AutoCloner

Multiple sequence alignment - TraesCS5B01G401700

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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	TraesCS5B01G401700	chr5B	100.000	4139	0	0	1	4139	578534339	578538477	0.000000e+00	7644.0
1	TraesCS5B01G401700	chr5D	93.422	4211	142	46	1	4139	472231647	472235794	0.000000e+00	6117.0
2	TraesCS5B01G401700	chr5D	87.547	265	33	0	2109	2373	303407552	303407816	1.450000e-79	307.0
3	TraesCS5B01G401700	chr5D	94.964	139	7	0	3979	4117	549703909	549704047	6.970000e-53	219.0
4	TraesCS5B01G401700	chr5D	90.370	135	9	2	3979	4113	362655988	362656118	1.530000e-39	174.0
5	TraesCS5B01G401700	chr5D	88.462	104	9	2	3890	3990	449629261	449629158	5.620000e-24	122.0
6	TraesCS5B01G401700	chr5D	83.333	114	6	2	3890	3990	298070745	298070632	4.410000e-15	93.5
7	TraesCS5B01G401700	chr5A	86.397	2448	210	68	1488	3872	591439405	591441792	0.000000e+00	2562.0
8	TraesCS5B01G401700	chr5A	86.484	910	78	22	573	1455	591438524	591439415	0.000000e+00	957.0
9	TraesCS5B01G401700	chr5A	94.775	555	16	3	1	555	591392173	591392714	0.000000e+00	852.0
10	TraesCS5B01G401700	chr5A	87.658	316	30	5	7	313	591437981	591438296	3.930000e-95	359.0
11	TraesCS5B01G401700	chr5A	93.296	179	8	2	379	555	591438295	591438471	1.140000e-65	261.0
12	TraesCS5B01G401700	chr5A	90.566	106	10	0	1832	1937	603998490	603998385	1.550000e-29	141.0
13	TraesCS5B01G401700	chr5A	97.260	73	2	0	573	645	591392767	591392839	1.560000e-24	124.0
14	TraesCS5B01G401700	chr2B	82.498	1057	138	31	1588	2644	37325665	37324656	0.000000e+00	883.0
15	TraesCS5B01G401700	chr2B	90.580	138	13	0	3979	4116	768127677	768127814	2.540000e-42	183.0
16	TraesCS5B01G401700	chr1B	82.492	891	116	26	1201	2083	533759059	533758201	0.000000e+00	745.0
17	TraesCS5B01G401700	chr1B	82.235	895	115	28	1201	2083	640478827	640477965	0.000000e+00	732.0
18	TraesCS5B01G401700	chr1B	81.967	122	9	2	3882	3990	58862887	58862766	1.580000e-14	91.6
19	TraesCS5B01G401700	chr1B	93.103	58	3	1	3887	3943	45121824	45121767	2.650000e-12	84.2
20	TraesCS5B01G401700	chr6D	88.302	265	31	0	2109	2373	79884311	79884047	6.680000e-83	318.0
21	TraesCS5B01G401700	chr3D	87.970	266	31	1	2109	2373	536420291	536420556	3.110000e-81	313.0
22	TraesCS5B01G401700	chr3D	87.547	265	32	1	2109	2373	19630324	19630587	5.200000e-79	305.0
23	TraesCS5B01G401700	chr1A	80.386	311	42	10	1198	1496	551506568	551506871	6.970000e-53	219.0
24	TraesCS5B01G401700	chr1A	89.286	84	2	3	312	389	11617140	11617222	9.470000e-17	99.0
25	TraesCS5B01G401700	chr1A	81.373	102	7	4	3890	3980	269092670	269092770	5.740000e-09	73.1
