AutoCloner

Multiple sequence alignment - TraesCS3D01G457000

Loading Multiple Alignment...

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	TraesCS3D01G457000	chr3D	100.000	3329	0	0	1	3329	562537221	562540549	0.000000e+00	6148
1	TraesCS3D01G457000	chr3D	87.076	2213	214	46	1023	3202	562504180	562506353	0.000000e+00	2436
2	TraesCS3D01G457000	chr3D	81.087	1380	196	40	965	2324	562545090	562546424	0.000000e+00	1042
3	TraesCS3D01G457000	chr3D	78.123	1545	253	50	1023	2520	561462583	561461077	0.000000e+00	902
4	TraesCS3D01G457000	chr3D	77.298	1458	252	50	1023	2444	561456406	561454992	0.000000e+00	785
5	TraesCS3D01G457000	chr3D	96.407	167	4	2	5	170	549120982	549120817	1.180000e-69	274
6	TraesCS3D01G457000	chr3D	95.322	171	6	2	1	170	549113085	549112916	1.520000e-68	270
7	TraesCS3D01G457000	chr3D	85.246	122	17	1	3208	3329	562512005	562512125	1.250000e-24	124
8	TraesCS3D01G457000	chr3A	94.544	2346	81	12	702	3021	697673131	697675455	0.000000e+00	3579
9	TraesCS3D01G457000	chr3A	86.474	1486	144	24	1223	2694	697617717	697619159	0.000000e+00	1578
10	TraesCS3D01G457000	chr3A	80.435	1380	200	39	965	2324	697679882	697681211	0.000000e+00	989
11	TraesCS3D01G457000	chr3A	77.102	1594	236	82	1023	2550	697438034	697436504	0.000000e+00	802
12	TraesCS3D01G457000	chr3A	77.598	1357	225	45	1025	2347	697391456	697390145	0.000000e+00	749
13	TraesCS3D01G457000	chr3A	76.087	1196	209	51	990	2146	697457501	697456344	1.350000e-153	553
14	TraesCS3D01G457000	chr3A	94.624	279	15	0	3051	3329	697675455	697675733	1.830000e-117	433
15	TraesCS3D01G457000	chr3A	83.333	432	46	12	2777	3202	697619318	697619729	3.140000e-100	375
16	TraesCS3D01G457000	chr3A	92.135	89	6	1	3241	3329	697685443	697685530	1.250000e-24	124
17	TraesCS3D01G457000	chr3B	92.614	1733	96	8	883	2593	749859757	749861479	0.000000e+00	2462
18	TraesCS3D01G457000	chr3B	86.538	2028	208	39	988	2983	749725732	749727726	0.000000e+00	2172
19	TraesCS3D01G457000	chr3B	81.331	1382	200	36	966	2324	749979276	749980622	0.000000e+00	1070
20	TraesCS3D01G457000	chr3B	93.604	641	30	7	2685	3321	749861494	749862127	0.000000e+00	946
21	TraesCS3D01G457000	chr3B	77.625	1457	242	52	1023	2444	748779500	748778093	0.000000e+00	808
22	TraesCS3D01G457000	chr3B	89.552	201	18	1	3005	3202	749727812	749728012	5.510000e-63	252
23	TraesCS3D01G457000	chr5D	96.259	695	19	6	1	689	33736675	33735982	0.000000e+00	1133
24	TraesCS3D01G457000	chr5D	96.812	596	17	1	88	681	33744788	33744193	0.000000e+00	994
25	TraesCS3D01G457000	chr5D	96.552	580	17	2	105	681	236729565	236728986	0.000000e+00	957
26	TraesCS3D01G457000	chr4D	96.204	685	22	3	1	681	25701743	25702427	0.000000e+00	1118
27	TraesCS3D01G457000	chr4D	96.204	685	21	4	1	681	25709588	25710271	0.000000e+00	1116
