AutoCloner

Multiple sequence alignment - TraesCS5A01G042500

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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	TraesCS5A01G042500	chr5A	100.000	5413	0	0	1	5413	38709864	38715276	0.000000e+00	9997.0
1	TraesCS5A01G042500	chr5A	94.578	830	37	5	3	828	342343903	342344728	0.000000e+00	1277.0
2	TraesCS5A01G042500	chr5A	92.410	830	38	13	1	827	697873493	697872686	0.000000e+00	1160.0
3	TraesCS5A01G042500	chr5A	92.240	799	47	9	31	825	488438825	488438038	0.000000e+00	1118.0
4	TraesCS5A01G042500	chr5A	100.000	28	0	0	805	832	83968324	83968351	1.000000e-02	52.8
5	TraesCS5A01G042500	chr5B	91.445	4243	261	39	826	5030	51788953	51793131	0.000000e+00	5731.0
6	TraesCS5A01G042500	chr5B	93.784	370	19	3	5047	5413	51793178	51793546	2.200000e-153	553.0
7	TraesCS5A01G042500	chr5D	96.343	3199	98	9	2222	5413	49018198	49021384	0.000000e+00	5241.0
8	TraesCS5A01G042500	chr5D	93.690	1363	57	14	830	2181	49016856	49018200	0.000000e+00	2013.0
9	TraesCS5A01G042500	chr6A	94.478	833	37	6	1	827	566597983	566597154	0.000000e+00	1275.0
10	TraesCS5A01G042500	chr3A	93.990	832	44	5	1	830	667309390	667308563	0.000000e+00	1254.0
11	TraesCS5A01G042500	chr3A	88.755	827	47	18	1	826	656431812	656432593	0.000000e+00	970.0
12	TraesCS5A01G042500	chr2A	93.961	828	44	4	1	825	738124209	738125033	0.000000e+00	1247.0
13	TraesCS5A01G042500	chr1A	93.713	684	35	6	31	709	490793422	490794102	0.000000e+00	1018.0
14	TraesCS5A01G042500	chr7A	89.924	794	58	16	1	786	202749455	202748676	0.000000e+00	1003.0
15	TraesCS5A01G042500	chr7A	94.885	391	20	0	2431	2821	303955066	303955456	3.580000e-171	612.0
16	TraesCS5A01G042500	chr7A	83.028	654	88	13	1680	2327	303950133	303950769	6.080000e-159	571.0
17	TraesCS5A01G042500	chr7A	83.694	601	64	15	3159	3753	303956024	303956596	2.220000e-148	536.0
18	TraesCS5A01G042500	chr7A	97.619	84	2	0	3850	3933	303956804	303956721	1.570000e-30	145.0
19	TraesCS5A01G042500	chr1D	94.608	612	28	3	1	611	335078457	335079064	0.000000e+00	942.0
20	TraesCS5A01G042500	chr7D	95.325	385	18	0	2431	2815	271751301	271751685	3.580000e-171	612.0
21	TraesCS5A01G042500	chr7D	83.028	601	68	15	3159	3753	271752247	271752819	1.040000e-141	514.0
22	TraesCS5A01G042500	chr7D	81.555	656	81	18	1678	2327	271748205	271748826	6.260000e-139	505.0
23	TraesCS5A01G042500	chr7D	86.552	290	20	12	3850	4130	271753164	271753443	8.810000e-78	302.0
24	TraesCS5A01G042500	chr7B	94.373	391	22	0	2431	2821	267337705	267337315	7.760000e-168	601.0
25	TraesCS5A01G042500	chr7B	82.587	603	65	21	3159	3753	267336764	267336194	3.770000e-136	496.0
26	TraesCS5A01G042500	chr7B	79.610	667	91	23	1683	2333	267341287	267340650	2.320000e-118	436.0
