AutoCloner

Multiple sequence alignment - TraesCS4B01G127200

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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	TraesCS4B01G127200	chr4B	100.000	5313	0	0	1	5313	166560932	166555620	0.000000e+00	9812.0
1	TraesCS4B01G127200	chr4B	93.902	82	4	1	4346	4427	625077148	625077228	7.230000e-24	122.0
2	TraesCS4B01G127200	chr4D	96.326	2014	48	3	3318	5313	131824588	131826593	0.000000e+00	3286.0
3	TraesCS4B01G127200	chr4D	93.879	1356	56	6	2059	3399	131823266	131824609	0.000000e+00	2019.0
4	TraesCS4B01G127200	chr4D	88.554	166	6	3	1756	1908	131822727	131822892	7.020000e-44	189.0
5	TraesCS4B01G127200	chr4D	88.235	68	6	2	3337	3404	131824519	131824584	4.410000e-11	80.5
6	TraesCS4B01G127200	chr4A	91.291	1596	105	12	1832	3404	432537240	432535656	0.000000e+00	2146.0
7	TraesCS4B01G127200	chr4A	92.420	752	41	5	4574	5313	432530621	432529874	0.000000e+00	1059.0
8	TraesCS4B01G127200	chr4A	95.994	649	26	0	3326	3974	432535126	432534478	0.000000e+00	1055.0
9	TraesCS4B01G127200	chr4A	89.291	635	68	0	4	638	692437113	692436479	0.000000e+00	797.0
10	TraesCS4B01G127200	chr4A	88.997	309	22	2	4291	4587	432531577	432531269	6.500000e-99	372.0
11	TraesCS4B01G127200	chr4A	88.444	225	17	3	3180	3404	432535383	432535168	4.080000e-66	263.0
12	TraesCS4B01G127200	chr4A	83.566	286	35	9	1408	1685	625090197	625090478	1.900000e-64	257.0
13	TraesCS4B01G127200	chr4A	94.118	170	7	1	4113	4282	432532141	432531975	6.830000e-64	255.0
14	TraesCS4B01G127200	chr4A	92.763	152	1	2	3972	4113	432534450	432534299	1.500000e-50	211.0
15	TraesCS4B01G127200	chr5B	94.380	1121	44	14	651	1764	255894765	255893657	0.000000e+00	1703.0
16	TraesCS4B01G127200	chr5B	95.768	638	27	0	1	638	697339696	697339059	0.000000e+00	1029.0
17	TraesCS4B01G127200	chr5B	89.308	636	67	1	1	636	37469901	37469267	0.000000e+00	797.0
18	TraesCS4B01G127200	chr5B	79.654	462	63	6	4864	5313	569939193	569938751	2.400000e-78	303.0
19	TraesCS4B01G127200	chr7D	93.722	1131	48	12	644	1762	41522910	41521791	0.000000e+00	1674.0
20	TraesCS4B01G127200	chr7D	91.003	678	41	8	1098	1759	333634871	333634198	0.000000e+00	896.0
21	TraesCS4B01G127200	chr7D	90.352	653	42	10	651	1292	569138703	569138061	0.000000e+00	837.0
22	TraesCS4B01G127200	chr7D	96.070	458	11	2	644	1101	333650296	333649846	0.000000e+00	739.0
23	TraesCS4B01G127200	chr7D	79.371	509	79	18	4809	5313	55651991	55652477	8.530000e-88	335.0
24	TraesCS4B01G127200	chr7D	92.254	142	11	0	1621	1762	569138059	569137918	9.020000e-48	202.0
