AutoCloner

Multiple sequence alignment - TraesCS3B01G271100

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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	TraesCS3B01G271100	chr3B	100.000	3657	0	0	1	3657	436729446	436725790	0.000000e+00	6754.0
1	TraesCS3B01G271100	chr3B	89.883	1028	97	6	1399	2421	436574738	436575763	0.000000e+00	1315.0
2	TraesCS3B01G271100	chr3D	94.342	2775	106	26	258	3007	338350962	338348214	0.000000e+00	4207.0
3	TraesCS3B01G271100	chr3D	88.900	1027	104	5	1403	2421	338321170	338322194	0.000000e+00	1256.0
4	TraesCS3B01G271100	chr3D	94.825	657	28	4	3005	3657	338348166	338347512	0.000000e+00	1020.0
5	TraesCS3B01G271100	chr3D	96.935	261	8	0	1	261	338351250	338350990	4.340000e-119	438.0
6	TraesCS3B01G271100	chr3A	92.197	1948	91	30	1108	3008	456700944	456699011	0.000000e+00	2699.0
7	TraesCS3B01G271100	chr3A	89.731	1042	96	7	1389	2421	456452183	456453222	0.000000e+00	1321.0
8	TraesCS3B01G271100	chr3A	93.303	657	31	5	3005	3657	456698982	456698335	0.000000e+00	957.0
9	TraesCS3B01G271100	chr3A	87.544	843	64	20	258	1072	456701772	456700943	0.000000e+00	937.0
10	TraesCS3B01G271100	chr3A	91.418	268	11	5	1	260	456703470	456703207	1.250000e-94	357.0
11	TraesCS3B01G271100	chr2D	93.333	135	8	1	1517	1650	536380669	536380803	8.010000e-47	198.0
12	TraesCS3B01G271100	chr2B	92.537	134	10	0	1517	1650	637775928	637776061	3.730000e-45	193.0
13	TraesCS3B01G271100	chr6B	92.308	65	5	0	1846	1910	347591962	347591898	3.890000e-15	93.5
14	TraesCS3B01G271100	chr6B	93.750	48	3	0	2582	2629	40678305	40678258	5.070000e-09	73.1
15	TraesCS3B01G271100	chr1D	91.667	48	4	0	2582	2629	327220586	327220539	2.360000e-07	67.6
16	TraesCS3B01G271100	chr7D	85.484	62	9	0	2572	2633	103820622	103820561	8.480000e-07	65.8
17	TraesCS3B01G271100	chr5A	85.938	64	6	3	2572	2633	427829165	427829103	8.480000e-07	65.8
18	TraesCS3B01G271100	chr2A	82.051	78	12	1	2573	2648	713152778	713152855	8.480000e-07	65.8
19	TraesCS3B01G271100	chr4B	88.462	52	6	0	2582	2633	536409015	536408964	3.050000e-06	63.9
20	TraesCS3B01G271100	chr1A	89.583	48	5	0	2582	2629	251695777	251695730	1.100000e-05	62.1

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	TraesCS3B01G271100	chr3B	436725790	436729446	3656	True	6754.000000	6754	100.000000	1	3657	1	chr3B.!!$R1	3656
