AutoCloner

Multiple sequence alignment - TraesCS1B01G300000

Loading Multiple Alignment...

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	TraesCS1B01G300000	chr1B	100.000	6194	0	0	1	6194	520780259	520786452	0.000000e+00	11439.0
1	TraesCS1B01G300000	chr1D	94.318	6248	198	72	2	6189	387422373	387428523	0.000000e+00	9426.0
2	TraesCS1B01G300000	chr1A	95.644	4431	125	29	1801	6189	487089598	487094002	0.000000e+00	7051.0
3	TraesCS1B01G300000	chr1A	90.944	1049	58	16	759	1783	487088510	487089545	0.000000e+00	1376.0
4	TraesCS1B01G300000	chr1A	84.134	479	66	6	4179	4650	403390326	403390801	7.320000e-124	455.0
5	TraesCS1B01G300000	chr7D	81.186	877	114	22	4179	5037	530712659	530713502	0.000000e+00	658.0
6	TraesCS1B01G300000	chr7D	86.371	587	70	6	38	618	186793190	186793772	3.150000e-177	632.0
7	TraesCS1B01G300000	chr7D	84.577	603	85	7	15	616	630507958	630507363	5.350000e-165	592.0
8	TraesCS1B01G300000	chr7B	81.050	876	116	23	4179	5036	570062779	570063622	0.000000e+00	652.0
9	TraesCS1B01G300000	chr7B	85.861	389	49	3	4179	4562	570173783	570174170	5.780000e-110	409.0
10	TraesCS1B01G300000	chr3A	85.089	617	86	6	2	616	640842108	640842720	5.270000e-175	625.0
11	TraesCS1B01G300000	chr3A	83.654	208	23	5	1374	1581	374728692	374728888	1.060000e-42	185.0
12	TraesCS1B01G300000	chr5A	84.590	610	85	8	2	608	539071777	539071174	1.150000e-166	597.0
13	TraesCS1B01G300000	chr5A	80.492	528	67	24	4524	5037	670228542	670229047	7.580000e-99	372.0
14	TraesCS1B01G300000	chr5A	85.833	120	16	1	4532	4650	640561166	640561047	6.520000e-25	126.0
15	TraesCS1B01G300000	chr4D	84.160	625	81	14	2	616	78863438	78862822	1.920000e-164	590.0
16	TraesCS1B01G300000	chr4D	85.052	582	84	2	43	624	399731100	399730522	1.920000e-164	590.0
17	TraesCS1B01G300000	chr4D	81.495	535	62	19	4524	5044	488358241	488357730	7.480000e-109	405.0
18	TraesCS1B01G300000	chr6B	84.590	597	87	4	12	607	626462146	626461554	6.920000e-164	588.0
19	TraesCS1B01G300000	chr6B	94.444	36	2	0	5159	5194	39197852	39197887	8.670000e-04	56.5
20	TraesCS1B01G300000	chr4B	83.575	621	95	4	1	616	666298475	666299093	5.380000e-160	575.0
21	TraesCS1B01G300000	chr4B	80.943	488	56	13	4524	4982	624402876	624402397	9.880000e-93	351.0
22	TraesCS1B01G300000	chr7A	78.947	266	30	16	4972	5215	610941662	610941923	2.310000e-34	158.0
23	TraesCS1B01G300000	chr2B	85.437	103	11	3	4729	4827	289174835	289174733	3.050000e-18	104.0
24	TraesCS1B01G300000	chr5D	94.737	38	2	0	1218	1255	222435992	222435955	6.710000e-05	60.2