26	TraesCS5B01G401700	chr2A	93.333	135	9	0	3982	4116	565077335	565077201	2.520000e-47	200.0
27	TraesCS5B01G401700	chr2A	92.593	135	9	1	3982	4116	143844079	143843946	4.220000e-45	193.0
28	TraesCS5B01G401700	chr2A	90.909	77	5	2	311	385	754467810	754467886	7.320000e-18	102.0
29	TraesCS5B01G401700	chr2A	90.541	74	3	2	311	380	675885097	675885170	1.220000e-15	95.3
30	TraesCS5B01G401700	chr4D	91.971	137	10	1	3982	4117	50663175	50663039	1.520000e-44	191.0
31	TraesCS5B01G401700	chr4D	94.545	55	2	1	3890	3943	66224845	66224899	2.650000e-12	84.2
32	TraesCS5B01G401700	chr7A	90.580	138	12	1	3979	4116	725736860	725736996	9.140000e-42	182.0
33	TraesCS5B01G401700	chr2D	89.209	139	12	3	3979	4116	281670627	281670763	1.980000e-38	171.0
34	TraesCS5B01G401700	chr2D	91.429	70	4	2	311	380	447497036	447496969	1.220000e-15	95.3
35	TraesCS5B01G401700	chr2D	89.706	68	4	3	3878	3943	236114125	236114191	2.650000e-12	84.2
36	TraesCS5B01G401700	chr7D	93.243	74	4	1	312	385	18437347	18437275	1.570000e-19	108.0
37	TraesCS5B01G401700	chr7D	80.833	120	11	3	3883	3990	255305516	255305397	2.650000e-12	84.2
38	TraesCS5B01G401700	chr6B	91.304	69	4	1	312	380	706122030	706121964	4.410000e-15	93.5
39	TraesCS5B01G401700	chr4A	90.411	73	3	2	312	380	540014943	540015015	4.410000e-15	93.5
40	TraesCS5B01G401700	chrUn	84.000	100	3	3	3890	3976	94995892	94995793	2.650000e-12	84.2

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	TraesCS5B01G401700	chr5B	578534339	578538477	4138	False	7644.00	7644	100.00000	1	4139	1	chr5B.!!$F1	4138
1	TraesCS5B01G401700	chr5D	472231647	472235794	4147	False	6117.00	6117	93.42200	1	4139	1	chr5D.!!$F3	4138
2	TraesCS5B01G401700	chr5A	591437981	591441792	3811	False	1034.75	2562	88.45875	7	3872	4	chr5A.!!$F2	3865
3	TraesCS5B01G401700	chr5A	591392173	591392839	666	False	488.00	852	96.01750	1	645	2	chr5A.!!$F1	644
4	TraesCS5B01G401700	chr2B	37324656	37325665	1009	True	883.00	883	82.49800	1588	2644	1	chr2B.!!$R1	1056
5	TraesCS5B01G401700	chr1B	533758201	533759059	858	True	745.00	745	82.49200	1201	2083	1	chr1B.!!$R3	882
6	TraesCS5B01G401700	chr1B	640477965	640478827	862	True	732.00	732	82.23500	1201	2083	1	chr1B.!!$R4	882

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
286	298	0.459899	TAGCACTATGGTCACTGGCG	59.540	55.000	0.00	0.0	0.0	5.69	F
1479	1593	0.111639	TTTTACACCCCCACCTGCTC	59.888	55.000	0.00	0.0	0.0	4.26	F
1578	1715	0.837272	TCCAGGGCCTACATTGCTAC	59.163	55.000	5.28	0.0	0.0	3.58	F
