Locus 6983

Sequence ID 3L_DroMel_CAF1
Location 18,850,899 – 18,851,132
Length 233
Max. P 0.999262
window11328 window11329 window11330 window11331 window11332

overview

Window 8

Location 18,850,899 – 18,851,000
Length 101
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 71.26
Mean single sequence MFE -26.65
Consensus MFE -14.19
Energy contribution -14.50
Covariance contribution 0.31
Combinations/Pair 1.14
Mean z-score -1.91
Structure conservation index 0.53
SVM decision value 1.34
SVM RNA-class probability 0.943565
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18850899 101 + 23771897
UAGCAAUUUCAGUGCUCAUACACA-CUUAUGUAUAUUGGAAAACACUCUG-----UGAAGA------AGAAAGAGUGUGCCAAAUG----UUGGUGCAUUCUAAUCUGUACGCCAUA
..((..((((((((..((((....-..))))..))))))))........(-----((.(((------....((((((..(((....----.)))..))))))..))).))))).... ( -26.50)
>DroSec_CAF1 16061 97 + 1
UAGCAAUUUUAGUGCGCAUACACA-CUUAU----GUUGGAAAACACUCUG-----UGAAAGG---CGAAAAAGAGUGUGCCAAAUG----UUGGUGCAUUCUAGUCUA---GUCAUA
...((((...((((.(....).))-))...----))))..........((-----(((.(((---(.....((((((..(((....----.)))..)))))).)))).---.))))) ( -25.70)
>DroSim_CAF1 16008 95 + 1
UAGCAAUUUUAGUGCUCAUACACA-CUUAU----AUUGGAAAACACUCUG-----UGAAAAG-----AGAAAGAGUGUGCCAAAUG----UUGGUGCAUUCUAGUCUA---GUCAUA
...((((...((((........))-))...----))))..........((-----(((..((-----(...((((((..(((....----.)))..))))))..))).---.))))) ( -24.90)
>DroEre_CAF1 16467 102 + 1
UAGCAAUUUUGGUGUUCGUACACA-CUUAU----AUUGGAAAACACUCUACACUUUGUAGG------GGAAAGAGUGUGCCAAAUG----UUGGUGCAUUCGAGUUUGUAUGCCAGA
.......((((((....(((((.(-(((..----...........((((((.....)))))------)....(((((..(((....----.)))..))))))))).))))))))))) ( -32.30)
>DroYak_CAF1 16782 102 + 1
UAGCAAUUUUAGUGUCCACACACA-CUUGU----AUUGGAAAACACUCUACUCAAUGUAGG------AGAAAGAGUGUGCCAAAUG----CUGGUGCAUUCGAACUUGCCCGCCAGA
..((((.(((.(((....))).((-((.((----(((((...(((((((.(((.......)------))..))))))).)).))))----).)))).....))).))))........ ( -28.30)
>DroAna_CAF1 17597 98 + 1
UAGCCGCCUUAGUGUUCAUGCGAGUAGUCC----AUUGAAAAGCCGUCUA-----UAAACGCAUUUGGUUAAGAGUGUGCCAAAUGCUUGUUGGUGCAGU----------UGCUAGA
((((.((.((((((..(.((....)))..)----)))))...(((((...-----...))(((((((((.........))))))))).....)))...))----------.)))).. ( -22.20)
>consensus
UAGCAAUUUUAGUGCUCAUACACA_CUUAU____AUUGGAAAACACUCUA_____UGAAGG______AGAAAGAGUGUGCCAAAUG____UUGGUGCAUUCUAGUCUG___GCCAGA
..((.......(((......))).................................................(((((..((((.......))))..)))))..........)).... (-14.19 = -14.50 +   0.31)