27	TraesCS5A01G042500	chr7B	85.473	296	24	12	3850	4136	267335950	267335665	1.910000e-74	291.0
28	TraesCS5A01G042500	chr3D	95.122	41	2	0	1374	1414	26665589	26665629	1.260000e-06	65.8

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	TraesCS5A01G042500	chr5A	38709864	38715276	5412	False	9997.00	9997	100.00000	1	5413	1	chr5A.!!$F1	5412
1	TraesCS5A01G042500	chr5A	342343903	342344728	825	False	1277.00	1277	94.57800	3	828	1	chr5A.!!$F3	825
2	TraesCS5A01G042500	chr5A	697872686	697873493	807	True	1160.00	1160	92.41000	1	827	1	chr5A.!!$R2	826
3	TraesCS5A01G042500	chr5A	488438038	488438825	787	True	1118.00	1118	92.24000	31	825	1	chr5A.!!$R1	794
4	TraesCS5A01G042500	chr5B	51788953	51793546	4593	False	3142.00	5731	92.61450	826	5413	2	chr5B.!!$F1	4587
5	TraesCS5A01G042500	chr5D	49016856	49021384	4528	False	3627.00	5241	95.01650	830	5413	2	chr5D.!!$F1	4583
6	TraesCS5A01G042500	chr6A	566597154	566597983	829	True	1275.00	1275	94.47800	1	827	1	chr6A.!!$R1	826
7	TraesCS5A01G042500	chr3A	667308563	667309390	827	True	1254.00	1254	93.99000	1	830	1	chr3A.!!$R1	829
8	TraesCS5A01G042500	chr3A	656431812	656432593	781	False	970.00	970	88.75500	1	826	1	chr3A.!!$F1	825
9	TraesCS5A01G042500	chr2A	738124209	738125033	824	False	1247.00	1247	93.96100	1	825	1	chr2A.!!$F1	824
10	TraesCS5A01G042500	chr1A	490793422	490794102	680	False	1018.00	1018	93.71300	31	709	1	chr1A.!!$F1	678
11	TraesCS5A01G042500	chr7A	202748676	202749455	779	True	1003.00	1003	89.92400	1	786	1	chr7A.!!$R1	785
12	TraesCS5A01G042500	chr7A	303955066	303956596	1530	False	574.00	612	89.28950	2431	3753	2	chr7A.!!$F2	1322
13	TraesCS5A01G042500	chr7A	303950133	303950769	636	False	571.00	571	83.02800	1680	2327	1	chr7A.!!$F1	647
14	TraesCS5A01G042500	chr1D	335078457	335079064	607	False	942.00	942	94.60800	1	611	1	chr1D.!!$F1	610
15	TraesCS5A01G042500	chr7D	271748205	271753443	5238	False	483.25	612	86.61500	1678	4130	4	chr7D.!!$F1	2452
16	TraesCS5A01G042500	chr7B	267335665	267341287	5622	True	456.00	601	85.51075	1683	4136	4	chr7B.!!$R1	2453

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	Hairpin	End Stability	Orientation
383	387	0.323087	TGGGAGGTCGATCTTCACGA	60.323	55.000	6.26	37.43	4.35	F
391	395	1.128136	TCGATCTTCACGACAGACGAC	59.872	52.381	0.00	45.77	4.34	F
913	971	1.135139	GCCATCAGCGTAAGTGAGAGA	59.865	52.381	0.00	41.68	3.10	F
1737	1825	0.902516	GCAATAACCTGTTGGCCCCA	60.903	55.000	0.00	36.63	4.96	F
2015	2103	0.385598	CGTGTCGACTCTTCGCTCAA	60.386	55.000	17.92	45.46	3.02	F
3441	7136	0.032217	GGGCCATCATCAAGGGGAAA	60.032	55.000	4.39	0.00	3.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1711	1799	1.204467	CAACAGGTTATTGCCGCCATT	59.796	47.619	0.00	0.00	3.16	R
1722	1810	1.765074	GAGTGGGGCCAACAGGTTA	59.235	57.895	14.90	0.00	2.85	R