25	TraesCS4B01G127200	chr7D	95.181	83	3	1	4346	4427	634756902	634756820	4.320000e-26	130.0
26	TraesCS4B01G127200	chr7D	93.976	83	4	1	4346	4427	634718355	634718273	2.010000e-24	124.0
27	TraesCS4B01G127200	chr7D	92.683	82	6	0	4346	4427	481835888	481835969	9.350000e-23	119.0
28	TraesCS4B01G127200	chr7D	92.771	83	5	1	4345	4427	634737403	634737322	9.350000e-23	119.0
29	TraesCS4B01G127200	chr5D	92.356	1125	66	11	644	1759	540006939	540008052	0.000000e+00	1583.0
30	TraesCS4B01G127200	chr6A	92.117	1091	64	11	644	1727	72843709	72842634	0.000000e+00	1519.0
31	TraesCS4B01G127200	chr6A	85.249	1166	94	38	644	1759	426255733	426254596	0.000000e+00	1129.0
32	TraesCS4B01G127200	chr1A	85.860	1174	84	40	644	1764	315264492	315263348	0.000000e+00	1173.0
33	TraesCS4B01G127200	chr1A	89.308	636	68	0	1	636	576657007	576657642	0.000000e+00	798.0
34	TraesCS4B01G127200	chr1A	95.946	74	3	0	4354	4427	119739090	119739017	2.600000e-23	121.0
35	TraesCS4B01G127200	chr2B	95.298	638	30	0	1	638	2454705	2454068	0.000000e+00	1013.0
36	TraesCS4B01G127200	chr2B	85.729	995	81	31	806	1754	12087092	12088071	0.000000e+00	994.0
37	TraesCS4B01G127200	chr3A	85.699	965	68	36	644	1558	707699669	707700613	0.000000e+00	953.0
38	TraesCS4B01G127200	chr3A	88.832	197	14	4	1564	1759	707833284	707833473	8.900000e-58	235.0
39	TraesCS4B01G127200	chrUn	85.216	974	74	34	644	1567	303635703	303634750	0.000000e+00	937.0
40	TraesCS4B01G127200	chrUn	87.659	786	56	21	644	1406	383713699	383712932	0.000000e+00	876.0
41	TraesCS4B01G127200	chrUn	89.028	638	67	2	1	638	50137473	50138107	0.000000e+00	787.0
42	TraesCS4B01G127200	chr1B	91.693	638	49	4	1	636	349356135	349356770	0.000000e+00	881.0
43	TraesCS4B01G127200	chr1B	90.738	637	56	3	1	636	8125142	8125776	0.000000e+00	846.0
44	TraesCS4B01G127200	chr1B	94.332	247	14	0	1505	1751	4033030	4032784	3.880000e-101	379.0
45	TraesCS4B01G127200	chr1B	90.000	160	14	2	1434	1591	161326453	161326612	6.970000e-49	206.0
46	TraesCS4B01G127200	chr7B	89.879	662	45	8	644	1290	633236846	633237500	0.000000e+00	832.0
47	TraesCS4B01G127200	chr7B	90.094	636	63	0	1	636	448649024	448648389	0.000000e+00	826.0
48	TraesCS4B01G127200	chr6D	79.191	519	69	15	4809	5313	424548427	424547934	1.850000e-84	324.0
49	TraesCS4B01G127200	chr5A	80.357	168	27	6	5006	5171	625002826	625002663	7.230000e-24	122.0
50	TraesCS4B01G127200	chr7A	93.827	81	3	1	4347	4427	731255743	731255821	2.600000e-23	121.0

