AutoCloner

Multiple sequence alignment - TraesCS2D01G264700

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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	TraesCS2D01G264700	chr2D	100.000	3350	0	0	1	3350	323647053	323650402	0.000000e+00	6187
1	TraesCS2D01G264700	chr2A	94.060	2660	88	23	1	2604	406769364	406766719	0.000000e+00	3973
2	TraesCS2D01G264700	chr2A	82.979	141	18	5	3215	3350	758503031	758502892	4.540000e-24	122
3	TraesCS2D01G264700	chr2B	92.809	1947	69	28	722	2606	391769179	391771116	0.000000e+00	2754
4	TraesCS2D01G264700	chr2B	96.676	692	23	0	1	692	391768394	391769085	0.000000e+00	1151
5	TraesCS2D01G264700	chr2B	94.355	124	6	1	2601	2723	391771373	391771496	4.410000e-44	189
6	TraesCS2D01G264700	chr3D	84.469	631	58	20	2728	3350	130973098	130972500	1.340000e-163	586
7	TraesCS2D01G264700	chr3D	77.919	394	56	24	2973	3348	104300491	104300871	2.020000e-52	217
8	TraesCS2D01G264700	chr3B	81.833	633	71	25	2728	3349	242495025	242494426	3.000000e-135	492
9	TraesCS2D01G264700	chr3B	80.365	219	22	17	3128	3330	688169420	688169633	2.690000e-31	147
10	TraesCS2D01G264700	chr4B	82.940	551	69	11	2805	3350	592279482	592278952	1.090000e-129	473
11	TraesCS2D01G264700	chr6B	80.725	524	72	19	2832	3347	569392338	569391836	6.780000e-102	381
12	TraesCS2D01G264700	chr6B	80.038	531	70	25	2832	3349	718899032	718899539	8.840000e-96	361
13	TraesCS2D01G264700	chr6B	77.960	549	65	31	2832	3349	718882768	718882245	3.270000e-75	292
14	TraesCS2D01G264700	chr4D	80.377	530	58	29	2832	3349	286115641	286116136	8.840000e-96	361
15	TraesCS2D01G264700	chr3A	78.799	533	66	32	2832	3347	28998353	28998855	6.980000e-82	315
16	TraesCS2D01G264700	chr3A	78.261	529	76	25	2832	3347	28968030	28968532	1.510000e-78	303
17	TraesCS2D01G264700	chr7D	79.080	435	59	25	2933	3349	422595587	422595167	1.530000e-68	270
18	TraesCS2D01G264700	chr7D	76.960	421	62	28	2954	3349	618172817	618172407	1.220000e-49	207
19	TraesCS2D01G264700	chr7A	80.506	395	40	23	2963	3350	116894196	116893832	5.510000e-68	268
20	TraesCS2D01G264700	chr7B	80.102	196	30	8	3162	3350	20389580	20389773	1.620000e-28	137

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	TraesCS2D01G264700	chr2D	323647053	323650402	3349	False	6187.000000	6187	100.000000	1	3350	1	chr2D.!!$F1	3349
1	TraesCS2D01G264700	chr2A	406766719	406769364	2645	True	3973.000000	3973	94.060000	1	2604	1	chr2A.!!$R1	2603
2	TraesCS2D01G264700	chr2B	391768394	391771496	3102	False	1364.666667	2754	94.613333	1	2723	3	chr2B.!!$F1	2722
3	TraesCS2D01G264700	chr3D	130972500	130973098	598	True	586.000000	586	84.469000	2728	3350	1	chr3D.!!$R1	622
