AutoCloner

Multiple sequence alignment - TraesCS3B01G262300

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	TraesCS3B01G262300	chr3B	100.000	2339	0	0	1	2339	420878661	420876323	0.000000e+00	4320
1	TraesCS3B01G262300	chr3B	88.670	1271	116	14	108	1360	1790694	1789434	0.000000e+00	1524
2	TraesCS3B01G262300	chr3A	94.128	1652	86	8	90	1739	434851504	434849862	0.000000e+00	2503
3	TraesCS3B01G262300	chr3A	91.333	600	22	4	1741	2339	434844609	434844039	0.000000e+00	793
4	TraesCS3B01G262300	chr3D	93.921	1612	80	10	90	1687	300565557	300567164	0.000000e+00	2418
5	TraesCS3B01G262300	chr3D	88.478	946	85	16	90	1017	188362169	188363108	0.000000e+00	1122
6	TraesCS3B01G262300	chr3D	90.371	862	66	11	514	1360	93477873	93477014	0.000000e+00	1116
7	TraesCS3B01G262300	chr3D	96.594	411	4	4	1929	2339	300567964	300568364	0.000000e+00	673
8	TraesCS3B01G262300	chr3D	97.479	238	6	0	1679	1916	300567547	300567784	7.780000e-110	407
9	TraesCS3B01G262300	chr3D	93.590	156	8	2	1378	1532	61184578	61184732	5.030000e-57	231
10	TraesCS3B01G262300	chr2D	90.443	1287	101	14	90	1360	574398634	574397354	0.000000e+00	1676
11	TraesCS3B01G262300	chr2D	92.547	161	10	2	1373	1532	556055817	556055658	1.810000e-56	230
12	TraesCS3B01G262300	chr7D	90.227	1279	105	10	90	1352	439710561	439709287	0.000000e+00	1652
13	TraesCS3B01G262300	chr7D	94.340	159	7	2	1375	1532	457148792	457148949	2.320000e-60	243
14	TraesCS3B01G262300	chr6D	89.120	1296	118	11	90	1367	48683397	48682107	0.000000e+00	1591
15	TraesCS3B01G262300	chr6D	89.594	1134	92	15	259	1370	32688758	32687629	0.000000e+00	1417
16	TraesCS3B01G262300	chr6D	87.500	104	13	0	1	104	14405791	14405894	1.140000e-23	121
17	TraesCS3B01G262300	chr7B	89.219	1280	120	8	90	1352	651392809	651391531	0.000000e+00	1583
18	TraesCS3B01G262300	chr4A	90.073	1229	103	10	90	1301	662511573	662512799	0.000000e+00	1576
19	TraesCS3B01G262300	chr4A	89.150	765	65	5	604	1352	4888741	4889503	0.000000e+00	937
20	TraesCS3B01G262300	chr4A	91.824	159	11	2	1378	1535	38011476	38011319	1.090000e-53	220
21	TraesCS3B01G262300	chr5A	88.768	1291	122	15	90	1361	592306803	592305517	0.000000e+00	1559
22	TraesCS3B01G262300	chr1B	89.193	694	56	10	675	1352	415252312	415253002	0.000000e+00	848
23	TraesCS3B01G262300	chr1B	91.489	94	8	0	1	94	152847883	152847976	1.890000e-26	130