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	TraesCS4B01G127200	chr4B	166555620	166560932	5312	True	9812.000000	9812	100.000000	1	5313	1	chr4B.!!$R1	5312
1	TraesCS4B01G127200	chr4D	131822727	131826593	3866	False	1393.625000	3286	91.748500	1756	5313	4	chr4D.!!$F1	3557
2	TraesCS4B01G127200	chr4A	692436479	692437113	634	True	797.000000	797	89.291000	4	638	1	chr4A.!!$R1	634
3	TraesCS4B01G127200	chr4A	432529874	432537240	7366	True	765.857143	2146	92.003857	1832	5313	7	chr4A.!!$R2	3481
4	TraesCS4B01G127200	chr5B	255893657	255894765	1108	True	1703.000000	1703	94.380000	651	1764	1	chr5B.!!$R2	1113
5	TraesCS4B01G127200	chr5B	697339059	697339696	637	True	1029.000000	1029	95.768000	1	638	1	chr5B.!!$R4	637
6	TraesCS4B01G127200	chr5B	37469267	37469901	634	True	797.000000	797	89.308000	1	636	1	chr5B.!!$R1	635
7	TraesCS4B01G127200	chr7D	41521791	41522910	1119	True	1674.000000	1674	93.722000	644	1762	1	chr7D.!!$R1	1118
8	TraesCS4B01G127200	chr7D	333634198	333634871	673	True	896.000000	896	91.003000	1098	1759	1	chr7D.!!$R2	661
9	TraesCS4B01G127200	chr7D	569137918	569138703	785	True	519.500000	837	91.303000	651	1762	2	chr7D.!!$R7	1111
10	TraesCS4B01G127200	chr5D	540006939	540008052	1113	False	1583.000000	1583	92.356000	644	1759	1	chr5D.!!$F1	1115
11	TraesCS4B01G127200	chr6A	72842634	72843709	1075	True	1519.000000	1519	92.117000	644	1727	1	chr6A.!!$R1	1083
12	TraesCS4B01G127200	chr6A	426254596	426255733	1137	True	1129.000000	1129	85.249000	644	1759	1	chr6A.!!$R2	1115
13	TraesCS4B01G127200	chr1A	315263348	315264492	1144	True	1173.000000	1173	85.860000	644	1764	1	chr1A.!!$R2	1120
14	TraesCS4B01G127200	chr1A	576657007	576657642	635	False	798.000000	798	89.308000	1	636	1	chr1A.!!$F1	635
15	TraesCS4B01G127200	chr2B	2454068	2454705	637	True	1013.000000	1013	95.298000	1	638	1	chr2B.!!$R1	637
16	TraesCS4B01G127200	chr2B	12087092	12088071	979	False	994.000000	994	85.729000	806	1754	1	chr2B.!!$F1	948
17	TraesCS4B01G127200	chr3A	707699669	707700613	944	False	953.000000	953	85.699000	644	1558	1	chr3A.!!$F1	914
18	TraesCS4B01G127200	chrUn	303634750	303635703	953	True	937.000000	937	85.216000	644	1567	1	chrUn.!!$R1	923
19	TraesCS4B01G127200	chrUn	383712932	383713699	767	True	876.000000	876	87.659000	644	1406	1	chrUn.!!$R2	762
20	TraesCS4B01G127200	chrUn	50137473	50138107	634	False	787.000000	787	89.028000	1	638	1	chrUn.!!$F1	637
21	TraesCS4B01G127200	chr1B	349356135	349356770	635	False	881.000000	881	91.693000	1	636	1	chr1B.!!$F3	635
22	TraesCS4B01G127200	chr1B	8125142	8125776	634	False	846.000000	846	90.738000	1	636	1	chr1B.!!$F1	635
