AutoCloner

Multiple sequence alignment - TraesCS3B01G236300

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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	TraesCS3B01G236300	chr3B	100.000	2699	0	0	1	2699	368884062	368881364	0.000000e+00	4985
1	TraesCS3B01G236300	chrUn	96.819	1949	56	5	1	1945	189394034	189395980	0.000000e+00	3251
2	TraesCS3B01G236300	chrUn	97.679	517	12	0	2183	2699	171047543	171048059	0.000000e+00	889
3	TraesCS3B01G236300	chrUn	97.679	517	12	0	2183	2699	189396298	189396814	0.000000e+00	889
4	TraesCS3B01G236300	chrUn	97.292	517	14	0	2183	2699	399419721	399419205	0.000000e+00	878
5	TraesCS3B01G236300	chrUn	96.552	261	8	1	1939	2198	171047269	171047529	5.340000e-117	431
6	TraesCS3B01G236300	chrUn	96.552	261	8	1	1939	2198	189396024	189396284	5.340000e-117	431
7	TraesCS3B01G236300	chr5B	96.817	1948	57	4	1	1945	679660392	679662337	0.000000e+00	3249
8	TraesCS3B01G236300	chr5B	97.292	517	14	0	2183	2699	679662654	679663170	0.000000e+00	878
9	TraesCS3B01G236300	chr5B	97.308	260	7	0	1939	2198	679662381	679662640	2.470000e-120	442
10	TraesCS3B01G236300	chr4D	96.817	1948	57	4	1	1945	123414377	123416322	0.000000e+00	3249
11	TraesCS3B01G236300	chr4D	97.485	517	13	0	2183	2699	398043100	398042584	0.000000e+00	883
12	TraesCS3B01G236300	chr7B	96.766	1948	58	4	1	1945	743087694	743089639	0.000000e+00	3243
13	TraesCS3B01G236300	chr7B	96.923	260	8	0	1939	2198	743089683	743089942	1.150000e-118	436
14	TraesCS3B01G236300	chr5A	96.715	1948	59	4	1	1945	16601428	16599483	0.000000e+00	3238
15	TraesCS3B01G236300	chr5A	96.509	1948	63	4	1	1945	300074474	300076419	0.000000e+00	3216
16	TraesCS3B01G236300	chr5A	96.923	260	8	0	1939	2198	16599439	16599180	1.150000e-118	436
17	TraesCS3B01G236300	chr5A	96.935	261	7	1	1939	2198	300076463	300076723	1.150000e-118	436
18	TraesCS3B01G236300	chr2A	96.715	1948	59	4	1	1945	618278461	618276516	0.000000e+00	3238
19	TraesCS3B01G236300	chr2A	97.679	517	12	0	2183	2699	735196409	735196925	0.000000e+00	889
20	TraesCS3B01G236300	chr7D	96.610	1947	60	5	3	1945	203554849	203552905	0.000000e+00	3225
21	TraesCS3B01G236300	chr7D	97.679	517	12	0	2183	2699	626694018	626693502	0.000000e+00	889
22	TraesCS3B01G236300	chr7D	96.935	261	7	1	1939	2198	203552861	203552601	1.150000e-118	436
23	TraesCS3B01G236300	chr6A	96.509	1948	63	4	1	1945	289130125	289132070	0.000000e+00	3216
24	TraesCS3B01G236300	chr6A	97.292	517	14	0	2183	2699	289132387	289132903	0.000000e+00	878
25	TraesCS3B01G236300	chr6A	96.923	260	8	0	1939	2198	289132114	289132373	1.150000e-118	436
26	TraesCS3B01G236300	chr1A	94.312	1178	44	5	769	1945	115939003	115937848	0.000000e+00	1783
