AutoCloner

Multiple sequence alignment - TraesCS3B01G070100

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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	TraesCS3B01G070100	chr3B	100.000	2970	0	0	333	3302	41856354	41859323	0.000000e+00	5485.0
1	TraesCS3B01G070100	chr3B	80.699	772	96	26	1361	2079	456981475	456980704	4.820000e-153	551.0
2	TraesCS3B01G070100	chr3B	100.000	106	0	0	1	106	41856022	41856127	2.600000e-46	196.0
3	TraesCS3B01G070100	chr3B	96.610	59	2	0	2758	2816	662534650	662534592	7.540000e-17	99.0
4	TraesCS3B01G070100	chr3D	94.206	2054	62	30	349	2357	23743374	23745415	0.000000e+00	3081.0
5	TraesCS3B01G070100	chr3D	90.827	665	38	13	1012	1665	23746380	23747032	0.000000e+00	869.0
6	TraesCS3B01G070100	chr3D	80.720	778	92	25	1360	2079	355795771	355794994	1.340000e-153	553.0
7	TraesCS3B01G070100	chr3D	87.864	206	25	0	1050	1255	355796036	355795831	3.290000e-60	243.0
8	TraesCS3B01G070100	chr3D	93.750	48	1	2	977	1023	23746315	23746361	1.640000e-08	71.3
9	TraesCS3B01G070100	chr3A	96.603	1354	34	8	1012	2357	32999777	33001126	0.000000e+00	2235.0
10	TraesCS3B01G070100	chr3A	92.708	288	18	3	338	624	32998854	32999139	2.370000e-111	412.0
11	TraesCS3B01G070100	chr3A	89.939	328	18	5	615	933	32999321	32999642	3.070000e-110	409.0
12	TraesCS3B01G070100	chr3A	83.896	385	25	20	825	1178	33142080	33142458	1.900000e-87	333.0
13	TraesCS3B01G070100	chr3A	87.379	206	26	0	1050	1255	474811975	474811770	1.530000e-58	237.0
14	TraesCS3B01G070100	chr3A	89.524	105	0	3	920	1023	32999664	32999758	4.470000e-24	122.0
15	TraesCS3B01G070100	chr6B	96.791	935	28	2	2369	3302	17642501	17641568	0.000000e+00	1559.0
16	TraesCS3B01G070100	chr6B	96.764	927	27	2	2376	3302	124548535	124549458	0.000000e+00	1543.0
17	TraesCS3B01G070100	chr6B	94.989	938	42	3	2369	3302	10218149	10219085	0.000000e+00	1467.0
18	TraesCS3B01G070100	chr2B	97.020	906	26	1	2397	3302	519690232	519691136	0.000000e+00	1522.0
19	TraesCS3B01G070100	chr2B	96.866	702	22	0	2601	3302	468656206	468656907	0.000000e+00	1175.0
20	TraesCS3B01G070100	chr2B	80.949	1328	178	37	1047	2310	144034397	144035713	0.000000e+00	981.0
21	TraesCS3B01G070100	chr2B	82.726	631	109	0	1672	2302	143969442	143970072	2.220000e-156	562.0
22	TraesCS3B01G070100	chr2B	96.596	235	6	2	2376	2609	468655497	468655730	4.000000e-104	388.0
23	TraesCS3B01G070100	chr2B	83.730	252	33	4	1021	1266	144078467	144078218	7.130000e-57	231.0
24	TraesCS3B01G070100	chr5B	95.811	931	37	2	2373	3302	711259158	711260087	0.000000e+00	1502.0
25	TraesCS3B01G070100	chr5B	95.685	927	36	2	2376	3302	579370148	579371070	0.000000e+00	1487.0
26	TraesCS3B01G070100	chr7B	94.839	930	30	2	2373	3302	157672159	157673070	0.000000e+00	1435.0
27	TraesCS3B01G070100	chr7B	94.239	486	28	0	2817	3302	191526408	191525923	0.000000e+00	743.0
