AutoCloner

Multiple sequence alignment - TraesCS2D01G021200

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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	TraesCS2D01G021200	chr2D	100.000	2693	0	0	1	2693	9871288	9868596	0.000000e+00	4974.0
1	TraesCS2D01G021200	chr2D	77.629	1940	357	61	800	2690	63229250	63227339	0.000000e+00	1107.0
2	TraesCS2D01G021200	chr2D	92.491	546	40	1	48	593	324121158	324120614	0.000000e+00	780.0
3	TraesCS2D01G021200	chr7D	90.014	2093	182	10	612	2693	626922457	626920381	0.000000e+00	2682.0
4	TraesCS2D01G021200	chr7D	80.995	1105	174	20	652	1733	215147223	215146132	0.000000e+00	845.0
5	TraesCS2D01G021200	chr5D	90.756	1601	139	7	612	2205	520827998	520826400	0.000000e+00	2128.0
6	TraesCS2D01G021200	chr5D	89.669	484	45	4	2211	2693	520812869	520812390	1.770000e-171	612.0
7	TraesCS2D01G021200	chr5D	96.154	52	2	0	1	52	285104365	285104416	4.780000e-13	86.1
8	TraesCS2D01G021200	chr5D	97.959	49	1	0	4	52	311092318	311092270	4.780000e-13	86.1
9	TraesCS2D01G021200	chr1D	79.322	2036	337	65	705	2690	375244134	375246135	0.000000e+00	1351.0
10	TraesCS2D01G021200	chr1D	97.959	49	1	0	4	52	153266619	153266571	4.780000e-13	86.1
11	TraesCS2D01G021200	chr7A	90.428	982	85	2	613	1594	36977883	36976911	0.000000e+00	1284.0
12	TraesCS2D01G021200	chr7A	88.865	943	88	10	1592	2532	36968712	36967785	0.000000e+00	1144.0
13	TraesCS2D01G021200	chr7A	89.051	274	23	4	48	318	95949864	95949595	1.550000e-87	333.0
14	TraesCS2D01G021200	chr7A	89.759	166	17	0	2528	2693	36966364	36966199	2.100000e-51	213.0
15	TraesCS2D01G021200	chr6D	77.850	1991	369	57	749	2690	427254004	427255971	0.000000e+00	1168.0
16	TraesCS2D01G021200	chr4D	80.624	1058	175	21	739	1773	46120737	46121787	0.000000e+00	791.0
17	TraesCS2D01G021200	chr7B	73.853	2027	438	72	726	2693	218525123	218523130	0.000000e+00	723.0
18	TraesCS2D01G021200	chr3A	90.816	490	39	3	48	537	736927856	736927373	0.000000e+00	651.0
19	TraesCS2D01G021200	chr3A	90.408	490	41	3	48	537	540605762	540605279	8.130000e-180	640.0
20	TraesCS2D01G021200	chr1A	90.833	480	38	3	58	537	74737030	74736557	2.920000e-179	638.0
21	TraesCS2D01G021200	chr2A	90.000	490	43	3	48	537	191906545	191907028	1.760000e-176	628.0
22	TraesCS2D01G021200	chr2B	89.184	490	43	4	48	537	188447604	188447125	1.070000e-168	603.0
23	TraesCS2D01G021200	chr4A	75.605	1115	213	40	980	2053	567180427	567179331	5.180000e-137	497.0
24	TraesCS2D01G021200	chr1B	88.889	315	28	4	48	359	144793639	144793329	5.440000e-102	381.0
