AutoCloner

Multiple sequence alignment - TraesCS6A01G017400

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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	TraesCS6A01G017400	chr6A	100.000	2774	0	0	1	2774	8625506	8622733	0.000000e+00	5123
1	TraesCS6A01G017400	chr6A	87.598	2032	163	30	686	2678	8711950	8713931	0.000000e+00	2274
2	TraesCS6A01G017400	chr6A	90.343	466	31	7	1	456	8710844	8711305	1.420000e-167	599
3	TraesCS6A01G017400	chr6D	89.499	1876	134	21	935	2774	8147261	8145413	0.000000e+00	2314
4	TraesCS6A01G017400	chr6D	88.758	1788	147	29	985	2739	8249774	8251540	0.000000e+00	2139
5	TraesCS6A01G017400	chr6D	78.991	1209	217	31	985	2177	7484803	7483616	0.000000e+00	791
6	TraesCS6A01G017400	chr6D	78.798	1165	212	28	1043	2188	7651582	7652730	0.000000e+00	750
7	TraesCS6A01G017400	chr6D	87.946	224	19	5	462	679	8244990	8245211	9.860000e-65	257
8	TraesCS6A01G017400	chr6D	84.343	198	28	3	2574	2769	8817590	8817786	1.010000e-44	191
9	TraesCS6A01G017400	chr6D	81.651	218	33	5	2559	2773	8971021	8971234	1.020000e-39	174
10	TraesCS6A01G017400	chr6B	88.150	1519	115	28	852	2352	15115829	15114358	0.000000e+00	1748
11	TraesCS6A01G017400	chr6B	91.552	1231	96	8	962	2188	21458671	21459897	0.000000e+00	1690
12	TraesCS6A01G017400	chr6B	77.859	1224	238	25	984	2188	14311106	14312315	0.000000e+00	728
13	TraesCS6A01G017400	chr6B	79.516	991	182	17	1526	2508	65158559	65157582	0.000000e+00	686
14	TraesCS6A01G017400	chr6B	91.170	453	27	8	13	456	15117117	15116669	1.100000e-168	603
15	TraesCS6A01G017400	chr6B	90.052	382	26	5	83	456	21457322	21457699	4.150000e-133	484
16	TraesCS6A01G017400	chr6B	85.610	410	34	10	2387	2774	15114362	15113956	9.250000e-110	407
17	TraesCS6A01G017400	chr6B	85.776	232	21	8	462	682	15116136	15115906	4.620000e-58	235
18	TraesCS6A01G017400	chr6B	86.026	229	20	8	462	679	21458231	21458458	4.620000e-58	235
19	TraesCS6A01G017400	chr6B	83.784	185	17	9	2553	2728	53061096	53060916	2.210000e-36	163
20	TraesCS6A01G017400	chr2B	77.947	1510	277	42	984	2463	89494604	89496087	0.000000e+00	893
21	TraesCS6A01G017400	chr3B	76.936	1201	239	31	983	2170	761047753	761046578	0.000000e+00	649
22	TraesCS6A01G017400	chr5B	78.261	989	191	19	1526	2499	621235474	621234495	5.080000e-172	614
23	TraesCS6A01G017400	chr5D	77.888	1004	186	27	1526	2508	499862079	499861091	2.380000e-165	592
