AutoCloner

Multiple sequence alignment - TraesCS7A01G265100

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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	TraesCS7A01G265100	chr7A	100.000	7747	0	0	1	7747	265353931	265361677	0.000000e+00	14307
1	TraesCS7A01G265100	chr7A	92.518	4317	278	31	3460	7747	458659525	458655225	0.000000e+00	6141
2	TraesCS7A01G265100	chr7A	82.822	2870	383	64	4902	7747	347900547	347897764	0.000000e+00	2468
3	TraesCS7A01G265100	chr7A	91.667	204	16	1	1	203	386957909	386957706	1.650000e-71	281
4	TraesCS7A01G265100	chr4D	93.393	5252	267	32	1	5218	144583624	144578419	0.000000e+00	7703
5	TraesCS7A01G265100	chr3D	94.219	4480	203	24	3318	7747	323153475	323157948	0.000000e+00	6787
6	TraesCS7A01G265100	chr3D	94.712	3328	153	20	1	3320	323150133	323153445	0.000000e+00	5149
7	TraesCS7A01G265100	chr3D	94.853	2681	132	6	642	3320	395858070	395860746	0.000000e+00	4181
8	TraesCS7A01G265100	chr5D	94.115	4452	226	14	3318	7747	190782088	190777651	0.000000e+00	6737
9	TraesCS7A01G265100	chr5D	91.166	2049	147	14	1927	3947	378823912	378821870	0.000000e+00	2750
10	TraesCS7A01G265100	chr1D	94.123	4441	216	32	3318	7747	371718999	371723405	0.000000e+00	6713
11	TraesCS7A01G265100	chr1D	93.031	4319	243	27	3456	7747	88010003	88005716	0.000000e+00	6255
12	TraesCS7A01G265100	chr1D	92.188	4109	256	34	3456	7531	78751762	78747686	0.000000e+00	5749
13	TraesCS7A01G265100	chr1D	94.154	2891	159	9	138	3021	371714919	371717806	0.000000e+00	4394
14	TraesCS7A01G265100	chr1D	92.320	1940	117	21	5	1937	88013066	88011152	0.000000e+00	2728
15	TraesCS7A01G265100	chr2D	93.563	4319	237	21	3454	7747	259244709	259240407	0.000000e+00	6397
16	TraesCS7A01G265100	chr2D	94.617	2675	139	5	642	3315	412327584	412330254	0.000000e+00	4137
17	TraesCS7A01G265100	chr2D	92.784	1940	110	17	5	1937	259247772	259245856	0.000000e+00	2780
18	TraesCS7A01G265100	chr5A	92.089	3982	274	27	3454	7407	154815318	154811350	0.000000e+00	5570
19	TraesCS7A01G265100	chr5A	92.164	1876	119	13	1927	3779	625197150	625199020	0.000000e+00	2625
20	TraesCS7A01G265100	chr7D	94.471	3599	185	11	4158	7747	291611850	291615443	0.000000e+00	5531
21	TraesCS7A01G265100	chr2A	90.790	4115	293	51	3454	7528	230715346	230719414	0.000000e+00	5421
22	TraesCS7A01G265100	chr2A	92.050	3547	242	23	3456	6974	433266723	433270257	0.000000e+00	4951
23	TraesCS7A01G265100	chr2A	91.718	1944	152	9	1	1937	378108105	378110046	0.000000e+00	2689
24	TraesCS7A01G265100	chr2B	90.434	3366	260	26	4395	7747	780380601	780383917	0.000000e+00	4375
25	TraesCS7A01G265100	chr1B	91.630	2043	144	11	1927	3947	273127531	273125494	0.000000e+00	2800
26	TraesCS7A01G265100	chr1B	90.695	1956	156	18	5	1937	256494602	256492650	0.000000e+00	2580
