AutoCloner

Multiple sequence alignment - TraesCS2B01G505900

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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	TraesCS2B01G505900	chr2B	100.000	3444	0	0	1	3444	701270997	701267554	0.000000e+00	6360
1	TraesCS2B01G505900	chr2B	92.483	3459	231	25	1	3444	514557011	514553567	0.000000e+00	4920
2	TraesCS2B01G505900	chr2B	95.581	430	16	2	1	428	536000030	536000458	0.000000e+00	686
3	TraesCS2B01G505900	chr2B	89.823	226	20	2	1	226	599874843	599875065	1.560000e-73	287
4	TraesCS2B01G505900	chr3B	93.595	3466	179	24	1	3444	300387409	300390853	0.000000e+00	5131
5	TraesCS2B01G505900	chr5A	92.830	3459	217	26	1	3444	141902095	141905537	0.000000e+00	4985
6	TraesCS2B01G505900	chr5A	92.579	3436	225	22	22	3444	465654136	465657554	0.000000e+00	4905
7	TraesCS2B01G505900	chr2A	92.692	3462	218	27	1	3444	685104323	685100879	0.000000e+00	4959
8	TraesCS2B01G505900	chr2A	92.692	3462	216	24	1	3444	572969920	572966478	0.000000e+00	4957
9	TraesCS2B01G505900	chr2A	92.661	3461	218	28	1	3444	384174891	384171450	0.000000e+00	4951
10	TraesCS2B01G505900	chr2A	92.486	3460	222	29	1	3444	80119631	80123068	0.000000e+00	4915
11	TraesCS2B01G505900	chr2A	92.399	3460	231	26	1	3444	284799909	284803352	0.000000e+00	4903

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	TraesCS2B01G505900	chr2B	701267554	701270997	3443	True	6360	6360	100.000	1	3444	1	chr2B.!!$R2	3443
1	TraesCS2B01G505900	chr2B	514553567	514557011	3444	True	4920	4920	92.483	1	3444	1	chr2B.!!$R1	3443
2	TraesCS2B01G505900	chr3B	300387409	300390853	3444	False	5131	5131	93.595	1	3444	1	chr3B.!!$F1	3443
3	TraesCS2B01G505900	chr5A	141902095	141905537	3442	False	4985	4985	92.830	1	3444	1	chr5A.!!$F1	3443
4	TraesCS2B01G505900	chr5A	465654136	465657554	3418	False	4905	4905	92.579	22	3444	1	chr5A.!!$F2	3422
5	TraesCS2B01G505900	chr2A	685100879	685104323	3444	True	4959	4959	92.692	1	3444	1	chr2A.!!$R3	3443
6	TraesCS2B01G505900	chr2A	572966478	572969920	3442	True	4957	4957	92.692	1	3444	1	chr2A.!!$R2	3443
7	TraesCS2B01G505900	chr2A	384171450	384174891	3441	True	4951	4951	92.661	1	3444	1	chr2A.!!$R1	3443
8	TraesCS2B01G505900	chr2A	80119631	80123068	3437	False	4915	4915	92.486	1	3444	1	chr2A.!!$F1	3443
9	TraesCS2B01G505900	chr2A	284799909	284803352	3443	False	4903	4903	92.399	1	3444	1	chr2A.!!$F2	3443

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
687	701	0.482446	AGTGGGATTTGGCAGGTCAA	59.518	50.0	4.04	0.00	3.18	F
1176	1202	0.321653	CCAGCGTACCAGAAAAGGCT	60.322	55.0	0.00	37.31	4.58	F