28	TraesCS3B01G070100	chr2D	80.801	1323	182	33	1047	2310	92831865	92833174	0.000000e+00	970.0
29	TraesCS3B01G070100	chr2D	82.323	990	151	17	1337	2311	92889070	92890050	0.000000e+00	837.0
30	TraesCS3B01G070100	chr2D	82.268	485	85	1	1827	2310	92863337	92863821	5.100000e-113	418.0
31	TraesCS3B01G070100	chr2D	81.452	372	42	17	1320	1668	92891844	92892211	2.510000e-71	279.0
32	TraesCS3B01G070100	chr2D	82.857	210	29	5	1047	1253	92882216	92882421	7.280000e-42	182.0
33	TraesCS3B01G070100	chr7A	95.062	486	24	0	2817	3302	611541972	611542457	0.000000e+00	765.0
34	TraesCS3B01G070100	chr4B	83.679	386	21	18	2374	2759	9065864	9065521	3.180000e-85	326.0

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	TraesCS3B01G070100	chr3B	41856022	41859323	3301	False	2840.500000	5485	100.000000	1	3302	2	chr3B.!!$F1	3301
1	TraesCS3B01G070100	chr3B	456980704	456981475	771	True	551.000000	551	80.699000	1361	2079	1	chr3B.!!$R1	718
2	TraesCS3B01G070100	chr3D	23743374	23747032	3658	False	1340.433333	3081	92.927667	349	2357	3	chr3D.!!$F1	2008
3	TraesCS3B01G070100	chr3D	355794994	355796036	1042	True	398.000000	553	84.292000	1050	2079	2	chr3D.!!$R1	1029
4	TraesCS3B01G070100	chr3A	32998854	33001126	2272	False	794.500000	2235	92.193500	338	2357	4	chr3A.!!$F2	2019
5	TraesCS3B01G070100	chr6B	17641568	17642501	933	True	1559.000000	1559	96.791000	2369	3302	1	chr6B.!!$R1	933
6	TraesCS3B01G070100	chr6B	124548535	124549458	923	False	1543.000000	1543	96.764000	2376	3302	1	chr6B.!!$F2	926
7	TraesCS3B01G070100	chr6B	10218149	10219085	936	False	1467.000000	1467	94.989000	2369	3302	1	chr6B.!!$F1	933
8	TraesCS3B01G070100	chr2B	519690232	519691136	904	False	1522.000000	1522	97.020000	2397	3302	1	chr2B.!!$F3	905
9	TraesCS3B01G070100	chr2B	144034397	144035713	1316	False	981.000000	981	80.949000	1047	2310	1	chr2B.!!$F2	1263
10	TraesCS3B01G070100	chr2B	468655497	468656907	1410	False	781.500000	1175	96.731000	2376	3302	2	chr2B.!!$F4	926
11	TraesCS3B01G070100	chr2B	143969442	143970072	630	False	562.000000	562	82.726000	1672	2302	1	chr2B.!!$F1	630
12	TraesCS3B01G070100	chr5B	711259158	711260087	929	False	1502.000000	1502	95.811000	2373	3302	1	chr5B.!!$F2	929
13	TraesCS3B01G070100	chr5B	579370148	579371070	922	False	1487.000000	1487	95.685000	2376	3302	1	chr5B.!!$F1	926
14	TraesCS3B01G070100	chr7B	157672159	157673070	911	False	1435.000000	1435	94.839000	2373	3302	1	chr7B.!!$F1	929
15	TraesCS3B01G070100	chr2D	92831865	92833174	1309	False	970.000000	970	80.801000	1047	2310	1	chr2D.!!$F1	1263
16	TraesCS3B01G070100	chr2D	92889070	92892211	3141	False	558.000000	837	81.887500	1320	2311	2	chr2D.!!$F4	991

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
