Locus 9725

Sequence ID 3R_DroMel_CAF1
Location 25,733,064 – 25,733,218
Length 154
Max. P 0.998273
window15535 window15536 window15537

overview

Window 5

Location 25,733,064 – 25,733,179
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.12
Mean single sequence MFE -26.96
Consensus MFE -14.24
Energy contribution -15.42
Covariance contribution 1.18
Combinations/Pair 1.16
Mean z-score -2.67
Structure conservation index 0.53
SVM decision value 3.05
SVM RNA-class probability 0.998273
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25733064 115 + 27905053
CAACAAUAGAUACAUAUG----UAUGGCAUAAAAUGUAUGCUGCCAGUUGGUUUGUCAUGUUUGCCAUCUGAGCAAGCUAAGAAACUUGUUUAA-ACCUAAUGGCUAAUUAUUGUUAAUU
.((((((((((((....)----)))((((((.....))))))((((...((((((....(((((((....).))))))((((...))))..)))-)))...))))...)))))))).... ( -29.70)
>DroSec_CAF1 28404 105 + 1
CAACAAUAAAUACACAUG----UAUGGCACGAAAUGUAUGCUGCCACUUGGUU---------UGCCAUCUCAGCAAGCUAAGAAACUUGUUUAA-ACCU-AUGGCUAAUUAUUGUUAAUU
.((((((((.((..((((----..(((((((.......)).)))))(((((((---------(((.......))))))))))............-...)-)))..)).)))))))).... ( -25.70)
>DroSim_CAF1 28901 109 + 1
CUACAAUAGAUACAUAUGUAUGUAUGGCACAAAACGUAUGCUGCCACUUGGUU---------UGCCAUCUCAGCAAGCUAAGAAACUUGUUUAA-ACCU-AUGGCUAAUUAUUGUUAAUU
..(((((((...(((((((.(((.....)))..)))))))..(((((((((((---------(((.......))))))))))(((....)))..-....-.))))...)))))))..... ( -25.80)
>DroEre_CAF1 29660 93 + 1
UAACAAUGGAUAUGUAUG-------------------------GCAGUUUGUUUUCCAUGUUUGCUAUCUAAGCAAGUUAAGAAACUUGUUUAA-ACAU-ACGGCUAAUUAUUGUUAAUU
(((((((((...((((((-------------------------((((..((.....))...))))....((((((((((....)))))))))).-.)))-))).....)))))))))... ( -23.30)
>DroYak_CAF1 29457 118 + 1
U-ACAAUGGAUAUGUAUAGAUGGAUGGCACACAAUGCAUGUUGCCAGUUGGCUAUCCAUGUUUGCUAUGGAAGCAAGUUAAGAAACUUGUUUAAAACUU-UUGGCUAAUUAUUGUUAAUU
.-((((((((((((.((((.....(((((.(((.....)))))))).....)))).)))))).((((.(.(((((((((....)))))))))....)..-.))))....))))))..... ( -30.30)
>consensus
CAACAAUAGAUACAUAUG____UAUGGCACAAAAUGUAUGCUGCCAGUUGGUU___CAUGUUUGCCAUCUAAGCAAGCUAAGAAACUUGUUUAA_ACCU_AUGGCUAAUUAUUGUUAAUU
.((((((((...............(((((............))))).................(((((..(((((((........)))))))........)))))...)))))))).... (-14.24 = -15.42 +   1.18)