27	TraesCS3B01G236300	chr4A	97.292	517	14	0	2183	2699	67583772	67583256	0.000000e+00	878
28	TraesCS3B01G236300	chr7A	97.308	260	7	0	1939	2198	4963326	4963585	2.470000e-120	442

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	TraesCS3B01G236300	chr3B	368881364	368884062	2698	True	4985.000000	4985	100.000000	1	2699	1	chr3B.!!$R1	2698
1	TraesCS3B01G236300	chrUn	189394034	189396814	2780	False	1523.666667	3251	97.016667	1	2699	3	chrUn.!!$F2	2698
2	TraesCS3B01G236300	chrUn	399419205	399419721	516	True	878.000000	878	97.292000	2183	2699	1	chrUn.!!$R1	516
3	TraesCS3B01G236300	chrUn	171047269	171048059	790	False	660.000000	889	97.115500	1939	2699	2	chrUn.!!$F1	760
4	TraesCS3B01G236300	chr5B	679660392	679663170	2778	False	1523.000000	3249	97.139000	1	2699	3	chr5B.!!$F1	2698
5	TraesCS3B01G236300	chr4D	123414377	123416322	1945	False	3249.000000	3249	96.817000	1	1945	1	chr4D.!!$F1	1944
6	TraesCS3B01G236300	chr4D	398042584	398043100	516	True	883.000000	883	97.485000	2183	2699	1	chr4D.!!$R1	516
7	TraesCS3B01G236300	chr7B	743087694	743089942	2248	False	1839.500000	3243	96.844500	1	2198	2	chr7B.!!$F1	2197
8	TraesCS3B01G236300	chr5A	16599180	16601428	2248	True	1837.000000	3238	96.819000	1	2198	2	chr5A.!!$R1	2197
9	TraesCS3B01G236300	chr5A	300074474	300076723	2249	False	1826.000000	3216	96.722000	1	2198	2	chr5A.!!$F1	2197
10	TraesCS3B01G236300	chr2A	618276516	618278461	1945	True	3238.000000	3238	96.715000	1	1945	1	chr2A.!!$R1	1944
11	TraesCS3B01G236300	chr2A	735196409	735196925	516	False	889.000000	889	97.679000	2183	2699	1	chr2A.!!$F1	516
12	TraesCS3B01G236300	chr7D	203552601	203554849	2248	True	1830.500000	3225	96.772500	3	2198	2	chr7D.!!$R2	2195
13	TraesCS3B01G236300	chr7D	626693502	626694018	516	True	889.000000	889	97.679000	2183	2699	1	chr7D.!!$R1	516
14	TraesCS3B01G236300	chr6A	289130125	289132903	2778	False	1510.000000	3216	96.908000	1	2699	3	chr6A.!!$F1	2698
15	TraesCS3B01G236300	chr1A	115937848	115939003	1155	True	1783.000000	1783	94.312000	769	1945	1	chr1A.!!$R1	1176
16	TraesCS3B01G236300	chr4A	67583256	67583772	516	True	878.000000	878	97.292000	2183	2699	1	chr4A.!!$R1	516

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
34	35	0.174845	CCCGCTCGGTCTCAATACAA	59.825	55.0	7.59	0.0	0.0	2.41	F
848	852	0.179234	TTTTCCGATATGCCGCTCCA	59.821	50.0	0.00	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1531	1537	1.112315	CCAGATCGGCTAGTGCTCCT	61.112	60.0	0.00	0.00	39.59	3.69	R
2251	2340	1.373570	CTTCACTCGCAGGGAATTCC	58.626	55.0	16.74	16.74	36.96	3.01	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