893	1096	0.102481	ACTGTATGTTAGAGCCGCGG	59.898	55.0	24.05	24.05	0.0	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2359	2770	0.191314	GGGTAGGCCTGGAGGAGTAT	59.809	60.0	17.99	0.0	37.39	2.12	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
23	24	6.458232	GATCTAGATGGCCGACTATGTATT	57.542	41.667	10.74	0.00	0.00	1.89
24	25	7.569639	GATCTAGATGGCCGACTATGTATTA	57.430	40.000	10.74	0.00	0.00	0.98
25	26	8.172352	GATCTAGATGGCCGACTATGTATTAT	57.828	38.462	10.74	0.00	0.00	1.28
26	27	7.956328	TCTAGATGGCCGACTATGTATTATT	57.044	36.000	8.76	0.00	0.00	1.40
27	28	8.362464	TCTAGATGGCCGACTATGTATTATTT	57.638	34.615	8.76	0.00	0.00	1.40
28	29	9.470399	TCTAGATGGCCGACTATGTATTATTTA	57.530	33.333	8.76	0.00	0.00	1.40
31	32	9.787435	AGATGGCCGACTATGTATTATTTAAAA	57.213	29.630	0.00	0.00	0.00	1.52
56	57	8.973835	AAAAATCGGCGTAATATTTCTGAAAA	57.026	26.923	6.85	0.00	0.00	2.29
57	58	8.973835	AAAATCGGCGTAATATTTCTGAAAAA	57.026	26.923	6.85	0.00	0.00	1.94
58	59	9.581099	AAAATCGGCGTAATATTTCTGAAAAAT	57.419	25.926	6.85	0.00	0.00	1.82
60	61	9.878599	AATCGGCGTAATATTTCTGAAAAATAG	57.121	29.630	6.85	0.00	0.00	1.73
61	62	8.428186	TCGGCGTAATATTTCTGAAAAATAGT	57.572	30.769	6.85	0.00	0.00	2.12
62	63	8.885722	TCGGCGTAATATTTCTGAAAAATAGTT	58.114	29.630	6.85	1.54	0.00	2.24
100	101	5.789710	TTCTAAAAATTAGCCGGAGAACG	57.210	39.130	5.05	0.00	43.80	3.95
101	102	2.913777	AAAAATTAGCCGGAGAACGC	57.086	45.000	5.05	0.00	42.52	4.84
102	103	1.092348	AAAATTAGCCGGAGAACGCC	58.908	50.000	5.05	0.00	42.52	5.68
103	104	0.746923	AAATTAGCCGGAGAACGCCC	60.747	55.000	5.05	0.00	42.52	6.13
104	105	2.604299	AATTAGCCGGAGAACGCCCC	62.604	60.000	5.05	0.00	42.52	5.80
105	106	4.772231	TAGCCGGAGAACGCCCCT	62.772	66.667	5.05	0.00	42.52	4.79
409	414	1.682451	CCGGAGAACGCCCCTCATAA	61.682	60.000	0.00	0.00	42.52	1.90
502	507	7.482169	TGGAGCTACAGAGAAAAGATAAGAA	57.518	36.000	0.00	0.00	0.00	2.52
534	539	2.235016	GTACAATGTGTGGGCCAGAAA	58.765	47.619	6.40	0.00	0.00	2.52
703	899	5.154932	CGTAGTGTTTGGTTTGTTTGACAA	58.845	37.500	0.00	0.00	36.11	3.18
712	910	4.527038	TGGTTTGTTTGACAAGTAAACCCA	59.473	37.500	27.78	19.60	45.97	4.51
784	987	8.345565	CGATCAAATTCCTCGGATTAAAATCTT	58.654	33.333	2.91	0.00	35.73	2.40
798	1001	3.683365	AAATCTTGTTGGACCATTGCC	57.317	42.857	0.00	0.00	0.00	4.52
822	1025	1.468520	AGTTCCATTTTGCGTCATCGG	59.531	47.619	0.00	0.00	37.56	4.18
873	1076	4.657952	GGCCTGCCCGACTTAAAT	57.342	55.556	0.00	0.00	0.00	1.40
874	1077	3.792712	GGCCTGCCCGACTTAAATA	57.207	52.632	0.00	0.00	0.00	1.40
875	1078	1.306148	GGCCTGCCCGACTTAAATAC	58.694	55.000	0.00	0.00	0.00	1.89
876	1079	1.134189	GGCCTGCCCGACTTAAATACT	60.134	52.381	0.00	0.00	0.00	2.12
877	1080	1.940613	GCCTGCCCGACTTAAATACTG	59.059	52.381	0.00	0.00	0.00	2.74
888	1091	7.381678	CCCGACTTAAATACTGTATGTTAGAGC	59.618	40.741	10.19	2.76	0.00	4.09
893	1096	0.102481	ACTGTATGTTAGAGCCGCGG	59.898	55.000	24.05	24.05	0.00	6.46
