AutoCloner

Multiple sequence alignment - TraesCS2D01G169800

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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	TraesCS2D01G169800	chr2D	100.000	3809	0	0	1	3809	113512312	113508504	0.000000e+00	7035.0
1	TraesCS2D01G169800	chr2A	95.295	1828	57	14	2001	3809	115141190	115139373	0.000000e+00	2872.0
2	TraesCS2D01G169800	chr2A	91.874	923	67	3	1	917	115143296	115142376	0.000000e+00	1282.0
3	TraesCS2D01G169800	chr2A	92.284	648	44	1	917	1564	115142346	115141705	0.000000e+00	915.0
4	TraesCS2D01G169800	chr2A	94.393	428	16	3	1580	2006	115141639	115141219	0.000000e+00	651.0
5	TraesCS2D01G169800	chr2A	85.000	160	15	5	3074	3231	141506470	141506318	1.830000e-33	154.0
6	TraesCS2D01G169800	chr2B	93.756	1089	25	12	2001	3075	164108523	164107464	0.000000e+00	1594.0
7	TraesCS2D01G169800	chr2B	91.529	1086	57	6	943	2006	164109624	164108552	0.000000e+00	1463.0
8	TraesCS2D01G169800	chr2B	84.369	531	47	20	3230	3744	164107465	164106955	4.420000e-134	488.0
9	TraesCS2D01G169800	chr2B	83.333	168	17	7	3070	3234	190023046	190022887	1.100000e-30	145.0
10	TraesCS2D01G169800	chr2B	91.071	56	5	0	3746	3801	164106852	164106797	4.080000e-10	76.8
11	TraesCS2D01G169800	chr1D	87.706	911	105	6	13	917	299695885	299694976	0.000000e+00	1055.0
12	TraesCS2D01G169800	chr4B	86.522	920	117	7	1	917	94952146	94951231	0.000000e+00	1005.0
13	TraesCS2D01G169800	chr4B	85.246	915	100	13	7	917	412112158	412111275	0.000000e+00	909.0
14	TraesCS2D01G169800	chr4B	85.185	162	15	5	3072	3231	106227407	106227561	1.420000e-34	158.0
15	TraesCS2D01G169800	chr6D	90.052	774	74	3	1	772	418533035	418532263	0.000000e+00	1000.0
16	TraesCS2D01G169800	chrUn	85.961	926	85	22	1	917	39800127	39801016	0.000000e+00	948.0
17	TraesCS2D01G169800	chrUn	85.961	926	85	22	1	917	300440903	300441792	0.000000e+00	948.0
18	TraesCS2D01G169800	chr7A	83.550	924	134	13	1	917	191279348	191278436	0.000000e+00	848.0
19	TraesCS2D01G169800	chr3D	86.262	808	78	18	114	917	271485383	271484605	0.000000e+00	846.0
20	TraesCS2D01G169800	chr1B	83.749	923	121	22	1	917	538721857	538720958	0.000000e+00	846.0
21	TraesCS2D01G169800	chr1B	82.941	170	19	8	3074	3240	328643677	328643839	1.100000e-30	145.0
22	TraesCS2D01G169800	chr6A	84.472	161	16	6	3074	3232	411770253	411770406	2.370000e-32	150.0
23	TraesCS2D01G169800	chr7D	83.735	166	16	7	3073	3234	583068890	583069048	3.070000e-31	147.0
24	TraesCS2D01G169800	chr1A	83.951	162	16	7	3074	3232	155857706	155857860	3.070000e-31	147.0
25	TraesCS2D01G169800	chr3B	83.851	161	16	6	3074	3230	404830472	404830318	1.100000e-30	145.0

