Locus 4383

Sequence ID	3L_DroMel_CAF1
Location	12,856,963 – 12,857,207
Length	244
Max. P	0.895705

overview

Window 7

Location	12,856,963 – 12,857,079
Length	116
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	91.75
Mean single sequence MFE	-32.98
Consensus MFE	-24.34
Energy contribution	-25.58
Covariance contribution	1.24
Combinations/Pair	1.08
Mean z-score	-1.94
Structure conservation index	0.74
SVM decision value	0.26
SVM RNA-class probability	0.656583
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12856963 116 - 23771897
UGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGACAGGGUUACUGCAGUGAAGGCAGCAGAUGCUUAGGACGAGCAUUGCU-GGGUGGAAAUUAUUGAUUUUCCGAUAGUUUGCUG
(.(((((((.(((((.....)))))..((((((....))))))))))))).)...((((((.(((((.....))))))))))-)...(.(((((((((......))))))))).).. ( -32.90)
>DroSec_CAF1 95341 116 - 1
UGAUUGCAGUAACUUAAUGAAAGUGCAUAAUUCGACAGGGUCACUGCAGUCAUGGCAGCAGAUGCUUAGAACGAGCAUAGCU-GGGUGGAAAUUAUUGAUUUUCAGAUAGUUUGCUG
((((((((((.((((..((((.........))))...)))).))))))))))...((((((((((((.....)))))).(((-(..((((((((...))))))))..)))))))))) ( -35.80)
>DroSim_CAF1 96823 116 - 1
UGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGACAGGGUCACUGCAGUCAUGGCAGCAGAUGCUUAGGACGAGCAAUGCU-GGGUGAAGAUUAUUGAUUUUCAGAUAGUUUGCUG
((((((((((.((((..((((.........))))...)))).))))))))))...((((((.(((((.....)))))..(((-(..((((((((...))))))))..)))))))))) ( -35.20)
>DroEre_CAF1 100659 115 - 1
UGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGAUAGGGUCACUGCAGUCAAGGCAGCAGAUGCUUAGGACAAGGAUUGCU-GGGAGGAAAUUAUUGAUUUUCU-AUAGGUUGCUG
((((((((((..((((.((((.........)))).))))...)))))))))).((((((.(((.(((.....))).))).((-(..((((((((...))))))))-.))))))))). ( -33.20)
>DroYak_CAF1 106774 117 - 1
UGAUUGCAGUUAGUUAAUGAAAGUGCAUAAUUCGAUAGGGUCACUGCAGUCAAGGCAACAGAUGCUUAGGACAAGGAUUGCUUGGGGGGAAACUAUUGAUUUUCGGAUAGUUUGCUG
((((((((((......(((......))).((((....)))).))))))))))(((((.....)))))....((((.....))))..((.((((((((........)))))))).)). ( -27.80)
>consensus
UGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGACAGGGUCACUGCAGUCAAGGCAGCAGAUGCUUAGGACGAGCAUUGCU_GGGUGGAAAUUAUUGAUUUUCAGAUAGUUUGCUG
((((((((((.((((..((((.........))))...)))).)))))))))).((((((((.(((((.....)))))))))).......((((((((........))))))))))). (-24.34 = -25.58 +   1.24)

