AutoCloner

Multiple sequence alignment - TraesCS1D01G158500

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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	TraesCS1D01G158500	chr1D	100.000	4260	0	0	1	4260	223394297	223390038	0.000000e+00	7867.0
1	TraesCS1D01G158500	chr1D	92.734	578	35	5	4	575	53055888	53055312	0.000000e+00	828.0
2	TraesCS1D01G158500	chr1D	83.764	813	70	35	1274	2047	223367138	223366349	0.000000e+00	713.0
3	TraesCS1D01G158500	chr1D	87.234	188	16	2	2241	2428	223364320	223364141	1.550000e-49	207.0
4	TraesCS1D01G158500	chr1D	91.729	133	11	0	2899	3031	223391273	223391141	7.270000e-43	185.0
5	TraesCS1D01G158500	chr1D	91.729	133	11	0	3025	3157	223391399	223391267	7.270000e-43	185.0
6	TraesCS1D01G158500	chr1D	94.231	104	5	1	2422	2525	223364033	223363931	1.590000e-34	158.0
7	TraesCS1D01G158500	chr1D	100.000	33	0	0	2015	2047	223392250	223392218	1.280000e-05	62.1
8	TraesCS1D01G158500	chr1D	100.000	33	0	0	2048	2080	223392283	223392251	1.280000e-05	62.1
9	TraesCS1D01G158500	chr1D	100.000	32	0	0	2049	2080	223366380	223366349	4.600000e-05	60.2
10	TraesCS1D01G158500	chr1B	92.461	1207	54	16	2280	3485	322728399	322727229	0.000000e+00	1690.0
11	TraesCS1D01G158500	chr1B	93.842	812	30	4	776	1583	322730126	322729331	0.000000e+00	1205.0
12	TraesCS1D01G158500	chr1B	90.404	396	21	4	3882	4260	340426322	340425927	4.920000e-139	505.0
13	TraesCS1D01G158500	chr1B	85.743	505	32	20	1578	2042	322729306	322728802	8.230000e-137	497.0
14	TraesCS1D01G158500	chr1B	96.016	251	5	2	2048	2293	322728829	322728579	1.840000e-108	403.0
15	TraesCS1D01G158500	chr1B	90.604	149	13	1	3741	3889	340426893	340426746	3.360000e-46	196.0
16	TraesCS1D01G158500	chr1B	91.729	133	11	0	2899	3031	322727672	322727540	7.270000e-43	185.0
17	TraesCS1D01G158500	chr1B	90.977	133	12	0	3025	3157	322727798	322727666	3.380000e-41	180.0
18	TraesCS1D01G158500	chr1B	86.928	153	16	4	574	724	322713694	322713544	7.330000e-38	169.0
19	TraesCS1D01G158500	chr1B	92.308	117	7	2	569	683	322735893	322735777	9.480000e-37	165.0
20	TraesCS1D01G158500	chr1A	90.884	1086	52	15	2411	3481	290346628	290345575	0.000000e+00	1413.0
21	TraesCS1D01G158500	chr1A	88.372	1204	83	31	874	2047	290349783	290348607	0.000000e+00	1395.0
22	TraesCS1D01G158500	chr1A	91.878	788	47	1	3486	4256	527020339	527021126	0.000000e+00	1085.0
23	TraesCS1D01G158500	chr1A	90.811	185	12	2	2244	2428	290346829	290346650	4.260000e-60	243.0
24	TraesCS1D01G158500	chr1A	92.949	156	9	1	2048	2201	290348639	290348484	4.290000e-55	226.0
25	TraesCS1D01G158500	chr1A	93.985	133	8	0	2899	3031	290346041	290345909	7.220000e-48	202.0
26	TraesCS1D01G158500	chr1A	88.722	133	15	0	3025	3157	290346167	290346035	3.410000e-36	163.0
27	TraesCS1D01G158500	chr1A	87.500	112	10	4	596	705	290317965	290317856	4.470000e-25	126.0
28	TraesCS1D01G158500	chr1A	88.764	89	5	1	638	726	290350410	290350327	2.100000e-18	104.0
29	TraesCS1D01G158500	chr1A	96.774	31	1	0	740	770	572350333	572350363	8.000000e-03	52.8
30	TraesCS1D01G158500	chr7D	93.916	789	29	6	3486	4257	88212049	88212835	0.000000e+00	1173.0
31	TraesCS1D01G158500	chr7D	89.796	49	2	1	724	772	91855257	91855302	4.600000e-05	60.2