23	TraesCS4B01G127200	chr7B	633236846	633237500	654	False	832.000000	832	89.879000	644	1290	1	chr7B.!!$F1	646
24	TraesCS4B01G127200	chr7B	448648389	448649024	635	True	826.000000	826	90.094000	1	636	1	chr7B.!!$R1	635

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
279	280	1.211703	TGTCTGACTCCCTGTTTGCAA	59.788	47.619	9.51	0.0	0.00	4.08	F
1822	1924	0.104304	CACCGTATGTCTAGCCCCAC	59.896	60.000	0.00	0.0	0.00	4.61	F
2277	2610	0.034059	CACACAAAGAGGACCTCGCT	59.966	55.000	15.97	4.6	35.36	4.93	F
2581	2914	0.318529	CGAGGACGATGATGCTGAGG	60.319	60.000	0.00	0.0	42.66	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2259	2592	0.034059	CAGCGAGGTCCTCTTTGTGT	59.966	55.000	17.0	0.00	3.72	R
3266	3617	2.305635	ACATAGCCATCTGGTGTGTCAA	59.694	45.455	0.0	42.23	3.18	R
3904	4854	0.944311	GCGAGGACGTTGCTTGAGAA	60.944	55.000	0.0	41.98	2.87	R
4378	7928	1.324005	GCTTAGGGTGCGAGAGGTCT	61.324	60.000	0.0	0.00	3.85	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
145	146	2.918934	TGGATCACAGGAAAATCAGGGA	59.081	45.455	0.00	0.00	0.00	4.20
158	159	4.640771	AATCAGGGAAAGCTTGACTACA	57.359	40.909	0.00	0.00	0.00	2.74
177	178	4.322057	ACAAATGGGAGCCTGAATTAGT	57.678	40.909	0.00	0.00	0.00	2.24
250	251	8.889717	CAAGTACAAAAAGTAGAGGAGAAACAA	58.110	33.333	0.00	0.00	32.19	2.83
279	280	1.211703	TGTCTGACTCCCTGTTTGCAA	59.788	47.619	9.51	0.00	0.00	4.08
440	442	5.913137	TCAAAAGCTTTCTCAAAGTCCAA	57.087	34.783	13.10	0.00	40.64	3.53
461	463	5.397899	CCAATTTGAGGAGGACAATAGGCTA	60.398	44.000	0.00	0.00	0.00	3.93
555	557	6.548251	TGATGAAGCCATATTGATTGATGTGT	59.452	34.615	0.00	0.00	32.09	3.72
638	641	5.574188	AGTGCAATTGAGAAGGGAAATAGT	58.426	37.500	10.34	0.00	0.00	2.12
639	642	5.416952	AGTGCAATTGAGAAGGGAAATAGTG	59.583	40.000	10.34	0.00	0.00	2.74
640	643	4.158394	TGCAATTGAGAAGGGAAATAGTGC	59.842	41.667	10.34	0.00	0.00	4.40
641	644	4.158394	GCAATTGAGAAGGGAAATAGTGCA	59.842	41.667	10.34	0.00	0.00	4.57
642	645	5.336690	GCAATTGAGAAGGGAAATAGTGCAA	60.337	40.000	10.34	0.00	0.00	4.08
968	984	5.869344	GGTGCATAGCATCAACGAAGATATA	59.131	40.000	0.00	0.00	41.91	0.86
1122	1147	0.755686	GGATCCAGAGCCGATGACTT	59.244	55.000	6.95	0.00	0.00	3.01
1328	1369	1.226859	CGTTCGCCGGCTGATCTTA	60.227	57.895	26.68	5.61	0.00	2.10
1350	1399	4.360951	TCTAAAAGATCGGTTGGGTTGT	57.639	40.909	0.00	0.00	0.00	3.32
1390	1439	1.167851	CTCCGTCATTGCAACATGGT	58.832	50.000	15.18	0.00	0.00	3.55
1391	1440	1.131126	CTCCGTCATTGCAACATGGTC	59.869	52.381	15.18	3.40	0.00	4.02
