AutoCloner

Multiple sequence alignment - TraesCS3B01G215800

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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	TraesCS3B01G215800	chr3B	100.000	5285	0	0	1	5285	256788205	256782921	0.000000e+00	9760.0
1	TraesCS3B01G215800	chr3B	98.780	82	1	0	1	82	435957116	435957197	4.270000e-31	147.0
2	TraesCS3B01G215800	chr3B	96.000	50	2	0	3619	3668	256784494	256784445	1.220000e-11	82.4
3	TraesCS3B01G215800	chr3B	96.000	50	2	0	3712	3761	256784587	256784538	1.220000e-11	82.4
4	TraesCS3B01G215800	chr3A	96.306	3790	81	15	200	3959	219801965	219798205	0.000000e+00	6168.0
5	TraesCS3B01G215800	chr3A	93.873	1371	38	19	3938	5285	219798191	219796844	0.000000e+00	2025.0
6	TraesCS3B01G215800	chr3A	92.929	99	6	1	101	199	219802109	219802012	5.520000e-30	143.0
7	TraesCS3B01G215800	chr3A	93.617	94	6	0	1	94	492706611	492706704	1.980000e-29	141.0
8	TraesCS3B01G215800	chr3A	98.000	50	1	0	3712	3761	219798548	219798499	2.620000e-13	87.9
9	TraesCS3B01G215800	chr3A	94.000	50	3	0	3619	3668	219798455	219798406	5.680000e-10	76.8
10	TraesCS3B01G215800	chr3D	96.688	2234	48	10	1375	3604	178535696	178533485	0.000000e+00	3692.0
11	TraesCS3B01G215800	chr3D	92.241	1392	45	16	3938	5285	178533214	178531842	0.000000e+00	1914.0
12	TraesCS3B01G215800	chr3D	94.641	1213	34	10	200	1386	178537888	178536681	0.000000e+00	1851.0
13	TraesCS3B01G215800	chr3D	93.452	168	8	1	3638	3805	178533487	178533323	4.090000e-61	246.0
14	TraesCS3B01G215800	chr3D	100.000	45	0	0	3895	3939	178533295	178533251	3.390000e-12	84.2
15	TraesCS3B01G215800	chr3D	100.000	31	0	0	3731	3761	178533487	178533457	2.060000e-04	58.4
16	TraesCS3B01G215800	chr1B	91.653	2492	176	12	1238	3713	622187222	622184747	0.000000e+00	3421.0
17	TraesCS3B01G215800	chr1B	85.721	2248	270	38	1391	3624	585882356	585884566	0.000000e+00	2326.0
18	TraesCS3B01G215800	chr1B	85.801	662	63	11	3938	4572	622184603	622183946	0.000000e+00	673.0
19	TraesCS3B01G215800	chr1B	85.397	315	35	10	948	1251	622187552	622187238	3.070000e-82	316.0
20	TraesCS3B01G215800	chr1B	83.186	339	39	12	4069	4392	585884753	585885088	1.440000e-75	294.0
21	TraesCS3B01G215800	chr1B	95.506	89	4	0	1	89	570480248	570480160	5.520000e-30	143.0
22	TraesCS3B01G215800	chr1D	91.320	2477	165	21	1238	3692	452341963	452344411	0.000000e+00	3338.0
23	TraesCS3B01G215800	chr1D	85.778	2257	264	42	1391	3624	433516610	433518832	0.000000e+00	2337.0
24	TraesCS3B01G215800	chr1D	86.798	659	50	13	3938	4570	452344741	452345388	0.000000e+00	701.0
25	TraesCS3B01G215800	chr1D	91.589	214	18	0	948	1161	452341601	452341814	4.000000e-76	296.0
26	TraesCS3B01G215800	chr1D	83.283	329	43	7	4069	4385	433519198	433519526	5.180000e-75	292.0
27	TraesCS3B01G215800	chr1D	97.561	82	2	0	1	82	315462311	315462230	1.980000e-29	141.0
