AutoCloner

Multiple sequence alignment - TraesCS2A01G230300

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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	TraesCS2A01G230300	chr2A	100.000	2027	0	0	256	2282	262821962	262819936	0.000000e+00	3744
1	TraesCS2A01G230300	chr2A	96.763	834	27	0	1449	2282	32281981	32282814	0.000000e+00	1391
2	TraesCS2A01G230300	chr2A	96.403	834	30	0	1449	2282	155306251	155305418	0.000000e+00	1375
3	TraesCS2A01G230300	chr2A	96.283	834	31	0	1449	2282	155374650	155373817	0.000000e+00	1369
4	TraesCS2A01G230300	chr2A	96.283	834	31	0	1449	2282	763555969	763555136	0.000000e+00	1369
5	TraesCS2A01G230300	chr2A	86.767	529	64	5	925	1450	702409727	702410252	3.270000e-163	584
6	TraesCS2A01G230300	chr2A	100.000	88	0	0	1	88	262822217	262822130	1.810000e-36	163
7	TraesCS2A01G230300	chr7A	97.112	831	24	0	1452	2282	690693699	690692869	0.000000e+00	1402
8	TraesCS2A01G230300	chr7A	97.727	88	2	0	1	88	112772206	112772293	3.930000e-33	152
9	TraesCS2A01G230300	chr6A	96.643	834	28	0	1449	2282	337298015	337297182	0.000000e+00	1386
10	TraesCS2A01G230300	chr6A	96.287	835	30	1	1449	2282	92234290	92235124	0.000000e+00	1369
11	TraesCS2A01G230300	chr6A	86.239	545	70	5	908	1450	610215995	610216536	9.080000e-164	586
12	TraesCS2A01G230300	chr3A	96.287	835	29	2	1449	2282	2497589	2498422	0.000000e+00	1369
13	TraesCS2A01G230300	chr5A	96.283	834	30	1	1449	2282	217142339	217143171	0.000000e+00	1367
14	TraesCS2A01G230300	chr1B	87.060	966	77	18	344	1289	588245127	588244190	0.000000e+00	1048
15	TraesCS2A01G230300	chr1B	78.771	179	20	11	522	685	497825890	497826065	1.120000e-18	104
16	TraesCS2A01G230300	chr1A	87.121	528	64	3	925	1450	353279788	353280313	1.510000e-166	595
17	TraesCS2A01G230300	chr1A	86.981	530	65	3	925	1452	97261565	97262092	5.430000e-166	593
18	TraesCS2A01G230300	chr1A	86.654	532	69	2	925	1455	563186131	563185601	2.530000e-164	588
19	TraesCS2A01G230300	chr1A	97.727	88	2	0	1	88	509107032	509106945	3.930000e-33	152
20	TraesCS2A01G230300	chr6B	86.289	547	65	9	908	1450	647587320	647586780	9.080000e-164	586
21	TraesCS2A01G230300	chr4B	86.081	546	70	5	908	1450	460376078	460376620	1.170000e-162	582
22	TraesCS2A01G230300	chr7D	86.004	543	70	4	909	1446	123493743	123493202	5.470000e-161	577
23	TraesCS2A01G230300	chr2D	84.982	546	78	4	908	1450	19527781	19527237	3.310000e-153	551
24	TraesCS2A01G230300	chr2D	81.073	671	78	32	256	910	19528470	19527833	7.330000e-135	490