27	TraesCS7A01G265100	chr4B	91.064	2048	141	17	1927	3947	379337353	379335321	0.000000e+00	2730
28	TraesCS7A01G265100	chr4A	83.021	1973	250	49	1	1937	278134350	278132427	0.000000e+00	1709
29	TraesCS7A01G265100	chr3B	90.300	1165	78	17	6586	7747	247180995	247182127	0.000000e+00	1493
30	TraesCS7A01G265100	chr5B	90.385	208	19	1	1	208	139268716	139268510	9.910000e-69	272
31	TraesCS7A01G265100	chr1A	90.863	197	18	0	1	197	174032920	174033116	1.660000e-66	265

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	TraesCS7A01G265100	chr7A	265353931	265361677	7746	False	14307.0	14307	100.0000	1	7747	1	chr7A.!!$F1	7746
1	TraesCS7A01G265100	chr7A	458655225	458659525	4300	True	6141.0	6141	92.5180	3460	7747	1	chr7A.!!$R3	4287
2	TraesCS7A01G265100	chr7A	347897764	347900547	2783	True	2468.0	2468	82.8220	4902	7747	1	chr7A.!!$R1	2845
3	TraesCS7A01G265100	chr4D	144578419	144583624	5205	True	7703.0	7703	93.3930	1	5218	1	chr4D.!!$R1	5217
4	TraesCS7A01G265100	chr3D	323150133	323157948	7815	False	5968.0	6787	94.4655	1	7747	2	chr3D.!!$F2	7746
5	TraesCS7A01G265100	chr3D	395858070	395860746	2676	False	4181.0	4181	94.8530	642	3320	1	chr3D.!!$F1	2678
6	TraesCS7A01G265100	chr5D	190777651	190782088	4437	True	6737.0	6737	94.1150	3318	7747	1	chr5D.!!$R1	4429
7	TraesCS7A01G265100	chr5D	378821870	378823912	2042	True	2750.0	2750	91.1660	1927	3947	1	chr5D.!!$R2	2020
8	TraesCS7A01G265100	chr1D	78747686	78751762	4076	True	5749.0	5749	92.1880	3456	7531	1	chr1D.!!$R1	4075
9	TraesCS7A01G265100	chr1D	371714919	371723405	8486	False	5553.5	6713	94.1385	138	7747	2	chr1D.!!$F1	7609
10	TraesCS7A01G265100	chr1D	88005716	88013066	7350	True	4491.5	6255	92.6755	5	7747	2	chr1D.!!$R2	7742
11	TraesCS7A01G265100	chr2D	259240407	259247772	7365	True	4588.5	6397	93.1735	5	7747	2	chr2D.!!$R1	7742
12	TraesCS7A01G265100	chr2D	412327584	412330254	2670	False	4137.0	4137	94.6170	642	3315	1	chr2D.!!$F1	2673
13	TraesCS7A01G265100	chr5A	154811350	154815318	3968	True	5570.0	5570	92.0890	3454	7407	1	chr5A.!!$R1	3953
14	TraesCS7A01G265100	chr5A	625197150	625199020	1870	False	2625.0	2625	92.1640	1927	3779	1	chr5A.!!$F1	1852
15	TraesCS7A01G265100	chr7D	291611850	291615443	3593	False	5531.0	5531	94.4710	4158	7747	1	chr7D.!!$F1	3589
16	TraesCS7A01G265100	chr2A	230715346	230719414	4068	False	5421.0	5421	90.7900	3454	7528	1	chr2A.!!$F1	4074
17	TraesCS7A01G265100	chr2A	433266723	433270257	3534	False	4951.0	4951	92.0500	3456	6974	1	chr2A.!!$F3	3518
18	TraesCS7A01G265100	chr2A	378108105	378110046	1941	False	2689.0	2689	91.7180	1	1937	1	chr2A.!!$F2	1936
19	TraesCS7A01G265100	chr2B	780380601	780383917	3316	False	4375.0	4375	90.4340	4395	7747	1	chr2B.!!$F1	3352
20	TraesCS7A01G265100	chr1B	273125494	273127531	2037	True	2800.0	2800	91.6300	1927	3947	1	chr1B.!!$R2	2020