28	TraesCS3B01G215800	chr1A	91.466	2449	167	18	1281	3713	547255037	547257459	0.000000e+00	3326.0
29	TraesCS3B01G215800	chr1A	86.783	2005	217	33	1627	3624	532103565	532105528	0.000000e+00	2191.0
30	TraesCS3B01G215800	chr1A	87.215	657	55	14	3938	4570	547257603	547258254	0.000000e+00	721.0
31	TraesCS3B01G215800	chr1A	86.032	315	33	9	948	1251	547254493	547254807	1.420000e-85	327.0
32	TraesCS3B01G215800	chr1A	83.383	337	42	9	4069	4392	532105705	532106040	3.090000e-77	300.0
33	TraesCS3B01G215800	chr1A	89.051	137	15	0	1010	1146	532102433	532102569	2.530000e-38	171.0
34	TraesCS3B01G215800	chr1A	85.455	165	21	3	3761	3924	547257389	547257551	9.100000e-38	169.0
35	TraesCS3B01G215800	chr5B	90.429	606	54	2	1234	1835	239395958	239395353	0.000000e+00	795.0
36	TraesCS3B01G215800	chr5B	85.079	315	36	8	948	1251	239396286	239395972	1.430000e-80	311.0
37	TraesCS3B01G215800	chr5B	96.552	87	3	0	1	87	557060873	557060959	1.530000e-30	145.0
38	TraesCS3B01G215800	chr2B	89.982	569	55	2	1234	1800	184124804	184124236	0.000000e+00	734.0
39	TraesCS3B01G215800	chr2B	83.178	214	25	8	1049	1251	184125033	184124820	9.040000e-43	185.0
40	TraesCS3B01G215800	chr2A	82.857	315	38	11	953	1251	203826104	203825790	8.720000e-68	268.0
41	TraesCS3B01G215800	chr5A	95.455	88	4	0	1	88	382088537	382088624	1.980000e-29	141.0
42	TraesCS3B01G215800	chr4B	97.561	82	2	0	1	82	645456702	645456783	1.980000e-29	141.0
43	TraesCS3B01G215800	chr4B	92.708	96	5	2	1	95	672122125	672122219	2.570000e-28	137.0
44	TraesCS3B01G215800	chr7B	96.471	85	2	1	1	85	2765349	2765266	7.140000e-29	139.0

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	TraesCS3B01G215800	chr3B	256782921	256788205	5284	True	3308.266667	9760	97.333333	1	5285	3	chr3B.!!$R1	5284
1	TraesCS3B01G215800	chr3A	219796844	219802109	5265	True	1700.140000	6168	95.021600	101	5285	5	chr3A.!!$R1	5184
2	TraesCS3B01G215800	chr3D	178531842	178537888	6046	True	1307.600000	3692	96.170333	200	5285	6	chr3D.!!$R1	5085
3	TraesCS3B01G215800	chr1B	622183946	622187552	3606	True	1470.000000	3421	87.617000	948	4572	3	chr1B.!!$R2	3624
4	TraesCS3B01G215800	chr1B	585882356	585885088	2732	False	1310.000000	2326	84.453500	1391	4392	2	chr1B.!!$F1	3001
5	TraesCS3B01G215800	chr1D	452341601	452345388	3787	False	1445.000000	3338	89.902333	948	4570	3	chr1D.!!$F2	3622
6	TraesCS3B01G215800	chr1D	433516610	433519526	2916	False	1314.500000	2337	84.530500	1391	4385	2	chr1D.!!$F1	2994
7	TraesCS3B01G215800	chr1A	547254493	547258254	3761	False	1135.750000	3326	87.542000	948	4570	4	chr1A.!!$F2	3622
8	TraesCS3B01G215800	chr1A	532102433	532106040	3607	False	887.333333	2191	86.405667	1010	4392	3	chr1A.!!$F1	3382
9	TraesCS3B01G215800	chr5B	239395353	239396286	933	True	553.000000	795	87.754000	948	1835	2	chr5B.!!$R1	887