25	TraesCS2A01G230300	chr3D	81.614	669	75	31	256	910	7706021	7706655	5.620000e-141	510
26	TraesCS2A01G230300	chr3B	98.864	88	1	0	1	88	702176327	702176414	8.440000e-35	158
27	TraesCS2A01G230300	chr5B	97.727	88	2	0	1	88	74014416	74014329	3.930000e-33	152
28	TraesCS2A01G230300	chr4D	97.727	88	2	0	1	88	54587997	54588084	3.930000e-33	152
29	TraesCS2A01G230300	chr4A	97.727	88	2	0	1	88	183882756	183882843	3.930000e-33	152
30	TraesCS2A01G230300	chr6D	96.591	88	3	0	1	88	14513508	14513595	1.830000e-31	147
31	TraesCS2A01G230300	chr1D	96.591	88	3	0	1	88	83852689	83852602	1.830000e-31	147
32	TraesCS2A01G230300	chr1D	96.591	88	3	0	1	88	308654543	308654630	1.830000e-31	147

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	TraesCS2A01G230300	chr2A	262819936	262822217	2281	True	1953.5	3744	100.0000	1	2282	2	chr2A.!!$R4	2281
1	TraesCS2A01G230300	chr2A	32281981	32282814	833	False	1391.0	1391	96.7630	1449	2282	1	chr2A.!!$F1	833
2	TraesCS2A01G230300	chr2A	155305418	155306251	833	True	1375.0	1375	96.4030	1449	2282	1	chr2A.!!$R1	833
3	TraesCS2A01G230300	chr2A	155373817	155374650	833	True	1369.0	1369	96.2830	1449	2282	1	chr2A.!!$R2	833
4	TraesCS2A01G230300	chr2A	763555136	763555969	833	True	1369.0	1369	96.2830	1449	2282	1	chr2A.!!$R3	833
5	TraesCS2A01G230300	chr2A	702409727	702410252	525	False	584.0	584	86.7670	925	1450	1	chr2A.!!$F2	525
6	TraesCS2A01G230300	chr7A	690692869	690693699	830	True	1402.0	1402	97.1120	1452	2282	1	chr7A.!!$R1	830
7	TraesCS2A01G230300	chr6A	337297182	337298015	833	True	1386.0	1386	96.6430	1449	2282	1	chr6A.!!$R1	833
8	TraesCS2A01G230300	chr6A	92234290	92235124	834	False	1369.0	1369	96.2870	1449	2282	1	chr6A.!!$F1	833
9	TraesCS2A01G230300	chr6A	610215995	610216536	541	False	586.0	586	86.2390	908	1450	1	chr6A.!!$F2	542
10	TraesCS2A01G230300	chr3A	2497589	2498422	833	False	1369.0	1369	96.2870	1449	2282	1	chr3A.!!$F1	833
11	TraesCS2A01G230300	chr5A	217142339	217143171	832	False	1367.0	1367	96.2830	1449	2282	1	chr5A.!!$F1	833
12	TraesCS2A01G230300	chr1B	588244190	588245127	937	True	1048.0	1048	87.0600	344	1289	1	chr1B.!!$R1	945
13	TraesCS2A01G230300	chr1A	353279788	353280313	525	False	595.0	595	87.1210	925	1450	1	chr1A.!!$F2	525
14	TraesCS2A01G230300	chr1A	97261565	97262092	527	False	593.0	593	86.9810	925	1452	1	chr1A.!!$F1	527
15	TraesCS2A01G230300	chr1A	563185601	563186131	530	True	588.0	588	86.6540	925	1455	1	chr1A.!!$R2	530