32	TraesCS1D01G158500	chr6D	92.734	578	38	4	1	575	329583922	329584498	0.000000e+00	832.0
33	TraesCS1D01G158500	chr6D	92.548	577	40	3	1	575	327063623	327063048	0.000000e+00	824.0
34	TraesCS1D01G158500	chr4D	92.708	576	40	2	1	575	494806815	494807389	0.000000e+00	830.0
35	TraesCS1D01G158500	chr4D	92.548	577	38	4	1	575	380240231	380239658	0.000000e+00	822.0
36	TraesCS1D01G158500	chr3D	92.708	576	40	2	1	575	177519938	177520512	0.000000e+00	830.0
37	TraesCS1D01G158500	chr3D	96.875	32	1	0	739	770	549065966	549065935	2.000000e-03	54.7
38	TraesCS1D01G158500	chr2D	92.548	577	40	3	1	575	443465976	443465401	0.000000e+00	824.0
39	TraesCS1D01G158500	chr2D	96.774	31	1	0	740	770	405628008	405628038	8.000000e-03	52.8
40	TraesCS1D01G158500	chr5B	91.626	609	29	2	3666	4257	569241912	569242515	0.000000e+00	822.0
41	TraesCS1D01G158500	chr5B	91.461	609	30	2	3666	4257	569140736	569141339	0.000000e+00	817.0
42	TraesCS1D01G158500	chr5B	92.215	578	40	5	1	575	53235584	53236159	0.000000e+00	813.0
43	TraesCS1D01G158500	chr5D	92.201	577	42	3	1	575	544357066	544356491	0.000000e+00	813.0
44	TraesCS1D01G158500	chr2A	91.304	46	2	1	724	769	70926553	70926510	1.280000e-05	62.1
45	TraesCS1D01G158500	chr2A	91.304	46	1	1	727	772	16582032	16581990	4.600000e-05	60.2
46	TraesCS1D01G158500	chr4A	100.000	28	0	0	743	770	614910288	614910261	8.000000e-03	52.8
47	TraesCS1D01G158500	chr3A	96.774	31	1	0	740	770	584292488	584292518	8.000000e-03	52.8
48	TraesCS1D01G158500	chr2B	100.000	28	0	0	743	770	774443749	774443722	8.000000e-03	52.8

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	TraesCS1D01G158500	chr1D	223390038	223394297	4259	True	1672.240000	7867	96.691600	1	4260	5	chr1D.!!$R3	4259
1	TraesCS1D01G158500	chr1D	53055312	53055888	576	True	828.000000	828	92.734000	4	575	1	chr1D.!!$R1	571
2	TraesCS1D01G158500	chr1D	223363931	223367138	3207	True	284.550000	713	91.307250	1274	2525	4	chr1D.!!$R2	1251
3	TraesCS1D01G158500	chr1B	322727229	322730126	2897	True	693.333333	1690	91.794667	776	3485	6	chr1B.!!$R3	2709
4	TraesCS1D01G158500	chr1B	340425927	340426893	966	True	350.500000	505	90.504000	3741	4260	2	chr1B.!!$R4	519
5	TraesCS1D01G158500	chr1A	527020339	527021126	787	False	1085.000000	1085	91.878000	3486	4256	1	chr1A.!!$F1	770
6	TraesCS1D01G158500	chr1A	290345575	290350410	4835	True	535.142857	1413	90.641000	638	3481	7	chr1A.!!$R2	2843
7	TraesCS1D01G158500	chr7D	88212049	88212835	786	False	1173.000000	1173	93.916000	3486	4257	1	chr7D.!!$F1	771
8	TraesCS1D01G158500	chr6D	329583922	329584498	576	False	832.000000	832	92.734000	1	575	1	chr6D.!!$F1	574
9	TraesCS1D01G158500	chr6D	327063048	327063623	575	True	824.000000	824	92.548000	1	575	1	chr6D.!!$R1	574
10	TraesCS1D01G158500	chr4D	494806815	494807389	574	False	830.000000	830	92.708000	1	575	1	chr4D.!!$F1	574
11	TraesCS1D01G158500	chr4D	380239658	380240231	573	True	822.000000	822	92.548000	1	575	1	chr4D.!!$R1	574
12	TraesCS1D01G158500	chr3D	177519938	177520512	574	False	830.000000	830	92.708000	1	575	1	chr3D.!!$F1	574
13	TraesCS1D01G158500	chr2D	443465401	443465976	575	True	824.000000	824	92.548000	1	575	1	chr2D.!!$R1	574
