AutoCloner

Multiple sequence alignment - TraesCS4D01G063900

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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	TraesCS4D01G063900	chr4D	100.000	2083	0	0	507	2589	39395156	39393074	0.000000e+00	3847.0
1	TraesCS4D01G063900	chr4D	91.667	300	13	4	1122	1415	39353761	39354054	3.100000e-109	405.0
2	TraesCS4D01G063900	chr4D	100.000	144	0	0	1	144	39395662	39395519	1.530000e-67	267.0
3	TraesCS4D01G063900	chr4D	91.765	85	7	0	1132	1216	418358169	418358085	4.530000e-23	119.0
4	TraesCS4D01G063900	chr4D	96.667	60	2	0	884	943	39353582	39353641	1.640000e-17	100.0
5	TraesCS4D01G063900	chr4B	85.397	1890	176	31	731	2589	57806733	57804913	0.000000e+00	1869.0
6	TraesCS4D01G063900	chr4B	91.246	297	17	2	1122	1415	57801621	57801331	1.870000e-106	396.0
7	TraesCS4D01G063900	chr4B	90.674	193	10	3	522	707	57807016	57806825	1.540000e-62	250.0
8	TraesCS4D01G063900	chr4B	98.039	102	1	1	1	102	57807118	57807018	2.650000e-40	176.0
9	TraesCS4D01G063900	chr4A	83.106	1101	54	40	589	1627	560951122	560952152	0.000000e+00	881.0
10	TraesCS4D01G063900	chr4A	78.076	894	121	41	1623	2502	560961830	560962662	1.790000e-136	496.0
11	TraesCS4D01G063900	chr4A	91.850	319	18	6	1122	1433	560964951	560965268	3.060000e-119	438.0
12	TraesCS4D01G063900	chr4A	92.941	85	6	0	1132	1216	46561064	46561148	9.730000e-25	124.0
13	TraesCS4D01G063900	chr4A	83.333	144	9	10	1	137	560950858	560950993	4.530000e-23	119.0
14	TraesCS4D01G063900	chr4A	98.305	59	1	0	532	590	560951007	560951065	1.270000e-18	104.0
15	TraesCS4D01G063900	chr4A	80.451	133	6	3	830	943	560964698	560964829	1.650000e-12	84.2
16	TraesCS4D01G063900	chr5B	83.504	685	106	5	1911	2589	13097102	13096419	1.310000e-177	632.0
17	TraesCS4D01G063900	chr5B	81.295	695	126	4	1898	2589	368125462	368124769	6.260000e-156	560.0
18	TraesCS4D01G063900	chr1D	83.041	684	109	7	1911	2589	32758915	32759596	4.730000e-172	614.0
19	TraesCS4D01G063900	chr7A	82.845	682	106	8	1912	2588	642874359	642875034	3.690000e-168	601.0
20	TraesCS4D01G063900	chr7A	80.934	771	131	11	1827	2589	4596601	4597363	1.720000e-166	595.0
21	TraesCS4D01G063900	chr7B	82.284	683	114	6	1912	2589	385919895	385919215	3.710000e-163	584.0
22	TraesCS4D01G063900	chr7B	90.476	84	8	0	1132	1215	469742206	469742289	7.570000e-21	111.0
23	TraesCS4D01G063900	chr3A	82.370	675	106	10	1909	2574	524756091	524755421	2.230000e-160	575.0
24	TraesCS4D01G063900	chr6B	81.215	708	122	10	1889	2589	276749279	276748576	6.260000e-156	560.0
