AutoCloner

Multiple sequence alignment - TraesCS6D01G381400

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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	TraesCS6D01G381400	chr6D	100.000	3654	0	0	1	3654	461857190	461853537	0.000000e+00	6748.0
1	TraesCS6D01G381400	chr6D	84.961	1782	205	33	1172	2925	462014285	462012539	0.000000e+00	1748.0
2	TraesCS6D01G381400	chr6D	81.570	1503	235	26	1172	2646	461924109	461925597	0.000000e+00	1203.0
3	TraesCS6D01G381400	chr6D	80.948	1223	198	23	1172	2371	68365251	68364041	0.000000e+00	935.0
4	TraesCS6D01G381400	chr6D	91.653	599	27	10	3060	3654	462012331	462011752	0.000000e+00	808.0
5	TraesCS6D01G381400	chr6D	73.269	1444	314	52	1158	2576	461797442	461796046	2.570000e-126	462.0
6	TraesCS6D01G381400	chr6D	77.984	377	51	24	601	965	461923508	461923864	1.330000e-49	207.0
7	TraesCS6D01G381400	chr6D	94.203	69	4	0	2924	2992	462012396	462012328	4.990000e-19	106.0
8	TraesCS6D01G381400	chr6B	92.188	2432	102	29	583	2940	704305312	704302895	0.000000e+00	3358.0
9	TraesCS6D01G381400	chr6B	85.065	1781	205	32	1172	2925	704183882	704182136	0.000000e+00	1759.0
10	TraesCS6D01G381400	chr6B	83.126	1529	210	24	1172	2676	704177939	704176435	0.000000e+00	1351.0
11	TraesCS6D01G381400	chr6B	80.135	1626	275	21	1077	2666	704187341	704188954	0.000000e+00	1170.0
12	TraesCS6D01G381400	chr6B	91.199	534	26	8	3129	3654	704181840	704181320	0.000000e+00	706.0
13	TraesCS6D01G381400	chr6B	86.248	509	66	3	74	578	529871522	529871014	1.920000e-152	549.0
14	TraesCS6D01G381400	chr6B	90.244	123	4	6	3060	3182	704181954	704181840	1.760000e-33	154.0
15	TraesCS6D01G381400	chr6B	82.667	75	4	5	2769	2841	704189116	704189183	1.420000e-04	58.4
16	TraesCS6D01G381400	chr6A	84.512	1782	212	34	1172	2925	608861089	608859344	0.000000e+00	1703.0
17	TraesCS6D01G381400	chr6A	83.433	1503	204	23	1172	2650	608902286	608900805	0.000000e+00	1354.0
18	TraesCS6D01G381400	chr6A	77.862	2114	332	71	601	2646	608709633	608711678	0.000000e+00	1186.0
19	TraesCS6D01G381400	chr6A	90.033	602	31	13	3060	3654	608859138	608858559	0.000000e+00	752.0
20	TraesCS6D01G381400	chr6A	83.010	824	113	20	1837	2656	608968557	608969357	0.000000e+00	721.0
21	TraesCS6D01G381400	chr6A	89.720	214	17	4	2684	2895	608969417	608969627	6.010000e-68	268.0
22	TraesCS6D01G381400	chr6A	82.873	181	15	9	3338	3509	608862620	608862447	8.180000e-32	148.0
23	TraesCS6D01G381400	chr5D	84.833	600	56	15	1	577	236433172	236432585	4.090000e-159	571.0
