AutoCloner

Multiple sequence alignment - TraesCS1B01G014000

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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	TraesCS1B01G014000	chr1B	100.000	2543	0	0	1	2543	6480674	6483216	0.000000e+00	4697.0
1	TraesCS1B01G014000	chr1B	93.791	1691	74	17	797	2464	5760432	5758750	0.000000e+00	2512.0
2	TraesCS1B01G014000	chr1B	91.266	229	16	3	1	228	5761203	5760978	2.460000e-80	309.0
3	TraesCS1B01G014000	chr1B	87.319	276	23	6	517	786	5760682	5760413	3.180000e-79	305.0
4	TraesCS1B01G014000	chr1B	82.011	378	39	16	1379	1739	5750003	5749638	6.880000e-76	294.0
5	TraesCS1B01G014000	chr1B	94.444	126	5	2	2340	2464	5699677	5699553	2.580000e-45	193.0
6	TraesCS1B01G014000	chr1B	91.304	138	9	3	2337	2472	6065219	6065083	4.320000e-43	185.0
7	TraesCS1B01G014000	chr1B	79.118	340	16	22	2177	2461	7697699	7698038	1.550000e-42	183.0
8	TraesCS1B01G014000	chr1B	85.987	157	8	7	2177	2319	22666002	22666158	3.390000e-34	156.0
9	TraesCS1B01G014000	chr1B	88.281	128	14	1	2337	2464	6285911	6285785	4.380000e-33	152.0
10	TraesCS1B01G014000	chr1B	84.768	151	8	6	2182	2317	5699896	5699746	1.230000e-28	137.0
11	TraesCS1B01G014000	chr1B	94.382	89	4	1	2456	2543	5758727	5758639	4.410000e-28	135.0
12	TraesCS1B01G014000	chr1A	89.350	1446	97	22	272	1690	4504152	4502737	0.000000e+00	1764.0
13	TraesCS1B01G014000	chr1A	89.350	1446	97	22	272	1690	5498425	5499840	0.000000e+00	1764.0
14	TraesCS1B01G014000	chr1A	86.950	1318	106	28	386	1690	6334758	6336022	0.000000e+00	1421.0
15	TraesCS1B01G014000	chr1A	91.408	710	38	8	982	1690	5500631	5501318	0.000000e+00	952.0
16	TraesCS1B01G014000	chr1A	81.426	603	49	26	1754	2319	6336149	6336725	3.890000e-118	435.0
17	TraesCS1B01G014000	chr1A	94.419	215	12	0	21	235	5498119	5498333	5.240000e-87	331.0
18	TraesCS1B01G014000	chr1A	93.989	183	11	0	53	235	4504426	4504244	6.930000e-71	278.0
19	TraesCS1B01G014000	chr1A	86.364	154	7	1	2177	2316	6293641	6293794	3.390000e-34	156.0
20	TraesCS1B01G014000	chr1A	90.789	76	6	1	1691	1766	6336051	6336125	1.610000e-17	100.0
21	TraesCS1B01G014000	chr1A	89.474	76	4	2	1694	1766	4502705	4502631	2.690000e-15	93.5
22	TraesCS1B01G014000	chr1A	88.608	79	5	2	1691	1766	5499869	5499946	2.690000e-15	93.5
23	TraesCS1B01G014000	chr1A	88.608	79	5	2	1691	1766	5501347	5501424	2.690000e-15	93.5
24	TraesCS1B01G014000	chr1D	91.286	1182	74	6	517	1690	3968425	3969585	0.000000e+00	1585.0
25	TraesCS1B01G014000	chr1D	84.358	748	61	32	1760	2461	3969724	3970461	0.000000e+00	682.0