25	TraesCS4D01G063900	chr7D	80.159	756	121	16	1844	2589	74954488	74955224	2.930000e-149	538.0

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	TraesCS4D01G063900	chr4D	39393074	39395662	2588	True	2057.00	3847	100.000	1	2589	2	chr4D.!!$R2	2588
1	TraesCS4D01G063900	chr4B	57801331	57807118	5787	True	672.75	1869	91.339	1	2589	4	chr4B.!!$R1	2588
2	TraesCS4D01G063900	chr4A	560950858	560952152	1294	False	368.00	881	88.248	1	1627	3	chr4A.!!$F2	1626
3	TraesCS4D01G063900	chr4A	560961830	560965268	3438	False	339.40	496	83.459	830	2502	3	chr4A.!!$F3	1672
4	TraesCS4D01G063900	chr5B	13096419	13097102	683	True	632.00	632	83.504	1911	2589	1	chr5B.!!$R1	678
5	TraesCS4D01G063900	chr5B	368124769	368125462	693	True	560.00	560	81.295	1898	2589	1	chr5B.!!$R2	691
6	TraesCS4D01G063900	chr1D	32758915	32759596	681	False	614.00	614	83.041	1911	2589	1	chr1D.!!$F1	678
7	TraesCS4D01G063900	chr7A	642874359	642875034	675	False	601.00	601	82.845	1912	2588	1	chr7A.!!$F2	676
8	TraesCS4D01G063900	chr7A	4596601	4597363	762	False	595.00	595	80.934	1827	2589	1	chr7A.!!$F1	762
9	TraesCS4D01G063900	chr7B	385919215	385919895	680	True	584.00	584	82.284	1912	2589	1	chr7B.!!$R1	677
10	TraesCS4D01G063900	chr3A	524755421	524756091	670	True	575.00	575	82.370	1909	2574	1	chr3A.!!$R1	665
11	TraesCS4D01G063900	chr6B	276748576	276749279	703	True	560.00	560	81.215	1889	2589	1	chr6B.!!$R1	700
12	TraesCS4D01G063900	chr7D	74954488	74955224	736	False	538.00	538	80.159	1844	2589	1	chr7D.!!$F1	745

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
620	689	1.629345	CTTTTACGGACCCGAACGGC	61.629	60.0	16.07	0.0	42.83	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1840	2036	0.035598	TCGAATTTGCCAAGTCCGGA	59.964	50.0	0.0	0.0	0.0	5.14	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
100	101	3.564225	CCTCCGTTCACTACTTGCTTTTT	59.436	43.478	0.00	0.00	0.00	1.94
137	147	3.487372	GGTTCCCTTCACTACTTGCTTT	58.513	45.455	0.00	0.00	0.00	3.51
138	148	3.889538	GGTTCCCTTCACTACTTGCTTTT	59.110	43.478	0.00	0.00	0.00	2.27
529	539	5.693814	GAATGAACTTCACTACTTGCTTGG	58.306	41.667	0.00	0.00	33.78	3.61
530	540	4.150897	TGAACTTCACTACTTGCTTGGT	57.849	40.909	0.00	0.00	0.00	3.67
560	570	3.059603	GCCTTTTCGCGAGTCCATA	57.940	52.632	9.59	0.00	0.00	2.74
620	689	1.629345	CTTTTACGGACCCGAACGGC	61.629	60.000	16.07	0.00	42.83	5.68
712	794	4.962836	AGCCCACACTGCTGCACC	62.963	66.667	0.00	0.00	37.76	5.01
714	796	4.584518	CCCACACTGCTGCACCCA	62.585	66.667	0.00	0.00	0.00	4.51