24	TraesCS6A01G017400	chr5A	80.721	555	88	11	1969	2508	624202300	624201750	5.530000e-112	414
25	TraesCS6A01G017400	chr7B	77.945	730	109	28	1824	2508	32346791	32346069	2.570000e-110	409

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	TraesCS6A01G017400	chr6A	8622733	8625506	2773	True	5123.00	5123	100.0000	1	2774	1	chr6A.!!$R1	2773
1	TraesCS6A01G017400	chr6A	8710844	8713931	3087	False	1436.50	2274	88.9705	1	2678	2	chr6A.!!$F1	2677
2	TraesCS6A01G017400	chr6D	8145413	8147261	1848	True	2314.00	2314	89.4990	935	2774	1	chr6D.!!$R2	1839
3	TraesCS6A01G017400	chr6D	8249774	8251540	1766	False	2139.00	2139	88.7580	985	2739	1	chr6D.!!$F3	1754
4	TraesCS6A01G017400	chr6D	7483616	7484803	1187	True	791.00	791	78.9910	985	2177	1	chr6D.!!$R1	1192
5	TraesCS6A01G017400	chr6D	7651582	7652730	1148	False	750.00	750	78.7980	1043	2188	1	chr6D.!!$F1	1145
6	TraesCS6A01G017400	chr6B	21457322	21459897	2575	False	803.00	1690	89.2100	83	2188	3	chr6B.!!$F2	2105
7	TraesCS6A01G017400	chr6B	15113956	15117117	3161	True	748.25	1748	87.6765	13	2774	4	chr6B.!!$R3	2761
8	TraesCS6A01G017400	chr6B	14311106	14312315	1209	False	728.00	728	77.8590	984	2188	1	chr6B.!!$F1	1204
9	TraesCS6A01G017400	chr6B	65157582	65158559	977	True	686.00	686	79.5160	1526	2508	1	chr6B.!!$R2	982
10	TraesCS6A01G017400	chr2B	89494604	89496087	1483	False	893.00	893	77.9470	984	2463	1	chr2B.!!$F1	1479
11	TraesCS6A01G017400	chr3B	761046578	761047753	1175	True	649.00	649	76.9360	983	2170	1	chr3B.!!$R1	1187
12	TraesCS6A01G017400	chr5B	621234495	621235474	979	True	614.00	614	78.2610	1526	2499	1	chr5B.!!$R1	973
13	TraesCS6A01G017400	chr5D	499861091	499862079	988	True	592.00	592	77.8880	1526	2508	1	chr5D.!!$R1	982
14	TraesCS6A01G017400	chr5A	624201750	624202300	550	True	414.00	414	80.7210	1969	2508	1	chr5A.!!$R1	539
15	TraesCS6A01G017400	chr7B	32346069	32346791	722	True	409.00	409	77.9450	1824	2508	1	chr7B.!!$R1	684

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
560	1108	0.169009	AAGAGCGGCGCTTCAAAATC	59.831	50.0	36.73	20.96	39.88	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2491	3190	0.67895	CGGCCAAAACTGTTTCCCAT	59.321	50.0	6.2	0.0	0.0	4.0	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
30	31	8.682710	CGAATCCCTTCCAATTTTCATAAACTA	58.317	33.333	0.00	0.00	0.00	2.24