21	TraesCS7A01G265100	chr1B	256492650	256494602	1952	True	2580.0	2580	90.6950	5	1937	1	chr1B.!!$R1	1932
22	TraesCS7A01G265100	chr4B	379335321	379337353	2032	True	2730.0	2730	91.0640	1927	3947	1	chr4B.!!$R1	2020
23	TraesCS7A01G265100	chr4A	278132427	278134350	1923	True	1709.0	1709	83.0210	1	1937	1	chr4A.!!$R1	1936
24	TraesCS7A01G265100	chr3B	247180995	247182127	1132	False	1493.0	1493	90.3000	6586	7747	1	chr3B.!!$F1	1161

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
812	1017	1.072648	CAAGGGACTACAAACGGGGAA	59.927	52.381	0.00	0.00	38.49	3.97	F
2491	7120	0.109153	TGACTGATGTTGCAGCCAGT	59.891	50.000	11.24	11.24	41.96	4.00	F
2600	7229	0.029567	CCTCATCGAGTACGCAGGAC	59.970	60.000	0.00	0.00	39.58	3.85	F
2695	7324	2.224402	GCGGGAGGCTGAGAAATTCTAT	60.224	50.000	0.00	0.00	39.11	1.98	F
3754	9328	2.696707	TCGCTTATAAACAGGTCCGGAT	59.303	45.455	7.81	0.00	0.00	4.18	F
5340	10968	0.593008	CAACCTCGTCGACGTTCACA	60.593	55.000	34.40	16.33	40.80	3.58	F
6406	12064	0.111061	AGCATTGGAGGTGACAAGCA	59.889	50.000	0.00	0.00	0.00	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2563	7192	0.036294	GGTTGTCTGGTAGTGGGCTC	60.036	60.000	0.00	0.00	4.70	R
3664	9211	0.320858	ACACGACGCTCTCTCTCTCA	60.321	55.000	0.00	0.00	3.27	R
3815	9389	0.531311	TAGATAGCTCGTCCACGCGA	60.531	55.000	15.93	39.60	5.87	R
3899	9478	1.733402	TTTGCCTTGCCGTCTGGTTG	61.733	55.000	0.00	37.67	3.77	R
5431	11060	0.034059	CACCTCGTCAGCCTTGTCTT	59.966	55.000	0.00	0.00	3.01	R
6576	12241	0.701731	CTGGTCCCCCATGGTTTGTA	59.298	55.000	11.73	40.90	2.41	R
7265	12963	5.612725	TTGATGGTTCTTTGCTTTTCCTT	57.387	34.783	0.00	0.00	3.36	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
320	326	3.395941	AGTCCCAGTTCAGAAAGACCATT	59.604	43.478	0.00	0.00	0.00	3.16
485	512	6.279123	ACATTAGCATCACACATAGTCTCAG	58.721	40.000	0.00	0.00	0.00	3.35
508	535	9.747898	TCAGTGGTATTTGGTAAGTTCAATTAT	57.252	29.630	0.00	0.00	0.00	1.28
535	563	2.097110	TCACCAGTCCAAGTACCACT	57.903	50.000	0.00	0.00	0.00	4.00
605	633	5.545723	AGTGGGATAAGCAGCTGATAAGTAT	59.454	40.000	20.43	6.08	0.00	2.12
700	729	4.701765	AGCAGATCATAAGTACAGCTTGG	58.298	43.478	0.00	0.00	38.05	3.61
812	1017	1.072648	CAAGGGACTACAAACGGGGAA	59.927	52.381	0.00	0.00	38.49	3.97
848	1064	4.939368	CACGCCCCCAACGAACCA	62.939	66.667	0.00	0.00	0.00	3.67
876	1092	2.438975	ATCCCCGTCGACGCACTA	60.439	61.111	31.73	16.53	38.18	2.74
939	1161	1.332144	CCACCATTGCCCCTTCCATG	61.332	60.000	0.00	0.00	0.00	3.66
951	1173	1.162698	CTTCCATGTCCACTGCACAG	58.837	55.000	0.00	0.00	0.00	3.66
968	1190	4.219507	TGCACAGAAACCAAAAACTTCTCA	59.780	37.500	0.00	0.00	0.00	3.27
969	1191	5.167845	GCACAGAAACCAAAAACTTCTCAA	58.832	37.500	0.00	0.00	0.00	3.02
1113	1335	2.224209	CGAGTACACCAAAACCCTCACT	60.224	50.000	0.00	0.00	0.00	3.41