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	TraesCS2D01G169800	chr2D	113508504	113512312	3808	True	7035.00	7035	100.00000	1	3809	1	chr2D.!!$R1	3808
1	TraesCS2D01G169800	chr2A	115139373	115143296	3923	True	1430.00	2872	93.46150	1	3809	4	chr2A.!!$R2	3808
2	TraesCS2D01G169800	chr2B	164106797	164109624	2827	True	905.45	1594	90.18125	943	3801	4	chr2B.!!$R2	2858
3	TraesCS2D01G169800	chr1D	299694976	299695885	909	True	1055.00	1055	87.70600	13	917	1	chr1D.!!$R1	904
4	TraesCS2D01G169800	chr4B	94951231	94952146	915	True	1005.00	1005	86.52200	1	917	1	chr4B.!!$R1	916
5	TraesCS2D01G169800	chr4B	412111275	412112158	883	True	909.00	909	85.24600	7	917	1	chr4B.!!$R2	910
6	TraesCS2D01G169800	chr6D	418532263	418533035	772	True	1000.00	1000	90.05200	1	772	1	chr6D.!!$R1	771
7	TraesCS2D01G169800	chrUn	39800127	39801016	889	False	948.00	948	85.96100	1	917	1	chrUn.!!$F1	916
8	TraesCS2D01G169800	chrUn	300440903	300441792	889	False	948.00	948	85.96100	1	917	1	chrUn.!!$F2	916
9	TraesCS2D01G169800	chr7A	191278436	191279348	912	True	848.00	848	83.55000	1	917	1	chr7A.!!$R1	916
10	TraesCS2D01G169800	chr3D	271484605	271485383	778	True	846.00	846	86.26200	114	917	1	chr3D.!!$R1	803
11	TraesCS2D01G169800	chr1B	538720958	538721857	899	True	846.00	846	83.74900	1	917	1	chr1B.!!$R1	916

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
854	952	0.322975	TGAGAGCAGAAACCTGAGGC	59.677	55.0	0.0	0.0	33.56	4.70	F
1318	1457	0.034616	GCTCAGTGTTCAGGTGCTCT	59.965	55.0	0.0	0.0	0.00	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1817	2008	0.819582	CGGATTGAAGGCAGGCAAAT	59.180	50.000	0.0	0.0	0.0	2.32	R
3204	3445	3.438087	CCCTCTGTTCACAATGTAAGCTG	59.562	47.826	0.0	0.0	0.0	4.24	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
131	132	1.550072	TCACCAAGATCGAGTCATGCA	59.450	47.619	0.00	0.00	0.00	3.96
149	150	3.554934	TGCAAGAAATGGACAGAGTGTT	58.445	40.909	0.00	0.00	0.00	3.32
347	348	0.391793	CGCCAAGAGGGAGGAGAAAC	60.392	60.000	0.00	0.00	40.01	2.78
361	362	4.699522	AAACCCGAGGCGAGGTGC	62.700	66.667	0.00	0.00	45.38	5.01
405	406	1.335964	CGTCAAGCTCGACCTTCTCAA	60.336	52.381	0.00	0.00	31.91	3.02
668	693	3.905678	CCCTACGGCAGAGGAGCG	61.906	72.222	3.27	0.00	35.99	5.03
713	740	2.544267	GGTTCCTATCCTTTTGATCGCG	59.456	50.000	0.00	0.00	34.76	5.87
753	848	4.447389	CGATCGTTAACATGTGGCATGATA	59.553	41.667	15.03	5.69	0.00	2.15
827	925	7.915508	AGCGGGAAAAAGAACTTTAAATTTTG	58.084	30.769	0.00	0.00	31.63	2.44
828	926	7.551262	AGCGGGAAAAAGAACTTTAAATTTTGT	59.449	29.630	0.00	0.00	31.63	2.83
839	937	7.820044	ACTTTAAATTTTGTTGCGTTTGAGA	57.180	28.000	0.00	0.00	0.00	3.27