59	60	9.880157	TTACCTTGTATTTACTCATACTGTTCC	57.120	33.333	0.00	0.00	31.73	3.62
64	65	7.207383	TGTATTTACTCATACTGTTCCGATGG	58.793	38.462	0.00	0.00	31.73	3.51
75	76	4.062293	CTGTTCCGATGGTCAGTAAACAA	58.938	43.478	0.00	0.00	0.00	2.83
89	90	9.801873	GGTCAGTAAACAATATGCACAAATATT	57.198	29.630	0.00	0.00	33.85	1.28
247	248	4.080863	AGGAATTAGTTGAGGTGCCTACTG	60.081	45.833	4.39	0.00	0.00	2.74
279	280	5.304614	TCAACAGTTGGTAGTTCTAGAAGCT	59.695	40.000	13.52	8.85	0.00	3.74
302	303	7.014230	AGCTAGTAAACCTTGATTGCTTTTGAA	59.986	33.333	0.00	0.00	0.00	2.69
304	305	9.696917	CTAGTAAACCTTGATTGCTTTTGAAAT	57.303	29.630	0.00	0.00	0.00	2.17
367	369	9.919348	GCCAAATTATAGTGCATACAAAATTTG	57.081	29.630	19.55	19.55	39.27	2.32
482	1025	3.279434	ACAATACTCTTCCGCCAAATCC	58.721	45.455	0.00	0.00	0.00	3.01
484	1027	2.691409	TACTCTTCCGCCAAATCCAG	57.309	50.000	0.00	0.00	0.00	3.86
486	1029	1.073923	ACTCTTCCGCCAAATCCAGTT	59.926	47.619	0.00	0.00	0.00	3.16
490	1033	1.459450	TCCGCCAAATCCAGTTAAGC	58.541	50.000	0.00	0.00	0.00	3.09
507	1050	6.422400	CAGTTAAGCTAAATTTGCCCGAAAAA	59.578	34.615	0.00	0.00	0.00	1.94
508	1051	7.117667	CAGTTAAGCTAAATTTGCCCGAAAAAT	59.882	33.333	0.00	0.00	0.00	1.82
509	1052	5.861222	AAGCTAAATTTGCCCGAAAAATG	57.139	34.783	0.00	0.00	0.00	2.32
560	1108	0.169009	AAGAGCGGCGCTTCAAAATC	59.831	50.000	36.73	20.96	39.88	2.17
561	1109	0.955428	AGAGCGGCGCTTCAAAATCA	60.955	50.000	36.73	0.00	39.88	2.57
585	1133	0.746563	ACATGGAAATGTACGCCGGG	60.747	55.000	2.18	0.00	32.14	5.73
600	1148	1.804748	GCCGGGCACATAATAGTAAGC	59.195	52.381	15.62	0.00	0.00	3.09
640	1188	4.566545	TTTGTGATCATTTTGCGTGACT	57.433	36.364	0.00	0.00	0.00	3.41
641	1189	3.811722	TGTGATCATTTTGCGTGACTC	57.188	42.857	0.00	0.00	0.00	3.36
643	1191	1.731709	TGATCATTTTGCGTGACTCGG	59.268	47.619	0.00	0.00	40.26	4.63
644	1192	0.447801	ATCATTTTGCGTGACTCGGC	59.552	50.000	0.00	0.00	40.26	5.54
645	1193	0.602638	TCATTTTGCGTGACTCGGCT	60.603	50.000	0.00	0.00	40.26	5.52
656	1210	4.578601	CGTGACTCGGCTAAAAATTGATC	58.421	43.478	0.00	0.00	35.71	2.92
664	1218	6.711579	TCGGCTAAAAATTGATCGACATTAC	58.288	36.000	0.00	0.00	0.00	1.89
679	1233	4.674362	CGACATTACTCCACTCGATGAACA	60.674	45.833	0.00	0.00	0.00	3.18
680	1234	5.344743	ACATTACTCCACTCGATGAACAT	57.655	39.130	0.00	0.00	0.00	2.71
681	1235	5.111989	ACATTACTCCACTCGATGAACATG	58.888	41.667	0.00	0.00	0.00	3.21