840	999	3.124921	CAACTACTTGCCCCCGCG	61.125	66.667	0.00	0.00	38.08	6.46
998	1173	4.144703	GCCGTTCCCCCGTCTCTC	62.145	72.222	0.00	0.00	0.00	3.20
1029	1204	4.889856	AGCACACGACGCAGCACA	62.890	61.111	9.03	0.00	0.00	4.57
1035	1210	3.842126	CGACGCAGCACACATCCG	61.842	66.667	0.00	0.00	0.00	4.18
1046	1221	4.157120	ACATCCGCCGTAGCCACC	62.157	66.667	0.00	0.00	34.57	4.61
1070	1245	1.363744	CTCCTAGCTTGCTTGTTCCG	58.636	55.000	0.00	0.00	0.00	4.30
1071	1246	0.685097	TCCTAGCTTGCTTGTTCCGT	59.315	50.000	0.00	0.00	0.00	4.69
1072	1247	1.071699	TCCTAGCTTGCTTGTTCCGTT	59.928	47.619	0.00	0.00	0.00	4.44
1074	1249	1.873591	CTAGCTTGCTTGTTCCGTTGT	59.126	47.619	0.00	0.00	0.00	3.32
1075	1250	1.102978	AGCTTGCTTGTTCCGTTGTT	58.897	45.000	0.00	0.00	0.00	2.83
1076	1251	1.065551	AGCTTGCTTGTTCCGTTGTTC	59.934	47.619	0.00	0.00	0.00	3.18
1077	1252	1.741993	CTTGCTTGTTCCGTTGTTCG	58.258	50.000	0.00	0.00	39.52	3.95
1078	1253	0.248296	TTGCTTGTTCCGTTGTTCGC	60.248	50.000	0.00	0.00	38.35	4.70
1079	1254	1.370051	GCTTGTTCCGTTGTTCGCC	60.370	57.895	0.00	0.00	38.35	5.54
1080	1255	1.083015	CTTGTTCCGTTGTTCGCCG	60.083	57.895	0.00	0.00	38.35	6.46
1081	1256	2.438385	CTTGTTCCGTTGTTCGCCGG	62.438	60.000	0.00	0.00	45.55	6.13
1082	1257	4.379143	GTTCCGTTGTTCGCCGGC	62.379	66.667	19.07	19.07	43.87	6.13
1095	1270	2.047274	CCGGCGGCAGAGAAAGAA	60.047	61.111	15.42	0.00	0.00	2.52
1096	1271	2.103042	CCGGCGGCAGAGAAAGAAG	61.103	63.158	15.42	0.00	0.00	2.85
1097	1272	2.103042	CGGCGGCAGAGAAAGAAGG	61.103	63.158	10.53	0.00	0.00	3.46
1098	1273	2.402572	GGCGGCAGAGAAAGAAGGC	61.403	63.158	3.07	0.00	0.00	4.35
1099	1274	1.672356	GCGGCAGAGAAAGAAGGCA	60.672	57.895	0.00	0.00	0.00	4.75
1117	1292	4.156477	AGGCAGACAGAGGAGGAATATAC	58.844	47.826	0.00	0.00	0.00	1.47
1144	1323	2.676839	GAGATGTCGAAGTACGTGGAGA	59.323	50.000	0.00	0.00	43.13	3.71
1243	1422	2.203451	AGTCCACCTCCACGTCGT	60.203	61.111	0.00	0.00	0.00	4.34
1244	1423	2.257676	GTCCACCTCCACGTCGTC	59.742	66.667	0.00	0.00	0.00	4.20
1245	1424	3.359523	TCCACCTCCACGTCGTCG	61.360	66.667	0.00	0.00	43.34	5.12
1456	1643	7.878408	GGCGACGAATTCTAATTTCTAAAAG	57.122	36.000	0.00	0.00	0.00	2.27
1457	1644	6.905609	GGCGACGAATTCTAATTTCTAAAAGG	59.094	38.462	0.00	0.00	0.00	3.11
1458	1645	7.201582	GGCGACGAATTCTAATTTCTAAAAGGA	60.202	37.037	0.00	0.00	0.00	3.36
1459	1646	7.846592	GCGACGAATTCTAATTTCTAAAAGGAG	59.153	37.037	0.00	0.00	0.00	3.69
1460	1647	9.084164	CGACGAATTCTAATTTCTAAAAGGAGA	57.916	33.333	3.52	0.00	0.00	3.71
1513	1704	5.343249	GGCCAATGAGTTGATTGATTGTAC	58.657	41.667	0.00	0.00	37.53	2.90