2054	2086	0.455633	GCTGCAGCATGAAAAGTCGG	60.456	55.0	33.36	39.69	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self end TH	Hairpin	End Stability	Orientation
2052	2084	0.386731	GAAACCGGCAAATGTGACCG	60.387	55.000	10.69	41.34	4.79	R
2418	2450	0.556258	AGTAAAGGGGCAATAGGGGC	59.444	55.000	0.00	0.00	5.80	R
3222	3275	1.444553	GCTCACCAGTCGAACTCCG	60.445	63.158	0.00	40.25	4.63	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
127	130	2.480037	TGATGCAAAACGCTACTGTCAG	59.520	45.455	0.00	0.00	43.06	3.51
143	147	1.801178	GTCAGCCAGTAACTCAGCAAC	59.199	52.381	0.00	0.00	0.00	4.17
144	148	1.416030	TCAGCCAGTAACTCAGCAACA	59.584	47.619	0.00	0.00	0.00	3.33
242	250	6.270064	GCATAGTAAAACAAACACACCAGTT	58.730	36.000	0.00	0.00	0.00	3.16
250	258	3.619929	ACAAACACACCAGTTAACGACTC	59.380	43.478	0.00	0.00	36.10	3.36
253	261	4.067972	ACACACCAGTTAACGACTCAAT	57.932	40.909	0.00	0.00	36.10	2.57
254	262	4.448210	ACACACCAGTTAACGACTCAATT	58.552	39.130	0.00	0.00	36.10	2.32
652	666	3.378112	ACAGTAAAATGCCATCATCACCG	59.622	43.478	0.00	0.00	31.27	4.94
660	674	1.596203	CATCATCACCGCCGCAGAT	60.596	57.895	0.00	0.00	0.00	2.90
687	701	0.482446	AGTGGGATTTGGCAGGTCAA	59.518	50.000	4.04	0.00	0.00	3.18
737	751	9.743057	CAGTTCAATAGTAAAAACCATTTCACA	57.257	29.630	0.00	0.00	0.00	3.58
757	771	5.044919	TCACATGGATGGTTAGTTCTTCCAT	60.045	40.000	0.00	0.00	44.72	3.41
789	803	2.669569	CACCCACTGAGCGGTTGG	60.670	66.667	0.00	0.00	0.00	3.77
807	821	1.391157	GGCACAAGGGACTGCAAACA	61.391	55.000	0.00	0.00	40.86	2.83
828	842	4.887190	ACCCCACGCCACAACACC	62.887	66.667	0.00	0.00	0.00	4.16
852	875	4.367023	CCCGAACGAACCGCCTCA	62.367	66.667	0.00	0.00	0.00	3.86
853	876	2.809601	CCGAACGAACCGCCTCAG	60.810	66.667	0.00	0.00	0.00	3.35
854	877	2.809601	CGAACGAACCGCCTCAGG	60.810	66.667	0.00	0.00	37.30	3.86
893	918	4.634004	CGCACTACACAAAATCCCATTCTA	59.366	41.667	0.00	0.00	0.00	2.10
1101	1127	0.386858	GCGAGAAGTGCGAGTACACA	60.387	55.000	0.00	0.00	43.23	3.72
1149	1175	0.737715	GCAACGAGACGCTGGAGATT	60.738	55.000	0.00	0.00	0.00	2.40
1176	1202	0.321653	CCAGCGTACCAGAAAAGGCT	60.322	55.000	0.00	0.00	37.31	4.58
1219	1245	1.304713	ATGAAGCTTGGTGGCAGGG	60.305	57.895	2.10	0.00	34.17	4.45
1395	1421	9.467258	CCTGCATATGGTTTATCTGTTTTATTG	57.533	33.333	4.56	0.00	0.00	1.90
1396	1422	8.870160	TGCATATGGTTTATCTGTTTTATTGC	57.130	30.769	4.56	0.00	0.00	3.56
1427	1453	9.076596	GTATCCTGAAAAATTAATCACACTTGC	57.923	33.333	0.00	0.00	0.00	4.01
1740	1768	1.967319	TGGTGAAGCACTGGTTTCTC	58.033	50.000	0.00	0.00	35.50	2.87
1750	1778	3.262420	CACTGGTTTCTCTGTTATCCCG	58.738	50.000	0.00	0.00	0.00	5.14