24	TraesCS3B01G262300	chr1B	90.526	95	9	0	1	95	647038392	647038298	2.440000e-25	126
25	TraesCS3B01G262300	chr7A	93.038	158	9	2	1376	1532	130229539	130229695	1.810000e-56	230
26	TraesCS3B01G262300	chr1A	92.357	157	10	2	1377	1532	36791923	36791768	3.030000e-54	222
27	TraesCS3B01G262300	chr1A	89.143	175	13	5	1375	1547	516570465	516570635	1.820000e-51	213
28	TraesCS3B01G262300	chr6B	94.505	91	5	0	1	91	658384171	658384261	8.710000e-30	141
29	TraesCS3B01G262300	chr6B	91.489	94	8	0	1	94	107818478	107818385	1.890000e-26	130
30	TraesCS3B01G262300	chr2B	93.617	94	6	0	1	94	473339573	473339480	8.710000e-30	141
31	TraesCS3B01G262300	chr4B	92.473	93	7	0	1	93	25825556	25825648	1.460000e-27	134
32	TraesCS3B01G262300	chr4B	91.398	93	8	0	2	94	522288883	522288791	6.780000e-26	128
33	TraesCS3B01G262300	chr4D	91.579	95	6	2	1	94	488769644	488769551	1.890000e-26	130
34	TraesCS3B01G262300	chr5B	91.139	79	6	1	1534	1612	454871434	454871357	3.180000e-19	106

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	TraesCS3B01G262300	chr3B	420876323	420878661	2338	True	4320	4320	100.000	1	2339	1	chr3B.!!$R2	2338
1	TraesCS3B01G262300	chr3B	1789434	1790694	1260	True	1524	1524	88.670	108	1360	1	chr3B.!!$R1	1252
2	TraesCS3B01G262300	chr3A	434849862	434851504	1642	True	2503	2503	94.128	90	1739	1	chr3A.!!$R2	1649
3	TraesCS3B01G262300	chr3A	434844039	434844609	570	True	793	793	91.333	1741	2339	1	chr3A.!!$R1	598
4	TraesCS3B01G262300	chr3D	300565557	300568364	2807	False	1166	2418	95.998	90	2339	3	chr3D.!!$F3	2249
5	TraesCS3B01G262300	chr3D	188362169	188363108	939	False	1122	1122	88.478	90	1017	1	chr3D.!!$F2	927
6	TraesCS3B01G262300	chr3D	93477014	93477873	859	True	1116	1116	90.371	514	1360	1	chr3D.!!$R1	846
7	TraesCS3B01G262300	chr2D	574397354	574398634	1280	True	1676	1676	90.443	90	1360	1	chr2D.!!$R2	1270
8	TraesCS3B01G262300	chr7D	439709287	439710561	1274	True	1652	1652	90.227	90	1352	1	chr7D.!!$R1	1262
9	TraesCS3B01G262300	chr6D	48682107	48683397	1290	True	1591	1591	89.120	90	1367	1	chr6D.!!$R2	1277
10	TraesCS3B01G262300	chr6D	32687629	32688758	1129	True	1417	1417	89.594	259	1370	1	chr6D.!!$R1	1111
11	TraesCS3B01G262300	chr7B	651391531	651392809	1278	True	1583	1583	89.219	90	1352	1	chr7B.!!$R1	1262
12	TraesCS3B01G262300	chr4A	662511573	662512799	1226	False	1576	1576	90.073	90	1301	1	chr4A.!!$F2	1211
