Locus 3691

Sequence ID X_DroMel_CAF1
Location 9,839,453 – 9,839,610
Length 157
Max. P 0.854560
window6042 window6043 window6044 window6045

overview

Window 2

Location 9,839,453 – 9,839,553
Length 100
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 78.51
Mean single sequence MFE -31.77
Consensus MFE -11.77
Energy contribution -12.30
Covariance contribution 0.53
Combinations/Pair 1.18
Mean z-score -2.58
Structure conservation index 0.37
SVM decision value 0.21
SVM RNA-class probability 0.637014
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9839453 100 - 22224390
AAACAAUGCUAAAAACUGGCCAGCUCUCUGGACGAAUA-----G-UUUCGGCUAACAAAUUAGCA-GGGGGCUGGGUGUACGGGGUGCUAAUUG-CCGACACAGUGAU
.......(((.........((((((((((...((((..-----.-.))))(((((....))))))-)))))))))((((.(((.(.......).-))))))))))... ( -34.10)
>DroPse_CAF1 8023 95 - 1
AAACAAUGCUAAAA-----------CGCAGACCGAACAAAAGAGUUUUUGGGUAACAAAUUAGCACAGGGGCUGGC--CAGGGAGUGUUAAUUGGCCAGCACAAUGGU
......((((((..-----------.....(((((((......))))...)))......))))))((..(((((((--(((..........))))))))).)..)).. ( -27.12)
>DroSec_CAF1 1159 100 - 1
AAACAAUGCUAAAAACUGGCAAGCUCUCUAGCCGAAUA-----G-UUUCGGCUAACAAAUUAGCA-GGGGGCUGGGUGUACGGGGUGCUAAUUG-CCGACACAUUGAU
...((((((((.....)))).(((((((((((((((..-----.-.)))))))...........)-)))))))..((((.(((.(.......).-))))))))))).. ( -32.30)
>DroSim_CAF1 1358 100 - 1
AAACAAUGCUAAAAACUGGCCAGCUCUCUGGCCGAAUA-----G-UUUCGGCUAACAAAUUAGCA-GGGGGCUGGGUGUACGGGGUGCUAAUUG-CCGACACAGUGAU
.......(((.........(((((((((((((((((..-----.-.))))))(((....))).))-)))))))))((((.(((.(.......).-))))))))))... ( -36.50)
>DroEre_CAF1 1147 96 - 1
AAACAAUGCUA--AACUGGCCAGCUCUCUGGCCGAAUA-----G-U-UCGGCUAACAAAUUAGCA-GGGGGCUGGGUGUACGG-GUGCUAAUUG-CCGACACAGUGAU
.......(((.--......((((((((((((((((...-----.-.-)))))(((....))).))-)))))))))((((.(((-..........-))))))))))... ( -33.50)
>DroPer_CAF1 8178 95 - 1
AAACAAUGCUAAAA-----------CGCAGACCGAACAAAAGAGUUUUUGGGUAACAAAUUAGCACAGGGGCUGGC--CAGGUAGUGUUAAUUGGCCAGCACAAUGGU
......((((((..-----------.....(((((((......))))...)))......))))))((..(((((((--(((..........))))))))).)..)).. ( -27.12)
>consensus
AAACAAUGCUAAAAACUGGCCAGCUCUCUGGCCGAAUA_____G_UUUCGGCUAACAAAUUAGCA_GGGGGCUGGGUGUACGGGGUGCUAAUUG_CCGACACAGUGAU
...((.((....................((((((((..........))))))))...((((((((.....((.....))......))))))))........)).)).. (-11.77 = -12.30 +   0.53)

