AutoCloner

Multiple sequence alignment - TraesCS6B01G032300

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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	TraesCS6B01G032300	chr6B	100.000	4274	0	0	1	4274	18858888	18854615	0.000000e+00	7893.0
1	TraesCS6B01G032300	chr6B	94.834	542	18	2	167	707	18869034	18869566	0.000000e+00	837.0
2	TraesCS6B01G032300	chr6B	95.814	215	8	1	1	215	719682349	719682136	3.160000e-91	346.0
3	TraesCS6B01G032300	chr6B	95.349	215	9	1	1	215	687846328	687846541	1.470000e-89	340.0
4	TraesCS6B01G032300	chr6B	91.057	246	16	5	1	240	459163412	459163657	1.150000e-85	327.0
5	TraesCS6B01G032300	chr6B	84.127	63	8	1	804	866	210283649	210283589	4.620000e-05	60.2
6	TraesCS6B01G032300	chr6D	94.454	3588	164	15	712	4274	10325228	10321651	0.000000e+00	5491.0
7	TraesCS6B01G032300	chr6D	93.478	46	2	1	793	838	249956977	249956933	2.760000e-07	67.6
8	TraesCS6B01G032300	chr6D	94.595	37	1	1	842	878	344209415	344209380	5.970000e-04	56.5
9	TraesCS6B01G032300	chr6A	94.004	3586	160	21	712	4274	11788401	11784848	0.000000e+00	5380.0
10	TraesCS6B01G032300	chr6A	90.811	370	27	3	170	535	158948303	158947937	4.970000e-134	488.0
11	TraesCS6B01G032300	chr6A	92.562	242	16	1	1	240	159730237	159729996	3.160000e-91	346.0
12	TraesCS6B01G032300	chr5B	89.474	570	26	10	170	708	685295121	685294555	0.000000e+00	689.0
13	TraesCS6B01G032300	chr5B	96.744	215	7	0	1	215	685303511	685303725	4.060000e-95	359.0
14	TraesCS6B01G032300	chr5B	85.714	350	16	9	391	706	685304023	685304372	5.290000e-89	339.0
15	TraesCS6B01G032300	chr5B	97.561	41	1	0	799	839	312761944	312761904	2.130000e-08	71.3
16	TraesCS6B01G032300	chr4B	89.180	573	28	19	167	708	87429017	87429586	0.000000e+00	684.0
17	TraesCS6B01G032300	chr4B	96.744	215	7	0	1	215	87421867	87421653	4.060000e-95	359.0
18	TraesCS6B01G032300	chr4B	95.349	215	9	1	1	215	396854194	396854407	1.470000e-89	340.0
19	TraesCS6B01G032300	chr1A	87.302	567	44	13	167	708	52481332	52481895	1.310000e-174	623.0
20	TraesCS6B01G032300	chr1A	85.639	571	43	22	170	705	434698275	434697709	8.020000e-157	564.0
21	TraesCS6B01G032300	chr7A	86.783	575	36	22	170	709	603506276	603505707	4.730000e-169	604.0
22	TraesCS6B01G032300	chr7A	86.285	576	42	14	167	708	714028080	714028652	3.680000e-165	592.0
23	TraesCS6B01G032300	chr7A	95.349	43	2	0	796	838	590778472	590778430	7.670000e-08	69.4
24	TraesCS6B01G032300	chr2A	89.125	423	38	6	167	584	726336861	726337280	1.760000e-143	520.0
25	TraesCS6B01G032300	chr3A	83.016	577	57	24	167	707	184665919	184665348	6.430000e-133	484.0
