AutoCloner

Multiple sequence alignment - TraesCS2D01G116700

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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	TraesCS2D01G116700	chr2D	100.000	4984	0	0	1	4984	65693851	65688868	0.000000e+00	9204.0
1	TraesCS2D01G116700	chr2D	92.553	470	28	4	287	749	421802649	421802180	0.000000e+00	667.0
2	TraesCS2D01G116700	chr2D	100.000	29	0	0	3245	3273	121704705	121704677	3.000000e-03	54.7
3	TraesCS2D01G116700	chr2B	94.203	3381	141	23	951	4310	105537564	105540910	0.000000e+00	5107.0
4	TraesCS2D01G116700	chr2B	83.838	396	61	3	287	681	402675462	402675855	1.690000e-99	374.0
5	TraesCS2D01G116700	chr2B	92.174	115	7	1	4499	4611	105541725	105541839	1.440000e-35	161.0
6	TraesCS2D01G116700	chr2B	97.059	34	0	1	4608	4641	105541892	105541924	6.970000e-04	56.5
7	TraesCS2D01G116700	chr2A	94.658	3276	137	18	885	4136	68878207	68881468	0.000000e+00	5046.0
8	TraesCS2D01G116700	chr2A	87.363	364	19	10	4646	4982	68882388	68882751	4.680000e-105	392.0
9	TraesCS2D01G116700	chr2A	85.944	249	10	5	4364	4607	68881865	68882093	4.980000e-60	243.0
10	TraesCS2D01G116700	chr2A	88.235	187	19	3	3599	3783	68886250	68886435	2.340000e-53	220.0
11	TraesCS2D01G116700	chr3A	87.879	462	50	4	286	744	82344277	82344735	5.680000e-149	538.0
12	TraesCS2D01G116700	chr3A	94.595	37	2	0	3239	3275	10500664	10500700	1.940000e-04	58.4
13	TraesCS2D01G116700	chr3D	87.118	458	58	1	287	743	346195326	346195783	7.400000e-143	518.0
14	TraesCS2D01G116700	chr3D	75.862	638	125	24	3147	3762	143459608	143460238	1.050000e-76	298.0
15	TraesCS2D01G116700	chr3B	86.087	460	57	6	287	742	720959706	720959250	5.800000e-134	488.0
16	TraesCS2D01G116700	chr1B	86.321	424	58	0	319	742	579607021	579607444	3.510000e-126	462.0
17	TraesCS2D01G116700	chr1B	91.026	78	7	0	3352	3429	687278426	687278349	6.820000e-19	106.0
18	TraesCS2D01G116700	chr1B	77.368	190	31	7	3240	3423	222209479	222209662	8.830000e-18	102.0
19	TraesCS2D01G116700	chr5D	81.360	456	82	3	287	740	305814854	305815308	7.880000e-98	368.0
20	TraesCS2D01G116700	chr5D	88.889	81	7	2	3625	3704	11950020	11949941	1.140000e-16	99.0
21	TraesCS2D01G116700	chr1D	81.176	425	79	1	318	742	64751614	64751191	1.720000e-89	340.0
22	TraesCS2D01G116700	chr1D	89.744	78	8	0	3352	3429	494011709	494011632	3.170000e-17	100.0
23	TraesCS2D01G116700	chr7B	79.212	457	92	3	287	742	48254720	48254266	1.040000e-81	315.0
24	TraesCS2D01G116700	chr7B	89.474	57	6	0	3240	3296	376934981	376934925	6.920000e-09	73.1
25	TraesCS2D01G116700	chr7D	86.631	187	17	8	4803	4984	174123585	174123402	3.040000e-47	200.0
26	TraesCS2D01G116700	chr7D	94.737	38	2	0	3238	3275	176160394	176160431	5.390000e-05	60.2
27	TraesCS2D01G116700	chr1A	91.026	78	7	0	3352	3429	592530824	592530747	6.820000e-19	106.0
28	TraesCS2D01G116700	chr1A	87.500	80	10	0	3625	3704	99868409	99868330	5.310000e-15	93.5
29	TraesCS2D01G116700	chr4A	74.721	269	43	16	3169	3423	532794329	532794586	4.110000e-16	97.1
30	TraesCS2D01G116700	chr4A	85.714	84	10	2	3623	3705	532796845	532796927	2.470000e-13	87.9
31	TraesCS2D01G116700	chr5B	79.861	144	15	9	3625	3765	11771812	11771680	5.310000e-15	93.5
32	TraesCS2D01G116700	chr4D	86.747	83	9	2	3623	3704	397094311	397094230	1.910000e-14	91.6
33	TraesCS2D01G116700	chr4D	82.828	99	15	2	3623	3720	63585447	63585350	2.470000e-13	87.9
34	TraesCS2D01G116700	chrUn	94.737	38	2	0	3238	3275	35540818	35540781	5.390000e-05	60.2
35	TraesCS2D01G116700	chrUn	94.737	38	2	0	3238	3275	244207322	244207359	5.390000e-05	60.2