16	TraesCS2A01G230300	chr6B	647586780	647587320	540	True	586.0	586	86.2890	908	1450	1	chr6B.!!$R1	542
17	TraesCS2A01G230300	chr4B	460376078	460376620	542	False	582.0	582	86.0810	908	1450	1	chr4B.!!$F1	542
18	TraesCS2A01G230300	chr7D	123493202	123493743	541	True	577.0	577	86.0040	909	1446	1	chr7D.!!$R1	537
19	TraesCS2A01G230300	chr2D	19527237	19528470	1233	True	520.5	551	83.0275	256	1450	2	chr2D.!!$R1	1194
20	TraesCS2A01G230300	chr3D	7706021	7706655	634	False	510.0	510	81.6140	256	910	1	chr3D.!!$F1	654

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
706	725	0.166814	CAACTTCAGGCGCTACAAGC	59.833	55.0	7.64	0.0	38.02	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2110	2211	2.766263	CAGCCACCACTACCTCATCTTA	59.234	50.0	0.0	0.0	0.0	2.1	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
18	19	3.623848	TTGTCTTGCGTACCATGCT	57.376	47.368	0.00	0.00	0.00	3.79
19	20	1.890876	TTGTCTTGCGTACCATGCTT	58.109	45.000	0.00	0.00	0.00	3.91
20	21	1.438651	TGTCTTGCGTACCATGCTTC	58.561	50.000	0.00	0.00	0.00	3.86
21	22	0.727398	GTCTTGCGTACCATGCTTCC	59.273	55.000	0.00	0.00	0.00	3.46
22	23	0.739462	TCTTGCGTACCATGCTTCCG	60.739	55.000	0.00	0.00	0.00	4.30
23	24	1.705337	CTTGCGTACCATGCTTCCGG	61.705	60.000	0.00	0.00	0.00	5.14
24	25	3.573491	GCGTACCATGCTTCCGGC	61.573	66.667	0.00	0.00	42.22	6.13
25	26	3.261951	CGTACCATGCTTCCGGCG	61.262	66.667	0.00	0.00	45.43	6.46
26	27	2.895372	GTACCATGCTTCCGGCGG	60.895	66.667	22.51	22.51	45.43	6.13
27	28	4.169696	TACCATGCTTCCGGCGGG	62.170	66.667	27.98	12.42	45.43	6.13
30	31	4.473520	CATGCTTCCGGCGGGTCT	62.474	66.667	27.98	3.72	45.43	3.85
31	32	4.162690	ATGCTTCCGGCGGGTCTC	62.163	66.667	27.98	13.30	45.43	3.36
34	35	3.391382	CTTCCGGCGGGTCTCCTT	61.391	66.667	27.98	0.00	33.83	3.36
35	36	3.372554	CTTCCGGCGGGTCTCCTTC	62.373	68.421	27.98	0.00	33.83	3.46
38	39	4.493747	CGGCGGGTCTCCTTCGAC	62.494	72.222	0.00	0.00	0.00	4.20
39	40	4.493747	GGCGGGTCTCCTTCGACG	62.494	72.222	0.00	0.00	34.75	5.12
40	41	3.745803	GCGGGTCTCCTTCGACGT	61.746	66.667	0.00	0.00	34.75	4.34
41	42	2.178521	CGGGTCTCCTTCGACGTG	59.821	66.667	0.00	0.00	34.75	4.49
42	43	2.330372	CGGGTCTCCTTCGACGTGA	61.330	63.158	0.00	0.00	34.75	4.35
43	44	1.507174	GGGTCTCCTTCGACGTGAG	59.493	63.158	0.00	0.00	34.75	3.51
44	45	1.153997	GGTCTCCTTCGACGTGAGC	60.154	63.158	0.00	0.00	34.75	4.26
45	46	1.587933	GGTCTCCTTCGACGTGAGCT	61.588	60.000	0.00	0.00	34.75	4.09
