Locus 2322

Sequence ID 2R_DroMel_CAF1
Location 8,529,965 – 8,530,155
Length 190
Max. P 0.987909
window3823 window3824 window3825 window3826

overview

Window 3

Location 8,529,965 – 8,530,079
Length 114
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 84.59
Mean single sequence MFE -22.00
Consensus MFE -15.84
Energy contribution -15.73
Covariance contribution -0.10
Combinations/Pair 1.14
Mean z-score -1.78
Structure conservation index 0.72
SVM decision value 0.00
SVM RNA-class probability 0.534171
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8529965 114 + 20766785
AUUAUGAGUUAGCAUAAUCGCUUGAAGAGAAUUUUUAAGUGAAAUGGCACUGUUUUGCAUGAAUUUCAAAAUAUUUCUGCCUGAUUUCGGCAGACAUUUUAUUGCGAAAUU-CAU
.(((((......)))))(((((((((((...)))))))))))....(((......)))(((((((((..((((..((((((.......)))))).....))))..))))))-))) ( -30.50)
>DroSec_CAF1 5490 101 + 1
AU--------------AUCGUUUAAAGAGAAUAUUUAAGUGAAAUUUCACUGUUUUGCAUUAAUUUCGAAAUAUUUCAGCCUGAUUUCGGCAGACAUUUUAUUGCAAAAUUCCAU
..--------------..........(.((((.....(((((....)))))..((((((.(((..(((((....))).(((.......))).))....))).))))))))))).. ( -16.70)
>DroSim_CAF1 8740 101 + 1
AU--------------AUCGUUUGAAGAGAAUAUUUAAGUGAAAUUUCACUGUUUCGCAUCAAUUUCAAAAUAUUUCUGCCUGAUUUCGGCAGACAUUUUAUUGCAAAAUUCCAU
..--------------....((((...(((((......(((((((......))))))).................((((((.......)))))).)))))....))))....... ( -18.80)
>consensus
AU______________AUCGUUUGAAGAGAAUAUUUAAGUGAAAUUUCACUGUUUUGCAUCAAUUUCAAAAUAUUUCUGCCUGAUUUCGGCAGACAUUUUAUUGCAAAAUUCCAU
.................(((((((((.......))))))))).........((((((((........(((((...((((((.......)))))).)))))..))))))))..... (-15.84 = -15.73 +  -0.10)

alignment

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secondary structure

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Window 4

Location 8,529,965 – 8,530,079
Length 114
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 84.59
Mean single sequence MFE -19.93
Consensus MFE -15.32
Energy contribution -16.77
Covariance contribution 1.45
Combinations/Pair 1.04
Mean z-score -1.86
Structure conservation index 0.77
SVM decision value 0.23
SVM RNA-class probability 0.646490
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8529965 114 - 20766785
AUG-AAUUUCGCAAUAAAAUGUCUGCCGAAAUCAGGCAGAAAUAUUUUGAAAUUCAUGCAAAACAGUGCCAUUUCACUUAAAAAUUCUCUUCAAGCGAUUAUGCUAACUCAUAAU
(((-(((((((.((((.....((((((.......))))))..)))).)))))))))).......((((......))))...............(((......))).......... ( -23.70)
>DroSec_CAF1 5490 101 - 1
AUGGAAUUUUGCAAUAAAAUGUCUGCCGAAAUCAGGCUGAAAUAUUUCGAAAUUAAUGCAAAACAGUGAAAUUUCACUUAAAUAUUCUCUUUAAACGAU--------------AU
..(((((((((((.(((.......(((.......)))((((....))))...))).))))))).(((((....)))))......))))...........--------------.. ( -15.50)
>DroSim_CAF1 8740 101 - 1
AUGGAAUUUUGCAAUAAAAUGUCUGCCGAAAUCAGGCAGAAAUAUUUUGAAAUUGAUGCGAAACAGUGAAAUUUCACUUAAAUAUUCUCUUCAAACGAU--------------AU
.((((((((..(..(((((((((((((.......))))))..))))))).......((.....)))..)))))))).......................--------------.. ( -20.60)
>consensus
AUGGAAUUUUGCAAUAAAAUGUCUGCCGAAAUCAGGCAGAAAUAUUUUGAAAUUAAUGCAAAACAGUGAAAUUUCACUUAAAUAUUCUCUUCAAACGAU______________AU
.(((((((((((..(((((((((((((.......))))))..))))))).......((.....)))))))))))))....................................... (-15.32 = -16.77 +   1.45)