1	TraesCS3B01G271100	chr3B	436574738	436575763	1025	False	1315.000000	1315	89.883000	1399	2421	1	chr3B.!!$F1	1022
2	TraesCS3B01G271100	chr3D	338347512	338351250	3738	True	1888.333333	4207	95.367333	1	3657	3	chr3D.!!$R1	3656
3	TraesCS3B01G271100	chr3D	338321170	338322194	1024	False	1256.000000	1256	88.900000	1403	2421	1	chr3D.!!$F1	1018
4	TraesCS3B01G271100	chr3A	456452183	456453222	1039	False	1321.000000	1321	89.731000	1389	2421	1	chr3A.!!$F1	1032
5	TraesCS3B01G271100	chr3A	456698335	456703470	5135	True	1237.500000	2699	91.115500	1	3657	4	chr3A.!!$R1	3656

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
120	129	0.524862	CCAGCTAACCGTAGTCGTGT	59.475	55.0	0.0	0.0	35.01	4.49	F
1343	2848	0.246360	TACACCTGGACGAGTGCATG	59.754	55.0	0.0	0.0	37.51	4.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1387	2892	0.106335	TCGCAACAACTCCCGGTAAA	59.894	50.0	0.0	0.0	0.0	2.01	R
2720	4265	0.603065	GTGGATTTGGTCTTGCCCAC	59.397	55.0	0.0	0.0	37.5	4.61	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
120	129	0.524862	CCAGCTAACCGTAGTCGTGT	59.475	55.000	0.00	0.00	35.01	4.49
224	233	5.977635	TGAGTGGGAATGACAGTATTACAG	58.022	41.667	0.00	0.00	0.00	2.74
233	242	9.517609	GGAATGACAGTATTACAGTGTTACTAG	57.482	37.037	0.00	2.68	41.06	2.57
270	1716	3.881688	CTGATGCTTTGTAGATCCCTTGG	59.118	47.826	0.00	0.00	0.00	3.61
284	1730	4.150897	TCCCTTGGTTGCATACTATCAC	57.849	45.455	0.00	0.00	0.00	3.06
294	1740	5.728637	TGCATACTATCACTACCAGATGG	57.271	43.478	0.00	0.00	42.17	3.51
311	1757	5.345702	CAGATGGTACCAATGAATTTGCAG	58.654	41.667	20.76	0.00	33.73	4.41
588	2034	5.062308	GCTAGTCGAGGTTTTGTATGTCTTG	59.938	44.000	0.00	0.00	0.00	3.02
589	2035	3.746492	AGTCGAGGTTTTGTATGTCTTGC	59.254	43.478	0.00	0.00	0.00	4.01
624	2072	2.293122	TGGCAGTTGTTGTAGTTCATGC	59.707	45.455	0.00	0.00	0.00	4.06
713	2161	8.981647	CGAAATCAAATTCAGAAAATGGTCTTT	58.018	29.630	0.00	0.00	0.00	2.52
768	2243	3.851976	ATCTTACACTGACGAGGTGTC	57.148	47.619	13.68	0.00	45.23	3.67
931	2407	5.297029	GGCTGTAATCCACCAGTTCTAATTC	59.703	44.000	0.00	0.00	0.00	2.17
960	2438	4.161377	GGTACAGAGAGGAGAAAGAAGCAT	59.839	45.833	0.00	0.00	0.00	3.79
1001	2479	5.567037	TGGATGATGGAATAAAGACCGAT	57.433	39.130	0.00	0.00	0.00	4.18
1081	2559	2.289565	CGGAAGCTTAACCATTCCCTC	58.710	52.381	0.00	0.00	39.50	4.30
1083	2561	2.656002	GAAGCTTAACCATTCCCTCCC	58.344	52.381	0.00	0.00	0.00	4.30
1085	2563	2.288525	AGCTTAACCATTCCCTCCCTT	58.711	47.619	0.00	0.00	0.00	3.95