1514	1705	5.126061	GGCCAATGAGTTGATTGATTGTACT	59.874	40.000	0.00	0.00	37.53	2.73
1515	1706	6.318648	GGCCAATGAGTTGATTGATTGTACTA	59.681	38.462	0.00	0.00	37.53	1.82
1550	1741	8.647143	AACATCATTCTTTTGTTAGTTTGTGG	57.353	30.769	0.00	0.00	32.09	4.17
1572	1763	3.066621	GCCGTGCTGGAATTGATCAAATA	59.933	43.478	13.09	0.00	42.00	1.40
1666	1859	5.998363	GTCCTAGTTGATTTGTCCAAGTCTT	59.002	40.000	4.50	0.00	0.00	3.01
1685	1878	1.449601	GCCACCATCGATTGACCGT	60.450	57.895	3.08	0.00	0.00	4.83
1699	1893	1.271325	TGACCGTCTTGGAATGCACAT	60.271	47.619	0.00	0.00	42.00	3.21
1706	1900	5.050091	CCGTCTTGGAATGCACATATTCTAC	60.050	44.000	0.00	0.00	42.00	2.59
1709	1903	6.318648	GTCTTGGAATGCACATATTCTACCAA	59.681	38.462	0.00	0.00	37.26	3.67
1711	1905	7.395772	TCTTGGAATGCACATATTCTACCAAAA	59.604	33.333	0.00	0.00	37.26	2.44
1720	1914	8.243426	GCACATATTCTACCAAAAGATGTTGAA	58.757	33.333	0.00	0.00	36.65	2.69
1754	1948	8.680903	CATTGCAACTTACTAATGGAGAAGAAT	58.319	33.333	0.00	0.00	0.00	2.40
1755	1949	8.635765	TTGCAACTTACTAATGGAGAAGAATT	57.364	30.769	0.00	0.00	0.00	2.17
1819	2015	2.093553	TGGGGTGCTACGGTTTACATAC	60.094	50.000	0.00	0.00	0.00	2.39
1820	2016	2.169144	GGGGTGCTACGGTTTACATACT	59.831	50.000	0.00	0.00	0.00	2.12
1821	2017	3.192466	GGGTGCTACGGTTTACATACTG	58.808	50.000	0.00	0.00	0.00	2.74
1822	2018	3.368739	GGGTGCTACGGTTTACATACTGT	60.369	47.826	0.00	0.00	40.59	3.55
1823	2019	4.142182	GGGTGCTACGGTTTACATACTGTA	60.142	45.833	0.00	0.00	38.53	2.74
1824	2020	5.452356	GGGTGCTACGGTTTACATACTGTAT	60.452	44.000	0.00	0.00	38.74	2.29
1862	2058	0.168128	GGACTTGGCAAATTCGACCG	59.832	55.000	0.00	0.00	0.00	4.79
1881	2077	1.890041	CTCAAACACCCGCGGACAA	60.890	57.895	30.73	3.32	0.00	3.18
1882	2078	1.440938	CTCAAACACCCGCGGACAAA	61.441	55.000	30.73	3.92	0.00	2.83
1884	2080	1.749638	AAACACCCGCGGACAAACA	60.750	52.632	30.73	0.00	0.00	2.83
1891	2087	2.659244	GCGGACAAACACGACCGA	60.659	61.111	0.00	0.00	45.28	4.69
1932	2128	3.199677	CCGGTCACGCCTCAAATATTTA	58.800	45.455	0.00	0.00	39.22	1.40
2085	2282	1.529152	TAGTTCGGTCGCCAGCAAGA	61.529	55.000	0.00	0.00	0.00	3.02
2099	2296	3.834813	CCAGCAAGATAGAGTAGGGCATA	59.165	47.826	0.00	0.00	0.00	3.14
2127	2324	1.376037	CCGGCTCAAGGGACTCAAC	60.376	63.158	0.00	0.00	38.49	3.18
2128	2325	1.371183	CGGCTCAAGGGACTCAACA	59.629	57.895	0.00	0.00	38.49	3.33
2266	2478	4.752879	GTTGCGGCGCCTGGACTA	62.753	66.667	30.82	5.38	0.00	2.59
2319	2533	3.129502	CCTCGCCGACGTCCACTA	61.130	66.667	10.58	0.00	41.18	2.74
2507	2738	2.355837	GAGGCAGCGACGACACAA	60.356	61.111	0.00	0.00	0.00	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
