Locus 5211

Sequence ID 3L_DroMel_CAF1
Location 14,364,362 – 14,364,541
Length 179
Max. P 0.989210
window8244 window8245 window8246 window8247

overview

Window 4

Location 14,364,362 – 14,364,461
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 86.52
Mean single sequence MFE -17.32
Consensus MFE -13.58
Energy contribution -13.74
Covariance contribution 0.16
Combinations/Pair 1.11
Mean z-score -1.51
Structure conservation index 0.78
SVM decision value 0.03
SVM RNA-class probability 0.550401
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14364362 99 + 23771897
UCCAUCUGCAGGCCUACCCACAAUAGUUAACAGCAUUGUUACACUUUUAAACGGUAUACUUACACCCAUUCCUAUUGAUUCGAAUGGGUAUAUUGCCAU
..........(((.((((......(((((((......)))).))).......)))).......((((((((..........)))))))).....))).. ( -20.92)
>DroSec_CAF1 188596 99 + 1
UCCAUUUGCAGGCCUACCCACAAUAGUUAACAGCAUUGUUACACUUUUAAACGGUAUACUUACACCCAUUCCAAGUGAUUCGAAUGGGUAUAUUAACAU
.......(.(((..((((......(((((((......)))).))).......))))..))).)((((((((.((....)).)))))))).......... ( -20.02)
>DroSim_CAF1 184273 99 + 1
UCCAUCUGCAGGCCUACCCACAAUAGUUAACAGCAUUGUUACACUUUUAAACGGUAUACUUACACCCAUUCCAAGUGAUUCGAAUGGGUAUAUUAACAU
.......(.(((..((((......(((((((......)))).))).......))))..))).)((((((((.((....)).)))))))).......... ( -20.02)
>DroEre_CAF1 187282 88 + 1
UC-----------CUACCCACAAUAGUUAACAGCAUUGUUACACUUUUAAACGGUAUACUUACACCCAGUCCCAGUGAUUCGACAGGGUAUACUGCCAU
..-----------.((((((((((.((.....)))))))..((((.......(((........))).......))))........)))))......... ( -14.24)
>DroYak_CAF1 194882 88 + 1
UU-----------CUAUCCACAAUAGUUAACAGCAUUGUUACACCUUUAAACGGUAUACUUACACCCAGUCCUAGUGAUUCGACAGGGCAUACUGACAU
..-----------......(((((.((.....)))))))............((((((.......(((.(((..(....)..))).))).)))))).... ( -11.40)
>consensus
UCCAU_UGCAGGCCUACCCACAAUAGUUAACAGCAUUGUUACACUUUUAAACGGUAUACUUACACCCAUUCCAAGUGAUUCGAAUGGGUAUAUUGACAU
..............((((......(((((((......)))).))).......)))).......((((((((..........)))))))).......... (-13.58 = -13.74 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,364,362 – 14,364,461
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 86.52
Mean single sequence MFE -26.76
Consensus MFE -20.90
Energy contribution -20.70
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -2.41
Structure conservation index 0.78
SVM decision value 1.63
SVM RNA-class probability 0.968577
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14364362 99 - 23771897
AUGGCAAUAUACCCAUUCGAAUCAAUAGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUUAACUAUUGUGGGUAGGCCUGCAGAUGGA
.......(((((((((((..........)))))))))))......((((((...(((.(((((....))))))))...(..((....))..))))))). ( -29.50)
>DroSec_CAF1 188596 99 - 1
AUGUUAAUAUACCCAUUCGAAUCACUUGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUUAACUAUUGUGGGUAGGCCUGCAAAUGGA
.......(((((((((((.((....)).)))))))))))......((((((...(((.(((((....))))))))...(..((....))..))))))). ( -30.90)
>DroSim_CAF1 184273 99 - 1
AUGUUAAUAUACCCAUUCGAAUCACUUGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUUAACUAUUGUGGGUAGGCCUGCAGAUGGA
.......(((((((((((.((....)).)))))))))))......((((((...(((.(((((....))))))))...(..((....))..))))))). ( -31.00)
>DroEre_CAF1 187282 88 - 1
AUGGCAGUAUACCCUGUCGAAUCACUGGGACUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUUAACUAUUGUGGGUAG-----------GA
...((..(((((((.(((..........))).))))))).)).((((...(((.(((.(((((....)))))))).)))..)))).-----------.. ( -20.60)
>DroYak_CAF1 194882 88 - 1
AUGUCAGUAUGCCCUGUCGAAUCACUAGGACUGGGUGUAAGUAUACCGUUUAAAGGUGUAACAAUGCUGUUAACUAUUGUGGAUAG-----------AA
.((((..(((((((.(((..........))).)))))))..((((((.......))))))((((((........)))))).)))).-----------.. ( -21.80)
>consensus
AUGUCAAUAUACCCAUUCGAAUCACUAGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUUAACUAUUGUGGGUAGGCCUGCA_AUGGA
.......(((((((((((..........)))))))))))....((((...(((.(((.(((((....)))))))).)))..)))).............. (-20.90 = -20.70 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,364,390 – 14,364,501
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 77.91
Mean single sequence MFE -24.10
