Locus 7180

Sequence ID 3R_DroMel_CAF1
Location 18,928,876 – 18,929,007
Length 131
Max. P 0.943297
window11613 window11614 window11615

overview

Window 3

Location 18,928,876 – 18,928,990
Length 114
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 84.64
Mean single sequence MFE -33.78
Consensus MFE -21.72
Energy contribution -22.16
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.90
Structure conservation index 0.64
SVM decision value 1.33
SVM RNA-class probability 0.943297
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18928876 114 + 27905053
UAUGCCUAUUUUUUCGACCUGAGCUGUAUGGCUAUAUCCUCAAGCGCAAAUAUUAUAUGUACAACAUAUAUUUCGCUGGGGACAGUAAAGUGUUCUAAUGCCACACACAGGCAA
..(((((...........(((((((....))))...((((((.(((.(((((...((((.....)))))))))))))))))))))....((((.........))))..))))). ( -30.10)
>DroSec_CAF1 39989 114 + 1
AAUGCCUAUUUUUUCGACCUCAGCUGUAUGGCUACAUCCUCAAGCGCGAGUUUUAUAUGUACAACAUAUAUUUCGCUGGGGACAGCAAAGUGUUCUAAUGCGACACAAAGGCAA
..(((((...............((((((((....)))(((((...(((((...((((((.....)))))).)))))))))))))))...(((((.......)))))..))))). ( -34.60)
>DroSim_CAF1 39966 114 + 1
AAUGCCUAUUUUUUUGACCUGCGCUGUAUGGCUCUAUCCUCAAGCGCGAGUUUUAUAUGUACAACAUAUAUUUCGCUGGGGACAGCAAAGUGUUCUAAUGCGACACAAAGGCAA
..(((((.............(((((....((......))...)))))(((...((((((.....)))))).)))((((....))))...(((((.......)))))..))))). ( -35.20)
>DroEre_CAF1 40132 99 + 1
UGUGCCUAUUUUUGCGACUUGAGCUGUGUGG---------------CAAGUGUUAUAUGCACAACAUAUACUUAGCUGGGGACAGCAAAGUGUUCUAAUGCGACACAAAGGAAA
....(((......((.......))(((((.(---------------((.((((.....)))).....((((((.((((....)))).)))))).....))).))))).)))... ( -32.60)
>DroYak_CAF1 41237 113 + 1
UGUGCCUAUUUUUUUGGCCUCAGCUGUGUGGCCAUAUUCUCG-GCGCAAGUAUUAUAUGUACAACAUAUAUUUAGCUGGGGACAGCAAAGUGUUCUAGUGCGACACAAAGGCAA
..(((((.......(((((.((....)).)))))........-((((..((((.....)))).....((((((.((((....)))).))))))....)))).......))))). ( -36.40)
>consensus
UAUGCCUAUUUUUUCGACCUGAGCUGUAUGGCUAUAUCCUCAAGCGCAAGUAUUAUAUGUACAACAUAUAUUUCGCUGGGGACAGCAAAGUGUUCUAAUGCGACACAAAGGCAA
..(((((...............(((....))).....................((((((.....))))))....((((....))))...(((((.......)))))..))))). (-21.72 = -22.16 +   0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,928,876 – 18,928,990
Length 114
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 84.64
Mean single sequence MFE -28.84
Consensus MFE -18.88
Energy contribution -19.48
Covariance contribution 0.60
Combinations/Pair 1.07
Mean z-score -1.85
Structure conservation index 0.65
SVM decision value 0.10
SVM RNA-class probability 0.584927
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18928876 114 - 27905053
UUGCCUGUGUGUGGCAUUAGAACACUUUACUGUCCCCAGCGAAAUAUAUGUUGUACAUAUAAUAUUUGCGCUUGAGGAUAUAGCCAUACAGCUCAGGUCGAAAAAAUAGGCAUA
.((((((((((((((..((((....)))).((((((.((((((((((((((.....)))).)))))).)))).).)))))..)))))))...((.....))....))))))).. ( -32.90)
>DroSec_CAF1 39989 114 - 1
UUGCCUUUGUGUCGCAUUAGAACACUUUGCUGUCCCCAGCGAAAUAUAUGUUGUACAUAUAAAACUCGCGCUUGAGGAUGUAGCCAUACAGCUGAGGUCGAAAAAAUAGGCAUU
.(((((..(((((......).))))(((((((....))))))).((((((.....))))))....(((.((((.((..((((....)))).)).)))))))......))))).. ( -29.60)
>DroSim_CAF1 39966 114 - 1