26	TraesCS6B01G032300	chr3A	92.975	242	15	1	1	240	184677538	184677779	6.800000e-93	351.0
27	TraesCS6B01G032300	chr3D	95.349	215	10	0	1	215	496176271	496176057	4.090000e-90	342.0
28	TraesCS6B01G032300	chr3D	84.532	278	33	6	1	270	83489820	83490095	2.530000e-67	267.0
29	TraesCS6B01G032300	chr3D	84.173	278	34	6	1	270	285003566	285003841	1.180000e-65	261.0
30	TraesCS6B01G032300	chr7B	85.143	350	18	10	391	706	147529890	147529541	1.150000e-85	327.0
31	TraesCS6B01G032300	chr7B	84.900	351	19	15	391	707	147530659	147531009	1.480000e-84	324.0
32	TraesCS6B01G032300	chr7B	97.561	41	1	0	799	839	65752897	65752937	2.130000e-08	71.3
33	TraesCS6B01G032300	chr7B	97.561	41	1	0	798	838	648760061	648760021	2.130000e-08	71.3
34	TraesCS6B01G032300	chrUn	85.971	278	29	6	1	270	22363968	22364243	5.410000e-74	289.0
35	TraesCS6B01G032300	chrUn	94.156	154	7	2	555	707	351356015	351356167	2.570000e-57	233.0
36	TraesCS6B01G032300	chr7D	85.252	278	31	6	1	270	109165996	109166271	1.170000e-70	278.0
37	TraesCS6B01G032300	chr2B	94.872	156	7	1	555	709	111677592	111677437	4.270000e-60	243.0
38	TraesCS6B01G032300	chr2D	97.561	41	1	0	799	839	72212557	72212517	2.130000e-08	71.3
39	TraesCS6B01G032300	chr2D	81.818	77	9	4	798	872	514950048	514950121	4.620000e-05	60.2
40	TraesCS6B01G032300	chr5D	93.478	46	2	1	802	846	350684044	350683999	2.760000e-07	67.6

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	TraesCS6B01G032300	chr6B	18854615	18858888	4273	True	7893	7893	100.000	1	4274	1	chr6B.!!$R1	4273
1	TraesCS6B01G032300	chr6B	18869034	18869566	532	False	837	837	94.834	167	707	1	chr6B.!!$F1	540
2	TraesCS6B01G032300	chr6D	10321651	10325228	3577	True	5491	5491	94.454	712	4274	1	chr6D.!!$R1	3562
3	TraesCS6B01G032300	chr6A	11784848	11788401	3553	True	5380	5380	94.004	712	4274	1	chr6A.!!$R1	3562
4	TraesCS6B01G032300	chr5B	685294555	685295121	566	True	689	689	89.474	170	708	1	chr5B.!!$R2	538
5	TraesCS6B01G032300	chr5B	685303511	685304372	861	False	349	359	91.229	1	706	2	chr5B.!!$F1	705
6	TraesCS6B01G032300	chr4B	87429017	87429586	569	False	684	684	89.180	167	708	1	chr4B.!!$F1	541
7	TraesCS6B01G032300	chr1A	52481332	52481895	563	False	623	623	87.302	167	708	1	chr1A.!!$F1	541
8	TraesCS6B01G032300	chr1A	434697709	434698275	566	True	564	564	85.639	170	705	1	chr1A.!!$R1	535
9	TraesCS6B01G032300	chr7A	603505707	603506276	569	True	604	604	86.783	170	709	1	chr7A.!!$R2	539
10	TraesCS6B01G032300	chr7A	714028080	714028652	572	False	592	592	86.285	167	708	1	chr7A.!!$F1	541