14	TraesCS1D01G158500	chr5B	569241912	569242515	603	False	822.000000	822	91.626000	3666	4257	1	chr5B.!!$F3	591
15	TraesCS1D01G158500	chr5B	569140736	569141339	603	False	817.000000	817	91.461000	3666	4257	1	chr5B.!!$F2	591
16	TraesCS1D01G158500	chr5B	53235584	53236159	575	False	813.000000	813	92.215000	1	575	1	chr5B.!!$F1	574
17	TraesCS1D01G158500	chr5D	544356491	544357066	575	True	813.000000	813	92.201000	1	575	1	chr5D.!!$R1	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
663	674	0.108329	AGACCCGTCTATTTGCCACG	60.108	55.0	0.00	0.00	38.35	4.94	F
853	933	0.109086	AACCTCGTGATCTGAGTGCG	60.109	55.0	12.56	3.11	0.00	5.34	F
933	1340	0.389391	TCTCGATGATCCCCTTTCGC	59.611	55.0	0.00	0.00	0.00	4.70	F
1322	1741	0.462047	AATGCCGATTCGTCAGGTCC	60.462	55.0	5.20	0.00	0.00	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1583	2004	1.967319	ACCGTGCAGAGAACACAATT	58.033	45.000	0.00	37.93	2.32	R
2570	6824	2.182842	CCTGGTATTGCTGCCTCGC	61.183	63.158	0.00	0.00	5.03	R
3046	7300	1.801512	CACGTCGCAGATCTCGCAA	60.802	57.895	14.69	40.67	4.85	R
3431	7722	0.541392	TATTGTCATGCAGAGGCCGT	59.459	50.000	0.00	40.13	5.68	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
197	199	1.156736	GGGATCACAACCAACACGAG	58.843	55.000	0.00	0.00	0.00	4.18
240	242	3.923563	GAGCACCGACAGCGCTTCT	62.924	63.158	7.50	0.00	35.75	2.85
246	248	0.452184	CCGACAGCGCTTCTCTAAGA	59.548	55.000	7.50	0.00	34.18	2.10
571	582	1.068588	TGGACTCACTTGTGGACTTCG	59.931	52.381	0.64	0.00	0.00	3.79
572	583	1.140816	GACTCACTTGTGGACTTCGC	58.859	55.000	0.64	0.00	0.00	4.70
574	585	1.284982	CTCACTTGTGGACTTCGCGG	61.285	60.000	6.13	0.00	0.00	6.46
575	586	2.030562	ACTTGTGGACTTCGCGGG	59.969	61.111	6.13	1.80	0.00	6.13
576	587	3.423154	CTTGTGGACTTCGCGGGC	61.423	66.667	6.13	0.00	0.00	6.13
577	588	3.883744	CTTGTGGACTTCGCGGGCT	62.884	63.158	6.13	0.00	0.00	5.19
578	589	3.469863	TTGTGGACTTCGCGGGCTT	62.470	57.895	6.13	0.00	0.00	4.35
579	590	3.119096	GTGGACTTCGCGGGCTTC	61.119	66.667	6.13	0.00	0.00	3.86
580	591	3.621805	TGGACTTCGCGGGCTTCA	61.622	61.111	6.13	0.00	0.00	3.02
581	592	2.815647	GGACTTCGCGGGCTTCAG	60.816	66.667	6.13	0.00	0.00	3.02
582	593	2.048127	GACTTCGCGGGCTTCAGT	60.048	61.111	6.13	0.00	0.00	3.41
583	594	1.668151	GACTTCGCGGGCTTCAGTT	60.668	57.895	6.13	0.00	0.00	3.16
584	595	0.389426	GACTTCGCGGGCTTCAGTTA	60.389	55.000	6.13	0.00	0.00	2.24
585	596	0.249398	ACTTCGCGGGCTTCAGTTAT	59.751	50.000	6.13	0.00	0.00	1.89
586	597	1.479323	ACTTCGCGGGCTTCAGTTATA	59.521	47.619	6.13	0.00	0.00	0.98
587	598	2.102588	ACTTCGCGGGCTTCAGTTATAT	59.897	45.455	6.13	0.00	0.00	0.86
588	599	2.148916	TCGCGGGCTTCAGTTATATG	57.851	50.000	6.13	0.00	0.00	1.78
589	600	1.148310	CGCGGGCTTCAGTTATATGG	58.852	55.000	0.00	0.00	0.00	2.74
590	601	1.270094	CGCGGGCTTCAGTTATATGGA	60.270	52.381	0.00	0.00	0.00	3.41
591	602	2.417719	GCGGGCTTCAGTTATATGGAG	58.582	52.381	0.00	0.00	0.00	3.86
595	606	2.417719	GCTTCAGTTATATGGAGCCGG	58.582	52.381	0.00	0.00	44.75	6.13
596	607	2.872038	GCTTCAGTTATATGGAGCCGGG	60.872	54.545	2.18	0.00	44.75	5.73
597	608	1.348064	TCAGTTATATGGAGCCGGGG	58.652	55.000	2.18	0.00	0.00	5.73
598	609	1.132977	TCAGTTATATGGAGCCGGGGA	60.133	52.381	2.18	0.00	0.00	4.81