1086	2564	3.470868	AGCTTAACCATTCCCTCCCTTA	58.529	45.455	0.00	0.00	0.00	2.69
1087	2565	3.202373	AGCTTAACCATTCCCTCCCTTAC	59.798	47.826	0.00	0.00	0.00	2.34
1088	2566	3.053917	GCTTAACCATTCCCTCCCTTACA	60.054	47.826	0.00	0.00	0.00	2.41
1089	2567	4.386424	GCTTAACCATTCCCTCCCTTACAT	60.386	45.833	0.00	0.00	0.00	2.29
1091	2569	3.151542	ACCATTCCCTCCCTTACATCT	57.848	47.619	0.00	0.00	0.00	2.90
1093	2571	3.048600	CCATTCCCTCCCTTACATCTGA	58.951	50.000	0.00	0.00	0.00	3.27
1094	2572	3.072184	CCATTCCCTCCCTTACATCTGAG	59.928	52.174	0.00	0.00	0.00	3.35
1095	2573	1.794714	TCCCTCCCTTACATCTGAGC	58.205	55.000	0.00	0.00	0.00	4.26
1099	2577	2.364970	CCTCCCTTACATCTGAGCAGAG	59.635	54.545	6.34	1.73	41.33	3.35
1101	2579	1.483827	CCCTTACATCTGAGCAGAGCA	59.516	52.381	6.34	0.00	41.33	4.26
1103	2581	2.483363	CCTTACATCTGAGCAGAGCAGG	60.483	54.545	6.34	4.90	41.33	4.85
1104	2582	0.463204	TACATCTGAGCAGAGCAGGC	59.537	55.000	6.34	0.00	41.33	4.85
1105	2583	1.883544	CATCTGAGCAGAGCAGGCG	60.884	63.158	6.34	0.00	41.33	5.52
1304	2782	0.673022	CTCAAGCTGGTCAGTGCTCC	60.673	60.000	0.00	0.00	38.75	4.70
1305	2783	2.031516	CAAGCTGGTCAGTGCTCCG	61.032	63.158	0.00	0.00	38.75	4.63
1308	2786	1.185618	AGCTGGTCAGTGCTCCGTAA	61.186	55.000	0.00	0.00	33.90	3.18
1317	2795	1.137513	GTGCTCCGTAATCCGTATGC	58.862	55.000	0.00	0.00	33.66	3.14
1324	2802	2.349275	CCGTAATCCGTATGCGTTTGTT	59.651	45.455	1.69	0.00	36.15	2.83
1325	2803	3.551082	CCGTAATCCGTATGCGTTTGTTA	59.449	43.478	1.69	0.00	36.15	2.41
1329	2834	2.067766	TCCGTATGCGTTTGTTACACC	58.932	47.619	1.69	0.00	36.15	4.16
1336	2841	1.855513	CGTTTGTTACACCTGGACGA	58.144	50.000	0.00	0.00	0.00	4.20
1343	2848	0.246360	TACACCTGGACGAGTGCATG	59.754	55.000	0.00	0.00	37.51	4.06
1428	2935	1.272147	GGTTGATGCAGGAAGAACCCT	60.272	52.381	0.00	0.00	40.05	4.34
1653	3160	2.345880	CGGACTACATCCCGTTCCGG	62.346	65.000	0.00	0.00	46.04	5.14
2136	3652	1.450312	GCTGCCGCACCTCTACATT	60.450	57.895	0.00	0.00	35.78	2.71
2537	4067	2.771372	GGGGTTAATGATGTGCCCAATT	59.229	45.455	0.00	0.00	41.02	2.32
2538	4068	3.181466	GGGGTTAATGATGTGCCCAATTC	60.181	47.826	0.00	0.00	41.02	2.17
2576	4108	8.700973	ACCCAATTTGACATATTGGTTTATACC	58.299	33.333	26.37	0.00	46.91	2.73
2583	4115	4.042435	ACATATTGGTTTATACCCTCCCCG	59.958	45.833	0.00	0.00	44.35	5.73
2609	4141	9.683069	GTCCCATAATATAAGATGTTTTTGCAG	57.317	33.333	0.00	0.00	0.00	4.41