842	940	2.929531	TTTTGTTGCGTTTGAGAGCA	57.070	40.000	0.00	0.00	42.15	4.26
851	949	2.483876	CGTTTGAGAGCAGAAACCTGA	58.516	47.619	0.00	0.00	33.56	3.86
854	952	0.322975	TGAGAGCAGAAACCTGAGGC	59.677	55.000	0.00	0.00	33.56	4.70
855	953	0.739112	GAGAGCAGAAACCTGAGGCG	60.739	60.000	0.00	0.00	33.56	5.52
856	954	1.004440	GAGCAGAAACCTGAGGCGT	60.004	57.895	0.00	0.00	33.56	5.68
857	955	1.294659	GAGCAGAAACCTGAGGCGTG	61.295	60.000	0.00	0.00	33.56	5.34
866	964	2.032528	TGAGGCGTGGGCTGAAAG	59.967	61.111	0.00	0.00	38.98	2.62
920	1051	2.937959	AAACGCCCAAAGCCCTGGAA	62.938	55.000	3.19	0.00	38.96	3.53
925	1056	0.545071	CCCAAAGCCCTGGAAATGGT	60.545	55.000	3.19	0.00	38.96	3.55
928	1059	2.250924	CAAAGCCCTGGAAATGGTTCT	58.749	47.619	0.00	0.00	33.92	3.01
930	1061	1.928868	AGCCCTGGAAATGGTTCTTG	58.071	50.000	0.00	0.00	33.92	3.02
939	1070	3.429410	GGAAATGGTTCTTGTATGCTGCC	60.429	47.826	0.00	0.00	33.92	4.85
942	1073	2.985896	TGGTTCTTGTATGCTGCCTAC	58.014	47.619	7.97	7.97	0.00	3.18
1032	1171	6.157123	TGATCGGATAAGCTCTCCTATCTCTA	59.843	42.308	21.02	7.35	36.45	2.43
1033	1172	6.569127	TCGGATAAGCTCTCCTATCTCTAT	57.431	41.667	12.18	0.00	0.00	1.98
1034	1173	6.588204	TCGGATAAGCTCTCCTATCTCTATC	58.412	44.000	12.18	1.06	0.00	2.08
1035	1174	6.385759	TCGGATAAGCTCTCCTATCTCTATCT	59.614	42.308	12.18	0.00	0.00	1.98
1036	1175	6.706270	CGGATAAGCTCTCCTATCTCTATCTC	59.294	46.154	12.18	0.00	0.00	2.75
1037	1176	7.419057	CGGATAAGCTCTCCTATCTCTATCTCT	60.419	44.444	12.18	0.00	0.00	3.10
1083	1222	0.543749	AGCAGGCAATGGAGTCTACC	59.456	55.000	0.00	0.00	0.00	3.18
1100	1239	7.828223	GGAGTCTACCCTAATCACGAGATTATA	59.172	40.741	14.45	5.34	43.71	0.98
1107	1246	5.484290	CCTAATCACGAGATTATACCCCCTT	59.516	44.000	14.45	0.00	43.71	3.95
1114	1253	1.907255	GATTATACCCCCTTCTCCCCG	59.093	57.143	0.00	0.00	0.00	5.73
1146	1285	2.123077	AGGCCCCTCTCCTCATCG	60.123	66.667	0.00	0.00	0.00	3.84
1198	1337	1.338107	TTCCTTCTCTTCCGTCAGCA	58.662	50.000	0.00	0.00	0.00	4.41
1219	1358	4.980805	GTGGCGTCTTGCGTCCCA	62.981	66.667	0.00	0.00	46.01	4.37
1318	1457	0.034616	GCTCAGTGTTCAGGTGCTCT	59.965	55.000	0.00	0.00	0.00	4.09
1346	1485	3.262420	CCCGACCACTAGTCTGAATTTG	58.738	50.000	0.00	0.00	43.91	2.32
1353	1492	5.163195	ACCACTAGTCTGAATTTGGAACACT	60.163	40.000	11.12	0.00	39.29	3.55
1357	1496	2.484264	GTCTGAATTTGGAACACTCCGG	59.516	50.000	0.00	0.00	45.85	5.14
1390	1529	4.757502	TGTTATTATCTTCGATTTGCGCG	58.242	39.130	0.00	0.00	40.61	6.86
1392	1531	2.990774	TTATCTTCGATTTGCGCGAC	57.009	45.000	12.10	0.88	40.61	5.19
1509	1648	3.949113	GGATTCTCGAGAGTCAGGTAGTT	59.051	47.826	31.35	0.00	33.10	2.24
