Locus 4240

Sequence ID X_DroMel_CAF1
Location 11,123,286 – 11,123,458
Length 172
Max. P 0.797206
window6965 window6966 window6967 window6968

overview

Window 5

Location 11,123,286 – 11,123,386
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 89.83
Mean single sequence MFE -29.50
Consensus MFE -22.40
Energy contribution -22.65
Covariance contribution 0.25
Combinations/Pair 1.15
Mean z-score -1.91
Structure conservation index 0.76
SVM decision value 0.50
SVM RNA-class probability 0.759161
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11123286 100 + 22224390
UUAACGAAGCACUCGCCCCGUGGCCAAAACCCAAUUAAAAUGCAGUUAACCGAGAUUGCCUGCCUUGAUUUGGCCUGAUUAUGUUUCUGGACACUGGCUA
..............(((..(((.(((((((..(((((....((((((......))))))..(((.......))).)))))..)))).))).))).))).. ( -22.70)
>DroSec_CAF1 38592 100 + 1
UUGACGAAGCACUCGCCCCGUGGCCGAAACCCAAUUAAAAUGCAGUUAACUGAGAUUGACUGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCCACUGGCUA
..............(((..(((((((((((((((....((.((((((((......)))))))).))...)))).........))))).)))))).))).. ( -32.00)
>DroEre_CAF1 37333 100 + 1
CUAACGAAACACUCGUCCAGUGGCCAAAACCCAAUUAGUAUGCAGUUAACUGGGAUUUGCUGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCUACUGGCUC
...((((.....))))((((((((((((((..((((((..(.(((....))).).......(((.......)))))))))..)))).))))))))))... ( -31.30)
>DroYak_CAF1 41395 99 + 1
UCAACGAAGCACUCGCCC-GUGGCCAAAGCCCAAUUAGAAUGCAGUUAACUGAGAUUCCCAGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCCACUGGCUA
..............(((.-(((((((((((..((((((....(((....))).........(((.......)))))))))..)))).))))))).))).. ( -32.00)
>consensus
UUAACGAAGCACUCGCCCCGUGGCCAAAACCCAAUUAAAAUGCAGUUAACUGAGAUUGCCUGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCCACUGGCUA
..............(((..(((((((((((..((((((....(((....))).........(((.......)))))))))..)))).))))))).))).. (-22.40 = -22.65 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,123,286 – 11,123,386
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -30.70
Consensus MFE -25.41
Energy contribution -26.35
Covariance contribution 0.94
Combinations/Pair 1.10
Mean z-score -1.75
Structure conservation index 0.83
SVM decision value 0.59
SVM RNA-class probability 0.792277
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11123286 100 - 22224390
UAGCCAGUGUCCAGAAACAUAAUCAGGCCAAAUCAAGGCAGGCAAUCUCGGUUAACUGCAUUUUAAUUGGGUUUUGGCCACGGGGCGAGUGCUUCGUUAA
......((((......)))).....(((((((((((.((((..(((....)))..)))).......))))..)))))))(((((((....)))))))... ( -27.10)
>DroSec_CAF1 38592 100 - 1
UAGCCAGUGGCCAGAAACAUAAUCAGGCCAAAUCAAGGCAGUCAAUCUCAGUUAACUGCAUUUUAAUUGGGUUUCGGCCACGGGGCGAGUGCUUCGUCAA
...((.((((((.(((((........(((.......)))........((((((((.......)))))))))))))))))))))((((((...)))))).. ( -32.10)
>DroEre_CAF1 37333 100 - 1
GAGCCAGUAGCCAGAAACAUAAUCAGGCCAAAUCAAGGCAGCAAAUCCCAGUUAACUGCAUACUAAUUGGGUUUUGGCCACUGGACGAGUGUUUCGUUAG
...(((((.(((((((..........(((.......))).......((((((((.........))))))))))))))).)))))(((((...)))))... ( -30.50)
>DroYak_CAF1 41395 99 - 1
UAGCCAGUGGCCAGAAACAUAAUCAGGCCAAAUCAAGGCUGGGAAUCUCAGUUAACUGCAUUCUAAUUGGGCUUUGGCCAC-GGGCGAGUGCUUCGUUGA
..(((.(((((((((..(.......((((.......)))).(((((..(((....))).))))).....)..)))))))))-.))).............. ( -33.10)
>consensus
UAGCCAGUGGCCAGAAACAUAAUCAGGCCAAAUCAAGGCAGGCAAUCUCAGUUAACUGCAUUCUAAUUGGGUUUUGGCCACGGGGCGAGUGCUUCGUUAA
...((.((((((((((..........(((.......))).......(((((((((.......))))))))))))))))))).))(((((...)))))... (-25.41 = -26.35 +   0.94)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,123,346 – 11,123,458
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.94
Mean single sequence MFE -30.57