1815	1903	1.902508	GAGACCATGAAGAGTCCCACA	59.097	52.381	0.00	33.29	4.17	R
3441	7136	0.764369	TGCCAACTGAGTGGAGGTCT	60.764	55.000	5.45	41.65	3.85	R
3975	7942	0.538287	ACCTTGCTTGCCTCCAGTTC	60.538	55.000	0.00	0.00	3.01	R
5218	9227	0.106419	GGGTGTGGGTGGTTTTCTCA	60.106	55.000	0.00	0.00	3.27	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
86	87	0.389817	CCGGACGCAGATGAACTTCA	60.390	55.000	0.00	0.00	0.00	3.02
256	260	3.518998	CTGGAGGACGTCGCCGAT	61.519	66.667	17.80	0.00	38.24	4.18
383	387	0.323087	TGGGAGGTCGATCTTCACGA	60.323	55.000	6.26	0.00	37.43	4.35
391	395	1.128136	TCGATCTTCACGACAGACGAC	59.872	52.381	0.00	0.00	45.77	4.34
428	432	2.184830	TGGCTCGATACCTCGGACG	61.185	63.158	6.23	0.00	45.10	4.79
496	501	7.295340	TGGAGTAGTTTCTATCTAGTATGCCA	58.705	38.462	0.00	0.00	0.00	4.92
913	971	1.135139	GCCATCAGCGTAAGTGAGAGA	59.865	52.381	0.00	0.00	41.68	3.10
973	1031	1.497286	GTAGGCCCAACCATCCCAATA	59.503	52.381	0.00	0.00	43.14	1.90
1562	1624	5.543507	AGACTTATATCCTGTGGAGCTTG	57.456	43.478	0.00	0.00	34.05	4.01
1563	1625	4.965532	AGACTTATATCCTGTGGAGCTTGT	59.034	41.667	0.00	0.00	34.05	3.16
1564	1626	6.136857	AGACTTATATCCTGTGGAGCTTGTA	58.863	40.000	0.00	0.00	34.05	2.41
1565	1627	6.266558	AGACTTATATCCTGTGGAGCTTGTAG	59.733	42.308	0.00	0.00	34.05	2.74
1593	1655	3.624410	TGTTTCTGCTGCTATGCATACTG	59.376	43.478	1.16	5.72	42.48	2.74
1594	1656	3.825143	TTCTGCTGCTATGCATACTGA	57.175	42.857	1.16	0.18	42.48	3.41
1595	1657	3.382048	TCTGCTGCTATGCATACTGAG	57.618	47.619	1.16	0.00	42.48	3.35
1624	1700	6.429385	GCCTAGCAAATAGTCATATTCTTGCT	59.571	38.462	11.40	11.40	43.24	3.91
1668	1744	2.412847	GCGCAGATTCTTGTGTTGTACC	60.413	50.000	0.30	0.00	0.00	3.34
1711	1799	2.044252	AGCCCTCGCCTTCGACTA	60.044	61.111	0.00	0.00	40.21	2.59
1722	1810	1.299541	CTTCGACTAATGGCGGCAAT	58.700	50.000	18.31	11.08	0.00	3.56
1727	1815	2.572290	GACTAATGGCGGCAATAACCT	58.428	47.619	18.31	0.00	0.00	3.50
1737	1825	0.902516	GCAATAACCTGTTGGCCCCA	60.903	55.000	0.00	0.00	36.63	4.96
1754	1842	3.295273	ACTCGTCGAGCTGTGGCA	61.295	61.111	22.00	0.00	41.70	4.92
1755	1843	2.049156	CTCGTCGAGCTGTGGCAA	60.049	61.111	9.74	0.00	41.70	4.52
1782	1870	1.136828	TGCAACCGCTAGGGGATTAT	58.863	50.000	31.00	11.80	43.47	1.28
2015	2103	0.385598	CGTGTCGACTCTTCGCTCAA	60.386	55.000	17.92	0.00	45.46	3.02
2043	2131	0.664761	ATGCATATGTTGAGGTGCGC	59.335	50.000	0.00	0.00	40.34	6.09
2100	2189	9.903682	CATCAATAATTCATGTCAATAGTTCCC	57.096	33.333	0.00	0.00	0.00	3.97
2133	2222	7.952671	TGGTATCCATAGATTTCTCACTGTAC	58.047	38.462	0.00	0.00	33.67	2.90
2186	2286	6.731164	ACACAAAATAAAGTTGTTAGTCCCG	58.269	36.000	0.00	0.00	37.09	5.14
2220	2320	1.131638	TCACTCTGGAAGGTGTTGCT	58.868	50.000	0.00	0.00	36.76	3.91