11	TraesCS6B01G032300	chr3A	184665348	184665919	571	True	484	484	83.016	167	707	1	chr3A.!!$R1	540

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	Hairpin	End Stability	Orientation
915	1098	0.109132	CAAACGAGAAATGGGCCTGC	60.109	55.0	4.53	0.00	4.85	F
934	1117	0.180406	CGTGCTAGGCCCATAACCTT	59.820	55.0	0.00	38.81	3.50	F
2373	2559	0.116342	TCTCCTGGACTGCCCTTGTA	59.884	55.0	0.00	35.38	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2301	2487	0.248539	GGTGTGCGTCCTCGATACTC	60.249	60.0	0.00	0.00	39.71	2.59	R
2916	3102	0.039764	AGGGGTGAGACTGATCGTCA	59.960	55.0	16.37	2.54	45.32	4.35	R
3283	3469	0.030101	GCGGTGTGCAGCTTTAACAA	59.970	50.0	0.00	0.00	45.45	2.83	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
68	69	0.464036	TCACGAGTGAAAGTGCCTGT	59.536	50.000	3.11	0.00	38.19	4.00
109	110	5.128827	TCTGTTCTTACACACTCAGAAGGTT	59.871	40.000	0.00	0.00	0.00	3.50
146	147	2.590291	TTGCGCACGGAGCAGAAA	60.590	55.556	11.12	0.00	46.01	2.52
353	477	4.838152	GCCTCGGAATCAGCGCCA	62.838	66.667	2.29	0.00	0.00	5.69
440	586	3.790437	CTGGGCCCGCATCAGACT	61.790	66.667	19.37	0.00	0.00	3.24
733	909	3.160545	CGATCGTTCAAATTTTGGACCG	58.839	45.455	13.71	8.62	35.68	4.79
813	992	6.896883	AGGTGTACAATTTATTACTCCCTCC	58.103	40.000	0.00	0.00	33.93	4.30
829	1010	5.019657	TCCCTCCGTCCCATAATATAAGT	57.980	43.478	0.00	0.00	0.00	2.24
833	1014	3.575256	TCCGTCCCATAATATAAGTGCGT	59.425	43.478	0.00	0.00	0.00	5.24
834	1015	4.039488	TCCGTCCCATAATATAAGTGCGTT	59.961	41.667	0.00	0.00	0.00	4.84
868	1049	4.524802	TTTGGTACGGAGGGAGTAGATA	57.475	45.455	0.00	0.00	0.00	1.98
870	1051	5.848286	TTGGTACGGAGGGAGTAGATATA	57.152	43.478	0.00	0.00	0.00	0.86
872	1053	7.515004	TTGGTACGGAGGGAGTAGATATATA	57.485	40.000	0.00	0.00	0.00	0.86
915	1098	0.109132	CAAACGAGAAATGGGCCTGC	60.109	55.000	4.53	0.00	0.00	4.85
932	1115	1.892391	GCGTGCTAGGCCCATAACC	60.892	63.158	0.00	0.00	0.00	2.85
933	1116	1.830145	CGTGCTAGGCCCATAACCT	59.170	57.895	0.00	0.00	41.57	3.50
934	1117	0.180406	CGTGCTAGGCCCATAACCTT	59.820	55.000	0.00	0.00	38.81	3.50
936	1119	1.211949	GTGCTAGGCCCATAACCTTCA	59.788	52.381	0.00	0.00	38.81	3.02
959	1142	0.468226	TATGGATCGCGAAGGGCTTT	59.532	50.000	15.24	0.00	41.64	3.51
961	1144	2.472909	GGATCGCGAAGGGCTTTGG	61.473	63.158	15.24	0.00	41.64	3.28
963	1146	2.869503	GATCGCGAAGGGCTTTGGGA	62.870	60.000	15.24	0.00	45.83	4.37
964	1147	3.431725	CGCGAAGGGCTTTGGGAC	61.432	66.667	0.00	0.00	38.70	4.46
1539	1725	2.267006	CACTGCCAGATCCTGCGT	59.733	61.111	0.00	0.00	0.00	5.24
1662	1848	2.423538	GGGCAAGAATGTGGTGATGTAC	59.576	50.000	0.00	0.00	0.00	2.90