1392	1441	1.167851	CCGTCATTGCAACATGGTCT	58.832	50.000	0.00	0.00	0.00	3.85
1394	1443	2.587956	CGTCATTGCAACATGGTCTTG	58.412	47.619	0.00	0.00	0.00	3.02
1395	1444	2.030893	CGTCATTGCAACATGGTCTTGT	60.031	45.455	0.00	0.00	0.00	3.16
1423	1497	4.708726	AAATCTGCAGTAAAGGTCATGC	57.291	40.909	14.67	0.00	39.14	4.06
1432	1507	3.503748	AGTAAAGGTCATGCTGCAGTTTC	59.496	43.478	16.64	0.00	0.00	2.78
1591	1679	4.502087	GCCAAAGAAAAACATCAGAAGCCT	60.502	41.667	0.00	0.00	0.00	4.58
1766	1856	5.333339	CGTGCATGCTTAATAGTGTACATCC	60.333	44.000	20.33	0.00	0.00	3.51
1783	1873	0.703488	TCCATGATCCAACAGCCCAA	59.297	50.000	0.00	0.00	0.00	4.12
1822	1924	0.104304	CACCGTATGTCTAGCCCCAC	59.896	60.000	0.00	0.00	0.00	4.61
1897	2003	4.462483	AGCGGATCAATGTGTGGTAATTTT	59.538	37.500	0.00	0.00	0.00	1.82
1913	2019	9.447040	GTGGTAATTTTTGAGTCTTTTGTAGTC	57.553	33.333	0.00	0.00	0.00	2.59
1914	2020	8.626526	TGGTAATTTTTGAGTCTTTTGTAGTCC	58.373	33.333	0.00	0.00	0.00	3.85
1982	2088	2.613595	TGATGAGTTGCATGTTATCGGC	59.386	45.455	0.00	0.00	37.34	5.54
1985	2091	3.194861	TGAGTTGCATGTTATCGGCTAC	58.805	45.455	0.00	0.00	34.29	3.58
1991	2097	3.194861	GCATGTTATCGGCTACAGTTCA	58.805	45.455	0.00	0.00	0.00	3.18
2012	2118	2.158475	ACAGAGGAAATGGCAAAGACCA	60.158	45.455	0.00	0.00	45.82	4.02
2026	2132	2.607750	ACCAGCACGACCTCCCAT	60.608	61.111	0.00	0.00	0.00	4.00
2030	2136	0.804989	CAGCACGACCTCCCATTTTC	59.195	55.000	0.00	0.00	0.00	2.29
2081	2410	0.621609	TCCCGGTTCAAATACCCCTG	59.378	55.000	0.00	0.00	34.56	4.45
2097	2426	1.664873	CTGCTCTCCTATGGCCTCG	59.335	63.158	3.32	0.00	0.00	4.63
2259	2592	0.322456	AGAAATTGCTACAGGGCGCA	60.322	50.000	10.83	0.00	34.52	6.09
2277	2610	0.034059	CACACAAAGAGGACCTCGCT	59.966	55.000	15.97	4.60	35.36	4.93
2278	2611	0.034059	ACACAAAGAGGACCTCGCTG	59.966	55.000	15.97	17.78	35.36	5.18
2376	2709	2.126189	GCCGCTAAGGACGTCGTT	60.126	61.111	24.97	24.97	45.00	3.85
2403	2736	4.398319	ACACAAGCTATATTATGGGTGCC	58.602	43.478	0.00	0.00	0.00	5.01
2581	2914	0.318529	CGAGGACGATGATGCTGAGG	60.319	60.000	0.00	0.00	42.66	3.86
2727	3066	8.451748	TCTATATATGACACCGAGAAGAAATCG	58.548	37.037	0.00	0.00	39.86	3.34
2823	3174	6.756074	ACGATGATGATGAGAAGAAAGAGAAC	59.244	38.462	0.00	0.00	0.00	3.01
2856	3207	2.783828	AGGATGACGACGATGATGAC	57.216	50.000	0.00	0.00	0.00	3.06
2875	3226	7.855545	TGATGACGAGAAGAAAGAAAAGAAAG	58.144	34.615	0.00	0.00	0.00	2.62
2907	3258	5.136816	AGGATGATGACGATGATGAGAAG	57.863	43.478	0.00	0.00	0.00	2.85
2961	3312	1.736586	GTCCGAGGATGATGACGCT	59.263	57.895	0.00	0.00	0.00	5.07