26	TraesCS1B01G014000	chr1D	84.946	372	43	11	1324	1692	3618233	3617872	5.170000e-97	364.0
27	TraesCS1B01G014000	chr1D	93.304	224	12	2	2	225	3967899	3968119	6.780000e-86	327.0
28	TraesCS1B01G014000	chr1D	81.723	383	26	16	1975	2319	5130323	5130699	1.930000e-71	279.0
29	TraesCS1B01G014000	chr5B	83.780	820	87	22	879	1688	55504715	55503932	0.000000e+00	736.0
30	TraesCS1B01G014000	chr5B	82.266	203	22	7	2151	2342	55503523	55503324	2.020000e-36	163.0
31	TraesCS1B01G014000	chr5D	85.435	666	74	14	865	1519	52327723	52327070	0.000000e+00	671.0
32	TraesCS1B01G014000	chr5D	84.571	175	16	7	2151	2317	52326494	52326323	2.020000e-36	163.0

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	TraesCS1B01G014000	chr1B	6480674	6483216	2542	False	4697.000000	4697	100.000000	1	2543	1	chr1B.!!$F1	2542
1	TraesCS1B01G014000	chr1B	5758639	5761203	2564	True	815.250000	2512	91.689500	1	2543	4	chr1B.!!$R5	2542
2	TraesCS1B01G014000	chr1A	4502631	4504426	1795	True	711.833333	1764	90.937667	53	1766	3	chr1A.!!$R1	1713
3	TraesCS1B01G014000	chr1A	6334758	6336725	1967	False	652.000000	1421	86.388333	386	2319	3	chr1A.!!$F3	1933
4	TraesCS1B01G014000	chr1A	5498119	5501424	3305	False	646.800000	1764	90.478600	21	1766	5	chr1A.!!$F2	1745
5	TraesCS1B01G014000	chr1D	3967899	3970461	2562	False	864.666667	1585	89.649333	2	2461	3	chr1D.!!$F2	2459
6	TraesCS1B01G014000	chr5B	55503324	55504715	1391	True	449.500000	736	83.023000	879	2342	2	chr5B.!!$R1	1463
7	TraesCS1B01G014000	chr5D	52326323	52327723	1400	True	417.000000	671	85.003000	865	2317	2	chr5D.!!$R1	1452

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
117	119	0.033796	AACTGTGGATGCCCTCATGG	60.034	55.000	0.00	0.0	35.61	3.66	F
892	1027	1.006998	ACAGGGCCCAGCAATTCATTA	59.993	47.619	27.56	0.0	0.00	1.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1173	1312	0.519077	GAAAAGGCAGAACAGGAGCG	59.481	55.0	0.0	0.0	0.00	5.03	R
2501	3022	0.906775	AGCAAGGGCATGGATTTTGG	59.093	50.0	0.0	0.0	44.61	3.28	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
72	74	4.161377	GGTGATCCTGCTAATAGATCCCTC	59.839	50.000	0.00	0.00	36.41	4.30
117	119	0.033796	AACTGTGGATGCCCTCATGG	60.034	55.000	0.00	0.00	35.61	3.66
197	199	3.194116	TGCTTTCATGAGGCCTTCAATTC	59.806	43.478	6.77	0.00	39.77	2.17
198	200	3.429960	GCTTTCATGAGGCCTTCAATTCC	60.430	47.826	6.77	0.00	39.77	3.01
228	230	5.239744	TGGTTGTGCGATTATGTTGTTAAGT	59.760	36.000	0.00	0.00	0.00	2.24
235	237	8.178964	GTGCGATTATGTTGTTAAGTGGAATTA	58.821	33.333	0.00	0.00	0.00	1.40