2683	4227	5.411977	AGATCTTGTCGAAGTCGTCTCTAAA	59.588	40.000	0.00	0.00	40.80	1.85
2690	4234	5.062308	GTCGAAGTCGTCTCTAAATTGCATT	59.938	40.000	0.00	0.00	40.80	3.56
2702	4247	2.818130	ATTGCATTGTGTTCCACCAC	57.182	45.000	0.00	0.00	32.73	4.16
2707	4252	2.575532	CATTGTGTTCCACCACTGACT	58.424	47.619	0.00	0.00	36.30	3.41
2708	4253	2.036958	TTGTGTTCCACCACTGACTG	57.963	50.000	0.00	0.00	36.30	3.51
2711	4256	2.102420	TGTGTTCCACCACTGACTGTAG	59.898	50.000	0.00	0.00	36.30	2.74
2790	4344	9.479549	AGATTGTAAATAAGTGGGATCACATTT	57.520	29.630	10.82	10.82	45.91	2.32
2817	4371	5.778862	TGATCGCGGATGAATAGTTATTGA	58.221	37.500	6.13	0.00	0.00	2.57
2851	4405	7.775053	ACAAAGGCTTATGGTTTGAATCTAA	57.225	32.000	0.00	0.00	35.55	2.10
2873	4427	2.113139	CAGGTGCACCCCGAGTTT	59.887	61.111	32.29	9.20	36.42	2.66
2890	4444	2.635427	AGTTTCTTGAGAGGGTGGAGAC	59.365	50.000	0.00	0.00	0.00	3.36
2907	4463	3.466836	GAGACACAACATGGAACTCACA	58.533	45.455	0.00	0.00	31.74	3.58
3001	4557	4.729868	AGTGCTAACATCAAAAGGACCTT	58.270	39.130	0.00	0.00	32.55	3.50
3062	4668	5.409520	GGAAATGTTTCATCAAAAGGGCTTC	59.590	40.000	7.69	0.00	38.92	3.86
3133	4739	1.963515	GAAAGGTGATTGTTGCAGGGT	59.036	47.619	0.00	0.00	0.00	4.34
3136	4742	1.039856	GGTGATTGTTGCAGGGTTGT	58.960	50.000	0.00	0.00	0.00	3.32
3141	4747	1.846007	TTGTTGCAGGGTTGTCAACT	58.154	45.000	15.17	0.00	39.69	3.16
3323	4930	8.851106	AGGCCATATGAATCTAGAGAATGATA	57.149	34.615	5.01	0.00	0.00	2.15
3468	5075	7.542477	AGTTCTTATCAGTACTCAAACATGACG	59.458	37.037	0.00	0.00	0.00	4.35
3469	5076	6.920817	TCTTATCAGTACTCAAACATGACGT	58.079	36.000	0.00	0.00	0.00	4.34
3572	5182	7.437267	CCTAAAATTGATGATGCTGAAACCATC	59.563	37.037	0.00	0.00	39.56	3.51
3573	5183	6.540438	AAATTGATGATGCTGAAACCATCT	57.460	33.333	0.00	0.00	39.76	2.90
3598	5208	2.832129	TGCCGAGAAGAAGTGGTTCTAT	59.168	45.455	0.00	0.00	42.59	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.140623	TCCCCAAGCGTTACAGTTTAAC	58.859	45.455	0.00	0.00	0.00	2.01
120	129	2.550277	TGAGGTGCCTCTCCTTATCA	57.450	50.000	17.96	0.00	43.12	2.15
270	1716	5.928839	CCATCTGGTAGTGATAGTATGCAAC	59.071	44.000	0.00	0.00	0.00	4.17
284	1730	6.460123	GCAAATTCATTGGTACCATCTGGTAG	60.460	42.308	17.17	4.28	43.84	3.18
294	1740	3.193267	TCAGGCTGCAAATTCATTGGTAC	59.807	43.478	10.34	0.00	39.54	3.34
300	1746	2.161855	TCGTTCAGGCTGCAAATTCAT	58.838	42.857	10.34	0.00	0.00	2.57