1732	1869	1.207089	TGGGCGGAGTACAAGATCAAG	59.793	52.381	0.00	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1600	1737	0.107456	CATTCAGGGATCAGGGTCCG	59.893	60.0	0.00	0.00	39.26	4.79	R
2443	2586	0.824759	GGAGGACAACCGTATCAGCT	59.175	55.0	0.00	0.00	41.83	4.24	R
2504	2647	4.583907	GGAGTTACCACTACCATAGACTCC	59.416	50.0	3.74	3.74	43.37	3.85	R
3522	3688	7.908193	TTTTGAAACAAAGATAGAAGAACGC	57.092	32.0	0.00	0.00	0.00	4.84	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
98	99	7.092716	CAGCCTGAAACTTTATGCTAAACATT	58.907	34.615	0.00	0.00	40.38	2.71
175	180	0.899720	TAGTCTTAGCCCGGGTGTTG	59.100	55.000	24.63	10.80	0.00	3.33
259	264	6.595326	CGCTTCTATCTGGAATATGGCATTTA	59.405	38.462	4.78	0.00	0.00	1.40
263	268	9.676861	TTCTATCTGGAATATGGCATTTATCTG	57.323	33.333	4.78	0.00	0.00	2.90
286	298	0.459899	TAGCACTATGGTCACTGGCG	59.540	55.000	0.00	0.00	0.00	5.69
287	299	1.079127	GCACTATGGTCACTGGCGT	60.079	57.895	0.00	0.00	0.00	5.68
298	310	2.046892	CTGGCGTGTCCTCCCTTG	60.047	66.667	0.00	0.00	35.26	3.61
353	365	3.553105	ACTCGTCGTGGTTTTAGTTCAAC	59.447	43.478	0.00	0.00	0.00	3.18
386	398	3.958798	TGGAACGGAGGGAGTATAAGAAG	59.041	47.826	0.00	0.00	0.00	2.85
387	399	4.213513	GGAACGGAGGGAGTATAAGAAGA	58.786	47.826	0.00	0.00	0.00	2.87
388	400	4.648307	GGAACGGAGGGAGTATAAGAAGAA	59.352	45.833	0.00	0.00	0.00	2.52
555	567	2.724454	CTCTCTTCTTACCCAGACCGA	58.276	52.381	0.00	0.00	0.00	4.69
801	898	2.930168	CGCAGCGCTGTATTTTTCC	58.070	52.632	35.80	17.13	0.00	3.13
805	902	3.317150	GCAGCGCTGTATTTTTCCTTTT	58.683	40.909	35.80	0.00	0.00	2.27
806	903	4.481463	GCAGCGCTGTATTTTTCCTTTTA	58.519	39.130	35.80	0.00	0.00	1.52
807	904	4.920927	GCAGCGCTGTATTTTTCCTTTTAA	59.079	37.500	35.80	0.00	0.00	1.52
809	906	5.059221	CAGCGCTGTATTTTTCCTTTTAACG	59.941	40.000	29.24	0.00	0.00	3.18
810	907	4.201456	GCGCTGTATTTTTCCTTTTAACGC	60.201	41.667	0.00	0.00	0.00	4.84
824	926	6.312918	TCCTTTTAACGCTAGAAACTGCATAG	59.687	38.462	0.00	0.00	0.00	2.23
825	927	6.092259	CCTTTTAACGCTAGAAACTGCATAGT	59.908	38.462	0.00	0.00	39.32	2.12
826	928	7.277098	CCTTTTAACGCTAGAAACTGCATAGTA	59.723	37.037	0.00	0.00	35.69	1.82
827	929	7.515957	TTTAACGCTAGAAACTGCATAGTAC	57.484	36.000	0.00	0.00	35.69	2.73
828	930	4.043037	ACGCTAGAAACTGCATAGTACC	57.957	45.455	0.00	0.00	35.69	3.34
829	931	3.446161	ACGCTAGAAACTGCATAGTACCA	59.554	43.478	0.00	0.00	35.69	3.25
830	932	4.045104	CGCTAGAAACTGCATAGTACCAG	58.955	47.826	0.00	0.00	35.69	4.00
831	933	4.202020	CGCTAGAAACTGCATAGTACCAGA	60.202	45.833	0.00	0.00	35.69	3.86
848	950	8.896722	AGTACCAGATTAGAAGTAGGAAAAGA	57.103	34.615	0.00	0.00	0.00	2.52
849	956	9.322769	AGTACCAGATTAGAAGTAGGAAAAGAA	57.677	33.333	0.00	0.00	0.00	2.52