236	238	8.178964	TGCGATTATGTTGTTAAGTGGAATTAC	58.821	33.333	0.00	0.00	0.00	1.89
237	239	8.178964	GCGATTATGTTGTTAAGTGGAATTACA	58.821	33.333	0.00	0.00	0.00	2.41
238	240	9.702726	CGATTATGTTGTTAAGTGGAATTACAG	57.297	33.333	0.00	0.00	0.00	2.74
240	242	5.699097	TGTTGTTAAGTGGAATTACAGGC	57.301	39.130	0.00	0.00	0.00	4.85
241	243	5.381757	TGTTGTTAAGTGGAATTACAGGCT	58.618	37.500	0.00	0.00	0.00	4.58
242	244	6.535540	TGTTGTTAAGTGGAATTACAGGCTA	58.464	36.000	0.00	0.00	0.00	3.93
243	245	6.653320	TGTTGTTAAGTGGAATTACAGGCTAG	59.347	38.462	0.00	0.00	0.00	3.42
244	246	6.368779	TGTTAAGTGGAATTACAGGCTAGT	57.631	37.500	0.00	0.00	0.00	2.57
245	247	6.403878	TGTTAAGTGGAATTACAGGCTAGTC	58.596	40.000	0.00	0.00	0.00	2.59
246	248	4.489306	AAGTGGAATTACAGGCTAGTCC	57.511	45.455	0.00	0.00	0.00	3.85
247	249	2.431057	AGTGGAATTACAGGCTAGTCCG	59.569	50.000	0.00	0.00	40.77	4.79
270	272	4.761235	TTACGAAGATATGCTAGTCCGG	57.239	45.455	0.00	0.00	0.00	5.14
305	376	3.005684	TGCACCTCAACATTTTGTGATCC	59.994	43.478	0.00	0.00	34.02	3.36
306	377	3.256631	GCACCTCAACATTTTGTGATCCT	59.743	43.478	0.00	0.00	34.02	3.24
396	467	2.423538	ACTTGCCCGCATATTTCTTCAC	59.576	45.455	0.00	0.00	0.00	3.18
497	568	7.316640	AGTACTAAAAGCAGTGAGTCAGTATG	58.683	38.462	0.00	0.00	37.54	2.39
510	581	9.003658	AGTGAGTCAGTATGTTTTCCAATTAAG	57.996	33.333	0.00	0.00	37.40	1.85
588	677	3.992643	TGAATGTTGCAAAACATCAGGG	58.007	40.909	0.00	0.00	42.13	4.45
593	687	4.583871	TGTTGCAAAACATCAGGGTTTTT	58.416	34.783	0.00	0.00	45.89	1.94
730	833	1.380785	ATGCCCTGCCCTCATGTTG	60.381	57.895	0.00	0.00	0.00	3.33
734	837	1.890573	GCCCTGCCCTCATGTTGTTAA	60.891	52.381	0.00	0.00	0.00	2.01
774	901	7.141758	AGAGCCCAGATATTCATTCTGTTAA	57.858	36.000	0.00	0.00	39.16	2.01
800	932	2.716814	GCATCCATGAGGCCTTCAG	58.283	57.895	6.77	0.00	39.68	3.02
821	956	5.170748	CAGTTTTTGAACTGGAAAGCTTGT	58.829	37.500	0.00	0.00	44.77	3.16
832	967	3.128589	TGGAAAGCTTGTGTGTTCAAGAC	59.871	43.478	0.00	2.78	45.11	3.01
850	985	4.928661	AGACTTGTGCGATTATGTTGTC	57.071	40.909	0.00	0.00	0.00	3.18
858	993	2.777845	GCGATTATGTTGTCAATGCACG	59.222	45.455	0.00	0.00	0.00	5.34
873	1008	1.737236	TGCACGCCATTCATTCAGTAC	59.263	47.619	0.00	0.00	0.00	2.73
892	1027	1.006998	ACAGGGCCCAGCAATTCATTA	59.993	47.619	27.56	0.00	0.00	1.90
902	1038	6.035975	GCCCAGCAATTCATTATGTTTAACAC	59.964	38.462	0.00	0.00	0.00	3.32
939	1077	7.775053	TGTTTGCTTGAATTAACCTCCTTAT	57.225	32.000	0.00	0.00	0.00	1.73
940	1078	8.871629	TGTTTGCTTGAATTAACCTCCTTATA	57.128	30.769	0.00	0.00	0.00	0.98
995	1134	4.828939	TGATGCTGTTTCAGGATTCTTGTT	59.171	37.500	5.35	0.00	42.36	2.83
