Locus 809

Sequence ID 3L_DroMel_CAF1
Location 2,454,073 – 2,454,204
Length 131
Max. P 0.933632
window1245 window1246 window1247

overview

Window 5

Location 2,454,073 – 2,454,181
Length 108
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.99
Mean single sequence MFE -27.22
Consensus MFE -19.81
Energy contribution -21.01
Covariance contribution 1.20
Combinations/Pair 1.13
Mean z-score -1.15
Structure conservation index 0.73
SVM decision value 0.09
SVM RNA-class probability 0.580929
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2454073 108 - 23771897
UUCUGGCCAUAAAAAC----GAAUAGAUUUAUGGCCAUGGCCACUAUG-GUGGCGUCCAAGCA-UAAAAGGAUGUGAUGCGCUGGCCGAAA-AAUGACUCAUG---AAAUGUGCA-CUA
(((((((((((((...----.......)))))))))).(((((.....-((.((((((.....-.....)))))).))....)))))))).-...........---.........-... ( -30.20)
>DroPse_CAF1 87310 103 - 1
UUCUGGCCAUAAAAAAUGACUGCUAAAUUGAUGGCUAUU-UGACUGUGUUUCAGCUCCAGGCAGUAAAAGGAAGCGA----AUGGCCAAAACUAUGACUCACCAUCAA-----------
...(((((((........((((((....((..((((...-.(((...)))..)))).))))))))....(....)..----)))))))....................----------- ( -19.50)
>DroSec_CAF1 77779 108 - 1
UUCUGGCCAUAAAACC----GAAUAGAUUUAUGGGCAUGGCCACUAUG-GUGGCGUCCAAGCA-UAAAAGGAUGUGAUGCGCUGGCCGAAA-AAUGACUCAUG---AAAUGUGCA-CUA
......(((((((.(.----.....).)))))))(((((((((.....-((.((((((.....-.....)))))).))....)))))((..-......))...---....)))).-... ( -26.60)
>DroSim_CAF1 71812 109 - 1
UUCUGGCCAUAAAACC----GAAUAGAUUUAUGACCAUGGCCACUAUG-GUGGCGUCCAAGCA-UAAAAGGAUGUGAUGCGCUGGCCGAAA-AAUGACUCAUG---AAAUGUGCAACUA
(((.((((........----.............(((((((...)))))-))(((((....(((-(......))))...)))))))))))).-...........---............. ( -24.70)
>DroEre_CAF1 72032 107 - 1
UUCUGGCCAUAAAACA----GAAUAGAUUUAUGGUCAUGGCCACUAUG-GUGGCGUCCAGGCA-UAAAAGGAUGUGAUGCGCUGGCC-AAA-AAUGACUCAUG---AAAUAUGCA-CUA
(((((.........))----)))....(((((((((((.(((((....-)))))(.(((((((-(...........)))).)))).)-...-.))))).))))---)).......-... ( -31.90)
>DroYak_CAF1 74966 96 - 1
UUCUGGCCAUAAAACC----GACUAGAUUUAUGGCCAUGGUCACUAUG-GUGGCGUCCGAGCA-UAAAAGGAUGUGAUGCGCUGGCC-AAA-AAUGACUCAUG---A------------
....(((((((((.(.----.....).)))))))))(((((((...((-(((((((....(((-(......))))...))))).)))-)..-..)))).))).---.------------ ( -30.40)
>consensus
UUCUGGCCAUAAAACC____GAAUAGAUUUAUGGCCAUGGCCACUAUG_GUGGCGUCCAAGCA_UAAAAGGAUGUGAUGCGCUGGCCGAAA_AAUGACUCAUG___AAAUGUGCA_CUA
...((((((((((..............)))))))))).(((((......((.((((((...........)))))).))....)))))................................ (-19.81 = -21.01 +   1.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,454,108 – 2,454,204
Length 96
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.41
Mean single sequence MFE -32.63
Consensus MFE -23.00
Energy contribution -26.39
Covariance contribution 3.39
Combinations/Pair 1.15
Mean z-score -2.95
Structure conservation index 0.70
SVM decision value 1.23
SVM RNA-class probability 0.933632
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2454108 96 + 23771897
CAUCACAUCCUUUUA-UGCUUGGACGCCAC-CAUAGUGGCCAUGGCCAUAAAUCUAUUC----GUUUUUAUGGCCAGAAGCGGAAACGUGAGUCGCCGCUUU-----------------
.......(((.....-.....))).(((((-....)))))..((((((((((.......----...))))))))))(((((((..((....))..)))))))----------------- ( -37.30)
>DroPse_CAF1 87337 116 + 1
--UCGCUUCCUUUUACUGCCUGGAGCUGAAACACAGUCA-AAUAGCCAUCAAUUUAGCAGUCAUUUUUUAUGGCCAGAAGCGAGAACGUGAUUCGCCGUUUGACUCAUCCCCAAAGGGG
--..(((.((...........)))))........(((((-((..((.((((.(((.((.(((((.....))))).....)).)))...))))..))..)))))))...((((...)))) ( -25.50)
>DroSec_CAF1 77814 96 + 1
CAUCACAUCCUUUUA-UGCUUGGACGCCAC-CAUAGUGGCCAUGCCCAUAAAUCUAUUC----GGUUUUAUGGCCAGAAGCGGAAACGUGAGUCGCCGCUUU-----------------