25	TraesCS2D01G021200	chr1B	92.982	57	4	0	1	57	658360887	658360831	1.720000e-12	84.2
26	TraesCS2D01G021200	chr3D	81.693	437	68	9	659	1086	156981140	156981573	1.190000e-93	353.0
27	TraesCS2D01G021200	chr3D	79.661	413	78	5	1124	1533	614196880	614196471	2.620000e-75	292.0
28	TraesCS2D01G021200	chr3D	97.959	49	1	0	4	52	78836822	78836774	4.780000e-13	86.1
29	TraesCS2D01G021200	chr3D	96.154	52	2	0	1	52	529133762	529133813	4.780000e-13	86.1
30	TraesCS2D01G021200	chr5B	91.795	195	8	4	343	537	166704514	166704328	5.720000e-67	265.0
31	TraesCS2D01G021200	chr5B	97.959	49	1	0	4	52	437862793	437862745	4.780000e-13	86.1
32	TraesCS2D01G021200	chr3B	90.909	176	12	2	153	325	813590929	813590755	1.610000e-57	233.0
33	TraesCS2D01G021200	chr4B	98.000	50	1	0	1	50	365624986	365624937	1.330000e-13	87.9
34	TraesCS2D01G021200	chr4B	92.857	56	2	2	10	65	429724755	429724702	2.220000e-11	80.5

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	TraesCS2D01G021200	chr2D	9868596	9871288	2692	True	4974.0	4974	100.000	1	2693	1	chr2D.!!$R1	2692
1	TraesCS2D01G021200	chr2D	63227339	63229250	1911	True	1107.0	1107	77.629	800	2690	1	chr2D.!!$R2	1890
2	TraesCS2D01G021200	chr2D	324120614	324121158	544	True	780.0	780	92.491	48	593	1	chr2D.!!$R3	545
3	TraesCS2D01G021200	chr7D	626920381	626922457	2076	True	2682.0	2682	90.014	612	2693	1	chr7D.!!$R2	2081
4	TraesCS2D01G021200	chr7D	215146132	215147223	1091	True	845.0	845	80.995	652	1733	1	chr7D.!!$R1	1081
5	TraesCS2D01G021200	chr5D	520826400	520827998	1598	True	2128.0	2128	90.756	612	2205	1	chr5D.!!$R3	1593
6	TraesCS2D01G021200	chr1D	375244134	375246135	2001	False	1351.0	1351	79.322	705	2690	1	chr1D.!!$F1	1985
7	TraesCS2D01G021200	chr7A	36976911	36977883	972	True	1284.0	1284	90.428	613	1594	1	chr7A.!!$R1	981
8	TraesCS2D01G021200	chr7A	36966199	36968712	2513	True	678.5	1144	89.312	1592	2693	2	chr7A.!!$R3	1101
9	TraesCS2D01G021200	chr6D	427254004	427255971	1967	False	1168.0	1168	77.850	749	2690	1	chr6D.!!$F1	1941
10	TraesCS2D01G021200	chr4D	46120737	46121787	1050	False	791.0	791	80.624	739	1773	1	chr4D.!!$F1	1034
11	TraesCS2D01G021200	chr7B	218523130	218525123	1993	True	723.0	723	73.853	726	2693	1	chr7B.!!$R1	1967
12	TraesCS2D01G021200	chr4A	567179331	567180427	1096	True	497.0	497	75.605	980	2053	1	chr4A.!!$R1	1073

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
503	504	0.033796	AATCCATGGGCTCCACACAG	60.034	55.000	13.02	0.0	35.8	3.66	F