599	610	1.276421	CAGTTATATGGAGCCGGGGAG	59.724	57.143	2.18	0.00	0.00	4.30
600	611	1.132817	AGTTATATGGAGCCGGGGAGT	60.133	52.381	2.18	0.00	0.00	3.85
601	612	1.002087	GTTATATGGAGCCGGGGAGTG	59.998	57.143	2.18	0.00	0.00	3.51
602	613	0.190069	TATATGGAGCCGGGGAGTGT	59.810	55.000	2.18	0.00	0.00	3.55
603	614	0.694444	ATATGGAGCCGGGGAGTGTT	60.694	55.000	2.18	0.00	0.00	3.32
604	615	1.335132	TATGGAGCCGGGGAGTGTTC	61.335	60.000	2.18	0.00	0.00	3.18
605	616	3.003763	GGAGCCGGGGAGTGTTCT	61.004	66.667	2.18	0.00	0.00	3.01
606	617	2.579738	GAGCCGGGGAGTGTTCTC	59.420	66.667	2.18	0.00	39.76	2.87
645	656	8.622948	AAAGATAAGTTGGACCTTTACAGAAG	57.377	34.615	0.00	0.00	0.00	2.85
650	661	1.621814	TGGACCTTTACAGAAGACCCG	59.378	52.381	0.00	0.00	0.00	5.28
663	674	0.108329	AGACCCGTCTATTTGCCACG	60.108	55.000	0.00	0.00	38.35	4.94
679	690	4.803426	CGCTGTCACCTCGGAGGC	62.803	72.222	23.84	8.51	39.63	4.70
680	691	4.803426	GCTGTCACCTCGGAGGCG	62.803	72.222	23.84	14.98	39.63	5.52
681	692	4.135153	CTGTCACCTCGGAGGCGG	62.135	72.222	23.84	16.01	39.63	6.13
682	693	4.988716	TGTCACCTCGGAGGCGGT	62.989	66.667	23.84	2.47	39.63	5.68
683	694	4.131088	GTCACCTCGGAGGCGGTC	62.131	72.222	23.84	10.39	39.63	4.79
689	700	1.738099	CTCGGAGGCGGTCAACAAG	60.738	63.158	0.00	0.00	0.00	3.16
721	732	2.749076	TGCCACATCAGCAGAATACAAC	59.251	45.455	0.00	0.00	34.69	3.32
726	737	4.864806	CACATCAGCAGAATACAACGTACT	59.135	41.667	0.00	0.00	0.00	2.73
727	738	5.004821	CACATCAGCAGAATACAACGTACTC	59.995	44.000	0.00	0.00	0.00	2.59
728	739	4.106029	TCAGCAGAATACAACGTACTCC	57.894	45.455	0.00	0.00	0.00	3.85
730	741	3.097614	AGCAGAATACAACGTACTCCCT	58.902	45.455	0.00	0.00	0.00	4.20
731	742	3.130693	AGCAGAATACAACGTACTCCCTC	59.869	47.826	0.00	0.00	0.00	4.30
732	743	3.737355	GCAGAATACAACGTACTCCCTCC	60.737	52.174	0.00	0.00	0.00	4.30
733	744	3.446161	CAGAATACAACGTACTCCCTCCA	59.554	47.826	0.00	0.00	0.00	3.86
734	745	4.099573	CAGAATACAACGTACTCCCTCCAT	59.900	45.833	0.00	0.00	0.00	3.41
743	763	7.014038	ACAACGTACTCCCTCCATAAACTATAG	59.986	40.741	0.00	0.00	0.00	1.31
747	767	9.240734	CGTACTCCCTCCATAAACTATAGTAAT	57.759	37.037	5.65	0.28	0.00	1.89
771	791	8.918961	ATATAAGAGCGTTTAGATCACTATGC	57.081	34.615	0.00	0.00	37.82	3.14
772	792	3.633235	AGAGCGTTTAGATCACTATGCG	58.367	45.455	0.00	0.00	37.82	4.73
773	793	3.315470	AGAGCGTTTAGATCACTATGCGA	59.685	43.478	0.00	0.00	37.82	5.10
774	794	3.633235	AGCGTTTAGATCACTATGCGAG	58.367	45.455	0.00	0.00	32.32	5.03
794	874	4.495844	CGAGAAAAAGACCATAAATCGGGC	60.496	45.833	0.00	0.00	0.00	6.13
815	895	6.294120	CGGGCATTCTTGAATATATTGAGCAA	60.294	38.462	1.78	0.63	0.00	3.91
853	933	0.109086	AACCTCGTGATCTGAGTGCG	60.109	55.000	12.56	3.11	0.00	5.34
855	935	1.875813	CTCGTGATCTGAGTGCGGC	60.876	63.158	7.22	0.00	0.00	6.53
914	1321	0.755327	GCCAGGTGAACCAACCAACT	60.755	55.000	1.62	0.00	43.20	3.16
916	1323	1.133792	CCAGGTGAACCAACCAACTCT	60.134	52.381	1.62	0.00	43.20	3.24
933	1340	0.389391	TCTCGATGATCCCCTTTCGC	59.611	55.000	0.00	0.00	0.00	4.70
1069	1478	0.602106	CATTGCCGATCGATCAGGCT	60.602	55.000	37.21	26.27	42.68	4.58
1075	1484	2.610479	GCCGATCGATCAGGCTATCAAA	60.610	50.000	34.17	0.00	40.66	2.69
1089	1498	3.553917	GCTATCAAAGAGGAAGACGAAGC	59.446	47.826	0.00	0.00	0.00	3.86