2983	3334	6.320944	GCTGAGAAGAAATCTAAAAGCAAGG	58.679	40.000	0.00	0.00	38.96	3.61
2985	3336	6.306987	TGAGAAGAAATCTAAAAGCAAGGGT	58.693	36.000	0.00	0.00	38.96	4.34
2994	3345	4.783227	TCTAAAAGCAAGGGTGAGTCCTAT	59.217	41.667	0.00	0.00	35.80	2.57
3102	3453	3.136763	CGATGAATCTATGCCAGCTGTT	58.863	45.455	13.81	0.00	0.00	3.16
3112	3463	2.591429	CAGCTGTTGACACGCCCA	60.591	61.111	5.25	0.00	0.00	5.36
3156	3507	1.529244	GACCAAGCCACAGTTGCCT	60.529	57.895	0.00	0.00	0.00	4.75
3208	3559	3.302344	CCACGGCCCAACCAAAGG	61.302	66.667	0.00	0.00	39.03	3.11
3279	3630	1.276138	TCAGCGATTGACACACCAGAT	59.724	47.619	0.00	0.00	0.00	2.90
3288	3639	2.305635	TGACACACCAGATGGCTATGTT	59.694	45.455	0.00	0.00	39.32	2.71
3531	4481	1.061570	CTACCCGTACGAGTGCGAC	59.938	63.158	18.76	0.00	41.16	5.19
3904	4854	2.992114	AGAAGGTGCTCGCGGAGT	60.992	61.111	6.13	0.00	31.39	3.85
4096	5085	4.905429	TGACTGTTTATATGGCTGTGTGT	58.095	39.130	0.00	0.00	0.00	3.72
4097	5086	4.694982	TGACTGTTTATATGGCTGTGTGTG	59.305	41.667	0.00	0.00	0.00	3.82
4231	7464	3.443037	TGTGAATGCCAAGTTTCAAACG	58.557	40.909	0.00	0.00	33.90	3.60
4321	7557	5.406780	CAGAGTCTGACGCAGATTAAACTTT	59.593	40.000	15.46	0.00	42.73	2.66
4378	7928	2.415168	GCATTCCGTGAATTGAACTCGA	59.585	45.455	0.00	0.00	28.87	4.04
4398	7948	1.605058	GACCTCTCGCACCCTAAGCA	61.605	60.000	0.00	0.00	0.00	3.91
4487	8037	3.951979	AAAGTTTGTGTTCTCGCTCTG	57.048	42.857	0.00	0.00	0.00	3.35
4708	8921	7.259290	ACCCACTTATAAATGCACTAATTCG	57.741	36.000	0.00	0.00	0.00	3.34
4723	8936	7.095649	TGCACTAATTCGTTATGCATGATAGAC	60.096	37.037	10.16	0.00	41.18	2.59
5002	9215	6.310956	CGTCATTAACCATGTGCATTTTTCAT	59.689	34.615	0.00	0.00	34.06	2.57
5146	9359	5.643379	TGTTCATATTTTCTGAAGGTGGC	57.357	39.130	0.00	0.00	33.49	5.01
5171	9384	4.833390	ACCTACTTTGTGATAGTGCTTCC	58.167	43.478	0.00	0.00	0.00	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	85	1.197036	CTCATATTGCCTGCTGATGCG	59.803	52.381	0.00	0.00	43.34	4.73
145	146	3.507622	GCTCCCATTTGTAGTCAAGCTTT	59.492	43.478	0.00	0.00	34.88	3.51
158	159	5.420104	CAGAAACTAATTCAGGCTCCCATTT	59.580	40.000	0.00	0.00	40.72	2.32
177	178	5.898174	CTTAATGAAGCCATGCATCAGAAA	58.102	37.500	0.00	0.00	39.56	2.52
250	251	1.551329	GGGAGTCAGACAAGGAGACCT	60.551	57.143	2.66	0.00	33.87	3.85
279	280	2.108952	AGTGCCAGGGAAACTCTTTCAT	59.891	45.455	0.00	0.00	41.43	2.57
367	368	7.039011	TGTTATTCTGAGAGCTAGAGGTTTTGA	60.039	37.037	0.00	0.00	0.00	2.69
440	442	4.971924	AGTAGCCTATTGTCCTCCTCAAAT	59.028	41.667	0.00	0.00	0.00	2.32