13	TraesCS3B01G262300	chr4A	4888741	4889503	762	False	937	937	89.150	604	1352	1	chr4A.!!$F1	748
14	TraesCS3B01G262300	chr5A	592305517	592306803	1286	True	1559	1559	88.768	90	1361	1	chr5A.!!$R1	1271
15	TraesCS3B01G262300	chr1B	415252312	415253002	690	False	848	848	89.193	675	1352	1	chr1B.!!$F2	677

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
32	33	0.039527	GCCCGCAATGACGTTTTTCT	60.04	50.0	0.0	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1595	1619	0.116342	TTAGGGTCAGTGGAGGAGCA	59.884	55.0	0.0	0.0	34.56	4.26	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
28	29	3.732892	CGGCCCGCAATGACGTTT	61.733	61.111	0.00	0.00	0.00	3.60
29	30	2.648454	GGCCCGCAATGACGTTTT	59.352	55.556	0.00	0.00	0.00	2.43
30	31	1.006688	GGCCCGCAATGACGTTTTT	60.007	52.632	0.00	0.00	0.00	1.94
31	32	1.006825	GGCCCGCAATGACGTTTTTC	61.007	55.000	0.00	0.00	0.00	2.29
32	33	0.039527	GCCCGCAATGACGTTTTTCT	60.040	50.000	0.00	0.00	0.00	2.52
33	34	1.685302	CCCGCAATGACGTTTTTCTG	58.315	50.000	0.00	0.00	0.00	3.02
34	35	1.052287	CCGCAATGACGTTTTTCTGC	58.948	50.000	0.00	0.00	0.00	4.26
35	36	0.697010	CGCAATGACGTTTTTCTGCG	59.303	50.000	14.03	14.03	45.38	5.18
36	37	2.031037	GCAATGACGTTTTTCTGCGA	57.969	45.000	0.00	0.00	0.00	5.10
37	38	2.380660	GCAATGACGTTTTTCTGCGAA	58.619	42.857	0.00	0.00	0.00	4.70
38	39	2.151172	GCAATGACGTTTTTCTGCGAAC	59.849	45.455	0.00	0.00	0.00	3.95
39	40	3.617669	CAATGACGTTTTTCTGCGAACT	58.382	40.909	0.00	0.00	0.00	3.01
40	41	3.963383	ATGACGTTTTTCTGCGAACTT	57.037	38.095	0.00	0.00	0.00	2.66
41	42	3.313274	TGACGTTTTTCTGCGAACTTC	57.687	42.857	0.00	0.00	0.00	3.01
42	43	2.673862	TGACGTTTTTCTGCGAACTTCA	59.326	40.909	0.00	0.00	33.41	3.02
43	44	3.125487	TGACGTTTTTCTGCGAACTTCAA	59.875	39.130	0.00	0.00	33.06	2.69
44	45	4.086199	ACGTTTTTCTGCGAACTTCAAA	57.914	36.364	0.00	0.00	0.00	2.69
45	46	3.849708	ACGTTTTTCTGCGAACTTCAAAC	59.150	39.130	0.00	6.39	0.00	2.93
46	47	3.062772	CGTTTTTCTGCGAACTTCAAACG	60.063	43.478	16.39	16.39	39.08	3.60
50	51	4.582452	GCGAACTTCAAACGCGTT	57.418	50.000	20.79	20.79	42.65	4.84
51	52	2.396689	GCGAACTTCAAACGCGTTC	58.603	52.632	26.77	10.02	42.65	3.95
52	53	0.042448	GCGAACTTCAAACGCGTTCT	60.042	50.000	26.77	12.71	42.65	3.01
53	54	1.647748	CGAACTTCAAACGCGTTCTG	58.352	50.000	26.77	23.01	35.95	3.02
54	55	1.385999	GAACTTCAAACGCGTTCTGC	58.614	50.000	26.77	7.04	41.47	4.26