1129	1351	2.352805	CTGGGGTTGAGCTCCACC	59.647	66.667	25.41	25.41	44.40	4.61
1180	1402	1.070786	GAACCAGACAAGGCCGACA	59.929	57.895	0.00	0.00	0.00	4.35
1347	1575	2.650196	GCAGCGGCCACAAAATGA	59.350	55.556	2.24	0.00	0.00	2.57
1476	1706	5.373222	TGTAAAAAGTGGATGCACTACTGT	58.627	37.500	21.06	8.63	40.15	3.55
1779	2010	9.617523	AAGTAAACTAAACTAGTACCAAAGCAA	57.382	29.630	0.00	0.00	38.26	3.91
1793	2024	7.984617	AGTACCAAAGCAAAACATACAACATTT	59.015	29.630	0.00	0.00	0.00	2.32
2049	6675	7.687757	GTGTTGTGCAATTGAACAAAAGTAAAG	59.312	33.333	29.54	0.00	44.57	1.85
2297	6926	3.334054	GCCTCTCCCCTTGCAGGT	61.334	66.667	0.00	0.00	31.93	4.00
2318	6947	1.301716	AAGCGCCTGAACGACATGT	60.302	52.632	2.29	0.00	34.06	3.21
2360	6989	2.224257	ACATTTGCCGGTTTCAGCATTT	60.224	40.909	1.90	0.00	39.11	2.32
2428	7057	4.984161	CCCAACAAGTTCATCAACATTCAC	59.016	41.667	0.00	0.00	34.60	3.18
2433	7062	2.485426	AGTTCATCAACATTCACCGCAG	59.515	45.455	0.00	0.00	34.60	5.18
2491	7120	0.109153	TGACTGATGTTGCAGCCAGT	59.891	50.000	11.24	11.24	41.96	4.00
2572	7201	1.681327	GTGGAGGACGAGCCCACTA	60.681	63.158	0.00	0.00	45.08	2.74
2600	7229	0.029567	CCTCATCGAGTACGCAGGAC	59.970	60.000	0.00	0.00	39.58	3.85
2651	7280	6.447162	TGGATCATAATCGACTACATCACAC	58.553	40.000	0.00	0.00	32.24	3.82
2695	7324	2.224402	GCGGGAGGCTGAGAAATTCTAT	60.224	50.000	0.00	0.00	39.11	1.98
2738	7370	8.553085	TTTTAGGGATGAAGATACATCAGAGA	57.447	34.615	0.00	0.00	45.68	3.10
2788	7420	5.177511	GCTTGCCTTTTATCTTGTTGTTTCC	59.822	40.000	0.00	0.00	0.00	3.13
2790	7422	5.841810	TGCCTTTTATCTTGTTGTTTCCAG	58.158	37.500	0.00	0.00	0.00	3.86
2833	7469	6.489603	TGGGTTGAACCAGTATGATTATGTT	58.510	36.000	17.27	0.00	41.02	2.71
3040	8541	4.862574	TGTTCCATGTCTAGTTTCGATTCG	59.137	41.667	0.00	0.00	0.00	3.34
3090	8591	9.376075	TGAAAACAATCAGCAAAATTTGAGTTA	57.624	25.926	10.26	0.00	0.00	2.24
3321	8856	4.101741	ACAAAGAAGGAGCAGTCTGTAAGT	59.898	41.667	0.93	0.00	33.76	2.24
3360	8895	9.122779	GGACTATCAGTACAACTTAGTCTACAT	57.877	37.037	17.39	0.00	38.07	2.29
3389	8924	7.680730	AGTACCATAGTTCTGAAAATGACACT	58.319	34.615	12.96	11.80	0.00	3.55
3487	9025	8.612619	CACTTACACAAAACTGACAAGAACTAT	58.387	33.333	0.00	0.00	0.00	2.12
3612	9159	3.181485	ACGCTGCTAGATACTTGAACTCC	60.181	47.826	0.00	0.00	0.00	3.85
3617	9164	3.386402	GCTAGATACTTGAACTCCAGCCT	59.614	47.826	0.00	0.00	0.00	4.58
3664	9211	4.052518	GCAGGGCCCACAGGTCAT	62.053	66.667	27.56	0.00	40.78	3.06
3754	9328	2.696707	TCGCTTATAAACAGGTCCGGAT	59.303	45.455	7.81	0.00	0.00	4.18
3783	9357	3.649023	TGACTAGCAAGGTGGGACTAAAA	59.351	43.478	0.00	0.00	0.00	1.52
3784	9358	4.103469	TGACTAGCAAGGTGGGACTAAAAA	59.897	41.667	0.00	0.00	0.00	1.94
3815	9389	2.961721	CACGTCGCACTGCACAGT	60.962	61.111	1.11	0.00	43.61	3.55
3899	9478	3.194755	CCACCAATAAGCCCAGTTAAACC	59.805	47.826	0.00	0.00	0.00	3.27