46	47	0.455295	GTCTCCTTCGACGTGAGCTG	60.455	60.000	0.00	0.00	0.00	4.24
47	48	1.803519	CTCCTTCGACGTGAGCTGC	60.804	63.158	0.00	0.00	0.00	5.25
48	49	3.175240	CCTTCGACGTGAGCTGCG	61.175	66.667	0.00	0.00	0.00	5.18
49	50	3.175240	CTTCGACGTGAGCTGCGG	61.175	66.667	11.28	0.00	0.00	5.69
50	51	3.898627	CTTCGACGTGAGCTGCGGT	62.899	63.158	11.28	0.00	0.00	5.68
51	52	4.700365	TCGACGTGAGCTGCGGTG	62.700	66.667	11.28	4.12	0.00	4.94
54	55	4.687215	ACGTGAGCTGCGGTGCAT	62.687	61.111	11.28	0.00	38.13	3.96
55	56	3.857854	CGTGAGCTGCGGTGCATC	61.858	66.667	0.00	0.00	38.13	3.91
56	57	2.743538	GTGAGCTGCGGTGCATCA	60.744	61.111	0.00	0.00	38.13	3.07
57	58	2.743538	TGAGCTGCGGTGCATCAC	60.744	61.111	0.00	0.00	38.13	3.06
66	67	4.388499	GTGCATCACCCCCGACGT	62.388	66.667	0.00	0.00	0.00	4.34
67	68	4.077184	TGCATCACCCCCGACGTC	62.077	66.667	5.18	5.18	0.00	4.34
69	70	3.445687	CATCACCCCCGACGTCGA	61.446	66.667	37.65	18.21	43.02	4.20
70	71	3.138798	ATCACCCCCGACGTCGAG	61.139	66.667	37.65	26.22	43.02	4.04
75	76	3.512516	CCCCGACGTCGAGGGTAC	61.513	72.222	36.50	6.47	46.17	3.34
76	77	2.747460	CCCGACGTCGAGGGTACA	60.747	66.667	37.65	0.00	42.67	2.90
77	78	2.482374	CCGACGTCGAGGGTACAC	59.518	66.667	37.65	0.00	43.02	2.90
78	79	2.097160	CGACGTCGAGGGTACACG	59.903	66.667	33.35	1.15	43.02	4.49
79	80	2.482374	GACGTCGAGGGTACACGG	59.518	66.667	10.27	0.00	37.86	4.94
80	81	2.281761	ACGTCGAGGGTACACGGT	60.282	61.111	10.27	0.00	37.86	4.83
81	82	2.177531	CGTCGAGGGTACACGGTG	59.822	66.667	6.58	6.58	0.00	4.94
82	83	2.327343	CGTCGAGGGTACACGGTGA	61.327	63.158	16.29	0.00	0.00	4.02
83	84	1.211190	GTCGAGGGTACACGGTGAC	59.789	63.158	16.29	8.49	0.00	3.67
281	283	2.213059	AAGTTAGGGGCCCCACCT	59.787	61.111	42.48	29.56	42.15	4.00
287	289	1.237459	TAGGGGCCCCACCTAGGTAA	61.237	60.000	42.48	12.77	39.54	2.85
372	385	0.463654	TTTCAGGCTTCACGCACACT	60.464	50.000	0.00	0.00	41.67	3.55
396	410	1.298859	GGATCGCAAGCCAAACGAGT	61.299	55.000	0.00	0.00	39.48	4.18
406	420	2.434359	AAACGAGTAGCAGCGGCC	60.434	61.111	4.82	0.00	42.56	6.13
452	466	0.976641	AGCGACCACTTCCTTCATCA	59.023	50.000	0.00	0.00	0.00	3.07
457	471	3.620374	CGACCACTTCCTTCATCATTCAG	59.380	47.826	0.00	0.00	0.00	3.02
526	544	0.657840	CGATCGTGATTTCCCAAGCC	59.342	55.000	7.03	0.00	0.00	4.35
595	613	4.856801	CCGCCGGGCTGTTGCTAT	62.857	66.667	18.34	0.00	39.59	2.97
616	634	7.072961	TGCTATTTCCTAATTCCCTTCTCATCT	59.927	37.037	0.00	0.00	0.00	2.90
638	656	2.025605	TCTTCCTAAGCTAGTCCACCGA	60.026	50.000	0.00	0.00	0.00	4.69