24	TraesCS6D01G381400	chr7D	83.828	606	74	10	1	582	20074591	20073986	4.120000e-154	555.0
25	TraesCS6D01G381400	chr3B	83.748	603	72	14	1	579	828436981	828437581	6.900000e-152	547.0
26	TraesCS6D01G381400	chr3B	86.255	502	60	9	82	577	687657995	687658493	1.490000e-148	536.0
27	TraesCS6D01G381400	chr4B	83.444	604	74	14	1	579	574061593	574060991	4.150000e-149	538.0
28	TraesCS6D01G381400	chr2A	83.527	601	72	15	2	577	18172765	18173363	1.490000e-148	536.0
29	TraesCS6D01G381400	chr1B	85.714	511	65	4	74	579	524158805	524159312	1.930000e-147	532.0
30	TraesCS6D01G381400	chr3D	85.602	507	69	3	77	579	380492175	380491669	2.500000e-146	529.0

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	TraesCS6D01G381400	chr6D	461853537	461857190	3653	True	6748.000000	6748	100.000000	1	3654	1	chr6D.!!$R3	3653
1	TraesCS6D01G381400	chr6D	68364041	68365251	1210	True	935.000000	935	80.948000	1172	2371	1	chr6D.!!$R1	1199
2	TraesCS6D01G381400	chr6D	462011752	462014285	2533	True	887.333333	1748	90.272333	1172	3654	3	chr6D.!!$R4	2482
3	TraesCS6D01G381400	chr6D	461923508	461925597	2089	False	705.000000	1203	79.777000	601	2646	2	chr6D.!!$F1	2045
4	TraesCS6D01G381400	chr6D	461796046	461797442	1396	True	462.000000	462	73.269000	1158	2576	1	chr6D.!!$R2	1418
5	TraesCS6D01G381400	chr6B	704302895	704305312	2417	True	3358.000000	3358	92.188000	583	2940	1	chr6B.!!$R2	2357
6	TraesCS6D01G381400	chr6B	704176435	704183882	7447	True	992.500000	1759	87.408500	1172	3654	4	chr6B.!!$R3	2482
7	TraesCS6D01G381400	chr6B	704187341	704189183	1842	False	614.200000	1170	81.401000	1077	2841	2	chr6B.!!$F1	1764
8	TraesCS6D01G381400	chr6B	529871014	529871522	508	True	549.000000	549	86.248000	74	578	1	chr6B.!!$R1	504
9	TraesCS6D01G381400	chr6A	608900805	608902286	1481	True	1354.000000	1354	83.433000	1172	2650	1	chr6A.!!$R1	1478
10	TraesCS6D01G381400	chr6A	608709633	608711678	2045	False	1186.000000	1186	77.862000	601	2646	1	chr6A.!!$F1	2045
11	TraesCS6D01G381400	chr6A	608858559	608862620	4061	True	867.666667	1703	85.806000	1172	3654	3	chr6A.!!$R2	2482
12	TraesCS6D01G381400	chr6A	608968557	608969627	1070	False	494.500000	721	86.365000	1837	2895	2	chr6A.!!$F2	1058
13	TraesCS6D01G381400	chr5D	236432585	236433172	587	True	571.000000	571	84.833000	1	577	1	chr5D.!!$R1	576
14	TraesCS6D01G381400	chr7D	20073986	20074591	605	True	555.000000	555	83.828000	1	582	1	chr7D.!!$R1	581
