Locus 3420

Sequence ID 2L_DroMel_CAF1
Location 9,903,831 – 9,903,973
Length 142
Max. P 0.851002
window5416 window5417 window5418

overview

Window 6

Location 9,903,831 – 9,903,949
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.53
Mean single sequence MFE -41.25
Consensus MFE -29.42
Energy contribution -29.57
Covariance contribution 0.14
Combinations/Pair 1.35
Mean z-score -1.66
Structure conservation index 0.71
SVM decision value 0.38
SVM RNA-class probability 0.711114
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9903831 118 - 22407834
ACUUUCAGAUUGAGUGCUUGUUUUAUGUUUUGACCUGUAUUGGCCAGGACAUGGAGCAGCAGUUGCCCCAGCAACUGGAGUUACUCAUGAGUCUGGUUCGCGAUGCCUUUUUGAAUGC
.....(((((((((((((((((((((((((((.((......)).)))))))))))))..(((((((....)))))))))).))))))...)))))(((((.((.....)).))))).. ( -41.60)
>DroVir_CAF1 116 118 - 1
AUUUGCAGAUUGAGUGCCUGUUCUAUGUUUUGACCUGCAUUGGCCAGGAUAUGGAGCAGCAGCUGCCGCAGCAGCUGGAGCUGCUCAUGUCCCUGGUGCGCGAUGCGUUCCUCAAUGC
....((((((((((((((((((((((((((((.((......)).)))))))))))))))(((((((....)))))))..)).))))).)))...((.((((...)))).))....))) ( -48.70)
>DroGri_CAF1 116 118 - 1
AUAUGAAGAUUGAGUGCCUGUUUUACGUUUUGACCUGCAUUGGACAGGACAUGGAGCAACAGCUGCCACAGCAAUUGGAGCUGCUCAUGUCCUUGGUGCGCGAUGCGUUUCUCAAUGC
........((((((..........((((.(((....((((..(...(((((((.((((...(((.(((.......))))))))))))))))))..)))).))).))))..)))))).. ( -35.70)
>DroMoj_CAF1 116 118 - 1
UUUUAUAGAUUGAGUCCUUAUUCUAUGUACUGACCUGCAUUGGUCAGGAUAUGGAGCAGCAGCUGCCGCAGCAGUUGGAGCAACUGAUGUCCGUGGUGCGCGAUGCGUUCCUCAAUGC
........((((((.......(((((((.((((((......)))))).)))))))(((...((((((((..((((((...))))))......)))))).))..)))....)))))).. ( -40.80)
>DroAna_CAF1 332 118 - 1
CCCUUUAGAUUGAGUGCCUUUUCUAUGUGCUCACCUGCAUCGGUCAGGAUAUGGAGCAGCAGCUGCCACAACAAUUGGAGCUACUUAUGGGCCUCGUUCGUGAUGCUUUUCUGAAUGC
...........(((.((((.((((((((.((.(((......))).)).)))))))).((.((((.(((.......))))))).))...)))))))(((((.((......))))))).. ( -32.20)
>DroPer_CAF1 2939 118 - 1
CGUUCCAGGUUGAGUGUCUGUUCUAUGUUCUAACCUGCAUUGGCCAGGACGUGGAGCAGCAGCUGCCCCAGCAGCUGGAGCUGCUCAUGAGCCUCGUGCGCGAUGCCUUCUUGAAUGC
(((((.((((...((((((((((((((((((..((......))..))))))))))))))(((((((....)))))))(((..(((....))))))..))))...))))....))))). ( -48.50)
>consensus
AUUUGCAGAUUGAGUGCCUGUUCUAUGUUCUGACCUGCAUUGGCCAGGACAUGGAGCAGCAGCUGCCACAGCAACUGGAGCUACUCAUGUCCCUGGUGCGCGAUGCGUUCCUCAAUGC
..........((((((((((((((((((((((.((......)).)))))))))))))))(((((((....)))))))..)).)))))............................... (-29.42 = -29.57 +   0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,903,871 – 9,903,973
Length 102
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 81.53
Mean single sequence MFE -27.72
Consensus MFE -20.53
Energy contribution -21.03
Covariance contribution 0.50
Combinations/Pair 1.24
Mean z-score -2.06
Structure conservation index 0.74
SVM decision value 0.77
SVM RNA-class probability 0.846646
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9903871 102 + 22407834
CCAGUUGCUGGGGCAACUGCUGCUCCAUGUCCUGGCCAAUACAGGUCAAAACAUAAAACAAGCACUCAAUCUGAAAGUU-AUGAAU------AGUAA----UCACAUGUAUUA-
.(((.((((((((((.....))))))((((..(((((......)))))..))))......))))......)))...(((-((....------.))))----)...........- ( -22.70)
>DroGri_CAF1 156 106 + 1
CCAAUUGCUGUGGCAGCUGUUGCUCCAUGUCCUGUCCAAUGCAGGUCAAAACGUAAAACAGGCACUCAAUCUUCAUAUGCAAGAAUUA----AAUAA----AUAAAUGGAAUAC
(((..((((((((.(((....)))))))(.(((((.....))))).).............)))).....(((((....).))))....----.....----.....)))..... ( -21.50)
>DroSec_CAF1 156 101 + 1
CCAGUUGCUGGGGCAGUUGCUGCUCCAUGUCCUGGCCAAUACAGGUCAGUACAUAGAACAGGCACUCAAUCUGCAUGUU-AAUAAU------AGUAA----UUA-AUGUUUUA-