514	515	1.400846	CTCCACACAGATGATGCAAGC	59.599	52.381	0.00	0.0	0.0	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1373	1405	0.114560	GGATGGATCCCCCGACTCTA	59.885	60.0	9.90	0.0	41.20	2.43	R
2195	2245	1.103811	TAAGGTCTTCCCCCTGGGTA	58.896	55.0	12.71	0.0	44.74	3.69	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
41	42	9.947433	TTAGAAAGACAAATATTTAGGAACGGA	57.053	29.630	0.00	0.00	0.00	4.69
42	43	8.494016	AGAAAGACAAATATTTAGGAACGGAG	57.506	34.615	0.00	0.00	0.00	4.63
43	44	7.553044	AGAAAGACAAATATTTAGGAACGGAGG	59.447	37.037	0.00	0.00	0.00	4.30
44	45	5.681639	AGACAAATATTTAGGAACGGAGGG	58.318	41.667	0.00	0.00	0.00	4.30
45	46	5.427481	AGACAAATATTTAGGAACGGAGGGA	59.573	40.000	0.00	0.00	0.00	4.20
46	47	5.681639	ACAAATATTTAGGAACGGAGGGAG	58.318	41.667	0.00	0.00	0.00	4.30
52	53	1.849977	AGGAACGGAGGGAGTACTTC	58.150	55.000	0.00	0.00	0.00	3.01
58	59	0.460722	GGAGGGAGTACTTCGGAAGC	59.539	60.000	17.37	2.61	0.00	3.86
59	60	0.460722	GAGGGAGTACTTCGGAAGCC	59.539	60.000	17.37	10.15	0.00	4.35
77	78	2.514592	GGCAATAGCAGCGGCAGA	60.515	61.111	12.44	0.00	44.61	4.26
79	80	1.817099	GCAATAGCAGCGGCAGAGT	60.817	57.895	12.44	0.00	44.61	3.24
80	81	1.770085	GCAATAGCAGCGGCAGAGTC	61.770	60.000	12.44	0.00	44.61	3.36
83	84	1.459455	ATAGCAGCGGCAGAGTCGAT	61.459	55.000	12.44	0.00	44.61	3.59
92	93	1.079612	CAGAGTCGATGCAGCCACA	60.080	57.895	1.83	0.00	0.00	4.17
94	95	1.812922	GAGTCGATGCAGCCACAGG	60.813	63.158	1.83	0.00	0.00	4.00
106	107	1.654220	CCACAGGCTGGACAAAACG	59.346	57.895	20.34	0.00	43.95	3.60
111	112	2.224426	ACAGGCTGGACAAAACGTGATA	60.224	45.455	20.34	0.00	0.00	2.15
127	128	7.932120	AACGTGATAAGATTACTACTGCATC	57.068	36.000	0.00	0.00	0.00	3.91
169	170	6.016777	AGGACTCTTTCACAAATCATGTCAAC	60.017	38.462	0.00	0.00	41.46	3.18
235	236	3.452755	TGGCATATACAGTCCTGAACG	57.547	47.619	0.40	0.00	0.00	3.95
257	258	5.628134	CGTAAGTTTCAAAATAGCAGGTCC	58.372	41.667	0.00	0.00	0.00	4.46
276	277	4.261447	GGTCCGTTGTAGCAGTGAATTTTT	60.261	41.667	0.00	0.00	0.00	1.94
288	289	7.820648	AGCAGTGAATTTTTCCTAATGTACTG	58.179	34.615	0.00	0.00	36.44	2.74
318	319	2.029838	AGCATCTGCCTAACCTTTCG	57.970	50.000	0.00	0.00	43.38	3.46
321	322	1.927174	CATCTGCCTAACCTTTCGTCG	59.073	52.381	0.00	0.00	0.00	5.12
329	330	4.668431	GCCTAACCTTTCGTCGTGAATTTC	60.668	45.833	0.00	0.00	36.22	2.17
389	390	9.915629	ACATTAGTTAGTGTAGACAAAGAAGAG	57.084	33.333	0.00	0.00	0.00	2.85
410	411	2.924290	GTTGAGCTTCCAGTACGTCATC	59.076	50.000	0.00	0.00	0.00	2.92
443	444	4.949966	TCCTAACTACCTCTCTCTGGTT	57.050	45.455	0.00	0.00	38.88	3.67