.......(((.....-.....))).(((((-....)))))..((.(((((((.((....----)).))))))).))(((((((..((....))..)))))))----------------- ( -31.40)
>DroSim_CAF1 71848 96 + 1
CAUCACAUCCUUUUA-UGCUUGGACGCCAC-CAUAGUGGCCAUGGUCAUAAAUCUAUUC----GGUUUUAUGGCCAGAAGCGGAAACGUGAGUCGCCGCUUU-----------------
.......(((.....-.....))).(((((-....)))))..((((((((((.((....----)).))))))))))(((((((..((....))..)))))))----------------- ( -35.80)
>DroEre_CAF1 72066 96 + 1
CAUCACAUCCUUUUA-UGCCUGGACGCCAC-CAUAGUGGCCAUGACCAUAAAUCUAUUC----UGUUUUAUGGCCAGAAGCGGAAACGUGAGUCGCCGCUUU-----------------
...............-...((((..(((((-....))))).....(((((((.(.....----.).)))))))))))((((((..((....))..)))))).----------------- ( -32.80)
>DroYak_CAF1 74989 96 + 1
CAUCACAUCCUUUUA-UGCUCGGACGCCAC-CAUAGUGACCAUGGCCAUAAAUCUAGUC----GGUUUUAUGGCCAGAAGCGGAAACGUGAGUCGCCGCUUU-----------------
...............-.....((.(((...-....))).)).((((((((((.((....----)).))))))))))(((((((..((....))..)))))))----------------- ( -33.00)
>consensus
CAUCACAUCCUUUUA_UGCUUGGACGCCAC_CAUAGUGGCCAUGGCCAUAAAUCUAUUC____GGUUUUAUGGCCAGAAGCGGAAACGUGAGUCGCCGCUUU_________________
.......(((...........))).(((((.....)))))..((((((((((..............))))))))))(((((((..((....))..)))))))................. (-23.00 = -26.39 +   3.39)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,454,108 – 2,454,204
Length 96
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.41
Mean single sequence MFE -31.23
Consensus MFE -24.75
Energy contribution -25.06
Covariance contribution 0.31
Combinations/Pair 1.21
Mean z-score -1.85
Structure conservation index 0.79
SVM decision value 0.74
SVM RNA-class probability 0.837043
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2454108 96 - 23771897
-----------------AAAGCGGCGACUCACGUUUCCGCUUCUGGCCAUAAAAAC----GAAUAGAUUUAUGGCCAUGGCCACUAUG-GUGGCGUCCAAGCA-UAAAAGGAUGUGAUG
-----------------.((((((.(((....))).)))))).((((((((((...----.......))))))))))..(((((....-)))))((((.....-.....))))...... ( -34.10)
>DroPse_CAF1 87337 116 - 1
CCCCUUUGGGGAUGAGUCAAACGGCGAAUCACGUUCUCGCUUCUGGCCAUAAAAAAUGACUGCUAAAUUGAUGGCUAUU-UGACUGUGUUUCAGCUCCAGGCAGUAAAAGGAAGCGA--
(((....)))(((..(((....)))..)))......((((((((((((((....(((.........))).)))))).((-(.(((((.(.........).))))).)))))))))))-- ( -30.00)
>DroSec_CAF1 77814 96 - 1
-----------------AAAGCGGCGACUCACGUUUCCGCUUCUGGCCAUAAAACC----GAAUAGAUUUAUGGGCAUGGCCACUAUG-GUGGCGUCCAAGCA-UAAAAGGAUGUGAUG
-----------------.((((((.(((....))).)))))).((.(((((((.(.----.....).))))))).))..(((((....-)))))((((.....-.....))))...... ( -30.20)
>DroSim_CAF1 71848 96 - 1
-----------------AAAGCGGCGACUCACGUUUCCGCUUCUGGCCAUAAAACC----GAAUAGAUUUAUGACCAUGGCCACUAUG-GUGGCGUCCAAGCA-UAAAAGGAUGUGAUG
-----------------.((((((.(((....))).)))))).(((.((((((.(.----.....).)))))).)))..(((((....-)))))((((.....-.....))))...... ( -27.70)
>DroEre_CAF1 72066 96 - 1
-----------------AAAGCGGCGACUCACGUUUCCGCUUCUGGCCAUAAAACA----GAAUAGAUUUAUGGUCAUGGCCACUAUG-GUGGCGUCCAGGCA-UAAAAGGAUGUGAUG
-----------------.((((((.(((....))).)))))).((((((((((.(.----.....).))))))))))..(((((....-)))))((((.....-.....))))...... ( -32.60)
>DroYak_CAF1 74989 96 - 1
-----------------AAAGCGGCGACUCACGUUUCCGCUUCUGGCCAUAAAACC----GACUAGAUUUAUGGCCAUGGUCACUAUG-GUGGCGUCCGAGCA-UAAAAGGAUGUGAUG
-----------------.((((((.(((....))).)))))).((((((((((.(.----.....).))))))))))..(((((....-)))))((((.....-.....))))...... ( -32.80)
>consensus
_________________AAAGCGGCGACUCACGUUUCCGCUUCUGGCCAUAAAACC____GAAUAGAUUUAUGGCCAUGGCCACUAUG_GUGGCGUCCAAGCA_UAAAAGGAUGUGAUG
..................((((((.(((....))).)))))).((((((((((..............))))))))))..(((((.....)))))((((...........))))...... (-24.75 = -25.06 +   0.31)

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 09:51:45 2006