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	TraesCS1B01G300000	chr1B	520780259	520786452	6193	False	11439.0	11439	100.000	1	6194	1	chr1B.!!$F1	6193
1	TraesCS1B01G300000	chr1D	387422373	387428523	6150	False	9426.0	9426	94.318	2	6189	1	chr1D.!!$F1	6187
2	TraesCS1B01G300000	chr1A	487088510	487094002	5492	False	4213.5	7051	93.294	759	6189	2	chr1A.!!$F2	5430
3	TraesCS1B01G300000	chr7D	530712659	530713502	843	False	658.0	658	81.186	4179	5037	1	chr7D.!!$F2	858
4	TraesCS1B01G300000	chr7D	186793190	186793772	582	False	632.0	632	86.371	38	618	1	chr7D.!!$F1	580
5	TraesCS1B01G300000	chr7D	630507363	630507958	595	True	592.0	592	84.577	15	616	1	chr7D.!!$R1	601
6	TraesCS1B01G300000	chr7B	570062779	570063622	843	False	652.0	652	81.050	4179	5036	1	chr7B.!!$F1	857
7	TraesCS1B01G300000	chr3A	640842108	640842720	612	False	625.0	625	85.089	2	616	1	chr3A.!!$F2	614
8	TraesCS1B01G300000	chr5A	539071174	539071777	603	True	597.0	597	84.590	2	608	1	chr5A.!!$R1	606
9	TraesCS1B01G300000	chr5A	670228542	670229047	505	False	372.0	372	80.492	4524	5037	1	chr5A.!!$F1	513
10	TraesCS1B01G300000	chr4D	78862822	78863438	616	True	590.0	590	84.160	2	616	1	chr4D.!!$R1	614
11	TraesCS1B01G300000	chr4D	399730522	399731100	578	True	590.0	590	85.052	43	624	1	chr4D.!!$R2	581
12	TraesCS1B01G300000	chr4D	488357730	488358241	511	True	405.0	405	81.495	4524	5044	1	chr4D.!!$R3	520
13	TraesCS1B01G300000	chr6B	626461554	626462146	592	True	588.0	588	84.590	12	607	1	chr6B.!!$R1	595
14	TraesCS1B01G300000	chr4B	666298475	666299093	618	False	575.0	575	83.575	1	616	1	chr4B.!!$F1	615

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
477	488	0.104304	GGTATGGGAGCGACGACAAT	59.896	55.000	0.00	0.00	0.00	2.71	F
971	1013	0.318441	GGTCCAAGCAAAAGGAAGCC	59.682	55.000	0.00	0.00	35.29	4.35	F
1912	2023	0.386113	GGAGAAGGAAGATCGACCCG	59.614	60.000	7.43	0.00	0.00	5.28	F
2138	2249	0.980423	AAGAGGTCAAGGAGGTCAGC	59.020	55.000	0.00	0.00	0.00	4.26	F
3104	3221	1.888512	CCAACATGGGGAACTCTGTTG	59.111	52.381	0.00	7.17	44.70	3.33	F
3351	3468	1.359848	AACGGTATTGCTCTTGCTCG	58.640	50.000	0.00	0.00	40.48	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2120	2231	0.178921	TGCTGACCTCCTTGACCTCT	60.179	55.000	0.00	0.00	0.00	3.69	R
2767	2884	0.109272	GTCGATCGGAGTGCTGTCAA	60.109	55.000	16.41	0.00	0.00	3.18	R
3104	3221	4.767255	CACCCTGGAGTGCTCGCC	62.767	72.222	1.11	1.11	0.00	5.54	R
3267	3384	5.106396	GCATCACCAGAAGGATATATGCAAC	60.106	44.000	7.02	0.33	38.12	4.17	R
4302	4428	1.466167	CTGATGAAAGGAGTTGCACCG	59.534	52.381	0.00	0.00	0.00	4.94	R