1173	1312	2.361737	GAACCCAAGAGCAGCCCC	60.362	66.667	0.00	0.00	0.00	5.80
1194	1339	1.819305	GCTCCTGTTCTGCCTTTTCCA	60.819	52.381	0.00	0.00	0.00	3.53
1272	1417	2.461110	GGTGGAAGCCATACGCACG	61.461	63.158	0.00	0.00	41.38	5.34
1386	1531	0.183492	ACAAGGAGTTCAAGCTGCCA	59.817	50.000	0.00	0.00	0.00	4.92
1398	1543	0.916358	AGCTGCCATACCAGAACCCT	60.916	55.000	0.00	0.00	34.77	4.34
1399	1544	0.749454	GCTGCCATACCAGAACCCTG	60.749	60.000	0.00	0.00	40.09	4.45
1440	1585	4.530857	GGGTGCGCCGAGTGCTAT	62.531	66.667	10.86	0.00	40.03	2.97
1541	1695	3.407083	TGCCGCCATGGGAGCTTA	61.407	61.111	15.13	0.00	38.63	3.09
1542	1696	2.592861	GCCGCCATGGGAGCTTAG	60.593	66.667	15.13	0.00	38.63	2.18
1544	1698	2.190313	CGCCATGGGAGCTTAGCA	59.810	61.111	15.13	0.00	0.00	3.49
1545	1699	1.451927	CGCCATGGGAGCTTAGCAA	60.452	57.895	15.13	0.00	0.00	3.91
1546	1700	0.820891	CGCCATGGGAGCTTAGCAAT	60.821	55.000	15.13	0.00	0.00	3.56
1547	1701	0.672342	GCCATGGGAGCTTAGCAATG	59.328	55.000	15.13	4.76	0.00	2.82
1548	1702	1.325355	CCATGGGAGCTTAGCAATGG	58.675	55.000	7.07	10.02	0.00	3.16
1549	1703	1.325355	CATGGGAGCTTAGCAATGGG	58.675	55.000	7.07	0.00	0.00	4.00
1550	1704	1.133699	CATGGGAGCTTAGCAATGGGA	60.134	52.381	7.07	0.00	0.00	4.37
1551	1705	0.548031	TGGGAGCTTAGCAATGGGAG	59.452	55.000	7.07	0.00	0.00	4.30
1552	1706	0.839946	GGGAGCTTAGCAATGGGAGA	59.160	55.000	7.07	0.00	0.00	3.71
1553	1707	1.202746	GGGAGCTTAGCAATGGGAGAG	60.203	57.143	7.07	0.00	0.00	3.20
1554	1708	1.202746	GGAGCTTAGCAATGGGAGAGG	60.203	57.143	7.07	0.00	0.00	3.69
1555	1709	0.842635	AGCTTAGCAATGGGAGAGGG	59.157	55.000	7.07	0.00	0.00	4.30
1556	1710	0.179006	GCTTAGCAATGGGAGAGGGG	60.179	60.000	0.00	0.00	0.00	4.79
1557	1711	1.216990	CTTAGCAATGGGAGAGGGGT	58.783	55.000	0.00	0.00	0.00	4.95
1558	1712	1.566231	CTTAGCAATGGGAGAGGGGTT	59.434	52.381	0.00	0.00	0.00	4.11
1559	1713	0.918983	TAGCAATGGGAGAGGGGTTG	59.081	55.000	0.00	0.00	0.00	3.77
1560	1714	2.054453	GCAATGGGAGAGGGGTTGC	61.054	63.158	0.00	0.00	38.43	4.17
1561	1715	1.750399	CAATGGGAGAGGGGTTGCG	60.750	63.158	0.00	0.00	0.00	4.85
1565	1719	2.579738	GGAGAGGGGTTGCGAGTC	59.420	66.667	0.00	0.00	0.00	3.36
1819	2173	4.053469	CCGTTTGTTTGGGATGAGTTTT	57.947	40.909	0.00	0.00	0.00	2.43
1822	2176	4.739716	CGTTTGTTTGGGATGAGTTTTGAG	59.260	41.667	0.00	0.00	0.00	3.02
1836	2190	6.908825	TGAGTTTTGAGTAACCATTGTATGC	58.091	36.000	0.00	0.00	0.00	3.14
1890	2244	4.622313	GCTGCAAAATGAAACATGAATCGA	59.378	37.500	0.00	0.00	0.00	3.59
1891	2245	5.290158	GCTGCAAAATGAAACATGAATCGAT	59.710	36.000	0.00	0.00	0.00	3.59