77	78	4.530857	GACGGGATGCGGGGTCTG	62.531	72.222	0.00	0.00	0.00	3.51
80	81	3.161450	GGGATGCGGGGTCTGCTA	61.161	66.667	0.30	0.00	0.00	3.49
81	82	2.423446	GGATGCGGGGTCTGCTAG	59.577	66.667	0.30	0.00	0.00	3.42
82	83	2.134287	GGATGCGGGGTCTGCTAGA	61.134	63.158	0.00	0.00	0.00	2.43
83	84	1.365633	GATGCGGGGTCTGCTAGAG	59.634	63.158	0.00	0.00	0.00	2.43
84	85	1.381872	ATGCGGGGTCTGCTAGAGT	60.382	57.895	0.00	0.00	0.00	3.24
85	86	0.978146	ATGCGGGGTCTGCTAGAGTT	60.978	55.000	0.00	0.00	0.00	3.01
86	87	1.153549	GCGGGGTCTGCTAGAGTTG	60.154	63.158	0.00	0.00	0.00	3.16
87	88	1.153549	CGGGGTCTGCTAGAGTTGC	60.154	63.158	0.00	0.00	0.00	4.17
88	89	1.608717	CGGGGTCTGCTAGAGTTGCT	61.609	60.000	0.00	0.00	0.00	3.91
184	185	5.754782	TGATTAGACAAACTATGTGGCCAT	58.245	37.500	9.72	0.00	44.12	4.40
193	194	3.995199	ACTATGTGGCCATTCGATGTAG	58.005	45.455	9.72	6.57	32.29	2.74
197	198	3.884895	TGTGGCCATTCGATGTAGAAAT	58.115	40.909	9.72	0.00	33.43	2.17
245	246	7.436970	GCAACATGATATGCAAGATTTCATTGA	59.563	33.333	14.81	0.00	42.12	2.57
286	289	4.823157	TGGTATTTTCTCGGTTCGATCAA	58.177	39.130	0.00	0.00	34.61	2.57
387	390	6.070656	CCCTATTTGGAGCAAGATATGGAAA	58.929	40.000	0.00	0.00	38.35	3.13
462	465	3.903783	CCATGCCGGGTTACACTG	58.096	61.111	2.18	0.00	0.00	3.66
498	502	0.190815	AGGTTTCACCCATTTGCCCT	59.809	50.000	0.00	0.00	39.75	5.19
583	588	1.566231	CTGGAAAAGGCTAGGGATGGT	59.434	52.381	0.00	0.00	0.00	3.55
874	894	3.185797	CCTCCAAGAGGTTTCGTTAAACG	59.814	47.826	2.28	0.00	44.97	3.60
889	909	6.660722	TCGTTAAACGTAATGTTGATGCTTT	58.339	32.000	0.00	0.00	43.14	3.51
934	954	2.669133	CCATGGGAGCGGTCCTTCA	61.669	63.158	31.09	22.19	43.36	3.02
976	997	1.157585	GCTGGAGGGAACGAGAAAAC	58.842	55.000	0.00	0.00	0.00	2.43
1184	1206	7.333174	TCATTATGCTTGTGATTTCGTTACTGA	59.667	33.333	0.00	0.00	0.00	3.41
1410	1433	8.991275	TCCGTTCCCTAATATAAGACCTTTTAA	58.009	33.333	0.00	0.00	0.00	1.52
1522	1545	8.090788	AGCTAAAAGGTCTTATATTGAGGACA	57.909	34.615	0.00	0.00	0.00	4.02
1585	1609	6.142818	TCTTGAACTTTGTACACCCATTTG	57.857	37.500	0.00	0.00	0.00	2.32
1673	1697	2.545742	GCAACAACAAGGTTTGCTAGGG	60.546	50.000	0.00	0.00	0.00	3.53
1791	2206	8.251026	AGTAAAGCCAGTTCAAATATTAAAGGC	58.749	33.333	0.00	0.00	39.82	4.35
1891	2306	4.703645	TCAGGACTTATGAGTGAACTCG	57.296	45.455	6.01	0.00	45.72	4.18
1899	2314	2.438868	TGAGTGAACTCGTGGTCATG	57.561	50.000	8.67	0.00	45.72	3.07