UUGCCUUUGUGUCGCAUUAGAACACUUUGCUGUCCCCAGCGAAAUAUAUGUUGUACAUAUAAAACUCGCGCUUGAGGAUAGAGCCAUACAGCGCAGGUCAAAAAAAUAGGCAUU
.(((((..(((((......).))))(((((((....))))))).((((((.....))))))..((..(((((((.((......)).)).)))))..)).........))))).. ( -30.20)
>DroEre_CAF1 40132 99 - 1
UUUCCUUUGUGUCGCAUUAGAACACUUUGCUGUCCCCAGCUAAGUAUAUGUUGUGCAUAUAACACUUG---------------CCACACAGCUCAAGUCGCAAAAAUAGGCACA
.......((((((((((......((((.((((....)))).)))).......)))).........(((---------------(.((.........)).)))).....)))))) ( -22.42)
>DroYak_CAF1 41237 113 - 1
UUGCCUUUGUGUCGCACUAGAACACUUUGCUGUCCCCAGCUAAAUAUAUGUUGUACAUAUAAUACUUGCGC-CGAGAAUAUGGCCACACAGCUGAGGCCAAAAAAAUAGGCACA
.((((((((.(.((((............((((....))))....((((((.....)))))).....)))))-))).....(((((.((....)).))))).......))))).. ( -29.10)
>consensus
UUGCCUUUGUGUCGCAUUAGAACACUUUGCUGUCCCCAGCGAAAUAUAUGUUGUACAUAUAAAACUUGCGCUUGAGGAUAUAGCCAUACAGCUCAGGUCGAAAAAAUAGGCAUA
.(((((.(((((.((..........(((((((....))))))).((((((.....)))))).....................)).)))))((....)).........))))).. (-18.88 = -19.48 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,928,911 – 18,929,007
Length 96
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 79.75
Mean single sequence MFE -25.38
Consensus MFE -17.28
Energy contribution -17.78
Covariance contribution 0.50
Combinations/Pair 1.22
Mean z-score -2.17
Structure conservation index 0.68
SVM decision value 1.12
SVM RNA-class probability 0.918272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18928911 96 + 27905053
AUCCUCAAGCGCAAAUAUUAUAUGUACAACAUAUAUUUCGCUGGGGACAGUAAAGUGUUCU-AAUGCCACACACAGGCAAUUGCCGACGCCUUGUUU
.((((((.(((.(((((...((((.....))))))))))))))))))...(((.(((((.(-((((((.......))).))))..))))).)))... ( -23.30)
>DroSec_CAF1 40024 96 + 1
AUCCUCAAGCGCGAGUUUUAUAUGUACAACAUAUAUUUCGCUGGGGACAGCAAAGUGUUCU-AAUGCGACACAAAGGCAAUUGCCGUCGCCUUGUUU
.....((((.(((((...((((((.....))))))...)((((....))))...(((((..-.....)))))...(((....))).))))))))... ( -30.50)
>DroSim_CAF1 40001 96 + 1
AUCCUCAAGCGCGAGUUUUAUAUGUACAACAUAUAUUUCGCUGGGGACAGCAAAGUGUUCU-AAUGCGACACAAAGGCAAUUGCCGCCGCCUUGUUU
.....((((.(((.((..((((((.....))))))....((((....))))...(((((..-.....)))))...(((....))))))))))))... ( -29.20)
>DroEre_CAF1 40163 85 + 1
-----------CAAGUGUUAUAUGCACAACAUAUACUUAGCUGGGGACAGCAAAGUGUUCU-AAUGCGACACAAAGGAAAUUGCCGCCGCCUUGUUU
-----------...(((((....(((......((((((.((((....)))).))))))...-..)))))))).((((............)))).... ( -22.60)
>DroYak_CAF1 41272 95 + 1
AUUCUCG-GCGCAAGUAUUAUAUGUACAACAUAUAUUUAGCUGGGGACAGCAAAGUGUUCU-AGUGCGACACAAAGGCAAUUGCCGCCGCCUUGUUU
......(-((((..........(((((.....((((((.((((....)))).))))))...-.))))).......(((....)))).))))...... ( -28.80)
>DroAna_CAF1 41967 80 + 1
--------------UUUCUAAGUGUAUUUUAUAUAUUUAACUGGAGACAACAAAGUUUCCUUUAUGUGACACACAGGCAAUUGCCAGCGCCUUG---
--------------.......((((...(((((((.......((((((......))))))..))))))).)))).(((....))).........--- ( -17.90)
>consensus
AUCCUCA_GCGCAAGUUUUAUAUGUACAACAUAUAUUUAGCUGGGGACAGCAAAGUGUUCU_AAUGCGACACAAAGGCAAUUGCCGCCGCCUUGUUU
..................((((((.....))))))....((((....))))...(((((........)))))...(((....)))............ (-17.28 = -17.78 +   0.50)

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 12:39:24 2006