899	1006	4.864704	ATTTGGGTTGCAATACGTCTTT	57.135	36.364	0.59	0.00	0.00	2.52
943	1050	3.716601	GATAAGGTTCAGAGAGCAGCTC	58.283	50.000	15.25	15.25	44.29	4.09
957	1064	0.839477	CAGCTCAACGCAAAAACACG	59.161	50.000	0.00	0.00	42.61	4.49
961	1068	1.507120	CTCAACGCAAAAACACGAACG	59.493	47.619	0.00	0.00	0.00	3.95
986	1093	3.382832	CCTCCCGCTTCACTCCGT	61.383	66.667	0.00	0.00	0.00	4.69
1014	1121	3.451894	GCCATGGCGGAAACCCTG	61.452	66.667	23.48	0.00	36.56	4.45
1271	1381	1.507141	CGCCCTCCGCCATTCATAAC	61.507	60.000	0.00	0.00	0.00	1.89
1278	1388	1.032014	CGCCATTCATAACCCCCAAG	58.968	55.000	0.00	0.00	0.00	3.61
1302	1412	2.652095	CCTGCTTCCGGGTCCGTAA	61.652	63.158	0.00	0.00	37.81	3.18
1306	1416	1.271488	TGCTTCCGGGTCCGTAATTTT	60.271	47.619	0.00	0.00	37.81	1.82
1307	1417	1.814394	GCTTCCGGGTCCGTAATTTTT	59.186	47.619	0.00	0.00	37.81	1.94
1308	1418	2.414957	GCTTCCGGGTCCGTAATTTTTG	60.415	50.000	0.00	0.00	37.81	2.44
1309	1419	1.823797	TCCGGGTCCGTAATTTTTGG	58.176	50.000	0.00	0.00	37.81	3.28
1310	1420	1.073603	TCCGGGTCCGTAATTTTTGGT	59.926	47.619	0.00	0.00	37.81	3.67
1311	1421	1.887854	CCGGGTCCGTAATTTTTGGTT	59.112	47.619	8.67	0.00	37.81	3.67
1314	1424	4.379708	CCGGGTCCGTAATTTTTGGTTAAG	60.380	45.833	8.67	0.00	37.81	1.85
1315	1425	4.216042	CGGGTCCGTAATTTTTGGTTAAGT	59.784	41.667	0.55	0.00	34.35	2.24
1316	1426	5.411053	CGGGTCCGTAATTTTTGGTTAAGTA	59.589	40.000	0.55	0.00	34.35	2.24
1317	1427	6.093909	CGGGTCCGTAATTTTTGGTTAAGTAT	59.906	38.462	0.55	0.00	34.35	2.12
1318	1428	7.361971	CGGGTCCGTAATTTTTGGTTAAGTATT	60.362	37.037	0.55	0.00	34.35	1.89
1319	1429	8.306038	GGGTCCGTAATTTTTGGTTAAGTATTT	58.694	33.333	0.00	0.00	0.00	1.40
1342	1452	0.867746	TCTGTGTGCAGCAATTCGAC	59.132	50.000	0.00	0.00	42.29	4.20
1452	1562	1.448540	GCTCCCGGTGACACTGATG	60.449	63.158	16.28	6.76	0.00	3.07
1461	1571	4.635765	CCGGTGACACTGATGTTGATATTT	59.364	41.667	16.28	0.00	39.95	1.40
1465	1575	7.692291	CGGTGACACTGATGTTGATATTTTTAC	59.308	37.037	8.88	0.00	39.95	2.01
1466	1576	8.511321	GGTGACACTGATGTTGATATTTTTACA	58.489	33.333	5.39	0.00	39.95	2.41
1468	1578	8.511321	TGACACTGATGTTGATATTTTTACACC	58.489	33.333	0.00	0.00	39.95	4.16
1479	1593	0.111639	TTTTACACCCCCACCTGCTC	59.888	55.000	0.00	0.00	0.00	4.26
1527	1664	2.810274	TGCATCTTCAGTCAAGTCAAGC	59.190	45.455	0.00	0.00	33.27	4.01
1563	1700	2.028839	TGCAAGCATTTTGACCATCCAG	60.029	45.455	0.00	0.00	0.00	3.86
1572	1709	2.544768	GACCATCCAGGGCCTACAT	58.455	57.895	5.28	0.00	40.85	2.29
1573	1710	0.846693	GACCATCCAGGGCCTACATT	59.153	55.000	5.28	0.00	40.85	2.71