1896	2250	6.513806	AAATGAAACATGAATCGATGGTGA	57.486	33.333	0.00	0.00	0.00	4.02
2012	2373	7.122055	TGGTTATTGGTAAAATCCATGTCTGAC	59.878	37.037	0.00	0.00	37.33	3.51
2020	2381	2.839486	TCCATGTCTGACTGGTTGAC	57.161	50.000	19.06	0.00	34.03	3.18
2024	2386	3.251729	CCATGTCTGACTGGTTGACAAAG	59.748	47.826	9.51	8.99	42.80	2.77
2036	2421	6.777580	ACTGGTTGACAAAGAATTATGGAACT	59.222	34.615	0.00	0.00	0.00	3.01
2143	2538	3.981071	ATGGTGCAAGAAGCTACAGTA	57.019	42.857	0.00	0.00	45.94	2.74
2355	2843	6.703857	CAGAGCAAGAAAATCGACAGATAAG	58.296	40.000	0.00	0.00	35.74	1.73
2388	2876	9.191995	AGTTGAAAAACTTTACTGAACAAGTTG	57.808	29.630	0.00	0.00	41.42	3.16
2461	2950	3.865011	AGATAGCTCACAGACACACAG	57.135	47.619	0.00	0.00	0.00	3.66
2501	3022	5.821204	ACTTGTACATTTGTTCAGAGCAAC	58.179	37.500	0.00	0.00	0.00	4.17
2509	3030	4.320608	TTGTTCAGAGCAACCAAAATCC	57.679	40.909	0.00	0.00	0.00	3.01
2524	3045	4.764771	TCCATGCCCTTGCTGCCC	62.765	66.667	0.00	0.00	38.71	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	32	8.720562	GGATCACCATTTTATTTTTCAACCTTG	58.279	33.333	0.00	0.00	35.97	3.61
117	119	8.171840	GCTCTAAACTGAATTCTACATTGACAC	58.828	37.037	7.05	0.00	0.00	3.67
197	199	1.234615	AATCGCACAACCAGTTCGGG	61.235	55.000	0.00	0.00	37.47	5.14
198	200	1.434555	TAATCGCACAACCAGTTCGG	58.565	50.000	0.00	0.00	37.47	4.30
228	230	2.463752	ACGGACTAGCCTGTAATTCCA	58.536	47.619	0.00	0.00	0.00	3.53
235	237	1.538047	TCGTAAACGGACTAGCCTGT	58.462	50.000	2.24	0.00	40.29	4.00
236	238	2.163010	TCTTCGTAAACGGACTAGCCTG	59.837	50.000	2.24	0.00	40.29	4.85
237	239	2.440409	TCTTCGTAAACGGACTAGCCT	58.560	47.619	2.24	0.00	40.29	4.58
238	240	2.927553	TCTTCGTAAACGGACTAGCC	57.072	50.000	2.24	0.00	40.29	3.93
239	241	4.382160	GCATATCTTCGTAAACGGACTAGC	59.618	45.833	2.24	0.00	40.29	3.42
240	242	5.759963	AGCATATCTTCGTAAACGGACTAG	58.240	41.667	2.24	0.00	40.29	2.57
241	243	5.762825	AGCATATCTTCGTAAACGGACTA	57.237	39.130	2.24	0.00	40.29	2.59
242	244	4.650754	AGCATATCTTCGTAAACGGACT	57.349	40.909	2.24	0.00	40.29	3.85
243	245	5.517904	ACTAGCATATCTTCGTAAACGGAC	58.482	41.667	2.24	0.00	40.29	4.79
244	246	5.278169	GGACTAGCATATCTTCGTAAACGGA	60.278	44.000	2.24	0.00	40.29	4.69
245	247	4.916249	GGACTAGCATATCTTCGTAAACGG	59.084	45.833	2.24	0.00	40.29	4.44
246	248	4.611782	CGGACTAGCATATCTTCGTAAACG	59.388	45.833	0.00	0.00	41.45	3.60
247	249	4.916249	CCGGACTAGCATATCTTCGTAAAC	59.084	45.833	0.00	0.00	0.00	2.01
270	272	5.357878	TGTTGAGGTGCATCTGATTAATTCC	59.642	40.000	2.86	0.00	0.00	3.01