alignment

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secondary structure

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Window 9

Location 18,850,938 – 18,851,040
Length 102
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 72.55
Mean single sequence MFE -29.82
Consensus MFE -13.94
Energy contribution -15.22
Covariance contribution 1.28
Combinations/Pair 1.06
Mean z-score -3.48
Structure conservation index 0.47
SVM decision value 3.47
SVM RNA-class probability 0.999262
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18850938 102 + 23771897
AAACACUCUG-----UGAAGA------AGAAAGAGUGUGCCAAAUG----UUGGUGCAUUCUAAUCUGUACGCCAUAGCAGACUAAACAAGCACACUAAGUGAGUGAAAUUCCGAAA
...(((((.(-----((....------....((((((..(((....----.)))..))))))..(((((........)))))...........))).....)))))........... ( -27.50)
>DroSec_CAF1 16096 102 + 1
AAACACUCUG-----UGAAAGG---CGAAAAAGAGUGUGCCAAAUG----UUGGUGCAUUCUAGUCUA---GUCAUACCAGACUAAACAAACACAAUAAGUGAGUGAAAUUCAGAAA
...(((((((-----((.....---......((((((..(((....----.)))..)))))).((.((---(((......))))).))...))))......)))))........... ( -29.50)
>DroSim_CAF1 16043 100 + 1
AAACACUCUG-----UGAAAAG-----AGAAAGAGUGUGCCAAAUG----UUGGUGCAUUCUAGUCUA---GUCAUAACAGACUAAACAAACACACUAAGUGAGUGAAAUUCAGAAA
...(((((.(-----((.....-----....((((((..(((....----.)))..)))))).((.((---(((......))))).)).....))).....)))))........... ( -29.70)
>DroEre_CAF1 16502 104 + 1
AAACACUCUACACUUUGUAGG------GGAAAGAGUGUGCCAAAUG----UUGGUGCAUUCGAGUUUGUAUGCCAGACCAGACUAGGCAAACACACUAAGUGAGUGAAAUUCAG---
.....((((((.....)))))------)....(((((..(((....----.)))..)))))((((((((.((((((......)).)))).)).((((.....))))))))))..--- ( -34.90)
>DroYak_CAF1 16817 107 + 1
AAACACUCUACUCAAUGUAGG------AGAAAGAGUGUGCCAAAUG----CUGGUGCAUUCGAACUUGCCCGCCAGACCAGACUAGGCAAACACACCAAGUGAGUGAAAUUCAGAAA
...(((((.(((....(((((------.....(((((..(((....----.)))..)))))...)))))..(((((......)).)))..........))))))))........... ( -29.60)
>DroAna_CAF1 17633 96 + 1
AAGCCGUCUA-----UAAACGCAUUUGGUUAAGAGUGUGCCAAAUGCUUGUUGGUGCAGU----------UGCUAGACCAGUCUGAACAUUCAGAAUUA-----UGCAGUUCAGA-A
.....(((((-----..((((((((((((.........))))))))).(((....)))))----------)..)))))...(((((((...((......-----))..)))))))-. ( -27.70)
>consensus
AAACACUCUA_____UGAAGG______AGAAAGAGUGUGCCAAAUG____UUGGUGCAUUCUAGUCUG___GCCAGACCAGACUAAACAAACACACUAAGUGAGUGAAAUUCAGAAA