Consensus MFE -22.41
Energy contribution -23.85
Covariance contribution 1.44
Combinations/Pair 1.07
Mean z-score -2.08
Structure conservation index 0.73
SVM decision value 0.61
SVM RNA-class probability 0.797206
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11123346 112 + 22224390
UGCCUUGAUUUGGCCUGAUUAUGUUUCUGGACACUGGCUAAAAUAAGAGGGCGAUAUAAUUGAAGAAAACUGAAUUUUCUCUAAUUAUA--GGAGUUCAUUA------UAAGCCAAACGA
.((((((.(((((((......((((....))))..))))))).)))).((((..((((((((.((((((.....)))))).))))))))--...))))....------...))....... ( -25.40)
>DroSec_CAF1 38652 114 + 1
UGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCCACUGGCUAAAAUAAGAGGGCGAUUUAAUUGGAGGAAACUGAACUUGCUCUAAUUAUAGAGGAGUUCAUUA------UAAGCCAAAUGU
.(((((....(((((.((.......)).)))))((..........))))))).......((((((....))((((((.(((((....)))))))))))....------....)))).... ( -32.20)
>DroEre_CAF1 37393 112 + 1
UGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCUACUGGCUCAAAUAAGAGGGCGAUAUAAUUGGAGGAAACUGAAUUUUCUCUAAUUAUA--GGAGUUCAUUA------UAAGCCAAAUGA
..........(((((.((.......)).))))).(((((...((((..((((..(((((((((((((((.....)))))))))))))))--...)))).)))------).)))))..... ( -32.90)
>DroYak_CAF1 41454 118 + 1
AGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCCACUGGCUAAAAUAGGGUGGCGAUAUAAUUGGAGGAAACAGAAUUUUACCUAAUUAUA--GGAGUUCAUUACGAGCAUAAGCCAAAUGG
.......((((((((..((((((((....((((((..(((...)))))))))))))))))..).(....).........((((....))--)).((((.....))))....))))))).. ( -31.80)
>consensus
UGCCUUGAUUUGGCCUGAUUAUGUUUCUGGCCACUGGCUAAAAUAAGAGGGCGAUAUAAUUGGAGGAAACUGAAUUUUCUCUAAUUAUA__GGAGUUCAUUA______UAAGCCAAAUGA
.(((......(((((.((.......)).)))))..)))...........(((..(((((((((((((((.....)))))))))))))))...(....).............)))...... (-22.41 = -23.85 +   1.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,123,346 – 11,123,458
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.94
Mean single sequence MFE -22.87
Consensus MFE -15.76
Energy contribution -16.00
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -1.84
Structure conservation index 0.69
SVM decision value 0.13
SVM RNA-class probability 0.598174
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11123346 112 - 22224390
UCGUUUGGCUUA------UAAUGAACUCC--UAUAAUUAGAGAAAAUUCAGUUUUCUUCAAUUAUAUCGCCCUCUUAUUUUAGCCAGUGUCCAGAAACAUAAUCAGGCCAAAUCAAGGCA
.....(((((.(------(((.((.....--(((((((..(((((((...)))))))..)))))))......))))))...)))))((((......))))......(((.......))). ( -22.20)
>DroSec_CAF1 38652 114 - 1
ACAUUUGGCUUA------UAAUGAACUCCUCUAUAAUUAGAGCAAGUUCAGUUUCCUCCAAUUAAAUCGCCCUCUUAUUUUAGCCAGUGGCCAGAAACAUAAUCAGGCCAAAUCAAGGCA
..(((((((((.------...((((((.(((((....)))))..))))))(((((..(((.(((((............)))))....)))...)))))......)))))))))....... ( -26.80)
>DroEre_CAF1 37393 112 - 1
UCAUUUGGCUUA------UAAUGAACUCC--UAUAAUUAGAGAAAAUUCAGUUUCCUCCAAUUAUAUCGCCCUCUUAUUUGAGCCAGUAGCCAGAAACAUAAUCAGGCCAAAUCAAGGCA
...(((((((..------...((......--(((((((.(((.((((...)))).))).))))))).....(((......))).))..)))))))...........(((.......))). ( -20.90)
>DroYak_CAF1 41454 118 - 1
CCAUUUGGCUUAUGCUCGUAAUGAACUCC--UAUAAUUAGGUAAAAUUCUGUUUCCUCCAAUUAUAUCGCCACCCUAUUUUAGCCAGUGGCCAGAAACAUAAUCAGGCCAAAUCAAGGCU
(((((((((((...........(((..((--((....)))).....)))((((((.............(((((.(((...)))...)))))..)))))).....)))))))))...)).. ( -21.56)
>consensus
UCAUUUGGCUUA______UAAUGAACUCC__UAUAAUUAGAGAAAAUUCAGUUUCCUCCAAUUAUAUCGCCCUCUUAUUUUAGCCAGUGGCCAGAAACAUAAUCAGGCCAAAUCAAGGCA
...(((((((.........(((((.......(((((((.(((.(((.....))).))).)))))))........))))).........)))))))...........(((.......))). (-15.76 = -16.00 +   0.25)

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 11:20:00 2006