305	376	1.195115	TCAACCTACCTAGCCAGCAG	58.805	55.000	0.00	0.00	0.00	4.24
306	377	1.278127	GTTCAACCTACCTAGCCAGCA	59.722	52.381	0.00	0.00	0.00	4.41
378	449	1.064758	AGGTGAAGAAATATGCGGGCA	60.065	47.619	0.00	0.00	0.00	5.36
396	467	2.224719	GGATGGATGAGTGGATTGGAGG	60.225	54.545	0.00	0.00	0.00	4.30
476	547	7.426929	AAACATACTGACTCACTGCTTTTAG	57.573	36.000	0.00	0.00	0.00	1.85
485	556	8.999431	TCTTAATTGGAAAACATACTGACTCAC	58.001	33.333	0.00	0.00	0.00	3.51
497	568	5.817296	GCCCATGGATTCTTAATTGGAAAAC	59.183	40.000	15.22	0.00	0.00	2.43
510	581	4.401925	AGCAAATACTAGCCCATGGATTC	58.598	43.478	15.22	1.54	0.00	2.52
730	833	7.224949	GGGCTCTACACTGAATTCTACATTAAC	59.775	40.741	7.05	0.00	0.00	2.01
734	837	4.716784	TGGGCTCTACACTGAATTCTACAT	59.283	41.667	7.05	0.00	0.00	2.29
774	901	1.819305	GCCTCATGGATGCCGGTTAAT	60.819	52.381	1.90	0.00	34.57	1.40
780	912	1.895707	GAAGGCCTCATGGATGCCG	60.896	63.158	5.23	0.00	45.67	5.69
800	932	4.929211	ACACAAGCTTTCCAGTTCAAAAAC	59.071	37.500	0.00	0.00	35.50	2.43
821	956	2.017138	TCGCACAAGTCTTGAACACA	57.983	45.000	19.53	0.00	0.00	3.72
832	967	4.263677	GCATTGACAACATAATCGCACAAG	59.736	41.667	0.00	0.00	0.00	3.16
850	985	2.190161	CTGAATGAATGGCGTGCATTG	58.810	47.619	17.69	0.60	32.80	2.82
858	993	1.678101	GCCCTGTACTGAATGAATGGC	59.322	52.381	0.60	0.12	0.00	4.40
873	1008	1.779221	TAATGAATTGCTGGGCCCTG	58.221	50.000	25.70	24.72	0.00	4.45
892	1027	3.740115	AGGTCTCAAGCGTGTTAAACAT	58.260	40.909	0.00	0.00	0.00	2.71
902	1038	1.334869	AGCAAACAAAGGTCTCAAGCG	59.665	47.619	0.00	0.00	0.00	4.68
939	1077	6.721318	AGTCAGGGATTAACAGCAAGATTTA	58.279	36.000	0.00	0.00	0.00	1.40
940	1078	5.574188	AGTCAGGGATTAACAGCAAGATTT	58.426	37.500	0.00	0.00	0.00	2.17
995	1134	0.767998	TGTGTAGTCACCCATGGCAA	59.232	50.000	6.09	0.00	43.26	4.52
1053	1192	3.701542	TCTTCACCTGCTTATCGTCATCT	59.298	43.478	0.00	0.00	0.00	2.90
1062	1201	2.180276	GTCCTCCTCTTCACCTGCTTA	58.820	52.381	0.00	0.00	0.00	3.09
1173	1312	0.519077	GAAAAGGCAGAACAGGAGCG	59.481	55.000	0.00	0.00	0.00	5.03
1194	1339	1.203389	ACTGGTAGGTACATGGGTGGT	60.203	52.381	0.00	0.00	0.00	4.16
1386	1531	1.198759	ACGGTGCAGGGTTCTGGTAT	61.199	55.000	0.00	0.00	41.19	2.73
1440	1585	1.292223	GTCCTGCACGTTGCTCCTA	59.708	57.895	10.54	0.00	45.31	2.94
1540	1694	0.918983	CAACCCCTCTCCCATTGCTA	59.081	55.000	0.00	0.00	0.00	3.49
1541	1695	1.693640	CAACCCCTCTCCCATTGCT	59.306	57.895	0.00	0.00	0.00	3.91
1542	1696	2.054453	GCAACCCCTCTCCCATTGC	61.054	63.158	0.00	0.00	38.93	3.56
1544	1698	1.915078	CTCGCAACCCCTCTCCCATT	61.915	60.000	0.00	0.00	0.00	3.16