3907	9486	1.611977	GCCCAGTTAAACCAACCAGAC	59.388	52.381	0.00	0.00	37.93	3.51
4109	9696	9.668497	TCTAAAAAGAAGAGAACTTAATAGCCC	57.332	33.333	0.00	0.00	36.39	5.19
4265	9855	9.301153	ACAAGTTCAACTACTAAAATGCAAAAG	57.699	29.630	0.00	0.00	0.00	2.27
4431	10030	9.209175	ACTACTTCAACTACTAAAATGCAAGAG	57.791	33.333	0.00	0.00	0.00	2.85
4654	10261	4.142138	ACCAAATTTCAAAACCGCACACTA	60.142	37.500	0.00	0.00	0.00	2.74
4863	10472	8.138712	GGAAAAACAATACTTAACATCCACACA	58.861	33.333	0.00	0.00	0.00	3.72
4898	10509	6.018588	CACAAAACATACGTCACCTAAACAGA	60.019	38.462	0.00	0.00	0.00	3.41
4919	10530	2.167693	AGCAAAATGCCATCATCACCAG	59.832	45.455	0.00	0.00	46.52	4.00
4924	10535	1.076485	GCCATCATCACCAGCCCTT	60.076	57.895	0.00	0.00	0.00	3.95
5112	10736	2.308722	ACCCACGCCCCAGATGAAT	61.309	57.895	0.00	0.00	0.00	2.57
5172	10797	2.092538	CCCATTGTCTTCCATCTCTGCT	60.093	50.000	0.00	0.00	0.00	4.24
5213	10840	1.699656	CCGCTTCAATCTCCACTGCG	61.700	60.000	0.00	0.00	41.30	5.18
5246	10874	1.211456	CTTCTCTCTCCCAAGCCCAT	58.789	55.000	0.00	0.00	0.00	4.00
5255	10883	1.077787	CCAAGCCCATAGTCGCCAA	60.078	57.895	0.00	0.00	0.00	4.52
5318	10946	2.687805	CGAGCCGTCGGACAAGAGA	61.688	63.158	17.49	0.00	42.87	3.10
5340	10968	0.593008	CAACCTCGTCGACGTTCACA	60.593	55.000	34.40	16.33	40.80	3.58
5431	11060	0.885879	ATCGTCTACACCAGCGAACA	59.114	50.000	0.00	0.00	36.73	3.18
5544	11173	3.181472	CGATGATGAACCTCCACAGATGA	60.181	47.826	0.00	0.00	0.00	2.92
5545	11174	4.681512	CGATGATGAACCTCCACAGATGAA	60.682	45.833	0.00	0.00	0.00	2.57
5690	11320	8.410912	ACTTCATTAAACTTGTTTCCCAACTAC	58.589	33.333	1.72	0.00	33.58	2.73
5766	11396	6.092955	ACATGCATTTCTGAAACTGTGAAT	57.907	33.333	4.73	0.00	0.00	2.57
5867	11498	9.405587	GAACTTGATGTACTAGCATAGATTCTC	57.594	37.037	0.00	0.00	42.77	2.87
5936	11568	4.595781	TGTTTGGTGAAGTGGTATAGGTCT	59.404	41.667	0.00	0.00	0.00	3.85
6037	11688	9.227777	ACTGGTATAGGTCTTTTATTCAACAAC	57.772	33.333	0.00	0.00	0.00	3.32
6206	11862	8.857098	TGTGTACTAGTTTCTGAACTACATTCT	58.143	33.333	0.00	0.00	44.13	2.40
6314	11972	7.264373	AGAAGACTTGTCTTTAAATGTGTGG	57.736	36.000	15.94	0.00	0.00	4.17
6355	12013	1.630244	CGCCTCAAAGACTTCCTGCG	61.630	60.000	6.87	6.87	34.52	5.18
6406	12064	0.111061	AGCATTGGAGGTGACAAGCA	59.889	50.000	0.00	0.00	0.00	3.91
6484	12142	2.034685	GCAAGTGGAAAGACCCAAAGAC	59.965	50.000	0.00	0.00	38.06	3.01
6576	12241	1.949799	AGAAGATGGACAGGCAGACT	58.050	50.000	0.00	0.00	0.00	3.24
6583	12248	1.071699	TGGACAGGCAGACTACAAACC	59.928	52.381	0.00	0.00	0.00	3.27
6690	12355	2.948979	GACAACATTGTGACAGGTTGGA	59.051	45.455	25.39	0.00	43.61	3.53
6915	12580	5.216566	TCAAGTACATCGTTTGCTTATGC	57.783	39.130	0.00	0.00	40.20	3.14
6963	12630	9.204337	TCCTATTTTGTTGATCCATCATTTGAT	57.796	29.630	0.00	0.00	36.56	2.57
7009	12697	1.644786	GATGGCTACCACGCAACACC	61.645	60.000	0.00	0.00	35.80	4.16