1952	1984	6.804534	TTCATCGCTTGTAAAACAAAACAG	57.195	33.333	0.00	0.00	37.69	3.16
2054	2086	0.455633	GCTGCAGCATGAAAAGTCGG	60.456	55.000	33.36	0.00	39.69	4.79
2160	2192	1.023513	ATTCAGCGCAAGTGGAGAGC	61.024	55.000	11.47	0.00	41.68	4.09
2242	2274	5.185635	CCCATTCTACAAAGGCATGAAGAAA	59.814	40.000	0.00	0.00	0.00	2.52
2272	2304	3.319972	ACACGCAGGAAGACTACAAACTA	59.680	43.478	0.00	0.00	0.00	2.24
2314	2346	1.472276	GCAACCTCATCGAGTACGCG	61.472	60.000	13.19	13.19	39.58	6.01
2384	2416	3.992943	TCACAGACGGTTGGGAATATT	57.007	42.857	0.00	0.00	0.00	1.28
2385	2417	4.295141	TCACAGACGGTTGGGAATATTT	57.705	40.909	0.00	0.00	0.00	1.40
2418	2450	1.725164	GGCTGAAAACTTCTACGACCG	59.275	52.381	0.00	0.00	0.00	4.79
2454	2486	7.420680	CCCCTTTACTGGATGAAGATAACATCT	60.421	40.741	0.00	0.00	42.33	2.90
2477	2509	2.152016	GCCTGCCTTCGTTTTACTTCT	58.848	47.619	0.00	0.00	0.00	2.85
2479	2511	3.399330	CCTGCCTTCGTTTTACTTCTGA	58.601	45.455	0.00	0.00	0.00	3.27
2554	2586	4.759693	GGTTGAACCACTGTGATTATGTCA	59.240	41.667	9.98	0.77	38.42	3.58
2862	2896	8.260818	ACTATGAATGCACTATCAGTACAACTT	58.739	33.333	0.00	0.00	0.00	2.66
2930	2966	8.070171	AGACACTTGAGAATAATCACAAAAACG	58.930	33.333	0.00	0.00	31.78	3.60
3025	3063	8.379457	ACAAAAAGTATCAGTCCAAGTTACTC	57.621	34.615	0.00	0.00	0.00	2.59
3038	3076	3.644884	AGTTACTCGTGGAGTCAAGTG	57.355	47.619	0.85	0.00	42.40	3.16
3222	3275	1.801178	GCACTCAGGTAAGTGTTCAGC	59.199	52.381	5.97	0.00	46.77	4.26
3404	3460	3.648739	ACAAAACACCCCACCAATAAGT	58.351	40.909	0.00	0.00	0.00	2.24
3423	3479	7.691993	ATAAGTCCAGGTATACAAACCAGAT	57.308	36.000	5.01	0.00	42.40	2.90
3431	3487	0.693622	TACAAACCAGATGGCGGGAA	59.306	50.000	0.00	0.00	39.32	3.97
3435	3491	1.937191	AACCAGATGGCGGGAAAAAT	58.063	45.000	0.00	0.00	39.32	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.259425	CTGCTTCAGCGGGCACAAC	62.259	63.158	0.00	0.00	45.83	3.32
127	130	3.708563	TTTTGTTGCTGAGTTACTGGC	57.291	42.857	0.00	0.00	0.00	4.85
481	494	4.309099	TGAACGTACCAAATACCAGTGAC	58.691	43.478	0.00	0.00	0.00	3.67
652	666	2.100631	ACTTGCACGTATCTGCGGC	61.101	57.895	0.00	0.00	40.31	6.53
660	674	1.529226	CCAAATCCCACTTGCACGTA	58.471	50.000	0.00	0.00	0.00	3.57
687	701	7.553334	TGACTAGTCTTGTCAAGTTGTACTTT	58.447	34.615	23.01	0.37	40.89	2.66
789	803	0.031178	CTGTTTGCAGTCCCTTGTGC	59.969	55.000	0.00	0.00	40.29	4.57
828	842	2.735857	GTTCGTTCGGGGTCGTGG	60.736	66.667	0.00	0.00	37.69	4.94
852	875	1.304134	GTGGACGGGGATTTTGCCT	60.304	57.895	0.00	0.00	0.00	4.75
853	876	2.696759	CGTGGACGGGGATTTTGCC	61.697	63.158	0.00	0.00	35.37	4.52
854	877	2.874751	CGTGGACGGGGATTTTGC	59.125	61.111	0.00	0.00	35.37	3.68