2254	2355	1.265095	CTGAGTGCTTGCAATTCGTGT	59.735	47.619	0.00	0.00	0.00	4.49
2268	2369	6.423302	TGCAATTCGTGTAAGCATTTTTCAAT	59.577	30.769	0.00	0.00	0.00	2.57
2308	2409	7.671495	AGTTTGCCCAATAAATCATTTTGTC	57.329	32.000	0.00	0.00	0.00	3.18
2334	5690	8.781196	CACATTTCTCCTGTTCCATTATGATAG	58.219	37.037	0.00	0.00	0.00	2.08
2413	5779	2.908634	CTGCAGTTTCTTTGCTGTACG	58.091	47.619	5.25	0.00	42.02	3.67
2704	6095	5.187687	CACTGGTTGGTATATTTACCCGTT	58.812	41.667	9.57	0.00	46.41	4.44
2810	6201	3.307480	CCTCTCCTTTCACGGGTACAATT	60.307	47.826	0.00	0.00	0.00	2.32
3003	6683	3.630312	TCTTGCAGTAGTGTTTCCCAAAC	59.370	43.478	0.00	0.00	41.73	2.93
3086	6774	1.340017	GGCTGGTTCTGCATTACCTCA	60.340	52.381	15.89	0.00	35.41	3.86
3098	6786	6.261603	TCTGCATTACCTCATAGCATTTCTTG	59.738	38.462	0.00	0.00	34.35	3.02
3347	7038	4.320608	TGGGTTGAACTGCTGAAAATTC	57.679	40.909	0.00	0.00	0.00	2.17
3424	7118	1.541588	GCTTGGCTAACTGTTTCAGGG	59.458	52.381	0.00	0.00	35.51	4.45
3441	7136	0.032217	GGGCCATCATCAAGGGGAAA	60.032	55.000	4.39	0.00	0.00	3.13
3533	7229	5.049129	GCCTTCTCCACATATATGCAGTTTC	60.049	44.000	12.79	0.00	0.00	2.78
3787	7727	2.104792	ACCAACTGCTGTTTCTGCTCTA	59.895	45.455	6.20	0.00	33.52	2.43
3795	7735	7.849169	AACTGCTGTTTCTGCTCTATTATAGCA	60.849	37.037	2.72	3.99	39.33	3.49
3848	7806	3.844211	TCTTACTTGTCCTTATGCCACCT	59.156	43.478	0.00	0.00	0.00	4.00
4275	8243	4.472691	TTCTGCATTCTTGACACGAAAG	57.527	40.909	0.00	0.00	0.00	2.62
4357	8325	1.816224	GTTGTGGTTGAACAGGTGTGT	59.184	47.619	0.00	0.00	39.19	3.72
4434	8402	1.327303	TTTGTCCCATGAACAGTGGC	58.673	50.000	0.00	0.00	35.35	5.01
4588	8556	8.472007	TTTTTCTTTCCCAGCATAAAACTAGA	57.528	30.769	0.00	0.00	0.00	2.43
4910	8885	0.038455	AGTGAGTGAGCGGACTAGGT	59.962	55.000	0.00	0.00	0.00	3.08
4922	8897	3.429135	GCGGACTAGGTTTTCTCTGGTAG	60.429	52.174	0.00	0.00	0.00	3.18
4958	8933	8.363390	TGCAACATGAGTGGAAACATATTTAAA	58.637	29.630	0.00	0.00	46.14	1.52
5005	8980	2.813061	CAAGAACAAAGCAACCACCTG	58.187	47.619	0.00	0.00	0.00	4.00
5044	9050	1.202510	GGCATGAACAAAGCAACCACA	60.203	47.619	0.00	0.00	0.00	4.17
5045	9051	2.129607	GCATGAACAAAGCAACCACAG	58.870	47.619	0.00	0.00	0.00	3.66
5190	9199	5.879223	GCATAGATTTCTAGCTATGGTGCAT	59.121	40.000	13.66	0.00	46.16	3.96
5218	9227	0.251341	AAAAGAGGCAAGGCACCGAT	60.251	50.000	0.00	0.00	0.00	4.18
5329	9338	4.098654	TGCTTTGCTTGTTTGGCTACTTTA	59.901	37.500	0.00	0.00	0.00	1.85
5335	9344	4.560513	GCTTGTTTGGCTACTTTATTGGCA	60.561	41.667	0.00	0.00	36.84	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
187	191	1.824329	GTCCTCCTCGGCGATGAGA	60.824	63.158	33.98	21.07	38.28	3.27
428	432	0.738975	TCATCATCCTCGTCGGTGTC	59.261	55.000	0.00	0.00	0.00	3.67
496	501	7.284944	ACGGTGCAAGTAGATAGAAACTACTAT	59.715	37.037	0.00	0.00	46.29	2.12