7010	12698	2.032071	GGCTACCACGCAACACCT	59.968	61.111	0.00	0.00	0.00	4.00
7116	12812	2.915738	AGACTTGGACGCTTAGTACG	57.084	50.000	0.00	0.00	36.10	3.67
7122	12818	2.026641	TGGACGCTTAGTACGGCTTAT	58.973	47.619	6.87	0.00	39.01	1.73
7328	13027	2.304180	AGCATGCTAGGACTGACAGTTT	59.696	45.455	21.21	4.26	0.00	2.66
7413	13114	6.990798	TCAGTTTGCATTCCATAAAACATCA	58.009	32.000	0.00	0.00	35.46	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	1.001020	TCCAGCGGGCACAAATCAT	60.001	52.632	0.00	0.00	0.00	2.45
195	197	7.153217	TGTACTGACGACTGAGAATTATCAA	57.847	36.000	4.06	0.00	0.00	2.57
281	287	4.263905	TGGGACTGGCAGAAAAAGACATAT	60.264	41.667	23.66	0.00	0.00	1.78
289	295	1.214175	TGAACTGGGACTGGCAGAAAA	59.786	47.619	23.66	2.64	0.00	2.29
290	296	0.843309	TGAACTGGGACTGGCAGAAA	59.157	50.000	23.66	2.26	0.00	2.52
508	535	4.974645	ACTTGGACTGGTGATTGAAGTA	57.025	40.909	0.00	0.00	0.00	2.24
605	633	2.826128	ACTGATCCGTCTTGTCAAGCTA	59.174	45.455	7.78	0.00	0.00	3.32
700	729	1.074752	GCTGCACTGACTAGTCTTGC	58.925	55.000	29.01	29.01	38.75	4.01
741	946	1.025113	GGCCTGGAAGAAGTAACCGC	61.025	60.000	0.00	0.00	34.07	5.68
812	1017	3.868985	GTGTGGTGGTCGTGGGGT	61.869	66.667	0.00	0.00	0.00	4.95
840	1056	1.147600	GTGTGGGAGGTGGTTCGTT	59.852	57.895	0.00	0.00	0.00	3.85
848	1064	3.009115	CGGGGATGTGTGGGAGGT	61.009	66.667	0.00	0.00	0.00	3.85
876	1092	5.333566	TGGAAGAGAAAGGGGTATTTTGT	57.666	39.130	0.00	0.00	0.00	2.83
939	1161	1.388547	TTGGTTTCTGTGCAGTGGAC	58.611	50.000	8.00	8.00	0.00	4.02
951	1173	5.912892	TGGGATTGAGAAGTTTTTGGTTTC	58.087	37.500	0.00	0.00	0.00	2.78
968	1190	2.037847	GGCTGTGGGCTTGGGATT	59.962	61.111	0.00	0.00	41.46	3.01
969	1191	4.431131	CGGCTGTGGGCTTGGGAT	62.431	66.667	0.00	0.00	41.46	3.85
1005	1227	2.920912	TTGGCGGACGGTTCCTCT	60.921	61.111	0.00	0.00	40.23	3.69
1039	1261	0.321346	TTGCTGCTCTTGTCCGATGA	59.679	50.000	0.00	0.00	0.00	2.92
1041	1263	0.674895	GGTTGCTGCTCTTGTCCGAT	60.675	55.000	0.00	0.00	0.00	4.18
1113	1335	3.636231	CGGTGGAGCTCAACCCCA	61.636	66.667	30.90	10.90	0.00	4.96
1129	1351	2.290122	ATCTCCAGCGTCTCCTTGCG	62.290	60.000	0.00	0.00	35.87	4.85
1256	1484	0.179000	CTGGGGAGGTTCATCTTCGG	59.821	60.000	0.00	0.00	0.00	4.30
1300	1528	1.515952	CCAAGCAGAGCTCGTCGAG	60.516	63.158	18.08	18.08	38.25	4.04
1632	1862	8.562892	ACTACATCAAGTTCAGAAACATCTTTG	58.437	33.333	0.00	0.00	37.88	2.77
2006	6632	3.207265	ACACATAACCAGTGCTTCACA	57.793	42.857	0.00	0.00	40.59	3.58
2049	6675	7.829378	ATGTGCTGCTTTAGTACTAGTTTAC	57.171	36.000	0.00	0.00	41.93	2.01
2297	6926	2.357034	GTCGTTCAGGCGCTTGGA	60.357	61.111	20.24	8.36	0.00	3.53
2318	6947	4.065088	GTGAACAACCTCTCATGCTACAA	58.935	43.478	0.00	0.00	0.00	2.41
2360	6989	3.990092	TCAGCTTCTCTTTGTCGCTTTA	58.010	40.909	0.00	0.00	0.00	1.85
