AutoCloner

Multiple sequence alignment - TraesCS4B01G275800

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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	TraesCS4B01G275800	chr4B	100.000	2703	0	0	1	2703	553941485	553944187	0.000000e+00	4992.0
1	TraesCS4B01G275800	chr4B	93.899	2016	111	8	699	2703	99422503	99424517	0.000000e+00	3031.0
2	TraesCS4B01G275800	chr4B	97.778	90	2	0	1	90	553930899	553930988	3.600000e-34	156.0
3	TraesCS4B01G275800	chr6B	94.557	2627	129	11	90	2703	157515982	157518607	0.000000e+00	4047.0
4	TraesCS4B01G275800	chr6B	93.903	2575	126	7	160	2703	423037036	423039610	0.000000e+00	3856.0
5	TraesCS4B01G275800	chr6B	97.500	40	0	1	90	129	626805040	626805002	1.740000e-07	67.6
6	TraesCS4B01G275800	chr2B	93.632	2654	124	22	90	2703	732950228	732947580	0.000000e+00	3923.0
7	TraesCS4B01G275800	chr2B	92.247	2270	156	14	444	2703	107470453	107472712	0.000000e+00	3199.0
8	TraesCS4B01G275800	chr2B	93.174	1919	95	20	90	1976	693556435	693554521	0.000000e+00	2785.0
9	TraesCS4B01G275800	chr2B	81.713	1296	159	28	1325	2573	407988857	407990121	0.000000e+00	1009.0
10	TraesCS4B01G275800	chr2B	96.703	91	3	0	1	91	651115217	651115307	4.660000e-33	152.0
11	TraesCS4B01G275800	chr2B	95.556	90	4	0	1	90	222634437	222634526	7.800000e-31	145.0
12	TraesCS4B01G275800	chr2B	94.681	94	4	1	1	94	682881242	682881150	7.800000e-31	145.0
13	TraesCS4B01G275800	chr5B	93.557	2654	119	26	90	2703	672898663	672901304	0.000000e+00	3906.0
14	TraesCS4B01G275800	chr5B	95.556	90	4	0	1	90	268840266	268840177	7.800000e-31	145.0
15	TraesCS4B01G275800	chr3D	94.186	2580	109	20	160	2703	570580266	570582840	0.000000e+00	3895.0
16	TraesCS4B01G275800	chr3D	94.554	2479	99	18	160	2606	64791671	64794145	0.000000e+00	3797.0
17	TraesCS4B01G275800	chr6D	93.398	2575	119	13	162	2703	97829589	97832145	0.000000e+00	3766.0
18	TraesCS4B01G275800	chr1A	93.140	2580	135	17	160	2703	97922253	97919680	0.000000e+00	3746.0
19	TraesCS4B01G275800	chr7B	93.412	1700	81	14	90	1760	556721703	556723400	0.000000e+00	2490.0
20	TraesCS4B01G275800	chr7B	95.556	90	4	0	1	90	131504080	131503991	7.800000e-31	145.0
21	TraesCS4B01G275800	chr7B	95.556	90	4	0	1	90	183156782	183156871	7.800000e-31	145.0
22	TraesCS4B01G275800	chr7B	94.624	93	5	0	1	93	609975457	609975365	7.800000e-31	145.0
23	TraesCS4B01G275800	chr1B	93.348	1383	84	8	90	1468	50144425	50145803	0.000000e+00	2037.0
24	TraesCS4B01G275800	chr1B	97.561	41	0	1	90	130	603982952	603982991	4.830000e-08	69.4
