	2.34
60	61	0.391263	CGCCTTCCACACTCCTTACC	60.391	60.000	0.00	0.00	0.00	2.85
61	62	0.690762	GCCTTCCACACTCCTTACCA	59.309	55.000	0.00	0.00	0.00	3.25

Showing 1 to 25 of 233 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	3.187700	GTTCAGCGATCTCCGTTTACAT	58.812	45.455	0.00	0.00	41.15	2.29
2	3	2.602878	GTTCAGCGATCTCCGTTTACA	58.397	47.619	0.00	0.00	41.15	2.41
3	4	1.582502	CGTTCAGCGATCTCCGTTTAC	59.417	52.381	0.00	0.00	44.77	2.01
4	5	1.468565	CCGTTCAGCGATCTCCGTTTA	60.469	52.381	0.00	0.00	44.77	2.01
5	6	0.736325	CCGTTCAGCGATCTCCGTTT	60.736	55.000	0.00	0.00	44.77	3.60
6	7	1.153823	CCGTTCAGCGATCTCCGTT	60.154	57.895	0.00	0.00	44.77	4.44
7	8	2.490217	CCGTTCAGCGATCTCCGT	59.510	61.111	0.00	0.00	44.77	4.69
8	9	2.278857	CCCGTTCAGCGATCTCCG	60.279	66.667	0.00	0.00	44.77	4.63
9	10	2.107141	CCCCGTTCAGCGATCTCC	59.893	66.667	0.00	0.00	44.77	3.71
10	11	1.389609	TACCCCCGTTCAGCGATCTC	61.390	60.000	0.00	0.00	44.77	2.75
11	12	1.380785	TACCCCCGTTCAGCGATCT	60.381	57.895	0.00	0.00	44.77	2.75
12	13	1.227176	GTACCCCCGTTCAGCGATC	60.227	63.158	0.00	0.00	44.77	3.69
13	14	2.728435	GGTACCCCCGTTCAGCGAT	61.728	63.158	0.00	0.00	44.77	4.58
14	15	3.384532	GGTACCCCCGTTCAGCGA	61.385	66.667	0.00	0.00	44.77	4.93
24	25	3.531207	GACTACCCGCGGTACCCC	61.531	72.222	26.12	6.35	37.09	4.95
25	26	3.892581	CGACTACCCGCGGTACCC	61.893	72.222	26.12	8.03	37.09	3.69
26	27	4.559229	GCGACTACCCGCGGTACC	62.559	72.222	26.12	0.16	45.86	3.34
33	34	2.183555	GTGGAAGGCGACTACCCG	59.816	66.667	0.00	0.00	42.68	5.28
34	35	1.079336	GTGTGGAAGGCGACTACCC	60.079	63.158	0.00	0.00	42.68	3.69
35	36	0.108756	GAGTGTGGAAGGCGACTACC	60.109	60.000	0.00	0.00	42.68	3.18
36	37	0.108756	GGAGTGTGGAAGGCGACTAC	60.109	60.000	0.00	0.00	42.68	2.73
37	38	0.251653	AGGAGTGTGGAAGGCGACTA	60.252	55.000	0.00	0.00	42.68	2.59
39	40	0.606604	TAAGGAGTGTGGAAGGCGAC	59.393	55.000	0.00	0.00	0.00	5.19
40	41	0.606604	GTAAGGAGTGTGGAAGGCGA	59.393	55.000	0.00	0.00	0.00	5.54
41	42	0.391263	GGTAAGGAGTGTGGAAGGCG	60.391	60.000	0.00	0.00	0.00	5.52

Showing 1 to 25 of 232 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.