454	455	3.578716	CTCTCTCTGGTTGGTTGAAGGTA	59.421	47.826	0.00	0.00	0.00	3.08
467	468	4.566907	GGTTGAAGGTATGGAGTTTAGCCA	60.567	45.833	0.00	0.00	40.24	4.75
473	474	4.475016	AGGTATGGAGTTTAGCCATGTTCT	59.525	41.667	0.00	0.00	45.39	3.01
492	493	3.889815	TCTGCTGTAAGGAAATCCATGG	58.110	45.455	4.97	4.97	38.89	3.66
493	494	2.954318	CTGCTGTAAGGAAATCCATGGG	59.046	50.000	13.02	0.00	38.89	4.00
501	502	1.106285	GAAATCCATGGGCTCCACAC	58.894	55.000	13.02	0.00	35.80	3.82
503	504	0.033796	AATCCATGGGCTCCACACAG	60.034	55.000	13.02	0.00	35.80	3.66
514	515	1.400846	CTCCACACAGATGATGCAAGC	59.599	52.381	0.00	0.00	0.00	4.01
542	543	7.986085	AACAAGCTAGACTCACAACAAATAT	57.014	32.000	0.00	0.00	0.00	1.28
560	561	6.442564	ACAAATATTACCCTGGTACTGACAGA	59.557	38.462	10.08	0.00	38.20	3.41
564	565	5.927281	TTACCCTGGTACTGACAGATTAC	57.073	43.478	10.08	2.00	38.20	1.89
565	566	4.062490	ACCCTGGTACTGACAGATTACT	57.938	45.455	10.08	0.00	38.20	2.24
598	599	9.244292	TCAGTATACTTGTTCAGTCTTGATACT	57.756	33.333	1.56	0.00	35.32	2.12
599	600	9.509855	CAGTATACTTGTTCAGTCTTGATACTC	57.490	37.037	1.56	0.00	33.76	2.59
600	601	8.399425	AGTATACTTGTTCAGTCTTGATACTCG	58.601	37.037	0.00	0.00	31.75	4.18
601	602	4.238514	ACTTGTTCAGTCTTGATACTCGC	58.761	43.478	0.00	0.00	32.27	5.03
602	603	4.021894	ACTTGTTCAGTCTTGATACTCGCT	60.022	41.667	0.00	0.00	32.27	4.93
603	604	4.098055	TGTTCAGTCTTGATACTCGCTC	57.902	45.455	0.00	0.00	32.27	5.03
604	605	3.102276	GTTCAGTCTTGATACTCGCTCG	58.898	50.000	0.00	0.00	32.27	5.03
605	606	1.671328	TCAGTCTTGATACTCGCTCGG	59.329	52.381	0.00	0.00	0.00	4.63
606	607	1.671328	CAGTCTTGATACTCGCTCGGA	59.329	52.381	0.00	0.00	0.00	4.55
607	608	2.097629	CAGTCTTGATACTCGCTCGGAA	59.902	50.000	0.00	0.00	0.00	4.30
608	609	2.356382	AGTCTTGATACTCGCTCGGAAG	59.644	50.000	0.00	0.00	0.00	3.46
609	610	2.355132	GTCTTGATACTCGCTCGGAAGA	59.645	50.000	0.00	0.00	39.12	2.87
610	611	2.355132	TCTTGATACTCGCTCGGAAGAC	59.645	50.000	0.00	0.00	35.39	3.01
657	658	3.429141	GCGACTCGGGTGACTCGA	61.429	66.667	7.57	7.57	33.82	4.04
677	678	3.717294	GACCACCGCTCCCCACAT	61.717	66.667	0.00	0.00	0.00	3.21
779	784	4.137872	CTCTTCGCGGCGGGGTTA	62.138	66.667	23.46	8.90	0.00	2.85
837	842	2.528127	TTGGCCGGGTTCTCCTCA	60.528	61.111	2.18	0.00	0.00	3.86
852	857	1.554617	TCCTCATTGATGCGGAGAACA	59.445	47.619	0.00	0.00	36.80	3.18
1056	1071	4.636435	CCGGTGGCTGGGAAACGT	62.636	66.667	0.00	0.00	0.00	3.99
1069	1084	2.162809	GGGAAACGTAACGCATCCAAAT	59.837	45.455	0.00	0.00	36.88	2.32