656	675	2.292267	CGATGATTTCAGTTCAGGGGG	58.708	52.381	0.00	0.00	0.00	5.40
659	678	0.332972	GATTTCAGTTCAGGGGGCCT	59.667	55.000	0.84	0.00	0.00	5.19
664	683	1.229951	AGTTCAGGGGGCCTCATCA	60.230	57.895	5.99	0.00	0.00	3.07
669	688	1.005289	AGGGGGCCTCATCATCACT	59.995	57.895	5.99	0.00	0.00	3.41
688	707	0.776810	TCTTGGTCAATTGCTCCCCA	59.223	50.000	14.02	8.72	0.00	4.96
693	712	1.546029	GGTCAATTGCTCCCCAACTTC	59.454	52.381	0.00	0.00	35.99	3.01
700	719	3.249189	TCCCCAACTTCAGGCGCT	61.249	61.111	7.64	0.00	0.00	5.92
701	720	1.899437	CTCCCCAACTTCAGGCGCTA	61.899	60.000	7.64	0.00	0.00	4.26
702	721	1.745489	CCCCAACTTCAGGCGCTAC	60.745	63.158	7.64	0.00	0.00	3.58
703	722	1.003839	CCCAACTTCAGGCGCTACA	60.004	57.895	7.64	0.00	0.00	2.74
704	723	0.605319	CCCAACTTCAGGCGCTACAA	60.605	55.000	7.64	0.00	0.00	2.41
705	724	0.798776	CCAACTTCAGGCGCTACAAG	59.201	55.000	7.64	9.22	0.00	3.16
706	725	0.166814	CAACTTCAGGCGCTACAAGC	59.833	55.000	7.64	0.00	38.02	4.01
726	745	3.106552	GCAAACAGCACACCGACA	58.893	55.556	0.00	0.00	44.79	4.35
727	746	1.654220	GCAAACAGCACACCGACAT	59.346	52.632	0.00	0.00	44.79	3.06
761	780	6.600822	ACGAATTCAACCATCAGATCAGAATT	59.399	34.615	6.22	0.00	37.05	2.17
811	831	0.610687	TCGATGTGTATGTGGCACCA	59.389	50.000	16.26	5.52	36.11	4.17
830	850	7.065563	TGGCACCATTTAATAATTGATGCAAAC	59.934	33.333	14.06	1.09	32.19	2.93
831	851	7.118724	GCACCATTTAATAATTGATGCAAACG	58.881	34.615	8.82	0.00	0.00	3.60
833	853	9.295214	CACCATTTAATAATTGATGCAAACGTA	57.705	29.630	0.00	0.00	0.00	3.57
886	908	4.154015	CCAAGAAACAAGACGTATGCATCA	59.846	41.667	0.19	0.00	0.00	3.07
896	918	4.928020	AGACGTATGCATCAGATAGCAATG	59.072	41.667	0.19	0.00	44.88	2.82
1043	1119	3.376546	GGGCATGTCAGAGAAGTTGATTC	59.623	47.826	0.00	0.00	38.28	2.52
1117	1210	4.020928	TGGTTGTATCGGCTGAAAGAAGTA	60.021	41.667	0.00	0.00	34.07	2.24
1120	1213	6.759827	GGTTGTATCGGCTGAAAGAAGTATTA	59.240	38.462	0.00	0.00	34.07	0.98
1121	1214	7.042658	GGTTGTATCGGCTGAAAGAAGTATTAG	60.043	40.741	0.00	0.00	34.07	1.73
1126	1219	6.106673	TCGGCTGAAAGAAGTATTAGAAAGG	58.893	40.000	0.00	0.00	34.07	3.11
1408	1508	5.182487	GTGTTTATTAAGGGCCCCAAATTG	58.818	41.667	21.43	0.00	0.00	2.32
1411	1511	6.500751	TGTTTATTAAGGGCCCCAAATTGTAA	59.499	34.615	21.43	7.20	0.00	2.41
1505	1605	1.814248	GCTTTGAACGGTCTCCAACCT	60.814	52.381	0.33	0.00	46.87	3.50
1512	1612	2.322658	ACGGTCTCCAACCTGTTCTTA	58.677	47.619	0.00	0.00	46.87	2.10