461	463	7.397221	TCTTCATCAATGTCACCAATCTAAGT	58.603	34.615	0.00	0.00	0.00	2.24
555	557	5.181009	CAGGCTGTGATTCTCAAGATTGTA	58.819	41.667	6.28	0.00	0.00	2.41
608	611	8.593945	TTCCCTTCTCAATTGCACTATTAAAT	57.406	30.769	0.00	0.00	0.00	1.40
612	615	7.836183	ACTATTTCCCTTCTCAATTGCACTATT	59.164	33.333	0.00	0.00	0.00	1.73
638	641	4.771590	CTGAAAGTAGCCTTCAATTGCA	57.228	40.909	0.00	0.00	0.00	4.08
905	921	9.667107	CACTAAATTAGGAACCATCAAAGTAGA	57.333	33.333	4.92	0.00	0.00	2.59
906	922	8.893727	CCACTAAATTAGGAACCATCAAAGTAG	58.106	37.037	4.92	0.00	0.00	2.57
1328	1369	4.700213	CACAACCCAACCGATCTTTTAGAT	59.300	41.667	0.00	0.00	37.73	1.98
1420	1494	3.182341	TGCAAAAAGAAACTGCAGCAT	57.818	38.095	15.27	1.77	41.01	3.79
1423	1497	4.175516	TGAGTTGCAAAAAGAAACTGCAG	58.824	39.130	13.48	13.48	46.48	4.41
1432	1507	5.620467	CAACAAAACCTGAGTTGCAAAAAG	58.380	37.500	0.00	0.00	36.59	2.27
1562	1650	5.811613	TCTGATGTTTTTCTTTGGCAACTTG	59.188	36.000	0.00	0.00	37.61	3.16
1754	1844	6.499106	TGTTGGATCATGGATGTACACTAT	57.501	37.500	0.00	0.00	0.00	2.12
1766	1856	2.133281	TCTTGGGCTGTTGGATCATG	57.867	50.000	0.00	0.00	0.00	3.07
1897	2003	6.174720	ACAGATGGACTACAAAAGACTCAA	57.825	37.500	0.00	0.00	0.00	3.02
1913	2019	1.271543	TGAAGGCAGGACAACAGATGG	60.272	52.381	0.00	0.00	0.00	3.51
1914	2020	1.808945	GTGAAGGCAGGACAACAGATG	59.191	52.381	0.00	0.00	0.00	2.90
1982	2088	3.686726	GCCATTTCCTCTGTGAACTGTAG	59.313	47.826	0.00	0.00	0.00	2.74
1985	2091	2.507484	TGCCATTTCCTCTGTGAACTG	58.493	47.619	0.00	0.00	0.00	3.16
1991	2097	2.158475	TGGTCTTTGCCATTTCCTCTGT	60.158	45.455	0.00	0.00	32.81	3.41
2012	2118	0.322546	GGAAAATGGGAGGTCGTGCT	60.323	55.000	0.00	0.00	0.00	4.40
2041	2147	1.202769	GGGTAGTAGGTGGTTGGCCA	61.203	60.000	0.00	0.00	43.73	5.36
2081	2410	0.825840	ACTCGAGGCCATAGGAGAGC	60.826	60.000	18.41	0.00	0.00	4.09
2097	2426	0.596577	GCGGGGAAAAGTTTGGACTC	59.403	55.000	0.00	0.00	34.21	3.36
2211	2544	1.674764	CCTCCTCAGCAGTCATCGCT	61.675	60.000	0.00	0.00	41.47	4.93
2259	2592	0.034059	CAGCGAGGTCCTCTTTGTGT	59.966	55.000	17.00	0.00	0.00	3.72
2277	2610	5.588240	ACATTCGCGATACTGAGTTTATCA	58.412	37.500	10.88	0.00	36.21	2.15
2278	2611	5.164273	CGACATTCGCGATACTGAGTTTATC	60.164	44.000	10.88	0.32	31.14	1.75
2297	2630	1.112113	ATAAGCGTCTGGGTCGACAT	58.888	50.000	18.91	0.00	33.54	3.06
2370	2703	6.749216	ATATAGCTTGTGTTATCAACGACG	57.251	37.500	0.00	0.00	0.00	5.12
2376	2709	7.390440	GCACCCATAATATAGCTTGTGTTATCA	59.610	37.037	0.00	0.00	0.00	2.15
2403	2736	1.151668	CAGGTTTCTTCTCAGGCACG	58.848	55.000	0.00	0.00	0.00	5.34
