Locus 2054

Sequence ID 2R_DroMel_CAF1
Location 7,726,769 – 7,726,969
Length 200
Max. P 0.998941
window3404 window3405 window3406 window3407

overview

Window 4

Location 7,726,769 – 7,726,889
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.39
Mean single sequence MFE -29.74
Consensus MFE -27.96
Energy contribution -27.84
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -1.63
Structure conservation index 0.94
SVM decision value 0.76
SVM RNA-class probability 0.844014
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7726769 120 - 20766785
UUCAAUACACACCUGCGAUCGGGAUGGUCGACUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGAAAAUGUACACCCUUUCAAAUCGAACUAAGAAUAUGAAACA
.(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).)))))))..(((((.((((..(....)..))))...((.......))....))))). ( -30.60)
>DroSec_CAF1 16805 120 - 1
UUCAAUACACACCUGCGAUCGGGAUGGUCGCCUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGAAAAUGUACACCCUUUACAAUAGAACUAGGAAUAUAAAACA
.(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).))))))).((((((......((((.......))))..)))))).............. ( -30.10)
>DroSim_CAF1 15096 120 - 1
UUCAAUACACACCUGCGAUCGAGAUGGUCGCCUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGAAAAUGUACACCCUUUACAAUAGAACUAAGAAUAUAAAACA
.(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).))))))).((((((......((((.......))))..)))))).............. ( -31.00)
>DroEre_CAF1 10321 97 - 1
CUCAAUACACACCUGCGAUCGGGAUGGUCGCCUUCGCGAGAAGAAGCCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCG---------------UAAAUGUAUACUA--------AAACC
.(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).)))))))..(((((.(---------------((......))).)--------)))). ( -31.70)
>DroYak_CAF1 10548 102 - 1
CUCAAUACACACCUGCGAUCGGGAUGGUCGCCUGCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUGUACA----------CCCUUUAAGAUCGAACUA--------ACCUA
.(((((((.(((..((((((.....))))))..((((((((.(....).))))))))..))).))))))).........----------..................--------..... ( -25.30)
>consensus
UUCAAUACACACCUGCGAUCGGGAUGGUCGCCUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGAAAAUGUACACCCUUUAAAAUAGAACUA_GAAUAU_AAACA
.(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).))))))).................................................. (-27.96 = -27.84 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,726,809 – 7,726,929
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.25
Mean single sequence MFE -31.14
Consensus MFE -28.96
Energy contribution -29.96
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.93
SVM decision value 1.07
SVM RNA-class probability 0.909589
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7726809 120 + 20766785
UCGAAAACUGUCAACACUCACUGGCACAAAAUGGUUUCUUCUCGCGAAGUCGACCAUCCCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAACACAAAUCCGCGAUUGCAUUGGAAAAUCA
..((......((((.((.((((.((.....((((((.((((....))))..)))))).......)).)))).)).)))).(((((.((((((.(......).).)))))..))))).)). ( -28.60)
>DroSec_CAF1 16845 120 + 1
UCGAAAACUGUCAACACUCACUGGCACAAAAUGGUUUCUUCUCGCGAAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCA
........(((((........))))).....((((((....((((....))))(((...(((((((.(((.(((((((..........))))))).))).)))))))...))).)))))) ( -34.20)
>DroSim_CAF1 15136 120 + 1
UCGAAAACUGUCAACACUCACUGGCACAAAAUGGUUUCUUCUCGCGAAGGCGACCAUCUCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCA
........(((((........))))).....((((((....((((....))))(((...(((((((.(((.(((((((..........))))))).))).)))))))...))).)))))) ( -34.20)
>DroEre_CAF1 10339 119 + 1
-CGAAAACUGUCAACACUCACUGGCACAAAAUGGCUUCUUCUCGCGAAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAGUUUCCUUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCA
-.......(((((........)))))...............((((....))))(((...(((((((.(((.(((((((..........))))))).))).)))))))...)))....... ( -32.30)
>DroYak_CAF1 10571 119 + 1
-UGUACACUGUCAACACUCACUGGCACAAAAUGGUUUCUUCUCGCGCAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAGUUUCCUUGCAAGACAAAUCCCCGAUUGCAUUGGAAAAUCA
-.((((..(((((........))))).................((((..((((.(.....).))))..))))))))(((.(((((.(((((.............)))))..))))).))) ( -26.42)
>consensus
UCGAAAACUGUCAACACUCACUGGCACAAAAUGGUUUCUUCUCGCGAAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCA
........(((((........))))).....((((((....((((....))))(((...(((((((.(((.(((((((..........))))))).))).)))))))...))).)))))) (-28.96 = -29.96 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,726,809 – 7,726,929