1545	1699	2.285368	TCGCAACCCCTCTCCCAT	60.285	61.111	0.00	0.00	0.00	4.00
1546	1700	3.003173	CTCGCAACCCCTCTCCCA	61.003	66.667	0.00	0.00	0.00	4.37
1547	1701	3.003763	ACTCGCAACCCCTCTCCC	61.004	66.667	0.00	0.00	0.00	4.30
1548	1702	2.579738	GACTCGCAACCCCTCTCC	59.420	66.667	0.00	0.00	0.00	3.71
1549	1703	2.182030	CGACTCGCAACCCCTCTC	59.818	66.667	0.00	0.00	0.00	3.20
1550	1704	3.382832	CCGACTCGCAACCCCTCT	61.383	66.667	0.00	0.00	0.00	3.69
1551	1705	3.358076	CTCCGACTCGCAACCCCTC	62.358	68.421	0.00	0.00	0.00	4.30
1552	1706	3.382832	CTCCGACTCGCAACCCCT	61.383	66.667	0.00	0.00	0.00	4.79
1554	1708	4.070552	AGCTCCGACTCGCAACCC	62.071	66.667	0.00	0.00	0.00	4.11
1555	1709	2.811317	CAGCTCCGACTCGCAACC	60.811	66.667	0.00	0.00	0.00	3.77
1556	1710	1.803519	CTCAGCTCCGACTCGCAAC	60.804	63.158	0.00	0.00	0.00	4.17
1557	1711	2.268802	ACTCAGCTCCGACTCGCAA	61.269	57.895	0.00	0.00	0.00	4.85
1558	1712	2.673341	ACTCAGCTCCGACTCGCA	60.673	61.111	0.00	0.00	0.00	5.10
1559	1713	2.202544	CACTCAGCTCCGACTCGC	60.203	66.667	0.00	0.00	0.00	5.03
1560	1714	1.427419	CTCACTCAGCTCCGACTCG	59.573	63.158	0.00	0.00	0.00	4.18
1561	1715	1.138671	GCTCACTCAGCTCCGACTC	59.861	63.158	0.00	0.00	45.83	3.36
1779	2105	2.815158	GGGCTAAAATCCAAGGAACCA	58.185	47.619	0.00	0.00	0.00	3.67
1819	2173	6.653020	AGAATCAGCATACAATGGTTACTCA	58.347	36.000	0.00	0.00	39.29	3.41
1822	2176	6.511767	CGGAAGAATCAGCATACAATGGTTAC	60.512	42.308	0.00	0.00	39.29	2.50
1836	2190	5.171476	ACTTATGTGACACGGAAGAATCAG	58.829	41.667	20.35	4.35	31.22	2.90
1891	2245	9.638239	GAAGCTAAATCACATTAATTTTCACCA	57.362	29.630	0.00	0.00	0.00	4.17
2012	2373	7.219484	AGTTCCATAATTCTTTGTCAACCAG	57.781	36.000	0.00	0.00	0.00	4.00
2076	2467	1.597742	GCGGTGCACCAAGATGATAT	58.402	50.000	34.16	0.00	35.14	1.63
2089	2480	2.644992	CAAAAGACTGGGCGGTGC	59.355	61.111	0.00	0.00	0.00	5.01
2093	2484	1.228124	TCCACCAAAAGACTGGGCG	60.228	57.895	0.00	0.00	41.16	6.13
2143	2538	3.075283	TGGGGTGGTTGTTGTATCTGAAT	59.925	43.478	0.00	0.00	0.00	2.57
2355	2843	5.743872	CAGTAAAGTTTTTCAACTGTGGCTC	59.256	40.000	7.73	0.00	42.89	4.70
2388	2876	4.529109	AACTGAGAAGACACTAGCCTTC	57.471	45.455	10.45	10.45	39.14	3.46
2403	2891	7.487829	TGTTTTTGCTTTGCTTAGTTAACTGAG	59.512	33.333	20.18	20.18	33.25	3.35
2461	2950	2.604046	AGTCGTGATTGGCATCTACC	57.396	50.000	0.00	0.00	0.00	3.18
2501	3022	0.906775	AGCAAGGGCATGGATTTTGG	59.093	50.000	0.00	0.00	44.61	3.28
2509	3030	3.458163	CAGGGCAGCAAGGGCATG	61.458	66.667	0.00	0.00	44.61	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.