25	TraesCS4B01G275800	chr3B	95.604	91	4	0	1	91	671376225	671376135	2.170000e-31	147.0
26	TraesCS4B01G275800	chr3B	97.500	40	0	1	90	129	481633545	481633583	1.740000e-07	67.6

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	TraesCS4B01G275800	chr4B	553941485	553944187	2702	False	4992	4992	100.000	1	2703	1	chr4B.!!$F3	2702
1	TraesCS4B01G275800	chr4B	99422503	99424517	2014	False	3031	3031	93.899	699	2703	1	chr4B.!!$F1	2004
2	TraesCS4B01G275800	chr6B	157515982	157518607	2625	False	4047	4047	94.557	90	2703	1	chr6B.!!$F1	2613
3	TraesCS4B01G275800	chr6B	423037036	423039610	2574	False	3856	3856	93.903	160	2703	1	chr6B.!!$F2	2543
4	TraesCS4B01G275800	chr2B	732947580	732950228	2648	True	3923	3923	93.632	90	2703	1	chr2B.!!$R3	2613
5	TraesCS4B01G275800	chr2B	107470453	107472712	2259	False	3199	3199	92.247	444	2703	1	chr2B.!!$F1	2259
6	TraesCS4B01G275800	chr2B	693554521	693556435	1914	True	2785	2785	93.174	90	1976	1	chr2B.!!$R2	1886
7	TraesCS4B01G275800	chr2B	407988857	407990121	1264	False	1009	1009	81.713	1325	2573	1	chr2B.!!$F3	1248
8	TraesCS4B01G275800	chr5B	672898663	672901304	2641	False	3906	3906	93.557	90	2703	1	chr5B.!!$F1	2613
9	TraesCS4B01G275800	chr3D	570580266	570582840	2574	False	3895	3895	94.186	160	2703	1	chr3D.!!$F2	2543
10	TraesCS4B01G275800	chr3D	64791671	64794145	2474	False	3797	3797	94.554	160	2606	1	chr3D.!!$F1	2446
11	TraesCS4B01G275800	chr6D	97829589	97832145	2556	False	3766	3766	93.398	162	2703	1	chr6D.!!$F1	2541
12	TraesCS4B01G275800	chr1A	97919680	97922253	2573	True	3746	3746	93.140	160	2703	1	chr1A.!!$R1	2543
13	TraesCS4B01G275800	chr7B	556721703	556723400	1697	False	2490	2490	93.412	90	1760	1	chr7B.!!$F2	1670
14	TraesCS4B01G275800	chr1B	50144425	50145803	1378	False	2037	2037	93.348	90	1468	1	chr1B.!!$F1	1378

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
36	37	0.037697	ACGCACAAGATTAGTCGGCA	60.038	50.0	0.00	0.00	0.00	5.69	F
349	353	0.316204	AACAAGCAGAGCATGTTGCC	59.684	50.0	11.21	0.24	46.26	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1192	1220	1.062206	GCTCGATGCTCTGCTTTGC	59.938	57.895	0.00	0.0	38.95	3.68	R
2071	2162	0.463654	GCTGGTGTGTGTCCACTCAA	60.464	55.000	3.96	0.0	42.34	3.02	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
22	23	5.847670	ATCTCTGAAAGAACTTAACGCAC	57.152	39.130	0.00	0.00	46.34	5.34
23	24	4.689071	TCTCTGAAAGAACTTAACGCACA	58.311	39.130	0.00	0.00	46.34	4.57
24	25	5.113383	TCTCTGAAAGAACTTAACGCACAA	58.887	37.500	0.00	0.00	46.34	3.33
25	26	5.234329	TCTCTGAAAGAACTTAACGCACAAG	59.766	40.000	0.00	0.00	46.34	3.16