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.25
Mean single sequence MFE -38.48
Consensus MFE -37.32
Energy contribution -37.44
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.92
Structure conservation index 0.97
SVM decision value 3.29
SVM RNA-class probability 0.998941
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7726809 120 - 20766785
UGAUUUUCCAAUGCAAUCGCGGAUUUGUGUUGCAGGGAAAUUCAAUACACACCUGCGAUCGGGAUGGUCGACUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGA
..(((((((..(((((.((((....))))))))))))))))(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).))))))).......... ( -40.60)
>DroSec_CAF1 16845 120 - 1
UGAUUUUCCAAUGCAAUCGCGGAUUUGUAUUGCAGGGAAAUUCAAUACACACCUGCGAUCGGGAUGGUCGCCUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGA
..(((((((..((((((.(((....))))))))))))))))(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).))))))).......... ( -39.10)
>DroSim_CAF1 15136 120 - 1
UGAUUUUCCAAUGCAAUCGCGGAUUUGUAUUGCAGGGAAAUUCAAUACACACCUGCGAUCGAGAUGGUCGCCUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGA
..(((((((..((((((.(((....))))))))))))))))(((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).))))))).......... ( -40.00)
>DroEre_CAF1 10339 119 - 1
UGAUUUUCCAAUGCAAUCGCGGAUUUGUAUUGCAAGGAAACUCAAUACACACCUGCGAUCGGGAUGGUCGCCUUCGCGAGAAGAAGCCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCG-
........((((((((........))))))))...(((((((((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).)))))))..)))))).- ( -40.60)
>DroYak_CAF1 10571 119 - 1
UGAUUUUCCAAUGCAAUCGGGGAUUUGUCUUGCAAGGAAACUCAAUACACACCUGCGAUCGGGAUGGUCGCCUGCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUGUACA-
....(((((..(((((.(((....)))..))))).))))).(((((((.(((..((((((.....))))))..((((((((.(....).))))))))..))).))))))).........- ( -32.10)
>consensus
UGAUUUUCCAAUGCAAUCGCGGAUUUGUAUUGCAGGGAAAUUCAAUACACACCUGCGAUCGGGAUGGUCGCCUUCGCGAGAAGAAACCAUUUUGUGCCAGUGAGUGUUGACAGUUUUCGA
........((((((((........))))))))...(((((((((((((.(((..(((..(((((((((...((((....))))..))))))))))))..))).)))))))..)))))).. (-37.32 = -37.44 +   0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,726,849 – 7,726,969
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.58
Mean single sequence MFE -32.36
Consensus MFE -27.86
Energy contribution -28.90
Covariance contribution 1.04
Combinations/Pair 1.05
Mean z-score -1.34
Structure conservation index 0.86
SVM decision value 0.34
SVM RNA-class probability 0.696951
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7726849 120 + 20766785
CUCGCGAAGUCGACCAUCCCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAACACAAAUCCGCGAUUGCAUUGGAAAAUCACUAAAUUGUUCGAUCGUGUGAAGAAUCGUCCAUUUUCCAA
.(((((..((((((((...(((((((.(((.(((.(((..........))).))).))).)))))))...)))......((......)))))))..)))))................... ( -28.10)
>DroSec_CAF1 16885 120 + 1
CUCGCGAAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCACUAAAUUGUUCGAUCGUGUGAAGAAUCGUCCAUUUGCCAA
...(((((((((((((...(((((((.(((.(((((((..........))))))).))).)))))))...)))....((((...(((....)))...))))....))).)).)))))... ( -35.40)
>DroSim_CAF1 15176 120 + 1
CUCGCGAAGGCGACCAUCUCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCACUAAAUUGUUCGAUCGCGUAAAGAAUCGUCCAUUUUCCAA
.((((....))))......(((((((.(((.(((((((..........))))))).))).)))))))..((((((((.........((..(((((.......).))))..)))))))))) ( -33.60)
>DroEre_CAF1 10378 120 + 1
CUCGCGAAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAGUUUCCUUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCACUAAAUUGUUCGAUCGAGUGAAGAACCGUCCAUUUUCCAA
.((((....))))......(((((((.(((.(((((((..........))))))).))).)))))))..(((((((((((((..(((....)))..))))).((....))..)))))))) ( -36.00)
>DroYak_CAF1 10610 120 + 1
CUCGCGCAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAGUUUCCUUGCAAGACAAAUCCCCGAUUGCAUUGGAAAAUCACUAAGUUGUUUGAUCGAGUGAAGAACCGUCCAUUUUCCAA
((((..((((((((((..((.......))..))...(((.(((((.(((((.............)))))..))))).)))....))))))))..)))).(((((........)))))... ( -28.72)
>consensus
CUCGCGAAGGCGACCAUCCCGAUCGCAGGUGUGUAUUGAAUUUCCCUGCAAUACAAAUCCGCGAUUGCAUUGGAAAAUCACUAAAUUGUUCGAUCGAGUGAAGAAUCGUCCAUUUUCCAA
.((((....))))......(((((((.(((.(((((((..........))))))).))).)))))))..(((((((((......(((.((((......)))).))).....))))))))) (-27.86 = -28.90 +   1.04)

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 10:20:07 2006