5315	5474	2.821546	CGGCAGCAGCTATAACTAACA	58.178	47.619	0.00	0.00	41.70	2.41	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
52	54	0.809385	TTCTCTTCGATCTTCGCCGT	59.191	50.000	0.00	0.00	40.21	5.68
227	236	1.338136	GGGCTCCGATCCTCCTCAAA	61.338	60.000	0.00	0.00	0.00	2.69
243	252	2.546368	CTCAAATTCGTTTGTCGGGACA	59.454	45.455	0.00	0.00	39.98	4.02
434	445	1.004918	CGAAGACTTCCCGGCTGTT	60.005	57.895	9.63	0.00	0.00	3.16
442	453	0.828022	TTCCCGGCTGTTATCGACAT	59.172	50.000	0.00	0.00	37.69	3.06
477	488	0.104304	GGTATGGGAGCGACGACAAT	59.896	55.000	0.00	0.00	0.00	2.71
573	585	2.073252	TGTTTGGGGTGCATTGTACA	57.927	45.000	7.21	0.00	0.00	2.90
673	690	3.782656	TTTTTGGGACAGAGGGAGTAC	57.217	47.619	0.00	0.00	42.39	2.73
677	694	2.915869	TGGGACAGAGGGAGTACATTT	58.084	47.619	0.00	0.00	0.00	2.32
703	720	7.650834	TTTTGAACTTTTCAGGAGTGTTTTG	57.349	32.000	0.00	0.00	41.38	2.44
707	724	5.500645	ACTTTTCAGGAGTGTTTTGCTAC	57.499	39.130	0.00	0.00	0.00	3.58
722	739	9.341899	GTGTTTTGCTACTGGTTTGATTAATAG	57.658	33.333	0.00	0.00	0.00	1.73
723	740	9.073475	TGTTTTGCTACTGGTTTGATTAATAGT	57.927	29.630	0.00	0.00	0.00	2.12
791	813	6.866770	TCTTTTAGATCACTGTACGTCCAAAG	59.133	38.462	0.00	0.00	0.00	2.77
803	825	2.498078	ACGTCCAAAGGCTTTTTCCAAA	59.502	40.909	10.36	0.00	0.00	3.28
805	827	3.308595	CGTCCAAAGGCTTTTTCCAAAAC	59.691	43.478	10.36	0.69	0.00	2.43
806	828	4.257731	GTCCAAAGGCTTTTTCCAAAACA	58.742	39.130	10.36	0.00	0.00	2.83
807	829	4.697828	GTCCAAAGGCTTTTTCCAAAACAA	59.302	37.500	10.36	0.00	0.00	2.83
851	873	1.677300	TGGCAAATGGCACCTACCG	60.677	57.895	5.46	0.00	46.12	4.02
858	881	4.814294	GGCACCTACCGGCACTCG	62.814	72.222	0.00	0.00	38.88	4.18
880	903	2.280119	GCACAGTCACGTCTGGCA	60.280	61.111	8.89	0.00	39.48	4.92
970	1012	1.000171	CAGGTCCAAGCAAAAGGAAGC	60.000	52.381	0.00	0.00	35.29	3.86
971	1013	0.318441	GGTCCAAGCAAAAGGAAGCC	59.682	55.000	0.00	0.00	35.29	4.35
973	1015	1.178534	TCCAAGCAAAAGGAAGCCGG	61.179	55.000	0.00	0.00	0.00	6.13
1074	1140	1.822371	GTTCTCCTCGCTTTCTCCTCT	59.178	52.381	0.00	0.00	0.00	3.69
1329	1398	4.135153	CTGGCCTCGAGGGTCACG	62.135	72.222	32.06	6.67	45.98	4.35
1535	1604	3.960998	GTACGTGCGCGCGATCAG	61.961	66.667	45.30	22.53	42.83	2.90
1581	1651	1.958205	CTCCCGCAATCTCGATGCC	60.958	63.158	4.00	0.00	40.72	4.40
1598	1668	4.380761	CGATGCCCTCTGAATCTCTGATAG	60.381	50.000	0.00	0.00	0.00	2.08
1601	1671	4.085733	GCCCTCTGAATCTCTGATAGCTA	58.914	47.826	0.00	0.00	0.00	3.32
1635	1705	1.202222	CCGGCAAAGCATGTCAGAATC	60.202	52.381	0.00	0.00	31.20	2.52
1667	1743	6.377327	TCTCTTTTCCAAAACATGTCAGAC	57.623	37.500	0.00	0.00	0.00	3.51
