Locus 6885

Sequence ID 2L_DroMel_CAF1
Location 19,248,357 – 19,248,484
Length 127
Max. P 0.998989
window10976 window10977 window10978 window10979

overview

Window 6

Location 19,248,357 – 19,248,462
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 83.41
Mean single sequence MFE -30.74
Consensus MFE -22.10
Energy contribution -23.18
Covariance contribution 1.08
Combinations/Pair 1.11
Mean z-score -2.22
Structure conservation index 0.72
SVM decision value 1.07
SVM RNA-class probability 0.910603
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19248357 105 + 22407834
UGCUCCCCUGGGUCGCUUUUUGUUCACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUUAAUGGGGUCUAUUGAUUUCAUGGUGAGCACGGUG
.((.((....))..))....(((((((.(((.......((((((((((....))).)))))))..(((((((((((...)))))))))))))))))))))..... ( -32.20)
>DroSec_CAF1 68264 105 + 1
UGCUCCCCUGGGUCGCUUUUUGUUCACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCUGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCGUGGUGAGCAUGGUG
....((....)).((((...(((((((.(((((((........(((((....))).)))))))))(((((((((((...)))))))))))...))))))).)))) ( -31.20)
>DroSim_CAF1 69604 105 + 1
UGCUCCCCUGGGUCGCUUUUUGUUCACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCAUGGUGAGCAUGGUG
....((....)).((((...(((((((.(((.......((((((((((....))).)))))))..(((((((((((...))))))))))))))))))))).)))) ( -35.40)
>DroEre_CAF1 67466 80 + 1
UGCUCUGCUG-------------------------UUUUUUCUGCUGUUUUUGCACGCAGAAAUGGAAACCAAUGGGGUCUAUUGAUUUCAUGGCGAGCAUUGUG
(((((.((((-------------------------(((((((((((((....))).))))))...)))))..(((..(((....)))..)))))))))))..... ( -28.30)
>DroYak_CAF1 69693 104 + 1
UGCUCCCCUGGGUAGCUUUUUGUUCACGCAUUUC-UUUUUUCUGCUGUUUUUGUACGCAGAAAUGGCAAUGACUCGGGUCUAUUGAUUUCAUGGUGUGCAUGGCG
(((((....)))))(((...(((.(((.(((...-.......(((((((((((....)))))))))))..(((....)))..........)))))).))).))). ( -26.60)
>consensus
UGCUCCCCUGGGUCGCUUUUUGUUCACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCAUGGUGAGCAUGGUG
(((((.((..............................((((((((((....))).)))))))..(((((((((((...)))))))))))..)).)))))..... (-22.10 = -23.18 +   1.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,248,357 – 19,248,462
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -23.96
Consensus MFE -18.30
Energy contribution -19.54
Covariance contribution 1.24
Combinations/Pair 1.04
Mean z-score -2.73
Structure conservation index 0.76
SVM decision value 2.12
SVM RNA-class probability 0.988341
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19248357 105 - 22407834
CACCGUGCUCACCAUGAAAUCAAUAGACCCCAUUAAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGUGAACAAAAAGCGACCCAGGGGAGCA
.....(((((....((....))......(((....(((((...((((((((......)).)))))).....)))))((...........))......)))))))) ( -21.70)
>DroSec_CAF1 68264 105 - 1
CACCAUGCUCACCACGAAAUCAAUAGACCCCAUUGAUUUCCACUUCAGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGUGAACAAAAAGCGACCCAGGGGAGCA
(((((((((......(((((((((.......)))))))))......))))))........(((............))))))........((..((....)).)). ( -22.30)
>DroSim_CAF1 69604 105 - 1
CACCAUGCUCACCAUGAAAUCAAUAGACCCCAUUGAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGUGAACAAAAAGCGACCCAGGGGAGCA
.....((.((((((((((((((((.......)))))))))...((((((((......)).))))))........))).)))).))....((..((....)).)). ( -26.70)
>DroEre_CAF1 67466 80 - 1
CACAAUGCUCGCCAUGAAAUCAAUAGACCCCAUUGGUUUCCAUUUCUGCGUGCAAAAACAGCAGAAAAAA-------------------------CAGCAGAGCA
.....(((((((...(((((((((.......)))))))))..(((((((((......)).)))))))...-------------------------..)).))))) ( -23.80)
>DroYak_CAF1 69693 104 - 1
CGCCAUGCACACCAUGAAAUCAAUAGACCCGAGUCAUUGCCAUUUCUGCGUACAAAAACAGCAGAAAAAA-GAAAUGCGUGAACAAAAAGCUACCCAGGGGAGCA
...((((((...........((((.(((....)))))))...(((((((((......)).)))))))...-....))))))........(((.((....))))). ( -25.30)
>consensus
CACCAUGCUCACCAUGAAAUCAAUAGACCCCAUUGAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGUGAACAAAAAGCGACCCAGGGGAGCA
.....(((((.((..(((((((((.......)))))))))...((((((((......)).))))))...............................)).))))) (-18.30 = -19.54 +   1.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,248,382 – 19,248,484
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.52
Mean single sequence MFE -30.26