2613	2946	4.665833	TTTCTTCTCTTTGTCCTCGTCA	57.334	40.909	0.00	0.00	0.00	4.35
2727	3066	8.410912	TCATCATCATCATCATCCTTGTTTTTC	58.589	33.333	0.00	0.00	0.00	2.29
2823	3174	7.748683	TCGTCGTCATCCTTATTTTTCAATTTG	59.251	33.333	0.00	0.00	0.00	2.32
2835	3186	3.303791	CGTCATCATCGTCGTCATCCTTA	60.304	47.826	0.00	0.00	0.00	2.69
2856	3207	8.895932	TTTTCACTTTCTTTTCTTTCTTCTCG	57.104	30.769	0.00	0.00	0.00	4.04
2875	3226	7.919690	TCATCGTCATCATCCTTATTTTTCAC	58.080	34.615	0.00	0.00	0.00	3.18
2883	3234	6.491403	TCTTCTCATCATCGTCATCATCCTTA	59.509	38.462	0.00	0.00	0.00	2.69
2907	3258	8.614469	TCTCTTTGGATTTCTTCTCTTTCTTC	57.386	34.615	0.00	0.00	0.00	2.87
2961	3312	6.207417	CACCCTTGCTTTTAGATTTCTTCTCA	59.793	38.462	0.00	0.00	35.79	3.27
2994	3345	3.692593	TCTTATTGTCATCGTCGTCCTCA	59.307	43.478	0.00	0.00	0.00	3.86
3112	3463	3.479127	TTGGCGCTTGGTACCCGTT	62.479	57.895	10.07	0.00	0.00	4.44
3162	3513	3.936203	TGGCCGTCAGGTGTGTCC	61.936	66.667	0.00	0.00	40.50	4.02
3266	3617	2.305635	ACATAGCCATCTGGTGTGTCAA	59.694	45.455	0.00	0.00	42.23	3.18
3531	4481	4.957684	AGCCTGGCGATCGATGCG	62.958	66.667	21.57	7.78	0.00	4.73
3904	4854	0.944311	GCGAGGACGTTGCTTGAGAA	60.944	55.000	0.00	0.00	41.98	2.87
4096	5085	5.981174	ACTGTACATCATCATCATCACACA	58.019	37.500	0.00	0.00	0.00	3.72
4097	5086	7.205992	ACTACTGTACATCATCATCATCACAC	58.794	38.462	0.00	0.00	0.00	3.82
4231	7464	3.604582	CCTCAGATCCTGGACAAACTTC	58.395	50.000	0.00	0.00	31.51	3.01
4365	7915	4.442375	GAGAGGTCTCGAGTTCAATTCA	57.558	45.455	13.13	0.00	32.78	2.57
4378	7928	1.324005	GCTTAGGGTGCGAGAGGTCT	61.324	60.000	0.00	0.00	0.00	3.85
4387	7937	3.565902	GGTATGATTCTTGCTTAGGGTGC	59.434	47.826	0.00	0.00	0.00	5.01
4398	7948	6.543831	GCATTTGGTCTAGTGGTATGATTCTT	59.456	38.462	0.00	0.00	0.00	2.52
4487	8037	5.119125	GCCAAAACTTTCATGACTTGTATGC	59.881	40.000	0.00	0.00	0.00	3.14
4647	8860	7.998081	GCATTTAAGTGACATGCAAAATTTC	57.002	32.000	1.56	0.00	42.49	2.17
4723	8936	3.426859	GTCCGATCTACGCATGAGAATTG	59.573	47.826	2.50	0.00	41.07	2.32
4893	9106	4.141937	CGGGGAGAAATCAACTAGTGATGA	60.142	45.833	0.00	0.00	46.80	2.92
5002	9215	5.400066	TTCTATGACACTCAAATCCGTCA	57.600	39.130	0.00	0.00	42.19	4.35
5146	9359	4.579869	AGCACTATCACAAAGTAGGTTGG	58.420	43.478	0.00	0.00	32.50	3.77
5158	9371	2.704572	AGCACTTGGAAGCACTATCAC	58.295	47.619	0.00	0.00	0.00	3.06
5171	9384	9.955208	TGCATTAATGAATATTCTAAGCACTTG	57.045	29.630	19.73	4.48	0.00	3.16
5279	9503	7.652507	TCGCCAATCACGTTTGTATATGTATTA	59.347	33.333	0.00	0.00	0.00	0.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.