893	918	1.196012	GAACGAGGGAGAGGTGGAAT	58.804	55.000	0.00	0.00	0.00	3.01
1090	1116	0.466543	AGGGTTGTTGTGTACTCGCA	59.533	50.000	0.00	0.00	0.00	5.10
1149	1175	2.342279	GGTACGCTGGTGCAGACA	59.658	61.111	0.00	0.00	39.64	3.41
1176	1202	1.323271	GCCTGGAGATCACCTCGTCA	61.323	60.000	10.73	0.00	42.89	4.35
1202	1228	2.115910	CCCTGCCACCAAGCTTCA	59.884	61.111	0.00	0.00	0.00	3.02
1212	1238	1.672854	CGATCCTACGAACCCTGCCA	61.673	60.000	0.00	0.00	35.09	4.92
1219	1245	1.653533	CGCCGACGATCCTACGAAC	60.654	63.158	0.00	0.00	43.93	3.95
1395	1421	9.937175	GTGATTAATTTTTCAGGATACAGTAGC	57.063	33.333	0.00	0.00	41.41	3.58
1514	1540	5.452255	AGTAATCCATTGCATCAGGTTCAT	58.548	37.500	0.00	0.00	0.00	2.57
1528	1554	8.137437	CGCAAGATTTTCCAAATAGTAATCCAT	58.863	33.333	0.00	0.00	43.02	3.41
1740	1768	4.839668	TTTGGTTGAAACGGGATAACAG	57.160	40.909	0.00	0.00	0.00	3.16
1920	1951	6.698008	TTTACAAGCGATGAATCCATGAAT	57.302	33.333	0.00	0.00	32.09	2.57
2024	2056	1.742880	GCTGCAGCATCTCGGTCAA	60.743	57.895	33.36	0.00	41.59	3.18
2047	2079	0.591170	CGGCAAATGTGACCGACTTT	59.409	50.000	11.89	0.00	43.09	2.66
2052	2084	0.386731	GAAACCGGCAAATGTGACCG	60.387	55.000	0.00	10.69	41.34	4.79
2054	2086	1.930371	GCTGAAACCGGCAAATGTGAC	60.930	52.381	0.00	0.00	36.01	3.67
2160	2192	3.611766	ACTCTTTTCCGGTGTATGGAG	57.388	47.619	0.00	5.91	36.72	3.86
2242	2274	2.808543	GTCTTCCTGCGTGTTGATCTTT	59.191	45.455	0.00	0.00	0.00	2.52
2272	2304	2.943265	AGCTTGCTGGTCCCCCAT	60.943	61.111	0.00	0.00	40.90	4.00
2285	2317	2.282745	GAGGTTGCCTGGCAGCTT	60.283	61.111	30.27	25.39	40.61	3.74
2314	2346	1.007618	GGCGTACGCATCTACTCCC	60.008	63.158	37.99	16.23	44.11	4.30
2418	2450	0.556258	AGTAAAGGGGCAATAGGGGC	59.444	55.000	0.00	0.00	0.00	5.80
2454	2486	1.071699	AGTAAAACGAAGGCAGGCTCA	59.928	47.619	0.00	0.00	0.00	4.26
2477	2509	5.010922	ACAAGATAAAAGGCAAGCACAATCA	59.989	36.000	0.00	0.00	0.00	2.57
2479	2511	5.473066	ACAAGATAAAAGGCAAGCACAAT	57.527	34.783	0.00	0.00	0.00	2.71
2554	2586	5.266733	ACTTGTTCAAACATGACAAGCAT	57.733	34.783	18.97	3.77	40.80	3.79
2614	2646	9.999009	GAAGCTACCAAACCAAACTTATATAAC	57.001	33.333	0.00	0.00	0.00	1.89
2862	2896	5.188434	ACTATGGTACTTGCGTGTAGACTA	58.812	41.667	0.00	0.00	0.00	2.59
3025	3063	2.949451	ATCTAGCACTTGACTCCACG	57.051	50.000	0.00	0.00	0.00	4.94
3079	3128	2.174685	TCTAGCATTGTCAGGGCCTA	57.825	50.000	5.28	0.00	0.00	3.93
3222	3275	1.444553	GCTCACCAGTCGAACTCCG	60.445	63.158	0.00	0.00	40.25	4.63
3404	3460	3.118038	GCCATCTGGTTTGTATACCTGGA	60.118	47.826	0.00	0.00	39.04	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.