10	TraesCS3B01G215800	chr2B	184124236	184125033	797	True	459.500000	734	86.580000	1049	1800	2	chr2B.!!$R1	751

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
83	84	0.251519	AAAGGACGGAGGGAGTACGT	60.252	55.000	0.0	0.0	44.35	3.57	F
707	759	0.598680	GTGAGAGTTGCGTCACAGCT	60.599	55.000	0.0	0.0	43.38	4.24	F
1868	3708	1.010793	TCTCTCTCTCTCCCTCCCTCT	59.989	57.143	0.0	0.0	0.00	3.69	F
3279	5147	0.036388	TGCTGGAAAGAAGGCTACGG	60.036	55.000	0.0	0.0	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2016	3875	0.451783	GAGATTTGCCAATTCCGCGT	59.548	50.0	4.92	0.0	0.00	6.01	R
2481	4340	0.039074	ACAGCGACAAGTTCTCCTCG	60.039	55.0	0.00	0.0	0.00	4.63	R
3565	5435	0.527565	GTGGTTGCATGCCTACCAAG	59.472	55.0	31.64	0.0	43.13	3.61	R
4659	6857	0.872388	GTGTTTCATCCGACACACCC	59.128	55.0	1.35	0.0	43.88	4.61	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
50	51	7.848223	AAGTTTGATTTTCCAAGAAAGTTGG	57.152	32.000	0.00	0.00	40.87	3.77
51	52	7.181569	AGTTTGATTTTCCAAGAAAGTTGGA	57.818	32.000	2.24	2.24	46.08	3.53
59	60	5.367945	TCCAAGAAAGTTGGAAGTACACT	57.632	39.130	3.95	0.00	44.90	3.55
60	61	5.365619	TCCAAGAAAGTTGGAAGTACACTC	58.634	41.667	3.95	0.00	44.90	3.51
61	62	5.130477	TCCAAGAAAGTTGGAAGTACACTCT	59.870	40.000	3.95	0.00	44.90	3.24
62	63	5.823045	CCAAGAAAGTTGGAAGTACACTCTT	59.177	40.000	0.00	0.00	42.06	2.85
63	64	6.318900	CCAAGAAAGTTGGAAGTACACTCTTT	59.681	38.462	0.00	0.00	42.06	2.52
64	65	7.497909	CCAAGAAAGTTGGAAGTACACTCTTTA	59.502	37.037	0.00	0.00	42.06	1.85
65	66	8.889717	CAAGAAAGTTGGAAGTACACTCTTTAA	58.110	33.333	0.00	0.00	30.46	1.52
66	67	9.457436	AAGAAAGTTGGAAGTACACTCTTTAAA	57.543	29.630	0.00	0.00	30.46	1.52
67	68	9.110502	AGAAAGTTGGAAGTACACTCTTTAAAG	57.889	33.333	9.04	9.04	30.46	1.85
68	69	7.803279	AAGTTGGAAGTACACTCTTTAAAGG	57.197	36.000	15.13	8.48	0.00	3.11
69	70	7.133133	AGTTGGAAGTACACTCTTTAAAGGA	57.867	36.000	15.13	1.82	0.00	3.36
70	71	6.990939	AGTTGGAAGTACACTCTTTAAAGGAC	59.009	38.462	15.13	6.27	0.00	3.85
71	72	5.535333	TGGAAGTACACTCTTTAAAGGACG	58.465	41.667	15.13	6.90	0.00	4.79
72	73	4.928020	GGAAGTACACTCTTTAAAGGACGG	59.072	45.833	15.13	5.64	0.00	4.79
73	74	5.279156	GGAAGTACACTCTTTAAAGGACGGA	60.279	44.000	15.13	0.00	0.00	4.69
74	75	5.388408	AGTACACTCTTTAAAGGACGGAG	57.612	43.478	15.13	7.51	0.00	4.63
75	76	3.679824	ACACTCTTTAAAGGACGGAGG	57.320	47.619	15.13	2.85	0.00	4.30
76	77	2.302157	ACACTCTTTAAAGGACGGAGGG	59.698	50.000	15.13	8.51	34.07	4.30
77	78	2.565834	CACTCTTTAAAGGACGGAGGGA	59.434	50.000	15.13	0.00	29.82	4.20
78	79	2.832733	ACTCTTTAAAGGACGGAGGGAG	59.167	50.000	15.13	4.81	0.00	4.30
79	80	2.832733	CTCTTTAAAGGACGGAGGGAGT	59.167	50.000	15.13	0.00	0.00	3.85
80	81	4.021916	CTCTTTAAAGGACGGAGGGAGTA	58.978	47.826	15.13	0.00	0.00	2.59
81	82	3.766051	TCTTTAAAGGACGGAGGGAGTAC	59.234	47.826	15.13	0.00	0.00	2.73