117	127	5.515797	AAAAAGCAAGTAGTGAAGGGAAC	57.484	39.130	0.00	0.00	0.00	3.62
506	516	5.239525	ACCAAGCAAGTAGTGAAGTTCATTC	59.760	40.000	9.18	3.13	38.50	2.67
507	517	5.009010	CACCAAGCAAGTAGTGAAGTTCATT	59.991	40.000	9.18	7.53	31.79	2.57
508	518	4.516698	CACCAAGCAAGTAGTGAAGTTCAT	59.483	41.667	9.18	1.24	31.79	2.57
509	519	3.876914	CACCAAGCAAGTAGTGAAGTTCA	59.123	43.478	0.08	0.08	31.79	3.18
510	520	4.127171	TCACCAAGCAAGTAGTGAAGTTC	58.873	43.478	0.00	0.00	36.36	3.01
511	521	4.130118	CTCACCAAGCAAGTAGTGAAGTT	58.870	43.478	0.00	0.00	38.68	2.66
512	522	3.388024	TCTCACCAAGCAAGTAGTGAAGT	59.612	43.478	0.00	0.00	38.68	3.01
513	523	3.993081	CTCTCACCAAGCAAGTAGTGAAG	59.007	47.826	0.00	0.00	38.68	3.02
514	524	3.641436	TCTCTCACCAAGCAAGTAGTGAA	59.359	43.478	0.00	0.00	38.68	3.18
515	525	3.230976	TCTCTCACCAAGCAAGTAGTGA	58.769	45.455	0.00	0.00	37.65	3.41
516	526	3.006323	ACTCTCTCACCAAGCAAGTAGTG	59.994	47.826	0.00	0.00	0.00	2.74
517	527	3.235200	ACTCTCTCACCAAGCAAGTAGT	58.765	45.455	0.00	0.00	0.00	2.73
518	528	3.951775	ACTCTCTCACCAAGCAAGTAG	57.048	47.619	0.00	0.00	0.00	2.57
519	529	3.193691	GCTACTCTCTCACCAAGCAAGTA	59.806	47.826	0.00	0.00	0.00	2.24
520	530	2.028567	GCTACTCTCTCACCAAGCAAGT	60.029	50.000	0.00	0.00	0.00	3.16
521	531	2.615869	GCTACTCTCTCACCAAGCAAG	58.384	52.381	0.00	0.00	0.00	4.01
522	532	1.067565	CGCTACTCTCTCACCAAGCAA	60.068	52.381	0.00	0.00	0.00	3.91
523	533	0.528017	CGCTACTCTCTCACCAAGCA	59.472	55.000	0.00	0.00	0.00	3.91
524	534	0.804156	GCGCTACTCTCTCACCAAGC	60.804	60.000	0.00	0.00	0.00	4.01
525	535	0.179124	GGCGCTACTCTCTCACCAAG	60.179	60.000	7.64	0.00	0.00	3.61
526	536	0.612174	AGGCGCTACTCTCTCACCAA	60.612	55.000	7.64	0.00	0.00	3.67
527	537	0.612174	AAGGCGCTACTCTCTCACCA	60.612	55.000	7.64	0.00	0.00	4.17
528	538	0.533032	AAAGGCGCTACTCTCTCACC	59.467	55.000	7.64	0.00	0.00	4.02
529	539	2.263945	GAAAAGGCGCTACTCTCTCAC	58.736	52.381	7.64	0.00	0.00	3.51
530	540	1.135373	CGAAAAGGCGCTACTCTCTCA	60.135	52.381	7.64	0.00	0.00	3.27
560	570	4.211374	CGTTTTCTTTTCTCTCCACGTGAT	59.789	41.667	19.30	0.00	0.00	3.06
620	689	2.126463	TCTTTCACCGCTCGCTCG	60.126	61.111	0.00	0.00	0.00	5.03
697	779	4.584518	TGGGTGCAGCAGTGTGGG	62.585	66.667	19.06	0.00	0.00	4.61
708	790	3.426568	GCGAGACTTGCTGGGTGC	61.427	66.667	7.49	0.00	43.25	5.01
710	792	4.021925	GGGCGAGACTTGCTGGGT	62.022	66.667	14.42	0.00	0.00	4.51
712	794	3.883744	AACGGGCGAGACTTGCTGG	62.884	63.158	14.42	8.93	0.00	4.85
714	796	2.048127	GAACGGGCGAGACTTGCT	60.048	61.111	14.42	0.00	0.00	3.91