20	21	1.382522	CTTAATGCATGTCACCCGCT	58.617	50.000	0.00	0.00	0.00	5.52
23	24	4.758251	TGCATGTCACCCGCTCGG	62.758	66.667	0.48	0.48	37.81	4.63
34	35	0.174845	CCCGCTCGGTCTCAATACAA	59.825	55.000	7.59	0.00	0.00	2.41
51	52	6.265422	TCAATACAACAAGTGACTCTCTCTCA	59.735	38.462	0.00	0.00	0.00	3.27
52	53	4.314740	ACAACAAGTGACTCTCTCTCAC	57.685	45.455	0.00	0.00	38.70	3.51
59	60	4.406456	AGTGACTCTCTCTCACACAAGAT	58.594	43.478	0.00	0.00	40.56	2.40
93	94	5.937975	ACCGATTCATCCAATCCAATTTT	57.062	34.783	0.00	0.00	38.17	1.82
194	196	4.361783	TCTATCCAGATCAGGGTTGAACA	58.638	43.478	4.05	0.00	36.78	3.18
258	261	3.235200	AGAAACCAGTGACTCTACAGCT	58.765	45.455	0.00	0.00	0.00	4.24
278	281	1.188219	AGGGCTCGATGGCGATGTAT	61.188	55.000	0.00	0.00	46.80	2.29
399	402	8.749354	GGGATGACTTTTATTATCCAAGTTGTT	58.251	33.333	1.45	0.00	40.65	2.83
462	465	3.690460	CTTGTGGTAGAAGATTGGGCTT	58.310	45.455	0.00	0.00	0.00	4.35
481	484	3.806380	CTTTGCTATGCAGATCCACTCT	58.194	45.455	0.00	0.00	40.61	3.24
485	488	3.320256	TGCTATGCAGATCCACTCTACTG	59.680	47.826	0.00	0.00	33.32	2.74
554	557	9.635404	AGTTACTAGTAGCTAATCAAGTCAGAT	57.365	33.333	16.77	0.00	0.00	2.90
577	580	0.606673	GGTGGCCGAGAAGCTTCTTT	60.607	55.000	29.02	9.31	37.73	2.52
603	606	0.397564	CCCCCAAAAGCAAAGCACAT	59.602	50.000	0.00	0.00	0.00	3.21
614	617	5.152623	AGCAAAGCACATACTCTACTCAA	57.847	39.130	0.00	0.00	0.00	3.02
618	621	5.683876	AAGCACATACTCTACTCAACCAT	57.316	39.130	0.00	0.00	0.00	3.55
621	624	4.758688	CACATACTCTACTCAACCATGCA	58.241	43.478	0.00	0.00	0.00	3.96
650	653	2.965831	CCTACGGAGGGAGAAATCATCA	59.034	50.000	5.47	0.00	39.48	3.07
668	671	7.835728	ATCATCAAAATATCCTCATCCCCTA	57.164	36.000	0.00	0.00	0.00	3.53
818	822	4.355925	CGGGCCCGTATAGAAAGC	57.644	61.111	36.64	0.00	34.35	3.51
848	852	0.179234	TTTTCCGATATGCCGCTCCA	59.821	50.000	0.00	0.00	0.00	3.86
922	926	2.424601	CGTCATTCCATGGAAAGCATGT	59.575	45.455	30.28	10.74	37.69	3.21
1113	1118	8.486210	ACAGTGATGGCTATTCATTTAAGTCTA	58.514	33.333	0.00	0.00	0.00	2.59
1145	1150	3.496692	CCACCAGATCTTCAACAAGGTGA	60.497	47.826	21.68	0.00	45.92	4.02
1178	1183	6.474427	CGTATTTCGTATGTACATGTTCCTGT	59.526	38.462	18.81	2.19	34.52	4.00
1183	1188	2.949177	TGTACATGTTCCTGTGGCTT	57.051	45.000	2.30	0.00	0.00	4.35
1311	1317	7.399245	TGGTGCTTTTTCTACTTTGTTTACT	57.601	32.000	0.00	0.00	0.00	2.24
1380	1386	1.434555	TGTGGGATGCTCGTTTAACG	58.565	50.000	11.60	11.60	44.19	3.18
1382	1388	1.802365	GTGGGATGCTCGTTTAACGTT	59.198	47.619	17.16	5.88	43.14	3.99
1447	1453	2.341846	AAAGCTTCCTGTCAAACCGA	57.658	45.000	0.00	0.00	0.00	4.69
1507	1513	6.884836	ACCAATAATAAAGTCTCCAGTCAACC	59.115	38.462	0.00	0.00	0.00	3.77