26	27	5.113383	TCTGAAAGAACTTAACGCACAAGA	58.887	37.500	0.00	0.00	42.31	3.02
27	28	5.758296	TCTGAAAGAACTTAACGCACAAGAT	59.242	36.000	0.00	0.00	42.31	2.40
28	29	6.260050	TCTGAAAGAACTTAACGCACAAGATT	59.740	34.615	0.00	0.00	42.31	2.40
29	30	7.439955	TCTGAAAGAACTTAACGCACAAGATTA	59.560	33.333	0.00	0.00	42.31	1.75
30	31	7.572759	TGAAAGAACTTAACGCACAAGATTAG	58.427	34.615	0.00	0.00	0.00	1.73
31	32	7.225931	TGAAAGAACTTAACGCACAAGATTAGT	59.774	33.333	0.00	0.00	0.00	2.24
32	33	6.707599	AGAACTTAACGCACAAGATTAGTC	57.292	37.500	0.00	0.00	0.00	2.59
33	34	5.345202	AGAACTTAACGCACAAGATTAGTCG	59.655	40.000	0.00	0.00	0.00	4.18
34	35	3.924686	ACTTAACGCACAAGATTAGTCGG	59.075	43.478	0.00	0.00	0.00	4.79
35	36	1.076332	AACGCACAAGATTAGTCGGC	58.924	50.000	0.00	0.00	0.00	5.54
36	37	0.037697	ACGCACAAGATTAGTCGGCA	60.038	50.000	0.00	0.00	0.00	5.69
37	38	0.370273	CGCACAAGATTAGTCGGCAC	59.630	55.000	0.00	0.00	0.00	5.01
38	39	1.438651	GCACAAGATTAGTCGGCACA	58.561	50.000	0.00	0.00	0.00	4.57
39	40	1.804151	GCACAAGATTAGTCGGCACAA	59.196	47.619	0.00	0.00	0.00	3.33
40	41	2.159653	GCACAAGATTAGTCGGCACAAG	60.160	50.000	0.00	0.00	0.00	3.16
41	42	2.076863	ACAAGATTAGTCGGCACAAGC	58.923	47.619	0.00	0.00	41.10	4.01
42	43	2.076100	CAAGATTAGTCGGCACAAGCA	58.924	47.619	0.00	0.00	44.61	3.91
43	44	2.679837	CAAGATTAGTCGGCACAAGCAT	59.320	45.455	0.00	0.00	44.61	3.79
44	45	2.991250	AGATTAGTCGGCACAAGCATT	58.009	42.857	0.00	0.00	44.61	3.56
58	59	4.443913	CAAGCATTGTCATCAATCACCA	57.556	40.909	0.00	0.00	42.34	4.17
59	60	4.811908	CAAGCATTGTCATCAATCACCAA	58.188	39.130	0.00	0.00	42.34	3.67
60	61	5.231702	CAAGCATTGTCATCAATCACCAAA	58.768	37.500	0.00	0.00	42.34	3.28
61	62	5.471556	AGCATTGTCATCAATCACCAAAA	57.528	34.783	0.00	0.00	41.66	2.44
62	63	5.232463	AGCATTGTCATCAATCACCAAAAC	58.768	37.500	0.00	0.00	41.66	2.43
63	64	4.989797	GCATTGTCATCAATCACCAAAACA	59.010	37.500	0.00	0.00	41.66	2.83
64	65	5.107375	GCATTGTCATCAATCACCAAAACAC	60.107	40.000	0.00	0.00	41.66	3.32
65	66	4.582701	TGTCATCAATCACCAAAACACC	57.417	40.909	0.00	0.00	0.00	4.16
66	67	4.214310	TGTCATCAATCACCAAAACACCT	58.786	39.130	0.00	0.00	0.00	4.00
67	68	4.648762	TGTCATCAATCACCAAAACACCTT	59.351	37.500	0.00	0.00	0.00	3.50
68	69	4.984161	GTCATCAATCACCAAAACACCTTG	59.016	41.667	0.00	0.00	0.00	3.61
76	77	3.636153	CCAAAACACCTTGGGGAAAAA	57.364	42.857	0.00	0.00	41.96	1.94
77	78	4.163441	CCAAAACACCTTGGGGAAAAAT	57.837	40.909	0.00	0.00	41.96	1.82
78	79	5.297569	CCAAAACACCTTGGGGAAAAATA	57.702	39.130	0.00	0.00	41.96	1.40