1578	1715	0.837272	TCCAGGGCCTACATTGCTAC	59.163	55.000	5.28	0.00	0.00	3.58
1583	1720	3.763897	CAGGGCCTACATTGCTACTTTTT	59.236	43.478	5.28	0.00	0.00	1.94
1584	1721	3.763897	AGGGCCTACATTGCTACTTTTTG	59.236	43.478	2.82	0.00	0.00	2.44
1585	1722	3.511699	GGCCTACATTGCTACTTTTTGC	58.488	45.455	0.00	0.00	0.00	3.68
1640	1777	8.132995	TGAATGATGTATCTGCAATTGTGATTC	58.867	33.333	16.92	13.63	0.00	2.52
1641	1778	6.051646	TGATGTATCTGCAATTGTGATTCG	57.948	37.500	16.92	0.00	0.00	3.34
1642	1779	5.585844	TGATGTATCTGCAATTGTGATTCGT	59.414	36.000	16.92	14.05	0.00	3.85
1732	1869	1.207089	TGGGCGGAGTACAAGATCAAG	59.793	52.381	0.00	0.00	0.00	3.02
1800	1937	6.915300	TGAAGTTCGTGGACATTTATTTTGTG	59.085	34.615	0.00	0.00	0.00	3.33
2008	2149	1.826720	TCCACTACCTTCGGCGTTTAT	59.173	47.619	6.85	0.00	0.00	1.40
2016	2157	2.869801	CCTTCGGCGTTTATCTGCATTA	59.130	45.455	6.85	0.00	0.00	1.90
2043	2184	5.249163	TGATGCCCTTATAGTATGATGCACT	59.751	40.000	0.00	0.00	0.00	4.40
2062	2203	4.558095	GCACTGCATCTGTTTTGACTTCAT	60.558	41.667	0.00	0.00	0.00	2.57
2329	2472	4.127171	CAGGGTCATGAAAAGGTATACCG	58.873	47.826	16.31	0.37	42.08	4.02
2504	2647	2.416547	CAGCTGGTTCAGGTATGTTTCG	59.583	50.000	5.57	0.00	40.40	3.46
2518	2661	5.301298	GGTATGTTTCGGAGTCTATGGTAGT	59.699	44.000	0.00	0.00	0.00	2.73
2524	2667	4.202441	TCGGAGTCTATGGTAGTGGTAAC	58.798	47.826	0.00	0.00	0.00	2.50
3522	3688	2.554806	TGAACGTGATGGTAGTAGCG	57.445	50.000	0.00	0.00	0.00	4.26
3753	3949	1.885887	CTTCCATCTGCCGAACCAAAA	59.114	47.619	0.00	0.00	0.00	2.44
3793	3989	9.119418	TGTGATCAATGTTAAGAGAAGTTTGAA	57.881	29.630	0.00	0.00	0.00	2.69
3908	4104	0.177141	TAGGGATGAAAACGGAGCGG	59.823	55.000	0.00	0.00	0.00	5.52
3935	4131	4.439057	GGACGAAATTGAGTGCTACCATA	58.561	43.478	0.00	0.00	0.00	2.74
4086	4295	7.716799	ATGAATTGGTTACATGGCTAGAAAA	57.283	32.000	0.00	0.00	0.00	2.29
4087	4296	7.716799	TGAATTGGTTACATGGCTAGAAAAT	57.283	32.000	0.00	0.00	0.00	1.82
4113	4322	8.681486	AATATGATTATGTCAGCAACTTAGCA	57.319	30.769	0.00	0.00	40.92	3.49
4114	4323	8.859236	ATATGATTATGTCAGCAACTTAGCAT	57.141	30.769	0.00	0.00	40.92	3.79
4115	4324	9.948964	ATATGATTATGTCAGCAACTTAGCATA	57.051	29.630	0.00	0.00	40.92	3.14
4116	4325	8.681486	ATGATTATGTCAGCAACTTAGCATAA	57.319	30.769	0.00	0.00	40.92	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
98	99	1.180456	TCGACGGGGTAGCAAGAACA	61.180	55.000	0.00	0.00	0.00	3.18
175	180	1.552226	CCGCAATGATCAATGTGCAC	58.448	50.000	17.21	10.75	36.80	4.57
259	264	4.467795	AGTGACCATAGTGCTACAACAGAT	59.532	41.667	0.00	0.00	0.00	2.90
263	268	3.262420	CCAGTGACCATAGTGCTACAAC	58.738	50.000	0.00	0.00	0.00	3.32