1683	1869	0.397941	ATACCATGATCACGGGGCTG	59.602	55.000	13.28	0.00	0.00	4.85
1989	2175	1.201812	GCGCTTGTTGACATGTACTCG	60.202	52.381	0.00	1.78	0.00	4.18
1994	2180	4.921515	GCTTGTTGACATGTACTCGAAGTA	59.078	41.667	0.00	0.00	0.00	2.24
2007	2193	1.751351	TCGAAGTACAGGAGCATCAGG	59.249	52.381	0.00	0.00	36.25	3.86
2088	2274	4.009675	TGATTGTTGGCTATGGACAGAAC	58.990	43.478	0.00	0.00	0.00	3.01
2095	2281	0.249120	CTATGGACAGAACGGGTGCA	59.751	55.000	0.00	0.00	40.90	4.57
2119	2305	1.003233	GAGGCTGTGAGGGTGTTCC	60.003	63.158	0.00	0.00	0.00	3.62
2160	2346	4.279420	GGGATTAAGCCTGATGATTTCACC	59.721	45.833	10.09	0.00	0.00	4.02
2277	2463	6.970613	CGTACATTACAGTGTCTAATGCACTA	59.029	38.462	15.63	2.50	44.43	2.74
2292	2478	2.892852	TGCACTAGTTACCTTGTACGGT	59.107	45.455	0.00	0.00	41.10	4.83
2298	2484	3.917988	AGTTACCTTGTACGGTAAGTGC	58.082	45.455	15.38	5.45	46.95	4.40
2301	2487	0.738412	CCTTGTACGGTAAGTGCGGG	60.738	60.000	0.00	0.00	38.36	6.13
2346	2532	3.189080	TGTTTGATGAGATGCCGTTTCAG	59.811	43.478	0.00	0.00	0.00	3.02
2352	2538	2.208431	GAGATGCCGTTTCAGGATCAG	58.792	52.381	0.00	0.00	0.00	2.90
2373	2559	0.116342	TCTCCTGGACTGCCCTTGTA	59.884	55.000	0.00	0.00	35.38	2.41
2374	2560	0.984230	CTCCTGGACTGCCCTTGTAA	59.016	55.000	0.00	0.00	35.38	2.41
2397	2583	1.135402	GGTTATGCGCAGTTTGGGAAG	60.135	52.381	18.32	0.00	31.21	3.46
2409	2595	3.118408	AGTTTGGGAAGGCAAAAGAAACC	60.118	43.478	0.00	0.00	0.00	3.27
2412	2598	3.850752	TGGGAAGGCAAAAGAAACCATA	58.149	40.909	0.00	0.00	0.00	2.74
2433	2619	8.517878	ACCATAGATTTGTTTGAGAAGATGTTG	58.482	33.333	0.00	0.00	0.00	3.33
2435	2621	9.552114	CATAGATTTGTTTGAGAAGATGTTGTC	57.448	33.333	0.00	0.00	0.00	3.18
2436	2622	7.814264	AGATTTGTTTGAGAAGATGTTGTCT	57.186	32.000	1.35	0.00	39.43	3.41
2463	2649	1.447314	GAAGCCTGACGGGGTAACG	60.447	63.158	5.20	0.00	46.33	3.18
2526	2712	0.391793	AGAAAGGCCGCAGCTACTTC	60.392	55.000	0.00	0.00	39.73	3.01
2529	2715	2.512515	GGCCGCAGCTACTTCCAG	60.513	66.667	0.00	0.00	39.73	3.86
2531	2717	1.376037	GCCGCAGCTACTTCCAGTT	60.376	57.895	0.00	0.00	35.50	3.16
2539	2725	2.012673	GCTACTTCCAGTTCATGCAGG	58.987	52.381	0.00	0.00	0.00	4.85
2542	2728	1.980765	ACTTCCAGTTCATGCAGGAGA	59.019	47.619	0.00	0.00	0.00	3.71
2565	2751	2.669781	CATGGTATTGTGCCCTTGGAT	58.330	47.619	0.00	0.00	0.00	3.41
2592	2778	9.416794	GATCACTATACTTGTATGATTGACCTG	57.583	37.037	3.75	0.00	30.23	4.00
2607	2793	4.184649	TGACCTGTATAGCAGATCAGGA	57.815	45.455	19.54	1.73	42.63	3.86
2754	2940	5.163205	TGAGAATCTCTTGAAAACTGACCCA	60.163	40.000	11.92	0.00	34.92	4.51
2814	3000	5.431765	CATGCTACTAAAGGTGAATGGAGT	58.568	41.667	0.00	0.00	0.00	3.85