1531	1537	4.377021	GTGGAATACATCGCATCAACCTA	58.623	43.478	0.00	0.00	0.00	3.08
1538	1544	0.175760	TCGCATCAACCTAGGAGCAC	59.824	55.000	17.98	0.00	0.00	4.40
1617	1623	4.062490	TGCTAACTTCCCCTTCTCTACT	57.938	45.455	0.00	0.00	0.00	2.57
1696	1703	5.880887	CCCTTAACGGAAGAAATAGAAGCTT	59.119	40.000	0.00	0.00	37.33	3.74
1826	1833	6.463190	GGCAAAATGGGTCAAAAAGTAGGTTA	60.463	38.462	0.00	0.00	0.00	2.85
1923	1930	7.271438	GCTTTTGGATTCTTATCGAAAGTGAAC	59.729	37.037	0.00	0.00	38.93	3.18
2095	2153	3.118884	GGTAAAGGAAGGCGTATCACAGA	60.119	47.826	0.00	0.00	0.00	3.41
2098	2156	0.530870	GGAAGGCGTATCACAGAGGC	60.531	60.000	0.00	0.00	0.00	4.70
2163	2222	6.808704	TGAAAACATGAACACAAACGAAATCA	59.191	30.769	0.00	0.00	0.00	2.57
2204	2293	5.542848	AAAGAAAAGGGAGGAGATGGATT	57.457	39.130	0.00	0.00	0.00	3.01
2251	2340	9.717892	CTTTGATGATCTTCAACACATCTATTG	57.282	33.333	20.34	2.10	39.54	1.90
2319	2408	6.865726	TCTTGAGCGCTATCTGATCTTATTTC	59.134	38.462	11.50	0.00	0.00	2.17
2320	2409	5.473931	TGAGCGCTATCTGATCTTATTTCC	58.526	41.667	11.50	0.00	0.00	3.13
2321	2410	4.826556	AGCGCTATCTGATCTTATTTCCC	58.173	43.478	8.99	0.00	0.00	3.97
2340	2429	4.980573	TCCCTATTTCAAATATGGGACCG	58.019	43.478	17.22	0.00	38.67	4.79
2414	2503	1.667154	CTCGACCAATCCTCGGAGCA	61.667	60.000	0.00	0.00	0.00	4.26
2487	2576	2.922740	ACCTTTAGCACTTCCGTTCA	57.077	45.000	0.00	0.00	0.00	3.18
2517	2606	1.134371	GGAGTATGGCTGGAAGGTCAC	60.134	57.143	0.00	0.00	0.00	3.67
2595	2684	7.061905	CGCTATTGAACTTCGGTACCTATATTG	59.938	40.741	10.90	0.00	0.00	1.90
2674	2763	5.957842	TCCACATTGAGGTGAAATTACAC	57.042	39.130	0.00	0.00	41.32	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	4.038763	AGTCACTTGTTGTATTGAGACCGA	59.961	41.667	0.00	0.00	0.00	4.69
23	24	6.451393	AGAGAGTCACTTGTTGTATTGAGAC	58.549	40.000	0.00	0.00	0.00	3.36
34	35	3.291584	TGTGTGAGAGAGAGTCACTTGT	58.708	45.455	4.96	0.00	44.02	3.16
51	52	7.406031	TCGGTAATCTTTCTCTATCTTGTGT	57.594	36.000	0.00	0.00	0.00	3.72
52	53	8.879342	AATCGGTAATCTTTCTCTATCTTGTG	57.121	34.615	0.00	0.00	0.00	3.33
59	60	7.597288	TGGATGAATCGGTAATCTTTCTCTA	57.403	36.000	0.00	0.00	0.00	2.43
93	94	7.498900	ACAACAACAATGAACTCACTTCTGATA	59.501	33.333	0.00	0.00	0.00	2.15
194	196	3.069443	TCTTTGGCTTTTCCATTCGCTTT	59.931	39.130	0.00	0.00	46.04	3.51
278	281	5.369699	CCCTAACTCCCCATTCTTTCTATCA	59.630	44.000	0.00	0.00	0.00	2.15
399	402	7.160049	TGTACTTGATTCACCCACGTAAATAA	58.840	34.615	0.00	0.00	0.00	1.40
462	465	3.963374	AGTAGAGTGGATCTGCATAGCAA	59.037	43.478	0.00	0.00	42.69	3.91
481	484	4.250464	CAATGCGTACTTCTTTCCCAGTA	58.750	43.478	0.00	0.00	0.00	2.74
485	488	2.084546	AGCAATGCGTACTTCTTTCCC	58.915	47.619	0.00	0.00	0.00	3.97