1720	1796	1.666209	GCCACATTGGTTGATCCGGG	61.666	60.000	0.00	0.00	40.46	5.73
1767	1843	7.652105	TCAGAGGATAATTAGCAAACGTATCAC	59.348	37.037	2.72	0.00	0.00	3.06
1790	1866	4.142513	CCTTGAAACTGAATCTTAGGCTGC	60.143	45.833	0.00	0.00	0.00	5.25
1861	1972	1.153289	CATGGCGGACTCCAAGGAG	60.153	63.158	14.44	14.44	46.91	3.69
1912	2023	0.386113	GGAGAAGGAAGATCGACCCG	59.614	60.000	7.43	0.00	0.00	5.28
1975	2086	5.041191	AGGAGATGTCTGACAACAACTTT	57.959	39.130	15.31	0.00	33.02	2.66
2033	2144	5.669164	AAGCTCTACCTTACCTTCTCTTG	57.331	43.478	0.00	0.00	0.00	3.02
2034	2145	4.936802	AGCTCTACCTTACCTTCTCTTGA	58.063	43.478	0.00	0.00	0.00	3.02
2068	2179	2.125512	GCCGGCGTCTTGATGAGT	60.126	61.111	12.58	0.00	0.00	3.41
2102	2213	2.048597	TGCGACAAGAACGGCGAT	60.049	55.556	16.62	0.00	0.00	4.58
2120	2231	3.329386	CGATGGAAAGCTCACAGAAGAA	58.671	45.455	0.00	0.00	0.00	2.52
2138	2249	0.980423	AAGAGGTCAAGGAGGTCAGC	59.020	55.000	0.00	0.00	0.00	4.26
2550	2667	3.118884	GCCCAATGCAGAAACAGATTCAT	60.119	43.478	0.00	0.00	40.72	2.57
2844	2961	6.598064	ACATAAACTTCCACAAGGTACATAGC	59.402	38.462	0.00	0.00	33.37	2.97
3104	3221	1.888512	CCAACATGGGGAACTCTGTTG	59.111	52.381	0.00	7.17	44.70	3.33
3351	3468	1.359848	AACGGTATTGCTCTTGCTCG	58.640	50.000	0.00	0.00	40.48	5.03
4108	4234	2.512515	GCAGAAGGCGCGGAAGAT	60.513	61.111	8.83	0.00	0.00	2.40
4302	4428	6.070824	TCCTTTTTCTTATTGGCCTTGGAATC	60.071	38.462	3.32	0.00	0.00	2.52
5024	5181	6.147581	CACCTGATCAAAATTGAAGTGTCAG	58.852	40.000	13.69	13.69	41.13	3.51
5100	5259	2.890311	TGCAGGTGTTTTCTATTGTGGG	59.110	45.455	0.00	0.00	0.00	4.61
5315	5474	8.090788	ACTATATGGAGTGAAAAGTATGTGGT	57.909	34.615	0.00	0.00	0.00	4.16
5522	5683	3.343941	TGAAACAAGATTACCCTCCGG	57.656	47.619	0.00	0.00	0.00	5.14
5580	5741	5.876357	TGTAAACCAAGTAGGAGCATTTCT	58.124	37.500	0.00	0.00	41.22	2.52
5595	5757	3.696051	GCATTTCTAGTCAATCTGCCCAA	59.304	43.478	0.00	0.00	0.00	4.12
5709	5872	6.199154	GCACACAAGCACATACTACTACATAG	59.801	42.308	0.00	0.00	36.89	2.23
5963	6135	1.923204	CAAGATCTGACGAGAAAGCCG	59.077	52.381	0.00	0.00	0.00	5.52
5964	6136	0.457851	AGATCTGACGAGAAAGCCGG	59.542	55.000	0.00	0.00	0.00	6.13
6000	6173	0.526211	CGTTAGGGGCTTTTGCTTCC	59.474	55.000	0.00	0.00	46.54	3.46
6008	6183	2.621668	GGGCTTTTGCTTCCTATCAGGT	60.622	50.000	0.00	0.00	46.54	4.00
6013	6188	3.906720	TTGCTTCCTATCAGGTACACC	57.093	47.619	0.00	0.00	36.53	4.16
6068	6243	3.452627	GGATAGACCAGTGAACCAGTGAT	59.547	47.826	3.54	0.00	36.99	3.06
6069	6244	2.847327	AGACCAGTGAACCAGTGATG	57.153	50.000	3.54	0.00	36.99	3.07
6070	6245	1.160137	GACCAGTGAACCAGTGATGC	58.840	55.000	3.54	0.00	36.99	3.91