1373	1405	1.571955	GTTTGGGCCATGGAGGAAAT	58.428	50.000	18.40	0.00	41.22	2.17
1561	1593	1.256812	GGAGATGGAGGAGCTAGAGC	58.743	60.000	0.00	0.00	42.49	4.09
1618	1653	2.334023	AGAAGAAGGAGAAGGTGCTGT	58.666	47.619	0.00	0.00	0.00	4.40
1667	1702	2.596851	GCTCACCAGGCCTCCTCAA	61.597	63.158	0.00	0.00	0.00	3.02
1678	1713	1.611936	GCCTCCTCAACCTCTCCAAAC	60.612	57.143	0.00	0.00	0.00	2.93
1688	1726	0.539051	CTCTCCAAACCTCCAGCGAT	59.461	55.000	0.00	0.00	0.00	4.58
2031	2079	5.363292	TCCCCAAAATTCATGACATATGGTG	59.637	40.000	7.80	3.37	0.00	4.17
2098	2146	2.107204	GGTGGAGATGGGATGCATTAGT	59.893	50.000	0.00	0.00	0.00	2.24
2195	2245	2.291800	CCCAACCCAGAGGACAATGATT	60.292	50.000	0.00	0.00	36.73	2.57
2270	2329	1.663702	CGGGTCAGTCGAACGCTTT	60.664	57.895	0.00	0.00	0.00	3.51
2351	2410	2.674754	GGGCGATTTGGTGGAGGA	59.325	61.111	0.00	0.00	0.00	3.71
2385	2445	2.649816	AGGGGAGGCAGAAACAACTATT	59.350	45.455	0.00	0.00	0.00	1.73
2435	2496	6.855914	GCGATAGATCTAGAAACTTCACTGAG	59.144	42.308	8.70	0.00	39.76	3.35
2468	2529	0.031616	GAGACTGGGATCAGGGGAGT	60.032	60.000	0.00	0.00	44.99	3.85
2469	2530	0.031616	AGACTGGGATCAGGGGAGTC	60.032	60.000	0.00	0.00	44.99	3.36
2495	2556	4.281941	AGCGATAATATGCAGAGGAGACAA	59.718	41.667	0.00	0.00	0.00	3.18
2522	2583	4.363991	ACAACAAGAGAAGGAGAAGCAT	57.636	40.909	0.00	0.00	0.00	3.79
2548	4035	3.333313	AGAGCAGGAGAGGATGAGATT	57.667	47.619	0.00	0.00	0.00	2.40
2549	4036	3.656496	AGAGCAGGAGAGGATGAGATTT	58.344	45.455	0.00	0.00	0.00	2.17
2561	4048	9.480053	GAGAGGATGAGATTTGAGAAAGATAAG	57.520	37.037	0.00	0.00	0.00	1.73
2592	4079	4.096833	TGAAGATCATGCAACAAGGTATGC	59.903	41.667	0.00	0.00	42.86	3.14
2632	4119	0.747852	GCTGGTAGTGGACTAGAGGC	59.252	60.000	0.00	0.00	38.94	4.70
2681	4168	6.808829	TGTTTTGCTTTCTCAATTGACTCAT	58.191	32.000	3.38	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	9.947433	TCCGTTCCTAAATATTTGTCTTTCTAA	57.053	29.630	11.05	0.00	0.00	2.10
16	17	9.595823	CTCCGTTCCTAAATATTTGTCTTTCTA	57.404	33.333	11.05	0.00	0.00	2.10
17	18	7.553044	CCTCCGTTCCTAAATATTTGTCTTTCT	59.447	37.037	11.05	0.00	0.00	2.52
18	19	7.201705	CCCTCCGTTCCTAAATATTTGTCTTTC	60.202	40.741	11.05	0.00	0.00	2.62
19	20	6.602009	CCCTCCGTTCCTAAATATTTGTCTTT	59.398	38.462	11.05	0.00	0.00	2.52
20	21	6.069847	TCCCTCCGTTCCTAAATATTTGTCTT	60.070	38.462	11.05	0.00	0.00	3.01
21	22	5.427481	TCCCTCCGTTCCTAAATATTTGTCT	59.573	40.000	11.05	0.00	0.00	3.41
22	23	5.677567	TCCCTCCGTTCCTAAATATTTGTC	58.322	41.667	11.05	0.00	0.00	3.18