alignment

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secondary structure

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Window 3

Location 9,839,492 – 9,839,591
Length 99
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 82.25
Mean single sequence MFE -22.43
Consensus MFE -13.39
Energy contribution -14.25
Covariance contribution 0.86
Combinations/Pair 1.04
Mean z-score -2.02
Structure conservation index 0.60
SVM decision value 0.03
SVM RNA-class probability 0.547549
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9839492 99 + 22224390
CC-UGCUAAUUUGUUAGCCGAAA-C-----UAUUCGUCCAGAGAGCUGGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU--UAUGGCUUUCACUUUGUGCAACAAAUUU
..-....((((((((.((((((.-.-----..))))..(((((.(..(((((.......((((......)))).....--..)))))..).))))).)))))))))). ( -22.34)
>DroPse_CAF1 8061 97 + 1
CUGUGCUAAUUUGUUACCCAAAAACUCUUUUGUUCGGUCUGCG-----------UUUUAGCAUUGUUUUAUGUCAAUUUCUGUGGCUUUCACUUUGUGCAACAAAUUU
..(((((((..(((.((((((((....)))))...)))..)))-----------..))))))).......((((((.....(((.....))).))).)))........ ( -16.00)
>DroSec_CAF1 1198 99 + 1
CC-UGCUAAUUUGUUAGCCGAAA-C-----UAUUCGGCUAGAGAGCUUGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU--UAUGGCUUUCACUUUGUGCAACAAAUUU
..-....(((((((((((((((.-.-----..))))))).(((((((....))))))).((((.((.....(((((..--.)))))....))...)))))))))))). ( -24.40)
>DroSim_CAF1 1397 99 + 1
CC-UGCUAAUUUGUUAGCCGAAA-C-----UAUUCGGCCAGAGAGCUGGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU--UAUGGCUUUCACUUUGUGCAACAAAUUU
..-....((((((((.((((((.-.-----..))))))(((((.(..(((((.......((((......)))).....--..)))))..).)))))...)))))))). ( -27.14)
>DroEre_CAF1 1185 96 + 1
CC-UGCUAAUUUGUUAGCCGA-A-C-----UAUUCGGCCAGAGAGCUGGCCAGUU--UAGCAUUGUUUUAUGUCAUAU--UUUGGCUUUCACUUUGUGCAACAAAUUU
..-((((((..((..((((((-(-.-----(((..((((((....))))))....--..((((......)))).))).--)))))))..))..))).)))........ ( -27.80)
>DroPer_CAF1 8216 97 + 1
CUGUGCUAAUUUGUUACCCAAAAACUCUUUUGUUCGGUCUGCG-----------UUUUAGCAUUGUUUUAUGUCAAUUUCUGUGACUUUCACUUUGUGCAACAAAUUU
..(((((((..(((.((((((((....)))))...)))..)))-----------..))))))).......((((((.....(((.....))).))).)))........ ( -16.90)
>consensus
CC_UGCUAAUUUGUUAGCCGAAA_C_____UAUUCGGCCAGAGAGCUGGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU__UAUGGCUUUCACUUUGUGCAACAAAUUU
.......((((((((.((((((..........)))))).....................((((.((.....((((.......))))....))...)))))))))))). (-13.39 = -14.25 +   0.86)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,839,515 – 9,839,610
Length 95
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 81.84
Mean single sequence MFE -22.82
Consensus MFE -15.99
Energy contribution -17.72
Covariance contribution 1.72
Combinations/Pair 1.08
Mean z-score -2.37
Structure conservation index 0.70
SVM decision value 0.80
SVM RNA-class probability 0.854560
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9839515 95 + 22224390
--UAUUCGUCCAGAGAGCUGGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU--UAUGGCUUUCACUUUGUGCAACAAAUUUGCACAAAUCUCCGAAAUCG
--..((((....(((((..(((((.......((((......)))).....--..)))))..)..(((((((((.....))))))))))))))))).... ( -24.64)
>DroPse_CAF1 8089 86 + 1
UUUGUUCGGUCUGCG-----------UUUUAGCAUUGUUUUAUGUCAAUUUCUGUGGCUUUCACUUUGUGCAACAAAUUUGCACAAAUGUCUGGUCU--
...........(((.-----------.....))).....................((((..((.(((((((((.....)))))))))))...)))).-- ( -16.80)