311	1757	1.468914	GGGAGACAAAATCGTTCAGGC	59.531	52.381	0.00	0.00	0.00	4.85
624	2072	1.078709	AGTTGCATGAACCGTGATCG	58.921	50.000	0.00	0.00	34.80	3.69
768	2243	3.309138	CAGCAAATCAGTCGAGGATCAAG	59.691	47.826	0.00	0.00	33.17	3.02
931	2407	2.382882	TCTCCTCTCTGTACCATGCTG	58.617	52.381	0.00	0.00	0.00	4.41
973	2451	6.122277	GTCTTTATTCCATCATCCAACCAGA	58.878	40.000	0.00	0.00	0.00	3.86
1001	2479	1.726571	GCGCGGCGAAACTTTTTATCA	60.727	47.619	28.54	0.00	0.00	2.15
1081	2559	1.483827	TGCTCTGCTCAGATGTAAGGG	59.516	52.381	0.00	0.00	36.76	3.95
1083	2561	2.823984	CCTGCTCTGCTCAGATGTAAG	58.176	52.381	0.00	0.00	36.76	2.34
1085	2563	0.463204	GCCTGCTCTGCTCAGATGTA	59.537	55.000	0.00	0.00	36.76	2.29
1086	2564	1.221293	GCCTGCTCTGCTCAGATGT	59.779	57.895	0.00	0.00	36.76	3.06
1087	2565	1.883544	CGCCTGCTCTGCTCAGATG	60.884	63.158	0.00	0.00	36.76	2.90
1088	2566	1.611474	TTCGCCTGCTCTGCTCAGAT	61.611	55.000	0.00	0.00	36.76	2.90
1089	2567	1.820010	TTTCGCCTGCTCTGCTCAGA	61.820	55.000	0.00	0.00	33.54	3.27
1091	2569	0.952497	CTTTTCGCCTGCTCTGCTCA	60.952	55.000	0.00	0.00	0.00	4.26
1093	2571	1.673665	CCTTTTCGCCTGCTCTGCT	60.674	57.895	0.00	0.00	0.00	4.24
1094	2572	2.873288	CCTTTTCGCCTGCTCTGC	59.127	61.111	0.00	0.00	0.00	4.26
1095	2573	1.919956	CTGCCTTTTCGCCTGCTCTG	61.920	60.000	0.00	0.00	0.00	3.35
1099	2577	3.673484	TGCTGCCTTTTCGCCTGC	61.673	61.111	0.00	0.00	0.00	4.85
1101	2579	2.113986	AGTGCTGCCTTTTCGCCT	59.886	55.556	0.00	0.00	0.00	5.52
1304	2782	5.995133	GTGTAACAAACGCATACGGATTACG	60.995	44.000	0.00	0.00	42.69	3.18
1305	2783	5.250332	GTGTAACAAACGCATACGGATTAC	58.750	41.667	0.00	0.00	39.79	1.89
1308	2786	2.674357	GGTGTAACAAACGCATACGGAT	59.326	45.455	0.00	0.00	41.46	4.18
1317	2795	1.790623	CTCGTCCAGGTGTAACAAACG	59.209	52.381	0.00	0.00	39.98	3.60
1324	2802	0.246360	CATGCACTCGTCCAGGTGTA	59.754	55.000	0.00	0.00	36.03	2.90
1325	2803	1.004560	CATGCACTCGTCCAGGTGT	60.005	57.895	0.00	0.00	36.03	4.16
1329	2834	2.819422	CAAATCATGCACTCGTCCAG	57.181	50.000	0.00	0.00	0.00	3.86
1343	2848	1.006805	CGCGAATGTGCAATGCAAATC	60.007	47.619	11.79	8.52	41.47	2.17
1380	2885	3.293337	ACAACTCCCGGTAAAGCTTTTT	58.707	40.909	18.47	0.00	0.00	1.94
1381	2886	2.940158	ACAACTCCCGGTAAAGCTTTT	58.060	42.857	18.47	1.58	0.00	2.27
1382	2887	2.621526	CAACAACTCCCGGTAAAGCTTT	59.378	45.455	17.30	17.30	0.00	3.51
1383	2888	2.227194	CAACAACTCCCGGTAAAGCTT	58.773	47.619	0.00	0.00	0.00	3.74