79	80	5.875224	CCAAAACACCTTGGGGAAAAATAT	58.125	37.500	0.00	0.00	41.96	1.28
80	81	5.704978	CCAAAACACCTTGGGGAAAAATATG	59.295	40.000	0.00	0.00	41.96	1.78
81	82	6.295249	CAAAACACCTTGGGGAAAAATATGT	58.705	36.000	0.00	0.00	36.25	2.29
82	83	5.738619	AACACCTTGGGGAAAAATATGTC	57.261	39.130	0.00	0.00	36.25	3.06
83	84	4.093743	ACACCTTGGGGAAAAATATGTCC	58.906	43.478	0.00	0.00	36.25	4.02
84	85	4.202781	ACACCTTGGGGAAAAATATGTCCT	60.203	41.667	0.00	0.00	34.10	3.85
85	86	4.777366	CACCTTGGGGAAAAATATGTCCTT	59.223	41.667	0.00	0.00	34.10	3.36
86	87	5.955355	CACCTTGGGGAAAAATATGTCCTTA	59.045	40.000	0.00	0.00	34.10	2.69
87	88	5.955959	ACCTTGGGGAAAAATATGTCCTTAC	59.044	40.000	0.00	0.00	34.10	2.34
88	89	5.955355	CCTTGGGGAAAAATATGTCCTTACA	59.045	40.000	0.00	0.00	35.69	2.41
258	262	5.529430	AGTCTACTAGATGATGAGAACACCG	59.471	44.000	0.00	0.00	0.00	4.94
349	353	0.316204	AACAAGCAGAGCATGTTGCC	59.684	50.000	11.21	0.24	46.26	4.52
611	625	1.242076	AAGTTGTCATGCCACTGAGC	58.758	50.000	0.00	0.00	0.00	4.26
810	832	3.839293	AGAATCGTCTCGACAAGAAAGG	58.161	45.455	0.00	0.00	39.18	3.11
979	1007	6.188407	ACCTACAGTGTGTATCTGTATCTGT	58.812	40.000	5.88	0.00	44.07	3.41
1103	1131	2.943033	ACAGACGTTTTGAAGTCCTTGG	59.057	45.455	7.85	0.00	38.08	3.61
1192	1220	3.062763	CAGCTATGGAGGAAGCATTACG	58.937	50.000	0.00	0.00	41.32	3.18
1273	1301	5.120830	AGCAAGTAAGACAAGAAGCATTACG	59.879	40.000	0.00	0.00	32.82	3.18
1414	1470	8.565896	TCTCAGTTGAACATAATTAGTTGCAT	57.434	30.769	0.00	0.00	0.00	3.96
1427	1505	7.587037	AATTAGTTGCATAGTGCCACATAAT	57.413	32.000	8.56	6.86	44.23	1.28
1452	1530	6.875948	AGTTGCACAGTGACACATAATTAA	57.124	33.333	4.15	0.00	0.00	1.40
1547	1629	2.158769	AGCAATGAGTGTGGTCTGTTCA	60.159	45.455	0.00	0.00	0.00	3.18
1603	1686	0.630673	TGCCCAACTATGAGCCCAAT	59.369	50.000	0.00	0.00	0.00	3.16
1833	1919	7.041635	TCAATGTCATCACTTTTGTTCACAT	57.958	32.000	0.00	0.00	0.00	3.21
1852	1939	4.212004	CACATATTACGAGAACTGGGCATG	59.788	45.833	0.00	0.00	0.00	4.06
1994	2083	3.561143	TGTATGTGTCCACTTTTTGCCT	58.439	40.909	0.00	0.00	0.00	4.75
2067	2158	5.639506	ACAAACGATACAAGAGAATCACAGG	59.360	40.000	0.00	0.00	37.82	4.00
2071	2162	4.202101	CGATACAAGAGAATCACAGGAGCT	60.202	45.833	0.00	0.00	37.82	4.09
2337	2456	2.649843	TTTTTCGCGCAACCACGACC	62.650	55.000	8.75	0.00	38.17	4.79
2392	2511	4.305769	GCAATTAATTGGTTGCTGTGTGA	58.694	39.130	25.61	0.00	45.41	3.58
2506	2625	4.685924	AGTTTGTTTGTCTTGATGCTTGG	58.314	39.130	0.00	0.00	0.00	3.61
2514	2633	4.713553	TGTCTTGATGCTTGGACTAACAA	58.286	39.130	0.00	0.00	0.00	2.83