1092	1501	0.670854	AAAGAGGAAGACGAAGCGGC	60.671	55.000	0.00	0.00	33.59	6.53
1140	1551	1.009389	CACGGCGACCAAGAAGACTC	61.009	60.000	16.62	0.00	0.00	3.36
1312	1731	1.255882	TGTTTCCTGCAATGCCGATT	58.744	45.000	1.53	0.00	0.00	3.34
1322	1741	0.462047	AATGCCGATTCGTCAGGTCC	60.462	55.000	5.20	0.00	0.00	4.46
1411	1830	2.125106	GCGGACATCACCCTGGAC	60.125	66.667	0.00	0.00	0.00	4.02
1583	2004	7.043961	TGTTTTGAAACTGGCACATTGTATA	57.956	32.000	7.97	0.00	39.59	1.47
1676	2134	2.153645	TCTGCTGCACATAGTTGTTGG	58.846	47.619	0.00	0.00	32.34	3.77
1681	2139	3.052036	CTGCACATAGTTGTTGGTTTGC	58.948	45.455	0.00	0.00	32.34	3.68
1863	2350	5.052436	CGCAATTAAGTGTTCACAAACAGTG	60.052	40.000	4.65	0.00	46.10	3.66
1895	2382	5.783111	ACAAGTTTTCCCAACAATGCTATC	58.217	37.500	0.00	0.00	0.00	2.08
1920	2407	5.843673	TGTTGCTTGAAATACTGGAACAA	57.156	34.783	0.00	0.00	37.69	2.83
1973	2460	2.656002	TCGGAGACATAGTTGAGAGGG	58.344	52.381	0.00	0.00	0.00	4.30
2293	6240	6.607689	TCACATTTCCTGCTACGTAAATTTG	58.392	36.000	0.00	0.00	0.00	2.32
2538	6792	4.421479	CTCCGGCGTTCGACAGCT	62.421	66.667	6.01	0.00	42.43	4.24
2688	6942	1.537397	TCCAGAAGCAGAGGCCACT	60.537	57.895	5.01	0.00	42.56	4.00
3046	7300	0.734942	CCGGTGAGATAAACGTGCGT	60.735	55.000	0.00	0.00	0.00	5.24
3055	7309	0.711670	TAAACGTGCGTTGCGAGATC	59.288	50.000	10.81	0.00	38.47	2.75
3206	7475	4.566004	TGCTAGTACCAGCTAACAACTTG	58.434	43.478	14.47	0.00	42.30	3.16
3266	7553	3.926616	ACTGTCCTGTAAGTGTGCATAC	58.073	45.455	5.29	5.29	0.00	2.39
3381	7668	5.860941	TGTTTTACTTGGATTTGCCTTGA	57.139	34.783	0.00	0.00	37.63	3.02
3395	7682	8.037166	GGATTTGCCTTGATGATTTTTCTTAGT	58.963	33.333	0.00	0.00	0.00	2.24
3396	7683	9.428097	GATTTGCCTTGATGATTTTTCTTAGTT	57.572	29.630	0.00	0.00	0.00	2.24
3397	7684	8.592105	TTTGCCTTGATGATTTTTCTTAGTTG	57.408	30.769	0.00	0.00	0.00	3.16
3398	7685	7.288810	TGCCTTGATGATTTTTCTTAGTTGT	57.711	32.000	0.00	0.00	0.00	3.32
3399	7686	8.402798	TGCCTTGATGATTTTTCTTAGTTGTA	57.597	30.769	0.00	0.00	0.00	2.41
3514	7805	1.808133	GCCGCTAAGTGATCAGGAAGG	60.808	57.143	0.00	0.00	0.00	3.46
3560	7851	4.405756	TTTCTCAGGAGTCCTAGGAACT	57.594	45.455	14.65	13.10	46.37	3.01
3575	7866	3.486383	AGGAACTCCAAGCGAAATTTCA	58.514	40.909	17.99	0.00	38.89	2.69
3599	7890	2.155279	GCTTTCTGTTGGGACTTCCTC	58.845	52.381	0.00	0.00	36.20	3.71
3610	7901	6.069440	TGTTGGGACTTCCTCAATATCAATCT	60.069	38.462	0.00	0.00	36.20	2.40
3618	7909	6.644248	TCCTCAATATCAATCTGGCAAATG	57.356	37.500	0.00	0.00	0.00	2.32
3698	7989	3.767630	AACTGACAAAGCGCCCGGT	62.768	57.895	2.29	0.00	0.00	5.28
3753	8044	4.292186	TGCTGGGATATCATTAAGGAGC	57.708	45.455	4.83	1.73	0.00	4.70
4103	8842	0.036765	GTGTCCTGGCCGTACATTCA	60.037	55.000	7.76	0.00	0.00	2.57
4106	8845	1.153168	CCTGGCCGTACATTCAGGG	60.153	63.158	14.22	0.00	42.12	4.45
4240	8979	1.454847	AAGTGCGGGTTCAGGCAAA	60.455	52.632	0.00	0.00	41.46	3.68
4257	8996	1.696097	AAAGCGACCCACTGTCACCT	61.696	55.000	0.00	0.00	44.71	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
124	126	2.746279	AGGAGGAGACATCATCGAGT	57.254	50.000	0.00	0.00	37.11	4.18
197	199	1.449601	CACCATCACCACTACGCCC	60.450	63.158	0.00	0.00	0.00	6.13
203	205	1.455849	CACCACCACCATCACCACT	59.544	57.895	0.00	0.00	0.00	4.00