15	TraesCS6D01G381400	chr3B	828436981	828437581	600	False	547.000000	547	83.748000	1	579	1	chr3B.!!$F2	578
16	TraesCS6D01G381400	chr4B	574060991	574061593	602	True	538.000000	538	83.444000	1	579	1	chr4B.!!$R1	578
17	TraesCS6D01G381400	chr2A	18172765	18173363	598	False	536.000000	536	83.527000	2	577	1	chr2A.!!$F1	575
18	TraesCS6D01G381400	chr1B	524158805	524159312	507	False	532.000000	532	85.714000	74	579	1	chr1B.!!$F1	505
19	TraesCS6D01G381400	chr3D	380491669	380492175	506	True	529.000000	529	85.602000	77	579	1	chr3D.!!$R1	502

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
821	860	0.545548	AAAGCCTCCTCCGTCTCCTT	60.546	55.0	0.0	0.0	0.0	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2798	9275	1.011968	GCACGATACTGCACGACCAA	61.012	55.0	1.06	0.0	37.11	3.67	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
37	38	1.223487	GGCACCTAATTCCGAGGCA	59.777	57.895	0.00	0.00	37.63	4.75
56	57	2.486663	CCGATGTCCATCCGGTCGA	61.487	63.158	9.68	0.00	34.40	4.20
80	100	2.231478	GTCTTTGACCGTGAGATGAGGA	59.769	50.000	0.00	0.00	0.00	3.71
113	133	4.030452	GCTTTGCGGCTTGCTCGT	62.030	61.111	0.00	0.00	46.63	4.18
128	148	0.671781	CTCGTCAGTTTGGAGGCAGG	60.672	60.000	0.00	0.00	0.00	4.85
146	166	1.132500	GGTAGCCTTGGGTCTAGCAT	58.868	55.000	0.00	0.00	33.46	3.79
292	312	3.263489	TGATACTCGGTCTCTTCGACT	57.737	47.619	0.00	0.00	42.44	4.18
338	359	0.879090	GGATTTGGTGGTGTCCGTTC	59.121	55.000	0.00	0.00	0.00	3.95
395	416	1.022735	GTAGAAGTGCGAGGGATCGA	58.977	55.000	1.17	0.00	34.64	3.59
410	431	2.218603	GATCGAGGTTGTTGTGTGGTT	58.781	47.619	0.00	0.00	0.00	3.67
438	461	4.041762	TCGGGTTGACCATGGGGC	62.042	66.667	18.09	8.37	40.22	5.80
456	479	3.056536	GGGGCCATGAAGTTTCTTTCTTC	60.057	47.826	4.39	0.00	40.89	2.87
468	491	2.434428	TCTTTCTTCGCGAGTAGTCCT	58.566	47.619	9.59	0.00	0.00	3.85
475	498	0.733150	CGCGAGTAGTCCTCATGTGA	59.267	55.000	0.00	0.00	40.48	3.58
486	509	8.634444	AGTAGTCCTCATGTGATCTATTTGTAC	58.366	37.037	0.00	0.00	0.00	2.90
496	520	5.123344	GTGATCTATTTGTACCGGTTTTGCT	59.877	40.000	15.04	0.00	0.00	3.91
534	562	7.968014	ATTAATTGGGCAATTCTCTTCTTCT	57.032	32.000	0.00	0.00	40.99	2.85
535	563	7.781324	TTAATTGGGCAATTCTCTTCTTCTT	57.219	32.000	0.00	0.00	40.99	2.52
694	731	1.749634	TCGAAGAAGGAAGGGATCGAC	59.250	52.381	0.00	0.00	34.74	4.20
800	839	7.700322	TTCTACGCTAGCTTCAATAAGATTG	57.300	36.000	13.93	0.00	34.37	2.67
821	860	0.545548	AAAGCCTCCTCCGTCTCCTT	60.546	55.000	0.00	0.00	0.00	3.36
822	861	1.261238	AAGCCTCCTCCGTCTCCTTG	61.261	60.000	0.00	0.00	0.00	3.61