4	TraesCS2D01G264700	chr3B	242494426	242495025	599	True	492.000000	492	81.833000	2728	3349	1	chr3B.!!$R1	621
5	TraesCS2D01G264700	chr4B	592278952	592279482	530	True	473.000000	473	82.940000	2805	3350	1	chr4B.!!$R1	545
6	TraesCS2D01G264700	chr6B	569391836	569392338	502	True	381.000000	381	80.725000	2832	3347	1	chr6B.!!$R1	515
7	TraesCS2D01G264700	chr6B	718899032	718899539	507	False	361.000000	361	80.038000	2832	3349	1	chr6B.!!$F1	517
8	TraesCS2D01G264700	chr6B	718882245	718882768	523	True	292.000000	292	77.960000	2832	3349	1	chr6B.!!$R2	517
9	TraesCS2D01G264700	chr3A	28998353	28998855	502	False	315.000000	315	78.799000	2832	3347	1	chr3A.!!$F2	515
10	TraesCS2D01G264700	chr3A	28968030	28968532	502	False	303.000000	303	78.261000	2832	3347	1	chr3A.!!$F1	515

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	Hairpin	End Stability	Orientation
782	851	0.249657	GCAGAGCCCTGATTCCTACG	60.250	60.000	43.02	3.51	F
1506	1608	0.955919	GGGACAAGGAAGCCAACGAG	60.956	60.000	0.00	4.18	F
2146	2282	1.376037	GACAAGGACAAGGGCGAGG	60.376	63.158	0.00	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
2107	2219	0.178873	TTGGCCTCCTTGTACTCCCT	60.179	55.000	3.32	4.20	R
2323	2459	0.396811	CAGGTCCAGGTTCGGTCTTT	59.603	55.000	0.00	2.52	R
3131	3611	5.514274	ACAATTTCTGAAAACACGACCAT	57.486	34.783	6.95	3.55	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
109	110	3.687102	TCGGTGCGGGTCGTTGAT	61.687	61.111	0.00	0.00	0.00	2.57
328	329	1.035932	ATCTCCAGCATTGCACAGCC	61.036	55.000	11.91	0.00	0.00	4.85
565	566	5.063564	CACTATTTTCTGTAGAAGGAACCGC	59.936	44.000	0.00	0.00	35.21	5.68
590	591	7.220108	GCGTTTATTATTTCTGGAATTCGCTTT	59.780	33.333	0.00	0.00	35.66	3.51
609	610	2.198827	TGTTACTCTGGTGCCATTGG	57.801	50.000	0.00	0.00	0.00	3.16
692	693	6.401394	TCTCATTGCCTGGAGAATATAATCG	58.599	40.000	0.00	0.00	37.23	3.34
718	784	8.219769	GTCATTCAGCTATAAAATGATCGACAG	58.780	37.037	13.05	0.00	40.44	3.51
767	833	1.419381	TACTTGGGTGTCACTGCAGA	58.581	50.000	23.35	0.00	0.00	4.26
770	836	2.359230	GGGTGTCACTGCAGAGCC	60.359	66.667	23.35	13.38	0.00	4.70
782	851	0.249657	GCAGAGCCCTGATTCCTACG	60.250	60.000	0.00	0.00	43.02	3.51
861	930	3.708631	TCCAATCCTGAAGTCTGGAGATC	59.291	47.826	11.92	0.00	45.24	2.75
906	975	2.048222	TCACGGAAGGAGCAAGCG	60.048	61.111	0.00	0.00	0.00	4.68
987	1086	2.693591	CGAGGCCAAGGTAGATACAGAA	59.306	50.000	5.01	0.00	0.00	3.02
1032	1131	3.502572	GGCAACGATCTGAAGGCC	58.497	61.111	0.00	0.00	0.00	5.19
1086	1185	2.359230	GTGGACAGTGAGCTGCCC	60.359	66.667	0.00	0.00	46.30	5.36