2892	3078	3.497640	GCTGCAGCTGGATCAAGTATAAG	59.502	47.826	31.33	0.00	38.21	1.73
2955	3141	4.576463	CCCTTCTCCGGAACAATTTATGAG	59.424	45.833	5.23	0.00	0.00	2.90
3015	3201	2.936919	ACAAGCCTGATGTCAGTTCA	57.063	45.000	9.03	0.00	42.27	3.18
3144	3330	0.804989	GGGTTGTCAAGAATCTGCGG	59.195	55.000	0.00	0.00	0.00	5.69
3147	3333	1.197721	GTTGTCAAGAATCTGCGGGTG	59.802	52.381	0.00	0.00	0.00	4.61
3207	3393	5.373981	AGATAACCGGTCGTGATATTCTC	57.626	43.478	8.04	0.00	0.00	2.87
3208	3394	4.825634	AGATAACCGGTCGTGATATTCTCA	59.174	41.667	8.04	0.00	0.00	3.27
3283	3469	4.506802	GGGACTTCTGGTAATTCCACTGTT	60.507	45.833	0.00	0.00	41.93	3.16
3288	3474	7.057894	ACTTCTGGTAATTCCACTGTTTGTTA	58.942	34.615	0.00	0.00	41.93	2.41
3289	3475	7.558444	ACTTCTGGTAATTCCACTGTTTGTTAA	59.442	33.333	0.00	0.00	41.93	2.01
3290	3476	7.883391	TCTGGTAATTCCACTGTTTGTTAAA	57.117	32.000	0.00	0.00	41.93	1.52
3291	3477	7.936584	TCTGGTAATTCCACTGTTTGTTAAAG	58.063	34.615	0.00	0.00	41.93	1.85
3293	3479	6.322712	TGGTAATTCCACTGTTTGTTAAAGCT	59.677	34.615	0.00	0.00	41.93	3.74
3294	3480	6.640907	GGTAATTCCACTGTTTGTTAAAGCTG	59.359	38.462	0.00	0.00	35.97	4.24
3296	3482	3.020274	TCCACTGTTTGTTAAAGCTGCA	58.980	40.909	1.02	0.00	0.00	4.41
3297	3483	3.115554	CCACTGTTTGTTAAAGCTGCAC	58.884	45.455	1.02	0.00	0.00	4.57
3298	3484	3.428725	CCACTGTTTGTTAAAGCTGCACA	60.429	43.478	1.02	0.00	0.00	4.57
3299	3485	3.547468	CACTGTTTGTTAAAGCTGCACAC	59.453	43.478	1.02	0.00	0.00	3.82
3300	3486	3.115554	CTGTTTGTTAAAGCTGCACACC	58.884	45.455	1.02	0.00	0.00	4.16
3349	3535	5.703130	GTCAGAAGTGCTACTGGAAGAAAAT	59.297	40.000	0.00	0.00	37.43	1.82
3363	3549	5.776716	TGGAAGAAAATGAGGAAAGCTGAAT	59.223	36.000	0.00	0.00	0.00	2.57
3369	3555	2.440409	TGAGGAAAGCTGAATGAAGCC	58.560	47.619	0.00	0.00	44.68	4.35
3431	3617	5.050363	GTGTGACACAGTACGAACAAATCAT	60.050	40.000	11.43	0.00	34.08	2.45
3485	3671	7.882791	AGGTGTGTTTATGTCATCATGAAACTA	59.117	33.333	0.00	0.00	32.73	2.24
3618	3804	6.543831	GGTATAAGGATTGTGCATGACTTCTT	59.456	38.462	0.00	0.00	0.00	2.52
3619	3805	6.690194	ATAAGGATTGTGCATGACTTCTTC	57.310	37.500	0.00	0.00	0.00	2.87
3620	3806	4.298103	AGGATTGTGCATGACTTCTTCT	57.702	40.909	0.00	0.00	0.00	2.85
3624	3810	6.989169	AGGATTGTGCATGACTTCTTCTATAC	59.011	38.462	0.00	0.00	0.00	1.47
3633	3819	7.389053	GCATGACTTCTTCTATACCCTTATTGG	59.611	40.741	0.00	0.00	0.00	3.16
3641	3827	6.824958	TCTATACCCTTATTGGCTCTTGTT	57.175	37.500	0.00	0.00	0.00	2.83
3661	3847	5.318630	TGTTTACCAAAGTGGAAGGGTATC	58.681	41.667	0.18	0.00	40.96	2.24
3665	3851	2.042433	CCAAAGTGGAAGGGTATCCCAA	59.958	50.000	7.60	0.00	43.26	4.12