1939	2547	4.956075	TGTATTCAGCAGGACTCACATAGA	59.044	41.667	0.00	0.00	0.00	1.98
1940	2548	5.422012	TGTATTCAGCAGGACTCACATAGAA	59.578	40.000	0.00	0.00	0.00	2.10
1941	2549	3.876274	TCAGCAGGACTCACATAGAAC	57.124	47.619	0.00	0.00	0.00	3.01
1942	2550	3.435275	TCAGCAGGACTCACATAGAACT	58.565	45.455	0.00	0.00	0.00	3.01
1943	2551	4.600062	TCAGCAGGACTCACATAGAACTA	58.400	43.478	0.00	0.00	0.00	2.24
1944	2552	5.204292	TCAGCAGGACTCACATAGAACTAT	58.796	41.667	0.00	0.00	0.00	2.12
1945	2553	5.658634	TCAGCAGGACTCACATAGAACTATT	59.341	40.000	0.00	0.00	0.00	1.73
1946	2554	5.752472	CAGCAGGACTCACATAGAACTATTG	59.248	44.000	0.00	0.00	0.00	1.90
1947	2555	5.423610	AGCAGGACTCACATAGAACTATTGT	59.576	40.000	0.00	0.00	0.00	2.71
1948	2556	5.521735	GCAGGACTCACATAGAACTATTGTG	59.478	44.000	13.12	13.12	0.00	3.33
1949	2557	5.521735	CAGGACTCACATAGAACTATTGTGC	59.478	44.000	13.86	7.70	31.17	4.57
1950	2558	5.423610	AGGACTCACATAGAACTATTGTGCT	59.576	40.000	13.86	0.00	35.85	4.40
1951	2559	6.607600	AGGACTCACATAGAACTATTGTGCTA	59.392	38.462	0.00	0.00	38.59	3.49
1952	2560	6.697892	GGACTCACATAGAACTATTGTGCTAC	59.302	42.308	0.00	9.71	37.16	3.58
1953	2561	7.170393	ACTCACATAGAACTATTGTGCTACA	57.830	36.000	0.00	0.00	37.16	2.74
1954	2562	7.261325	ACTCACATAGAACTATTGTGCTACAG	58.739	38.462	0.00	0.00	37.16	2.74
1955	2563	6.573434	TCACATAGAACTATTGTGCTACAGG	58.427	40.000	0.00	0.00	37.16	4.00
1956	2564	5.755375	CACATAGAACTATTGTGCTACAGGG	59.245	44.000	0.00	0.00	37.16	4.45
1957	2565	3.268023	AGAACTATTGTGCTACAGGGC	57.732	47.619	0.00	0.00	28.11	5.19
1958	2566	1.933853	GAACTATTGTGCTACAGGGCG	59.066	52.381	0.00	0.00	34.52	6.13
1959	2567	0.902531	ACTATTGTGCTACAGGGCGT	59.097	50.000	0.00	0.00	34.52	5.68
1960	2568	1.290203	CTATTGTGCTACAGGGCGTG	58.710	55.000	5.50	5.50	34.52	5.34
1961	2569	0.742990	TATTGTGCTACAGGGCGTGC	60.743	55.000	7.17	0.00	34.52	5.34
1962	2570	2.746412	ATTGTGCTACAGGGCGTGCA	62.746	55.000	7.17	0.00	34.52	4.57
1963	2571	2.668212	GTGCTACAGGGCGTGCAA	60.668	61.111	7.17	0.00	34.75	4.08
1964	2572	2.358615	TGCTACAGGGCGTGCAAG	60.359	61.111	7.17	6.45	31.51	4.01
2006	2614	2.094182	ACGGAATAACGTGATCTGCAGT	60.094	45.455	14.67	0.42	46.64	4.40
2143	2751	3.118482	TGCAAAGCTTGGAACCAATTTGA	60.118	39.130	24.48	13.61	37.76	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	2.741116	AAAAACGTCATTGCGGGCCG	62.741	55.000	24.35	24.35	35.98	6.13
