Locus 2573

Sequence ID 2R_DroMel_CAF1
Location 9,085,490 – 9,085,689
Length 199
Max. P 0.975822
window4243 window4244 window4245 window4246 window4247

overview

Window 3

Location 9,085,490 – 9,085,610
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -28.05
Consensus MFE -25.23
Energy contribution -24.98
Covariance contribution -0.25
Combinations/Pair 1.15
Mean z-score -1.83
Structure conservation index 0.90
SVM decision value 0.91
SVM RNA-class probability 0.880843
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9085490 120 + 20766785
GCUGUUUUUUAUGUUUGCCUGGUGCAUGAAUAUUGAUUUUUCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGUCCAGGCUGCAUUACAAAUGUAUUUA
...((((...((((..(((((.((((.(....((((((......)))))).)))))..............((((((((..........))))))))))))).))))...))))....... ( -27.60)
>DroSec_CAF1 50264 119 + 1
GCUGUU-UUUAUGUUUGCCUGGUGCAUGAAUAUUGAUUUUUCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUUCAAAUGUAUUUU
...(((-(..((((..(((((.((((.(....((((((......)))))).)))))..............((((((((..........))))))))))))).))))...))))....... ( -30.00)
>DroSim_CAF1 52476 120 + 1
GCUGUUUUUUAUGUUUUCUUGGUGCAUGAAUAUUAAUUUUUCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUACAAAUGUAUUUA
...((((...((((...((((.((((.(....((((((......)))))).)))))..............((((((((..........))))))))))))..))))...))))....... ( -23.80)
>DroEre_CAF1 57589 120 + 1
GCUGUUAUUUUUGCUUGCCUGGUGCAUGAAAAUGGAUUUUUCUUGAUUAAACUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUAGAAAAAUAUUUA
..((((.(((((((..((((((((..((((((((.(.(((........))).).).))))))))))....((((((((..........))))))))))))).)))..)))).)))).... ( -30.80)
>consensus
GCUGUUUUUUAUGUUUGCCUGGUGCAUGAAUAUUGAUUUUUCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUACAAAUGUAUUUA
...........(((..(((((.((((.(....((((((......)))))).)))))..............((((((((..........))))))))))))).)))............... (-25.23 = -24.98 +  -0.25)

alignment

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secondary structure

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Window 4

Location 9,085,490 – 9,085,610
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -32.58
Consensus MFE -27.75
Energy contribution -28.38
Covariance contribution 0.62
Combinations/Pair 1.06
Mean z-score -3.41
Structure conservation index 0.85
SVM decision value 1.73
SVM RNA-class probability 0.974277
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9085490 120 - 20766785
UAAAUACAUUUGUAAUGCAGCCUGGACAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGAAAAAUCAAUAUUCAUGCACCAGGCAAACAUAAAAAACAGC
....(((....))).....((((((.((((((((......))))))))))(((.(((((((.((((...(((....)))......)))).))))))))))))))................ ( -31.10)
>DroSec_CAF1 50264 119 - 1
AAAAUACAUUUGAAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGAAAAAUCAAUAUUCAUGCACCAGGCAAACAUAAA-AACAGC
...................((((.((((((((((......))))))))))(((.(((((((.((((...(((....)))......)))).)))))))))))))).........-...... ( -34.60)
>DroSim_CAF1 52476 120 - 1
UAAAUACAUUUGUAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGAAAAAUUAAUAUUCAUGCACCAAGAAAACAUAAAAAACAGC
....(((....))).......(((((((((((((......))))))))))(((.(((((((.((((...(((....)))......)))).))))))))))................))). ( -28.60)
>DroEre_CAF1 57589 120 - 1
UAAAUAUUUUUCUAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGUUUAAUCAAGAAAAAUCCAUUUUCAUGCACCAGGCAAGCAAAAAUAACAGC
....((((((.....(((.((((.((((((((((......))))))))))(((.((((((((((.(...(((......)))....).)))))))))))))))))..)))))))))..... ( -36.00)
>consensus
UAAAUACAUUUGUAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGAAAAAUCAAUAUUCAUGCACCAGGCAAACAUAAAAAACAGC
...................((((.((((((((((......))))))))))(((.(((((((.((((...(((....)))......)))).))))))))))))))................ (-27.75 = -28.38 +   0.62)

alignment

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secondary structure

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Window 5

Location 9,085,530 – 9,085,649
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.40
Mean single sequence MFE -28.22
Consensus MFE -24.35
Energy contribution -24.66
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.86
SVM decision value 0.76
SVM RNA-class probability 0.844382
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9085530 119 + 20766785
UCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGUCCAGGCUGCAUUACAAAUGUAUUUAAAAUGCAUUUAUUUUUAUUCCCAUGCAACAGGU-UGCAGG
...........(((((((((......(.((((((((((..........)))))).)).)))(((((...((((((((.....))))))))............)))))..))))-))))). ( -26.26)
>DroSec_CAF1 50303 119 + 1
UCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUUCAAAUGUAUUUUAAAUGCAUUUAUUUUCUUUCCCAUGCAACAGGU-UGCAGG
...........(((((((((......(.((((((((((..........))))))))..)))(((((...((((((((.....))))))))............)))))..))))-))))). ( -28.66)
>DroSim_CAF1 52516 119 + 1
UCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUACAAAUGUAUUUAAAAUGCAUUUAUUUUCUUUCCCAUGCAACAGGU-UGCAGG
...........(((((((((......(.((((((((((..........))))))))..)))(((((...((((((((.....))))))))............)))))..))))-))))). ( -28.66)
>DroEre_CAF1 57629 120 + 1
UCUUGAUUAAACUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUAGAAAAAUAUUUAAAAUGCAUUUAUUUUCUUUGCCAUGCAACAGGUUUGCAGG
...........(((((..........((((((((((((..........))))))))..(((((((((..(((....)))..))))))............)))........))))))))). ( -29.30)
>consensus
UCUUGAUUAAGCUGCAAUUUUCACACGACCGGCAGAUGCAUUUUCCCACAUCUGCCCAGGCUGCAUUACAAAUGUAUUUAAAAUGCAUUUAUUUUCUUUCCCAUGCAACAGGU_UGCAGG
...........(((((...........(((((((((((..........))))))))...(.(((((...((((((((.....))))))))............))))).).))).))))). (-24.35 = -24.66 +   0.31)

