Locus 7389

Sequence ID 3L_DroMel_CAF1
Location 19,849,134 – 19,849,251
Length 117
Max. P 0.849835
window12003 window12004

overview

Window 3

Location 19,849,134 – 19,849,251
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.71
Mean single sequence MFE -45.65
Consensus MFE -24.26
Energy contribution -24.52
Covariance contribution 0.25
Combinations/Pair 1.33
Mean z-score -2.24
Structure conservation index 0.53
SVM decision value 0.78
SVM RNA-class probability 0.849835
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19849134 117 + 23771897
AGGACAAGGAGCAGCAGCCGGAGCUCUCCGACGAGGACCAGCAGCUGCAGGAGGAGCUGGAGCUGCUGGUGCAGCACUUGCAGGAGCCGGAUGCCAAGCUCUACCAGCCGACGCUGG
.......(((((.(((.((((....((((.....(.((((((((((.(((......))).)))))))))).).((....)).)))))))).)))...))))).(((((....))))) ( -57.80)
>DroVir_CAF1 34838 112 + 1
-----AAGGAGCAGCAGCCAGAGCUAUCCGACGAGGAUCAACAGCUGCAGGAGGAGCUAGAGAUGUUGGUGCUGCGCCUGCAGGAAAAGGACAAGAAAUUGUAUCAGCCAGCAUUGG
-----.(((.((((((.((((..((((((.....))))....((((.(....).))))..))...)))))))))).)))((.((......((((....)))).....)).))..... ( -37.40)
>DroPse_CAF1 33680 108 + 1
------AGG---AGCAGCCCGAGCUGUCGGACGAGGAUCAGCAGCUGCAGGAGGAACUGGAGAUGCUCGUGCUGCGUCUGCAGGAGAACGACAUAAAGUUGUACCAGCCAGCGCUGG
------.((---......))...(((.((((((((.((.((((.((.(((......))).)).)))).)).)).)))))))))....(((((.....))))).(((((....))))) ( -39.50)
>DroGri_CAF1 34983 112 + 1
-----AAAGAACAGCAACCGGAGCUGUCCGACGAGGAUCAGCAGUUACAGGAGGAGCUGGAGAUGCUGGUGCAGCGCCUCACGGAGAACGACAAGCAGCUGUAUCAGCCAGCGCUAG
-----.......(((.......(((((((.....))).)))).............((((.....(((((((((((((....((.....))....)).)))))))))))))))))).. ( -39.60)
>DroAna_CAF1 32520 114 + 1
AGGACAAGGAG---CAGCCCGAGCUGUCCGAUGAGGACCAGCAGCUGCAGGAGGAGCUGGAGCUGCUGGUCCAGCGCCUGCAGGAGUCGGACAAGAAGCUCUACCAGCCGGCCCUGG
(((.(..(((.---((((....))))))).....((((((((((((.(((......))).))))))))))))...)))).((((.(((((...((.....)).....))))))))). ( -57.10)
>DroPer_CAF1 33911 108 + 1
------AGG---AGCAGCCCGAGCUGUCGGACGAGGAUCAGCAGUUGCAGGAGGAACUGGAGAUGCUCGUGCUGCGUCUGCAGGAGAACGACAUAAAGUUGUACCAGCCAGCGCUGG
------((.---.(((((((((....))))(((((.(((..(((((.(....).)))))..))).))))))))))..))........(((((.....))))).(((((....))))) ( -42.50)
>consensus
_____AAGGAG_AGCAGCCCGAGCUGUCCGACGAGGAUCAGCAGCUGCAGGAGGAGCUGGAGAUGCUGGUGCAGCGCCUGCAGGAGAACGACAAGAAGCUGUACCAGCCAGCGCUGG
.............(((((......(((((.....(.(((((((.((.(((......))).)).))))))).)....((....))....)))))....))))).(((((....))))) (-24.26 = -24.52 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 19,849,134 – 19,849,251
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 78.71
Mean single sequence MFE -41.75
Consensus MFE -19.33
Energy contribution -20.78
Covariance contribution 1.45
Combinations/Pair 1.38
Mean z-score -2.25
Structure conservation index 0.46
SVM decision value 0.29
SVM RNA-class probability 0.671506
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19849134 117 - 23771897
CCAGCGUCGGCUGGUAGAGCUUGGCAUCCGGCUCCUGCAAGUGCUGCACCAGCAGCUCCAGCUCCUCCUGCAGCUGCUGGUCCUCGUCGGAGAGCUCCGGCUGCUGCUCCUUGUCCU
(((((....)))))..(((((.((...)))))))..(((((.((.((((((((((((.(((......))).))))))))))....((((((....)))))).)).))..)))))... ( -53.20)
>DroVir_CAF1 34838 112 - 1
CCAAUGCUGGCUGAUACAAUUUCUUGUCCUUUUCCUGCAGGCGCAGCACCAACAUCUCUAGCUCCUCCUGCAGCUGUUGAUCCUCGUCGGAUAGCUCUGGCUGCUGCUCCUU-----
....(((.((..((.((((....))))..))..)).)))((.(((((((((.........((.......))((((((((((....))).))))))).))).)))))).))..----- ( -31.30)
>DroPse_CAF1 33680 108 - 1
CCAGCGCUGGCUGGUACAACUUUAUGUCGUUCUCCUGCAGACGCAGCACGAGCAUCUCCAGUUCCUCCUGCAGCUGCUGAUCCUCGUCCGACAGCUCGGGCUGCU---CCU------
(((((....)))))...........(((((......)).)))((((((((((.(((..(((((.(....).)))))..))).)))))((((....))))))))).---...------ ( -37.70)
>DroGri_CAF1 34983 112 - 1
CUAGCGCUGGCUGAUACAGCUGCUUGUCGUUCUCCGUGAGGCGCUGCACCAGCAUCUCCAGCUCCUCCUGUAACUGCUGAUCCUCGUCGGACAGCUCCGGUUGCUGUUCUUU-----
.((((....))))..(((((.(((.(..(((.(((((((((.((((...)))).....((((.............))))..))))).)))).)))..)))).))))).....----- ( -34.82)
>DroAna_CAF1 32520 114 - 1
CCAGGGCCGGCUGGUAGAGCUUCUUGUCCGACUCCUGCAGGCGCUGGACCAGCAGCUCCAGCUCCUCCUGCAGCUGCUGGUCCUCAUCGGACAGCUCGGGCUG---CUCCUUGUCCU
.(((((.(((((....(((((....((((((.....((....)).((((((((((((.(((......))).))))))))))))...))))))))))).)))))---..))))).... ( -55.80)
>DroPer_CAF1 33911 108 - 1
CCAGCGCUGGCUGGUACAACUUUAUGUCGUUCUCCUGCAGACGCAGCACGAGCAUCUCCAGUUCCUCCUGCAACUGCUGAUCCUCGUCCGACAGCUCGGGCUGCU---CCU------
(((((....)))))...........(((((......)).)))((((((((((.(((..(((((.(....).)))))..))).)))))((((....))))))))).---...------ ( -37.70)
>consensus
CCAGCGCUGGCUGGUACAACUUCUUGUCCUUCUCCUGCAGGCGCAGCACCAGCAUCUCCAGCUCCUCCUGCAGCUGCUGAUCCUCGUCGGACAGCUCGGGCUGCU_CUCCUU_____
...(((((.((.((.((.((.....)).))...)).)).))))).(((.(((((.((.(((......))).)).)))))......((((((....)))))))))............. (-19.33 = -20.78 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:45 2006