2428	7057	2.060383	TGGATCTCTCCACCTGCGG	61.060	63.158	0.00	0.00	46.95	5.69
2442	7071	4.441079	CGTACTCTTTTCCGGTGTATGGAT	60.441	45.833	0.00	0.00	34.91	3.41
2491	7120	4.567537	CCTTTGTAGAATGGGTGGATGACA	60.568	45.833	0.00	0.00	0.00	3.58
2558	7187	1.682684	CTGGTAGTGGGCTCGTCCT	60.683	63.158	0.00	0.00	34.39	3.85
2563	7192	0.036294	GGTTGTCTGGTAGTGGGCTC	60.036	60.000	0.00	0.00	0.00	4.70
2572	7201	1.633774	ACTCGATGAGGTTGTCTGGT	58.366	50.000	0.00	0.00	33.35	4.00
2600	7229	2.316792	GTACATGGCGTACGCATCTAG	58.683	52.381	37.99	24.48	41.13	2.43
2651	7280	4.305769	TCTTTTGCAAATTCCGAACCATG	58.694	39.130	13.65	0.00	0.00	3.66
2695	7324	0.849094	AAGGGGCAATAGGGTGGTCA	60.849	55.000	0.00	0.00	0.00	4.02
2738	7370	1.539827	CGGAAGGAAAACGAAGGCATT	59.460	47.619	0.00	0.00	0.00	3.56
2788	7420	5.049405	CCCAACAAGAGCAAACTACTAACTG	60.049	44.000	0.00	0.00	0.00	3.16
2790	7422	4.820173	ACCCAACAAGAGCAAACTACTAAC	59.180	41.667	0.00	0.00	0.00	2.34
2833	7469	2.373224	TGTTCAACCATGACAAGCACA	58.627	42.857	0.00	0.00	34.61	4.57
3079	8580	8.185505	TGAAGCGTTGTTAAGTAACTCAAATTT	58.814	29.630	3.07	0.00	37.12	1.82
3090	8591	5.945155	TCAACTTTTGAAGCGTTGTTAAGT	58.055	33.333	8.00	0.00	39.14	2.24
3307	8809	3.859411	AGTAGCACTTACAGACTGCTC	57.141	47.619	1.25	0.00	40.47	4.26
3321	8856	7.724061	TGTACTGATAGTCCATTCATAGTAGCA	59.276	37.037	0.00	0.00	0.00	3.49
3360	8895	6.939730	TCATTTTCAGAACTATGGTACTTGCA	59.060	34.615	0.00	0.00	0.00	4.08
3389	8924	7.733773	TGTGATTATTCTCAAGGGTCTTCTA	57.266	36.000	0.00	0.00	0.00	2.10
3487	9025	9.841295	AGTAACTTGGACTGATACTTTTTGTTA	57.159	29.630	0.00	0.00	0.00	2.41
3625	9172	3.131396	GTTGTGCGGATTACTAGGGATG	58.869	50.000	0.00	0.00	0.00	3.51
3658	9205	1.064758	ACGCTCTCTCTCTCATGACCT	60.065	52.381	0.00	0.00	0.00	3.85
3660	9207	1.003972	CGACGCTCTCTCTCTCATGAC	60.004	57.143	0.00	0.00	0.00	3.06
3664	9211	0.320858	ACACGACGCTCTCTCTCTCA	60.321	55.000	0.00	0.00	0.00	3.27
3815	9389	0.531311	TAGATAGCTCGTCCACGCGA	60.531	55.000	15.93	0.00	39.60	5.87
3859	9434	3.056179	GGTGGGGTGTTTGTAAATGATGG	60.056	47.826	0.00	0.00	0.00	3.51
3899	9478	1.733402	TTTGCCTTGCCGTCTGGTTG	61.733	55.000	0.00	0.00	37.67	3.77
3907	9486	5.650543	AGTTTATATTTCTTTGCCTTGCCG	58.349	37.500	0.00	0.00	0.00	5.69
4402	10001	8.896320	TGCATTTTAGTAGTTGAAGTAGTCAA	57.104	30.769	0.00	0.00	44.20	3.18
4480	10079	2.224079	CGTTGAGGTGTGGACAGATTTG	59.776	50.000	0.00	0.00	0.00	2.32
4557	10163	8.479313	TGTCATATGTATGTTTGAACTGAGTC	57.521	34.615	1.90	0.00	35.26	3.36
4757	10364	7.422399	TGTTGCTCAAAACTGGTACTTATTTC	58.578	34.615	0.00	0.00	0.00	2.17
4863	10472	7.431084	GTGACGTATGTTTTGTGATGTTTTTCT	59.569	33.333	0.00	0.00	0.00	2.52
4898	10509	2.167693	CTGGTGATGATGGCATTTTGCT	59.832	45.455	0.00	0.00	44.28	3.91
4919	10530	1.098050	CCACTTGCATGTCTAAGGGC	58.902	55.000	1.56	0.00	0.00	5.19