23	24	5.191124	ACTCCCTCCGTTCCTAAATATTTGT	59.809	40.000	11.05	0.00	0.00	2.83
24	25	5.681639	ACTCCCTCCGTTCCTAAATATTTG	58.318	41.667	11.05	1.40	0.00	2.32
25	26	5.970501	ACTCCCTCCGTTCCTAAATATTT	57.029	39.130	5.89	5.89	0.00	1.40
26	27	6.141790	AGTACTCCCTCCGTTCCTAAATATT	58.858	40.000	0.00	0.00	0.00	1.28
27	28	5.713807	AGTACTCCCTCCGTTCCTAAATAT	58.286	41.667	0.00	0.00	0.00	1.28
28	29	5.134725	AGTACTCCCTCCGTTCCTAAATA	57.865	43.478	0.00	0.00	0.00	1.40
29	30	3.991683	AGTACTCCCTCCGTTCCTAAAT	58.008	45.455	0.00	0.00	0.00	1.40
30	31	3.463048	AGTACTCCCTCCGTTCCTAAA	57.537	47.619	0.00	0.00	0.00	1.85
31	32	3.359950	GAAGTACTCCCTCCGTTCCTAA	58.640	50.000	0.00	0.00	0.00	2.69
32	33	2.681976	CGAAGTACTCCCTCCGTTCCTA	60.682	54.545	0.00	0.00	0.00	2.94
33	34	1.849977	GAAGTACTCCCTCCGTTCCT	58.150	55.000	0.00	0.00	0.00	3.36
34	35	0.455005	CGAAGTACTCCCTCCGTTCC	59.545	60.000	0.00	0.00	0.00	3.62
35	36	0.455005	CCGAAGTACTCCCTCCGTTC	59.545	60.000	0.00	0.00	0.00	3.95
36	37	0.038744	TCCGAAGTACTCCCTCCGTT	59.961	55.000	0.00	0.00	0.00	4.44
37	38	0.038744	TTCCGAAGTACTCCCTCCGT	59.961	55.000	0.00	0.00	0.00	4.69
38	39	0.739561	CTTCCGAAGTACTCCCTCCG	59.260	60.000	0.00	0.00	0.00	4.63
39	40	0.460722	GCTTCCGAAGTACTCCCTCC	59.539	60.000	9.87	0.00	0.00	4.30
40	41	0.460722	GGCTTCCGAAGTACTCCCTC	59.539	60.000	9.87	0.00	0.00	4.30
41	42	2.593128	GGCTTCCGAAGTACTCCCT	58.407	57.895	9.87	0.00	0.00	4.20
59	60	3.945434	CTGCCGCTGCTATTGCCG	61.945	66.667	0.70	0.00	38.71	5.69
75	76	1.217511	CTGTGGCTGCATCGACTCT	59.782	57.895	0.50	0.00	0.00	3.24
77	78	2.267006	CCTGTGGCTGCATCGACT	59.733	61.111	0.50	0.00	0.00	4.18
92	93	2.851263	TATCACGTTTTGTCCAGCCT	57.149	45.000	0.00	0.00	0.00	4.58
94	95	4.946784	ATCTTATCACGTTTTGTCCAGC	57.053	40.909	0.00	0.00	0.00	4.85
97	98	8.592998	CAGTAGTAATCTTATCACGTTTTGTCC	58.407	37.037	0.00	0.00	0.00	4.02
106	107	9.967346	TTAGTGATGCAGTAGTAATCTTATCAC	57.033	33.333	0.00	0.00	41.92	3.06
111	112	9.672673	ACAATTTAGTGATGCAGTAGTAATCTT	57.327	29.630	0.00	0.00	0.00	2.40
127	128	5.934625	AGAGTCCTACTTGCACAATTTAGTG	59.065	40.000	0.00	0.00	42.37	2.74
169	170	2.611292	CCTCTTCAAATTGCTAGCCTCG	59.389	50.000	13.29	0.00	0.00	4.63
235	236	5.180680	ACGGACCTGCTATTTTGAAACTTAC	59.819	40.000	0.00	0.00	0.00	2.34
250	251	1.004918	ACTGCTACAACGGACCTGC	60.005	57.895	0.00	0.00	0.00	4.85
257	258	5.108385	AGGAAAAATTCACTGCTACAACG	57.892	39.130	0.00	0.00	0.00	4.10
276	277	7.343574	TGCTAATGAGGTTACAGTACATTAGGA	59.656	37.037	20.16	17.28	44.58	2.94
288	289	4.078639	AGGCAGATGCTAATGAGGTTAC	57.921	45.455	4.59	0.00	41.70	2.50