240	242	0.609957	TTGTCCCGGCGACTCTTAGA	60.610	55.000	19.61	0.00	42.49	2.10
263	265	2.229784	CCCGTTACTTCGTAGTTCCACT	59.770	50.000	0.00	0.00	35.78	4.00
275	277	1.342175	CCCCTCTCTCTCCCGTTACTT	60.342	57.143	0.00	0.00	0.00	2.24
389	394	2.393646	CAAGTCCTCTCCCCCTTAGAG	58.606	57.143	0.00	0.00	40.21	2.43
571	582	2.417719	CTCCATATAACTGAAGCCCGC	58.582	52.381	0.00	0.00	0.00	6.13
572	583	2.417719	GCTCCATATAACTGAAGCCCG	58.582	52.381	0.00	0.00	0.00	6.13
574	585	2.417719	CGGCTCCATATAACTGAAGCC	58.582	52.381	1.10	1.10	37.79	4.35
575	586	2.417719	CCGGCTCCATATAACTGAAGC	58.582	52.381	0.00	0.00	0.00	3.86
576	587	2.289694	CCCCGGCTCCATATAACTGAAG	60.290	54.545	0.00	0.00	0.00	3.02
577	588	1.697432	CCCCGGCTCCATATAACTGAA	59.303	52.381	0.00	0.00	0.00	3.02
578	589	1.132977	TCCCCGGCTCCATATAACTGA	60.133	52.381	0.00	0.00	0.00	3.41
579	590	1.276421	CTCCCCGGCTCCATATAACTG	59.724	57.143	0.00	0.00	0.00	3.16
580	591	1.132817	ACTCCCCGGCTCCATATAACT	60.133	52.381	0.00	0.00	0.00	2.24
581	592	1.002087	CACTCCCCGGCTCCATATAAC	59.998	57.143	0.00	0.00	0.00	1.89
582	593	1.348064	CACTCCCCGGCTCCATATAA	58.652	55.000	0.00	0.00	0.00	0.98
583	594	0.190069	ACACTCCCCGGCTCCATATA	59.810	55.000	0.00	0.00	0.00	0.86
584	595	0.694444	AACACTCCCCGGCTCCATAT	60.694	55.000	0.00	0.00	0.00	1.78
585	596	1.306654	AACACTCCCCGGCTCCATA	60.307	57.895	0.00	0.00	0.00	2.74
586	597	2.610859	AACACTCCCCGGCTCCAT	60.611	61.111	0.00	0.00	0.00	3.41
587	598	3.319198	GAACACTCCCCGGCTCCA	61.319	66.667	0.00	0.00	0.00	3.86
588	599	3.003763	AGAACACTCCCCGGCTCC	61.004	66.667	0.00	0.00	0.00	4.70
589	600	2.579738	GAGAACACTCCCCGGCTC	59.420	66.667	0.00	0.00	0.00	4.70
590	601	3.003763	GGAGAACACTCCCCGGCT	61.004	66.667	0.00	0.00	43.01	5.52
618	629	8.990163	TCTGTAAAGGTCCAACTTATCTTTTT	57.010	30.769	0.00	0.00	0.00	1.94
619	630	8.990163	TTCTGTAAAGGTCCAACTTATCTTTT	57.010	30.769	0.00	0.00	0.00	2.27
620	631	8.437575	TCTTCTGTAAAGGTCCAACTTATCTTT	58.562	33.333	0.00	0.00	0.00	2.52
621	632	7.878644	GTCTTCTGTAAAGGTCCAACTTATCTT	59.121	37.037	0.00	0.00	0.00	2.40
622	633	7.387643	GTCTTCTGTAAAGGTCCAACTTATCT	58.612	38.462	0.00	0.00	0.00	1.98
623	634	6.594547	GGTCTTCTGTAAAGGTCCAACTTATC	59.405	42.308	0.00	0.00	0.00	1.75
624	635	6.473758	GGTCTTCTGTAAAGGTCCAACTTAT	58.526	40.000	0.00	0.00	0.00	1.73
625	636	5.221783	GGGTCTTCTGTAAAGGTCCAACTTA	60.222	44.000	0.00	0.00	0.00	2.24
626	637	4.445879	GGGTCTTCTGTAAAGGTCCAACTT	60.446	45.833	0.00	0.00	0.00	2.66
627	638	3.072622	GGGTCTTCTGTAAAGGTCCAACT	59.927	47.826	0.00	0.00	0.00	3.16
628	639	3.409570	GGGTCTTCTGTAAAGGTCCAAC	58.590	50.000	0.00	0.00	0.00	3.77
629	640	2.038033	CGGGTCTTCTGTAAAGGTCCAA	59.962	50.000	0.00	0.00	0.00	3.53
630	641	1.621814	CGGGTCTTCTGTAAAGGTCCA	59.378	52.381	0.00	0.00	0.00	4.02
631	642	1.622312	ACGGGTCTTCTGTAAAGGTCC	59.378	52.381	0.00	0.00	32.15	4.46
632	643	2.561858	AGACGGGTCTTCTGTAAAGGTC	59.438	50.000	0.00	0.00	36.31	3.85
633	644	2.606378	AGACGGGTCTTCTGTAAAGGT	58.394	47.619	0.00	0.00	36.31	3.50
634	645	5.340439	AATAGACGGGTCTTCTGTAAAGG	57.660	43.478	6.65	0.00	40.93	3.11
635	646	5.063564	GCAAATAGACGGGTCTTCTGTAAAG	59.936	44.000	6.65	0.00	40.93	1.85
636	647	4.933400	GCAAATAGACGGGTCTTCTGTAAA	59.067	41.667	6.65	0.00	40.93	2.01