alignment

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secondary structure

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dotplot

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Window 6

Location 25,733,064 – 25,733,179
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.12
Mean single sequence MFE -23.04
Consensus MFE -12.83
Energy contribution -13.40
Covariance contribution 0.57
Combinations/Pair 1.29
Mean z-score -2.23
Structure conservation index 0.56
SVM decision value 1.96
SVM RNA-class probability 0.983922
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25733064 115 - 27905053
AAUUAACAAUAAUUAGCCAUUAGGU-UUAAACAAGUUUCUUAGCUUGCUCAGAUGGCAAACAUGACAAACCAACUGGCAGCAUACAUUUUAUGCCAUA----CAUAUGUAUCUAUUGUUG
...((((((((....((((...(((-((...((((((....)))))).....(((.....)))...)))))...)))).(((((.....))))).(((----(....)))).)))))))) ( -24.90)
>DroSec_CAF1 28404 105 - 1
AAUUAACAAUAAUUAGCCAU-AGGU-UUAAACAAGUUUCUUAGCUUGCUGAGAUGGCA---------AACCAAGUGGCAGCAUACAUUUCGUGCCAUA----CAUGUGUAUUUAUUGUUG
...(((((((((...(((((-.(((-((...((....((((((....))))))))..)---------))))..)))))...(((((...((((.....----)))))))))))))))))) ( -26.60)
>DroSim_CAF1 28901 109 - 1
AAUUAACAAUAAUUAGCCAU-AGGU-UUAAACAAGUUUCUUAGCUUGCUGAGAUGGCA---------AACCAAGUGGCAGCAUACGUUUUGUGCCAUACAUACAUAUGUAUCUAUUGUAG
.....((((((....(((((-.(((-((...((....((((((....))))))))..)---------))))..))))).(((((.....))))).((((((....)))))).)))))).. ( -27.10)
>DroEre_CAF1 29660 93 - 1
AAUUAACAAUAAUUAGCCGU-AUGU-UUAAACAAGUUUCUUAACUUGCUUAGAUAGCAAACAUGGAAAACAAACUGC-------------------------CAUACAUAUCCAUUGUUA
...(((((((........((-.(((-((((.((((((....)))))).)))))))))....((((...........)-------------------------)))........))))))) ( -15.90)
>DroYak_CAF1 29457 118 - 1
AAUUAACAAUAAUUAGCCAA-AAGUUUUAAACAAGUUUCUUAACUUGCUUCCAUAGCAAACAUGGAUAGCCAACUGGCAACAUGCAUUGUGUGCCAUCCAUCUAUACAUAUCCAUUGU-A
.....(((((..........-..((((.....(((((....)))))(((.....)))))))((((((.((((....((.....))....)).)).))))))............)))))-. ( -20.70)
>consensus
AAUUAACAAUAAUUAGCCAU_AGGU_UUAAACAAGUUUCUUAGCUUGCUGAGAUGGCAAACAUG___AACCAACUGGCAGCAUACAUUUUGUGCCAUA____CAUAUGUAUCUAUUGUUG
...((((((((....((((...(((.......(((((....)))))(((.....)))...........)))...)))).(((((.....)))))..................)))))))) (-12.83 = -13.40 +   0.57)

alignment

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secondary structure

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dotplot

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Window 7

Location 25,733,100 – 25,733,218
Length 118
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 82.42
Mean single sequence MFE -22.76
Consensus MFE -15.78
Energy contribution -15.90
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.61
Structure conservation index 0.69
SVM decision value 0.04
SVM RNA-class probability 0.555585
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25733100 118 - 27905053
GCUUUACUGUAAGCACACAAAAGUGUUAAAAGCUUGAUUAAUUAACAAUAAUUAGCCAUUAGGU-UUAAACAAGUUUCUUAGCUUGCUCAGAUGGCAAACAUGACAAACCAACUGGCAG
((......((((((((((....))))...(((((((..((((((....))))))(((....)))-.....)))))))....)))))).(((.(((.............))).))))).. ( -24.92)
>DroSec_CAF1 28440 108 - 1
GCUUUACUGUAAGCAUAAAAAAGUGUUAAAAGCUUGAUUAAUUAACAAUAAUUAGCCAU-AGGU-UUAAACAAGUUUCUUAGCUUGCUGAGAUGGCA---------AACCAAGUGGCAG
(((..(((((((((.((((((..((((.(((.((((..((((((....))))))..)).-)).)-)).))))..))).))))))))).....(((..---------..))))))))).. ( -22.70)
>DroSim_CAF1 28941 108 - 1
GCUUUACUGUAAGCAUACAAAAGUGUUAAAAGCUUGAUUAAUUAACAAUAAUUAGCCAU-AGGU-UUAAACAAGUUUCUUAGCUUGCUGAGAUGGCA---------AACCAAGUGGCAG
((((......))))......((((.......))))...((((((....))))))(((((-.(((-((...((....((((((....))))))))..)---------))))..))))).. ( -22.60)
>DroEre_CAF1 29678 111 - 1
GCUUU---GUAAGCAUAUCACUACGUUUAAAGCUUGAUUAAUUAACAAUAAUUAGCCGU-AUGU-UUAAACAAGUUUCUUAACUUGCUUAGAUAGCAAACAUGGAAAACAAACUGC---
(((.(---.(((((..........(((((((...((..((((((....))))))..)).-...)-))))))(((((....)))))))))).).)))....................--- ( -19.60)
>DroYak_CAF1 29496 115 - 1
GCUUU---CUAAGCAUAGCAAAGUGUUAAAAGCUUGAUUAAUUAACAAUAAUUAGCCAA-AAGUUUUAAACAAGUUUCUUAACUUGCUUCCAUAGCAAACAUGGAUAGCCAACUGGCAA
(((..---..(((((.((.((..((((.(((((((..(((((((....)))))))....-))))))).))))..)).)).....)))))....)))...........(((....))).. ( -24.00)
>consensus
GCUUUACUGUAAGCAUACAAAAGUGUUAAAAGCUUGAUUAAUUAACAAUAAUUAGCCAU_AGGU_UUAAACAAGUUUCUUAGCUUGCUGAGAUGGCAAACAUG___AACCAACUGGCAG
((((......))))..........((((((((((((..((((((....))))))(((....)))......))))))).))))).((((.....))))...................... (-15.78 = -15.90 +   0.12)

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 13:40:45 2006