3683	3869	4.646945	TCCCAAGTTTTGTAATTCTGTGCA	59.353	37.500	0.00	0.00	0.00	4.57
3738	3924	2.224548	ACCACCACTCTTCTGCCTTAAC	60.225	50.000	0.00	0.00	0.00	2.01
3748	3934	4.345257	TCTTCTGCCTTAACAGTCTGAGTT	59.655	41.667	6.91	0.00	38.84	3.01
3827	4013	2.645838	TGCCAGATAAAGCTCCATCC	57.354	50.000	4.34	0.00	0.00	3.51
3829	4015	1.546548	GCCAGATAAAGCTCCATCCCC	60.547	57.143	4.34	0.00	0.00	4.81
3830	4016	1.271054	CCAGATAAAGCTCCATCCCCG	60.271	57.143	4.34	0.00	0.00	5.73
3876	4062	4.201960	ACGTAATGTTTGATGTTGCACACA	60.202	37.500	4.56	4.56	40.71	3.72
4005	4191	1.270550	AGCAAAGGGAACAAAGCGATG	59.729	47.619	0.00	0.00	0.00	3.84
4189	4389	9.046296	GTGAGTCATGTAAAGGGTATATTTCTG	57.954	37.037	0.00	0.00	0.00	3.02
4190	4390	8.768397	TGAGTCATGTAAAGGGTATATTTCTGT	58.232	33.333	0.00	0.00	0.00	3.41
4195	4395	8.830580	CATGTAAAGGGTATATTTCTGTCAGTG	58.169	37.037	0.00	0.00	0.00	3.66
4204	4404	0.535780	TTCTGTCAGTGCTGCTTGGG	60.536	55.000	0.00	0.00	0.00	4.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	8.567285	AAGAACAGAGAGAAAGAAAAACTCAA	57.433	30.769	0.00	0.00	33.69	3.02
109	110	0.321919	GCACACTGGCATCCTCTTCA	60.322	55.000	0.00	0.00	0.00	3.02
422	559	4.864334	GTCTGATGCGGGCCCAGG	62.864	72.222	24.92	7.60	0.00	4.45
708	884	2.661195	CCAAAATTTGAACGATCGGCAC	59.339	45.455	20.98	10.48	0.00	5.01
709	885	2.554462	TCCAAAATTTGAACGATCGGCA	59.446	40.909	20.98	14.21	0.00	5.69
710	886	2.914838	GTCCAAAATTTGAACGATCGGC	59.085	45.455	20.98	11.58	0.00	5.54
717	893	4.561735	TGAGACGGTCCAAAATTTGAAC	57.438	40.909	7.37	0.00	0.00	3.18
783	962	6.174760	AGTAATAAATTGTACACCTTCCGCA	58.825	36.000	0.00	0.00	0.00	5.69
794	973	5.070847	GGGACGGAGGGAGTAATAAATTGTA	59.929	44.000	0.00	0.00	0.00	2.41
813	992	5.917541	AAACGCACTTATATTATGGGACG	57.082	39.130	0.00	0.00	0.00	4.79
838	1019	6.070078	ACTCCCTCCGTACCAAAATATAACAA	60.070	38.462	0.00	0.00	0.00	2.83
840	1021	5.922053	ACTCCCTCCGTACCAAAATATAAC	58.078	41.667	0.00	0.00	0.00	1.89
852	1033	7.404104	TCCAGTTATATATCTACTCCCTCCGTA	59.596	40.741	0.00	0.00	0.00	4.02
855	1036	7.064229	CCTCCAGTTATATATCTACTCCCTCC	58.936	46.154	0.00	0.00	0.00	4.30
899	1082	2.436646	CGCAGGCCCATTTCTCGT	60.437	61.111	0.00	0.00	0.00	4.18
915	1098	0.180406	AAGGTTATGGGCCTAGCACG	59.820	55.000	4.53	0.00	32.76	5.34
959	1142	2.747686	GAAACCGGCTCAGTCCCA	59.252	61.111	0.00	0.00	0.00	4.37
961	1144	2.046217	GGGAAACCGGCTCAGTCC	60.046	66.667	0.00	0.53	43.64	3.85
1287	1473	1.880340	GAAGAGCCGCTCCATGTCG	60.880	63.158	16.99	0.00	0.00	4.35
1539	1725	4.064768	TAGGCCCCGAACCCGAGA	62.065	66.667	0.00	0.00	38.22	4.04
