Locus 5574

Sequence ID 3R_DroMel_CAF1
Location 14,739,417 – 14,739,547
Length 130
Max. P 0.849199
window9084 window9085

overview

Window 4

Location 14,739,417 – 14,739,516
Length 99
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 79.84
Mean single sequence MFE -28.98
Consensus MFE -19.52
Energy contribution -19.40
Covariance contribution -0.12
Combinations/Pair 1.24
Mean z-score -1.63
Structure conservation index 0.67
SVM decision value 0.19
SVM RNA-class probability 0.626388
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14739417 99 - 27905053
UAGCUGGCUGGCUGGCUUAAAUUAGCCGGCCGAUGAUUCAUUUUGGGGGUUGUCCACUUACAUAAGAUG-AGCU-CACCCAAUGUGAAAACUCUUUAGUCG
.....((((((((((((......)))))))).....(((((.(((((....(..(((((....))).))-..).-..))))).)))))........)))). ( -34.50)
>DroSec_CAF1 6333 88 - 1
UAGCUG-CUGGCUGGCUAAAAUUAGCCGGCCGAUGACUCAUUUUGGGGGUUGUCCACUUACAUAAGAGC-UGCUUUACCCA-----------CUUAAGUCG
.(((.(-(((((((((((....)))))))))((..((((.......))))..))............)))-.))).......-----------......... ( -30.40)
>DroSim_CAF1 6921 88 - 1
UAGCUG-CUGGCUGGCUAAAAUUAGCCGGCCGAUGAUUCAUUUUGGGGGUUGUCCACUUACAUAAGAGC-UGCUUUACCCA-----------CUUUAGUCG
.(((.(-(((((((((((....)))))))))((..((((.......))))..))............)))-.))).......-----------......... ( -28.00)
>DroEre_CAF1 6630 97 - 1
UAGCUG-CUGCCUGGUUCAAAAAAGCCGGCCGAUGAUUCAUUUGGGGGGUUGUCCACUUACAUCAGAGC-UUCU-GACCCACC-AUGACACGCGUUACCCG
((((.(-(.(((.((((......))))))).......((((.((((.((....)).......((((...-..))-))))))..-))))...)))))).... ( -22.90)
>DroYak_CAF1 6413 99 - 1
UUCCUG-CUGGCUGGCUAAAAUUAGUCGGCCAAUGAUUCAUUUUGGGGGUUGUCCACUUACAUAAGAGCCUUCU-AACCCACUGAUGACACGUAUUAGGCG
..((((-.((((((((((....))))))))))(((..(((((....((((((....(((......))).....)-)))))...)))))..)))..)))).. ( -29.10)
>consensus
UAGCUG_CUGGCUGGCUAAAAUUAGCCGGCCGAUGAUUCAUUUUGGGGGUUGUCCACUUACAUAAGAGC_UGCU_UACCCA______A_AC_CUUUAGUCG
..((((..(((((((((......)))))))))............(((((....)).(((....)))...........)))...............)))).. (-19.52 = -19.40 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,739,451 – 14,739,547
Length 96
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 80.53
Mean single sequence MFE -30.95
Consensus MFE -20.12
Energy contribution -20.93
Covariance contribution 0.81
Combinations/Pair 1.32
Mean z-score -2.10
Structure conservation index 0.65
SVM decision value 0.78
SVM RNA-class probability 0.849199
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14739451 96 - 27905053
-----GUGCAGGGCAAAAAGGGGGUGGCUUAAACUGUAGCUG-GCU-GGCUGGCUUAAAUUAGCCGGCCGAUGAUUCAUUUUG-GGGGUUGUCCACUUACAUAA
-----.....((((((.....((.(((((........)))))-.))-((((((((......))))))))..............-....)))))).......... ( -30.40)
>DroSec_CAF1 6357 94 - 1
-----AUGUAGGUCAAAAAGG-GGUCACUUAAGCUGUAGCUG--CU-GGCUGGCUAAAAUUAGCCGGCCGAUGACUCAUUUUG-GGGGUUGUCCACUUACAUAA
-----(((((((((((((..(-(((((....(((....))).--.(-(((((((((....)))))))))).)))))).)))))-(((....))))))))))).. ( -37.00)
>DroSim_CAF1 6945 94 - 1
-----AUGUAGGUCAAAAAGG-GGUGGCUUGAACUGUAGCUG--CU-GGCUGGCUAAAAUUAGCCGGCCGAUGAUUCAUUUUG-GGGGUUGUCCACUUACAUAA
-----((((((((........-((..(((........)))..--))-(((((((((....)))))))))((..((((......-.))))..)).)))))))).. ( -36.10)
>DroEre_CAF1 6663 94 - 1
-----AUGUAGUGCAAAAAAG-GGUGUCUGCAACUGUAGCUG--CU-GCCUGGUUCAAAAAAGCCGGCCGAUGAUUCAUUUGG-GGGGUUGUCCACUUACAUCA
-----((((((((........-((((.((((....)))).))--))-(((.((((......))))))).((..((((......-.))))..))))).))))).. ( -22.40)
>DroYak_CAF1 6448 93 - 1
-----AUGUAGUGCAAA-AGG-GGUGGCUUUAACUGUUCCUG--CU-GGCUGGCUAAAAUUAGUCGGCCAAUGAUUCAUUUUG-GGGGUUGUCCACUUACAUAA
-----((((((((....-(((-((..(......)..))))).--.(-(((((((((....))))))))))(..((((......-.))))..).))).))))).. ( -28.00)
>DroAna_CAF1 7299 100 - 1
CGGGAAUGGGCGGCAAAAAGG-GG---CCAAAACCUUAGCGACACUGAGCCGGCUAAAAUUAGUCGGUGAAUGAUUCGUUUCGAAGGGUUGUCCACUUACAUAA
.(..(.((((((((.......-.)---))..(((((((((((......((((((((....)))))))).......)))))....))))))))))).)..).... ( -31.82)
>consensus
_____AUGUAGGGCAAAAAGG_GGUGGCUUAAACUGUAGCUG__CU_GGCUGGCUAAAAUUAGCCGGCCGAUGAUUCAUUUUG_GGGGUUGUCCACUUACAUAA
.....(((((((...................................(((((((((....)))))))))((..((((........))))..))..))))))).. (-20.12 = -20.93 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:26 2006