Locus 4182

Sequence ID 2R_DroMel_CAF1
Location 13,769,030 – 13,769,161
Length 131
Max. P 0.853751
window6723 window6724 window6725 window6726

overview

Window 3

Location 13,769,030 – 13,769,146
Length 116
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 90.66
Mean single sequence MFE -25.32
Consensus MFE -19.58
Energy contribution -19.90
Covariance contribution 0.32
Combinations/Pair 1.10
Mean z-score -1.93
Structure conservation index 0.77
SVM decision value 0.80
SVM RNA-class probability 0.853751
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13769030 116 + 20766785
AAAUUAAGGCAAAUUGGUCCAUCCACUAUGCAAAUGGUUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCAC-CAACUUUUGCUAUUUUAAG
.......(((((((((((.....((((.(((....(((....)))(((....))).)))...)))).((((((((((......))))))))))..))-)))..))))))........ ( -28.30)
>DroSec_CAF1 70029 117 + 1
AAAUUAAGGCAAAUUGGCCCAUCCACUAUGCAAAUGGUUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCAUACAACUUUUGCUACUUAAAG
.......(((......)))..........(((((.((((...((.(((....))).))...(.(((.((((((((((......)))))))))).))).))))))))))......... ( -26.30)
>DroSim_CAF1 73901 117 + 1
AAAUUAAGGCAAAUUGGUCCAUCCACUAUGCAAAUGGUUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCGUACAACUUUUGCUACUUAAAG
...(((((......(((.....)))....(((((.((((...((.(((....))).)).....((((((((((((((......))))))))))..)))))))))))))..))))).. ( -28.10)
>DroEre_CAF1 70206 111 + 1
AAAUGAAGGCAAAUUGGUCCAUCCACUAUGCAAAUGGUUAUAUCCCAGUAAUCUGCACAGCGUGUGCAAUAAUAUGUUAAUUUUUGUAUUACUCCGC-UAAAUUUUUCUAUU-----
.......(((....(((.....)))..(((((((.((((((......))))))(((((.....)))))..............)))))))......))-).............----- ( -18.10)
>DroYak_CAF1 73442 116 + 1
AAAUUAAGGCAAAUUGGUCCAUCCACUAUGCAAAUGGUUAUAUCCCGGUAAUCGGCGCAGCGAGUGCAAUAAUAUGAUAAUUUUUAUAUUACUCCAC-CAACUUUUGCUACUAAAAA
.......(((((((((((.....((((.(((...(((((((......)))))))..)))...))))...((((((((......))))))))....))-)))..))))))........ ( -25.80)
>consensus
AAAUUAAGGCAAAUUGGUCCAUCCACUAUGCAAAUGGUUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCAC_CAACUUUUGCUACUUAAAG
.......((((((((((.......(((((....)))))......))))).....((((.....))))((((((((((......))))))))))...........)))))........ (-19.58 = -19.90 +   0.32)