6071	6246	0.473755	ACCAGTGAACCAGTGATGCA	59.526	50.000	3.54	0.00	36.99	3.96
6072	6247	1.133823	ACCAGTGAACCAGTGATGCAA	60.134	47.619	0.00	0.00	36.99	4.08
6189	6370	1.628846	AGGACGCCTGTTCATAAGGTT	59.371	47.619	0.00	0.00	37.13	3.50
6190	6371	2.039879	AGGACGCCTGTTCATAAGGTTT	59.960	45.455	0.00	0.00	37.13	3.27
6191	6372	2.161609	GGACGCCTGTTCATAAGGTTTG	59.838	50.000	0.00	0.00	37.13	2.93
6192	6373	3.071479	GACGCCTGTTCATAAGGTTTGA	58.929	45.455	0.00	0.00	37.13	2.69
6193	6374	3.074412	ACGCCTGTTCATAAGGTTTGAG	58.926	45.455	0.00	0.00	37.13	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	0.035343	GGCTTTCCCTAGTCGCCTTT	60.035	55.000	0.00	0.00	37.76	3.11
52	54	2.508439	GCGAATTCACGGGCTCGA	60.508	61.111	15.95	0.00	40.11	4.04
63	65	4.176752	GCGGAGGGGAGGCGAATT	62.177	66.667	0.00	0.00	0.00	2.17
104	109	0.988678	GCACCAGGAATACCCTCCCT	60.989	60.000	0.00	0.00	45.60	4.20
124	129	6.406624	CCAAAACTCTACCTATCTAAGCCGAA	60.407	42.308	0.00	0.00	0.00	4.30
227	236	0.395312	ACCTGTCCCGACAAACGAAT	59.605	50.000	0.00	0.00	45.77	3.34
434	445	1.070134	GCCAGCCTAACCATGTCGATA	59.930	52.381	0.00	0.00	0.00	2.92
442	453	2.808761	TACCGGAGCCAGCCTAACCA	62.809	60.000	9.46	0.00	0.00	3.67
548	560	6.437477	TGTACAATGCACCCCAAACATAATAA	59.563	34.615	0.00	0.00	0.00	1.40
549	561	5.952347	TGTACAATGCACCCCAAACATAATA	59.048	36.000	0.00	0.00	0.00	0.98
624	641	6.340522	AGTTCTGGGATTTTTGTCAAACTTG	58.659	36.000	0.00	0.00	0.00	3.16
680	697	5.637387	GCAAAACACTCCTGAAAAGTTCAAA	59.363	36.000	0.00	0.00	39.58	2.69
683	700	4.998788	AGCAAAACACTCCTGAAAAGTTC	58.001	39.130	0.00	0.00	0.00	3.01
684	701	5.652452	AGTAGCAAAACACTCCTGAAAAGTT	59.348	36.000	0.00	0.00	0.00	2.66
685	702	5.066505	CAGTAGCAAAACACTCCTGAAAAGT	59.933	40.000	0.00	0.00	0.00	2.66
686	703	5.506317	CCAGTAGCAAAACACTCCTGAAAAG	60.506	44.000	0.00	0.00	0.00	2.27
687	704	4.338118	CCAGTAGCAAAACACTCCTGAAAA	59.662	41.667	0.00	0.00	0.00	2.29
688	705	3.882888	CCAGTAGCAAAACACTCCTGAAA	59.117	43.478	0.00	0.00	0.00	2.69
689	706	3.118038	ACCAGTAGCAAAACACTCCTGAA	60.118	43.478	0.00	0.00	0.00	3.02
690	707	2.438021	ACCAGTAGCAAAACACTCCTGA	59.562	45.455	0.00	0.00	0.00	3.86
691	708	2.851195	ACCAGTAGCAAAACACTCCTG	58.149	47.619	0.00	0.00	0.00	3.86
692	709	3.577805	AACCAGTAGCAAAACACTCCT	57.422	42.857	0.00	0.00	0.00	3.69
693	710	3.630312	TCAAACCAGTAGCAAAACACTCC	59.370	43.478	0.00	0.00	0.00	3.85
694	711	4.893424	TCAAACCAGTAGCAAAACACTC	57.107	40.909	0.00	0.00	0.00	3.51
695	712	5.852282	AATCAAACCAGTAGCAAAACACT	57.148	34.783	0.00	0.00	0.00	3.55