823	862	2.896443	CCTCCTCCGTCTCCTTGC	59.104	66.667	0.00	0.00	0.00	4.01
825	864	2.683933	TCCTCCGTCTCCTTGCCC	60.684	66.667	0.00	0.00	0.00	5.36
901	942	3.206957	TCGTCGATCGTCGGGCAT	61.207	61.111	28.94	0.00	40.88	4.40
1376	1737	3.998341	GTGACGGCAAACATCCTTAGTAA	59.002	43.478	0.00	0.00	0.00	2.24
1386	1747	5.695424	ACATCCTTAGTAAAAGGTCTCCC	57.305	43.478	3.83	0.00	38.55	4.30
1452	1816	2.124695	GGTCTCCCCATCGGCAAC	60.125	66.667	0.00	0.00	0.00	4.17
1496	1860	1.144057	AGAAACTAGATGCCGCCGG	59.856	57.895	0.00	0.00	0.00	6.13
1507	1871	2.340328	GCCGCCGGGTTTGAAATCT	61.340	57.895	4.77	0.00	34.97	2.40
1608	1972	0.179119	GTCCAGATGCATTTGCTGGC	60.179	55.000	22.34	15.62	46.82	4.85
2288	2691	2.035632	ACCTAGAGGAGCTTTCCATCG	58.964	52.381	1.60	0.00	38.94	3.84
2576	8949	3.374402	CACGGACCAGCGAGGAGT	61.374	66.667	5.19	0.13	41.22	3.85
2580	8953	1.376037	GGACCAGCGAGGAGTTTGG	60.376	63.158	5.19	0.00	41.22	3.28
2627	9000	1.099879	GTCGGCTACGGCTTCTCCTA	61.100	60.000	0.00	0.00	42.51	2.94
2738	9208	3.487544	GCATCTCGGCTACCAATTTGTTC	60.488	47.826	0.00	0.00	0.00	3.18
2812	9289	5.615984	CGTTTATGTTTTGGTCGTGCAGTAT	60.616	40.000	0.00	0.00	0.00	2.12
2855	9340	7.011763	ACAGTCAATATTCAGTTCGAATGATGG	59.988	37.037	0.00	0.00	44.32	3.51
2862	9347	4.641396	TCAGTTCGAATGATGGTCTGTTT	58.359	39.130	0.00	0.00	0.00	2.83
2863	9348	5.063204	TCAGTTCGAATGATGGTCTGTTTT	58.937	37.500	0.00	0.00	0.00	2.43
2895	9382	5.592104	TCTTGTATTTATGAGAGCCACGA	57.408	39.130	0.00	0.00	0.00	4.35
2970	9603	4.670221	GCTGGAAGAAGAAAATGCACGTAG	60.670	45.833	0.00	0.00	34.07	3.51
2971	9604	4.637276	TGGAAGAAGAAAATGCACGTAGA	58.363	39.130	0.00	0.00	0.00	2.59
2988	9621	1.082104	GAAAACGGCAGCGTTCCTG	60.082	57.895	1.18	0.00	44.67	3.86
2989	9622	1.782028	GAAAACGGCAGCGTTCCTGT	61.782	55.000	1.18	0.00	43.71	4.00
2990	9623	1.782028	AAAACGGCAGCGTTCCTGTC	61.782	55.000	1.18	0.00	43.71	3.51
2991	9624	4.681978	ACGGCAGCGTTCCTGTCC	62.682	66.667	0.00	0.00	43.34	4.02
2993	9626	4.021925	GGCAGCGTTCCTGTCCCT	62.022	66.667	0.00	0.00	43.71	4.20
2994	9627	2.743928	GCAGCGTTCCTGTCCCTG	60.744	66.667	0.00	0.00	43.71	4.45
2995	9628	2.046892	CAGCGTTCCTGTCCCTGG	60.047	66.667	0.00	0.00	36.79	4.45
2996	9629	2.526873	AGCGTTCCTGTCCCTGGT	60.527	61.111	0.00	0.00	0.00	4.00
2997	9630	2.147387	AGCGTTCCTGTCCCTGGTT	61.147	57.895	0.00	0.00	0.00	3.67
2998	9631	1.966451	GCGTTCCTGTCCCTGGTTG	60.966	63.158	0.00	0.00	0.00	3.77
2999	9632	1.966451	CGTTCCTGTCCCTGGTTGC	60.966	63.158	0.00	0.00	0.00	4.17