292	293	3.072184	AGGTTAGGCAGATGCTAATGAGG	59.928	47.826	4.59	0.00	41.70	3.86
299	300	1.279271	ACGAAAGGTTAGGCAGATGCT	59.721	47.619	4.59	0.00	41.70	3.79
318	319	5.725110	AGATGCATACAGAAATTCACGAC	57.275	39.130	0.00	0.00	0.00	4.34
321	322	5.049129	GGCCTAGATGCATACAGAAATTCAC	60.049	44.000	0.00	0.00	0.00	3.18
329	330	2.105477	ACTTGGGCCTAGATGCATACAG	59.895	50.000	21.96	0.00	0.00	2.74
389	390	2.433868	TGACGTACTGGAAGCTCAAC	57.566	50.000	0.00	0.00	37.60	3.18
410	411	6.156429	AGAGGTAGTTAGGAAAGGTGGTTATG	59.844	42.308	0.00	0.00	0.00	1.90
443	444	4.566907	GGCTAAACTCCATACCTTCAACCA	60.567	45.833	0.00	0.00	0.00	3.67
454	455	3.019564	GCAGAACATGGCTAAACTCCAT	58.980	45.455	0.00	0.00	44.70	3.41
467	468	4.922206	TGGATTTCCTTACAGCAGAACAT	58.078	39.130	0.00	0.00	36.82	2.71
473	474	2.949963	GCCCATGGATTTCCTTACAGCA	60.950	50.000	15.22	0.00	36.82	4.41
492	493	0.393402	TGCATCATCTGTGTGGAGCC	60.393	55.000	0.00	0.00	0.00	4.70
493	494	1.400846	CTTGCATCATCTGTGTGGAGC	59.599	52.381	0.00	0.00	0.00	4.70
501	502	1.469703	TGTTTCCGCTTGCATCATCTG	59.530	47.619	0.00	0.00	0.00	2.90
503	504	2.523015	CTTGTTTCCGCTTGCATCATC	58.477	47.619	0.00	0.00	0.00	2.92
514	515	3.026630	TGTGAGTCTAGCTTGTTTCCG	57.973	47.619	0.00	0.00	0.00	4.30
542	543	5.586877	AGTAATCTGTCAGTACCAGGGTAA	58.413	41.667	0.00	0.00	31.86	2.85
589	590	2.355132	GTCTTCCGAGCGAGTATCAAGA	59.645	50.000	0.00	0.00	33.17	3.02
593	594	0.935898	TCGTCTTCCGAGCGAGTATC	59.064	55.000	0.00	0.00	41.60	2.24
594	595	3.076104	TCGTCTTCCGAGCGAGTAT	57.924	52.632	0.00	0.00	41.60	2.12
595	596	4.604114	TCGTCTTCCGAGCGAGTA	57.396	55.556	0.00	0.00	41.60	2.59
603	604	1.409412	CTAATCGCCATCGTCTTCCG	58.591	55.000	0.00	0.00	36.96	4.30
604	605	1.140816	GCTAATCGCCATCGTCTTCC	58.859	55.000	0.00	0.00	36.96	3.46
605	606	1.523095	GTGCTAATCGCCATCGTCTTC	59.477	52.381	0.00	0.00	38.05	2.87
606	607	1.134818	TGTGCTAATCGCCATCGTCTT	60.135	47.619	0.00	0.00	38.05	3.01
607	608	0.459899	TGTGCTAATCGCCATCGTCT	59.540	50.000	0.00	0.00	38.05	4.18
608	609	0.577269	GTGTGCTAATCGCCATCGTC	59.423	55.000	0.00	0.00	38.05	4.20
609	610	1.145759	CGTGTGCTAATCGCCATCGT	61.146	55.000	0.00	0.00	38.05	3.73
610	611	1.559814	CGTGTGCTAATCGCCATCG	59.440	57.895	0.00	0.00	38.05	3.84
650	651	3.733960	CGGTGGTCGCTCGAGTCA	61.734	66.667	15.13	5.14	0.00	3.41
677	678	3.640257	CTCCCTCCGACCACTCCGA	62.640	68.421	0.00	0.00	0.00	4.55
702	703	2.126965	CGTTCGCCTCTCGTCGTT	60.127	61.111	0.00	0.00	39.67	3.85