2644	2783	1.355043	ACGAACCCTCTGAGTACTCCT	59.645	52.381	20.11	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.297547	TGTGCGTTAAGTTCTTTCAGAGAT	58.702	37.500	0.00	0.00	33.49	2.75
1	2	4.689071	TGTGCGTTAAGTTCTTTCAGAGA	58.311	39.130	0.00	0.00	0.00	3.10
2	3	5.234329	TCTTGTGCGTTAAGTTCTTTCAGAG	59.766	40.000	0.00	0.00	0.00	3.35
3	4	5.113383	TCTTGTGCGTTAAGTTCTTTCAGA	58.887	37.500	0.00	0.00	0.00	3.27
4	5	5.403897	TCTTGTGCGTTAAGTTCTTTCAG	57.596	39.130	0.00	0.00	0.00	3.02
5	6	6.371809	AATCTTGTGCGTTAAGTTCTTTCA	57.628	33.333	0.00	0.00	0.00	2.69
6	7	7.573627	ACTAATCTTGTGCGTTAAGTTCTTTC	58.426	34.615	0.00	0.00	0.00	2.62
7	8	7.492352	ACTAATCTTGTGCGTTAAGTTCTTT	57.508	32.000	0.00	0.00	0.00	2.52
8	9	6.128902	CGACTAATCTTGTGCGTTAAGTTCTT	60.129	38.462	0.00	0.00	0.00	2.52
9	10	5.345202	CGACTAATCTTGTGCGTTAAGTTCT	59.655	40.000	0.00	0.00	0.00	3.01
10	11	5.444218	CCGACTAATCTTGTGCGTTAAGTTC	60.444	44.000	0.00	0.00	0.00	3.01
11	12	4.387862	CCGACTAATCTTGTGCGTTAAGTT	59.612	41.667	0.00	0.00	0.00	2.66
12	13	3.924686	CCGACTAATCTTGTGCGTTAAGT	59.075	43.478	0.00	0.00	0.00	2.24
13	14	3.241995	GCCGACTAATCTTGTGCGTTAAG	60.242	47.826	0.00	0.00	0.00	1.85
14	15	2.669434	GCCGACTAATCTTGTGCGTTAA	59.331	45.455	0.00	0.00	0.00	2.01
15	16	2.264813	GCCGACTAATCTTGTGCGTTA	58.735	47.619	0.00	0.00	0.00	3.18
16	17	1.076332	GCCGACTAATCTTGTGCGTT	58.924	50.000	0.00	0.00	0.00	4.84
17	18	0.037697	TGCCGACTAATCTTGTGCGT	60.038	50.000	0.00	0.00	0.00	5.24
18	19	0.370273	GTGCCGACTAATCTTGTGCG	59.630	55.000	0.00	0.00	0.00	5.34
19	20	1.438651	TGTGCCGACTAATCTTGTGC	58.561	50.000	0.00	0.00	0.00	4.57
20	21	2.159653	GCTTGTGCCGACTAATCTTGTG	60.160	50.000	0.00	0.00	0.00	3.33
21	22	2.076863	GCTTGTGCCGACTAATCTTGT	58.923	47.619	0.00	0.00	0.00	3.16
22	23	2.076100	TGCTTGTGCCGACTAATCTTG	58.924	47.619	0.00	0.00	38.71	3.02
23	24	2.472695	TGCTTGTGCCGACTAATCTT	57.527	45.000	0.00	0.00	38.71	2.40
24	25	2.679837	CAATGCTTGTGCCGACTAATCT	59.320	45.455	0.00	0.00	38.71	2.40
25	26	2.420022	ACAATGCTTGTGCCGACTAATC	59.580	45.455	1.44	0.00	43.48	1.75
26	27	2.420022	GACAATGCTTGTGCCGACTAAT	59.580	45.455	6.31	0.00	45.52	1.73
27	28	1.804151	GACAATGCTTGTGCCGACTAA	59.196	47.619	6.31	0.00	45.52	2.24
28	29	1.270571	TGACAATGCTTGTGCCGACTA	60.271	47.619	6.31	0.00	45.52	2.59
29	30	0.534877	TGACAATGCTTGTGCCGACT	60.535	50.000	6.31	0.00	45.52	4.18
30	31	0.523072	ATGACAATGCTTGTGCCGAC	59.477	50.000	6.31	0.00	45.52	4.79
31	32	0.804364	GATGACAATGCTTGTGCCGA	59.196	50.000	6.31	0.00	45.52	5.54
32	33	0.522626	TGATGACAATGCTTGTGCCG	59.477	50.000	6.31	0.00	45.52	5.69