82	83	1.755179	TAAAGGACGGAGGGAGTACG	58.245	55.000	0.00	0.00	0.00	3.67
83	84	0.251519	AAAGGACGGAGGGAGTACGT	60.252	55.000	0.00	0.00	44.35	3.57
84	85	0.251519	AAGGACGGAGGGAGTACGTT	60.252	55.000	0.00	0.00	41.40	3.99
85	86	0.620556	AGGACGGAGGGAGTACGTTA	59.379	55.000	0.00	0.00	41.40	3.18
86	87	0.735471	GGACGGAGGGAGTACGTTAC	59.265	60.000	0.00	0.00	41.40	2.50
87	88	1.680249	GGACGGAGGGAGTACGTTACT	60.680	57.143	0.00	0.00	41.40	2.24
88	89	2.420129	GGACGGAGGGAGTACGTTACTA	60.420	54.545	0.00	0.00	41.40	1.82
89	90	3.471680	GACGGAGGGAGTACGTTACTAT	58.528	50.000	0.00	0.00	41.40	2.12
90	91	3.879892	GACGGAGGGAGTACGTTACTATT	59.120	47.826	0.00	0.00	41.40	1.73
91	92	3.629398	ACGGAGGGAGTACGTTACTATTG	59.371	47.826	0.00	0.00	39.59	1.90
92	93	3.629398	CGGAGGGAGTACGTTACTATTGT	59.371	47.826	0.00	0.00	39.59	2.71
93	94	4.096984	CGGAGGGAGTACGTTACTATTGTT	59.903	45.833	0.00	0.00	39.59	2.83
94	95	5.393461	CGGAGGGAGTACGTTACTATTGTTT	60.393	44.000	0.00	0.00	39.59	2.83
95	96	6.401394	GGAGGGAGTACGTTACTATTGTTTT	58.599	40.000	0.00	0.00	39.59	2.43
96	97	6.875726	GGAGGGAGTACGTTACTATTGTTTTT	59.124	38.462	0.00	0.00	39.59	1.94
292	340	1.935327	CTAGTCCCTATAGCCGCCGC	61.935	65.000	0.00	0.00	0.00	6.53
427	475	7.591006	TTTTCAGGTATAAGCTTTACAGTCG	57.409	36.000	3.20	0.00	0.00	4.18
434	482	2.200373	AGCTTTACAGTCGCCCAATT	57.800	45.000	0.00	0.00	0.00	2.32
435	483	1.812571	AGCTTTACAGTCGCCCAATTG	59.187	47.619	0.00	0.00	0.00	2.32
451	499	4.274705	CCCAATTGTTGCTTAAACCCAAAC	59.725	41.667	4.43	0.00	38.06	2.93
454	502	4.553330	TTGTTGCTTAAACCCAAACCAA	57.447	36.364	0.00	0.00	38.06	3.67
463	511	6.463190	GCTTAAACCCAAACCAATTAACCTCA	60.463	38.462	0.00	0.00	0.00	3.86
465	513	5.545063	AACCCAAACCAATTAACCTCAAG	57.455	39.130	0.00	0.00	0.00	3.02
466	514	4.552674	ACCCAAACCAATTAACCTCAAGT	58.447	39.130	0.00	0.00	0.00	3.16
686	738	1.263484	CTGTTGCTCATGCGATGATCC	59.737	52.381	0.00	0.00	43.34	3.36
707	759	0.598680	GTGAGAGTTGCGTCACAGCT	60.599	55.000	0.00	0.00	43.38	4.24
781	833	7.689953	TTATAGTCGAAAGGTTTAATCGCTC	57.310	36.000	0.00	0.00	36.56	5.03
842	913	6.594159	CCTAACTAATGTTCCAACGATCAAGT	59.406	38.462	0.00	0.00	37.59	3.16
843	914	6.877611	AACTAATGTTCCAACGATCAAGTT	57.122	33.333	0.00	0.00	34.15	2.66
844	915	6.877611	ACTAATGTTCCAACGATCAAGTTT	57.122	33.333	0.00	0.00	30.96	2.66
875	949	3.350219	TCTTTGCTAACTCATGGGGTC	57.650	47.619	0.00	0.00	0.00	4.46
885	959	2.779430	ACTCATGGGGTCAATGCATCTA	59.221	45.455	0.00	0.00	0.00	1.98
929	1003	7.552458	AAGATAAACATGTGTGCGAATCATA	57.448	32.000	0.00	0.00	0.00	2.15
1146	1221	5.542635	ACACTTCAGTTCTGGGTAAGTGATA	59.457	40.000	25.40	1.61	46.29	2.15
1178	1286	8.407064	TCAAGTATAATTCTCTCGTTTCTCTCC	58.593	37.037	0.00	0.00	0.00	3.71
1227	1340	6.861065	ACAATTACTGTGGACACTTTACTG	57.139	37.500	3.91	0.00	36.69	2.74
1251	1364	9.241317	CTGCCATGATAAATGTTTGAATAGTTC	57.759	33.333	0.00	0.00	0.00	3.01