682	1236	4.801330	TTACTCCACTCGATGAACATGT	57.199	40.909	0.00	0.00	0.00	3.21
683	1237	3.685139	ACTCCACTCGATGAACATGTT	57.315	42.857	11.78	11.78	0.00	2.71
684	1238	4.008074	ACTCCACTCGATGAACATGTTT	57.992	40.909	13.36	0.00	0.00	2.83
685	1239	5.147330	ACTCCACTCGATGAACATGTTTA	57.853	39.130	13.36	9.29	0.00	2.01
686	1240	5.171476	ACTCCACTCGATGAACATGTTTAG	58.829	41.667	13.36	8.14	0.00	1.85
687	1241	5.047306	ACTCCACTCGATGAACATGTTTAGA	60.047	40.000	13.36	8.92	0.00	2.10
688	1242	5.977635	TCCACTCGATGAACATGTTTAGAT	58.022	37.500	13.36	5.52	0.00	1.98
689	1243	7.107639	TCCACTCGATGAACATGTTTAGATA	57.892	36.000	13.36	0.00	0.00	1.98
690	1244	6.978659	TCCACTCGATGAACATGTTTAGATAC	59.021	38.462	13.36	0.00	0.00	2.24
691	1245	6.074835	CCACTCGATGAACATGTTTAGATACG	60.075	42.308	13.36	12.60	0.00	3.06
710	1264	4.223320	ACGGTGCTCATGTTTGTTTTAG	57.777	40.909	0.00	0.00	0.00	1.85
759	1317	1.137872	TCATGTTTGCAAGCGGGTTTT	59.862	42.857	8.84	0.00	0.00	2.43
799	1361	9.082313	AGGGATGCCTTGATTATTATTACTTTG	57.918	33.333	0.00	0.00	0.00	2.77
800	1362	8.860088	GGGATGCCTTGATTATTATTACTTTGT	58.140	33.333	0.00	0.00	0.00	2.83
801	1363	9.683069	GGATGCCTTGATTATTATTACTTTGTG	57.317	33.333	0.00	0.00	0.00	3.33
804	1366	9.679661	TGCCTTGATTATTATTACTTTGTGAGA	57.320	29.630	0.00	0.00	0.00	3.27
814	1376	9.643693	ATTATTACTTTGTGAGAAATTGCCTTG	57.356	29.630	0.00	0.00	0.00	3.61
815	1377	6.707440	TTACTTTGTGAGAAATTGCCTTGA	57.293	33.333	0.00	0.00	0.00	3.02
816	1378	5.796424	ACTTTGTGAGAAATTGCCTTGAT	57.204	34.783	0.00	0.00	0.00	2.57
817	1379	6.165700	ACTTTGTGAGAAATTGCCTTGATT	57.834	33.333	0.00	0.00	0.00	2.57
818	1380	7.288810	ACTTTGTGAGAAATTGCCTTGATTA	57.711	32.000	0.00	0.00	0.00	1.75
819	1381	7.899973	ACTTTGTGAGAAATTGCCTTGATTAT	58.100	30.769	0.00	0.00	0.00	1.28
820	1382	8.370182	ACTTTGTGAGAAATTGCCTTGATTATT	58.630	29.630	0.00	0.00	0.00	1.40
821	1383	9.211485	CTTTGTGAGAAATTGCCTTGATTATTT	57.789	29.630	0.00	0.00	0.00	1.40
827	1389	9.643693	GAGAAATTGCCTTGATTATTTTTGAGA	57.356	29.630	0.00	0.00	0.00	3.27
861	1423	1.148048	GAGATTCTCCAGCCCAGCC	59.852	63.158	1.97	0.00	0.00	4.85
862	1424	2.194326	GATTCTCCAGCCCAGCCC	59.806	66.667	0.00	0.00	0.00	5.19
863	1425	2.614969	ATTCTCCAGCCCAGCCCA	60.615	61.111	0.00	0.00	0.00	5.36
864	1426	2.621517	GATTCTCCAGCCCAGCCCAG	62.622	65.000	0.00	0.00	0.00	4.45