>DroSec_CAF1 1221 95 + 1
--UAUUCGGCUAGAGAGCUUGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU--UAUGGCUUUCACUUUGUGCAACAAAUUUGCACAAAUCUCCGAAAUCG
--..(((((..((((((...((((.......((((......)))).....--..)))).)))..(((((((((.....))))))))))))))))).... ( -25.14)
>DroSim_CAF1 1420 95 + 1
--UAUUCGGCCAGAGAGCUGGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU--UAUGGCUUUCACUUUGUGCAACAAAUUUGCACAAAUCUCCGAAAUCG
--..(((((..((((((..(((((.......((((......)))).....--..))))))))..(((((((((.....))))))))))))))))).... ( -26.14)
>DroEre_CAF1 1207 93 + 1
--UAUUCGGCCAGAGAGCUGGCCAGUU--UAGCAUUGUUUUAUGUCAUAU--UUUGGCUUUCACUUUGUGCAACAAAUUUGCACAAAUCUCCGAAAUCG
--..(((((..((((((..((((((..--((((((......))))..)).--.)))))))))..(((((((((.....))))))))))))))))).... ( -26.80)
>DroPer_CAF1 8244 86 + 1
UUUGUUCGGUCUGCG-----------UUUUAGCAUUGUUUUAUGUCAAUUUCUGUGACUUUCACUUUGUGCAACAAAUUUGCACAAAUGUCUGGUCU--
...........(((.-----------.....))).....................((((..((.(((((((((.....)))))))))))...)))).-- ( -17.40)
>consensus
__UAUUCGGCCAGAGAGCUGGCCAGUUUUUAGCAUUGUUUUAUGUCAUAU__UAUGGCUUUCACUUUGUGCAACAAAUUUGCACAAAUCUCCGAAAUCG
....(((((...(((((((............((((......))))..........)))))))..(((((((((.....)))))))))...))))).... (-15.99 = -17.72 +   1.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,839,515 – 9,839,610
Length 95
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 81.84
Mean single sequence MFE -20.42
Consensus MFE -11.88
Energy contribution -13.38
Covariance contribution 1.50
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.58
SVM decision value 0.20
SVM RNA-class probability 0.628751
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9839515 95 - 22224390
CGAUUUCGGAGAUUUGUGCAAAUUUGUUGCACAAAGUGAAAGCCAUA--AUAUGACAUAAAACAAUGCUAAAAACUGGCCAGCUCUCUGGACGAAUA--
....(((((((((((((((((.....)))))))))((....((((..--....(.(((......)))).......))))..))))))))))......-- ( -23.62)
>DroPse_CAF1 8089 86 - 1
--AGACCAGACAUUUGUGCAAAUUUGUUGCACAAAGUGAAAGCCACAGAAAUUGACAUAAAACAAUGCUAAAA-----------CGCAGACCGAACAAA
--....(((...(((((((((.....)))))))))(((.....))).....)))...........(((.....-----------.)))........... ( -14.20)
>DroSec_CAF1 1221 95 - 1
CGAUUUCGGAGAUUUGUGCAAAUUUGUUGCACAAAGUGAAAGCCAUA--AUAUGACAUAAAACAAUGCUAAAAACUGGCAAGCUCUCUAGCCGAAUA--
....(((((...(((((((((.....)))))))))..((.((((((.--..)))...........(((((.....))))).))).))...)))))..-- ( -22.20)
>DroSim_CAF1 1420 95 - 1
CGAUUUCGGAGAUUUGUGCAAAUUUGUUGCACAAAGUGAAAGCCAUA--AUAUGACAUAAAACAAUGCUAAAAACUGGCCAGCUCUCUGGCCGAAUA--
....(((((...(((((((((.....))))))))).......))...--...........................((((((....)))))))))..-- ( -23.40)
>DroEre_CAF1 1207 93 - 1
CGAUUUCGGAGAUUUGUGCAAAUUUGUUGCACAAAGUGAAAGCCAAA--AUAUGACAUAAAACAAUGCUA--AACUGGCCAGCUCUCUGGCCGAAUA--
....(((((...(((((((((.....))))))))).......))...--.....................--....((((((....)))))))))..-- ( -23.40)
>DroPer_CAF1 8244 86 - 1
--AGACCAGACAUUUGUGCAAAUUUGUUGCACAAAGUGAAAGUCACAGAAAUUGACAUAAAACAAUGCUAAAA-----------CGCAGACCGAACAAA
--.......((.(((((((((.....)))))))))))....((((.(....))))).........(((.....-----------.)))........... ( -15.70)
>consensus
CGAUUUCGGAGAUUUGUGCAAAUUUGUUGCACAAAGUGAAAGCCAUA__AUAUGACAUAAAACAAUGCUAAAAACUGGCCAGCUCUCUGGCCGAAUA__
......(((((((((((((((.....)))))))))(((.....))).....................................)))))).......... (-11.88 = -13.38 +   1.50)

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 11:05:46 2006