28	TraesCS3D01G457000	chr4D	96.334	682	19	5	5	681	68394454	68393774	0.000000e+00	1116
29	TraesCS3D01G457000	chr4D	95.359	668	16	4	19	683	68386248	68385593	0.000000e+00	1048
30	TraesCS3D01G457000	chr4D	92.105	608	31	13	80	681	398316861	398316265	0.000000e+00	841
31	TraesCS3D01G457000	chr4D	94.152	171	7	2	1	170	58511239	58511071	1.190000e-64	257
32	TraesCS3D01G457000	chr7D	91.873	566	34	10	131	690	173976443	173977002	0.000000e+00	780
33	TraesCS3D01G457000	chr1D	91.034	580	37	13	107	681	206904157	206904726	0.000000e+00	769

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	TraesCS3D01G457000	chr3D	562537221	562540549	3328	False	6148.0	6148	100.0000	1	3329	1	chr3D.!!$F3	3328
1	TraesCS3D01G457000	chr3D	562504180	562506353	2173	False	2436.0	2436	87.0760	1023	3202	1	chr3D.!!$F1	2179
2	TraesCS3D01G457000	chr3D	562545090	562546424	1334	False	1042.0	1042	81.0870	965	2324	1	chr3D.!!$F4	1359
3	TraesCS3D01G457000	chr3D	561461077	561462583	1506	True	902.0	902	78.1230	1023	2520	1	chr3D.!!$R4	1497
4	TraesCS3D01G457000	chr3D	561454992	561456406	1414	True	785.0	785	77.2980	1023	2444	1	chr3D.!!$R3	1421
5	TraesCS3D01G457000	chr3A	697673131	697675733	2602	False	2006.0	3579	94.5840	702	3329	2	chr3A.!!$F4	2627
6	TraesCS3D01G457000	chr3A	697679882	697681211	1329	False	989.0	989	80.4350	965	2324	1	chr3A.!!$F1	1359
7	TraesCS3D01G457000	chr3A	697617717	697619729	2012	False	976.5	1578	84.9035	1223	3202	2	chr3A.!!$F3	1979
8	TraesCS3D01G457000	chr3A	697436504	697438034	1530	True	802.0	802	77.1020	1023	2550	1	chr3A.!!$R2	1527
9	TraesCS3D01G457000	chr3A	697390145	697391456	1311	True	749.0	749	77.5980	1025	2347	1	chr3A.!!$R1	1322
10	TraesCS3D01G457000	chr3A	697456344	697457501	1157	True	553.0	553	76.0870	990	2146	1	chr3A.!!$R3	1156
11	TraesCS3D01G457000	chr3B	749859757	749862127	2370	False	1704.0	2462	93.1090	883	3321	2	chr3B.!!$F3	2438
12	TraesCS3D01G457000	chr3B	749725732	749728012	2280	False	1212.0	2172	88.0450	988	3202	2	chr3B.!!$F2	2214
13	TraesCS3D01G457000	chr3B	749979276	749980622	1346	False	1070.0	1070	81.3310	966	2324	1	chr3B.!!$F1	1358
14	TraesCS3D01G457000	chr3B	748778093	748779500	1407	True	808.0	808	77.6250	1023	2444	1	chr3B.!!$R1	1421
15	TraesCS3D01G457000	chr5D	33735982	33736675	693	True	1133.0	1133	96.2590	1	689	1	chr5D.!!$R1	688
16	TraesCS3D01G457000	chr5D	33744193	33744788	595	True	994.0	994	96.8120	88	681	1	chr5D.!!$R2	593
17	TraesCS3D01G457000	chr5D	236728986	236729565	579	True	957.0	957	96.5520	105	681	1	chr5D.!!$R3	576
18	TraesCS3D01G457000	chr4D	25701743	25702427	684	False	1118.0	1118	96.2040	1	681	1	chr4D.!!$F1	680
19	TraesCS3D01G457000	chr4D	25709588	25710271	683	False	1116.0	1116	96.2040	1	681	1	chr4D.!!$F2	680
20	TraesCS3D01G457000	chr4D	68393774	68394454	680	True	1116.0	1116	96.3340	5	681	1	chr4D.!!$R3	676