1384	2889	1.892209	CAACAACTCCCGGTAAAGCT	58.108	50.000	0.00	0.00	0.00	3.74
1385	2890	0.240145	GCAACAACTCCCGGTAAAGC	59.760	55.000	0.00	0.00	0.00	3.51
1386	2891	0.515564	CGCAACAACTCCCGGTAAAG	59.484	55.000	0.00	0.00	0.00	1.85
1387	2892	0.106335	TCGCAACAACTCCCGGTAAA	59.894	50.000	0.00	0.00	0.00	2.01
1388	2893	0.322322	ATCGCAACAACTCCCGGTAA	59.678	50.000	0.00	0.00	0.00	2.85
1428	2935	2.363276	ACCATCCGCCGGTAGTCA	60.363	61.111	1.63	0.00	34.02	3.41
1429	2936	1.745320	ATCACCATCCGCCGGTAGTC	61.745	60.000	1.63	0.00	34.02	2.59
2062	3578	2.126149	CTCGCTCTCGCTGTTGCT	60.126	61.111	0.00	0.00	36.97	3.91
2136	3652	3.257375	AGCAGATGTAGTCGTTGGTGTTA	59.743	43.478	0.00	0.00	0.00	2.41
2576	4108	4.359105	TCTTATATTATGGGACGGGGAGG	58.641	47.826	0.00	0.00	0.00	4.30
2583	4115	9.683069	CTGCAAAAACATCTTATATTATGGGAC	57.317	33.333	0.00	0.00	0.00	4.46
2609	4141	7.978975	TCCACAATTTTGCAAGTTAATATAGCC	59.021	33.333	0.00	0.00	0.00	3.93
2720	4265	0.603065	GTGGATTTGGTCTTGCCCAC	59.397	55.000	0.00	0.00	37.50	4.61
2790	4344	4.322080	ACTATTCATCCGCGATCAAAGA	57.678	40.909	8.23	0.00	0.00	2.52
2817	4371	9.845740	AAACCATAAGCCTTTGTTTTTAATCTT	57.154	25.926	0.00	0.00	0.00	2.40
2851	4405	2.257409	CTCGGGGTGCACCTGCTAAT	62.257	60.000	33.91	0.00	45.92	1.73
2873	4427	1.133167	TGTGTCTCCACCCTCTCAAGA	60.133	52.381	0.00	0.00	41.09	3.02
2927	4483	7.173907	TCCTAACTTCAGCAAAAATCTTCTCAG	59.826	37.037	0.00	0.00	0.00	3.35
3022	4628	3.737559	TTTCCTGCCATATTGGTCACT	57.262	42.857	0.00	0.00	40.46	3.41
3062	4668	7.220741	TCTTCCTCGTCATAGATATGAAAGG	57.779	40.000	18.24	18.24	43.65	3.11
3182	4788	7.765360	TGTTTAAAAGTGTACATACTATCCCCG	59.235	37.037	0.00	0.00	0.00	5.73
3190	4796	8.995220	TCAGACCATGTTTAAAAGTGTACATAC	58.005	33.333	0.00	0.00	30.53	2.39
3214	4821	1.629861	TCAGTGCCCATCAGAACATCA	59.370	47.619	0.00	0.00	0.00	3.07
3323	4930	6.962182	TCTGATAAACATTCTTCAGGTCCAT	58.038	36.000	0.00	0.00	36.95	3.41
3388	4995	7.498900	CCATGCTATCAATAGTAAACTTGGTCA	59.501	37.037	0.00	0.00	32.96	4.02
3468	5075	5.460419	CGTAGAAATCATAAGGAGTCAGCAC	59.540	44.000	0.00	0.00	0.00	4.40
3469	5076	5.127194	ACGTAGAAATCATAAGGAGTCAGCA	59.873	40.000	0.00	0.00	0.00	4.41
3572	5182	2.028930	ACCACTTCTTCTCGGCAACTAG	60.029	50.000	0.00	0.00	0.00	2.57
3573	5183	1.968493	ACCACTTCTTCTCGGCAACTA	59.032	47.619	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.