Consensus MFE -18.32
Energy contribution -20.32
Covariance contribution 2.00
Combinations/Pair 1.19
Mean z-score -2.95
Structure conservation index 0.61
SVM decision value 3.31
SVM RNA-class probability 0.998989
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19248382 102 + 22407834
ACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUUAAUGGGGUCUAUUGAUUUCAUGGUGAGCACGGUGAUUAAU------------------UAUUAUCCGUUAUGCA
..((((..((....(((((((((....))).))))))(((...((((.((..(((....)))..))))))...)))((((((....------------------.))))))))..)))). ( -29.30)
>DroSec_CAF1 68289 102 + 1
ACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCUGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCGUGGUGAGCAUGGUGAUUAAU------------------UAUUAUUCGCUAUGCA
.(((.........((((.(((((....))).)).))))..(((((((((((...))))))))))))))....(((((((((.((..------------------...)).))))))))). ( -32.00)
>DroSim_CAF1 69629 102 + 1
ACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCAUGGUGAGCAUGGUGAUUAAU------------------UAUUAUUCGCUAUGCA
.(((.........((((((((((....))).)))))))..(((((((((((...)))))))))))...))).(((((((((.((..------------------...)).))))))))). ( -36.10)
>DroEre_CAF1 67476 106 + 1
----------UUUUUUCUGCUGUUUUUGCACGCAGAAAUGGAAACCAAUGGGGUCUAUUGAUUUCAUGGCGAGCAUUGUGAUUAAUACAUUUCAC----ACAUUAAUAAUCUGCUAUAAU
----------...((((((((((....))).))))))).(((..(((.((..(((....)))..))))).......(((((..........))))----).........)))........ ( -24.10)
>DroYak_CAF1 69718 119 + 1
ACGCAUUUC-UUUUUUCUGCUGUUUUUGUACGCAGAAAUGGCAAUGACUCGGGUCUAUUGAUUUCAUGGUGUGCAUGGCGAUUUUCACAUUACAUAUGUACAUUAAUAACCCGCUAUUAU
..((.....-.......(((((((((((....))))))))))).......((((.(((((((..((((.((((.(((..........)))))))))))...)))))))))))))...... ( -29.80)
>consensus
ACGCAUUUCGUUUUUUCUGCUGUUUUUGCACGCAGAAGUGGAAAUCAAUGGGGUCUAUUGAUUUCAUGGUGAGCAUGGUGAUUAAU__________________UAUUAUCCGCUAUGCA
.(((.........((((((((((....))).)))))))..(((((((((((...)))))))))))...))).((((((((...............................)))))))). (-18.32 = -20.32 +   2.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,248,382 – 19,248,484
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.52
Mean single sequence MFE -20.74
Consensus MFE -10.42
Energy contribution -11.26
Covariance contribution 0.84
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.50
SVM decision value 0.85
SVM RNA-class probability 0.865201
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19248382 102 - 22407834
UGCAUAACGGAUAAUA------------------AUUAAUCACCGUGCUCACCAUGAAAUCAAUAGACCCCAUUAAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGU
.((((...(((....(------------------((((((...((((.....))))...((....))....))))))))))..((((((((......)).))))))........)))).. ( -16.90)
>DroSec_CAF1 68289 102 - 1
UGCAUAGCGAAUAAUA------------------AUUAAUCACCAUGCUCACCACGAAAUCAAUAGACCCCAUUGAUUUCCACUUCAGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGU
.((((..((.......------------------..........(((((......(((((((((.......)))))))))......)))))((.......))........))..)))).. ( -19.30)
>DroSim_CAF1 69629 102 - 1
UGCAUAGCGAAUAAUA------------------AUUAAUCACCAUGCUCACCAUGAAAUCAAUAGACCCCAUUGAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGU
.((((..((.......------------------.....................(((((((((.......)))))))))...((((((((......)).))))))....))..)))).. ( -22.10)
>DroEre_CAF1 67476 106 - 1
AUUAUAGCAGAUUAUUAAUGU----GUGAAAUGUAUUAAUCACAAUGCUCGCCAUGAAAUCAAUAGACCCCAUUGGUUUCCAUUUCUGCGUGCAAAAACAGCAGAAAAAA----------
.....((((....(((((((.----.(...)..))))))).....))))......(((((((((.......)))))))))..(((((((((......)).)))))))...---------- ( -22.00)
>DroYak_CAF1 69718 119 - 1
AUAAUAGCGGGUUAUUAAUGUACAUAUGUAAUGUGAAAAUCGCCAUGCACACCAUGAAAUCAAUAGACCCGAGUCAUUGCCAUUUCUGCGUACAAAAACAGCAGAAAAAA-GAAAUGCGU
.......((((((.......(((((.....)))))........((((.....)))).........)))))).(.((((....(((((((((......)).)))))))...-..))))).. ( -23.40)
>consensus
UGCAUAGCGGAUAAUA__________________AUUAAUCACCAUGCUCACCAUGAAAUCAAUAGACCCCAUUGAUUUCCACUUCUGCGUGCAAAAACAGCAGAAAAAACGAAAUGCGU
.......................................................(((((((((.......)))))))))...((((((((......)).)))))).............. (-10.42 = -11.26 +   0.84)

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 12:22:07 2006