Locus 6081

Sequence ID	3L_DroMel_CAF1
Location	16,159,009 – 16,159,193
Length	184
Max. P	0.998659

overview

Window 8

Location	16,159,009 – 16,159,117
Length	108
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	82.18
Mean single sequence MFE	-24.61
Consensus MFE	-17.40
Energy contribution	-17.85
Covariance contribution	0.45
Combinations/Pair	1.16
Mean z-score	-2.10
Structure conservation index	0.71
SVM decision value	0.73
SVM RNA-class probability	0.836339
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16159009 108 - 23771897
----------AUAUACAUAUAUAACCAUAUUCAGGGUGCUUCAGAACUCUAAGGCAAUUUGAAAAAAAAAAACCUGGCACUUUAAUUAUUGUCAUAGGUCCUGAGCAAACCUUGAAUU
----------..................((((((((((((.(((.((.(((.(((((((((((.................)))))..)))))).))))).))))))..))))))))). ( -24.23)
>DroSim_CAF1 18836 112 - 1
-----GUUAUAUAUACAUAUAUAACCAUAUUCAGGGUGCUUCAGUUCUCUAAGGCAAUUUGAAAAA-AAAAAGCUGGCACUUUAAUUAUUGUCAUAGGUCCUGAGCAAACGUUGAAUU
-----((((((((....))))))))...((((((.(((((.(((..(.(((.((((((((....))-).((((......)))).....))))).))))..))))))..)).)))))). ( -24.90)
>DroEre_CAF1 15971 111 - 1
GAGUAUGUAUAUAUAUAUGUAUAACCAUAUUCAGGGUGCUUCAGAACUCUAAGGCAUUUUGAAA------AAGCUGGCACUCUAAUUAUUGCCAUAGGUCCAGAACAAGUCUUGAAU-
(((((((..(((((....)))))..)))))))(((((((((.((....)).)))))))))((..------...((((.((.(((..........)))))))))......))......- ( -24.70)
>consensus
_______UAUAUAUACAUAUAUAACCAUAUUCAGGGUGCUUCAGAACUCUAAGGCAAUUUGAAAAA_AAAAAGCUGGCACUUUAAUUAUUGUCAUAGGUCCUGAGCAAACCUUGAAUU
............................(((((((((..(((((.((.(((.((((((.............................)))))).))))).)))))...))))))))). (-17.40 = -17.85 +   0.45)

alignment

secondary structure

dotplot

Window 9

Location	16,159,049 – 16,159,153
Length	104
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	80.40
Mean single sequence MFE	-23.50
Consensus MFE	-20.22
Energy contribution	-22.00
Covariance contribution	1.78
Combinations/Pair	1.09
Mean z-score	-1.79
Structure conservation index	0.86
SVM decision value	1.33
SVM RNA-class probability	0.942667
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16159049 104 + 23771897
GCCAGGUUUUUUUUUUUCAAAUUGCCUUAGAGUUCUGAAGCACCCUGAAUAUGGUUAUAUAUGUAUAU--------------AUGUAUAUAUUGUUCAGCCAGACAUUCGAUUGCUGC
((.((((..(((......)))..))))..((((((((.......(((((((....(((((((((....--------------))))))))).))))))).)))).))))....))... ( -19.10)
>DroSim_CAF1 18876 111 + 1
GCCAGCUUUUU-UUUUUCAAAUUGCCUUAGAGAACUGAAGCACCCUGAAUAUGGUUAUAUAUGUAUAUAUAAC------AAUAUAUACAUAUUCUUUAGCCAGACAUUCGAUUGCUGC
..((((.....-..........(((.((((....)))).)))...(((((.((((((.((((((((((((...------.))))))))))))....))))))...)))))...)))). ( -29.00)
>DroEre_CAF1 16010 112 + 1
GCCAGCUU------UUUCAAAAUGCCUUAGAGUUCUGAAGCACCCUGAAUAUGGUUAUACAUAUAUAUAUACAUACUCGUAUAUGUACGUAUUAUUCAGCCAGACAUUCGAUUGCCGC
((..((..------..((....(((.((((....)))).)))....((((.(((((((((.(((((((((........))))))))).)))).....)))))...))))))..)).)) ( -22.40)
>consensus
GCCAGCUUUUU_UUUUUCAAAUUGCCUUAGAGUUCUGAAGCACCCUGAAUAUGGUUAUAUAUGUAUAUAUA_________AUAUGUACAUAUUAUUCAGCCAGACAUUCGAUUGCUGC
..((((................(((.((((....)))).)))...(((((.(((((..((((((((((((((......)))))))))))))).....)))))...)))))...)))). (-20.22 = -22.00 +   1.78)