286	298	2.143925	CGAAAAGACAAGGGAGGACAC	58.856	52.381	0.00	0.00	0.00	3.67
287	299	1.071699	CCGAAAAGACAAGGGAGGACA	59.928	52.381	0.00	0.00	0.00	4.02
298	310	3.368220	GGAGGGAGTAGAACCGAAAAGAC	60.368	52.174	0.00	0.00	0.00	3.01
353	365	3.306019	CCCTCCGTTCCAAATTTCCAAAG	60.306	47.826	0.00	0.00	0.00	2.77
477	489	5.712004	TCCCGCATCGTTTCGATAAATATA	58.288	37.500	4.37	0.00	45.19	0.86
571	599	4.164030	TCTGCCCAGCTCAATAATGTTAGA	59.836	41.667	0.00	0.00	0.00	2.10
753	845	4.629200	GGATCAAGCTCAACTCTACACTTG	59.371	45.833	0.00	0.00	36.66	3.16
799	896	4.382291	TGCAGTTTCTAGCGTTAAAAGGA	58.618	39.130	0.00	0.00	0.00	3.36
801	898	7.061752	ACTATGCAGTTTCTAGCGTTAAAAG	57.938	36.000	0.00	0.00	0.00	2.27
805	902	5.125900	TGGTACTATGCAGTTTCTAGCGTTA	59.874	40.000	0.00	0.00	36.14	3.18
806	903	4.081862	TGGTACTATGCAGTTTCTAGCGTT	60.082	41.667	0.00	0.00	36.14	4.84
807	904	3.446161	TGGTACTATGCAGTTTCTAGCGT	59.554	43.478	0.00	0.00	36.14	5.07
809	906	5.263968	TCTGGTACTATGCAGTTTCTAGC	57.736	43.478	0.00	0.00	36.14	3.42
810	907	8.851145	TCTAATCTGGTACTATGCAGTTTCTAG	58.149	37.037	0.00	0.00	36.14	2.43
824	926	9.939802	TTTCTTTTCCTACTTCTAATCTGGTAC	57.060	33.333	0.00	0.00	0.00	3.34
826	928	9.862149	TTTTTCTTTTCCTACTTCTAATCTGGT	57.138	29.630	0.00	0.00	0.00	4.00
849	956	1.580815	CCATGGCAAAGCGTGTTTTT	58.419	45.000	0.00	0.00	0.00	1.94
871	978	5.006941	ACGTATTGCAACCCAAATACGTATC	59.993	40.000	24.40	0.00	43.65	2.24
883	990	4.469552	GTTGGTAAAGACGTATTGCAACC	58.530	43.478	0.00	12.83	0.00	3.77
884	991	4.145997	CGTTGGTAAAGACGTATTGCAAC	58.854	43.478	0.00	0.00	34.75	4.17
899	1006	2.601067	TGACCCTCGCCGTTGGTA	60.601	61.111	0.55	0.00	30.97	3.25
943	1050	0.045419	GCGTTCGTGTTTTTGCGTTG	60.045	50.000	0.00	0.00	0.00	4.10
957	1064	2.776913	CGGGAGGAGAGAGGCGTTC	61.777	68.421	0.00	0.00	0.00	3.95
961	1068	2.762043	AAGCGGGAGGAGAGAGGC	60.762	66.667	0.00	0.00	0.00	4.70
986	1093	3.671410	CCATGGCCAGTGGGGGAA	61.671	66.667	20.58	0.00	37.04	3.97
1263	1373	1.217942	GAGGCCTTGGGGGTTATGAAT	59.782	52.381	6.77	0.00	37.43	2.57
1306	1416	6.975772	GCACACAGACAAAAATACTTAACCAA	59.024	34.615	0.00	0.00	0.00	3.67
1307	1417	6.095580	TGCACACAGACAAAAATACTTAACCA	59.904	34.615	0.00	0.00	0.00	3.67
1308	1418	6.500041	TGCACACAGACAAAAATACTTAACC	58.500	36.000	0.00	0.00	0.00	2.85
1357	1467	1.514553	CGTGCTGATCTCCTGCTGA	59.485	57.895	0.00	0.00	40.01	4.26
1406	1516	0.622136	TGCATGAGGCTGATGAGGTT	59.378	50.000	18.49	0.00	45.15	3.50
1452	1562	5.020795	AGGTGGGGGTGTAAAAATATCAAC	58.979	41.667	0.00	0.00	0.00	3.18
1461	1571	0.770557	AGAGCAGGTGGGGGTGTAAA	60.771	55.000	0.00	0.00	0.00	2.01