1539	1679	6.452242	TCTTTCACTTACTCACTATCGCAAA	58.548	36.000	0.00	0.00	0.00	3.68
1541	1681	7.602644	TCTTTCACTTACTCACTATCGCAAATT	59.397	33.333	0.00	0.00	0.00	1.82
1574	1747	5.419542	TCTCTTGGGAAATTATGTCTGACG	58.580	41.667	2.98	0.00	0.00	4.35
1622	1813	9.458374	ACTACGGTTAATTTTCTTTTGTTCATG	57.542	29.630	0.00	0.00	0.00	3.07
1817	2008	0.042581	TGCCCAGATAGGTGTCCTCA	59.957	55.000	0.00	0.00	34.61	3.86
1860	2051	2.435372	TGACCTGAAACCATATGGGC	57.565	50.000	25.55	14.43	42.05	5.36
1936	2127	3.731652	TTGAAATTTCTGCCAGTGGTG	57.268	42.857	18.64	4.47	0.00	4.17
2018	2243	4.365514	TTTGCAATGACTGGGTAGAGAA	57.634	40.909	0.00	0.00	0.00	2.87
2460	2686	4.934356	ACCTGCTCCAGAAAATATGGAAA	58.066	39.130	0.00	0.00	46.04	3.13
2541	2767	6.308766	AGAAGCACGTCAAAATTTTATCATGC	59.691	34.615	16.01	16.01	0.00	4.06
2543	2769	4.323336	GCACGTCAAAATTTTATCATGCGT	59.677	37.500	2.44	5.64	0.00	5.24
2651	2877	1.561542	CCTTACAGGAATGGACTGCCT	59.438	52.381	0.00	0.00	37.67	4.75
2699	2925	1.207089	CAGGACCAAACTCGCTATGGA	59.793	52.381	0.00	0.00	37.66	3.41
2774	3014	6.404074	CCAGCTTTCTGAAATCACAGTTATCC	60.404	42.308	2.88	0.00	42.95	2.59
2775	3015	6.149973	CAGCTTTCTGAAATCACAGTTATCCA	59.850	38.462	2.88	0.00	42.95	3.41
3153	3394	3.230743	AGACAGTTTTGGTGTGTTTGC	57.769	42.857	0.00	0.00	0.00	3.68
3173	3414	7.120579	TGTTTGCTCATTAATTTCAGTCCGTAT	59.879	33.333	0.00	0.00	0.00	3.06
3174	3415	6.603237	TGCTCATTAATTTCAGTCCGTATG	57.397	37.500	0.00	0.00	0.00	2.39
3175	3416	5.527214	TGCTCATTAATTTCAGTCCGTATGG	59.473	40.000	0.00	0.00	0.00	2.74
3176	3417	5.527582	GCTCATTAATTTCAGTCCGTATGGT	59.472	40.000	0.00	0.00	36.30	3.55
3177	3418	6.704493	GCTCATTAATTTCAGTCCGTATGGTA	59.296	38.462	0.00	0.00	36.30	3.25
3192	3433	6.722590	TCCGTATGGTATGTAGTCCATATTGT	59.277	38.462	0.00	0.00	44.86	2.71
3234	3477	7.016153	ACATTGTGAACAGAGGGAGTATAAA	57.984	36.000	0.00	0.00	0.00	1.40
3252	3495	5.705609	ATAAACCAAGCAGTTTGACGAAT	57.294	34.783	9.11	0.00	40.15	3.34
3254	3497	4.385358	AACCAAGCAGTTTGACGAATTT	57.615	36.364	0.00	0.00	39.21	1.82
3274	3517	7.758980	CGAATTTTTGAATTCATGGTATGTCCA	59.241	33.333	9.40	0.00	40.02	4.02
3394	3637	8.952278	TCTATGGTGTGTTTAATGGAAATGTAC	58.048	33.333	0.00	0.00	0.00	2.90
3395	3638	6.961360	TGGTGTGTTTAATGGAAATGTACA	57.039	33.333	0.00	0.00	0.00	2.90
3396	3639	7.531857	TGGTGTGTTTAATGGAAATGTACAT	57.468	32.000	1.41	1.41	0.00	2.29
3553	3801	2.606725	GTGCTTCTTCGGTCTGATCATG	59.393	50.000	0.00	0.00	0.00	3.07
3624	3881	7.916450	TGGTAAAGTTTCCAGAAAAATACAACG	59.084	33.333	0.00	0.00	31.33	4.10
3724	3982	4.526970	GGAATGAGAGTTGCATAAAGGGA	58.473	43.478	0.00	0.00	0.00	4.20