1128	1227	1.821332	CTTCCGCATCCTCAAGGCC	60.821	63.158	0.00	0.00	34.44	5.19
1506	1608	0.955919	GGGACAAGGAAGCCAACGAG	60.956	60.000	0.00	0.00	0.00	4.18
1512	1614	1.966451	GGAAGCCAACGAGGTGGTG	60.966	63.158	9.13	0.00	41.12	4.17
2146	2282	1.376037	GACAAGGACAAGGGCGAGG	60.376	63.158	0.00	0.00	0.00	4.63
2384	2524	5.174761	GCTAATCAGTCTGCTAATTGAGTCG	59.825	44.000	0.00	0.00	0.00	4.18
2406	2553	1.202475	TGACTCACTGTGCGTGCTTAA	60.202	47.619	8.32	0.00	43.46	1.85
2435	2582	6.884187	TCTGCTAAATGTTTGTTTCGTACTC	58.116	36.000	0.00	0.00	0.00	2.59
2440	2587	6.780706	AAATGTTTGTTTCGTACTCTCGAT	57.219	33.333	0.00	0.00	39.57	3.59
2557	2709	1.070289	ACCGACTTTGTGGAGACTTCC	59.930	52.381	0.00	0.00	44.31	3.46
2568	2720	4.089361	GTGGAGACTTCCCCAAATTTGAT	58.911	43.478	19.86	0.00	43.33	2.57
2661	3075	0.535102	ACACGACCAAAGGGCTGAAG	60.535	55.000	0.00	0.00	37.90	3.02
2692	3107	2.838736	ACTTGTTGATCTTGTCGCTGT	58.161	42.857	0.00	0.00	0.00	4.40
2703	3118	2.048597	TCGCTGTGTACCGCTTGG	60.049	61.111	0.00	0.00	39.35	3.61
2720	3135	5.424121	GCTTGGCGTATTCATGTCTTATT	57.576	39.130	0.00	0.00	0.00	1.40
2721	3136	5.207768	GCTTGGCGTATTCATGTCTTATTG	58.792	41.667	0.00	0.00	0.00	1.90
2722	3137	4.811555	TGGCGTATTCATGTCTTATTGC	57.188	40.909	0.00	0.00	0.00	3.56
2723	3138	3.247411	TGGCGTATTCATGTCTTATTGCG	59.753	43.478	0.00	0.00	0.00	4.85
2724	3139	3.363970	GGCGTATTCATGTCTTATTGCGG	60.364	47.826	0.00	0.00	0.00	5.69
2725	3140	3.363970	GCGTATTCATGTCTTATTGCGGG	60.364	47.826	0.00	0.00	0.00	6.13
2726	3141	3.807622	CGTATTCATGTCTTATTGCGGGT	59.192	43.478	0.00	0.00	0.00	5.28
2748	3163	3.449377	TGGAATATCCTATTCGCCGCATA	59.551	43.478	0.00	0.00	37.46	3.14
2762	3177	3.133814	GCATATTGCGTCGAACAGC	57.866	52.632	0.00	0.00	31.71	4.40
2779	3194	2.383527	GCCGACCTTTCGCACAGAG	61.384	63.158	0.00	0.00	44.43	3.35
2780	3195	1.289066	CCGACCTTTCGCACAGAGA	59.711	57.895	0.00	0.00	44.43	3.10
2792	3208	3.125573	CAGAGACCGACCGAGCGA	61.126	66.667	0.00	0.00	0.00	4.93
2793	3209	2.820479	AGAGACCGACCGAGCGAG	60.820	66.667	0.00	0.00	0.00	5.03
2794	3210	4.539881	GAGACCGACCGAGCGAGC	62.540	72.222	0.00	0.00	0.00	5.03
2828	3244	1.381165	GCCCGTTACCGCATTCCATT	61.381	55.000	0.00	0.00	0.00	3.16
2830	3246	0.248458	CCGTTACCGCATTCCATTGC	60.248	55.000	0.00	0.00	39.29	3.56
3257	3756	8.105742	GGAATGTTTTTGTTCGTTTTTACAGAC	58.894	33.333	0.00	0.00	0.00	3.51
3280	3780	7.696453	AGACTTTTAAATAATGACCGCGATTTG	59.304	33.333	8.23	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
109	110	5.132502	ACTGTTCTTGTGATGGTGAAATGA	58.867	37.500	0.00	0.00	0.00	2.57
214	215	4.022068	GGGATGAAAAACTGACAATCTGCA	60.022	41.667	0.00	0.00	0.00	4.41