696	713	9.341899	CTATTAATCAAACCAGTAGCAAAACAC	57.658	33.333	0.00	0.00	0.00	3.32
697	714	9.073475	ACTATTAATCAAACCAGTAGCAAAACA	57.927	29.630	0.00	0.00	0.00	2.83
858	881	3.753539	GACGTGACTGTGCGACGC	61.754	66.667	14.19	14.19	36.56	5.19
1317	1386	1.507174	GAAGGACGTGACCCTCGAG	59.493	63.158	5.13	5.13	32.57	4.04
1535	1604	0.883370	AACAAGAAAGGACGGTCGGC	60.883	55.000	1.43	0.00	0.00	5.54
1581	1651	6.094048	GCTAGTAGCTATCAGAGATTCAGAGG	59.906	46.154	15.16	0.00	38.45	3.69
1598	1668	0.248539	CGGACCGTCAAGCTAGTAGC	60.249	60.000	14.62	14.62	42.84	3.58
1601	1671	3.003113	GCCGGACCGTCAAGCTAGT	62.003	63.158	13.94	0.00	0.00	2.57
1635	1705	2.743636	TGGAAAAGAGAGCACTACGG	57.256	50.000	0.00	0.00	0.00	4.02
1667	1743	1.067354	GCTGGCCAACCTGAAAATCTG	60.067	52.381	7.01	0.00	37.06	2.90
1717	1793	7.591057	TGATAAATAAACGATTACTACGTCCCG	59.409	37.037	0.00	0.00	43.16	5.14
1759	1835	5.794894	AGATTCAGTTTCAAGGTGATACGT	58.205	37.500	0.00	0.00	34.26	3.57
1760	1836	6.727824	AAGATTCAGTTTCAAGGTGATACG	57.272	37.500	0.00	0.00	34.26	3.06
1767	1843	4.142513	GCAGCCTAAGATTCAGTTTCAAGG	60.143	45.833	0.00	0.00	0.00	3.61
1861	1972	0.297820	CGAATACCTCGCTTGCGAAC	59.702	55.000	18.28	5.78	41.49	3.95
1881	1992	4.207281	TTCTCCTCGCCATCGCCG	62.207	66.667	0.00	0.00	35.26	6.46
1912	2023	0.322008	CCTTGGTGAGTCCTTGCTCC	60.322	60.000	0.00	0.00	37.07	4.70
1942	2053	1.326213	ACATCTCCTCCCAGCACTCG	61.326	60.000	0.00	0.00	0.00	4.18
2014	2125	5.126384	CCACTCAAGAGAAGGTAAGGTAGAG	59.874	48.000	3.73	0.00	0.00	2.43
2048	2159	3.869272	CATCAAGACGCCGGCAGC	61.869	66.667	28.98	17.68	38.52	5.25
2102	2213	3.244353	CCTCTTCTTCTGTGAGCTTTCCA	60.244	47.826	0.00	0.00	0.00	3.53
2120	2231	0.178921	TGCTGACCTCCTTGACCTCT	60.179	55.000	0.00	0.00	0.00	3.69
2157	2268	3.991725	GAGAAGGGCAGGCAGGCAG	62.992	68.421	5.69	0.00	46.44	4.85
2158	2269	4.039092	GAGAAGGGCAGGCAGGCA	62.039	66.667	5.69	0.00	46.44	4.75
2159	2270	4.811364	GGAGAAGGGCAGGCAGGC	62.811	72.222	0.00	0.00	43.27	4.85
2550	2667	0.809385	GGATGAAGTCGACGGTCTCA	59.191	55.000	18.99	15.89	0.00	3.27
2766	2883	0.817654	TCGATCGGAGTGCTGTCAAT	59.182	50.000	16.41	0.00	0.00	2.57
2767	2884	0.109272	GTCGATCGGAGTGCTGTCAA	60.109	55.000	16.41	0.00	0.00	3.18
3104	3221	4.767255	CACCCTGGAGTGCTCGCC	62.767	72.222	1.11	1.11	0.00	5.54
3267	3384	5.106396	GCATCACCAGAAGGATATATGCAAC	60.106	44.000	7.02	0.33	38.12	4.17
3351	3468	5.954335	ACTACTCTTGCCAAACATAATTGC	58.046	37.500	0.00	0.00	0.00	3.56
3896	4020	5.880887	CCCAAATAGGTTCCTTAGTTCTGTC	59.119	44.000	0.00	0.00	34.66	3.51
4136	4262	7.349598	ACATATCCTCAAGCAATTCCTTAAGT	58.650	34.615	0.97	0.00	0.00	2.24