3000	9633	1.603739	GTTCCTGTCCCTGGTTGCC	60.604	63.158	0.00	0.00	0.00	4.52
3001	9634	3.190738	TTCCTGTCCCTGGTTGCCG	62.191	63.158	0.00	0.00	0.00	5.69
3038	9671	2.742372	GAGGAGCTCGCCGCAAAA	60.742	61.111	7.83	0.00	42.61	2.44
3039	9672	2.743928	AGGAGCTCGCCGCAAAAG	60.744	61.111	7.83	0.00	42.61	2.27
3040	9673	3.050275	GGAGCTCGCCGCAAAAGT	61.050	61.111	7.83	0.00	42.61	2.66
3041	9674	1.740296	GGAGCTCGCCGCAAAAGTA	60.740	57.895	7.83	0.00	42.61	2.24
3042	9675	1.696832	GGAGCTCGCCGCAAAAGTAG	61.697	60.000	7.83	0.00	42.61	2.57
3043	9676	1.696832	GAGCTCGCCGCAAAAGTAGG	61.697	60.000	0.00	0.00	42.61	3.18
3044	9677	2.750888	GCTCGCCGCAAAAGTAGGG	61.751	63.158	0.00	0.00	38.92	3.53
3045	9678	2.046700	TCGCCGCAAAAGTAGGGG	60.047	61.111	0.00	0.00	41.62	4.79
3048	9681	3.590824	CCGCAAAAGTAGGGGCTG	58.409	61.111	0.00	0.00	32.05	4.85
3049	9682	2.700773	CCGCAAAAGTAGGGGCTGC	61.701	63.158	0.00	0.00	32.05	5.25
3050	9683	1.675641	CGCAAAAGTAGGGGCTGCT	60.676	57.895	0.00	0.00	0.00	4.24
3051	9684	1.885871	GCAAAAGTAGGGGCTGCTG	59.114	57.895	0.00	0.00	0.00	4.41
3052	9685	1.885871	CAAAAGTAGGGGCTGCTGC	59.114	57.895	7.10	7.10	38.76	5.25
3053	9686	0.895100	CAAAAGTAGGGGCTGCTGCA	60.895	55.000	17.89	0.88	41.91	4.41
3054	9687	0.895559	AAAAGTAGGGGCTGCTGCAC	60.896	55.000	17.89	14.12	43.08	4.57
3055	9688	2.067932	AAAGTAGGGGCTGCTGCACA	62.068	55.000	20.17	0.00	46.28	4.57
3056	9689	2.437359	GTAGGGGCTGCTGCACAG	60.437	66.667	20.17	10.75	46.28	3.66
3092	9725	4.957684	CAGCTCCGGCGCGATGAT	62.958	66.667	12.10	0.00	44.37	2.45
3093	9726	4.957684	AGCTCCGGCGCGATGATG	62.958	66.667	12.10	0.00	44.37	3.07
3094	9727	4.950062	GCTCCGGCGCGATGATGA	62.950	66.667	12.10	0.00	0.00	2.92
3095	9728	2.732468	CTCCGGCGCGATGATGAG	60.732	66.667	12.10	3.55	0.00	2.90
3096	9729	4.950062	TCCGGCGCGATGATGAGC	62.950	66.667	12.10	0.00	0.00	4.26
3097	9730	4.957684	CCGGCGCGATGATGAGCT	62.958	66.667	12.10	0.00	34.84	4.09
3098	9731	3.401411	CGGCGCGATGATGAGCTC	61.401	66.667	12.10	6.82	34.84	4.09
3186	9819	2.499289	TGCACTTGGGTTTTGAACACAT	59.501	40.909	0.00	0.00	45.71	3.21
3214	9847	0.036765	TGACGTGATGTGGGGTTAGC	60.037	55.000	0.00	0.00	0.00	3.09
3224	9857	0.037590	TGGGGTTAGCGACTTTGCAT	59.962	50.000	0.00	0.00	37.31	3.96
3260	9893	3.548214	GCCCGAAAGAAGTTCTTGTGTTC	60.548	47.826	18.70	11.21	36.71	3.18
3261	9894	3.877508	CCCGAAAGAAGTTCTTGTGTTCT	59.122	43.478	18.70	1.87	36.71	3.01
3262	9895	4.335594	CCCGAAAGAAGTTCTTGTGTTCTT	59.664	41.667	18.70	1.12	41.29	2.52
