AutoCloner

Multiple sequence alignment - TraesCS7B01G179700

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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	TraesCS7B01G179700	chr7B	100.000	3564	0	0	1	3564	265440759	265444322	0.000000e+00	6582.0
1	TraesCS7B01G179700	chr6A	96.980	2649	74	3	1	2649	364056727	364059369	0.000000e+00	4444.0
2	TraesCS7B01G179700	chr6A	96.316	923	27	6	2644	3564	364064101	364065018	0.000000e+00	1509.0
3	TraesCS7B01G179700	chr6A	78.632	234	37	7	3024	3245	315487050	315487282	3.710000e-30	143.0
4	TraesCS7B01G179700	chr3A	94.663	2342	112	6	1	2332	732495143	732492805	0.000000e+00	3620.0
5	TraesCS7B01G179700	chr3B	94.730	1632	80	3	384	2010	743143016	743141386	0.000000e+00	2532.0
6	TraesCS7B01G179700	chr3B	92.290	869	56	5	1996	2853	743139997	743139129	0.000000e+00	1223.0
7	TraesCS7B01G179700	chr3B	97.315	149	3	1	1	149	743143152	743143005	5.910000e-63	252.0
8	TraesCS7B01G179700	chr1A	78.205	234	38	7	3024	3245	53342383	53342151	1.730000e-28	137.0
9	TraesCS7B01G179700	chr1A	88.889	72	7	1	3174	3245	53334020	53333950	1.760000e-13	87.9
10	TraesCS7B01G179700	chr2A	77.350	234	41	6	3024	3245	20633878	20634111	1.040000e-25	128.0

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	TraesCS7B01G179700	chr7B	265440759	265444322	3563	False	6582.000000	6582	100.000000	1	3564	1	chr7B.!!$F1	3563
1	TraesCS7B01G179700	chr6A	364056727	364059369	2642	False	4444.000000	4444	96.980000	1	2649	1	chr6A.!!$F2	2648
2	TraesCS7B01G179700	chr6A	364064101	364065018	917	False	1509.000000	1509	96.316000	2644	3564	1	chr6A.!!$F3	920
3	TraesCS7B01G179700	chr3A	732492805	732495143	2338	True	3620.000000	3620	94.663000	1	2332	1	chr3A.!!$R1	2331
4	TraesCS7B01G179700	chr3B	743139129	743143152	4023	True	1335.666667	2532	94.778333	1	2853	3	chr3B.!!$R1	2852

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
189	190	2.383527	GCGTGCTGAAGAAGTCCCG	61.384	63.158	0.0	0.0	0.00	5.14	F
1291	1310	0.818938	TTGCATAGCAATGTGCCCAG	59.181	50.000	0.0	0.0	46.52	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1381	1400	0.820891	GCGGCCATCCACATTCTGAT	60.821	55.0	2.24	0.0	0.00	2.90	R
3133	4567	0.175989	AACTAGAACAGGCTAGCGGC	59.824	55.0	9.00	0.0	41.21	6.53	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
189	190	2.383527	GCGTGCTGAAGAAGTCCCG	61.384	63.158	0.00	0.00	0.00	5.14
339	340	5.950549	AGTTAAGACCGACATAGAAAGGAGA	59.049	40.000	0.00	0.00	0.00	3.71
340	341	4.993029	AAGACCGACATAGAAAGGAGAG	57.007	45.455	0.00	0.00	0.00	3.20
598	611	9.575783	GTAAAACACCAAAAACTATTCTCACAA	57.424	29.630	0.00	0.00	0.00	3.33
679	695	6.246420	ACATGTCAGTGCAAAATCTCTTAC	57.754	37.500	0.00	0.00	0.00	2.34
720	738	3.092192	CTTGCAGATGGAGCGTGCG	62.092	63.158	0.00	0.00	40.23	5.34
775	794	4.481870	GCAAATGGCACGTGATGG	57.518	55.556	22.23	2.70	43.97	3.51
934	953	5.363005	GGACTACAGGATAACAGGTACATGT	59.637	44.000	7.48	7.48	33.96	3.21
998	1017	4.997395	TCTTAGCTCTAACTTTTGTGCCAG	59.003	41.667	0.00	0.00	0.00	4.85
1291	1310	0.818938	TTGCATAGCAATGTGCCCAG	59.181	50.000	0.00	0.00	46.52	4.45