665	672	1.010797	CTAAAATGCAGCGCGCGAT	60.011	52.632	37.18	28.60	46.97	4.58
751	809	1.998285	CGCGCATCGTCTGATTTGA	59.002	52.632	8.75	0.00	30.49	2.69
804	862	3.869272	GCATCTCCAACAGGCGCG	61.869	66.667	0.00	0.00	0.00	6.86
868	926	0.856641	CGAACGTCGTTGTTGACCAT	59.143	50.000	16.75	0.00	35.40	3.55
1021	1079	3.063084	GTCCGTCGCTGGAGAGGT	61.063	66.667	0.00	0.00	39.14	3.85
1206	1265	4.717313	GTGGCCCAGTTCCCGACC	62.717	72.222	0.00	0.00	0.00	4.79
1562	1624	6.144724	GCATAGCAGCAGAAACATACTACTAC	59.855	42.308	0.00	0.00	0.00	2.73
1563	1625	6.183360	TGCATAGCAGCAGAAACATACTACTA	60.183	38.462	0.00	0.00	40.11	1.82
1564	1626	5.053145	GCATAGCAGCAGAAACATACTACT	58.947	41.667	0.00	0.00	0.00	2.57
1565	1627	4.811024	TGCATAGCAGCAGAAACATACTAC	59.189	41.667	0.00	0.00	40.11	2.73
1593	1655	4.408182	TGACTATTTGCTAGGCTTCCTC	57.592	45.455	0.00	0.00	36.32	3.71
1594	1656	6.694445	ATATGACTATTTGCTAGGCTTCCT	57.306	37.500	0.00	0.00	36.32	3.36
1595	1657	7.164803	AGAATATGACTATTTGCTAGGCTTCC	58.835	38.462	0.00	0.00	36.32	3.46
1647	1723	2.412847	GGTACAACACAAGAATCTGCGC	60.413	50.000	0.00	0.00	0.00	6.09
1648	1724	2.805671	TGGTACAACACAAGAATCTGCG	59.194	45.455	0.00	0.00	31.92	5.18
1668	1744	3.570638	CTCGAGGCTGCCGCATTG	61.571	66.667	22.18	6.35	38.10	2.82
1708	1796	2.297701	CAGGTTATTGCCGCCATTAGT	58.702	47.619	0.00	0.00	0.00	2.24
1711	1799	1.204467	CAACAGGTTATTGCCGCCATT	59.796	47.619	0.00	0.00	0.00	3.16
1722	1810	1.765074	GAGTGGGGCCAACAGGTTA	59.235	57.895	14.90	0.00	0.00	2.85
1727	1815	4.308458	CGACGAGTGGGGCCAACA	62.308	66.667	14.90	0.00	0.00	3.33
1737	1825	2.856628	TTGCCACAGCTCGACGAGT	61.857	57.895	24.80	10.04	40.80	4.18
1782	1870	2.125147	CTGCGCTTCCCGAATCCA	60.125	61.111	9.73	0.00	40.02	3.41
1815	1903	1.902508	GAGACCATGAAGAGTCCCACA	59.097	52.381	0.00	0.00	33.29	4.17
1908	1996	2.333926	CTGAACTCGAACACGGCATTA	58.666	47.619	0.00	0.00	0.00	1.90
1911	1999	1.954146	GCTGAACTCGAACACGGCA	60.954	57.895	10.07	0.00	35.13	5.69
2015	2103	6.709397	CACCTCAACATATGCATCAATACTCT	59.291	38.462	0.19	0.00	0.00	3.24
2043	2131	3.683822	GGAGAGAGCAAGAAGTGTTGATG	59.316	47.826	0.00	0.00	0.00	3.07
2093	2181	6.956102	TGGATACCAGTAAAAAGGGAACTA	57.044	37.500	0.00	0.00	42.68	2.24
2133	2222	8.035394	AGTTTCCACATACTACATTCTACACAG	58.965	37.037	0.00	0.00	0.00	3.66
2181	2281	3.813166	TGAATTTTGTCAGAGTTCGGGAC	59.187	43.478	0.00	0.00	0.00	4.46
2186	2286	5.760253	TCCAGAGTGAATTTTGTCAGAGTTC	59.240	40.000	0.00	0.00	0.00	3.01
2268	2369	6.948886	TGGGCAAACTAAATTATGGTTCAGTA	59.051	34.615	0.00	0.00	0.00	2.74
2334	5690	2.629656	GCATGCCACACCCACTCAC	61.630	63.158	6.36	0.00	0.00	3.51
2395	5761	3.813529	ATCGTACAGCAAAGAAACTGC	57.186	42.857	0.00	0.00	37.42	4.40
2704	6095	6.418101	CAATTTCCTCCATGTCTCTTCCTAA	58.582	40.000	0.00	0.00	0.00	2.69