328	329	6.983307	AGTGCACAAGTAAATCTCTGCTATAG	59.017	38.462	21.04	0.00	33.47	1.31
489	490	7.170393	TCTACATCCAGGATATATGTTTCCG	57.830	40.000	0.00	0.00	37.10	4.30
565	566	8.523464	CAAAGCGAATTCCAGAAATAATAAACG	58.477	33.333	0.00	0.00	0.00	3.60
590	591	1.423541	ACCAATGGCACCAGAGTAACA	59.576	47.619	0.00	0.00	0.00	2.41
609	610	9.144747	CATTGCAGATATGTATGTACTAGGAAC	57.855	37.037	0.00	0.00	0.00	3.62
664	665	0.986527	TCTCCAGGCAATGAGAAGCA	59.013	50.000	0.00	0.00	34.79	3.91
692	693	8.076714	TGTCGATCATTTTATAGCTGAATGAC	57.923	34.615	14.64	7.77	41.14	3.06
709	743	1.521457	GGCGCCATTCTGTCGATCA	60.521	57.895	24.80	0.00	0.00	2.92
713	747	1.851021	TTTGTGGCGCCATTCTGTCG	61.851	55.000	35.23	0.00	0.00	4.35
718	784	1.444895	CTGCTTTGTGGCGCCATTC	60.445	57.895	35.23	21.83	34.52	2.67
767	833	0.983378	AAGGCGTAGGAATCAGGGCT	60.983	55.000	0.00	0.00	38.19	5.19
770	836	5.890424	TTTTTAAAGGCGTAGGAATCAGG	57.110	39.130	0.00	0.00	0.00	3.86
806	875	7.336427	ACAGATTTGCAAACTTTGGAATTTTCA	59.664	29.630	15.41	0.00	40.72	2.69
861	930	5.200734	GCGAGATGCTACACATGATTATG	57.799	43.478	0.00	0.00	39.84	1.90
906	975	6.422400	GCCTTTATATAGCTGAGTGTTGAGAC	59.578	42.308	0.00	0.00	0.00	3.36
941	1011	1.221414	GGAGCTTACGCCATTAGCAG	58.779	55.000	0.00	0.00	44.04	4.24
987	1086	3.661944	CTGCGCCATGATTATCTCTCTT	58.338	45.455	4.18	0.00	0.00	2.85
1020	1119	1.068588	TCCATTACGGCCTTCAGATCG	59.931	52.381	0.00	0.00	33.14	3.69
1086	1185	2.930019	TCCAGCACCTCCCTGTGG	60.930	66.667	0.00	0.00	36.73	4.17
1097	1196	1.296392	CGGAAGATGTGGTCCAGCA	59.704	57.895	0.00	0.00	33.10	4.41
1128	1227	4.118410	CCGAGATGATCTTCTCCTTGTTG	58.882	47.826	25.14	14.13	39.19	3.33
1524	1626	3.717294	TCTTCGCCCTCCTTGCCC	61.717	66.667	0.00	0.00	0.00	5.36
1893	2004	2.507102	CAGTCGCTGTACGCCCTG	60.507	66.667	4.51	6.80	43.23	4.45
2107	2219	0.178873	TTGGCCTCCTTGTACTCCCT	60.179	55.000	3.32	0.00	0.00	4.20
2146	2282	1.567357	AGCTTGTCTTCCTCCTCCTC	58.433	55.000	0.00	0.00	0.00	3.71
2323	2459	0.396811	CAGGTCCAGGTTCGGTCTTT	59.603	55.000	0.00	0.00	0.00	2.52
2362	2498	5.043903	GCGACTCAATTAGCAGACTGATTA	58.956	41.667	6.65	0.00	31.34	1.75
2406	2553	5.520376	AAACAAACATTTAGCAGAGCACT	57.480	34.783	0.00	0.00	0.00	4.40
2435	2582	5.043248	AGAAAAACAAAAGGCACAATCGAG	58.957	37.500	0.00	0.00	0.00	4.04
2440	2587	5.059833	ACACAAGAAAAACAAAAGGCACAA	58.940	33.333	0.00	0.00	0.00	3.33
2661	3075	7.352739	ACAAGATCAACAAGTTTGACGAATAC	58.647	34.615	0.00	0.00	0.00	1.89
2703	3118	3.363970	CCCGCAATAAGACATGAATACGC	60.364	47.826	0.00	0.00	0.00	4.42
2709	3124	1.557371	TCCACCCGCAATAAGACATGA	59.443	47.619	0.00	0.00	0.00	3.07
2710	3125	2.036958	TCCACCCGCAATAAGACATG	57.963	50.000	0.00	0.00	0.00	3.21