1575	1761	6.209986	CCATCTTGGCATACATATCAACCAAT	59.790	38.462	0.00	0.00	36.63	3.16
1602	1788	3.740128	CTTGGCGTCCCCGATGAGG	62.740	68.421	0.00	0.00	40.63	3.86
1662	1848	1.202806	AGCCCCGTGATCATGGTATTG	60.203	52.381	28.32	15.22	35.70	1.90
1683	1869	1.675641	AACCATCTTGCACCGGAGC	60.676	57.895	17.78	17.78	0.00	4.70
1989	2175	3.265791	CAACCTGATGCTCCTGTACTTC	58.734	50.000	0.00	0.00	0.00	3.01
1994	2180	1.001641	GCCAACCTGATGCTCCTGT	60.002	57.895	0.00	0.00	0.00	4.00
2095	2281	3.073735	CCTCACAGCCTCCTCGCT	61.074	66.667	0.00	0.00	40.65	4.93
2119	2305	0.397187	CCATCCCTCTGCATCTCCAG	59.603	60.000	0.00	0.00	0.00	3.86
2120	2306	1.058428	CCCATCCCTCTGCATCTCCA	61.058	60.000	0.00	0.00	0.00	3.86
2160	2346	5.473504	ACAAGAACTTATAACACTGCCAAGG	59.526	40.000	0.00	0.00	0.00	3.61
2226	2412	2.110967	CCCTGAGACAAGCGCCATG	61.111	63.158	2.29	6.50	0.00	3.66
2292	2478	1.134007	TCCTCGATACTCCCGCACTTA	60.134	52.381	0.00	0.00	0.00	2.24
2298	2484	2.184830	TGCGTCCTCGATACTCCCG	61.185	63.158	0.00	0.00	39.71	5.14
2301	2487	0.248539	GGTGTGCGTCCTCGATACTC	60.249	60.000	0.00	0.00	39.71	2.59
2373	2559	1.269448	CCAAACTGCGCATAACCTGTT	59.731	47.619	12.24	7.71	0.00	3.16
2374	2560	0.881118	CCAAACTGCGCATAACCTGT	59.119	50.000	12.24	0.00	0.00	4.00
2397	2583	7.440856	TCAAACAAATCTATGGTTTCTTTTGCC	59.559	33.333	0.00	0.00	32.79	4.52
2409	2595	9.552114	GACAACATCTTCTCAAACAAATCTATG	57.448	33.333	0.00	0.00	0.00	2.23
2412	2598	7.814264	AGACAACATCTTCTCAAACAAATCT	57.186	32.000	0.00	0.00	31.62	2.40
2433	2619	1.623811	TCAGGCTTCACACCCTTAGAC	59.376	52.381	0.00	0.00	0.00	2.59
2435	2621	1.673033	CGTCAGGCTTCACACCCTTAG	60.673	57.143	0.00	0.00	0.00	2.18
2436	2622	0.320374	CGTCAGGCTTCACACCCTTA	59.680	55.000	0.00	0.00	0.00	2.69
2463	2649	3.335579	AGCAGAAAGGACACCGATAAAC	58.664	45.455	0.00	0.00	0.00	2.01
2469	2655	2.069273	CTACAAGCAGAAAGGACACCG	58.931	52.381	0.00	0.00	0.00	4.94
2526	2712	1.271543	TGGTTCTCCTGCATGAACTGG	60.272	52.381	19.56	4.60	41.42	4.00
2529	2715	1.747355	CCATGGTTCTCCTGCATGAAC	59.253	52.381	2.57	14.90	41.08	3.18
2531	2717	0.994247	ACCATGGTTCTCCTGCATGA	59.006	50.000	13.00	0.00	34.23	3.07
2539	2725	2.024414	GGGCACAATACCATGGTTCTC	58.976	52.381	25.38	6.70	0.00	2.87
2542	2728	2.178580	CAAGGGCACAATACCATGGTT	58.821	47.619	25.38	8.28	0.00	3.67
2565	2751	9.147732	AGGTCAATCATACAAGTATAGTGATCA	57.852	33.333	0.00	0.00	0.00	2.92
2592	2778	8.204836	TCTTTTAACCTTCCTGATCTGCTATAC	58.795	37.037	0.00	0.00	0.00	1.47
2607	2793	5.311844	ACTCCTCAGCTTCTTTTAACCTT	57.688	39.130	0.00	0.00	0.00	3.50
2691	2877	0.321210	CCATGTCACCACGCAACCTA	60.321	55.000	0.00	0.00	0.00	3.08