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	TraesCS2D01G116700	chr2D	65688868	65693851	4983	True	9204.000000	9204	100.000000	1	4984	1	chr2D.!!$R1	4983
1	TraesCS2D01G116700	chr2B	105537564	105541924	4360	False	1774.833333	5107	94.478667	951	4641	3	chr2B.!!$F2	3690
2	TraesCS2D01G116700	chr2A	68878207	68886435	8228	False	1475.250000	5046	89.050000	885	4982	4	chr2A.!!$F1	4097
3	TraesCS2D01G116700	chr3D	143459608	143460238	630	False	298.000000	298	75.862000	3147	3762	1	chr3D.!!$F1	615

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
646	647	0.030235	GTGACCGAAACTTGGGTTGC	59.970	55.0	0.00	0.00	39.53	4.17	F
649	650	0.106918	ACCGAAACTTGGGTTGCAGA	60.107	50.0	0.00	0.00	35.62	4.26	F
704	705	0.112412	ACTGTCCGGGGAATGCTTTT	59.888	50.0	0.00	0.00	0.00	2.27	F
905	906	0.169672	CTGATTCCGCTGCAGTTTGG	59.830	55.0	16.64	14.86	0.00	3.28	F
1008	1015	0.323725	ACACCAATGCCATGACTCCC	60.324	55.0	0.00	0.00	0.00	4.30	F
2535	2554	0.391228	TTACACAGCTCGACCTTGCA	59.609	50.0	0.00	0.00	0.00	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1486	1502	1.377202	GGGAGCTGACATTCGCCAA	60.377	57.895	0.00	0.00	0.00	4.52	R
2362	2381	1.739562	GCTCGACCAGCCTTGTCAG	60.740	63.158	0.00	0.00	43.17	3.51	R
2427	2446	2.046892	AGCGTGGACACATCAGCC	60.047	61.111	3.12	0.00	0.00	4.85	R
2839	2858	0.106708	ATGAGTATGGCGACGGCAAT	59.893	50.000	28.50	16.77	42.43	3.56	R
2881	2900	0.108615	CTCTGGCTCCGGTACTTGTG	60.109	60.000	0.00	0.00	0.00	3.33	R
4478	4855	0.247460	CACTAGGCAGCAGTAGCACA	59.753	55.000	0.00	0.00	45.49	4.57	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	9.716507	AACAATTATATGAAATCTTGTACGTGC	57.283	29.630	0.00	0.00	0.00	5.34
63	64	9.109393	ACAATTATATGAAATCTTGTACGTGCT	57.891	29.630	4.97	0.00	0.00	4.40
64	65	9.935682	CAATTATATGAAATCTTGTACGTGCTT	57.064	29.630	4.97	0.00	0.00	3.91
71	72	7.915508	TGAAATCTTGTACGTGCTTATTATGG	58.084	34.615	4.97	0.00	0.00	2.74
72	73	7.766738	TGAAATCTTGTACGTGCTTATTATGGA	59.233	33.333	4.97	0.00	0.00	3.41
73	74	7.478520	AATCTTGTACGTGCTTATTATGGAC	57.521	36.000	4.97	0.00	0.00	4.02
74	75	5.353938	TCTTGTACGTGCTTATTATGGACC	58.646	41.667	4.97	0.00	0.00	4.46
75	76	5.128171	TCTTGTACGTGCTTATTATGGACCT	59.872	40.000	4.97	0.00	0.00	3.85
76	77	6.321945	TCTTGTACGTGCTTATTATGGACCTA	59.678	38.462	4.97	0.00	0.00	3.08
77	78	6.659745	TGTACGTGCTTATTATGGACCTAT	57.340	37.500	4.97	0.00	0.00	2.57
78	79	7.764141	TGTACGTGCTTATTATGGACCTATA	57.236	36.000	4.97	0.00	0.00	1.31
79	80	8.180706	TGTACGTGCTTATTATGGACCTATAA	57.819	34.615	4.97	0.00	0.00	0.98
80	81	8.640651	TGTACGTGCTTATTATGGACCTATAAA	58.359	33.333	4.97	0.00	0.00	1.40
81	82	9.480053	GTACGTGCTTATTATGGACCTATAAAA	57.520	33.333	0.00	0.00	0.00	1.52
82	83	8.967664	ACGTGCTTATTATGGACCTATAAAAA	57.032	30.769	0.00	0.00	0.00	1.94
118	119	7.834068	ACAGTGATTTGTATAAGCTACACAG	57.166	36.000	0.00	0.00	0.00	3.66
119	120	7.611770	ACAGTGATTTGTATAAGCTACACAGA	58.388	34.615	0.00	0.00	0.00	3.41
120	121	8.094548	ACAGTGATTTGTATAAGCTACACAGAA	58.905	33.333	0.00	0.00	0.00	3.02
121	122	8.935844	CAGTGATTTGTATAAGCTACACAGAAA	58.064	33.333	0.00	0.00	0.00	2.52
122	123	9.502091	AGTGATTTGTATAAGCTACACAGAAAA	57.498	29.630	0.00	0.00	0.00	2.29
141	142	4.316205	AAAAACAAAATCCCTGTCGACC	57.684	40.909	14.12	0.00	0.00	4.79
142	143	2.649531	AACAAAATCCCTGTCGACCA	57.350	45.000	14.12	0.01	0.00	4.02
143	144	2.649531	ACAAAATCCCTGTCGACCAA	57.350	45.000	14.12	0.00	0.00	3.67
144	145	2.227194	ACAAAATCCCTGTCGACCAAC	58.773	47.619	14.12	0.00	0.00	3.77
145	146	1.539827	CAAAATCCCTGTCGACCAACC	59.460	52.381	14.12	0.00	0.00	3.77