21	TraesCS3D01G457000	chr4D	68385593	68386248	655	True	1048.0	1048	95.3590	19	683	1	chr4D.!!$R2	664
22	TraesCS3D01G457000	chr4D	398316265	398316861	596	True	841.0	841	92.1050	80	681	1	chr4D.!!$R4	601
23	TraesCS3D01G457000	chr7D	173976443	173977002	559	False	780.0	780	91.8730	131	690	1	chr7D.!!$F1	559
24	TraesCS3D01G457000	chr1D	206904157	206904726	569	False	769.0	769	91.0340	107	681	1	chr1D.!!$F1	574

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
783	801	0.179121	ACACGATAATCCAAGCGCGA	60.179	50.0	12.10	0.0	0.00	5.87	F
860	878	0.251341	AATCGCTTGAGGCCTTGGTT	60.251	50.0	6.77	0.0	37.74	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2187	2351	1.324383	TAACAGGAGAGACACGCACA	58.676	50.000	0.0	0.0	0.0	4.57	R
2814	3107	2.298610	TCACACGCCACATTTTTACCA	58.701	42.857	0.0	0.0	0.0	3.25	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
74	77	3.714001	GTGAGGGGGAACGGGGAC	61.714	72.222	0.00	0.00	0.00	4.46
526	534	3.992260	TTATTTGACAACACCCCAACG	57.008	42.857	0.00	0.00	0.00	4.10
536	544	2.300433	ACACCCCAACGGTTTAGTTTC	58.700	47.619	0.00	0.00	45.36	2.78
617	627	7.773864	TGAACTAACACGAGATTAACAACAA	57.226	32.000	0.00	0.00	0.00	2.83
634	644	3.306917	ACAATAATCGTGGTGACGTGA	57.693	42.857	0.00	0.00	46.20	4.35
654	664	6.809689	ACGTGACATCATTAACGTGAGATTAA	59.190	34.615	0.00	0.00	46.58	1.40
683	693	1.405872	ATTATCCGGGCGTCACAGTA	58.594	50.000	0.00	0.00	0.00	2.74
684	694	1.405872	TTATCCGGGCGTCACAGTAT	58.594	50.000	0.00	0.00	0.00	2.12
685	695	0.956633	TATCCGGGCGTCACAGTATC	59.043	55.000	0.00	0.00	0.00	2.24
686	696	0.755698	ATCCGGGCGTCACAGTATCT	60.756	55.000	0.00	0.00	0.00	1.98
687	697	0.968901	TCCGGGCGTCACAGTATCTT	60.969	55.000	0.00	0.00	0.00	2.40
688	698	0.742505	CCGGGCGTCACAGTATCTTA	59.257	55.000	0.00	0.00	0.00	2.10
689	699	1.535437	CCGGGCGTCACAGTATCTTAC	60.535	57.143	0.00	0.00	0.00	2.34
690	700	1.535437	CGGGCGTCACAGTATCTTACC	60.535	57.143	0.00	0.00	0.00	2.85
691	701	1.535437	GGGCGTCACAGTATCTTACCG	60.535	57.143	0.00	0.00	0.00	4.02
692	702	1.535437	GGCGTCACAGTATCTTACCGG	60.535	57.143	0.00	0.00	0.00	5.28
693	703	1.402968	GCGTCACAGTATCTTACCGGA	59.597	52.381	9.46	0.00	0.00	5.14
694	704	2.034305	GCGTCACAGTATCTTACCGGAT	59.966	50.000	9.46	0.00	0.00	4.18
695	705	3.490419	GCGTCACAGTATCTTACCGGATT	60.490	47.826	9.46	0.00	0.00	3.01
696	706	4.261322	GCGTCACAGTATCTTACCGGATTA	60.261	45.833	9.46	0.00	0.00	1.75
697	707	5.450171	CGTCACAGTATCTTACCGGATTAG	58.550	45.833	9.46	1.63	0.00	1.73
698	708	5.237996	CGTCACAGTATCTTACCGGATTAGA	59.762	44.000	9.46	8.00	0.00	2.10
699	709	6.437094	GTCACAGTATCTTACCGGATTAGAC	58.563	44.000	9.46	0.00	0.00	2.59
700	710	6.262720	GTCACAGTATCTTACCGGATTAGACT	59.737	42.308	9.46	0.61	0.00	3.24