alignment

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secondary structure

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Window 4

Location 13,769,030 – 13,769,146
Length 116
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 90.66
Mean single sequence MFE -27.51
Consensus MFE -19.94
Energy contribution -20.30
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.72
SVM decision value 0.07
SVM RNA-class probability 0.567654
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13769030 116 - 20766785
CUUAAAAUAGCAAAAGUUG-GUGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAACCAUUUGCAUAGUGGAUGGACCAAUUUGCCUUAAUUU
.........((((((((.(-(((.((((((((..........)))))))).)))).)))((.(((....))).)).....(((((..(...)..))))).....)))))........ ( -32.10)
>DroSec_CAF1 70029 117 - 1
CUUUAAGUAGCAAAAGUUGUAUGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAACCAUUUGCAUAGUGGAUGGGCCAAUUUGCCUUAAUUU
......(((((...(((.(((((..(((((......)))))))))).)))......)))))((((((...(((.((((..(((((.....))))))))).)))))))))........ ( -28.80)
>DroSim_CAF1 73901 117 - 1
CUUUAAGUAGCAAAAGUUGUACGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAACCAUUUGCAUAGUGGAUGGACCAAUUUGCCUUAAUUU
......(((((....(.....)(.((((((((..........)))))))).)....)))))((((((...(((.((((..(((((.....))))))))).)))))))))........ ( -27.20)
>DroEre_CAF1 70206 111 - 1
-----AAUAGAAAAAUUUA-GCGGAGUAAUACAAAAAUUAACAUAUUAUUGCACACGCUGUGCAGAUUACUGGGAUAUAACCAUUUGCAUAGUGGAUGGACCAAUUUGCCUUCAUUU
-----..............-(((((((((((...............))))))...(((((((((((....(((.......))))))))))))))..........)))))........ ( -22.56)
>DroYak_CAF1 73442 116 - 1
UUUUUAGUAGCAAAAGUUG-GUGGAGUAAUAUAAAAAUUAUCAUAUUAUUGCACUCGCUGCGCCGAUUACCGGGAUAUAACCAUUUGCAUAGUGGAUGGACCAAUUUGCCUUAAUUU
.........((((((((.(-(((.((((((((..........)))))))).)))).)))...(((.....))).......(((((..(...)..))))).....)))))........ ( -26.90)
>consensus
CUUUAAGUAGCAAAAGUUG_GUGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAACCAUUUGCAUAGUGGAUGGACCAAUUUGCCUUAAUUU
.........(((((..........((((((((..........)))))))).((..(((((.((((((....((.......)))))))).)))))..))......)))))........ (-19.94 = -20.30 +   0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,769,067 – 13,769,161
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.21
Mean single sequence MFE -22.70
Consensus MFE -14.56
Energy contribution -14.62
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -2.06
Structure conservation index 0.64
SVM decision value 0.75
SVM RNA-class probability 0.839470
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13769067 94 + 20766785
UUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCAC-CAACUUUUGCUAUUUUAAGCAGCCAAGUUUAUAU-------------------------
.....((.(((....))).))...(.(((.((((((((((......)))))))))).)))-)((((((((((......)))))..))))).....------------------------- ( -23.10)
>DroSec_CAF1 70066 95 + 1
UUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCAUACAACUUUUGCUACUUAAAGCAGGCAAGUUUAUAU-------------------------
.....(((..(((...(((((.....)))))(((((((((......)))))))))....)))......((((......)))))))..........------------------------- ( -22.60)
>DroSim_CAF1 73938 95 + 1
UUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCGUACAACUUUUGCUACUUAAAGCAGGCAAGUUUAUAU-------------------------
.....((.(((....))).)).((..((((((((((((((......))))))))))..)))).....(((((......)))))))..........------------------------- ( -23.40)
>DroYak_CAF1 73479 119 + 1
UUAUAUCCCGGUAAUCGGCGCAGCGAGUGCAAUAAUAUGAUAAUUUUUAUAUUACUCCAC-CAACUUUUGCUACUAAAAACAGACAAGGAUAUAUGUAUGGUUUGGUAAGACUGAAUGGA
.(((((((.(((.....((((.....))))..((((((((......))))))))....))-).....(((((.........)).))))))))))....(.(((..(.....)..))).). ( -21.70)
>consensus
UUAUAGCCCAGUAAUCUGCGCAGCGAGUGCAGUAAUAUGAUAAUUUUUAUAUUACUCCAC_CAACUUUUGCUACUUAAAGCAGGCAAGUUUAUAU_________________________
.(((((...(((.....((((.....))))((((((((((......)))))))))).......)))((((((......)))))).....))))).......................... (-14.56 = -14.62 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,769,067 – 13,769,161
Length 94
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.21
Mean single sequence MFE -21.88
Consensus MFE -14.77
Energy contribution -16.15
Covariance contribution 1.38
Combinations/Pair 1.08
Mean z-score -1.74
Structure conservation index 0.68
SVM decision value 0.30
SVM RNA-class probability 0.679216
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13769067 94 - 20766785
-------------------------AUAUAAACUUGGCUGCUUAAAAUAGCAAAAGUUG-GUGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAA
-------------------------.............((((......))))..(((.(-(((.((((((((..........)))))))).)))).)))((.(((....))).))..... ( -24.00)
>DroSec_CAF1 70066 95 - 1
-------------------------AUAUAAACUUGCCUGCUUUAAGUAGCAAAAGUUGUAUGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAA
-------------------------.....(((((...((((......)))).)))))(..((.((((((((..........)))))))).))..)...((.(((....))).))..... ( -20.30)
>DroSim_CAF1 73938 95 - 1
-------------------------AUAUAAACUUGCCUGCUUUAAGUAGCAAAAGUUGUACGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAA
-------------------------.....(((((...((((......)))).)))))....(.((((((((..........)))))))).).......((.(((....))).))..... ( -19.40)
>DroYak_CAF1 73479 119 - 1
UCCAUUCAGUCUUACCAAACCAUACAUAUAUCCUUGUCUGUUUUUAGUAGCAAAAGUUG-GUGGAGUAAUAUAAAAAUUAUCAUAUUAUUGCACUCGCUGCGCCGAUUACCGGGAUAUAA
..........................((((((((.((..(((....(((((.......(-(((.((((((((..........)))))))).)))).)))))...))).)).)))))))). ( -23.80)
>consensus
_________________________AUAUAAACUUGCCUGCUUUAAGUAGCAAAAGUUG_AUGGAGUAAUAUAAAAAUUAUCAUAUUACUGCACUCGCUGCGCAGAUUACUGGGCUAUAA
..............................(((((...((((......)))).)))))(.(((.((((((((..........)))))))).))).)...((.(((....))).))..... (-14.77 = -16.15 +   1.38)

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 11:13:44 2006