1691	1791	2.125952	GCAAGGGCCGATGCAAAC	60.126	61.111	25.96	2.97	42.12	2.93
1752	1852	8.780846	ACGTACAAAATATGTATCCAAACTCA	57.219	30.769	0.00	0.00	45.87	3.41
1778	1878	2.969827	GGCAACCCCACAAATCCG	59.030	61.111	0.00	0.00	0.00	4.18
1873	1973	7.918562	GCATACAAGAAAGTGTTTCACCTTTTA	59.081	33.333	2.44	0.00	42.10	1.52
1984	2084	3.170791	ACTCTCAACCGTCATATGCTG	57.829	47.619	0.00	0.00	0.00	4.41
2045	2146	4.458989	TGTAGATGCTCAAAATTCGGCTTT	59.541	37.500	0.00	0.00	0.00	3.51
2133	2234	1.915078	ATGAGGTAGTGGTGGCTGCC	61.915	60.000	12.87	12.87	40.86	4.85
2163	2264	5.934781	AGTTTAGCCCAGAATAAGAGGATG	58.065	41.667	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.804151	GAAGCATGGTACGCAAGACAA	59.196	47.619	0.00	0.00	43.62	3.18
1	2	1.438651	GAAGCATGGTACGCAAGACA	58.561	50.000	0.00	0.00	43.62	3.41
5	6	1.743623	CCGGAAGCATGGTACGCAA	60.744	57.895	14.26	0.00	0.00	4.85
6	7	2.125310	CCGGAAGCATGGTACGCA	60.125	61.111	14.26	0.00	0.00	5.24
7	8	3.573491	GCCGGAAGCATGGTACGC	61.573	66.667	5.05	7.97	42.97	4.42
8	9	3.261951	CGCCGGAAGCATGGTACG	61.262	66.667	5.05	13.13	44.04	3.67
9	10	2.895372	CCGCCGGAAGCATGGTAC	60.895	66.667	5.05	0.00	44.04	3.34
10	11	4.169696	CCCGCCGGAAGCATGGTA	62.170	66.667	5.05	0.00	44.04	3.25
13	14	4.473520	AGACCCGCCGGAAGCATG	62.474	66.667	5.05	0.00	44.04	4.06
14	15	4.162690	GAGACCCGCCGGAAGCAT	62.163	66.667	5.05	0.00	44.04	3.79
17	18	3.372554	GAAGGAGACCCGCCGGAAG	62.373	68.421	5.05	0.00	37.58	3.46
18	19	3.387947	GAAGGAGACCCGCCGGAA	61.388	66.667	5.05	0.00	37.58	4.30
21	22	4.493747	GTCGAAGGAGACCCGCCG	62.494	72.222	0.00	0.00	37.58	6.46
22	23	4.493747	CGTCGAAGGAGACCCGCC	62.494	72.222	0.00	0.00	37.85	6.13
23	24	3.745803	ACGTCGAAGGAGACCCGC	61.746	66.667	0.00	0.00	37.85	6.13
24	25	2.178521	CACGTCGAAGGAGACCCG	59.821	66.667	0.00	0.00	37.85	5.28
25	26	1.507174	CTCACGTCGAAGGAGACCC	59.493	63.158	0.00	0.00	37.85	4.46
26	27	1.153997	GCTCACGTCGAAGGAGACC	60.154	63.158	16.63	0.00	37.85	3.85
27	28	0.455295	CAGCTCACGTCGAAGGAGAC	60.455	60.000	16.63	10.11	37.76	3.36
28	29	1.876664	CAGCTCACGTCGAAGGAGA	59.123	57.895	16.63	7.92	0.00	3.71
29	30	1.803519	GCAGCTCACGTCGAAGGAG	60.804	63.158	0.00	7.74	0.00	3.69
30	31	2.258591	GCAGCTCACGTCGAAGGA	59.741	61.111	0.00	0.00	0.00	3.36
31	32	3.175240	CGCAGCTCACGTCGAAGG	61.175	66.667	0.00	0.00	0.00	3.46
32	33	3.175240	CCGCAGCTCACGTCGAAG	61.175	66.667	0.00	0.00	0.00	3.79
33	34	3.973516	ACCGCAGCTCACGTCGAA	61.974	61.111	0.00	0.00	0.00	3.71
34	35	4.700365	CACCGCAGCTCACGTCGA	62.700	66.667	0.00	0.00	0.00	4.20