2810	6201	8.450578	AATGTCACACAAGAATTAGTCAGAAA	57.549	30.769	0.00	0.00	0.00	2.52
2948	6628	3.849911	CTTCGCAGAACTTCATCAGGTA	58.150	45.455	0.00	0.00	45.90	3.08
2982	6662	3.243401	GGTTTGGGAAACACTACTGCAAG	60.243	47.826	0.00	0.00	43.15	4.01
3003	6683	9.801873	TTTCTTCACAAATAAAAAGAACTGAGG	57.198	29.630	0.00	0.00	37.44	3.86
3050	6738	3.105283	CCAGCCCCCTATATAGTACCAC	58.895	54.545	8.92	0.00	0.00	4.16
3086	6774	5.163581	GCCATCACTTGACAAGAAATGCTAT	60.164	40.000	21.95	0.00	0.00	2.97
3098	6786	7.826252	AGGACATAATATATGCCATCACTTGAC	59.174	37.037	11.01	0.00	0.00	3.18
3157	6845	8.131100	CAGGACATATATGGAAAACATGTTGAC	58.869	37.037	12.82	9.12	40.82	3.18
3347	7038	4.037208	GCAACATGATGGACCTAATCTTGG	59.963	45.833	0.00	0.00	34.90	3.61
3424	7118	2.027385	GTCTTTCCCCTTGATGATGGC	58.973	52.381	0.00	0.00	0.00	4.40
3441	7136	0.764369	TGCCAACTGAGTGGAGGTCT	60.764	55.000	5.45	0.00	41.65	3.85
3511	7207	6.294473	AGGAAACTGCATATATGTGGAGAAG	58.706	40.000	24.31	2.99	39.62	2.85
3533	7229	5.065731	GTCTGCAAATAAGTTGAGATCCAGG	59.934	44.000	0.00	0.00	39.87	4.45
3787	7727	6.639632	ATTTTGCACTTCCGATGCTATAAT	57.360	33.333	0.00	0.00	43.77	1.28
3795	7735	4.081752	TGCCATAAATTTTGCACTTCCGAT	60.082	37.500	0.00	0.00	0.00	4.18
3797	7737	3.583806	TGCCATAAATTTTGCACTTCCG	58.416	40.909	0.00	0.00	0.00	4.30
3848	7806	3.214328	GGAAGACTTCAACCTTCTGCAA	58.786	45.455	16.85	0.00	38.92	4.08
3975	7942	0.538287	ACCTTGCTTGCCTCCAGTTC	60.538	55.000	0.00	0.00	0.00	3.01
4275	8243	5.933790	TCGACAACAACAAATAATACTGCC	58.066	37.500	0.00	0.00	0.00	4.85
4357	8325	9.378551	CACAATAGTACTAGCAAATTCCTTGTA	57.621	33.333	8.85	0.00	37.36	2.41
4434	8402	8.908903	AGTAGTAGTTCATTAGATGTTCAGGAG	58.091	37.037	0.00	0.00	0.00	3.69
4788	8763	4.341783	AGGCAGCTGCAGTGACCC	62.342	66.667	37.63	19.72	44.36	4.46
4886	8861	0.458716	GTCCGCTCACTCACTAAGGC	60.459	60.000	0.00	0.00	0.00	4.35
4910	8885	5.526115	CACAACGTCTACTACCAGAGAAAA	58.474	41.667	0.00	0.00	0.00	2.29
4922	8897	2.800544	ACTCATGTTGCACAACGTCTAC	59.199	45.455	5.27	0.00	43.94	2.59
4958	8933	7.856145	AATTCTTAGTCAATCGAGCTTTGAT	57.144	32.000	2.78	0.00	35.68	2.57
5005	8980	1.545651	CCAAACCAAGTCACCTCCCTC	60.546	57.143	0.00	0.00	0.00	4.30
5044	9050	6.489361	AGAAGAAACAGCAATGAATCAGAACT	59.511	34.615	0.00	0.00	0.00	3.01
5045	9051	6.675987	AGAAGAAACAGCAATGAATCAGAAC	58.324	36.000	0.00	0.00	0.00	3.01
5129	9138	6.014840	GGGGCAATCAATATCATCAAGACAAT	60.015	38.462	0.00	0.00	0.00	2.71
5190	9199	3.880117	GCCTTGCCTCTTTTGGGGTAATA	60.880	47.826	0.00	0.00	43.73	0.98
5218	9227	0.106419	GGGTGTGGGTGGTTTTCTCA	60.106	55.000	0.00	0.00	0.00	3.27
5329	9338	4.706035	TCAGCAGAAAACAAATTGCCAAT	58.294	34.783	0.00	0.00	37.26	3.16
5335	9344	5.581874	CCAACAGTTCAGCAGAAAACAAATT	59.418	36.000	0.00	0.00	35.08	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.