33	34	2.728690	TTGATGACAATGCTTGTGCC	57.271	45.000	6.31	0.00	45.52	5.01
34	35	3.611113	GTGATTGATGACAATGCTTGTGC	59.389	43.478	6.31	0.00	45.52	4.57
35	36	4.171005	GGTGATTGATGACAATGCTTGTG	58.829	43.478	6.31	0.00	45.52	3.33
37	38	4.443913	TGGTGATTGATGACAATGCTTG	57.556	40.909	0.00	0.00	45.30	4.01
38	39	5.471556	TTTGGTGATTGATGACAATGCTT	57.528	34.783	0.00	0.00	45.30	3.91
39	40	5.221481	TGTTTTGGTGATTGATGACAATGCT	60.221	36.000	0.00	0.00	45.30	3.79
40	41	4.989797	TGTTTTGGTGATTGATGACAATGC	59.010	37.500	0.00	0.00	45.30	3.56
41	42	5.406175	GGTGTTTTGGTGATTGATGACAATG	59.594	40.000	0.00	0.00	45.30	2.82
43	44	4.648762	AGGTGTTTTGGTGATTGATGACAA	59.351	37.500	0.00	0.00	40.42	3.18
44	45	4.214310	AGGTGTTTTGGTGATTGATGACA	58.786	39.130	0.00	0.00	0.00	3.58
45	46	4.853924	AGGTGTTTTGGTGATTGATGAC	57.146	40.909	0.00	0.00	0.00	3.06
46	47	4.039004	CCAAGGTGTTTTGGTGATTGATGA	59.961	41.667	0.00	0.00	42.16	2.92
47	48	4.309099	CCAAGGTGTTTTGGTGATTGATG	58.691	43.478	0.00	0.00	42.16	3.07
48	49	3.324556	CCCAAGGTGTTTTGGTGATTGAT	59.675	43.478	4.29	0.00	44.98	2.57
49	50	2.697751	CCCAAGGTGTTTTGGTGATTGA	59.302	45.455	4.29	0.00	44.98	2.57
50	51	2.224257	CCCCAAGGTGTTTTGGTGATTG	60.224	50.000	4.29	0.00	44.98	2.67
51	52	2.046292	CCCCAAGGTGTTTTGGTGATT	58.954	47.619	4.29	0.00	44.98	2.57
52	53	1.219213	TCCCCAAGGTGTTTTGGTGAT	59.781	47.619	4.29	0.00	44.98	3.06
53	54	0.631753	TCCCCAAGGTGTTTTGGTGA	59.368	50.000	4.29	0.00	44.98	4.02
54	55	1.490574	TTCCCCAAGGTGTTTTGGTG	58.509	50.000	4.29	0.00	44.98	4.17
55	56	2.255770	TTTCCCCAAGGTGTTTTGGT	57.744	45.000	4.29	0.00	44.98	3.67
56	57	3.636153	TTTTTCCCCAAGGTGTTTTGG	57.364	42.857	0.00	0.00	45.83	3.28
57	58	6.295249	ACATATTTTTCCCCAAGGTGTTTTG	58.705	36.000	0.00	0.00	0.00	2.44
58	59	6.465178	GGACATATTTTTCCCCAAGGTGTTTT	60.465	38.462	0.00	0.00	0.00	2.43
59	60	5.012664	GGACATATTTTTCCCCAAGGTGTTT	59.987	40.000	0.00	0.00	0.00	2.83
60	61	4.530553	GGACATATTTTTCCCCAAGGTGTT	59.469	41.667	0.00	0.00	0.00	3.32
61	62	4.093743	GGACATATTTTTCCCCAAGGTGT	58.906	43.478	0.00	0.00	0.00	4.16
62	63	4.352893	AGGACATATTTTTCCCCAAGGTG	58.647	43.478	0.00	0.00	31.51	4.00
63	64	4.692523	AGGACATATTTTTCCCCAAGGT	57.307	40.909	0.00	0.00	31.51	3.50
64	65	5.955355	TGTAAGGACATATTTTTCCCCAAGG	59.045	40.000	0.00	0.00	31.51	3.61
65	66	7.178451	AGTTGTAAGGACATATTTTTCCCCAAG	59.822	37.037	0.00	0.00	34.86	3.61
66	67	7.013834	AGTTGTAAGGACATATTTTTCCCCAA	58.986	34.615	0.00	0.00	34.86	4.12
67	68	6.435904	CAGTTGTAAGGACATATTTTTCCCCA	59.564	38.462	0.00	0.00	34.86	4.96