889	1451	2.522185	CCCATCCAAGCCCATTATCAG	58.478	52.381	0.00	0.00	0.00	2.90
896	1458	3.162666	CAAGCCCATTATCAGATGGCAT	58.837	45.455	0.00	0.00	44.29	4.40
909	1471	1.483827	GATGGCATGTGAGGTGAGAGA	59.516	52.381	3.81	0.00	0.00	3.10
930	1492	4.357947	GACGCACGAGTCCAGCCA	62.358	66.667	0.00	0.00	35.22	4.75
938	1511	1.150536	GAGTCCAGCCACAAACCCA	59.849	57.895	0.00	0.00	0.00	4.51
1077	1692	0.923358	ATCTCTCTCCTCTCCACCGT	59.077	55.000	0.00	0.00	0.00	4.83
1228	1850	2.528127	TCAAGTCCCCCGCCAAGA	60.528	61.111	0.00	0.00	0.00	3.02
1242	1864	3.745803	AAGACCGACGCCGTCCTC	61.746	66.667	12.26	6.57	0.00	3.71
1483	2114	1.144936	CTCTTCGGCTCCATGGACC	59.855	63.158	11.44	15.95	0.00	4.46
1584	2221	4.514577	CGGGAGTGCGGGCTACAG	62.515	72.222	0.00	0.00	0.00	2.74
1708	2346	1.076485	ATGGCTCTGGGATGTTGGC	60.076	57.895	0.00	0.00	0.00	4.52
1975	2613	2.757099	CAGGCCCCGGTACTACGT	60.757	66.667	0.00	0.00	0.00	3.57
2053	2698	1.137872	AGTCATGATCACCGAGAAGGC	59.862	52.381	0.00	0.00	46.52	4.35
2198	2846	8.938906	AGCATGAAAATTGGTATGTTCATTTTC	58.061	29.630	0.00	8.59	43.24	2.29
2224	2878	9.545105	CTCATTCAATAGAGAAGAAAGCATAGT	57.455	33.333	0.00	0.00	33.74	2.12
2249	2909	4.517285	TGCTATCAACTTGTCCTTCATCC	58.483	43.478	0.00	0.00	0.00	3.51
2271	2933	5.065235	CCTGTCATATTGGCACACATATCA	58.935	41.667	0.00	0.00	39.29	2.15
2273	2935	6.349033	CCTGTCATATTGGCACACATATCATG	60.349	42.308	0.00	0.00	39.29	3.07
2398	3089	5.947228	TTTCAGTGCAATCTTCAACCTAG	57.053	39.130	0.00	0.00	0.00	3.02
2426	3117	7.077050	TCCATGAAAGAATGTTCCCATTTTT	57.923	32.000	0.00	0.00	41.37	1.94
2491	3190	5.358442	TGAAAATCGTGGACTTCTTTTTCCA	59.642	36.000	0.00	0.00	39.72	3.53
2508	3207	1.691434	TCCATGGGAAACAGTTTTGGC	59.309	47.619	13.02	0.00	0.00	4.52
2509	3208	1.270785	CCATGGGAAACAGTTTTGGCC	60.271	52.381	2.85	0.00	0.00	5.36
2510	3209	0.678950	ATGGGAAACAGTTTTGGCCG	59.321	50.000	0.00	0.00	0.00	6.13
2511	3210	1.300620	GGGAAACAGTTTTGGCCGC	60.301	57.895	0.00	0.00	0.00	6.53
2512	3211	1.439644	GGAAACAGTTTTGGCCGCA	59.560	52.632	0.00	0.00	0.00	5.69
2513	3212	0.874175	GGAAACAGTTTTGGCCGCAC	60.874	55.000	0.00	0.00	0.00	5.34
2515	3236	0.534873	AAACAGTTTTGGCCGCACTT	59.465	45.000	0.00	0.00	0.00	3.16
2540	3261	9.607988	TTTTGAACATGTATACCACTATGTAGG	57.392	33.333	0.00	0.00	32.26	3.18
2566	3287	6.661740	TTTTAGGTCCCCTGGTATTTGTAT	57.338	37.500	0.00	0.00	34.61	2.29