777	782	2.023404	TCCCCTGGTGATAGCAGAGTAA	60.023	50.000	9.40	0.00	45.98	2.24
779	784	0.339859	TCCCCTGGTGATAGCAGAGT	59.660	55.000	9.40	0.00	45.98	3.24
819	824	2.046217	GAGGAGAACCCGGCCAAC	60.046	66.667	2.24	0.00	40.87	3.77
837	842	2.086869	CAACCTGTTCTCCGCATCAAT	58.913	47.619	0.00	0.00	0.00	2.57
852	857	3.694746	TCGGCTGTCGATCAACCT	58.305	55.556	0.00	0.00	43.74	3.50
987	1002	1.651987	CATTCATGGCGGTAGTTCGT	58.348	50.000	0.00	0.00	0.00	3.85
1056	1071	2.096248	GGTGGGAATTTGGATGCGTTA	58.904	47.619	0.00	0.00	0.00	3.18
1069	1084	1.538876	CTGTGGGAGAGGGTGGGAA	60.539	63.158	0.00	0.00	0.00	3.97
1202	1234	3.178540	AACCAGGACACCACCTCGC	62.179	63.158	0.00	0.00	38.32	5.03
1373	1405	0.114560	GGATGGATCCCCCGACTCTA	59.885	60.000	9.90	0.00	41.20	2.43
1488	1520	2.266055	GGAACCCAGCGAGTCCTG	59.734	66.667	0.00	2.56	0.00	3.86
1489	1521	3.382832	CGGAACCCAGCGAGTCCT	61.383	66.667	0.00	0.00	0.00	3.85
1618	1653	3.338250	AGGGGATCGCCTTGGCAA	61.338	61.111	24.97	0.00	0.00	4.52
1657	1692	1.201429	TTGGAGAGGTTGAGGAGGCC	61.201	60.000	0.00	0.00	0.00	5.19
1667	1702	1.831652	CGCTGGAGGTTTGGAGAGGT	61.832	60.000	0.00	0.00	0.00	3.85
1711	1749	1.282875	GCCAGCAACCAGAAACGAC	59.717	57.895	0.00	0.00	0.00	4.34
2019	2067	4.586001	GCCCAATTTCTCACCATATGTCAT	59.414	41.667	1.24	0.00	0.00	3.06
2026	2074	3.104519	TCATGCCCAATTTCTCACCAT	57.895	42.857	0.00	0.00	0.00	3.55
2031	2079	5.909477	TGAAATCATCATGCCCAATTTCTC	58.091	37.500	16.50	2.15	37.28	2.87
2195	2245	1.103811	TAAGGTCTTCCCCCTGGGTA	58.896	55.000	12.71	0.00	44.74	3.69
2209	2268	6.858306	TGGGTTTATATATGTCCCCTTAAGGT	59.142	38.462	20.22	3.80	37.52	3.50
2214	2273	6.467339	GCTCTTGGGTTTATATATGTCCCCTT	60.467	42.308	14.75	0.00	37.52	3.95
2351	2410	2.997138	CCTCCCCTATTGAATCTCCCT	58.003	52.381	0.00	0.00	0.00	4.20
2385	2445	7.394816	CCTCCTTCATCCTTCTTTTTGTACTA	58.605	38.462	0.00	0.00	0.00	1.82
2399	2459	3.096092	AGATCTATCGCCTCCTTCATCC	58.904	50.000	0.00	0.00	0.00	3.51
2435	2496	2.684881	CCAGTCTCTCTTGCTCTCTCTC	59.315	54.545	0.00	0.00	0.00	3.20
2468	2529	2.599659	CTCTGCATATTATCGCTGCGA	58.400	47.619	28.01	28.01	41.13	5.10
2469	2530	1.657594	CCTCTGCATATTATCGCTGCG	59.342	52.381	17.25	17.25	38.75	5.18
2495	2556	5.815233	TCTCCTTCTCTTGTTGTTGATCT	57.185	39.130	0.00	0.00	0.00	2.75
2522	2583	2.612285	TCCTCTCCTGCTCTTCTTCA	57.388	50.000	0.00	0.00	0.00	3.02
2592	4079	3.495100	GCACTACCATTATCAGGGTCAGG	60.495	52.174	0.00	0.00	38.60	3.86
2632	4119	2.744202	AGGAGTTTTTGCTGCTGTATCG	59.256	45.455	0.00	0.00	35.81	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.