alignment

secondary structure

dotplot

Window 0

Location	16,159,049 – 16,159,153
Length	104
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	80.40
Mean single sequence MFE	-24.11
Consensus MFE	-17.97
Energy contribution	-19.20
Covariance contribution	1.23
Combinations/Pair	1.12
Mean z-score	-1.80
Structure conservation index	0.75
SVM decision value	0.68
SVM RNA-class probability	0.820674
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16159049 104 - 23771897
GCAGCAAUCGAAUGUCUGGCUGAACAAUAUAUACAU--------------AUAUACAUAUAUAACCAUAUUCAGGGUGCUUCAGAACUCUAAGGCAAUUUGAAAAAAAAAAACCUGGC
.((((.............)))).............(--------------((((....))))).......(((((.(((((.((....)).))))).(((....))).....))))). ( -15.52)
>DroSim_CAF1 18876 111 - 1
GCAGCAAUCGAAUGUCUGGCUAAAGAAUAUGUAUAUAUU------GUUAUAUAUACAUAUAUAACCAUAUUCAGGGUGCUUCAGUUCUCUAAGGCAAUUUGAAAAA-AAAAAGCUGGC
.((((......((((((......)))((((((((((((.------...)))))))))))).....))).((((((.(((((.((....)).))))).))))))...-.....)))).. ( -28.00)
>DroEre_CAF1 16010 112 - 1
GCGGCAAUCGAAUGUCUGGCUGAAUAAUACGUACAUAUACGAGUAUGUAUAUAUAUAUGUAUAACCAUAUUCAGGGUGCUUCAGAACUCUAAGGCAUUUUGAAA------AAGCUGGC
((((((......)))).((((.....(((((((.((((((......))))))...))))))).......((((((((((((.((....)).)))))))))))).------.)))).)) ( -28.80)
>consensus
GCAGCAAUCGAAUGUCUGGCUGAACAAUAUGUACAUAU_________UAUAUAUACAUAUAUAACCAUAUUCAGGGUGCUUCAGAACUCUAAGGCAAUUUGAAAAA_AAAAAGCUGGC
.((((...........(((.((....(((((((.((((((......)))))).))))))).)).)))..(((((..(((((.((....)).)))))..))))).........)))).. (-17.97 = -19.20 +   1.23)

alignment

secondary structure

dotplot

Window 1

Location	16,159,087 – 16,159,193
Length	106
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-32.43
Consensus MFE	-26.24
Energy contribution	-28.13
Covariance contribution	1.90
Combinations/Pair	1.11
Mean z-score	-3.66
Structure conservation index	0.81
SVM decision value	3.18
SVM RNA-class probability	0.998659
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16159087 106 + 23771897
AGCACCCUGAAUAUGGUUAUAUAUGUAUAU--------------AUGUAUAUAUUGUUCAGCCAGACAUUCGAUUGCUGCAGCCGGCAGCAGCAGCGGCAGCAAAACAAGGGCAAACAAU
....((((((((.(((((..((((((((..--------------..)))))))).....)))))...))))..(((((((.((..((....)).)).)))))))....))))........ ( -31.50)
>DroSim_CAF1 18913 108 + 1
AGCACCCUGAAUAUGGUUAUAUAUGUAUAUAUAAC------AAUAUAUACAUAUUCUUUAGCCAGACAUUCGAUUGCUGCAGCCGGCA------GCGGCAGCAAAACAAGGGCAAACAAU
....((((((((.((((((.((((((((((((...------.))))))))))))....))))))...))))..(((((((.((.....------)).)))))))....))))........ ( -38.00)
>DroEre_CAF1 16042 111 + 1
AGCACCCUGAAUAUGGUUAUACAUAUAUAUAUACAUACUCGUAUAUGUACGUAUUAUUCAGCCAGACAUUCGAUUGCCGCAGCCGGCA------G---CAGCAGAACAAGGGCAAACAAU
....((((((((.(((((((((.(((((((((........))))))))).)))).....)))))...))))(.((((((....)))))------)---).........))))........ ( -27.80)
>consensus
AGCACCCUGAAUAUGGUUAUAUAUGUAUAUAUA_________AUAUGUACAUAUUAUUCAGCCAGACAUUCGAUUGCUGCAGCCGGCA______GCGGCAGCAAAACAAGGGCAAACAAU
....((((((((.(((((..((((((((((((((......)))))))))))))).....)))))...))))..(((((((.((...........)).)))))))....))))........ (-26.24 = -28.13 +   1.90)

alignment

secondary structure

dotplot

Window 2

Location	16,159,087 – 16,159,193
Length	106
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	80.46
Mean single sequence MFE	-31.18
Consensus MFE	-20.74
Energy contribution	-22.30
Covariance contribution	1.56
Combinations/Pair	1.11
Mean z-score	-2.39
Structure conservation index	0.67
SVM decision value	1.38
SVM RNA-class probability	0.948554
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16159087 106 - 23771897
AUUGUUUGCCCUUGUUUUGCUGCCGCUGCUGCUGCCGGCUGCAGCAAUCGAAUGUCUGGCUGAACAAUAUAUACAU--------------AUAUACAUAUAUAACCAUAUUCAGGGUGCU
.......(((((....(((((((.(((((....).)))).)))))))..(((((..(((........(((((....--------------))))).........)))))))))))))... ( -28.13)
>DroSim_CAF1 18913 108 - 1
AUUGUUUGCCCUUGUUUUGCUGCCGC------UGCCGGCUGCAGCAAUCGAAUGUCUGGCUAAAGAAUAUGUAUAUAUU------GUUAUAUAUACAUAUAUAACCAUAUUCAGGGUGCU
.......(((((....(((((((.((------.....)).)))))))..((((((((......)))((((((((((((.------...)))))))))))).......))))))))))... ( -35.30)
>DroEre_CAF1 16042 111 - 1
AUUGUUUGCCCUUGUUCUGCUG---C------UGCCGGCUGCGGCAAUCGAAUGUCUGGCUGAAUAAUACGUACAUAUACGAGUAUGUAUAUAUAUAUGUAUAACCAUAUUCAGGGUGCU
((((((((((..((((((((((---(------........))))))...)))))...))).)))))))..((((......(((((((..(((((....)))))..)))))))...)))). ( -30.10)
>consensus
AUUGUUUGCCCUUGUUUUGCUGCCGC______UGCCGGCUGCAGCAAUCGAAUGUCUGGCUGAACAAUAUGUACAUAU_________UAUAUAUACAUAUAUAACCAUAUUCAGGGUGCU
.......(((((.....((((((.((...........)).))))))...(((((..(((.((....(((((((.((((((......)))))).))))))).)).)))))))))))))... (-20.74 = -22.30 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:35 2006