..((((((((((((((...)))))))((((.((((((......)))))).))))..((((.(((.......))).))))-......------)))))----)).-........- ( -31.80)
>DroSim_CAF1 156 102 + 1
CCAGUUGCUGGGGCAGCUGCUGCUCCAUGUCCUGGCCAAUACAGGUCAGUACAUAGAACAGGCACUCAAUCUGAAUGUU-AAGAAU------GGUAA----UCAUAUGUAUUA-
.(((((((....)))))))(((.((.((((.((((((......)))))).)))).)).)))..((.((.(((.......-.))).)------)))..----............- ( -30.40)
>DroEre_CAF1 156 111 + 1
CCAGUUGCUGGGGCAGCUGCUGCUCCAUGUCCUGGCCAAUACAGGUUAGUACAUAGAACAGGCACUCAAUCUGAAAAUU-AAGAAU-AUAAUCGUAGUUAUGUAUGUAUAUUA-
.(((((((....)))))))(((.((.((((.((((((......)))))).)))).)).)))(((.....(((.......-.)))((-(((((....))))))).)))......- ( -29.40)
>DroYak_CAF1 156 107 + 1
CCAGUUGCUGUGGCAGCUGCUGUUCCAUGUCCUGGCCAAUACAAGUCAGUACAUAGAACAGGCACUCAAUCUGAAAGUU-AAGAUU-ACAAUAAUAA----GUAUGUAUAUUA-
.(((((((....)))))))((((((.((((.(((((........))))).)))).))))))......(((((.......-.)))))-..........----............- ( -30.50)
>consensus
CCAGUUGCUGGGGCAGCUGCUGCUCCAUGUCCUGGCCAAUACAGGUCAGUACAUAGAACAGGCACUCAAUCUGAAAGUU_AAGAAU______AGUAA____UUAUAUGUAUUA_
.....(((((((((((...)))))))((((.((((((......)))))).))))......)))).................................................. (-20.53 = -21.03 +   0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,903,871 – 9,903,973
Length 102
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 81.53
Mean single sequence MFE -27.98
Consensus MFE -23.15
Energy contribution -22.98
Covariance contribution -0.16
Combinations/Pair 1.24
Mean z-score -1.84
Structure conservation index 0.83
SVM decision value 0.79
SVM RNA-class probability 0.851002
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9903871 102 - 22407834
-UAAUACAUGUGA----UUACU------AUUCAU-AACUUUCAGAUUGAGUGCUUGUUUUAUGUUUUGACCUGUAUUGGCCAGGACAUGGAGCAGCAGUUGCCCCAGCAACUGG
-.......(((((----.....------..))))-)((((.......))))..(((((((((((((((.((......)).)))))))))))))))(((((((....))))))). ( -31.50)
>DroGri_CAF1 156 106 - 1
GUAUUCCAUUUAU----UUAUU----UAAUUCUUGCAUAUGAAGAUUGAGUGCCUGUUUUACGUUUUGACCUGCAUUGGACAGGACAUGGAGCAACAGCUGCCACAGCAAUUGG
...((((((....----.((((----((((..((......))..))))))))(((((((...((........))...)))))))..))))))(((..((((...))))..))). ( -22.50)
>DroSec_CAF1 156 101 - 1
-UAAAACAU-UAA----UUACU------AUUAUU-AACAUGCAGAUUGAGUGCCUGUUCUAUGUACUGACCUGUAUUGGCCAGGACAUGGAGCAGCAACUGCCCCAGCAACUGG
-........-...----.....------......-.....((((.(((.....(((((((((((.(((.((......)).))).)))))))))))))))))).((((...)))) ( -28.70)
>DroSim_CAF1 156 102 - 1
-UAAUACAUAUGA----UUACC------AUUCUU-AACAUUCAGAUUGAGUGCCUGUUCUAUGUACUGACCUGUAUUGGCCAGGACAUGGAGCAGCAGCUGCCCCAGCAACUGG
-............----.....------......-..(((((.....))))).(((((((((((.(((.((......)).))).)))))))))))(((.(((....))).))). ( -30.60)
>DroEre_CAF1 156 111 - 1
-UAAUAUACAUACAUAACUACGAUUAU-AUUCUU-AAUUUUCAGAUUGAGUGCCUGUUCUAUGUACUAACCUGUAUUGGCCAGGACAUGGAGCAGCAGCUGCCCCAGCAACUGG
-..........................-...(((-((((....)))))))...(((((((((((.((..((......))..)).)))))))))))(((.(((....))).))). ( -26.80)
>DroYak_CAF1 156 107 - 1
-UAAUAUACAUAC----UUAUUAUUGU-AAUCUU-AACUUUCAGAUUGAGUGCCUGUUCUAUGUACUGACUUGUAUUGGCCAGGACAUGGAACAGCAGCUGCCACAGCAACUGG
-.....((((...----.......)))-).....-......(((......(((.((((((((((.(((.((......)).))).)))))))))))))((((...))))..))). ( -27.80)
>consensus
_UAAUACAUAUAA____UUACU______AUUCUU_AACAUUCAGAUUGAGUGCCUGUUCUAUGUACUGACCUGUAUUGGCCAGGACAUGGAGCAGCAGCUGCCCCAGCAACUGG
.........................................(((......(((.((((((((((.(((.((......)).))).)))))))))))))((((...))))..))). (-23.15 = -22.98 +  -0.16)

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 10:52:08 2006