37	38	4.687215	ATGCACCGCAGCTCACGT	62.687	61.111	5.06	0.00	43.65	4.49
38	39	3.857854	GATGCACCGCAGCTCACG	61.858	66.667	0.00	0.00	43.65	4.35
39	40	2.743538	TGATGCACCGCAGCTCAC	60.744	61.111	5.76	0.00	45.80	3.51
40	41	2.743538	GTGATGCACCGCAGCTCA	60.744	61.111	5.76	0.00	45.80	4.26
41	42	3.503363	GGTGATGCACCGCAGCTC	61.503	66.667	5.76	1.79	45.80	4.09
49	50	4.388499	ACGTCGGGGGTGATGCAC	62.388	66.667	0.00	0.00	0.00	4.57
50	51	4.077184	GACGTCGGGGGTGATGCA	62.077	66.667	0.00	0.00	0.00	3.96
52	53	3.411418	CTCGACGTCGGGGGTGATG	62.411	68.421	35.05	12.86	40.29	3.07
53	54	3.138798	CTCGACGTCGGGGGTGAT	61.139	66.667	35.05	0.00	40.29	3.06
59	60	2.747460	TGTACCCTCGACGTCGGG	60.747	66.667	35.05	32.90	46.26	5.14
60	61	2.482374	GTGTACCCTCGACGTCGG	59.518	66.667	35.05	24.95	40.29	4.79
61	62	2.097160	CGTGTACCCTCGACGTCG	59.903	66.667	31.30	31.30	41.45	5.12
62	63	2.328099	ACCGTGTACCCTCGACGTC	61.328	63.158	5.18	5.18	0.00	4.34
63	64	2.281761	ACCGTGTACCCTCGACGT	60.282	61.111	0.00	0.00	0.00	4.34
64	65	2.177531	CACCGTGTACCCTCGACG	59.822	66.667	0.00	0.00	0.00	5.12
65	66	1.211190	GTCACCGTGTACCCTCGAC	59.789	63.158	0.00	0.00	0.00	4.20
66	67	2.327343	CGTCACCGTGTACCCTCGA	61.327	63.158	0.00	0.00	0.00	4.04
67	68	2.177531	CGTCACCGTGTACCCTCG	59.822	66.667	0.00	0.00	0.00	4.63
267	268	1.237459	TACCTAGGTGGGGCCCCTAA	61.237	60.000	40.66	20.81	41.11	2.69
287	289	6.503944	AGCCTGCTATACCTAATACCTACAT	58.496	40.000	0.00	0.00	0.00	2.29
296	298	4.813479	GCCTACCTAGCCTGCTATACCTAA	60.813	50.000	0.00	0.00	0.00	2.69
299	301	1.826096	GCCTACCTAGCCTGCTATACC	59.174	57.143	0.00	0.00	0.00	2.73
372	385	0.250684	TTTGGCTTGCGATCCTGTGA	60.251	50.000	0.00	0.00	0.00	3.58
419	433	4.299316	CGCTAATCAAGGCGCGCC	62.299	66.667	42.34	42.34	44.64	6.53
466	481	2.791560	CGTGAAGGATAGCAGATCGTTG	59.208	50.000	10.26	0.00	0.00	4.10
583	601	4.038042	GGAATTAGGAAATAGCAACAGCCC	59.962	45.833	0.00	0.00	0.00	5.19
588	606	6.828785	TGAGAAGGGAATTAGGAAATAGCAAC	59.171	38.462	0.00	0.00	0.00	4.17
595	613	7.516450	AGAAGATGAGAAGGGAATTAGGAAA	57.484	36.000	0.00	0.00	0.00	3.13
616	634	2.758979	CGGTGGACTAGCTTAGGAAGAA	59.241	50.000	0.00	0.00	0.00	2.52
638	656	1.342374	GGCCCCCTGAACTGAAATCAT	60.342	52.381	0.00	0.00	0.00	2.45
656	675	2.093288	TGACCAAGAGTGATGATGAGGC	60.093	50.000	0.00	0.00	0.00	4.70
659	678	4.397103	GCAATTGACCAAGAGTGATGATGA	59.603	41.667	10.34	0.00	0.00	2.92
664	683	3.350833	GGAGCAATTGACCAAGAGTGAT	58.649	45.455	10.34	0.00	0.00	3.06
