Locus 4292

Sequence ID 3L_DroMel_CAF1
Location 12,588,292 – 12,588,405
Length 113
Max. P 0.998860
window6638 window6639 window6640

overview

Window 8

Location 12,588,292 – 12,588,384
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 73.96
Mean single sequence MFE -25.40
Consensus MFE -11.66
Energy contribution -12.30
Covariance contribution 0.64
Combinations/Pair 1.19
Mean z-score -2.09
Structure conservation index 0.46
SVM decision value 1.27
SVM RNA-class probability 0.938635
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12588292 92 + 23771897
UUGUCUUAGUGGUGAUUGCCUGCCCUUCAAAUGGUUUCUCACUGGCAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACUGGUUUUUGC
..(((((((((((....)))((((.....(((((((((((((((.....))))))))))).))))..))))..))))).))).......... ( -26.50)
>DroSec_CAF1 76367 86 + 1
UUGUCUUACUGGUGAUUGAAGGGCCUUUAGAUGGUUUCUCACUGGUAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACU------UGU
.......((.(((.((..(...(((....(((((((((((((((.....))))))))))).))))..)))....)..)).)))------.)) ( -26.70)
>DroSim_CAF1 79150 86 + 1
UCUUCUCACUGGCGAUUGAAGGGCCUUCAAAUUGUUUCUCACUGGUAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACU------UGC
(((((............)))))(((.......((((((((((((.....))))))))))))......))).............------... ( -21.52)
>DroEre_CAF1 79063 92 + 1
UCGAUUCACUGCAGAUUGCCUGCCCUUCAGAUGGAUUCGUACUGGCCAUUAGUGGGCAGCACAUUCUGGCCAUAUUGAUGGCUAGCUUUCGU
.(((((((((((((.....)))).....)).)))).)))..((((((((((((((.(((......))).))))..))))))))))....... ( -29.90)
>DroYak_CAF1 78704 76 + 1
UCGAUUCAC----------------UUCAGAUGGAUUCUUGCUGGCAAUUAGUGGGAAACACAUUCUGGCCAUAUUGAUGGCUAGUUUCCGU
..((.....----------------.))..(((((((((..(((.....)))..)))).......((((((((....))))))))..))))) ( -22.40)
>consensus
UCGUCUCACUGGUGAUUGAAGGCCCUUCAGAUGGUUUCUCACUGGCAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACU_G_UU_UGU
..........................(((((..(((((((((((.....)))))))))))....)))))....................... (-11.66 = -12.30 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,588,292 – 12,588,384
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 73.96
Mean single sequence MFE -19.84
Consensus MFE -6.02
Energy contribution -7.38
Covariance contribution 1.36
Combinations/Pair 1.07
Mean z-score -1.73
Structure conservation index 0.30
SVM decision value 0.18
SVM RNA-class probability 0.620415
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12588292 92 - 23771897
GCAAAAACCAGUCAUCAAUAUUGCCAGAAUGUGUUUCCCACUAAUUGCCAGUGAGAAACCAUUUGAAGGGCAGGCAAUCACCACUAAGACAA
..........(((........((((.(((((.(((((.((((.......)))).))))))))))....))))((......)).....))).. ( -24.00)
>DroSec_CAF1 76367 86 - 1
ACA------AGUCAUCAAUAUUGCCAGAAUGUGUUUCCCACUAAUUACCAGUGAGAAACCAUCUAAAGGCCCUUCAAUCACCAGUAAGACAA
...------.(((.........((((((.((.(((((.((((.......)))).))))))))))...))).((.........))...))).. ( -14.60)
>DroSim_CAF1 79150 86 - 1
GCA------AGUCAUCAAUAUUGCCAGAAUGUGUUUCCCACUAAUUACCAGUGAGAAACAAUUUGAAGGCCCUUCAAUCGCCAGUGAGAAGA
...------.............(((.((((.((((((.((((.......)))).))))))))))...))).((((..(((....))))))). ( -17.80)
>DroEre_CAF1 79063 92 - 1
ACGAAAGCUAGCCAUCAAUAUGGCCAGAAUGUGCUGCCCACUAAUGGCCAGUACGAAUCCAUCUGAAGGGCAGGCAAUCUGCAGUGAAUCGA
.(((..(((.(((((....)))))((((.(((.((((((.(..((((...........))))..)..))))))))).)))).)))...))). ( -29.10)
>DroYak_CAF1 78704 76 - 1
ACGGAAACUAGCCAUCAAUAUGGCCAGAAUGUGUUUCCCACUAAUUGCCAGCAAGAAUCCAUCUGAA----------------GUGAAUCGA
.(((..(((.(((((....)))))((((..(((.....)))...(((....))).......)))).)----------------))...))). ( -13.70)
>consensus
ACA_AA_C_AGUCAUCAAUAUUGCCAGAAUGUGUUUCCCACUAAUUGCCAGUGAGAAACCAUCUGAAGGCCAGGCAAUCACCAGUGAGACGA
........................((((.((.(((((.((((.......)))).)))))))))))........................... ( -6.02 =  -7.38 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 12,588,309 – 12,588,405
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 78.72
Mean single sequence MFE -31.48
Consensus MFE -22.82
Energy contribution -22.90
Covariance contribution 0.08
Combinations/Pair 1.21
Mean z-score -3.15
Structure conservation index 0.72
SVM decision value 3.26
SVM RNA-class probability 0.998860
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12588309 96 + 23771897
GCCUGCCCUUCAAAUGGUUUCUCACUGGCAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACUGGUUUUUGCAGGUCUUUGAUUUUGCUGGGU
....((((....(((((((((((((((.....))))))))))).))))..(((((.((..(.((((.((....)).)))).)..)).))))))))) ( -34.30)
>DroSec_CAF1 76384 90 + 1
GAAGGGCCUUUAGAUGGUUUCUCACUGGUAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACU------UGUAGGUCUUUGAUUUUGCUGGGC
.....((((...(((((((((((((((.....))))))))))).))))..(((((.((..(.((((------....)))).)..)).))))))))) ( -31.70)
>DroSim_CAF1 79167 90 + 1
GAAGGGCCUUCAAAUUGUUUCUCACUGGUAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACU------UGCGGGUCUUUGAUUUUGCUGGGU
((((...))))....((((((((((((.....))))))))))))...((..((((.((..(.((((------....)))).)..)).))))..)). ( -31.00)
>DroEre_CAF1 79080 96 + 1
GCCUGCCCUUCAGAUGGAUUCGUACUGGCCAUUAGUGGGCAGCACAUUCUGGCCAUAUUGAUGGCUAGCUUUCGUAGUUCUUUAAUUUGGCUGGAA
.((.(((........(((((((..((((((((((((((.(((......))).))))..))))))))))....)).)))))........))).)).. ( -33.89)
>DroYak_CAF1 78713 88 + 1
--------UUCAGAUGGAUUCUUGCUGGCAAUUAGUGGGAAACACAUUCUGGCCAUAUUGAUGGCUAGUUUCCGUAGCUCUUUGUUUUGGCUGGGA
--------....(((((.((((..(((.....)))..)))).).))))((((((((....))))))))..(((.((((.(........)))))))) ( -26.50)
>consensus
GAAGGCCCUUCAGAUGGUUUCUCACUGGCAAUUAGUGGGAAACACAUUCUGGCAAUAUUGAUGACU_G_UU_UGUAGGUCUUUGAUUUUGCUGGGA
............(((((((((((((((.....))))))))))).))))(..((((.(((((.((((..........)))).))))).))))..).. (-22.82 = -22.90 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:47 2006