Showing 1 to 25 of 591 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	9.716507	GCACGTACAAGATTTCATATAATTGTT	57.283	29.630	0.00	0.00	33.31	2.83
37	38	9.109393	AGCACGTACAAGATTTCATATAATTGT	57.891	29.630	0.00	0.00	35.28	2.71
38	39	9.935682	AAGCACGTACAAGATTTCATATAATTG	57.064	29.630	0.00	0.00	0.00	2.32
45	46	8.559536	CCATAATAAGCACGTACAAGATTTCAT	58.440	33.333	0.00	0.00	0.00	2.57
46	47	7.766738	TCCATAATAAGCACGTACAAGATTTCA	59.233	33.333	0.00	0.00	0.00	2.69
47	48	8.062448	GTCCATAATAAGCACGTACAAGATTTC	58.938	37.037	0.00	0.00	0.00	2.17
48	49	7.012044	GGTCCATAATAAGCACGTACAAGATTT	59.988	37.037	0.00	0.00	0.00	2.17
49	50	6.482308	GGTCCATAATAAGCACGTACAAGATT	59.518	38.462	0.00	0.00	0.00	2.40
50	51	5.989777	GGTCCATAATAAGCACGTACAAGAT	59.010	40.000	0.00	0.00	0.00	2.40
51	52	5.128171	AGGTCCATAATAAGCACGTACAAGA	59.872	40.000	0.00	0.00	0.00	3.02
52	53	5.357257	AGGTCCATAATAAGCACGTACAAG	58.643	41.667	0.00	0.00	0.00	3.16
53	54	5.347620	AGGTCCATAATAAGCACGTACAA	57.652	39.130	0.00	0.00	0.00	2.41
54	55	6.659745	ATAGGTCCATAATAAGCACGTACA	57.340	37.500	0.00	0.00	0.00	2.90
55	56	9.480053	TTTTATAGGTCCATAATAAGCACGTAC	57.520	33.333	0.00	0.00	0.00	3.67
57	58	8.967664	TTTTTATAGGTCCATAATAAGCACGT	57.032	30.769	0.00	0.00	0.00	4.49
92	93	9.534565	CTGTGTAGCTTATACAAATCACTGTAT	57.465	33.333	0.00	2.17	43.38	2.29
93	94	8.745590	TCTGTGTAGCTTATACAAATCACTGTA	58.254	33.333	0.00	0.00	36.27	2.74
94	95	7.611770	TCTGTGTAGCTTATACAAATCACTGT	58.388	34.615	0.00	0.00	29.24	3.55
95	96	8.479313	TTCTGTGTAGCTTATACAAATCACTG	57.521	34.615	0.00	0.00	29.24	3.66
96	97	9.502091	TTTTCTGTGTAGCTTATACAAATCACT	57.498	29.630	0.00	0.00	29.24	3.41
120	121	3.702045	TGGTCGACAGGGATTTTGTTTTT	59.298	39.130	18.91	0.00	0.00	1.94
121	122	3.292460	TGGTCGACAGGGATTTTGTTTT	58.708	40.909	18.91	0.00	0.00	2.43
122	123	2.938838	TGGTCGACAGGGATTTTGTTT	58.061	42.857	18.91	0.00	0.00	2.83
123	124	2.621526	GTTGGTCGACAGGGATTTTGTT	59.378	45.455	18.91	0.00	0.00	2.83
124	125	2.227194	GTTGGTCGACAGGGATTTTGT	58.773	47.619	18.91	0.00	0.00	2.83

Showing 1 to 25 of 665 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.