68	69	6.436218	ACAGTTGTAAGGACATATTTTTCCCC	59.564	38.462	0.00	0.00	34.86	4.81
69	70	7.462571	ACAGTTGTAAGGACATATTTTTCCC	57.537	36.000	0.00	0.00	34.86	3.97
70	71	9.227777	ACTACAGTTGTAAGGACATATTTTTCC	57.772	33.333	0.00	0.00	34.86	3.13
258	262	4.299796	TGGGGAGTTGGCTTGCCC	62.300	66.667	9.35	6.81	45.74	5.36
296	300	1.873591	GGTGGTACTGTGCAACTGAAG	59.126	52.381	3.40	0.00	39.30	3.02
349	353	6.749118	GTCTGCAATTTAAAGCACTATTCTGG	59.251	38.462	0.00	0.00	36.62	3.86
411	423	4.035208	ACAAAGTTAGCTTGAAAGGTCACG	59.965	41.667	0.00	0.00	36.17	4.35
740	762	8.173542	TCATTCGTATTGTAGATACCTTGCTA	57.826	34.615	0.00	0.00	0.00	3.49
793	815	3.120792	CAAACCTTTCTTGTCGAGACGA	58.879	45.455	0.00	0.00	33.02	4.20
810	832	0.102300	GGGCACAACACTCACCAAAC	59.898	55.000	0.00	0.00	0.00	2.93
979	1007	0.601576	ACCTGCACGCGTGAACAATA	60.602	50.000	41.19	17.84	0.00	1.90
1103	1131	6.604735	TGTCTTCTAGCTTTCTGTTTGAAC	57.395	37.500	0.00	0.00	33.88	3.18
1192	1220	1.062206	GCTCGATGCTCTGCTTTGC	59.938	57.895	0.00	0.00	38.95	3.68
1212	1240	5.416083	ACGTCGATGTCAATAATCTGGAAA	58.584	37.500	3.92	0.00	0.00	3.13
1427	1505	6.875948	AATTATGTGTCACTGTGCAACTAA	57.124	33.333	2.12	6.57	38.04	2.24
1520	1602	1.072173	ACCACACTCATTGCTGCAGTA	59.928	47.619	16.64	8.31	0.00	2.74
1547	1629	2.626743	ACTCAGTGGCGTTAAGTAGTGT	59.373	45.455	0.00	0.00	0.00	3.55
1603	1686	4.420206	TCTTCCTGAGGTTGAGATCTTCA	58.580	43.478	0.00	0.00	0.00	3.02
1833	1919	2.169561	TGCATGCCCAGTTCTCGTAATA	59.830	45.455	16.68	0.00	0.00	0.98
1888	1976	3.243704	TGGTTGCTATTTGTGCCTTTGTC	60.244	43.478	0.00	0.00	0.00	3.18
1994	2083	6.662865	TGATGGTTTTTGAGCAATTTAGGA	57.337	33.333	0.00	0.00	39.57	2.94
2067	2158	1.221414	GTGTGTGTCCACTCAAGCTC	58.779	55.000	3.96	0.00	42.34	4.09
2071	2162	0.463654	GCTGGTGTGTGTCCACTCAA	60.464	55.000	3.96	0.00	42.34	3.02
2124	2215	5.243954	GGAGCTACACCCAAAGAAGAAAAAT	59.756	40.000	0.00	0.00	0.00	1.82
2209	2300	7.776969	ACAAGCCTATGATGATTTTGTGTCTAT	59.223	33.333	0.00	0.00	0.00	1.98
2213	2304	5.622914	GCACAAGCCTATGATGATTTTGTGT	60.623	40.000	13.77	0.00	43.36	3.72
2258	2349	3.023949	GCTCGTGATGGTCCTGCCT	62.024	63.158	0.00	0.00	38.35	4.75
2337	2456	2.069273	GTGTGGTTGGAGAGAACATCG	58.931	52.381	0.00	0.00	0.00	3.84
2374	2493	8.948631	TTAATTTTCACACAGCAACCAATTAA	57.051	26.923	0.00	0.00	0.00	1.40
2506	2625	2.570838	GCGCGCGCTTTGTTAGTC	60.571	61.111	44.38	14.45	38.26	2.59
2628	2767	3.334280	ACTACAAGGAGTACTCAGAGGGT	59.666	47.826	23.91	15.32	0.00	4.34
2644	2783	1.281867	CTCCTCCCAATGGCACTACAA	59.718	52.381	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.