1410	2732	4.774586	TCGCAGTATTTTTGTTTGGTACG	58.225	39.130	0.00	0.00	0.00	3.67
1791	3623	6.016276	GTGTGGTCAAATCTCACAGGTAATTT	60.016	38.462	0.00	0.00	41.33	1.82
1855	3695	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1857	3697	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1860	3700	4.219115	TCTCTCTCTCTCTCTCTCTCTCC	58.781	52.174	0.00	0.00	0.00	3.71
1861	3701	3.309296	TCTCTCTCTCTCTCTCTCTCCC	58.691	54.545	0.00	0.00	0.00	4.30
1862	3702	3.051803	TCTCTCTCTCTCTCTCTCTCCCT	60.052	52.174	0.00	0.00	0.00	4.20
1867	3707	1.421646	CTCTCTCTCTCTCCCTCCCTC	59.578	61.905	0.00	0.00	0.00	4.30
1868	3708	1.010793	TCTCTCTCTCTCCCTCCCTCT	59.989	57.143	0.00	0.00	0.00	3.69
1869	3709	1.421646	CTCTCTCTCTCCCTCCCTCTC	59.578	61.905	0.00	0.00	0.00	3.20
1988	3830	1.272114	GACTATGCAGACGCGCTAGC	61.272	60.000	5.73	4.06	42.97	3.42
2016	3875	7.759489	AGTTACATCTGCTTATGTTGGAAAA	57.241	32.000	9.33	0.00	40.52	2.29
2118	3977	2.158885	GGATCTCCCAGGTGCTAAAGTC	60.159	54.545	0.00	0.00	34.14	3.01
2481	4340	8.739649	AATCTAAACGTAGAAACAGTACTGTC	57.260	34.615	28.04	16.78	39.36	3.51
2755	4614	5.276461	TGATCGGAATGCACAGTACTATT	57.724	39.130	0.00	0.00	0.00	1.73
3279	5147	0.036388	TGCTGGAAAGAAGGCTACGG	60.036	55.000	0.00	0.00	0.00	4.02
3706	5578	5.922544	AGTTACTATGTTTTCAACTACGCGT	59.077	36.000	19.17	19.17	0.00	6.01
3782	5654	5.763698	AGGCTTTTTCACTTGGACTAGTTAC	59.236	40.000	0.00	0.00	0.00	2.50
3893	5765	5.467035	TTTGATGAATTGGTTGGTCCTTC	57.533	39.130	0.00	0.00	37.07	3.46
4319	6496	8.715088	ACGATGTTAGTTAAATTGTGGTACTTC	58.285	33.333	0.00	0.00	0.00	3.01
4599	6797	6.942532	TGTTTCAAACTCAGTTGCTCTTAT	57.057	33.333	1.10	0.00	0.00	1.73
4652	6850	3.935993	GGCTGCACTTCAGTCCTTA	57.064	52.632	0.50	0.00	44.66	2.69
4659	6857	2.876079	GCACTTCAGTCCTTAACCCTGG	60.876	54.545	0.00	0.00	0.00	4.45
4776	6974	5.458779	CCTTTTGAAGTTTGGCTTAAAGACG	59.541	40.000	0.00	0.00	35.96	4.18
4787	6992	3.555518	GCTTAAAGACGAAAAGCACCTG	58.444	45.455	0.00	0.00	43.98	4.00
4791	6996	3.692791	AAGACGAAAAGCACCTGTTTC	57.307	42.857	0.00	0.00	0.00	2.78
4835	7040	8.749354	CAAAGTTAAGCCTAACCAAATATTCCT	58.251	33.333	1.48	0.00	38.59	3.36
4865	7070	1.892209	AAGGTTTTGACGTGGGCTAG	58.108	50.000	0.00	0.00	0.00	3.42
4868	7089	2.071540	GGTTTTGACGTGGGCTAGTAC	58.928	52.381	0.00	0.00	0.00	2.73
4871	7092	0.245539	TTGACGTGGGCTAGTACTGC	59.754	55.000	5.39	7.18	0.00	4.40
4889	7110	2.278596	CTACCGTGTCCGATGCCG	60.279	66.667	0.00	0.00	35.63	5.69
4921	7143	7.288810	TGACTGATTTGTCCAAATTTTAGCT	57.711	32.000	6.70	0.00	40.77	3.32
4922	7144	7.725251	TGACTGATTTGTCCAAATTTTAGCTT	58.275	30.769	6.70	0.00	40.77	3.74
5162	7386	5.408909	CACAATGCTGATCATAGAGGTCATC	59.591	44.000	0.00	0.00	34.33	2.92
5185	7409	0.809636	GCACAAACACCCAAACAGGC	60.810	55.000	0.00	0.00	35.39	4.85