12	13	1.006688	AAAAACGTCATTGCGGGCC	60.007	52.632	0.00	0.00	35.98	5.80
13	14	0.039527	AGAAAAACGTCATTGCGGGC	60.040	50.000	0.00	0.00	35.98	6.13
14	15	1.685302	CAGAAAAACGTCATTGCGGG	58.315	50.000	0.00	0.00	35.98	6.13
15	16	1.052287	GCAGAAAAACGTCATTGCGG	58.948	50.000	0.00	0.00	35.98	5.69
16	17	0.697010	CGCAGAAAAACGTCATTGCG	59.303	50.000	14.95	14.95	46.41	4.85
17	18	2.031037	TCGCAGAAAAACGTCATTGC	57.969	45.000	0.00	0.00	0.00	3.56
18	19	3.617669	AGTTCGCAGAAAAACGTCATTG	58.382	40.909	0.00	0.00	45.90	2.82
19	20	3.963383	AGTTCGCAGAAAAACGTCATT	57.037	38.095	0.00	0.00	45.90	2.57
20	21	3.311322	TGAAGTTCGCAGAAAAACGTCAT	59.689	39.130	0.00	0.00	45.90	3.06
21	22	2.673862	TGAAGTTCGCAGAAAAACGTCA	59.326	40.909	0.00	0.00	45.90	4.35
22	23	3.313274	TGAAGTTCGCAGAAAAACGTC	57.687	42.857	0.00	0.00	45.90	4.34
23	24	3.750639	TTGAAGTTCGCAGAAAAACGT	57.249	38.095	0.00	0.00	45.90	3.99
24	25	3.062772	CGTTTGAAGTTCGCAGAAAAACG	60.063	43.478	16.97	16.97	45.90	3.60
25	26	4.402473	CGTTTGAAGTTCGCAGAAAAAC	57.598	40.909	0.00	1.82	45.90	2.43
33	34	0.042448	AGAACGCGTTTGAAGTTCGC	60.042	50.000	27.32	9.70	46.19	4.70
34	35	1.647748	CAGAACGCGTTTGAAGTTCG	58.352	50.000	27.32	4.32	46.19	3.95
35	36	1.385999	GCAGAACGCGTTTGAAGTTC	58.614	50.000	27.32	11.54	43.13	3.01
36	37	3.526825	GCAGAACGCGTTTGAAGTT	57.473	47.368	27.32	0.19	0.00	2.66
60	61	4.530857	CAGACCCCGCATCCCGTC	62.531	72.222	0.00	0.00	34.38	4.79
63	64	3.161450	TAGCAGACCCCGCATCCC	61.161	66.667	0.00	0.00	0.00	3.85
64	65	2.093537	CTCTAGCAGACCCCGCATCC	62.094	65.000	0.00	0.00	0.00	3.51
65	66	1.365633	CTCTAGCAGACCCCGCATC	59.634	63.158	0.00	0.00	0.00	3.91
66	67	0.978146	AACTCTAGCAGACCCCGCAT	60.978	55.000	0.00	0.00	0.00	4.73
67	68	1.609501	AACTCTAGCAGACCCCGCA	60.610	57.895	0.00	0.00	0.00	5.69
68	69	1.153549	CAACTCTAGCAGACCCCGC	60.154	63.158	0.00	0.00	0.00	6.13
69	70	1.153549	GCAACTCTAGCAGACCCCG	60.154	63.158	0.00	0.00	0.00	5.73
70	71	0.176910	GAGCAACTCTAGCAGACCCC	59.823	60.000	0.00	0.00	0.00	4.95
71	72	1.190643	AGAGCAACTCTAGCAGACCC	58.809	55.000	0.00	0.00	39.28	4.46
72	73	3.181480	CCTTAGAGCAACTCTAGCAGACC	60.181	52.174	4.64	0.00	42.92	3.85
73	74	3.181480	CCCTTAGAGCAACTCTAGCAGAC	60.181	52.174	4.64	0.00	42.92	3.51
74	75	3.027412	CCCTTAGAGCAACTCTAGCAGA	58.973	50.000	4.64	0.00	42.92	4.26
75	76	3.027412	TCCCTTAGAGCAACTCTAGCAG	58.973	50.000	4.64	1.45	42.92	4.24