3264	9897	6.322491	CCGAAAGAAGTTCTTGTGTTCTTTT	58.678	36.000	18.70	0.00	45.91	2.27
3265	9898	6.806739	CCGAAAGAAGTTCTTGTGTTCTTTTT	59.193	34.615	18.70	0.00	45.91	1.94
3393	10027	4.266029	CGATGATTGCTATGGTTTTGTTGC	59.734	41.667	0.00	0.00	0.00	4.17
3401	10035	1.850377	TGGTTTTGTTGCTTGCATCG	58.150	45.000	0.00	0.00	0.00	3.84
3421	10055	5.749596	TCGACAACAACAAAATGACTGAT	57.250	34.783	0.00	0.00	0.00	2.90
3437	10071	4.880120	TGACTGATCTGATTTTGGATGAGC	59.120	41.667	6.60	0.00	28.71	4.26
3562	10198	6.056884	ACAACGTTGGGAGTAGAAAATGTTA	58.943	36.000	30.34	0.00	32.10	2.41
3567	10208	6.090898	CGTTGGGAGTAGAAAATGTTAGACTG	59.909	42.308	0.00	0.00	0.00	3.51
3601	10242	5.297029	GGCATGTTCCTACAAGAATAAGGAC	59.703	44.000	0.00	0.00	39.13	3.85
3610	10251	4.273318	ACAAGAATAAGGACTTGGATGCC	58.727	43.478	0.00	0.00	45.03	4.40
3611	10252	3.199880	AGAATAAGGACTTGGATGCCG	57.800	47.619	0.00	0.00	0.00	5.69
3624	10265	0.458370	GATGCCGCGCAAGGAAAAAT	60.458	50.000	8.75	0.00	43.62	1.82
3625	10266	0.737019	ATGCCGCGCAAGGAAAAATG	60.737	50.000	8.75	0.00	43.62	2.32
3629	10270	1.783434	GCGCAAGGAAAAATGCAGC	59.217	52.632	0.30	0.00	42.68	5.25
3638	10279	5.796424	AGGAAAAATGCAGCATTATAGGG	57.204	39.130	21.15	0.00	32.43	3.53
3642	10283	4.796038	AAATGCAGCATTATAGGGCATC	57.204	40.909	21.15	0.00	43.80	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	1.592669	GATGGACATCGGTGCCTCG	60.593	63.158	9.95	0.00	33.90	4.63
37	38	2.782222	CGACCGGATGGACATCGGT	61.782	63.158	20.61	20.61	42.75	4.69
56	57	0.966920	ATCTCACGGTCAAAGACGGT	59.033	50.000	4.76	4.76	44.70	4.83
80	100	1.594331	AAGCTTTTTCGCGAAGACCT	58.406	45.000	22.21	13.00	34.40	3.85
113	133	0.324943	GCTACCTGCCTCCAAACTGA	59.675	55.000	0.00	0.00	35.15	3.41
128	148	1.202698	CCATGCTAGACCCAAGGCTAC	60.203	57.143	0.00	0.00	0.00	3.58
146	166	2.493278	GCTAGAAGGAAAGCAATTGCCA	59.507	45.455	26.45	0.69	43.38	4.92
222	242	2.669569	GCGCCACTCTTCTTGCCA	60.670	61.111	0.00	0.00	0.00	4.92
338	359	5.277828	CCTCAACGAAACCAAGGTTAAAGAG	60.278	44.000	4.68	8.40	37.35	2.85
395	416	3.383185	CCATACAAACCACACAACAACCT	59.617	43.478	0.00	0.00	0.00	3.50
410	431	2.496111	GTCAACCCGACAACCATACAA	58.504	47.619	0.00	0.00	44.69	2.41
438	461	3.186409	TCGCGAAGAAAGAAACTTCATGG	59.814	43.478	6.20	0.00	42.39	3.66
443	466	4.618965	ACTACTCGCGAAGAAAGAAACTT	58.381	39.130	11.33	0.00	0.00	2.66
468	491	5.607939	ACCGGTACAAATAGATCACATGA	57.392	39.130	4.49	0.00	0.00	3.07
475	498	4.331717	CGAGCAAAACCGGTACAAATAGAT	59.668	41.667	8.00	0.00	0.00	1.98