819	978	2.359011	GGGGCAAGTAGTTGGGGG	59.641	66.667	12.19	0.00	33.87	5.40
856	1015	1.078708	ACATAAACGTGGCCCCTCG	60.079	57.895	0.00	5.31	38.64	4.63
1029	1204	4.157120	GGTGGCTACGGCGGATGT	62.157	66.667	13.24	0.00	39.81	3.06
1078	1253	2.047274	TTCTTTCTCTGCCGCCGG	60.047	61.111	0.00	0.00	0.00	6.13
1079	1254	2.103042	CCTTCTTTCTCTGCCGCCG	61.103	63.158	0.00	0.00	0.00	6.46
1080	1255	2.402572	GCCTTCTTTCTCTGCCGCC	61.403	63.158	0.00	0.00	0.00	6.13
1081	1256	1.642952	CTGCCTTCTTTCTCTGCCGC	61.643	60.000	0.00	0.00	0.00	6.53
1082	1257	0.036952	TCTGCCTTCTTTCTCTGCCG	60.037	55.000	0.00	0.00	0.00	5.69
1083	1258	1.271054	TGTCTGCCTTCTTTCTCTGCC	60.271	52.381	0.00	0.00	0.00	4.85
1084	1259	2.075338	CTGTCTGCCTTCTTTCTCTGC	58.925	52.381	0.00	0.00	0.00	4.26
1085	1260	3.587923	CTCTGTCTGCCTTCTTTCTCTG	58.412	50.000	0.00	0.00	0.00	3.35
1086	1261	2.566724	CCTCTGTCTGCCTTCTTTCTCT	59.433	50.000	0.00	0.00	0.00	3.10
1087	1262	2.564947	TCCTCTGTCTGCCTTCTTTCTC	59.435	50.000	0.00	0.00	0.00	2.87
1088	1263	2.566724	CTCCTCTGTCTGCCTTCTTTCT	59.433	50.000	0.00	0.00	0.00	2.52
1089	1264	2.354604	CCTCCTCTGTCTGCCTTCTTTC	60.355	54.545	0.00	0.00	0.00	2.62
1090	1265	1.627834	CCTCCTCTGTCTGCCTTCTTT	59.372	52.381	0.00	0.00	0.00	2.52
1091	1266	1.203237	TCCTCCTCTGTCTGCCTTCTT	60.203	52.381	0.00	0.00	0.00	2.52
1092	1267	0.411452	TCCTCCTCTGTCTGCCTTCT	59.589	55.000	0.00	0.00	0.00	2.85
1093	1268	1.270907	TTCCTCCTCTGTCTGCCTTC	58.729	55.000	0.00	0.00	0.00	3.46
1094	1269	1.963985	ATTCCTCCTCTGTCTGCCTT	58.036	50.000	0.00	0.00	0.00	4.35
1095	1270	2.856760	TATTCCTCCTCTGTCTGCCT	57.143	50.000	0.00	0.00	0.00	4.75
1096	1271	3.259625	GGTATATTCCTCCTCTGTCTGCC	59.740	52.174	0.00	0.00	0.00	4.85
1097	1272	3.057174	CGGTATATTCCTCCTCTGTCTGC	60.057	52.174	0.00	0.00	0.00	4.26
1098	1273	3.508012	CCGGTATATTCCTCCTCTGTCTG	59.492	52.174	0.00	0.00	0.00	3.51
1099	1274	3.140519	ACCGGTATATTCCTCCTCTGTCT	59.859	47.826	4.49	0.00	0.00	3.41
1144	1323	2.438975	CACGCCCATGTCCAGCAT	60.439	61.111	0.00	0.00	38.60	3.79
1301	1480	3.482232	AAGCCAGCAGCCACGTCTT	62.482	57.895	0.00	0.00	45.47	3.01
1302	1481	3.890936	GAAGCCAGCAGCCACGTCT	62.891	63.158	0.00	0.00	45.47	4.18
1459	1646	7.920160	AAAAATCTCATCAAAGAGACCTCTC	57.080	36.000	0.00	0.00	46.58	3.20
1543	1734	1.805428	ATTCCAGCACGGCCACAAAC	61.805	55.000	2.24	0.00	33.14	2.93
1549	1740	1.031571	TGATCAATTCCAGCACGGCC	61.032	55.000	0.00	0.00	33.14	6.13
1550	1741	0.810648	TTGATCAATTCCAGCACGGC	59.189	50.000	3.38	0.00	33.14	5.68