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	0.103390	TCGAAGAACAAGTGTCGGCA	59.897	50.000	0.00	0.00	34.32	5.69
131	132	2.887152	GCCAACACTCTGTCCATTTCTT	59.113	45.455	0.00	0.00	0.00	2.52
169	170	2.609737	CGGGTTGTAGACACTGTCCTTC	60.610	54.545	5.51	0.00	32.18	3.46
361	362	0.716108	GCTTCGTCATCAACACCGAG	59.284	55.000	0.00	0.00	0.00	4.63
366	367	1.795768	GTCCTGCTTCGTCATCAACA	58.204	50.000	0.00	0.00	0.00	3.33
405	406	3.569049	CTTCGGGCGACGTTGGTCT	62.569	63.158	4.64	0.00	44.69	3.85
450	454	2.313317	GTCGACATGTCTACCCCCATA	58.687	52.381	22.95	0.00	0.00	2.74
594	613	0.179215	CAACTTCAATGCTCGGCGTC	60.179	55.000	6.85	0.30	0.00	5.19
668	693	0.951558	ACATGGAACTCAAACGGCAC	59.048	50.000	0.00	0.00	0.00	5.01
713	740	3.487574	CGATCGAACATAGCCAAAGTCTC	59.512	47.826	10.26	0.00	0.00	3.36
753	848	2.503331	TCATGCCACAAGTTGACGATT	58.497	42.857	10.54	0.00	0.00	3.34
811	908	8.713271	TCAAACGCAACAAAATTTAAAGTTCTT	58.287	25.926	0.75	0.00	0.00	2.52
827	925	2.376032	GTTTCTGCTCTCAAACGCAAC	58.624	47.619	0.00	0.00	35.46	4.17
828	926	1.333619	GGTTTCTGCTCTCAAACGCAA	59.666	47.619	0.00	0.00	35.46	4.85
839	937	1.302033	CACGCCTCAGGTTTCTGCT	60.302	57.895	0.00	0.00	40.69	4.24
842	940	2.750350	CCCACGCCTCAGGTTTCT	59.250	61.111	0.00	0.00	0.00	2.52
851	949	3.909086	GAGCTTTCAGCCCACGCCT	62.909	63.158	0.00	0.00	43.77	5.52
854	952	1.424493	GATCGAGCTTTCAGCCCACG	61.424	60.000	0.00	0.00	43.77	4.94
855	953	1.092345	GGATCGAGCTTTCAGCCCAC	61.092	60.000	0.00	0.00	43.77	4.61
856	954	1.221840	GGATCGAGCTTTCAGCCCA	59.778	57.895	0.00	0.00	43.77	5.36
857	955	0.179034	ATGGATCGAGCTTTCAGCCC	60.179	55.000	0.00	0.00	43.77	5.19
863	961	2.369394	GGTTTGGATGGATCGAGCTTT	58.631	47.619	0.00	0.00	0.00	3.51
866	964	0.179084	TCGGTTTGGATGGATCGAGC	60.179	55.000	0.00	0.00	0.00	5.03
920	1051	3.091633	AGGCAGCATACAAGAACCATT	57.908	42.857	0.00	0.00	0.00	3.16
925	1056	2.496070	AGTCGTAGGCAGCATACAAGAA	59.504	45.455	17.04	0.00	0.00	2.52
928	1059	1.136305	GGAGTCGTAGGCAGCATACAA	59.864	52.381	17.04	0.00	0.00	2.41
930	1061	0.744874	TGGAGTCGTAGGCAGCATAC	59.255	55.000	7.17	7.17	0.00	2.39
1032	1171	1.454111	CTCCCCCGTCGTCAGAGAT	60.454	63.158	0.00	0.00	0.00	2.75
1033	1172	2.045242	CTCCCCCGTCGTCAGAGA	60.045	66.667	0.00	0.00	0.00	3.10
1034	1173	2.045242	TCTCCCCCGTCGTCAGAG	60.045	66.667	0.00	0.00	0.00	3.35
1035	1174	2.360852	GTCTCCCCCGTCGTCAGA	60.361	66.667	0.00	0.00	0.00	3.27
1036	1175	3.812019	CGTCTCCCCCGTCGTCAG	61.812	72.222	0.00	0.00	0.00	3.51
1083	1222	5.024118	AGGGGGTATAATCTCGTGATTAGG	58.976	45.833	20.76	0.00	45.11	2.69
1318	1457	2.036098	TAGTGGTCGGGGCGAGAA	59.964	61.111	0.00	0.00	36.23	2.87
1346	1485	1.617947	ATGGAGAGCCGGAGTGTTCC	61.618	60.000	5.05	4.70	40.33	3.62