645	656	1.702491	GCGTGGCAAATAGACGGGTC	61.702	60.000	0.00	0.00	33.68	4.46
650	661	1.128692	GTGACAGCGTGGCAAATAGAC	59.871	52.381	0.00	0.00	36.98	2.59
679	690	5.447279	GGCATATACTTTGACTTGTTGACCG	60.447	44.000	0.00	0.00	0.00	4.79
680	691	5.414454	TGGCATATACTTTGACTTGTTGACC	59.586	40.000	0.00	0.00	0.00	4.02
681	692	6.072728	TGTGGCATATACTTTGACTTGTTGAC	60.073	38.462	0.00	0.00	0.00	3.18
682	693	6.000840	TGTGGCATATACTTTGACTTGTTGA	58.999	36.000	0.00	0.00	0.00	3.18
683	694	6.252967	TGTGGCATATACTTTGACTTGTTG	57.747	37.500	0.00	0.00	0.00	3.33
689	700	4.576053	TGCTGATGTGGCATATACTTTGAC	59.424	41.667	0.00	0.00	34.56	3.18
721	732	8.627208	TTACTATAGTTTATGGAGGGAGTACG	57.373	38.462	11.40	0.00	0.00	3.67
747	767	7.021790	CGCATAGTGATCTAAACGCTCTTATA	58.978	38.462	0.00	0.00	0.00	0.98
748	768	5.859114	CGCATAGTGATCTAAACGCTCTTAT	59.141	40.000	0.00	0.00	0.00	1.73
751	771	3.315470	TCGCATAGTGATCTAAACGCTCT	59.685	43.478	0.00	0.00	32.43	4.09
753	773	3.315470	TCTCGCATAGTGATCTAAACGCT	59.685	43.478	0.00	0.00	32.43	5.07
755	775	6.569228	TTTTCTCGCATAGTGATCTAAACG	57.431	37.500	0.00	0.00	33.12	3.60
761	781	4.870426	TGGTCTTTTTCTCGCATAGTGATC	59.130	41.667	0.00	0.00	0.00	2.92
763	783	4.265904	TGGTCTTTTTCTCGCATAGTGA	57.734	40.909	0.00	0.00	0.00	3.41
764	784	6.662414	TTATGGTCTTTTTCTCGCATAGTG	57.338	37.500	0.00	0.00	0.00	2.74
765	785	7.254455	CGATTTATGGTCTTTTTCTCGCATAGT	60.254	37.037	0.00	0.00	0.00	2.12
766	786	7.065894	CGATTTATGGTCTTTTTCTCGCATAG	58.934	38.462	0.00	0.00	0.00	2.23
767	787	6.018262	CCGATTTATGGTCTTTTTCTCGCATA	60.018	38.462	0.00	0.00	0.00	3.14
768	788	5.220854	CCGATTTATGGTCTTTTTCTCGCAT	60.221	40.000	0.00	0.00	0.00	4.73
769	789	4.094294	CCGATTTATGGTCTTTTTCTCGCA	59.906	41.667	0.00	0.00	0.00	5.10
770	790	4.495844	CCCGATTTATGGTCTTTTTCTCGC	60.496	45.833	0.00	0.00	0.00	5.03
771	791	4.495844	GCCCGATTTATGGTCTTTTTCTCG	60.496	45.833	0.00	0.00	0.00	4.04
772	792	4.398044	TGCCCGATTTATGGTCTTTTTCTC	59.602	41.667	0.00	0.00	0.00	2.87
773	793	4.340617	TGCCCGATTTATGGTCTTTTTCT	58.659	39.130	0.00	0.00	0.00	2.52
774	794	4.712122	TGCCCGATTTATGGTCTTTTTC	57.288	40.909	0.00	0.00	0.00	2.29
834	914	0.109086	CGCACTCAGATCACGAGGTT	60.109	55.000	14.58	0.00	34.66	3.50
835	915	1.508545	CGCACTCAGATCACGAGGT	59.491	57.895	14.58	1.07	34.66	3.85
836	916	1.226802	CCGCACTCAGATCACGAGG	60.227	63.158	14.58	6.68	34.66	4.63
853	933	7.424001	CCAAAAGATCTAAAAGATGAGATGCC	58.576	38.462	0.00	0.00	34.53	4.40
855	935	7.776969	TCCCCAAAAGATCTAAAAGATGAGATG	59.223	37.037	0.00	0.00	34.53	2.90
914	1321	0.389391	GCGAAAGGGGATCATCGAGA	59.611	55.000	0.00	0.00	37.48	4.04
916	1323	0.830648	AAGCGAAAGGGGATCATCGA	59.169	50.000	0.00	0.00	37.48	3.59
1069	1478	3.428999	CCGCTTCGTCTTCCTCTTTGATA	60.429	47.826	0.00	0.00	0.00	2.15
1075	1484	2.574399	GCCGCTTCGTCTTCCTCT	59.426	61.111	0.00	0.00	0.00	3.69
1092	1501	4.129737	ATGCAGGGACGTCGACGG	62.130	66.667	37.89	22.50	44.95	4.79
1103	1514	2.047274	AACCCGACGTGATGCAGG	60.047	61.111	0.00	0.00	0.00	4.85
1140	1551	1.597742	GTTCATCCGGATGTCCATGG	58.402	55.000	36.95	15.80	39.72	3.66
1312	1731	0.033504	GTGCTTTGAGGACCTGACGA	59.966	55.000	0.00	0.00	29.54	4.20