5220	7444	1.289160	ATCCCAGCTCCAGCAAGTAA	58.711	50.000	0.48	0.00	45.16	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	8.729756	CCAACTTTCTTGGAAAATCAAACTTTT	58.270	29.630	0.00	0.00	42.06	2.27
25	26	8.100164	TCCAACTTTCTTGGAAAATCAAACTTT	58.900	29.630	0.00	0.00	44.90	2.66
26	27	7.619965	TCCAACTTTCTTGGAAAATCAAACTT	58.380	30.769	0.00	0.00	44.90	2.66
27	28	7.181569	TCCAACTTTCTTGGAAAATCAAACT	57.818	32.000	0.00	0.00	44.90	2.66
37	38	5.130477	AGAGTGTACTTCCAACTTTCTTGGA	59.870	40.000	0.00	0.00	46.08	3.53
38	39	5.368989	AGAGTGTACTTCCAACTTTCTTGG	58.631	41.667	0.00	0.00	40.87	3.61
39	40	6.927294	AAGAGTGTACTTCCAACTTTCTTG	57.073	37.500	0.00	0.00	0.00	3.02
40	41	9.457436	TTTAAAGAGTGTACTTCCAACTTTCTT	57.543	29.630	0.00	0.00	31.02	2.52
41	42	9.110502	CTTTAAAGAGTGTACTTCCAACTTTCT	57.889	33.333	9.77	0.00	31.02	2.52
42	43	8.343366	CCTTTAAAGAGTGTACTTCCAACTTTC	58.657	37.037	16.98	0.00	31.02	2.62
43	44	8.050930	TCCTTTAAAGAGTGTACTTCCAACTTT	58.949	33.333	16.98	0.00	32.26	2.66
44	45	7.498239	GTCCTTTAAAGAGTGTACTTCCAACTT	59.502	37.037	16.98	0.00	0.00	2.66
45	46	6.990939	GTCCTTTAAAGAGTGTACTTCCAACT	59.009	38.462	16.98	0.00	0.00	3.16
46	47	6.073927	CGTCCTTTAAAGAGTGTACTTCCAAC	60.074	42.308	16.98	0.00	0.00	3.77
47	48	5.987347	CGTCCTTTAAAGAGTGTACTTCCAA	59.013	40.000	16.98	0.00	0.00	3.53
48	49	5.510179	CCGTCCTTTAAAGAGTGTACTTCCA	60.510	44.000	16.98	0.00	0.00	3.53
49	50	4.928020	CCGTCCTTTAAAGAGTGTACTTCC	59.072	45.833	16.98	0.00	0.00	3.46
50	51	5.776744	TCCGTCCTTTAAAGAGTGTACTTC	58.223	41.667	16.98	0.00	0.00	3.01
51	52	5.279356	CCTCCGTCCTTTAAAGAGTGTACTT	60.279	44.000	16.98	0.00	0.00	2.24
52	53	4.220163	CCTCCGTCCTTTAAAGAGTGTACT	59.780	45.833	16.98	0.00	0.00	2.73
53	54	4.492611	CCTCCGTCCTTTAAAGAGTGTAC	58.507	47.826	16.98	5.84	0.00	2.90
54	55	3.512724	CCCTCCGTCCTTTAAAGAGTGTA	59.487	47.826	16.98	0.00	0.00	2.90
55	56	2.302157	CCCTCCGTCCTTTAAAGAGTGT	59.698	50.000	16.98	0.00	0.00	3.55
56	57	2.565834	TCCCTCCGTCCTTTAAAGAGTG	59.434	50.000	16.98	5.33	0.00	3.51
57	58	2.832733	CTCCCTCCGTCCTTTAAAGAGT	59.167	50.000	16.98	0.00	0.00	3.24
58	59	2.832733	ACTCCCTCCGTCCTTTAAAGAG	59.167	50.000	16.98	7.03	0.00	2.85
59	60	2.898662	ACTCCCTCCGTCCTTTAAAGA	58.101	47.619	16.98	0.24	0.00	2.52
60	61	3.428589	CGTACTCCCTCCGTCCTTTAAAG	60.429	52.174	8.32	8.32	0.00	1.85
61	62	2.493278	CGTACTCCCTCCGTCCTTTAAA	59.507	50.000	0.00	0.00	0.00	1.52
62	63	2.094675	CGTACTCCCTCCGTCCTTTAA	58.905	52.381	0.00	0.00	0.00	1.52
63	64	1.004745	ACGTACTCCCTCCGTCCTTTA	59.995	52.381	0.00	0.00	0.00	1.85
64	65	0.251519	ACGTACTCCCTCCGTCCTTT	60.252	55.000	0.00	0.00	0.00	3.11
65	66	0.251519	AACGTACTCCCTCCGTCCTT	60.252	55.000	0.00	0.00	32.95	3.36
66	67	0.620556	TAACGTACTCCCTCCGTCCT	59.379	55.000	0.00	0.00	32.95	3.85
67	68	0.735471	GTAACGTACTCCCTCCGTCC	59.265	60.000	0.00	0.00	32.95	4.79
68	69	1.743996	AGTAACGTACTCCCTCCGTC	58.256	55.000	0.00	0.00	32.47	4.79