701	711	6.262496	TCACAGTATCTTACCGGATTAGACTG	59.738	42.308	9.46	16.00	36.59	3.51
702	712	6.262496	CACAGTATCTTACCGGATTAGACTGA	59.738	42.308	23.76	7.34	35.28	3.41
703	713	7.005296	ACAGTATCTTACCGGATTAGACTGAT	58.995	38.462	23.76	12.33	35.28	2.90
704	714	7.506261	ACAGTATCTTACCGGATTAGACTGATT	59.494	37.037	23.76	8.41	35.28	2.57
705	715	8.361139	CAGTATCTTACCGGATTAGACTGATTT	58.639	37.037	9.46	0.00	34.38	2.17
706	716	8.578151	AGTATCTTACCGGATTAGACTGATTTC	58.422	37.037	9.46	0.00	0.00	2.17
761	779	7.866393	CGTGTATCCTTTACCTGTATCTAAAGG	59.134	40.741	9.14	9.14	45.76	3.11
783	801	0.179121	ACACGATAATCCAAGCGCGA	60.179	50.000	12.10	0.00	0.00	5.87
815	833	4.095334	GCGTAGAAACCGTAAAATGGGATT	59.905	41.667	0.00	0.00	0.00	3.01
845	863	5.116180	TGTAGCATTACTTGGAGGAAATCG	58.884	41.667	0.00	0.00	0.00	3.34
852	870	2.012673	CTTGGAGGAAATCGCTTGAGG	58.987	52.381	0.00	0.00	0.00	3.86
858	876	0.453390	GAAATCGCTTGAGGCCTTGG	59.547	55.000	6.77	0.85	37.74	3.61
860	878	0.251341	AATCGCTTGAGGCCTTGGTT	60.251	50.000	6.77	0.00	37.74	3.67
913	931	2.254546	TGATTTGGCAGTTCTCGTGT	57.745	45.000	0.00	0.00	0.00	4.49
961	985	2.306512	AGTGTTATTTTGCTCCCCCGTA	59.693	45.455	0.00	0.00	0.00	4.02
984	1016	4.803426	CTGCTCGCTCCCACCGAC	62.803	72.222	0.00	0.00	0.00	4.79
1986	2144	2.821366	GAGGGTCAGGCATGCACG	60.821	66.667	21.36	9.77	0.00	5.34
2303	2473	9.953697	GTTGTACTATCTAAACTGAGTATGAGG	57.046	37.037	0.00	0.00	0.00	3.86
2384	2558	4.392138	GCAGTCATGTAAGTTGGGTCTTAC	59.608	45.833	8.94	8.94	45.59	2.34
2751	2942	4.018870	TGTCCACAAAGCTATAATCCACCA	60.019	41.667	0.00	0.00	0.00	4.17
2814	3107	5.716228	TGAAGTTTTATCCCAATGTCATGCT	59.284	36.000	0.00	0.00	0.00	3.79
2816	3109	4.403432	AGTTTTATCCCAATGTCATGCTGG	59.597	41.667	0.00	0.00	0.00	4.85
2817	3110	3.668141	TTATCCCAATGTCATGCTGGT	57.332	42.857	3.39	0.00	0.00	4.00
2839	3133	0.516877	AAATGTGGCGTGTGATGTCG	59.483	50.000	0.00	0.00	0.00	4.35
3067	3434	5.052481	TCATTCGAGGCATCATTACAAGAG	58.948	41.667	0.00	0.00	0.00	2.85
3151	3518	2.680339	GCAAAGATTACAGGAGGTGCTC	59.320	50.000	0.00	0.00	0.00	4.26
3257	3624	4.695455	CACAATTGGTATTCCTTCTCACGT	59.305	41.667	10.83	0.00	34.23	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
583	593	7.416154	TCTCGTGTTAGTTCAAAATCGATTT	57.584	32.000	17.60	17.60	0.00	2.17
634	644	8.765219	GCTACATTAATCTCACGTTAATGATGT	58.235	33.333	18.95	12.83	45.63	3.06
648	658	7.565680	CCCGGATAATTAGGCTACATTAATCT	58.434	38.462	0.73	0.00	0.00	2.40
654	664	2.093658	CGCCCGGATAATTAGGCTACAT	60.094	50.000	0.73	0.00	43.48	2.29
683	693	6.516860	CGGAAATCAGTCTAATCCGGTAAGAT	60.517	42.308	0.00	0.00	46.97	2.40
684	694	5.221185	CGGAAATCAGTCTAATCCGGTAAGA	60.221	44.000	0.00	0.00	46.97	2.10
685	695	4.982916	CGGAAATCAGTCTAATCCGGTAAG	59.017	45.833	0.00	0.00	46.97	2.34
686	696	4.940463	CGGAAATCAGTCTAATCCGGTAA	58.060	43.478	0.00	0.00	46.97	2.85