alignment

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secondary structure

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Window 5

Location 8,530,001 – 8,530,119
Length 118
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 80.25
Mean single sequence MFE -24.65
Consensus MFE -14.88
Energy contribution -17.00
Covariance contribution 2.12
Combinations/Pair 1.10
Mean z-score -2.85
Structure conservation index 0.60
SVM decision value 2.10
SVM RNA-class probability 0.987909
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8530001 118 - 20766785
ACACUGAAUCAUUAACCACAUUUUGAAAAAUAUUCAUGGAAUG-AAUUUCGCAAUAAAAUGUCUGCCGAAAUCAGGCAGAAAUAUUUUGAAAUUCAUGCAAAACAGUGCCAUUUCACUU
.(((((.........(((.....((((.....))))))).(((-(((((((.((((.....((((((.......))))))..)))).))))))))))......)))))........... ( -29.40)
>DroSec_CAF1 5512 119 - 1
ACACUGAAUCAUUAACCACAUUGUGAACAAUAUUCAUGGAAUGGAAUUUUGCAAUAAAAUGUCUGCCGAAAUCAGGCUGAAAUAUUUCGAAAUUAAUGCAAAACAGUGAAAUUUCACUU
.(((((.........(((..(..((((.....))))..)..)))..(((((((.(((.......(((.......)))((((....))))...))).))))))))))))........... ( -25.10)
>DroSim_CAF1 8762 119 - 1
ACACUGAAUCAUUAACCACAUUGUGAACAACAUUCAUGGAAUGGAAUUUUGCAAUAAAAUGUCUGCCGAAAUCAGGCAGAAAUAUUUUGAAAUUGAUGCGAAACAGUGAAAUUUCACUU
.(((((.........(((..(..((((.....))))..)..)))..(((((((.(((((((((((((.......))))))..))))))).......))))))))))))........... ( -29.20)
>DroYak_CAF1 8514 92 - 1
ACACUGAAUCAAAAACCACAUUGUGAAUAAUAUUUAUGGAAUGGAAUUUCGCAUUAAAAUGUCCGCCAAAAUCAGGCAAAGAUAUUUUGUAA---------------------------
.....................((((((...(((((...)))))....)))))).(((((((((.(((.......)))...)))))))))...--------------------------- ( -14.90)
>consensus
ACACUGAAUCAUUAACCACAUUGUGAACAAUAUUCAUGGAAUGGAAUUUCGCAAUAAAAUGUCUGCCGAAAUCAGGCAGAAAUAUUUUGAAAUU_AUGCAAAACAGUGAAAUUUCACUU
.(((((.............((((((((...(((((...)))))....))))))))((((((((((((.......))))))..))))))...............)))))........... (-14.88 = -17.00 +   2.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,530,040 – 8,530,155
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.95
Mean single sequence MFE -20.91
Consensus MFE -19.08
Energy contribution -18.57
Covariance contribution -0.50
Combinations/Pair 1.19
Mean z-score -1.35
Structure conservation index 0.91
SVM decision value 0.09
SVM RNA-class probability 0.578731
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8530040 115 + 20766785
UCUGCCUGAUUUCGGCAGACAUUUUAUUGCGAAAUU-CAUUCCAUGAAUAUUUUUCAAAAUGUGGUUAAUGAUUCAGUGUCGCGCCUCCAUUUUGCAUAUUCCCAUCCCUUU-UUUU---
((((((.......)))))).................-........((((((....(((((((.(((...((((.....)))).)))..))))))).))))))..........-....--- ( -20.80)
>DroSec_CAF1 5551 116 + 1
UCAGCCUGAUUUCGGCAGACAUUUUAUUGCAAAAUUCCAUUCCAUGAAUAUUGUUCACAAUGUGGUUAAUGAUUCAGUGUCGCGCCUCCAUUUUGCAUAUUCCCAUCCCUUU-UUUU---
...((..(((...(((.((((((..(((........((((....(((((...)))))....)))).....)))..))))))..)))...)))..))................-....--- ( -19.22)
>DroSim_CAF1 8801 117 + 1
UCUGCCUGAUUUCGGCAGACAUUUUAUUGCAAAAUUCCAUUCCAUGAAUGUUGUUCACAAUGUGGUUAAUGAUUCAGUGUCGCGCCUCCAUUUUGCAUAUUCCCAUCCCUUUUUUUU---
((((((.......))))))........((((((((.((((....(((((...)))))....)))).....(((.....)))........))))))))....................--- ( -21.60)
>DroYak_CAF1 8526 119 + 1
UUUGCCUGAUUUUGGCGGACAUUUUAAUGCGAAAUUCCAUUCCAUAAAUAUUAUUCACAAUGUGGUUUUUGAUUCAGUGUCGCGCCUCCAUUUUGCAUUUUCCCAUCCCUUU-UUUUUUG
..(((..(((...((((((((((..(((.(((((..((((.....................)))).)))))))).)))))).))))...)))..)))...............-....... ( -22.00)
>consensus
UCUGCCUGAUUUCGGCAGACAUUUUAUUGCAAAAUUCCAUUCCAUGAAUAUUGUUCACAAUGUGGUUAAUGAUUCAGUGUCGCGCCUCCAUUUUGCAUAUUCCCAUCCCUUU_UUUU___
((((((.......))))))........((((((((............((((((....))))))(((...((((.....)))).)))...))))))))....................... (-19.08 = -18.57 +  -0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:50 2006