1381	1400	1.338973	AGGCAGTTACGTCGTGAAAGA	59.661	47.619	8.47	0.00	0.00	2.52
1729	1749	6.775142	TCAAGAATTATCAGAGAGACTCGGAT	59.225	38.462	15.73	15.73	44.75	4.18
1849	1869	0.244994	TCCAGAAGTTGCTCTCGCTC	59.755	55.000	0.00	0.00	36.97	5.03
2197	3620	8.894768	ATAACTATGTACCAGAATCTTGCTTC	57.105	34.615	0.00	0.00	0.00	3.86
2234	3657	3.998672	GGCAGGACCGGTTCGACA	61.999	66.667	9.42	0.00	0.00	4.35
2299	3722	1.018910	TGATGGCATCTGCATCAACG	58.981	50.000	26.49	0.00	44.36	4.10
2467	3890	1.544246	GATGAACCAAAGAAACCCCCG	59.456	52.381	0.00	0.00	0.00	5.73
2482	3905	1.090052	CCCCGAAGAAGGTTCGATGC	61.090	60.000	8.67	0.00	43.97	3.91
2590	4013	6.689669	GCAAAGTTGTCAACGTTAACTTATGT	59.310	34.615	21.75	9.11	42.11	2.29
2684	4112	6.147164	CGCTGAATTTGTTACTCTTACTCCAA	59.853	38.462	0.00	0.00	0.00	3.53
2869	4303	7.065443	GTCTACTTATGTTACCCATTTCACCAC	59.935	40.741	0.00	0.00	34.86	4.16
2977	4411	5.575157	TGATTAGTAAAGGCCATTGGTTGA	58.425	37.500	5.01	0.00	0.00	3.18
3056	4490	9.160496	TCAACATATTATTTTGGTTCCAATTGC	57.840	29.630	5.06	0.00	0.00	3.56
3058	4492	8.721019	ACATATTATTTTGGTTCCAATTGCAG	57.279	30.769	5.06	0.00	0.00	4.41
3133	4567	3.885484	ATGAGCGATAAAAAGCCATCG	57.115	42.857	0.00	0.00	45.27	3.84
3163	4597	3.326747	CTGTTCTAGTTTCCAGTTCCGG	58.673	50.000	0.00	0.00	0.00	5.14
3164	4598	2.038033	TGTTCTAGTTTCCAGTTCCGGG	59.962	50.000	0.00	0.00	0.00	5.73
3166	4600	2.612000	TCTAGTTTCCAGTTCCGGGAA	58.388	47.619	5.09	5.09	42.49	3.97
3167	4601	2.565834	TCTAGTTTCCAGTTCCGGGAAG	59.434	50.000	10.35	0.00	44.70	3.46
3168	4602	0.400594	AGTTTCCAGTTCCGGGAAGG	59.599	55.000	10.35	9.22	44.70	3.46
3171	4605	1.774894	TTCCAGTTCCGGGAAGGTGG	61.775	60.000	23.68	23.68	39.44	4.61
3172	4606	2.351276	CAGTTCCGGGAAGGTGGG	59.649	66.667	10.35	0.00	41.99	4.61
3173	4607	2.206036	AGTTCCGGGAAGGTGGGA	59.794	61.111	10.35	0.00	41.99	4.37
3175	4609	1.077716	GTTCCGGGAAGGTGGGATG	60.078	63.158	10.35	0.00	41.99	3.51
3176	4610	2.978946	TTCCGGGAAGGTGGGATGC	61.979	63.158	5.09	0.00	41.99	3.91
3201	4637	8.773645	GCCAGTTCTTTGCAAAATACTATTTTT	58.226	29.630	19.63	1.82	0.00	1.94
3307	4743	6.015180	CGATCCCCATGAAAATCCATTGTTAT	60.015	38.462	0.00	0.00	0.00	1.89
3331	4767	6.414732	TGTATATGCTTTCTGCCAACTAAGT	58.585	36.000	0.00	0.00	42.00	2.24
3373	4809	4.210120	CAGTTTTGTAGACACTCTCTGCAC	59.790	45.833	0.00	0.00	40.96	4.57
3374	4810	4.119862	GTTTTGTAGACACTCTCTGCACA	58.880	43.478	0.00	0.00	40.96	4.57
3397	4833	8.443160	CACATGTTTTGTAGATGTACTTACCTG	58.557	37.037	0.00	3.50	38.59	4.00
3398	4834	8.372459	ACATGTTTTGTAGATGTACTTACCTGA	58.628	33.333	1.30	0.00	38.84	3.86
3399	4835	8.873830	CATGTTTTGTAGATGTACTTACCTGAG	58.126	37.037	1.30	0.00	0.00	3.35
3400	4836	7.959175	TGTTTTGTAGATGTACTTACCTGAGT	58.041	34.615	1.30	0.00	0.00	3.41
3479	4915	5.510671	GCCAACCATTTCATTGAGTATACG	58.489	41.667	0.00	0.00	0.00	3.06
3543	4979	6.530019	ACAGAAAAAGGAATCACAAGTGTT	57.470	33.333	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
189	190	0.033504	TCAGACACCTCTTGCCGAAC	59.966	55.000	0.00	0.00	0.00	3.95