76	77	3.027412	CTCCCTTAGAGCAACTCTAGCA	58.973	50.000	4.64	0.00	42.92	3.49
77	78	2.364002	CCTCCCTTAGAGCAACTCTAGC	59.636	54.545	4.64	0.00	42.92	3.42
78	79	2.364002	GCCTCCCTTAGAGCAACTCTAG	59.636	54.545	4.64	0.00	42.92	2.43
79	80	2.292257	TGCCTCCCTTAGAGCAACTCTA	60.292	50.000	0.16	0.16	41.50	2.43
80	81	1.199615	GCCTCCCTTAGAGCAACTCT	58.800	55.000	2.23	2.23	43.83	3.24
81	82	0.905357	TGCCTCCCTTAGAGCAACTC	59.095	55.000	0.00	0.00	41.74	3.01
82	83	1.362224	TTGCCTCCCTTAGAGCAACT	58.638	50.000	0.00	0.00	41.74	3.16
83	84	1.454201	GTTGCCTCCCTTAGAGCAAC	58.546	55.000	10.52	10.52	45.99	4.17
84	85	1.064003	TGTTGCCTCCCTTAGAGCAA	58.936	50.000	0.00	0.00	41.74	3.91
85	86	1.003580	CTTGTTGCCTCCCTTAGAGCA	59.996	52.381	0.00	0.00	41.74	4.26
86	87	1.003696	ACTTGTTGCCTCCCTTAGAGC	59.996	52.381	0.00	0.00	41.74	4.09
87	88	3.425162	AACTTGTTGCCTCCCTTAGAG	57.575	47.619	0.00	0.00	42.83	2.43
88	89	4.349930	AGTTAACTTGTTGCCTCCCTTAGA	59.650	41.667	1.12	0.00	0.00	2.10
197	198	4.523083	CGGTAGGGGAAATGAAAGAATCA	58.477	43.478	0.00	0.00	43.67	2.57
208	209	0.693622	TCATGTTGCGGTAGGGGAAA	59.306	50.000	0.00	0.00	0.00	3.13
286	289	4.079958	GTGGTCCCACTCCATAAAATAGGT	60.080	45.833	9.24	0.00	43.12	3.08
312	315	7.054491	AGAGTGTTTTAATTTGCTTCCATGT	57.946	32.000	0.00	0.00	0.00	3.21
313	316	9.643693	ATTAGAGTGTTTTAATTTGCTTCCATG	57.356	29.630	0.00	0.00	0.00	3.66
387	390	3.418684	ACTTTTGCCGGACAGACTAAT	57.581	42.857	5.05	0.00	0.00	1.73
462	465	5.880332	TGAAACCTTCATATGTCTGTTAGCC	59.120	40.000	1.90	0.39	34.08	3.93
498	502	6.600882	ATCTTCTAAACCTCCGAACAAGTA	57.399	37.500	0.00	0.00	0.00	2.24
889	909	7.413446	ACCCCTAAGAAGATCATGATCAAAAA	58.587	34.615	31.99	15.30	40.22	1.94
934	954	2.052782	AAACCTGCCTTTGTCGTCTT	57.947	45.000	0.00	0.00	0.00	3.01
976	997	3.329386	ACACATCCACGACAGAAATCAG	58.671	45.455	0.00	0.00	0.00	2.90
1089	1111	6.406370	TCCATCATTCGTAGTTTCAATCACT	58.594	36.000	0.00	0.00	0.00	3.41
1103	1125	1.536922	CCGACTGTCCTCCATCATTCG	60.537	57.143	1.55	0.00	36.81	3.34
1184	1206	7.618019	TCCCTATTACAGTGCTCAAATCTAT	57.382	36.000	0.00	0.00	0.00	1.98
1521	1544	5.988561	GCTATTTTCTCATGTACTCCCTCTG	59.011	44.000	0.00	0.00	0.00	3.35
1522	1545	5.902431	AGCTATTTTCTCATGTACTCCCTCT	59.098	40.000	0.00	0.00	0.00	3.69
1585	1609	1.002011	GGAGGAGCAAGGTTCACCC	60.002	63.158	0.00	0.00	36.42	4.61
1595	1619	0.116342	TTAGGGTCAGTGGAGGAGCA	59.884	55.000	0.00	0.00	34.56	4.26