1593	1784	9.709495	ATGACAAATGCACAAATTAATACAAGT	57.291	25.926	0.00	0.00	0.00	3.16
1621	1812	5.348418	ACGAGATTCATGTTTGTTGTCAG	57.652	39.130	0.00	0.00	0.00	3.51
1666	1859	1.449423	CGGTCAATCGATGGTGGCA	60.449	57.895	0.00	0.00	0.00	4.92
1685	1878	6.000246	TGGTAGAATATGTGCATTCCAAGA	58.000	37.500	0.00	0.00	35.85	3.02
1699	1893	8.250332	GGCAATTCAACATCTTTTGGTAGAATA	58.750	33.333	0.00	0.00	28.83	1.75
1706	1900	3.337358	GGGGCAATTCAACATCTTTTGG	58.663	45.455	0.00	0.00	0.00	3.28
1709	1903	2.618794	TGGGGGCAATTCAACATCTTT	58.381	42.857	0.00	0.00	0.00	2.52
1711	1905	2.502538	CAATGGGGGCAATTCAACATCT	59.497	45.455	0.00	0.00	0.00	2.90
1754	1948	5.123186	CGCCACTAAATTGTGTATTCTCCAA	59.877	40.000	0.00	0.00	36.30	3.53
1755	1949	4.634004	CGCCACTAAATTGTGTATTCTCCA	59.366	41.667	0.00	0.00	36.30	3.86
1824	2020	9.848710	CCAAGTCCGGATATAGATACTCTTATA	57.151	37.037	7.81	0.00	0.00	0.98
1832	2028	6.620877	ATTTGCCAAGTCCGGATATAGATA	57.379	37.500	7.81	0.00	0.00	1.98
1838	2034	2.093394	TCGAATTTGCCAAGTCCGGATA	60.093	45.455	7.81	0.00	0.00	2.59
1840	2036	0.035598	TCGAATTTGCCAAGTCCGGA	59.964	50.000	0.00	0.00	0.00	5.14
1862	2058	3.723348	GTCCGCGGGTGTTTGAGC	61.723	66.667	27.83	0.72	0.00	4.26
1903	2099	1.217244	GGCGTGACCGGTGTCTATT	59.783	57.895	14.63	0.00	42.28	1.73
1908	2104	2.391724	ATTTGAGGCGTGACCGGTGT	62.392	55.000	14.63	0.00	46.52	4.16
1909	2105	0.390603	TATTTGAGGCGTGACCGGTG	60.391	55.000	14.63	0.00	46.52	4.94
1932	2128	8.575649	AATTTAAGATGTCCGGTTGTAGAATT	57.424	30.769	0.00	0.00	0.00	2.17
1981	2177	2.697431	TTAGGTTTCACGTTGCATGC	57.303	45.000	11.82	11.82	0.00	4.06
2025	2222	3.576356	CATCGGACATGGGCACGC	61.576	66.667	0.00	0.00	0.00	5.34
2048	2245	0.611618	TAACACTCCGGGGAGCGTAA	60.612	55.000	9.33	0.00	45.54	3.18
2050	2247	2.283388	TAACACTCCGGGGAGCGT	60.283	61.111	9.33	8.59	45.54	5.07
2085	2282	2.812591	CGTGTCGTATGCCCTACTCTAT	59.187	50.000	0.00	0.00	0.00	1.98
2141	2338	1.075050	ACGAGGAAGAGTAGGACACCA	59.925	52.381	0.00	0.00	0.00	4.17
2142	2339	1.744522	GACGAGGAAGAGTAGGACACC	59.255	57.143	0.00	0.00	0.00	4.16
2143	2340	1.397692	CGACGAGGAAGAGTAGGACAC	59.602	57.143	0.00	0.00	0.00	3.67
2189	2395	5.009410	TGGATCCATCATCGATCTGATATCG	59.991	44.000	11.44	1.06	42.38	2.92
2266	2478	4.467084	CGCCCCGTATGGTGCACT	62.467	66.667	17.98	0.00	32.38	4.40
2378	2608	1.136611	GCGTCGTCTGACACAAACATC	60.137	52.381	8.73	0.00	45.80	3.06
2467	2698	3.718210	GAGATGGTGCGGTCCGTCC	62.718	68.421	13.94	15.72	42.63	4.79
2507	2738	3.566853	CGCATGGATCGCGCTTGT	61.567	61.111	5.56	0.00	46.98	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.