339	340	1.414181	CACCACAAGAGACCAGACACT	59.586	52.381	0.00	0.00	0.00	3.55
340	341	1.871080	CACCACAAGAGACCAGACAC	58.129	55.000	0.00	0.00	0.00	3.67
679	695	8.475331	AAGCATTGATCTGCAAAAATTTCTAG	57.525	30.769	9.38	0.00	44.77	2.43
720	738	5.762218	AGTAGAAGGCATAACATCAGCAATC	59.238	40.000	0.00	0.00	0.00	2.67
775	794	5.301805	TCCCAAGTTTCTCCTTGATGTTTTC	59.698	40.000	2.62	0.00	43.65	2.29
934	953	2.290260	CCCTGCAGTGAAACACATCCTA	60.290	50.000	13.81	0.00	41.43	2.94
998	1017	1.601903	TCCGTTGTGTGCTTGACATTC	59.398	47.619	0.00	0.00	36.78	2.67
1157	1176	6.284459	ACTGTACTGTCAAGAAGAAAGAAGG	58.716	40.000	0.00	0.00	34.99	3.46
1223	1242	2.743636	TTCAGTAAGCTAAGCACGCT	57.256	45.000	0.00	0.00	39.94	5.07
1381	1400	0.820891	GCGGCCATCCACATTCTGAT	60.821	55.000	2.24	0.00	0.00	2.90
1849	1869	1.800805	TGGCTTTGAGCTCTTTCTCG	58.199	50.000	16.19	0.00	41.99	4.04
2197	3620	0.603707	CATCATCCCCGGAACCATCG	60.604	60.000	0.73	0.00	0.00	3.84
2299	3722	4.803426	CGGGCTGCGAGAGGTGTC	62.803	72.222	0.00	0.00	0.00	3.67
2440	3863	6.014584	GGGGTTTCTTTGGTTCATCATTTAGT	60.015	38.462	0.00	0.00	0.00	2.24
2467	3890	1.019278	TGCCGCATCGAACCTTCTTC	61.019	55.000	0.00	0.00	0.00	2.87
2560	3983	7.251994	AGTTAACGTTGACAACTTTGCATTAA	58.748	30.769	23.17	9.28	0.00	1.40
2601	4024	4.023726	TCGCCTTTAAGGGTACAACAAT	57.976	40.909	13.42	0.00	35.37	2.71
2684	4112	7.879160	ACAAAACATCACCATTGCAAATAGAAT	59.121	29.630	1.71	0.00	0.00	2.40
3044	4478	3.305267	CGTCAAATCTGCAATTGGAACCA	60.305	43.478	7.72	0.00	0.00	3.67
3056	4490	3.753272	ACCATGAAGAACCGTCAAATCTG	59.247	43.478	0.00	0.00	0.00	2.90
3058	4492	3.751175	TCACCATGAAGAACCGTCAAATC	59.249	43.478	0.00	0.00	0.00	2.17
3133	4567	0.175989	AACTAGAACAGGCTAGCGGC	59.824	55.000	9.00	0.00	41.21	6.53
3163	4597	0.681243	GAACTGGCATCCCACCTTCC	60.681	60.000	0.00	0.00	35.79	3.46
3164	4598	0.329596	AGAACTGGCATCCCACCTTC	59.670	55.000	0.00	0.00	35.79	3.46
3166	4600	0.779997	AAAGAACTGGCATCCCACCT	59.220	50.000	0.00	0.00	35.79	4.00
3167	4601	0.890683	CAAAGAACTGGCATCCCACC	59.109	55.000	0.00	0.00	35.79	4.61
3168	4602	0.244721	GCAAAGAACTGGCATCCCAC	59.755	55.000	0.00	0.00	35.79	4.61
3171	4605	2.818130	TTTGCAAAGAACTGGCATCC	57.182	45.000	8.05	0.00	37.39	3.51
3172	4606	5.473039	AGTATTTTGCAAAGAACTGGCATC	58.527	37.500	21.14	3.85	37.39	3.91
3173	4607	5.473066	AGTATTTTGCAAAGAACTGGCAT	57.527	34.783	21.14	9.85	37.39	4.40
3175	4609	7.889589	AAATAGTATTTTGCAAAGAACTGGC	57.110	32.000	26.45	11.14	0.00	4.85
3201	4637	7.502226	AGAACTGTCAAATCTACAATTGGAACA	59.498	33.333	10.83	0.29	0.00	3.18
3220	4656	1.407437	GGGATCGCCATGAAGAACTGT	60.407	52.381	0.00	0.00	35.15	3.55
3331	4767	3.201266	ACTGTTGTTCAACCTACTTGGGA	59.799	43.478	12.23	0.00	41.11	4.37
3373	4809	8.771920	TCAGGTAAGTACATCTACAAAACATG	57.228	34.615	0.00	0.00	0.00	3.21
3374	4810	8.594550	ACTCAGGTAAGTACATCTACAAAACAT	58.405	33.333	0.00	0.00	0.00	2.71
3414	4850	6.289064	CAAGGTAGTCTTGTTAACTGGTTCT	58.711	40.000	7.22	2.34	45.81	3.01
3479	4915	7.184779	AGTTTGACACTTTACTTTTAACGAGC	58.815	34.615	0.00	0.00	27.32	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.