1673	1697	7.839705	TCCTATGATACAACTATATCTCCACCC	59.160	40.741	0.00	0.00	33.42	4.61
1743	2158	2.166870	TGCAACAATGATGGGATGCTTC	59.833	45.455	2.31	0.00	36.39	3.86
1791	2206	5.008415	GTCTATCAGGCAAGGATGTTCATTG	59.992	44.000	0.00	0.00	40.72	2.82
1891	2306	2.988010	TGATCTGCCTACATGACCAC	57.012	50.000	0.00	0.00	0.00	4.16
1899	2314	7.277539	GCTGAATACAAGATATGATCTGCCTAC	59.722	40.741	0.00	0.00	40.13	3.18
1939	2547	1.278127	ACGCCCTGTAGCACAATAGTT	59.722	47.619	0.00	0.00	0.00	2.24
1940	2548	0.902531	ACGCCCTGTAGCACAATAGT	59.097	50.000	0.00	0.00	0.00	2.12
1941	2549	1.290203	CACGCCCTGTAGCACAATAG	58.710	55.000	0.00	0.00	0.00	1.73
1942	2550	0.742990	GCACGCCCTGTAGCACAATA	60.743	55.000	0.00	0.00	0.00	1.90
1943	2551	2.040544	GCACGCCCTGTAGCACAAT	61.041	57.895	0.00	0.00	0.00	2.71
1944	2552	2.668212	GCACGCCCTGTAGCACAA	60.668	61.111	0.00	0.00	0.00	3.33
1945	2553	3.468326	TTGCACGCCCTGTAGCACA	62.468	57.895	0.00	0.00	35.38	4.57
1946	2554	2.668212	TTGCACGCCCTGTAGCAC	60.668	61.111	0.00	0.00	35.38	4.40
1947	2555	2.358615	CTTGCACGCCCTGTAGCA	60.359	61.111	0.00	0.00	34.35	3.49
1948	2556	3.127533	CCTTGCACGCCCTGTAGC	61.128	66.667	0.00	0.00	0.00	3.58
1949	2557	2.436646	CCCTTGCACGCCCTGTAG	60.437	66.667	0.00	0.00	0.00	2.74
1950	2558	3.246112	ACCCTTGCACGCCCTGTA	61.246	61.111	0.00	0.00	0.00	2.74
1951	2559	4.954970	CACCCTTGCACGCCCTGT	62.955	66.667	0.00	0.00	0.00	4.00
1956	2564	3.853698	TAACCCCACCCTTGCACGC	62.854	63.158	0.00	0.00	0.00	5.34
1957	2565	1.228306	TTAACCCCACCCTTGCACG	60.228	57.895	0.00	0.00	0.00	5.34
1958	2566	1.183030	GGTTAACCCCACCCTTGCAC	61.183	60.000	14.16	0.00	0.00	4.57
1959	2567	1.154221	GGTTAACCCCACCCTTGCA	59.846	57.895	14.16	0.00	0.00	4.08
1960	2568	1.974875	CGGTTAACCCCACCCTTGC	60.975	63.158	19.09	0.00	0.00	4.01
1961	2569	1.303806	CCGGTTAACCCCACCCTTG	60.304	63.158	19.09	2.11	0.00	3.61
1962	2570	1.463804	TCCGGTTAACCCCACCCTT	60.464	57.895	19.09	0.00	0.00	3.95
1963	2571	2.207768	TCCGGTTAACCCCACCCT	59.792	61.111	19.09	0.00	0.00	4.34
1964	2572	2.066700	TTGTCCGGTTAACCCCACCC	62.067	60.000	19.09	3.59	0.00	4.61
2143	2751	1.066573	GGTATGTGACTGCTGAGCTGT	60.067	52.381	16.99	16.99	43.03	4.40
2304	2912	6.693315	TGACTCTTTCTTTACCCACAAAAG	57.307	37.500	0.00	0.00	35.66	2.27
2309	2917	7.039313	ACATTTTGACTCTTTCTTTACCCAC	57.961	36.000	0.00	0.00	0.00	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.