1353	1492	1.860641	TAACAGAATGGAGAGCCGGA	58.139	50.000	5.05	0.00	43.62	5.14
1357	1496	7.148641	TCGAAGATAATAACAGAATGGAGAGC	58.851	38.462	0.00	0.00	43.62	4.09
1390	1529	1.677637	CCTAACCCTCTCGGCCTGTC	61.678	65.000	0.00	0.00	33.26	3.51
1392	1531	1.381327	TCCTAACCCTCTCGGCCTG	60.381	63.158	0.00	0.00	33.26	4.85
1410	1549	1.818363	CAGCGCATCATGCCTGAGT	60.818	57.895	18.40	0.00	41.20	3.41
1509	1648	7.148390	CGATAGTGAGTAAGTGAAAGAGAGACA	60.148	40.741	0.00	0.00	0.00	3.41
1539	1679	6.423776	TTTCCCAAGAGAAATGAAGCAAAT	57.576	33.333	0.00	0.00	30.87	2.32
1541	1681	6.423776	AATTTCCCAAGAGAAATGAAGCAA	57.576	33.333	0.59	0.00	43.90	3.91
1574	1747	1.270550	CAGTCACTGCCCATTGGTTTC	59.729	52.381	1.20	0.00	0.00	2.78
1657	1848	6.184068	TCATCCATTCCCGTTTTATCTTCAA	58.816	36.000	0.00	0.00	0.00	2.69
1664	1855	5.317808	TCAGTTTCATCCATTCCCGTTTTA	58.682	37.500	0.00	0.00	0.00	1.52
1817	2008	0.819582	CGGATTGAAGGCAGGCAAAT	59.180	50.000	0.00	0.00	0.00	2.32
1860	2051	8.348285	TGGTCTTTTATGATGAAAACTTAGGG	57.652	34.615	0.00	0.00	0.00	3.53
1936	2127	3.551407	GATCAGGCGTCCCCCTCC	61.551	72.222	0.00	0.00	31.24	4.30
1986	2177	5.632347	CCAGTCATTGCAAAAATGAAGAGAC	59.368	40.000	1.71	1.28	38.27	3.36
2541	2767	6.410845	CGACCAAATGTTTACATGAGATACG	58.589	40.000	0.00	0.00	36.56	3.06
2543	2769	6.411376	ACCGACCAAATGTTTACATGAGATA	58.589	36.000	0.00	0.00	36.56	1.98
2699	2925	6.124340	TGATATGAACATGCTCAAGGACATT	58.876	36.000	2.34	0.00	0.00	2.71
2745	2971	4.914983	TGTGATTTCAGAAAGCTGGAGAT	58.085	39.130	12.28	0.00	42.53	2.75
2927	3167	3.706594	AGAGGACAACTTTCACAGAGACA	59.293	43.478	0.00	0.00	0.00	3.41
2929	3169	5.386060	TCTAGAGGACAACTTTCACAGAGA	58.614	41.667	0.00	0.00	0.00	3.10
3132	3373	4.013728	AGCAAACACACCAAAACTGTCTA	58.986	39.130	0.00	0.00	0.00	2.59
3138	3379	6.843069	ATTAATGAGCAAACACACCAAAAC	57.157	33.333	0.00	0.00	0.00	2.43
3153	3394	8.712363	CATACCATACGGACTGAAATTAATGAG	58.288	37.037	0.00	0.00	35.59	2.90
3196	3437	7.264221	TGTTCACAATGTAAGCTGTTTTTGAT	58.736	30.769	6.70	0.00	0.00	2.57
3204	3445	3.438087	CCCTCTGTTCACAATGTAAGCTG	59.562	47.826	0.00	0.00	0.00	4.24
3234	3477	4.385358	AAAATTCGTCAAACTGCTTGGT	57.615	36.364	0.00	0.00	35.56	3.67
3274	3517	5.615289	ACACACTTCATTCTAAGTTCAGCT	58.385	37.500	0.00	0.00	37.61	4.24
3373	3616	8.825667	AAATGTACATTTCCATTAAACACACC	57.174	30.769	24.88	0.00	36.34	4.16
3553	3801	5.929415	TGTAAATTTGCGAAAAATTCTCCCC	59.071	36.000	0.00	0.14	0.00	4.81
3624	3881	9.387123	GTCTGAATGAAAACATTCAACTAAGAC	57.613	33.333	20.65	18.91	46.84	3.01
3724	3982	2.238646	TGCGTCTAATCCCTCCACAAAT	59.761	45.455	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.