2580	3301	7.350382	TGGTATTTGTATGGGAGAAGCAAATA	58.650	34.615	0.00	0.00	39.51	1.40
2687	3411	9.895138	GGTTATGACCTTACCAAGTTAATTCTA	57.105	33.333	0.00	0.00	42.99	2.10
2744	3468	8.941995	AGCACTATCTGTATAGGTAATGAGAA	57.058	34.615	0.00	0.00	39.63	2.87
2746	3470	8.798402	GCACTATCTGTATAGGTAATGAGAACT	58.202	37.037	0.00	0.00	39.63	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	9.768215	TCTAGTTTATGAAAATTGGAAGGGATT	57.232	29.630	0.00	0.00	0.00	3.01
51	52	4.281435	TGTTTACTGACCATCGGAACAGTA	59.719	41.667	15.17	15.17	40.99	2.74
58	59	4.574421	TGCATATTGTTTACTGACCATCGG	59.426	41.667	0.00	0.00	0.00	4.18
59	60	5.064579	TGTGCATATTGTTTACTGACCATCG	59.935	40.000	0.00	0.00	0.00	3.84
126	127	9.040939	GCAAGGTTTGTAATAAAAACAACATCT	57.959	29.630	8.19	0.00	38.91	2.90
176	177	9.072375	AGCTAGAATATTTCCTTATTTTCTGCC	57.928	33.333	0.00	0.00	31.28	4.85
219	220	3.366374	GCACCTCAACTAATTCCTTGTGC	60.366	47.826	0.00	0.00	39.61	4.57
247	248	3.746492	ACTACCAACTGTTGATTTCGAGC	59.254	43.478	21.49	0.00	0.00	5.03
329	330	7.423199	CACTATAATTTGGCGAGTGAGTAGTA	58.577	38.462	0.00	0.00	39.94	1.82
330	331	6.273825	CACTATAATTTGGCGAGTGAGTAGT	58.726	40.000	0.00	0.00	39.94	2.73
331	332	5.175856	GCACTATAATTTGGCGAGTGAGTAG	59.824	44.000	4.58	0.00	39.94	2.57
332	333	5.047847	GCACTATAATTTGGCGAGTGAGTA	58.952	41.667	4.58	0.00	39.94	2.59
333	334	3.871594	GCACTATAATTTGGCGAGTGAGT	59.128	43.478	4.58	0.00	39.94	3.41
335	336	3.867857	TGCACTATAATTTGGCGAGTGA	58.132	40.909	4.58	0.00	39.94	3.41
340	342	7.928908	ATTTTGTATGCACTATAATTTGGCG	57.071	32.000	0.00	0.00	0.00	5.69
456	466	4.481368	TGGCGGAAGAGTATTGTATGTT	57.519	40.909	0.00	0.00	0.00	2.71
457	467	4.481368	TTGGCGGAAGAGTATTGTATGT	57.519	40.909	0.00	0.00	0.00	2.29
459	469	5.063880	GGATTTGGCGGAAGAGTATTGTAT	58.936	41.667	0.00	0.00	0.00	2.29
464	1007	2.505819	ACTGGATTTGGCGGAAGAGTAT	59.494	45.455	0.00	0.00	0.00	2.12
476	1019	6.313658	GGGCAAATTTAGCTTAACTGGATTTG	59.686	38.462	0.00	0.00	40.87	2.32
482	1025	4.695217	TCGGGCAAATTTAGCTTAACTG	57.305	40.909	0.00	0.00	0.00	3.16
484	1027	6.772770	TTTTTCGGGCAAATTTAGCTTAAC	57.227	33.333	0.00	0.00	0.00	2.01
486	1029	6.459923	ACATTTTTCGGGCAAATTTAGCTTA	58.540	32.000	0.00	0.00	0.00	3.09
526	1071	3.433598	CCGCTCTTTATTTGGATCCTCCA	60.434	47.826	14.23	0.00	46.61	3.86
548	1096	2.060284	TGTGCAATGATTTTGAAGCGC	58.940	42.857	0.00	0.00	0.00	5.92