554	557	1.198759	AAGCTTCTCGGCCACCCTAA	61.199	55.000	2.24	0.00	0.00	2.69
577	580	2.203625	GCTTTTGGGGGCACAGGA	60.204	61.111	0.00	0.00	0.00	3.86
603	606	5.880332	GGAAAATGCATGGTTGAGTAGAGTA	59.120	40.000	0.00	0.00	0.00	2.59
614	617	2.091541	CGTAGGTGGAAAATGCATGGT	58.908	47.619	0.00	0.00	0.00	3.55
668	671	4.084287	GTCCTATTTTCGGGTTCCCTTTT	58.916	43.478	6.31	0.00	0.00	2.27
685	688	2.775960	TCACCTATCCACTCTCGTCCTA	59.224	50.000	0.00	0.00	0.00	2.94
818	822	5.507985	GGCATATCGGAAAAAGAAGGATTGG	60.508	44.000	0.00	0.00	0.00	3.16
879	883	4.021456	CGGAATTCCCCTTGCTTAGTTTTT	60.021	41.667	19.01	0.00	0.00	1.94
969	973	1.412079	TGCCTTGCAAGTGGAACAAT	58.588	45.000	24.35	0.00	39.71	2.71
1113	1118	1.612442	ATCTGGTGGTGCTACCCGT	60.612	57.895	2.28	0.00	40.09	5.28
1330	1336	1.654137	CCCCACATAGGCATTCCCCA	61.654	60.000	0.00	0.00	35.39	4.96
1337	1343	1.562475	GAAAGGTACCCCACATAGGCA	59.438	52.381	8.74	0.00	35.39	4.75
1360	1366	2.006888	CGTTAAACGAGCATCCCACAT	58.993	47.619	0.00	0.00	46.05	3.21
1447	1453	3.535561	CAGCACGGATTGAAATAGGAGT	58.464	45.455	0.00	0.00	0.00	3.85
1507	1513	1.864565	TGATGCGATGTATTCCACCG	58.135	50.000	0.00	0.00	0.00	4.94
1531	1537	1.112315	CCAGATCGGCTAGTGCTCCT	61.112	60.000	0.00	0.00	39.59	3.69
1538	1544	4.527509	ATTGATGTACCAGATCGGCTAG	57.472	45.455	3.85	0.00	39.03	3.42
1617	1623	4.508461	TTCCAGAACGAACAAGATACGA	57.492	40.909	0.00	0.00	0.00	3.43
1696	1703	7.086685	AGGTTTTTAGTGGTATTCCTTCTCA	57.913	36.000	0.00	0.00	34.23	3.27
1923	1930	3.451540	GACTAAGGGAAGTGTTAGAGGGG	59.548	52.174	0.00	0.00	31.74	4.79
2004	2061	8.166422	TCCTTCTTTCCTTTGAAATTGTAGAC	57.834	34.615	0.00	0.00	39.65	2.59
2005	2062	8.760980	TTCCTTCTTTCCTTTGAAATTGTAGA	57.239	30.769	0.00	0.00	39.65	2.59
2006	2063	9.415544	CATTCCTTCTTTCCTTTGAAATTGTAG	57.584	33.333	0.00	0.00	39.65	2.74
2204	2293	8.748412	TCAAAGAAAGGAAAAAGACTGAATTCA	58.252	29.630	8.12	8.12	0.00	2.57
2251	2340	1.373570	CTTCACTCGCAGGGAATTCC	58.626	55.000	16.74	16.74	36.96	3.01
2319	2408	4.760204	GTCGGTCCCATATTTGAAATAGGG	59.240	45.833	18.86	18.86	37.65	3.53
2320	2409	4.760204	GGTCGGTCCCATATTTGAAATAGG	59.240	45.833	3.83	3.31	0.00	2.57
2321	2410	5.621193	AGGTCGGTCCCATATTTGAAATAG	58.379	41.667	3.83	0.00	36.75	1.73
2414	2503	4.184629	CTCGAGAATTCGTTCATCCCTTT	58.815	43.478	6.58	0.00	46.72	3.11
2487	2576	4.603171	TCCAGCCATACTCCATCCAATATT	59.397	41.667	0.00	0.00	0.00	1.28
2517	2606	3.243569	CCGATTGACAAGACTAGCTAGGG	60.244	52.174	24.35	12.89	0.00	3.53
2595	2684	3.206150	TGAAGGTCTGTCTTGTTTCAGC	58.794	45.455	0.00	0.00	0.00	4.26
2674	2763	7.736447	GTAGTCCAGGATTATTTTCCTCATG	57.264	40.000	0.00	0.00	44.54	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.