899	1106	0.466739	TGTTAGAGCCGCGGGATAGA	60.467	55.000	29.38	0.00	0.00	1.98
910	1117	0.103208	CGGGATAGACAGTCAGCCAC	59.897	60.000	2.66	0.00	0.00	5.01
1042	1315	4.308458	TTGTCCTGTCCGTGGCCG	62.308	66.667	0.00	0.00	0.00	6.13
1286	1568	2.726681	CGACGACGATGATGTGTACACA	60.727	50.000	29.70	29.70	43.15	3.72
1314	1623	4.951715	TCTTAATCACTGCCCGTCTTAGTA	59.048	41.667	0.00	0.00	0.00	1.82
1315	1624	3.521947	AATCACTGCCCGTCTTAGTAC	57.478	47.619	0.00	0.00	0.00	2.73
1316	1625	0.806868	TCACTGCCCGTCTTAGTACG	59.193	55.000	0.00	0.00	42.49	3.67
1317	1626	0.524862	CACTGCCCGTCTTAGTACGT	59.475	55.000	0.00	0.00	41.27	3.57
1670	2049	3.130633	GCACTGACCATGCATATTACGA	58.869	45.455	0.00	0.00	42.88	3.43
1674	2079	5.466393	CACTGACCATGCATATTACGATCAA	59.534	40.000	0.00	0.00	0.00	2.57
1915	2320	1.615124	TTCCTCGGCATCTTCCCCA	60.615	57.895	0.00	0.00	0.00	4.96
2218	2626	0.753867	TGTACACTTGACGGAGGCAA	59.246	50.000	0.00	0.00	0.00	4.52
2320	2731	1.827969	AGACTTGCGTGCCTAAGAGAT	59.172	47.619	0.00	0.00	0.00	2.75
2370	4613	6.935240	TGGAATTGGTATATACTCCTCCAG	57.065	41.667	12.54	0.00	0.00	3.86
2887	5893	1.372499	CGGTGGACGTCGACAATGT	60.372	57.895	28.33	5.22	37.93	2.71
2904	6008	1.081906	GTGGATTGTGTGCTGTGCG	60.082	57.895	0.00	0.00	0.00	5.34
3193	6301	2.987547	GGGGACAGTGGACGTCGA	60.988	66.667	9.92	1.86	34.04	4.20
3216	6324	3.053896	CGGCTTCGGGTGGTTTCC	61.054	66.667	0.00	0.00	0.00	3.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.458232	AATACATAGTCGGCCATCTAGATC	57.542	41.667	2.24	0.00	0.00	2.75
31	32	8.973835	TTTTCAGAAATATTACGCCGATTTTT	57.026	26.923	0.00	0.00	0.00	1.94
32	33	8.973835	TTTTTCAGAAATATTACGCCGATTTT	57.026	26.923	0.00	0.00	0.00	1.82
34	35	9.878599	CTATTTTTCAGAAATATTACGCCGATT	57.121	29.630	4.39	0.00	0.00	3.34
35	36	9.052759	ACTATTTTTCAGAAATATTACGCCGAT	57.947	29.630	4.39	0.00	0.00	4.18
36	37	8.428186	ACTATTTTTCAGAAATATTACGCCGA	57.572	30.769	4.39	0.00	0.00	5.54
74	75	8.392612	CGTTCTCCGGCTAATTTTTAGAAATAA	58.607	33.333	0.00	0.00	34.44	1.40
75	76	7.466320	GCGTTCTCCGGCTAATTTTTAGAAATA	60.466	37.037	0.00	0.00	34.05	1.40
76	77	6.677187	GCGTTCTCCGGCTAATTTTTAGAAAT	60.677	38.462	0.00	0.00	35.52	2.17
77	78	5.391203	GCGTTCTCCGGCTAATTTTTAGAAA	60.391	40.000	0.00	0.00	36.94	2.52
78	79	4.093850	GCGTTCTCCGGCTAATTTTTAGAA	59.906	41.667	0.00	0.00	36.94	2.10
79	80	3.619929	GCGTTCTCCGGCTAATTTTTAGA	59.380	43.478	0.00	0.00	36.94	2.10
80	81	3.936661	GCGTTCTCCGGCTAATTTTTAG	58.063	45.455	0.00	0.00	36.94	1.85
82	83	2.913777	GCGTTCTCCGGCTAATTTTT	57.086	45.000	0.00	0.00	36.94	1.94
336	337	0.678048	CTGAAACTGCTACAGCCCCC	60.678	60.000	0.00	0.00	41.18	5.40
391	396	0.393077	ATTATGAGGGGCGTTCTCCG	59.607	55.000	0.00	0.00	40.40	4.63
409	414	3.021356	TGGCTACCCCAAGTGCTAT	57.979	52.632	0.00	0.00	41.82	2.97
446	451	3.496160	CGTTCCTCCCTCTTTTCTTTCCA	60.496	47.826	0.00	0.00	0.00	3.53