687	697	4.579454	CGGAAATCAGTCTAATCCGGTA	57.421	45.455	0.00	0.00	46.97	4.02
688	698	3.454371	CGGAAATCAGTCTAATCCGGT	57.546	47.619	0.00	0.00	46.97	5.28
691	701	2.495084	GGCCGGAAATCAGTCTAATCC	58.505	52.381	5.05	0.00	0.00	3.01
692	702	2.135933	CGGCCGGAAATCAGTCTAATC	58.864	52.381	20.10	0.00	0.00	1.75
693	703	1.202651	CCGGCCGGAAATCAGTCTAAT	60.203	52.381	41.82	0.00	37.50	1.73
694	704	0.177141	CCGGCCGGAAATCAGTCTAA	59.823	55.000	41.82	0.00	37.50	2.10
695	705	0.685131	TCCGGCCGGAAATCAGTCTA	60.685	55.000	43.93	18.26	42.05	2.59
696	706	1.987855	TCCGGCCGGAAATCAGTCT	60.988	57.895	43.93	0.00	42.05	3.24
697	707	2.582436	TCCGGCCGGAAATCAGTC	59.418	61.111	43.93	0.00	42.05	3.51
705	715	0.614294	TCTTATTGTTTCCGGCCGGA	59.386	50.000	42.66	42.66	43.52	5.14
706	716	0.730840	GTCTTATTGTTTCCGGCCGG	59.269	55.000	39.13	39.13	0.00	6.13
761	779	2.705154	GCGCTTGGATTATCGTGTTTC	58.295	47.619	0.00	0.00	0.00	2.78
783	801	3.667360	ACGGTTTCTACGCAATTTAGGT	58.333	40.909	0.00	0.00	34.00	3.08
845	863	0.752658	ACAAAACCAAGGCCTCAAGC	59.247	50.000	5.23	0.00	42.60	4.01
852	870	3.801114	AGAGTGAAACAAAACCAAGGC	57.199	42.857	0.00	0.00	41.43	4.35
944	965	5.131475	AGAATACTACGGGGGAGCAAAATAA	59.869	40.000	0.00	0.00	0.00	1.40
961	985	0.461961	GTGGGAGCGAGCAGAATACT	59.538	55.000	0.00	0.00	0.00	2.12
984	1016	1.735455	TTTTTCTGGGGGAGGGGGTG	61.735	60.000	0.00	0.00	0.00	4.61
1161	1238	2.049156	CACCGCTTGCAGACGAGA	60.049	61.111	11.55	0.00	0.00	4.04
1581	1697	3.338249	CTTCCACAGATTCACCAACGAT	58.662	45.455	0.00	0.00	0.00	3.73
1582	1698	2.549992	CCTTCCACAGATTCACCAACGA	60.550	50.000	0.00	0.00	0.00	3.85
1584	1700	2.814336	GTCCTTCCACAGATTCACCAAC	59.186	50.000	0.00	0.00	0.00	3.77
1986	2144	4.767255	CTGTCCTCTGCACGGGGC	62.767	72.222	0.00	0.00	45.13	5.80
2187	2351	1.324383	TAACAGGAGAGACACGCACA	58.676	50.000	0.00	0.00	0.00	4.57
2190	2354	2.941453	TCATAACAGGAGAGACACGC	57.059	50.000	0.00	0.00	0.00	5.34
2303	2473	9.953697	CAAAGTACATACCTCTCTATTACAGAC	57.046	37.037	0.00	0.00	0.00	3.51
2444	2624	6.842437	AGAAGATCAGTGCAGTCTTACTAA	57.158	37.500	0.00	0.00	32.67	2.24
2445	2625	7.415765	GCTTAGAAGATCAGTGCAGTCTTACTA	60.416	40.741	0.00	0.22	32.67	1.82
2725	2914	6.428159	GGTGGATTATAGCTTTGTGGACATAG	59.572	42.308	0.00	0.00	0.00	2.23
2814	3107	2.298610	TCACACGCCACATTTTTACCA	58.701	42.857	0.00	0.00	0.00	3.25
2816	3109	3.896122	ACATCACACGCCACATTTTTAC	58.104	40.909	0.00	0.00	0.00	2.01
2817	3110	3.364465	CGACATCACACGCCACATTTTTA	60.364	43.478	0.00	0.00	0.00	1.52
2839	3133	5.705609	ATACCATTGTTGTGGAGTTTGTC	57.294	39.130	0.00	0.00	42.02	3.18
3067	3434	5.013599	AGGACCCTGGCTAATCTTTGATATC	59.986	44.000	0.00	0.00	0.00	1.63
3151	3518	8.507249	GGGATAAAACTCCATCTAATGAATTCG	58.493	37.037	0.04	0.00	37.01	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.