69	70	3.567478	ATAGTAACGTACTCCCTCCGT	57.433	47.619	0.00	0.00	40.14	4.69
70	71	3.629398	ACAATAGTAACGTACTCCCTCCG	59.371	47.826	0.00	0.00	40.14	4.63
71	72	5.588958	AACAATAGTAACGTACTCCCTCC	57.411	43.478	0.00	0.00	40.14	4.30
72	73	7.895975	AAAAACAATAGTAACGTACTCCCTC	57.104	36.000	0.00	0.00	40.14	4.30
99	100	0.804364	GCGTGGCATTGAGAACATCA	59.196	50.000	0.00	0.00	35.62	3.07
100	101	1.089920	AGCGTGGCATTGAGAACATC	58.910	50.000	0.00	0.00	0.00	3.06
101	102	0.806868	CAGCGTGGCATTGAGAACAT	59.193	50.000	0.00	0.00	0.00	2.71
102	103	1.855213	GCAGCGTGGCATTGAGAACA	61.855	55.000	0.00	0.00	0.00	3.18
103	104	1.154150	GCAGCGTGGCATTGAGAAC	60.154	57.895	0.00	0.00	0.00	3.01
104	105	1.300971	GAGCAGCGTGGCATTGAGAA	61.301	55.000	0.00	0.00	35.83	2.87
105	106	1.742880	GAGCAGCGTGGCATTGAGA	60.743	57.895	0.00	0.00	35.83	3.27
181	182	3.753434	CTCGACTCGGCAGCAGGT	61.753	66.667	0.00	0.00	0.00	4.00
215	262	1.000739	ATCGGGTCGGGTTGGACTA	59.999	57.895	0.00	0.00	37.12	2.59
239	287	9.197694	CGGTAGACCAGAAGAGATTTATTAATG	57.802	37.037	0.00	0.00	35.14	1.90
241	289	7.208080	GCGGTAGACCAGAAGAGATTTATTAA	58.792	38.462	0.00	0.00	35.14	1.40
427	475	2.224402	TGGGTTTAAGCAACAATTGGGC	60.224	45.455	10.83	12.91	37.07	5.36
434	482	4.762289	ATTGGTTTGGGTTTAAGCAACA	57.238	36.364	0.00	0.00	43.28	3.33
435	483	6.017770	GGTTAATTGGTTTGGGTTTAAGCAAC	60.018	38.462	0.00	0.00	43.28	4.17
451	499	5.236263	GGCACAAAAACTTGAGGTTAATTGG	59.764	40.000	9.51	2.59	38.28	3.16
454	502	4.500716	CCGGCACAAAAACTTGAGGTTAAT	60.501	41.667	0.00	0.00	37.12	1.40
463	511	2.093106	TGTACACCGGCACAAAAACTT	58.907	42.857	0.00	0.00	0.00	2.66
465	513	1.534385	GGTGTACACCGGCACAAAAAC	60.534	52.381	28.55	2.05	42.29	2.43
466	514	0.739561	GGTGTACACCGGCACAAAAA	59.260	50.000	28.55	0.00	42.29	1.94
686	738	1.278172	CTGTGACGCAACTCTCACGG	61.278	60.000	0.00	0.00	39.83	4.94
707	759	3.876914	GACTGACAATGACCACACTTCAA	59.123	43.478	0.00	0.00	0.00	2.69
781	833	6.100004	TCAGAAGAACCGAATTAGCAGTTAG	58.900	40.000	0.00	0.00	0.00	2.34
875	949	5.494632	TCACAAGCAGAATAGATGCATTG	57.505	39.130	0.00	0.00	46.31	2.82
885	959	9.985730	TTATCTTTTGATTTTCACAAGCAGAAT	57.014	25.926	0.00	0.00	40.19	2.40
929	1003	7.738437	AATGTTGGGGATCAATGAATAAGTT	57.262	32.000	0.00	0.00	37.73	2.66
1171	1279	5.854010	ATGTAGCAGTTAATCGGAGAGAA	57.146	39.130	0.00	0.00	43.63	2.87
1227	1340	8.416329	AGGAACTATTCAAACATTTATCATGGC	58.584	33.333	0.00	0.00	36.02	4.40
1251	1364	4.974368	AATCTTCAGAGTCGACTACAGG	57.026	45.455	20.09	8.42	0.00	4.00
1410	2732	8.932945	TGATAGATTCATTGAGACACTACAAC	57.067	34.615	0.00	0.00	0.00	3.32
1791	3623	6.899393	ATTACTCAACAATGAAAGCCAGAA	57.101	33.333	0.00	0.00	34.49	3.02
1855	3695	3.028130	GTTGTTAGAGAGGGAGGGAGAG	58.972	54.545	0.00	0.00	0.00	3.20
1857	3697	3.028130	GAGTTGTTAGAGAGGGAGGGAG	58.972	54.545	0.00	0.00	0.00	4.30