560	1108	2.853594	GCGTACATTTCCATGTGCAATG	59.146	45.455	0.00	7.04	44.13	2.82
561	1109	2.159254	GGCGTACATTTCCATGTGCAAT	60.159	45.455	0.00	0.00	44.13	3.56
640	1188	5.811399	AATGTCGATCAATTTTTAGCCGA	57.189	34.783	0.00	0.00	0.00	5.54
641	1189	6.715464	AGTAATGTCGATCAATTTTTAGCCG	58.285	36.000	0.00	0.00	0.00	5.52
643	1191	7.640240	GTGGAGTAATGTCGATCAATTTTTAGC	59.360	37.037	0.00	0.00	0.00	3.09
644	1192	8.883731	AGTGGAGTAATGTCGATCAATTTTTAG	58.116	33.333	0.00	0.00	0.00	1.85
645	1193	8.786826	AGTGGAGTAATGTCGATCAATTTTTA	57.213	30.769	0.00	0.00	0.00	1.52
656	1210	3.692791	TCATCGAGTGGAGTAATGTCG	57.307	47.619	0.00	0.00	0.00	4.35
664	1218	5.410924	TCTAAACATGTTCATCGAGTGGAG	58.589	41.667	12.39	0.00	0.00	3.86
679	1233	5.023533	ACATGAGCACCGTATCTAAACAT	57.976	39.130	0.00	0.00	0.00	2.71
680	1234	4.465632	ACATGAGCACCGTATCTAAACA	57.534	40.909	0.00	0.00	0.00	2.83
681	1235	5.121768	ACAAACATGAGCACCGTATCTAAAC	59.878	40.000	0.00	0.00	0.00	2.01
682	1236	5.242434	ACAAACATGAGCACCGTATCTAAA	58.758	37.500	0.00	0.00	0.00	1.85
683	1237	4.827692	ACAAACATGAGCACCGTATCTAA	58.172	39.130	0.00	0.00	0.00	2.10
684	1238	4.465632	ACAAACATGAGCACCGTATCTA	57.534	40.909	0.00	0.00	0.00	1.98
685	1239	3.334583	ACAAACATGAGCACCGTATCT	57.665	42.857	0.00	0.00	0.00	1.98
686	1240	4.419522	AAACAAACATGAGCACCGTATC	57.580	40.909	0.00	0.00	0.00	2.24
687	1241	4.846779	AAAACAAACATGAGCACCGTAT	57.153	36.364	0.00	0.00	0.00	3.06
688	1242	5.057819	TCTAAAACAAACATGAGCACCGTA	58.942	37.500	0.00	0.00	0.00	4.02
689	1243	3.880490	TCTAAAACAAACATGAGCACCGT	59.120	39.130	0.00	0.00	0.00	4.83
690	1244	4.481930	TCTAAAACAAACATGAGCACCG	57.518	40.909	0.00	0.00	0.00	4.94
691	1245	7.713764	AAAATCTAAAACAAACATGAGCACC	57.286	32.000	0.00	0.00	0.00	5.01
717	1271	4.394729	AGCCATCTCAAAAACGAAACCTA	58.605	39.130	0.00	0.00	0.00	3.08
799	1361	9.206870	TCAAAAATAATCAAGGCAATTTCTCAC	57.793	29.630	0.00	0.00	0.00	3.51
800	1362	9.426837	CTCAAAAATAATCAAGGCAATTTCTCA	57.573	29.630	0.00	0.00	0.00	3.27
801	1363	9.643693	TCTCAAAAATAATCAAGGCAATTTCTC	57.356	29.630	0.00	0.00	0.00	2.87
827	1389	8.859090	TGGAGAATCTCAAAAACACATTGTAAT	58.141	29.630	12.79	0.00	33.73	1.89
861	1423	2.441532	CTTGGATGGGCTGGCTGG	60.442	66.667	0.00	0.00	0.00	4.85
862	1424	3.145551	GCTTGGATGGGCTGGCTG	61.146	66.667	0.00	0.00	0.00	4.85
863	1425	4.453892	GGCTTGGATGGGCTGGCT	62.454	66.667	0.00	0.00	0.00	4.75