4245	4371	2.987413	TGTAATTTTGAGCTGGTGCG	57.013	45.000	0.00	0.00	45.42	5.34
4302	4428	1.466167	CTGATGAAAGGAGTTGCACCG	59.534	52.381	0.00	0.00	0.00	4.94
4387	4513	3.743269	TGCATCTGCACTCATGTATGAGG	60.743	47.826	22.02	13.64	46.64	3.86
5315	5474	2.821546	CGGCAGCAGCTATAACTAACA	58.178	47.619	0.00	0.00	41.70	2.41
5375	5534	4.222366	AGAAGCAGTCTCACTGATGAATGA	59.778	41.667	7.87	0.00	45.10	2.57
5522	5683	1.082104	CAAGCAAACGAAGCCGACC	60.082	57.895	0.00	0.00	39.50	4.79
5523	5684	0.517316	ATCAAGCAAACGAAGCCGAC	59.483	50.000	0.00	0.00	39.50	4.79
5550	5711	5.505159	GCTCCTACTTGGTTTACAACACAAC	60.505	44.000	0.00	0.00	34.76	3.32
5709	5872	1.410882	CCAGGGATTCCTCTTCGTCTC	59.589	57.143	2.01	0.00	42.67	3.36
5819	5982	6.096695	GGCTGTACTTCTTCTCTTCTTACTG	58.903	44.000	0.00	0.00	0.00	2.74
5945	6117	0.457851	CCGGCTTTCTCGTCAGATCT	59.542	55.000	0.00	0.00	0.00	2.75
6000	6173	3.895232	AACAGCTGGTGTACCTGATAG	57.105	47.619	19.93	3.87	39.03	2.08
6008	6183	5.336372	GGCATTTTATCAAACAGCTGGTGTA	60.336	40.000	19.93	3.36	39.03	2.90
6013	6188	7.042321	CCATATTGGCATTTTATCAAACAGCTG	60.042	37.037	13.48	13.48	0.00	4.24
6040	6215	5.928976	TGGTTCACTGGTCTATCCATATTG	58.071	41.667	0.00	0.00	46.12	1.90
6041	6216	5.667626	ACTGGTTCACTGGTCTATCCATATT	59.332	40.000	0.00	0.00	46.12	1.28
6042	6217	5.070981	CACTGGTTCACTGGTCTATCCATAT	59.929	44.000	0.00	0.00	46.12	1.78
6043	6218	4.405680	CACTGGTTCACTGGTCTATCCATA	59.594	45.833	0.00	0.00	46.12	2.74
6044	6219	3.198635	CACTGGTTCACTGGTCTATCCAT	59.801	47.826	0.00	0.00	46.12	3.41
6045	6220	2.567169	CACTGGTTCACTGGTCTATCCA	59.433	50.000	0.00	0.00	45.01	3.41
6046	6221	2.832129	TCACTGGTTCACTGGTCTATCC	59.168	50.000	0.00	0.00	0.00	2.59
6047	6222	4.437239	CATCACTGGTTCACTGGTCTATC	58.563	47.826	0.00	0.00	0.00	2.08
6048	6223	3.369892	GCATCACTGGTTCACTGGTCTAT	60.370	47.826	0.00	0.00	0.00	1.98
6049	6224	2.028112	GCATCACTGGTTCACTGGTCTA	60.028	50.000	0.00	0.00	0.00	2.59
6052	6227	0.473755	TGCATCACTGGTTCACTGGT	59.526	50.000	0.00	0.00	0.00	4.00
6068	6243	1.002576	CTCGAGTGTTGTTGCATTGCA	60.003	47.619	7.38	7.38	36.47	4.08
6069	6244	1.678360	CTCGAGTGTTGTTGCATTGC	58.322	50.000	3.62	0.46	0.00	3.56
6070	6245	1.002576	TGCTCGAGTGTTGTTGCATTG	60.003	47.619	15.13	0.00	0.00	2.82
6071	6246	1.308047	TGCTCGAGTGTTGTTGCATT	58.692	45.000	15.13	0.00	0.00	3.56
6072	6247	1.265095	CTTGCTCGAGTGTTGTTGCAT	59.735	47.619	15.13	0.00	0.00	3.96
6102	6277	8.668353	ACTATGTCTTACAACTGTAAATGCATG	58.332	33.333	0.00	0.00	39.70	4.06
6111	6286	5.701290	GGCTCAAACTATGTCTTACAACTGT	59.299	40.000	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.