4924	10535	4.199310	GCTAAATCCCACTTGCATGTCTA	58.801	43.478	1.56	0.00	0.00	2.59
5105	10729	0.179000	GTGTGGGAGGCGATTCATCT	59.821	55.000	0.00	0.00	0.00	2.90
5112	10736	3.399181	GGGATGTGTGGGAGGCGA	61.399	66.667	0.00	0.00	0.00	5.54
5172	10797	3.005684	GCAATGGTGGTTCTGTGAATGAA	59.994	43.478	0.00	0.00	0.00	2.57
5213	10840	4.998788	AGAGAGAAGTTTTTGGTTTGTGC	58.001	39.130	0.00	0.00	0.00	4.57
5318	10946	0.938168	GAACGTCGACGAGGTTGCTT	60.938	55.000	41.52	24.28	40.09	3.91
5388	11017	2.579201	CGTCTCCTTGCCGTGGAT	59.421	61.111	0.00	0.00	32.56	3.41
5431	11060	0.034059	CACCTCGTCAGCCTTGTCTT	59.966	55.000	0.00	0.00	0.00	3.01
5628	11257	9.938670	GTAGTACTAGTACAACAGATGAATGAG	57.061	37.037	29.87	0.00	38.48	2.90
5766	11396	8.049117	AGATGCTAATCTAGTGAAACAATCCAA	58.951	33.333	0.00	0.00	41.57	3.53
5936	11568	8.735692	TTGAGAAACATGTGCATCAAGATATA	57.264	30.769	13.10	0.00	0.00	0.86
6006	11638	8.764558	TGAATAAAAGACCTATACCAGTGCTTA	58.235	33.333	0.00	0.00	0.00	3.09
6037	11688	7.010367	TGCTGCTTGATTCAAGTTTAGTTTTTG	59.990	33.333	23.66	0.00	42.77	2.44
6148	11804	8.755696	TGAAATTAAATTCAACTACACCATGC	57.244	30.769	3.42	0.00	36.42	4.06
6298	11956	3.153919	GGGAGCCACACATTTAAAGACA	58.846	45.455	0.00	0.00	0.00	3.41
6299	11957	2.492088	GGGGAGCCACACATTTAAAGAC	59.508	50.000	0.00	0.00	0.00	3.01
6355	12013	5.476945	ACAAATGTGTACAATTTCTCCTCCC	59.523	40.000	0.00	0.00	35.72	4.30
6431	12089	3.366273	CGATGAAGTTGTTGGGGTTGATG	60.366	47.826	0.00	0.00	0.00	3.07
6484	12142	2.686915	AGGAGTCGTAGTATTTGTCGGG	59.313	50.000	0.00	0.00	0.00	5.14
6576	12241	0.701731	CTGGTCCCCCATGGTTTGTA	59.298	55.000	11.73	0.00	40.90	2.41
6690	12355	3.956848	GCCTCCTGCTCTTTGGAAATATT	59.043	43.478	0.00	0.00	36.87	1.28
6915	12580	2.290641	AGCTAGCAAACTTGTTGAACGG	59.709	45.455	18.83	0.00	0.00	4.44
6963	12630	6.657541	AGTTTCAACTTCAACCTACTTCAACA	59.342	34.615	0.00	0.00	35.21	3.33
6997	12685	1.148273	ATGACAGGTGTTGCGTGGT	59.852	52.632	0.00	0.00	37.30	4.16
7009	12697	6.418819	GTGTGATTTTTGTTTCTCCATGACAG	59.581	38.462	0.00	0.00	0.00	3.51
7010	12698	6.127507	TGTGTGATTTTTGTTTCTCCATGACA	60.128	34.615	0.00	0.00	0.00	3.58
7116	12812	6.566197	AGTACTACCGTACATGTATAAGCC	57.434	41.667	9.18	0.00	46.68	4.35
7122	12818	7.275183	AGTGTGATAGTACTACCGTACATGTA	58.725	38.462	4.31	0.08	46.68	2.29
7264	12962	6.723298	TTGATGGTTCTTTGCTTTTCCTTA	57.277	33.333	0.00	0.00	0.00	2.69
7265	12963	5.612725	TTGATGGTTCTTTGCTTTTCCTT	57.387	34.783	0.00	0.00	0.00	3.36
7323	13022	6.255453	CCATTTGTTCAAGTGTACCAAAACTG	59.745	38.462	7.14	0.00	0.00	3.16
7328	13027	5.886474	TGTACCATTTGTTCAAGTGTACCAA	59.114	36.000	7.14	0.00	29.84	3.67
7368	13069	7.182060	ACTGAAGCTTCCCATTCCTTTTTATA	58.818	34.615	23.42	0.00	0.00	0.98
7452	13154	9.471702	ACTTGCCTTATAGACTAAGTTGTACTA	57.528	33.333	0.00	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.