Consensus MFE -16.00
Energy contribution -15.96
Covariance contribution -0.04
Combinations/Pair 1.29
Mean z-score -1.49
Structure conservation index 0.66
SVM decision value 0.02
SVM RNA-class probability 0.544427
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14364390 111 - 23771897
GAAAGAUAUUCUGAGCUCUGAUUGAGUAUAAUUCUGAAAAAUGGCAAUAUACCCAUUCGAAUCAAUAGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUU
(((..((((((............))))))..))).....(((((((.(((((((((((..........)))))))))))..(((((.........)))))....))))))) ( -26.00)
>DroSec_CAF1 188624 95 - 1
GAAAGAUGUUCU----------------UAAUUUUGACAUAUGUUAAUAUACCCAUUCGAAUCACUUGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUU
...(((((....----------------.....(((((....)))))(((((((((((.((....)).))))))))))).......)))))...(((((....)))))... ( -20.70)
>DroSim_CAF1 184301 95 - 1
GAAAGAUGUUCU----------------UAAUUUUGACAUAUGUUAAUAUACCCAUUCGAAUCACUUGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUU
...(((((....----------------.....(((((....)))))(((((((((((.((....)).))))))))))).......)))))...(((((....)))))... ( -20.70)
>DroEre_CAF1 187299 109 - 1
UAAAAGUAUUCUGAGCUCUGAUAGA-UACUA-UCUGCUAAAUGGCAGUAUACCCUGUCGAAUCACUGGGACUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUU
....((((((.(..(((..((..((-((((.-.(((((....)))))(((((((.(((..........))).)))))))))))).)..))....)))...).))))))... ( -26.40)
>DroYak_CAF1 194899 106 - 1
----AGGAUUCUCAGCUCAGAUAGAGUAUUA-UCUGCAAAAUGUCAGUAUGCCCUGUCGAAUCACUAGGACUGGGUGUAAGUAUACCGUUUAAAGGUGUAACAAUGCUGUU
----........((((.(((((((....)))-)))).....(((...(((((((.(((..........))).)))))))..((((((.......)))))))))..)))).. ( -26.70)
>consensus
GAAAGAUAUUCU_AGCUC_GAU_GA_UAUAAUUCUGAAAAAUGUCAAUAUACCCAUUCGAAUCACUAGGAAUGGGUGUAAGUAUACCGUUUAAAAGUGUAACAAUGCUGUU
.................................(((((....)))))(((((((((((..........)))))))))))..(((((.........)))))........... (-16.00 = -15.96 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,364,421 – 14,364,541
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.70
Mean single sequence MFE -28.63
Consensus MFE -15.36
Energy contribution -14.92
Covariance contribution -0.44
Combinations/Pair 1.48
Mean z-score -2.21
Structure conservation index 0.54
SVM decision value 2.15
SVM RNA-class probability 0.989210
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14364421 120 - 23771897
AUUUCGUUGCUUAAGAAAAGGAUUGGCUUGAAGAGUUUACGAAAGAUAUUCUGAGCUCUGAUUGAGUAUAAUUCUGAAAAAUGGCAAUAUACCCAUUCGAAUCAAUAGGAAUGGGUGUAA
.....((((((.......((((((((((..(((((((((.(((.....)))))))))))..)..))).))))))).......))))))((((((((((..........)))))))))).. ( -37.74)
>DroSec_CAF1 188655 104 - 1
AUUUCGUUGCUUAAGAAUAGGAUUGGCUUGAAAAGUUUACGAAAGAUGUUCU----------------UAAUUUUGACAUAUGUUAAUAUACCCAUUCGAAUCACUUGGAAUGGGUGUAA
..........(((((((((.....((((.....))))..(....).))))))----------------)))..(((((....)))))(((((((((((.((....)).))))))))))). ( -26.00)
>DroSim_CAF1 184332 104 - 1
AUUUCGUUGCUUAAGAAUAGGAUUGGCUUGAAAAGUUUACGAAAGAUGUUCU----------------UAAUUUUGACAUAUGUUAAUAUACCCAUUCGAAUCACUUGGAAUGGGUGUAA
..........(((((((((.....((((.....))))..(....).))))))----------------)))..(((((....)))))(((((((((((.((....)).))))))))))). ( -26.00)
>DroEre_CAF1 187330 118 - 1
UUUUUCUUGCUCAAGCAUGGGAAUGGCUUAAGGAGUUUACUAAAAGUAUUCUGAGCUCUGAUAGA-UACUA-UCUGCUAAAUGGCAGUAUACCCUGUCGAAUCACUGGGACUGGGUGUAA
.((..(.(((....))).)..))...((...((((((((............))))))))...)).-.....-.(((((....)))))(((((((.(((..........))).))))))). ( -30.10)
>DroYak_CAF1 194930 105 - 1
AUUUACCUGCUUAAGAAUAGGAAAGGUUAU--------------AGGAUUCUCAGCUCAGAUAGAGUAUUA-UCUGCAAAAUGUCAGUAUGCCCUGUCGAAUCACUAGGACUGGGUGUAA
...(((((.((((....))))...((((.(--------------(((((((........(((((.((((..-.((((.....).))).)))).)))))))))).))).)))))))))... ( -23.30)
>consensus
AUUUCGUUGCUUAAGAAUAGGAUUGGCUUGAAAAGUUUACGAAAGAUAUUCU_AGCUC_GAU_GA_UAUAAUUCUGAAAAAUGUCAAUAUACCCAUUCGAAUCACUAGGAAUGGGUGUAA
.((((...(((.............)))..))))........................................(((((....)))))(((((((((((..........))))))))))). (-15.36 = -14.92 +  -0.44)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:38 2006