2692	2878	1.600636	CCATGTCACCACGCAACCT	60.601	57.895	0.00	0.00	0.00	3.50
2754	2940	1.271379	ACATAGCTCGCTGGGTTTTGT	60.271	47.619	0.85	0.00	0.00	2.83
2797	2983	3.910627	ACCTCACTCCATTCACCTTTAGT	59.089	43.478	0.00	0.00	0.00	2.24
2916	3102	0.039764	AGGGGTGAGACTGATCGTCA	59.960	55.000	16.37	2.54	45.32	4.35
2955	3141	0.036022	AGTTGAGCCACTGGAGCTTC	59.964	55.000	0.00	0.00	41.75	3.86
3015	3201	1.303806	TGCCACATCATGCAGCACT	60.304	52.632	0.00	0.00	32.77	4.40
3039	3225	1.998315	CTGAGCATGTGAACCTTCTCG	59.002	52.381	0.00	0.00	0.00	4.04
3144	3330	4.172625	TGGCAATCCACACACACC	57.827	55.556	0.00	0.00	37.47	4.16
3207	3393	5.006844	GTGAAATCTGACAGCATCTCTCATG	59.993	44.000	0.00	0.00	0.00	3.07
3208	3394	5.117584	GTGAAATCTGACAGCATCTCTCAT	58.882	41.667	0.00	0.00	0.00	2.90
3213	3399	4.649692	ACTTGTGAAATCTGACAGCATCT	58.350	39.130	0.00	0.00	0.00	2.90
3255	3441	3.610911	GAATTACCAGAAGTCCCCACAG	58.389	50.000	0.00	0.00	0.00	3.66
3283	3469	0.030101	GCGGTGTGCAGCTTTAACAA	59.970	50.000	0.00	0.00	45.45	2.83
3349	3535	2.224843	TGGCTTCATTCAGCTTTCCTCA	60.225	45.455	0.00	0.00	39.97	3.86
3363	3549	6.716628	GGAACTATTATCCATGATTGGCTTCA	59.283	38.462	0.00	0.00	43.29	3.02
3369	3555	5.416952	GGCCAGGAACTATTATCCATGATTG	59.583	44.000	0.00	0.00	39.55	2.67
3448	3634	7.039011	TGACATAAACACACCTCTTATCAGTCT	60.039	37.037	0.00	0.00	0.00	3.24
3453	3639	8.554528	CATGATGACATAAACACACCTCTTATC	58.445	37.037	0.00	0.00	35.09	1.75
3624	3810	4.340617	TGGTAAACAAGAGCCAATAAGGG	58.659	43.478	0.00	0.00	38.09	3.95
3633	3819	4.261614	CCTTCCACTTTGGTAAACAAGAGC	60.262	45.833	0.00	0.00	40.82	4.09
3641	3827	4.579647	GGATACCCTTCCACTTTGGTAA	57.420	45.455	0.00	0.00	39.03	2.85
3661	3847	4.744631	GTGCACAGAATTACAAAACTTGGG	59.255	41.667	13.17	0.00	34.12	4.12
3665	3851	9.893305	GTAATTAGTGCACAGAATTACAAAACT	57.107	29.630	34.62	17.13	42.04	2.66
3673	3859	7.754924	CGAATTTGGTAATTAGTGCACAGAATT	59.245	33.333	24.50	24.50	34.16	2.17
3683	3869	6.151985	TCAATGTGCCGAATTTGGTAATTAGT	59.848	34.615	13.49	0.00	34.16	2.24
3788	3974	4.177783	GCAAGAGGTTAAGCTCAGACTAC	58.822	47.826	30.59	13.60	0.00	2.73
3876	4062	6.952773	TTTTGCAGTTAGTAACCACTTGAT	57.047	33.333	9.46	0.00	36.14	2.57
3926	4112	4.018050	ACAAACTTGAGGCCCATCTCTAAT	60.018	41.667	0.00	0.00	34.98	1.73
3929	4115	1.707427	ACAAACTTGAGGCCCATCTCT	59.293	47.619	0.00	0.00	34.98	3.10
4005	4191	3.441572	CCAAACTCAGTGGATGGTGATTC	59.558	47.826	0.00	0.00	38.54	2.52
4189	4389	2.595463	TGCCCAAGCAGCACTGAC	60.595	61.111	0.81	0.00	46.52	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.