1465	1575	4.729918	GCAGAGCAGGTGGGGGTG	62.730	72.222	0.00	0.00	0.00	4.61
1466	1576	4.990910	AGCAGAGCAGGTGGGGGT	62.991	66.667	0.00	0.00	0.00	4.95
1468	1578	2.045536	GAAGCAGAGCAGGTGGGG	60.046	66.667	0.00	0.00	0.00	4.96
1479	1593	5.578727	GGAGTGAACATAGTAACTGAAGCAG	59.421	44.000	0.00	0.00	37.52	4.24
1527	1664	3.688185	TGCTTGCAGAAATCAGCTTAGAG	59.312	43.478	7.30	0.00	0.00	2.43
1563	1700	3.676049	GCAAAAAGTAGCAATGTAGGCCC	60.676	47.826	0.00	0.00	0.00	5.80
1567	1704	4.083537	TCCACGCAAAAAGTAGCAATGTAG	60.084	41.667	0.00	0.00	0.00	2.74
1572	1709	2.227865	GGATCCACGCAAAAAGTAGCAA	59.772	45.455	6.95	0.00	0.00	3.91
1573	1710	1.810151	GGATCCACGCAAAAAGTAGCA	59.190	47.619	6.95	0.00	0.00	3.49
1600	1737	0.107456	CATTCAGGGATCAGGGTCCG	59.893	60.000	0.00	0.00	39.26	4.79
1640	1777	4.368315	TGCTTGATATACAGCCTACAACG	58.632	43.478	3.68	0.00	0.00	4.10
1641	1778	4.752101	CCTGCTTGATATACAGCCTACAAC	59.248	45.833	3.68	0.00	0.00	3.32
1642	1779	4.743651	GCCTGCTTGATATACAGCCTACAA	60.744	45.833	3.68	0.00	0.00	2.41
1732	1869	6.268825	TCTACAGTGAACATGTTAGTCTCC	57.731	41.667	11.95	0.00	32.02	3.71
1800	1937	3.358076	CTCGGACCTCGGAGCCAAC	62.358	68.421	0.00	0.00	36.70	3.77
1999	2140	5.778161	TCATATAATGCAGATAAACGCCG	57.222	39.130	0.00	0.00	0.00	6.46
2016	2157	7.935755	GTGCATCATACTATAAGGGCATCATAT	59.064	37.037	0.00	0.00	32.16	1.78
2039	2180	3.243168	TGAAGTCAAAACAGATGCAGTGC	60.243	43.478	8.58	8.58	0.00	4.40
2040	2181	4.556942	TGAAGTCAAAACAGATGCAGTG	57.443	40.909	0.00	0.00	0.00	3.66
2043	2184	5.997129	TCTGTATGAAGTCAAAACAGATGCA	59.003	36.000	18.65	0.00	42.67	3.96
2329	2472	7.110155	TGGGATTCTAGTGACAAAGGATAAAC	58.890	38.462	0.00	0.00	0.00	2.01
2443	2586	0.824759	GGAGGACAACCGTATCAGCT	59.175	55.000	0.00	0.00	41.83	4.24
2504	2647	4.583907	GGAGTTACCACTACCATAGACTCC	59.416	50.000	3.74	3.74	43.37	3.85
2524	2667	9.323985	TCCATTTTTCTAAAACATTTGTTGGAG	57.676	29.630	0.00	0.00	38.44	3.86
3522	3688	7.908193	TTTTGAAACAAAGATAGAAGAACGC	57.092	32.000	0.00	0.00	0.00	4.84
3793	3989	1.026182	TGCGCTCGGAAATTCTGCAT	61.026	50.000	9.73	0.00	0.00	3.96
3908	4104	2.223377	AGCACTCAATTTCGTCCGTTTC	59.777	45.455	0.00	0.00	0.00	2.78
3913	4109	2.695359	TGGTAGCACTCAATTTCGTCC	58.305	47.619	0.00	0.00	0.00	4.79
3945	4153	7.362660	GGGGTTTCTATATTTGTTTTCGCTTCT	60.363	37.037	0.00	0.00	0.00	2.85
3952	4160	9.430623	CATTTTCGGGGTTTCTATATTTGTTTT	57.569	29.630	0.00	0.00	0.00	2.43
4087	4296	9.777297	TGCTAAGTTGCTGACATAATCATATTA	57.223	29.630	0.00	0.00	36.48	0.98
4111	4320	9.538508	AATTCAAGCTCCTGATTTTATTTATGC	57.461	29.630	0.00	0.00	0.00	3.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.