889	1451	1.483827	TCTCTCACCTCACATGCCATC	59.516	52.381	0.00	0.00	0.00	3.51
896	1458	0.952280	GTCGTGTCTCTCACCTCACA	59.048	55.000	0.00	0.00	43.51	3.58
909	1471	3.538028	CTGGACTCGTGCGTCGTGT	62.538	63.158	8.16	8.16	46.51	4.49
1183	1804	1.000396	GCTTGGTGGAGGCCTTGAT	60.000	57.895	6.77	0.00	0.00	2.57
1291	1922	4.473520	CAGCGGGTCCTTGGCGAT	62.474	66.667	0.00	0.00	0.00	4.58
1483	2114	1.165907	TTGAGCAACCGGAGCAAGTG	61.166	55.000	21.98	6.14	0.00	3.16
1584	2221	0.803380	GCTTGGCAATGTCGCAATCC	60.803	55.000	0.00	0.00	0.00	3.01
1708	2346	0.780002	GACAGCATGCAACGCTTTTG	59.220	50.000	21.98	9.14	42.53	2.44
1975	2613	6.432783	TCTGTTTTCCTTGAGAAACTTCACAA	59.567	34.615	2.94	2.94	44.20	3.33
2053	2698	5.450965	GGGCATATGAACTTCTCCACAAATG	60.451	44.000	6.97	0.00	0.00	2.32
2198	2846	9.545105	ACTATGCTTTCTTCTCTATTGAATGAG	57.455	33.333	0.00	0.00	0.00	2.90
2224	2878	5.738619	TGAAGGACAAGTTGATAGCAGTA	57.261	39.130	10.54	0.00	0.00	2.74
2249	2909	6.428771	TCATGATATGTGTGCCAATATGACAG	59.571	38.462	0.00	0.00	0.00	3.51
2271	2933	4.209538	CCTGATCTCTCACTCTCAGTCAT	58.790	47.826	0.00	0.00	34.62	3.06
2273	2935	2.951642	CCCTGATCTCTCACTCTCAGTC	59.048	54.545	0.00	0.00	34.62	3.51
2398	3089	4.021192	TGGGAACATTCTTTCATGGAAAGC	60.021	41.667	12.63	0.09	41.34	3.51
2426	3117	3.131577	GGCTTCAAATCATCTTCATGGCA	59.868	43.478	0.00	0.00	0.00	4.92
2491	3190	0.678950	CGGCCAAAACTGTTTCCCAT	59.321	50.000	6.20	0.00	0.00	4.00
2508	3207	4.155099	TGGTATACATGTTCAAAAGTGCGG	59.845	41.667	2.30	0.00	0.00	5.69
2509	3208	5.086058	GTGGTATACATGTTCAAAAGTGCG	58.914	41.667	2.30	0.00	0.00	5.34
2510	3209	6.254281	AGTGGTATACATGTTCAAAAGTGC	57.746	37.500	2.30	0.00	0.00	4.40
2511	3210	8.946085	ACATAGTGGTATACATGTTCAAAAGTG	58.054	33.333	2.30	0.00	31.46	3.16
2515	3236	8.764558	ACCTACATAGTGGTATACATGTTCAAA	58.235	33.333	2.30	0.00	34.81	2.69
2551	3272	3.053077	TCTCCCATACAAATACCAGGGG	58.947	50.000	0.00	0.00	36.92	4.79
2580	3301	3.070159	AGCATCATACCGTACAAGCATCT	59.930	43.478	0.00	0.00	0.00	2.90
2735	3459	7.280428	GCTAAGGGGTAAAGAAGTTCTCATTAC	59.720	40.741	15.00	15.00	37.45	1.89
2743	3467	8.749354	CAAAATATGCTAAGGGGTAAAGAAGTT	58.251	33.333	0.00	0.00	0.00	2.66
2744	3468	7.893833	ACAAAATATGCTAAGGGGTAAAGAAGT	59.106	33.333	0.00	0.00	0.00	3.01
2746	3470	8.658840	AACAAAATATGCTAAGGGGTAAAGAA	57.341	30.769	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.