...(((((........................(((((..((((.......))))..)))))..........((.............)).............)))))........... (-13.94 = -15.22 +   1.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,850,938 – 18,851,040
Length 102
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 72.55
Mean single sequence MFE -26.54
Consensus MFE -8.72
Energy contribution -9.80
Covariance contribution 1.08
Combinations/Pair 1.15
Mean z-score -2.59
Structure conservation index 0.33
SVM decision value 1.57
SVM RNA-class probability 0.964527
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18850938 102 - 23771897
UUUCGGAAUUUCACUCACUUAGUGUGCUUGUUUAGUCUGCUAUGGCGUACAGAUUAGAAUGCACCAA----CAUUUGGCACACUCUUUCU------UCUUCA-----CAGAGUGUUU
....((.....((((.....))))(((...(((((((((.(((...))))))))))))..)))))..----........(((((((....------......-----.))))))).. ( -21.50)
>DroSec_CAF1 16096 102 - 1
UUUCUGAAUUUCACUCACUUAUUGUGUUUGUUUAGUCUGGUAUGAC---UAGACUAGAAUGCACCAA----CAUUUGGCACACUCUUUUUCG---CCUUUCA-----CAGAGUGUUU
...........(((((.......((((...((((((((((.....)---)))))))))..))))...----.....(((............)---)).....-----..)))))... ( -26.60)
>DroSim_CAF1 16043 100 - 1
UUUCUGAAUUUCACUCACUUAGUGUGUUUGUUUAGUCUGUUAUGAC---UAGACUAGAAUGCACCAA----CAUUUGGCACACUCUUUCU-----CUUUUCA-----CAGAGUGUUU
.(((((..............((((((((.((((((((......)))---)))))..(((((......----)))))))))))))......-----.......-----)))))..... ( -23.13)
>DroEre_CAF1 16502 104 - 1
---CUGAAUUUCACUCACUUAGUGUGUUUGCCUAGUCUGGUCUGGCAUACAAACUCGAAUGCACCAA----CAUUUGGCACACUCUUUCC------CCUACAAAGUGUAGAGUGUUU
---........(((((....(((((((.((((.((......))))))........((((((......----)))))))))))))......------..(((.....))))))))... ( -24.80)
>DroYak_CAF1 16817 107 - 1
UUUCUGAAUUUCACUCACUUGGUGUGUUUGCCUAGUCUGGUCUGGCGGGCAAGUUCGAAUGCACCAG----CAUUUGGCACACUCUUUCU------CCUACAUUGAGUAGAGUGUUU
...........((((((((..(((((.((((((.(((......)))))))))((((((((((....)----))))))).)).........------..)))))..))).)))))... ( -37.00)
>DroAna_CAF1 17633 96 - 1
U-UCUGAACUGCA-----UAAUUCUGAAUGUUCAGACUGGUCUAGCA----------ACUGCACCAACAAGCAUUUGGCACACUCUUAACCAAAUGCGUUUA-----UAGACGGCUU
.-(((((((..((-----......))...)))))))...(((((((.----------...))........((((((((...........)))))))).....-----)))))..... ( -26.20)
>consensus
UUUCUGAAUUUCACUCACUUAGUGUGUUUGUUUAGUCUGGUAUGGC___CAGACUAGAAUGCACCAA____CAUUUGGCACACUCUUUCU______CCUUCA_____CAGAGUGUUU
...((((((..(((.........)))...))))))............................((((.......)))).(((((((......................))))))).. ( -8.72 =  -9.80 +   1.08)