2711	3126	2.799126	TTCCACCCGCAATAAGACAT	57.201	45.000	0.00	0.00	0.00	3.06
2712	3127	2.799126	ATTCCACCCGCAATAAGACA	57.201	45.000	0.00	0.00	0.00	3.41
2713	3128	3.751698	GGATATTCCACCCGCAATAAGAC	59.248	47.826	0.00	0.00	36.28	3.01
2714	3129	3.650942	AGGATATTCCACCCGCAATAAGA	59.349	43.478	0.00	0.00	39.61	2.10
2715	3130	4.021102	AGGATATTCCACCCGCAATAAG	57.979	45.455	0.00	0.00	39.61	1.73
2716	3131	5.772393	ATAGGATATTCCACCCGCAATAA	57.228	39.130	0.00	0.00	39.61	1.40
2717	3132	5.625886	CGAATAGGATATTCCACCCGCAATA	60.626	44.000	4.40	0.00	39.61	1.90
2718	3133	4.589908	GAATAGGATATTCCACCCGCAAT	58.410	43.478	0.00	0.00	39.61	3.56
2719	3134	3.556213	CGAATAGGATATTCCACCCGCAA	60.556	47.826	4.40	0.00	39.61	4.85
2720	3135	2.028476	CGAATAGGATATTCCACCCGCA	60.028	50.000	4.40	0.00	39.61	5.69
2721	3136	2.618053	CGAATAGGATATTCCACCCGC	58.382	52.381	4.40	0.00	39.61	6.13
2722	3137	2.618053	GCGAATAGGATATTCCACCCG	58.382	52.381	4.40	0.00	39.61	5.28
2723	3138	2.677037	CGGCGAATAGGATATTCCACCC	60.677	54.545	0.00	2.71	39.61	4.61
2724	3139	2.618053	CGGCGAATAGGATATTCCACC	58.382	52.381	0.00	5.47	39.61	4.61
2725	3140	2.000447	GCGGCGAATAGGATATTCCAC	59.000	52.381	12.98	0.00	39.61	4.02
2726	3141	1.621317	TGCGGCGAATAGGATATTCCA	59.379	47.619	12.98	0.00	39.61	3.53
2748	3163	2.048597	TCGGCTGTTCGACGCAAT	60.049	55.556	0.00	0.00	46.15	3.56
2766	3181	1.009389	GTCGGTCTCTGTGCGAAAGG	61.009	60.000	0.00	0.00	0.00	3.11
2767	3182	1.009389	GGTCGGTCTCTGTGCGAAAG	61.009	60.000	0.00	0.00	0.00	2.62
2768	3183	1.006571	GGTCGGTCTCTGTGCGAAA	60.007	57.895	0.00	0.00	0.00	3.46
2792	3208	4.404098	CCGGCCCAGGTTAACGCT	62.404	66.667	0.00	0.00	0.00	5.07
2820	3236	2.995258	CAAAACCGGAAGCAATGGAATG	59.005	45.455	9.46	0.00	0.00	2.67
2821	3237	2.028203	CCAAAACCGGAAGCAATGGAAT	60.028	45.455	9.46	0.00	0.00	3.01
2828	3244	0.747852	GTTTCCCAAAACCGGAAGCA	59.252	50.000	9.46	0.00	40.44	3.91
2830	3246	2.956333	AGAAGTTTCCCAAAACCGGAAG	59.044	45.455	9.46	0.00	44.87	3.46
3068	3526	9.883142	TTTTGAAGTTTCCAAACAAGTTATGAT	57.117	25.926	5.03	0.00	41.30	2.45
3072	3532	9.549078	AAGTTTTTGAAGTTTCCAAACAAGTTA	57.451	25.926	14.32	0.00	41.30	2.24
3075	3535	8.341903	ACAAAGTTTTTGAAGTTTCCAAACAAG	58.658	29.630	8.41	8.81	41.30	3.16
3131	3611	5.514274	ACAATTTCTGAAAACACGACCAT	57.486	34.783	6.95	0.00	0.00	3.55
3230	3718	7.813148	TCTGTAAAAACGAACAAAAACATTCCA	59.187	29.630	0.00	0.00	0.00	3.53
3257	3756	7.962934	TCAAATCGCGGTCATTATTTAAAAG	57.037	32.000	6.13	0.00	0.00	2.27
3280	3780	9.891828	ACAATTTTTGAAAACAGGAACTTTTTC	57.108	25.926	0.00	0.00	37.35	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.