1860	3700	5.483811	GAAAAGAGTTGTTAGAGAGGGAGG	58.516	45.833	0.00	0.00	0.00	4.30
1861	3701	5.247337	AGGAAAAGAGTTGTTAGAGAGGGAG	59.753	44.000	0.00	0.00	0.00	4.30
1862	3702	5.155905	AGGAAAAGAGTTGTTAGAGAGGGA	58.844	41.667	0.00	0.00	0.00	4.20
1867	3707	6.102897	TCCTGAGGAAAAGAGTTGTTAGAG	57.897	41.667	0.00	0.00	0.00	2.43
1868	3708	6.099845	AGTTCCTGAGGAAAAGAGTTGTTAGA	59.900	38.462	16.79	0.00	43.86	2.10
1869	3709	6.203723	CAGTTCCTGAGGAAAAGAGTTGTTAG	59.796	42.308	16.79	0.00	43.86	2.34
1988	3830	6.595326	TCCAACATAAGCAGATGTAACTTCAG	59.405	38.462	4.14	0.00	39.16	3.02
2016	3875	0.451783	GAGATTTGCCAATTCCGCGT	59.548	50.000	4.92	0.00	0.00	6.01
2097	3956	1.840635	ACTTTAGCACCTGGGAGATCC	59.159	52.381	0.00	0.00	0.00	3.36
2118	3977	3.419759	CGAACGCAAACCTCCCCG	61.420	66.667	0.00	0.00	0.00	5.73
2481	4340	0.039074	ACAGCGACAAGTTCTCCTCG	60.039	55.000	0.00	0.00	0.00	4.63
2755	4614	2.092429	GGCCCATGTCTTGAAGGATACA	60.092	50.000	0.00	0.00	41.41	2.29
3054	4920	6.071616	GCACCCTTCACAAATAGGAAATACAA	60.072	38.462	0.00	0.00	33.13	2.41
3279	5147	2.599612	GCCAAATTCTGTTTGCAAACGC	60.600	45.455	31.20	22.94	41.74	4.84
3565	5435	0.527565	GTGGTTGCATGCCTACCAAG	59.472	55.000	31.64	0.00	43.13	3.61
3633	5505	8.616076	GTCTAAGTGAAAAAGCATGCATACTAT	58.384	33.333	21.98	0.00	0.00	2.12
3706	5578	9.938280	ATACTACTAGAACAATAGCACAAAACA	57.062	29.630	0.00	0.00	0.00	2.83
3893	5765	0.240945	GGTTGCCATGTTGAGTTCCG	59.759	55.000	0.00	0.00	0.00	4.30
4319	6496	2.340337	GCTGCAACTTAATGCCCAAAG	58.660	47.619	0.00	0.00	45.83	2.77
4447	6644	1.796017	TCCCGGTATCAGTTGGCATA	58.204	50.000	0.00	0.00	0.00	3.14
4499	6696	5.112686	GGATCTGGATACGATAAGCCAATC	58.887	45.833	0.00	0.00	42.51	2.67
4659	6857	0.872388	GTGTTTCATCCGACACACCC	59.128	55.000	1.35	0.00	43.88	4.61
4776	6974	4.639135	AGAACAGAAACAGGTGCTTTTC	57.361	40.909	0.00	0.00	32.76	2.29
4787	6992	3.375642	GCTCAGCCAAAAGAACAGAAAC	58.624	45.455	0.00	0.00	0.00	2.78
4835	7040	6.537301	CCACGTCAAAACCTTAGCAGATATAA	59.463	38.462	0.00	0.00	0.00	0.98
4865	7070	1.138247	CGGACACGGTAGGCAGTAC	59.862	63.158	0.00	0.00	36.18	2.73
4868	7089	1.226974	CATCGGACACGGTAGGCAG	60.227	63.158	0.00	0.00	41.39	4.85
4871	7092	2.106332	GGCATCGGACACGGTAGG	59.894	66.667	0.00	0.00	41.39	3.18
4876	7097	2.431771	TTCACGGCATCGGACACG	60.432	61.111	0.00	0.00	41.39	4.49
4889	7110	2.485814	GGACAAATCAGTCAGCCTTCAC	59.514	50.000	0.00	0.00	40.29	3.18
4921	7143	5.505181	AAGCTGGAGGAGATAAAACAGAA	57.495	39.130	0.00	0.00	0.00	3.02
4922	7144	5.505181	AAAGCTGGAGGAGATAAAACAGA	57.495	39.130	0.00	0.00	0.00	3.41
4936	7158	4.365514	TGAATTGTCCTGTAAAGCTGGA	57.634	40.909	0.00	0.00	42.01	3.86
5162	7386	1.134580	TGTTTGGGTGTTTGTGCCATG	60.135	47.619	0.00	0.00	0.00	3.66
5185	7409	6.831976	AGCTGGGATATTTCTAGTTAAGGTG	58.168	40.000	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.