alignment

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secondary structure

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Window 1

Location 18,851,000 – 18,851,120
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.82
Mean single sequence MFE -33.08
Consensus MFE -19.42
Energy contribution -20.76
Covariance contribution 1.34
Combinations/Pair 1.19
Mean z-score -2.47
Structure conservation index 0.59
SVM decision value 1.09
SVM RNA-class probability 0.914319
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18851000 120 - 23771897
AGACAGGGCCAACCUGUCUACAUGUGAGCAGAUACAUUUGCUUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCAUUUCGGAAUUUCACUCACUUAGUGUGCUUGUUUAGUCUGC
(((((((.....)))))))........(((((((((.((((....)))).))).(((((((((...(((((....)))))...........((((.....))))))))))))).)))))) ( -35.60)
>DroSec_CAF1 16158 120 - 1
AGACAGGGCCAACCUGUCUACAUCUGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCAUUUCUGAAUUUCACUCACUUAUUGUGUUUGUUUAGUCUGG
(((((((.....))))))).((.(((((((((((((..((.(((.(.((((....)))........(((((....)))))...........).).))).)).)))))))))))))..)). ( -32.30)
>DroSim_CAF1 16103 120 - 1
AGACAGGGCCAACCUGUCUACAUGUGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCAUUUCUGAAUUUCACUCACUUAGUGUGUUUGUUUAGUCUGU
(((((((.....))))))).....((((((((((((((...(((.(.((((....)))........(((((....)))))...........).).)))..))))))))))))))...... ( -31.80)
>DroEre_CAF1 16569 117 - 1
AGACAGGGCCAACCUGUCUACAUGAGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUAAUAUAUAAUUAUGCA---CUGAAUUUCACUCACUUAGUGUGUUUGCCUAGUCUGG
(((((((.....))))))).....((.(((((((((((((.(((..((((((.....)).(((((((.....))))))))---))).....))).))...)))))))))))))....... ( -34.40)
>DroYak_CAF1 16884 120 - 1
AGACAGGGCCAACCUGUCUACAAGUGAGCAGAUACAUUUGAGAGUGCGGUUGUAAAACAAUGAUUGUGUAUAAUUAUGCAUUUCUGAAUUUCACUCACUUGGUGUGUUUGCCUAGUCUGG
(((((((.....))))))).((..(..(((((((((((.(.(((((..((((.....))))((..((((((....)))))).)).......))))).)..)))))))))))...)..)). ( -36.50)
>DroAna_CAF1 17695 97 - 1
UGACAGGGACAACCUGUCUGCUUAUGACCGGGUAUAGAUAUG--UAC-------AAAUAAAAAUAAU--------GUGCAU-UCUGAACUGCA-----UAAUUCUGAAUGUUCAGACUGG
.((((((.....)))))).........((((........(((--(((-------(...........)--------))))))-(((((((..((-----......))...))))))))))) ( -27.90)
>consensus
AGACAGGGCCAACCUGUCUACAUGUGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCAUUUCUGAAUUUCACUCACUUAGUGUGUUUGUUUAGUCUGG
(((((((.....))))))).....((((((((((((((.....(((..((((((..............))))))..)))......(.....)........))))))))))))))...... (-19.42 = -20.76 +   1.34)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,851,040 – 18,851,132
Length 92
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 80.71
Mean single sequence MFE -21.92
Consensus MFE -13.54
Energy contribution -14.90
Covariance contribution 1.36
Combinations/Pair 1.14
Mean z-score -1.64
Structure conservation index 0.62
SVM decision value 0.10
SVM RNA-class probability 0.583665
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18851040 92 - 23771897
AGACUU-------UUGACAAGACAGGGCCAACCUGUCUACAUGUGAGCAGAUACAUUUGCUUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCA
......-------.(.((((((((((.....)))))))...))).)(((.(((((..(((((((...........)))))))...))))).....))). ( -26.20)
>DroSec_CAF1 16198 99 - 1
AGACUUUUGACUUUUGACAAGACAGGGCCAACCUGUCUACAUCUGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCA
.....((((.(((..((..(((((((.....)))))))...)).)))))))((((.((((....)))).))))......((((..(.....)..)))). ( -21.80)
>DroSim_CAF1 16143 92 - 1
AGACUU-------UUGACAAGACAGGGCCAACCUGUCUACAUGUGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCA
......-------.(.((((((((((.....)))))))...))).)(((.(((((..(((.(((...........))).)))...))))).....))). ( -22.10)
>DroEre_CAF1 16606 91 - 1
AGACU--------UUGACAAGACAGGGCCAACCUGUCUACAUGAGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUAAUAUAUAAUUAUGCA
.(.((--------((.(..(((((((.....)))))))...).)))))...((((.((((....)))).))))......(((((((.....))))))). ( -23.20)
>DroYak_CAF1 16924 92 - 1
AGACUU-------UUGACAAGACAGGGCCAACCUGUCUACAAGUGAGCAGAUACAUUUGAGAGUGCGGUUGUAAAACAAUGAUUGUGUAUAAUUAUGCA
..((((-------(.....(((((((.....))))))).((((((........)))))))))))(((((..(......)..)))))((((....)))). ( -22.90)
>DroAna_CAF1 17729 75 - 1
AGACUU-------UUGACAUGACAGGGACAACCUGUCUGCUUAUGACCGGGUAUAGAUAUG--UAC-------AAAUAAAAAUAAU--------GUGCA
.....(-------(((((((((((((.....))))))(((((......))))).....)))--).)-------)))..........--------..... ( -15.30)
>consensus
AGACUU_______UUGACAAGACAGGGCCAACCUGUCUACAUGUGAGCAGAUACAUUUGCGUGUGCGGUUGUAAAACAAGUAUUUUGUAUAAUUAUGCA
...................(((((((.....)))))))........(((.(((((..(((.(((...........))).)))...))))).....))). (-13.54 = -14.90 +   1.36)

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 12:34:50 2006