Locus 7726

Sequence ID 3L_DroMel_CAF1
Location 20,619,503 – 20,619,622
Length 119
Max. P 0.962142
window12575 window12576 window12577 window12578

overview

Window 5

Location 20,619,503 – 20,619,603
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 99.00
Mean single sequence MFE -33.68
Consensus MFE -33.84
Energy contribution -33.90
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -3.07
Structure conservation index 1.00
SVM decision value 1.52
SVM RNA-class probability 0.960998
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20619503 100 + 23771897
GGGCUAAAAACUUAAAAGCCAGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUG
.((((...........))))...........((((.(((..(((((((.(((((.(.....).)))))....)))))))..))).))))........... ( -35.10)
>DroSec_CAF1 64277 100 + 1
GGGCUAAAAACUUAAAAGCCAGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUG
.((((...........))))...........((((.(((..(((((((.(((((.(.....).)))))....)))))))..))).))))........... ( -35.10)
>DroSim_CAF1 59185 100 + 1
GGGCUAAAAACUUAAAAGCCAGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUG
.((((...........))))...........((((.(((..(((((((.(((((.(.....).)))))....)))))))..))).))))........... ( -35.10)
>DroEre_CAF1 56843 100 + 1
GGGCUAAAAACUUAAAAGCCAGCAAACAAAACGCUGCUCUGCAUCUUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUG
.((((...........))))...........((((.(((..(((((...(((((.(.....).))))).....)).)))..))).))))........... ( -29.40)
>consensus
GGGCUAAAAACUUAAAAGCCAGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUG
.((((...........))))...........((((.(((..(((((((.(((((.(.....).)))))....)))))))..))).))))........... (-33.84 = -33.90 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,619,503 – 20,619,603
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 99.00
Mean single sequence MFE -28.23
Consensus MFE -28.21
Energy contribution -28.28
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.34
Structure conservation index 1.00
SVM decision value 1.04
SVM RNA-class probability 0.904546
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20619503 100 - 23771897
CAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCUGGCUUUUAAGUUUUUAGCCC
((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..))..((((...........)))). ( -29.30)
>DroSec_CAF1 64277 100 - 1
CAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCUGGCUUUUAAGUUUUUAGCCC
((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..))..((((...........)))). ( -29.30)
>DroSim_CAF1 59185 100 - 1
CAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCUGGCUUUUAAGUUUUUAGCCC
((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..))..((((...........)))). ( -29.30)
>DroEre_CAF1 56843 100 - 1
CAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAAGAUGCAGAGCAGCGUUUUGUUUGCUGGCUUUUAAGUUUUUAGCCC
((..((....(((((.(((..(((.((......((((((.....))))))....)))))..))).)))))..))..))..((((...........)))). ( -25.00)
>consensus
CAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCUGGCUUUUAAGUUUUUAGCCC
((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..))..((((...........)))). (-28.21 = -28.28 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,619,523 – 20,619,622
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.66
Mean single sequence MFE -35.87
Consensus MFE -27.40
Energy contribution -29.44
Covariance contribution 2.04
Combinations/Pair 1.04
Mean z-score -2.28
Structure conservation index 0.76
SVM decision value 1.54
SVM RNA-class probability 0.962142
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20619523 99 + 23771897
AGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUGCUGUAUGCUGG---------------------ACCGGGAA
((((.(((....(((.(((..(((((((.(((((.(.....).)))))....)))))))..))).)))(((.......)))))).))))..---------------------........ ( -35.80)
>DroSec_CAF1 64297 99 + 1
AGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUGCUGCAUGCUGG---------------------ACCGGGAA
((((..((...((((.(((..(((((((.(((((.(.....).)))))....)))))))..))).)))).....))..)))).........---------------------........ ( -35.60)
>DroAna_CAF1 86046 111 + 1
AGCAAACAAAACGCUGCUC-GCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGA--------GAGAGGGAGGCUGUGUCGCGGAUGAUGAUGGUGACGUGCCCUCCAUGCAA
.(((.......(.((.(((-((((((((.(((((.(.....).)))))....))))))))))--------))).)(((((.(..(((((...........)))))..).))))).))).. ( -42.30)
>DroSim_CAF1 59205 99 + 1
AGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUGCUGCAUGCUGG---------------------ACCGGGAA
((((..((...((((.(((..(((((((.(((((.(.....).)))))....)))))))..))).)))).....))..)))).........---------------------........ ( -35.60)
>DroEre_CAF1 56863 94 + 1
AGCAAACAAAACGCUGCUCUGCAUCUUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUGCUG-----UGG---------------------ACCGGGCA
.((........(((.((..(.(((((((((((.((((((....)).(((......))).))).).))))))))))).).)).)-----)).---------------------.....)). ( -30.04)
>consensus
AGCAAACAAAACGCUGCUCUGCAUUCUGUGCUGCCCAGCUAGAGCAGUUAAUUAGAAUGUGGAGGAGCGCGAGAUGGAUGCUGCAUGCUGG_____________________ACCGGGAA
((((..((...((((.((((((((((((.(((((.(.....).)))))....)))))))))))).)))).....))..))))...................................... (-27.40 = -29.44 +   2.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,619,523 – 20,619,622
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.66
Mean single sequence MFE -29.48
Consensus MFE -22.68
Energy contribution -24.36
Covariance contribution 1.68
Combinations/Pair 1.08
Mean z-score -2.00
Structure conservation index 0.77
SVM decision value 1.01
SVM RNA-class probability 0.900687
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20619523 99 - 23771897
UUCCCGGU---------------------CCAGCAUACAGCAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCU
........---------------------.........((((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..)))) ( -30.40)
>DroSec_CAF1 64297 99 - 1
UUCCCGGU---------------------CCAGCAUGCAGCAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCU
........---------------------.........((((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..)))) ( -30.40)
>DroAna_CAF1 86046 111 - 1
UUGCAUGGAGGGCACGUCACCAUCAUCAUCCGCGACACAGCCUCCCUCUC--------UCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGC-GAGCAGCGUUUUGUUUGCU
..(((.((..(((..(((.(...........).)))...)))..))....--------...............((((((.....)))))).(((((((((-.....))))))))).))). ( -30.10)
>DroSim_CAF1 59205 99 - 1
UUCCCGGU---------------------CCAGCAUGCAGCAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCU
........---------------------.........((((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..)))) ( -30.40)
>DroEre_CAF1 56863 94 - 1
UGCCCGGU---------------------CCA-----CAGCAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAAGAUGCAGAGCAGCGUUUUGUUUGCU
........---------------------...-----.((((..((....(((((.(((..(((.((......((((((.....))))))....)))))..))).)))))..))..)))) ( -26.10)
>consensus
UUCCCGGU_____________________CCAGCAUACAGCAUCCAUCUCGCGCUCCUCCACAUUCUAAUUAACUGCUCUAGCUGGGCAGCACAGAAUGCAGAGCAGCGUUUUGUUUGCU
......................................((((..((....(((((.(((..((((((......((((((.....))))))...))))))..))).)))))..))..)))) (-22.68 = -24.36 +   1.68)

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 12:55:13 2006