alignment

secondary structure

dotplot

Window 8

Location	12,857,002 – 12,857,103
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-23.51
Consensus MFE	-21.42
Energy contribution	-21.18
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-1.40
Structure conservation index	0.91
SVM decision value	0.99
SVM RNA-class probability	0.895705
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12857002 101 + 23771897
UGCUCGUCCUAAGCAUCUGCUGCCUUCACUGCAGUAACCCUGUCGAAUUAUGCACUUUCAUUAAGUAACUGCAAUCAGGCGAAUAAAAAUCCUUUCGAGAG
..((((.....(((....)))((((....((((((.((...((.(((.........)))))...)).))))))...))))...............)))).. ( -21.00)
>DroSec_CAF1 95380 101 + 1
UGCUCGUUCUAAGCAUCUGCUGCCAUGACUGCAGUGACCCUGUCGAAUUAUGCACUUUCAUUAAGUUACUGCAAUCAGGCGAAUAAAAAUCCUUUCGAGAG
..((((.....(((....)))(((.(((.(((((((((...((.(((.........)))))...))))))))).))))))...............)))).. ( -28.10)
>DroSim_CAF1 96862 101 + 1
UGCUCGUCCUAAGCAUCUGCUGCCAUGACUGCAGUGACCCUGUCGAAUUAUGCACUUUCAUUAAGUAACUGCAAUCAGGCGAAUAAAAAUCCUUUCGAGAG
..((((.....(((....)))(((.(((.(((((((((...))).........((((.....)))).)))))).))))))...............)))).. ( -25.30)
>DroEre_CAF1 100697 101 + 1
UCCUUGUCCUAAGCAUCUGCUGCCUUGACUGCAGUGACCCUAUCGAAUUAUGCACUUUCAUUAAGUAACUGCAAUCAGGCGAAUAAAAAUCCUUUCGAGAG
..((((.....(((....)))((((.((.((((((.((..((..(((.........)))..)).)).)))))).))))))...............)))).. ( -21.90)
>DroYak_CAF1 106814 101 + 1
UCCUUGUCCUAAGCAUCUGUUGCCUUGACUGCAGUGACCCUAUCGAAUUAUGCACUUUCAUUAACUAACUGCAAUCAGGCGAAUAAAAAUCCUUUCGAGAG
..((((.............((((((.((.((((((......((.(((.........)))))......)))))).)))))))).............)))).. ( -21.27)
>consensus
UGCUCGUCCUAAGCAUCUGCUGCCUUGACUGCAGUGACCCUGUCGAAUUAUGCACUUUCAUUAAGUAACUGCAAUCAGGCGAAUAAAAAUCCUUUCGAGAG
..((((.....(((....)))(((.(((.((((((.((...((.(((.........)))))...)).)))))).))))))...............)))).. (-21.42 = -21.18 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	12,857,002 – 12,857,103
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	95.25
Mean single sequence MFE	-27.68
Consensus MFE	-24.66
Energy contribution	-25.46
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.89
SVM decision value	0.78
SVM RNA-class probability	0.849275
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12857002 101 - 23771897
CUCUCGAAAGGAUUUUUAUUCGCCUGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGACAGGGUUACUGCAGUGAAGGCAGCAGAUGCUUAGGACGAGCA
..((((...((((....))))((((.(((((((.(((((.....)))))..((((((....)))))))))))))..))))(((....))).....)))).. ( -27.10)
>DroSec_CAF1 95380 101 - 1
CUCUCGAAAGGAUUUUUAUUCGCCUGAUUGCAGUAACUUAAUGAAAGUGCAUAAUUCGACAGGGUCACUGCAGUCAUGGCAGCAGAUGCUUAGAACGAGCA
..((((...((((....))))(((((((((((((.((((..((((.........))))...)))).)))))))))).)))(((....))).....)))).. ( -30.00)
>DroSim_CAF1 96862 101 - 1
CUCUCGAAAGGAUUUUUAUUCGCCUGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGACAGGGUCACUGCAGUCAUGGCAGCAGAUGCUUAGGACGAGCA
..((((...((((....))))(((((((((((((.((((..((((.........))))...)))).)))))))))).)))(((....))).....)))).. ( -30.00)
>DroEre_CAF1 100697 101 - 1
CUCUCGAAAGGAUUUUUAUUCGCCUGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGAUAGGGUCACUGCAGUCAAGGCAGCAGAUGCUUAGGACAAGGA
.((.(....)))(((((.((((((((((((((((..((((.((((.........)))).))))...))))))))).))))(((....)))..))).))))) ( -29.20)
>DroYak_CAF1 106814 101 - 1
CUCUCGAAAGGAUUUUUAUUCGCCUGAUUGCAGUUAGUUAAUGAAAGUGCAUAAUUCGAUAGGGUCACUGCAGUCAAGGCAACAGAUGCUUAGGACAAGGA
.(((..(..((((....))))(((((((((((((......(((......))).((((....)))).))))))))).)))).........)..)))...... ( -22.10)
>consensus
CUCUCGAAAGGAUUUUUAUUCGCCUGAUUGCAGUUACUUAAUGAAAGUGCAUAAUUCGACAGGGUCACUGCAGUCAAGGCAGCAGAUGCUUAGGACGAGCA
..((((...((((....))))(((((((((((((.((((..((((.........))))...)))).)))))))))).)))...............)))).. (-24.66 = -25.46 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	12,857,103 – 12,857,207
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	94.40
Mean single sequence MFE	-35.31
Consensus MFE	-30.02
Energy contribution	-30.18
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.26
Structure conservation index	0.85
SVM decision value	0.01
SVM RNA-class probability	0.540788
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12857103 104 + 23771897
CAAUCUGUUGGCUUGGCUGGCUGCCUUAACCUUGUGACUGGCUGAGCGUGGCUUAAUGCACUUUUAAUUGAGCCAAGCAUCCUGGGCUAGCUAGGGGGAAAUUG
...........((((((((((((((..............)))...((.(((((((((.........))))))))).))......)))))))))))......... ( -34.84)
>DroSec_CAF1 95481 104 + 1
CAAUCUGUUGGCUUGGCUGGCUGCCGUAACCUUGUGACUGGCUGAGCGUGGCUUAAUGCACUUUUAAUUGAGCCAAGCAUCCUGGGCUAGCGAGCGGGAAAUUG
((((...((.(((((.(((((((((((.((...)).)).)))...((.(((((((((.........))))))))).))......))))))))))).))..)))) ( -35.40)
>DroSim_CAF1 96963 104 + 1
CAAUCUGUUGGCUUGGCUGGCUGCCUUAACCUUGUGACUGGCUGAGCGUGGCUUAAUGCACUUUUAAUUGAGCCGAGCAUCCUGUUCUAGCGAGCGGGAAAUUG
.....((((.(((..((..(..((.........))..)..))..))).(((((((((.........)))))))))))))((((((((....))))))))..... ( -37.40)
>DroEre_CAF1 100798 100 + 1
CAAUCUGUUGGCUUGGCUGGCUGCCUUAACCUUCUGACUGGCUGAGCGUGGCUUAAUGCACUUUUAAUUGAGCCGAGCAUCCUGGG----CGAGCGGGAAAUUG
...((((((.(((..(...(((((((((.((........)).)))).))((((((((.........)))))))).)))...)..))----).))))))...... ( -34.50)
>DroYak_CAF1 106915 100 + 1
CAAUCUGUUGGCUUGGCUGGCUGCCUUAACCUUGUGACUGGCUGAGCGUGGCUUAAUGCACUUUUAAUUGAGCCGAGCAUCCUGGG----CGGGCGGGAAAUUG
...((((((.(((..(...(((((((((.((........)).)))).))((((((((.........)))))))).)))...)..))----).))))))...... ( -34.40)
>consensus
CAAUCUGUUGGCUUGGCUGGCUGCCUUAACCUUGUGACUGGCUGAGCGUGGCUUAAUGCACUUUUAAUUGAGCCGAGCAUCCUGGGCUAGCGAGCGGGAAAUUG
.....((((.(((..((..(..((.........))..)..))..))).(((((((((.........)))))))))))))(((((..........)))))..... (-30.02 = -30.18 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:12 2006