alignment

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secondary structure

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Window 6

Location 9,085,530 – 9,085,649
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.40
Mean single sequence MFE -37.20
Consensus MFE -33.30
Energy contribution -33.80
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -3.49
Structure conservation index 0.90
SVM decision value 1.76
SVM RNA-class probability 0.975822
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9085530 119 - 20766785
CCUGCA-ACCUGUUGCAUGGGAAUAAAAAUAAAUGCAUUUUAAAUACAUUUGUAAUGCAGCCUGGACAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGA
.(((((-(....(..(((((.............((((((.((((....)))).))))))..((((.((((((((......)))))))))))))))))..)...))))))........... ( -35.30)
>DroSec_CAF1 50303 119 - 1
CCUGCA-ACCUGUUGCAUGGGAAAGAAAAUAAAUGCAUUUAAAAUACAUUUGAAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGA
.(((((-(....(..((((..............(((((((.(((....))).)))))))(((..((((((((((......)))))))))))))))))..)...))))))........... ( -36.90)
>DroSim_CAF1 52516 119 - 1
CCUGCA-ACCUGUUGCAUGGGAAAGAAAAUAAAUGCAUUUUAAAUACAUUUGUAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGA
.(((((-(....(..((((..............((((((.((((....)))).))))))(((..((((((((((......)))))))))))))))))..)...))))))........... ( -37.00)
>DroEre_CAF1 57629 120 - 1
CCUGCAAACCUGUUGCAUGGCAAAGAAAAUAAAUGCAUUUUAAAUAUUUUUCUAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGUUUAAUCAAGA
.((((((.....(..((((((............((((((..(((....)))..)))))).....((((((((((......)))))))))).))))))..)...))))))........... ( -39.60)
>consensus
CCUGCA_ACCUGUUGCAUGGGAAAGAAAAUAAAUGCAUUUUAAAUACAUUUGUAAUGCAGCCUGGGCAGAUGUGGGAAAAUGCAUCUGCCGGUCGUGUGAAAAUUGCAGCUUAAUCAAGA
.(((((......(..(((((.............((((((.((((....)))).))))))..((((.((((((((......)))))))))))))))))..)....)))))........... (-33.30 = -33.80 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,085,570 – 9,085,689
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.17
Mean single sequence MFE -28.93
Consensus MFE -23.64
Energy contribution -24.70
Covariance contribution 1.06
Combinations/Pair 1.11
Mean z-score -1.66
Structure conservation index 0.82
SVM decision value 0.14
SVM RNA-class probability 0.602073
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9085570 119 - 20766785
AACCAGCAGAUGUUACGAAUCACACGAUGAUACGACUUUUCCUGCA-ACCUGUUGCAUGGGAAUAAAAAUAAAUGCAUUUUAAAUACAUUUGUAAUGCAGCCUGGACAGAUGUGGGAAAA
..((.(((..((((.((.((((.....)))).))...(((((((((-(....))))).)))))..........((((((.((((....)))).)))))).....))))..))).)).... ( -28.30)
>DroSec_CAF1 50343 119 - 1
AACUAGCAGAUGUUACGAAUCACACGAUGAUACGGCUUUUCCUGCA-ACCUGUUGCAUGGGAAAGAAAAUAAAUGCAUUUAAAAUACAUUUGAAAUGCAGCCUGGGCAGAUGUGGGAAAA
..((.(((..((((..(.((((.....)))).)(((((((((((((-(....))))).)))))).........(((((((.(((....))).))))))))))..))))..))).)).... ( -30.30)
>DroSim_CAF1 52556 119 - 1
AACCAGCAGAUGUUACGAAUCACACGAUGAUACGGCUUUUCCUGCA-ACCUGUUGCAUGGGAAAGAAAAUAAAUGCAUUUUAAAUACAUUUGUAAUGCAGCCUGGGCAGAUGUGGGAAAA
..((.(((..((((..(.((((.....)))).)(((((((((((((-(....))))).)))))).........((((((.((((....)))).)))))))))..))))..))).)).... ( -32.20)
>DroEre_CAF1 57669 120 - 1
AACCAGCAGAUGUUACGAGUCACACGAUUAUACGAUUCUUCCUGCAAACCUGUUGCAUGGCAAAGAAAAUAAAUGCAUUUUAAAUAUUUUUCUAAUGCAGCCUGGGCAGAUGUGGGAAAA
................(((((............)))))((((..((...(((((.((.(((............((((((..(((....)))..)))))))))))))))).))..)))).. ( -24.90)
>consensus
AACCAGCAGAUGUUACGAAUCACACGAUGAUACGACUUUUCCUGCA_ACCUGUUGCAUGGGAAAGAAAAUAAAUGCAUUUUAAAUACAUUUGUAAUGCAGCCUGGGCAGAUGUGGGAAAA
..((.(((..((((.((.((((.....)))).)).(((((((((((.......)))).)))))))........((((((.((((....)))).)))))).....))))..))).)).... (-23.64 = -24.70 +   1.06)

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 10:33:34 2006