496	520	5.862860	GCCCAATTAATTAACGAAAAACCGA	59.137	36.000	0.00	0.00	0.00	4.69
694	731	6.554334	TCCTTTTTCTCATACAAACCGAAG	57.446	37.500	0.00	0.00	0.00	3.79
782	821	6.205071	GCTTTCCAATCTTATTGAAGCTAGC	58.795	40.000	6.62	6.62	36.15	3.42
898	939	6.567050	TCTTGAAATTATGCTCCTTTCATGC	58.433	36.000	0.00	0.00	38.34	4.06
965	1006	1.164041	AAAACAGGACAAGGACGGCG	61.164	55.000	4.80	4.80	0.00	6.46
1293	1654	3.058450	GCTGAGATCGATGACAATCTGG	58.942	50.000	0.54	0.00	32.43	3.86
1386	1747	1.970917	GCTTGCGAACGGTGATCTGG	61.971	60.000	0.00	0.00	0.00	3.86
1496	1860	4.022849	CCCTCAGTGTCAAGATTTCAAACC	60.023	45.833	0.00	0.00	0.00	3.27
1507	1871	7.577426	GCAATTAAATGAATCCCTCAGTGTCAA	60.577	37.037	0.00	0.00	37.52	3.18
1608	1972	2.281070	AGTTGCAGCCGTGTGAGG	60.281	61.111	0.00	0.00	0.00	3.86
2288	2691	3.077359	GGCACTTATGATCCCATACTGC	58.923	50.000	0.00	0.00	37.89	4.40
2576	8949	4.243793	TCTTCTCCCTCAACAAACCAAA	57.756	40.909	0.00	0.00	0.00	3.28
2580	8953	4.389374	TGTCATCTTCTCCCTCAACAAAC	58.611	43.478	0.00	0.00	0.00	2.93
2627	9000	5.930135	ACCTAATGAGCGGAAGTGAATAAT	58.070	37.500	0.00	0.00	0.00	1.28
2656	9029	6.983890	GTCTTTCAGATAGAGGTTCATCTTCC	59.016	42.308	0.00	0.00	28.88	3.46
2717	9187	3.242413	CGAACAAATTGGTAGCCGAGATG	60.242	47.826	0.00	0.00	0.00	2.90
2738	9208	6.020916	TCGAAAATAGCTAAATGAGTCGTTCG	60.021	38.462	0.00	2.23	35.53	3.95
2791	9268	4.092237	CGATACTGCACGACCAAAACATAA	59.908	41.667	0.00	0.00	0.00	1.90
2798	9275	1.011968	GCACGATACTGCACGACCAA	61.012	55.000	1.06	0.00	37.11	3.67
2812	9289	5.474825	TGACTGTATTCAACATAAGCACGA	58.525	37.500	0.00	0.00	37.50	4.35
2895	9382	4.336433	CAGTGTCCATGAAAAACAGAGTGT	59.664	41.667	0.00	0.00	0.00	3.55
2951	9584	6.085068	CGTTTTCTACGTGCATTTTCTTCTTC	59.915	38.462	0.00	0.00	45.14	2.87
2981	9614	1.966451	GCAACCAGGGACAGGAACG	60.966	63.158	0.00	0.00	37.04	3.95
3027	9660	2.106683	CCCCTACTTTTGCGGCGAG	61.107	63.158	12.98	0.20	0.00	5.03
3028	9661	2.046700	CCCCTACTTTTGCGGCGA	60.047	61.111	12.98	0.00	0.00	5.54
3029	9662	3.810896	GCCCCTACTTTTGCGGCG	61.811	66.667	0.51	0.51	0.00	6.46
3030	9663	2.361230	AGCCCCTACTTTTGCGGC	60.361	61.111	0.00	0.00	40.03	6.53
3031	9664	2.700773	GCAGCCCCTACTTTTGCGG	61.701	63.158	0.00	0.00	0.00	5.69
3032	9665	1.675641	AGCAGCCCCTACTTTTGCG	60.676	57.895	0.00	0.00	39.63	4.85
3033	9666	1.885871	CAGCAGCCCCTACTTTTGC	59.114	57.895	0.00	0.00	35.09	3.68
3034	9667	0.895100	TGCAGCAGCCCCTACTTTTG	60.895	55.000	0.00	0.00	41.13	2.44
3035	9668	0.895559	GTGCAGCAGCCCCTACTTTT	60.896	55.000	0.00	0.00	41.13	2.27
