Locus 408

Sequence ID X_DroMel_CAF1
Location 1,186,961 – 1,187,222
Length 261
Max. P 0.876027
window627 window628 window629

overview

Window 7

Location 1,186,961 – 1,187,071
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 89.09
Mean single sequence MFE -38.43
Consensus MFE -33.17
Energy contribution -32.73
Covariance contribution -0.43
Combinations/Pair 1.17
Mean z-score -2.35
Structure conservation index 0.86
SVM decision value 0.89
SVM RNA-class probability 0.876027
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1186961 110 + 22224390
CAUCGCCAUCUUUCUGCUUGCCACUCUCGGUGGUGACAUUUUCCACGCUCUGACGCCUUUCUUUCAGAGUCUCAUCUUGGCCACUCUGAAGGGACUGCAGAUAGGCGGCG
...((((..((.((((((..((((.....))))..)..........((......))..((((((((((((..(......)..))))))))))))..))))).))..)))) ( -38.90)
>DroSec_CAF1 22841 110 + 1
CAUCGCCAUCUUUCUGCUUACCACUCUCGGUGGUGACAUUUUCCACGCUUUGACGCCUUGCUUUCAGAGUCUCAUCUUGGCCACUCUGAAGGGACUGCAGAUAGGCGGCG
...((((..((.((((((((((((.....)))))))....((((..((......))......((((((((..(......)..))))))))))))..))))).))..)))) ( -38.30)
>DroEre_CAF1 22188 110 + 1
CCUCACCAUCCCUCUGCUUGCCACUCUCCGUGGUGACAUUUGCCACGCUCUGCCGCCUCGCCUUCAGGGUCUCGUCUUGCCCAUUCUGAAGGGACUGCAGGUAGGCGGCA
..................((((.......((((..(...)..))))((.(((((((.((.((((((((((........))))....))))))))..)).))))))))))) ( -38.10)
>consensus
CAUCGCCAUCUUUCUGCUUGCCACUCUCGGUGGUGACAUUUUCCACGCUCUGACGCCUUGCUUUCAGAGUCUCAUCUUGGCCACUCUGAAGGGACUGCAGAUAGGCGGCG
....(((..((.((((((((((((.....)))))))..........((......))....((((((((((............))))))))))....))))).))..))). (-33.17 = -32.73 +  -0.43) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,187,071 – 1,187,185
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.20
Mean single sequence MFE -42.98
Consensus MFE -31.61
Energy contribution -30.92
Covariance contribution -0.69
Combinations/Pair 1.27
Mean z-score -1.60
Structure conservation index 0.74
SVM decision value 0.20
SVM RNA-class probability 0.628825
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1187071 114 + 22224390
UCUGGAUUGGGCCUUGGACUUGAUGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU------
....((((.(((....(((.....)))((((..((..(((((((..(((((.....)))))...((((((......)))))).))))))).))..))))..)))..))))....------ ( -39.90)
>DroSec_CAF1 22951 114 + 1
UCUGGAUUGGGCCUCGGACUCGACGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUUAGGCGCUGCAGCUCGCUGAGAUUGCUU------
(((((........)))))((((.((..((((..((..(((((((..(((((.....)))))...((((((......)))))).))))))).))..)))).)).)))).......------ ( -39.00)
>DroEre_CAF1 22298 114 + 1
UCUGGAUUGGGUAUCGCAGUUGACGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGAAGCUCGCUAAGAUUGCUU------
..(((((..(((((((((((.......))))))).))))..)))))(((((.....)))))...(((((.(((((.((..(((..((((...))))))))).))))))))))..------ ( -45.70)
>DroAna_CAF1 7583 114 + 1
UCCGGACUGGGCGUGGGAGU-GACCACCU-----UGACCUUGUCCAGGCUCACGUUGAGCUGCUGCAGCUCCUGGAGGUUACUGAUCAGACGCUGCAGUUCGCUCAGGUUGCCGCCACUG
...((((.((((((((....-..))))..-----.).))).)))).(((..((.((((((.((((((((..((((((....))..))))..))))))))..)))))))).)))....... ( -47.30)
>consensus
UCUGGAUUGGGCCUCGGACUUGACGUCGCUGUGGUUACCUGGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU______
...((((..((.........((....)).........))..)))).(((((.....)))))((((((((.(((((((....))..))))).))))))))..((.......))........ (-31.61 = -30.92 +  -0.69) 

alignment

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secondary structure

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dotplot

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Window 9

Location 1,187,111 – 1,187,222
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.10
Mean single sequence MFE -41.12
Consensus MFE -27.99
Energy contribution -29.43
Covariance contribution 1.44
Combinations/Pair 1.20
Mean z-score -1.60
Structure conservation index 0.68
SVM decision value 0.06
SVM RNA-class probability 0.562185
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1187111 111 + 22224390
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU---------UUGGAGUCAUCCCUUUUUUCCUUGGGUGCCUCGGGCU
(((((.(((((.....)))))((((((((.(((((((....))..))))).))))))))..((.......))..---------...(((.((.(((..........))))).)))))))) ( -37.30)
>DroSec_CAF1 22991 111 + 1
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUUAGGCGCUGCAGCUCGCUGAGAUUGCUU---------UUGGAGUCAUCCCUUUUUUCCUUGGGUGCCUCGGGCU
(((((((((((.((.((((((((.((...((.....))..(((.....))))).)))))))).)).))..))))---------...(((.((.(((..........))))).)))))))) ( -37.00)
>DroEre_CAF1 22338 111 + 1
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGAAGCUCGCUAAGAUUGCUU---------GUGGAGUCAUCCCGUUUUUUCUUGGCUGUCUCGGGCU
((((..(((((.....)))))...((((((......)))))).)))).(((.((((..(..(((((((..(..(---------(.(((....)))))..)..))))))).)..))))))) ( -36.70)
>DroAna_CAF1 7617 114 + 1
UGUCCAGGCUCACGUUGAGCUGCUGCAGCUCCUGGAGGUUACUGAUCAGACGCUGCAGUUCGCUCAGGUUGCCGCCACUGGCGGGGGAGUUCUCCCGCUUCUCCUUGGGCGUC------U
.((((((((..((.((((((.((((((((..((((((....))..))))..))))))))..)))))))).)))......((((((((....))))))))......)))))...------. ( -53.50)
>consensus
GGUCCAAGCUCACAUUGAGCUGUUGCAGUUCUUGGAGAUUGCUGAUCAGGCGCUGCAGCUCGCUGAGAUUGCUU_________GUGGAGUCAUCCCGUUUUUCCUUGGGUGCCUCGGGCU
(((((.(((((.....)))))((((((((.(((((((....))..))))).))))))))..((.......))..............(((.(((((...........))))).)))))))) (-27.99 = -29.43 +   1.44) 

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 09:43:54 2006