669	688	0.776810	TGGGGAGCAATTGACCAAGA	59.223	50.000	10.34	0.00	0.00	3.02
688	707	0.955919	GGCTTGTAGCGCCTGAAGTT	60.956	55.000	2.29	0.00	43.62	2.66
726	745	3.187700	GGTTGAATTCGTGAGAGCGTAT	58.812	45.455	0.04	0.00	43.69	3.06
727	746	2.029739	TGGTTGAATTCGTGAGAGCGTA	60.030	45.455	0.04	0.00	43.69	4.42
784	803	3.119137	CCACATACACATCGAGGAACAGA	60.119	47.826	3.06	0.00	0.00	3.41
786	805	2.676750	GCCACATACACATCGAGGAACA	60.677	50.000	3.06	0.00	0.00	3.18
793	813	1.667236	ATGGTGCCACATACACATCG	58.333	50.000	0.00	0.00	39.87	3.84
830	850	6.693315	AACCCACAATCCTGAAAATATACG	57.307	37.500	0.00	0.00	0.00	3.06
831	851	7.996644	TCCTAACCCACAATCCTGAAAATATAC	59.003	37.037	0.00	0.00	0.00	1.47
833	853	6.980577	TCCTAACCCACAATCCTGAAAATAT	58.019	36.000	0.00	0.00	0.00	1.28
834	854	6.395780	TCCTAACCCACAATCCTGAAAATA	57.604	37.500	0.00	0.00	0.00	1.40
835	855	5.269554	TCCTAACCCACAATCCTGAAAAT	57.730	39.130	0.00	0.00	0.00	1.82
886	908	7.233348	TGTTTCCTTTTCCTTTCATTGCTATCT	59.767	33.333	0.00	0.00	0.00	1.98
896	918	7.517614	AGAGAGAATGTTTCCTTTTCCTTTC	57.482	36.000	0.00	0.00	0.00	2.62
998	1074	6.460676	CCCAAAAATCTCCATAGCAGACATTC	60.461	42.308	0.00	0.00	0.00	2.67
1117	1210	8.519799	TTCTTCAACAGTTTCACCTTTCTAAT	57.480	30.769	0.00	0.00	0.00	1.73
1120	1213	7.410120	AATTCTTCAACAGTTTCACCTTTCT	57.590	32.000	0.00	0.00	0.00	2.52
1121	1214	9.750125	AATAATTCTTCAACAGTTTCACCTTTC	57.250	29.630	0.00	0.00	0.00	2.62
1126	1219	9.185192	CCTCAAATAATTCTTCAACAGTTTCAC	57.815	33.333	0.00	0.00	0.00	3.18
1168	1262	7.961326	ATGTAGCCAAATCATTTAACCTCTT	57.039	32.000	0.00	0.00	0.00	2.85
1241	1335	3.126001	TCCTCGATGCAAAGTCACTTT	57.874	42.857	0.00	0.00	33.58	2.66
1374	1474	9.127277	GGCCCTTAATAAACACATCATAGTAAA	57.873	33.333	0.00	0.00	0.00	2.01
1476	1576	0.882927	CCGTTCAAAGCTTCGTCCCA	60.883	55.000	0.00	0.00	0.00	4.37
1691	1791	9.031360	CATAAGAATTTGAAGCATGAAGATTGG	57.969	33.333	0.00	0.00	0.00	3.16
1778	1878	4.530388	CATCATGTTGTTCATCGGCATAC	58.470	43.478	0.00	0.00	34.09	2.39
1845	1945	5.009010	AGGTGAAACACTTTCTTGTATGCTG	59.991	40.000	0.00	0.00	39.98	4.41
1984	2084	6.027749	CCGAAAAATTACTAACATGAGGTGC	58.972	40.000	0.00	0.00	0.00	5.01
2110	2211	2.766263	CAGCCACCACTACCTCATCTTA	59.234	50.000	0.00	0.00	0.00	2.10
2133	2234	7.106239	TCTTATTCTGGGCTAAACTCTTCAAG	58.894	38.462	0.00	0.00	0.00	3.02
2163	2264	6.072112	TGTTGTTCAAGGAAAATAGCACTC	57.928	37.500	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.