534	539	7.604164	CAGGAAGACTACACACTCATACATTTT	59.396	37.037	0.00	0.00	0.00	1.82
542	547	2.891580	GACCAGGAAGACTACACACTCA	59.108	50.000	0.00	0.00	0.00	3.41
548	553	3.427573	TCGATTGACCAGGAAGACTACA	58.572	45.455	0.00	0.00	0.00	2.74
683	879	5.208463	ACTTGTCAAACAAACCAAACACT	57.792	34.783	0.00	0.00	37.69	3.55
712	910	1.075212	GCCTAGGGGAGAGTATACCGT	59.925	57.143	11.72	0.00	33.58	4.83
784	987	0.888736	CTCGTGGCAATGGTCCAACA	60.889	55.000	0.00	0.00	35.01	3.33
798	1001	1.262950	TGACGCAAAATGGAACTCGTG	59.737	47.619	0.00	0.00	0.00	4.35
822	1025	4.099585	CGTGTGTACGTGCGTCGC	62.100	66.667	11.10	11.10	44.99	5.19
867	1070	6.129168	CGCGGCTCTAACATACAGTATTTAAG	60.129	42.308	0.00	0.00	0.00	1.85
870	1073	4.049186	CGCGGCTCTAACATACAGTATTT	58.951	43.478	0.00	0.00	0.00	1.40
873	1076	1.335810	CCGCGGCTCTAACATACAGTA	59.664	52.381	14.67	0.00	0.00	2.74
874	1077	0.102481	CCGCGGCTCTAACATACAGT	59.898	55.000	14.67	0.00	0.00	3.55
875	1078	0.597637	CCCGCGGCTCTAACATACAG	60.598	60.000	22.85	0.00	0.00	2.74
876	1079	1.038681	TCCCGCGGCTCTAACATACA	61.039	55.000	22.85	0.00	0.00	2.29
877	1080	0.317479	ATCCCGCGGCTCTAACATAC	59.683	55.000	22.85	0.00	0.00	2.39
888	1091	1.360551	CTGACTGTCTATCCCGCGG	59.639	63.158	21.04	21.04	0.00	6.46
893	1096	1.103803	TCGTGGCTGACTGTCTATCC	58.896	55.000	9.51	7.79	0.00	2.59
899	1106	1.079543	GCAGATCGTGGCTGACTGT	60.080	57.895	0.00	0.00	35.39	3.55
910	1117	4.063689	AGCTTTTATGATGAGGCAGATCG	58.936	43.478	0.00	0.00	0.00	3.69
1016	1289	1.000607	CGGACAGGACAAGAAGAACGA	60.001	52.381	0.00	0.00	0.00	3.85
1286	1568	1.739067	GGGCAGTGATTAAGAACGCT	58.261	50.000	0.00	0.00	0.00	5.07
1291	1575	3.767673	ACTAAGACGGGCAGTGATTAAGA	59.232	43.478	0.00	0.00	0.00	2.10
1617	1968	4.979204	GCGCCATGCATGCATTAT	57.021	50.000	30.32	8.66	45.45	1.28
1670	2049	0.177604	CGCCTTCCTCTCTGCTTGAT	59.822	55.000	0.00	0.00	0.00	2.57
1674	2079	3.780173	GCCGCCTTCCTCTCTGCT	61.780	66.667	0.00	0.00	0.00	4.24
2218	2626	2.746142	CGTGGGCCATGATCTTGTATGT	60.746	50.000	21.47	0.00	0.00	2.29
2275	2683	2.255252	GCGGTTGCATGTGGACAC	59.745	61.111	0.00	0.00	42.15	3.67
2357	2768	2.044630	GGGTAGGCCTGGAGGAGTATAT	59.955	54.545	17.99	0.00	37.39	0.86
2359	2770	0.191314	GGGTAGGCCTGGAGGAGTAT	59.809	60.000	17.99	0.00	37.39	2.12
2360	2771	1.624753	GGGTAGGCCTGGAGGAGTA	59.375	63.158	17.99	0.00	37.39	2.59
2361	2772	2.369001	GGGTAGGCCTGGAGGAGT	59.631	66.667	17.99	0.00	37.39	3.85
2362	2773	2.446802	GGGGTAGGCCTGGAGGAG	60.447	72.222	17.99	0.00	37.39	3.69
2887	5893	2.260154	CCGCACAGCACACAATCCA	61.260	57.895	0.00	0.00	0.00	3.41
2904	6008	1.372087	CCAAGCAGATCCGAAGCACC	61.372	60.000	0.00	0.00	0.00	5.01
3038	6146	1.079127	CCCGGAGAGTCGTGCAATT	60.079	57.895	0.73	0.00	0.00	2.32
3216	6324	2.622629	CATCTCGGCGCACAATCG	59.377	61.111	10.83	2.53	0.00	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.