1322	1741	3.058708	ACATCGACATTGTGTGCTTTGAG	60.059	43.478	0.00	0.00	0.00	3.02
1550	1971	5.049828	GCCAGTTTCAAAACATGCTAAAGT	58.950	37.500	8.23	0.00	41.30	2.66
1583	2004	1.967319	ACCGTGCAGAGAACACAATT	58.033	45.000	0.00	0.00	37.93	2.32
1694	2153	6.363065	ACTGTACCATCCTAGAACGAGAATA	58.637	40.000	0.00	0.00	0.00	1.75
1696	2155	4.597004	ACTGTACCATCCTAGAACGAGAA	58.403	43.478	0.00	0.00	0.00	2.87
1720	2179	6.111382	TCAACAAATGCATTTTCCTGACAAA	58.889	32.000	21.95	1.85	0.00	2.83
1863	2350	5.929415	TGTTGGGAAAACTTGTTTTCTTCAC	59.071	36.000	27.30	21.91	39.99	3.18
1895	2382	5.221224	TGTTCCAGTATTTCAAGCAACAAGG	60.221	40.000	0.00	0.00	0.00	3.61
1902	2389	9.045223	AGAAATTTTTGTTCCAGTATTTCAAGC	57.955	29.630	0.00	0.00	35.51	4.01
1920	2407	8.755018	CAGAAGTTTGCGTTATTCAGAAATTTT	58.245	29.630	0.00	0.00	0.00	1.82
1973	2460	5.326069	TGCCTAGAGGTAGTTCTATCATCC	58.674	45.833	0.00	0.00	37.57	3.51
2047	2538	6.476378	ACTATCTTTCATACAGTGGCTGTTT	58.524	36.000	7.11	0.00	42.59	2.83
2048	2539	6.054860	ACTATCTTTCATACAGTGGCTGTT	57.945	37.500	7.11	0.00	42.59	3.16
2050	2541	6.344500	AGAACTATCTTTCATACAGTGGCTG	58.656	40.000	0.00	0.00	32.56	4.85
2052	2543	8.894768	AATAGAACTATCTTTCATACAGTGGC	57.105	34.615	0.00	0.00	37.10	5.01
2293	6240	6.937465	ACTGGAGTAATTCTTCTTCTGAAACC	59.063	38.462	0.00	0.00	0.00	3.27
2509	6763	2.681778	CCGGAGACAGCAGGAGGT	60.682	66.667	0.00	0.00	0.00	3.85
2538	6792	2.281484	GGAACTGGTTCTGCGGCA	60.281	61.111	1.29	1.29	39.45	5.69
2570	6824	2.182842	CCTGGTATTGCTGCCTCGC	61.183	63.158	0.00	0.00	0.00	5.03
3046	7300	1.801512	CACGTCGCAGATCTCGCAA	60.802	57.895	14.69	0.00	40.67	4.85
3055	7309	1.138636	CTGAGATGAGCACGTCGCAG	61.139	60.000	19.15	19.15	46.90	5.18
3206	7475	4.034510	CACTGGATAATCAAGTCGAAAGGC	59.965	45.833	0.00	0.00	0.00	4.35
3266	7553	4.453478	ACTGACACTGTGAATGCAGTAATG	59.547	41.667	15.86	0.00	46.81	1.90
3366	7653	6.877322	AGAAAAATCATCAAGGCAAATCCAAG	59.123	34.615	0.00	0.00	37.29	3.61
3411	7702	4.261447	CCGTGTACTCCCCTTTTCAAAAAG	60.261	45.833	8.02	8.02	43.82	2.27
3431	7722	0.541392	TATTGTCATGCAGAGGCCGT	59.459	50.000	0.00	0.00	40.13	5.68
3455	7746	3.974401	ACAAAATGAATTGCACGAGAACG	59.026	39.130	0.00	0.00	38.44	3.95
3496	7787	2.969628	ACCTTCCTGATCACTTAGCG	57.030	50.000	0.00	0.00	0.00	4.26
3514	7805	2.093341	TCACCAACCGCCTTAAGGATAC	60.093	50.000	26.21	6.62	37.39	2.24
3560	7851	1.132262	GCGGATGAAATTTCGCTTGGA	59.868	47.619	13.34	0.00	42.83	3.53
3575	7866	0.693049	AGTCCCAACAGAAAGCGGAT	59.307	50.000	0.00	0.00	0.00	4.18
3599	7890	6.151663	TGGACATTTGCCAGATTGATATTG	57.848	37.500	0.00	0.00	0.00	1.90
3610	7901	1.614903	CAAGCTCTTGGACATTTGCCA	59.385	47.619	1.79	0.00	36.95	4.92
3618	7909	5.009010	TGAAGTTTTGATCAAGCTCTTGGAC	59.991	40.000	19.16	10.48	40.78	4.02
3698	7989	3.154473	CCCGAGAAGCCATCCGGA	61.154	66.667	6.61	6.61	41.58	5.14
3753	8044	2.235650	TCTGGAAGACAAGGAGCAGATG	59.764	50.000	0.00	0.00	38.67	2.90
3853	8144	2.688817	CGGTAGTCTCCAATCCCCACTA	60.689	54.545	0.00	0.00	0.00	2.74
4103	8842	1.629353	CCATAGCTCTCATGATGCCCT	59.371	52.381	14.67	4.47	0.00	5.19
4106	8845	2.855209	ACCCATAGCTCTCATGATGC	57.145	50.000	11.49	11.49	0.00	3.91
4205	8944	1.202758	ACTTGTGCCAGATTCGTTCCA	60.203	47.619	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.