3036	9669	1.303643	GTGCAGCAGCCCCTACTTT	60.304	57.895	0.00	0.00	41.13	2.66
3037	9670	2.352805	GTGCAGCAGCCCCTACTT	59.647	61.111	0.00	0.00	41.13	2.24
3038	9671	2.930019	TGTGCAGCAGCCCCTACT	60.930	61.111	0.00	0.00	41.13	2.57
3039	9672	2.437359	CTGTGCAGCAGCCCCTAC	60.437	66.667	0.00	0.00	41.13	3.18
3047	9680	3.807631	GACGGACCACTGTGCAGCA	62.808	63.158	1.29	0.00	35.56	4.41
3048	9681	3.044305	GACGGACCACTGTGCAGC	61.044	66.667	1.29	0.00	35.56	5.25
3049	9682	2.357517	GGACGGACCACTGTGCAG	60.358	66.667	1.29	0.00	42.12	4.41
3050	9683	3.936203	GGGACGGACCACTGTGCA	61.936	66.667	1.29	0.00	43.87	4.57
3051	9684	4.699522	GGGGACGGACCACTGTGC	62.700	72.222	1.29	0.00	41.87	4.57
3052	9685	3.238497	TGGGGACGGACCACTGTG	61.238	66.667	0.00	0.00	43.74	3.66
3053	9686	2.923035	CTGGGGACGGACCACTGT	60.923	66.667	0.00	0.00	43.74	3.55
3054	9687	4.394712	GCTGGGGACGGACCACTG	62.395	72.222	0.00	0.62	43.74	3.66
3082	9715	3.040763	GGAGCTCATCATCGCGCC	61.041	66.667	17.19	0.00	38.86	6.53
3097	9730	1.687146	AGAGCTGCTCCCGAATGGA	60.687	57.895	25.09	0.00	42.41	3.41
3098	9731	1.523258	CAGAGCTGCTCCCGAATGG	60.523	63.158	25.09	3.82	0.00	3.16
3186	9819	4.441792	CCCACATCACGTCAGATAAATCA	58.558	43.478	0.00	0.00	0.00	2.57
3214	9847	3.492421	AATAGCCAACATGCAAAGTCG	57.508	42.857	0.00	0.00	0.00	4.18
3241	9874	7.796958	AAAAAGAACACAAGAACTTCTTTCG	57.203	32.000	0.92	0.00	41.33	3.46
3393	10027	4.739228	TCATTTTGTTGTTGTCGATGCAAG	59.261	37.500	0.00	0.00	0.00	4.01
3401	10035	6.728200	TCAGATCAGTCATTTTGTTGTTGTC	58.272	36.000	0.00	0.00	0.00	3.18
3421	10055	4.591929	TGATGTGCTCATCCAAAATCAGA	58.408	39.130	22.44	1.68	46.96	3.27
3476	10111	7.015584	ACCATTTCCAGCAAGTAAGAGAAAAAT	59.984	33.333	0.00	0.00	0.00	1.82
3492	10127	4.402474	CCCCTTAGCTTTTACCATTTCCAG	59.598	45.833	0.00	0.00	0.00	3.86
3539	10175	5.432885	AACATTTTCTACTCCCAACGTTG	57.567	39.130	21.47	21.47	0.00	4.10
3567	10208	4.458989	TGTAGGAACATGCCATGACTTTTC	59.541	41.667	12.53	4.50	0.00	2.29
3601	10242	4.183686	CCTTGCGCGGCATCCAAG	62.184	66.667	8.83	12.25	38.76	3.61
3610	10251	1.947934	GCTGCATTTTTCCTTGCGCG	61.948	55.000	0.00	0.00	41.80	6.86
3611	10252	0.945265	TGCTGCATTTTTCCTTGCGC	60.945	50.000	0.00	0.00	41.80	6.09
3615	10256	5.453762	GCCCTATAATGCTGCATTTTTCCTT	60.454	40.000	30.35	10.16	35.54	3.36
3624	10265	2.290514	GGAGATGCCCTATAATGCTGCA	60.291	50.000	4.13	4.13	36.23	4.41
3625	10266	2.026449	AGGAGATGCCCTATAATGCTGC	60.026	50.000	0.00	0.00	37.37	5.25

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.