Locus 7903

Sequence ID 3L_DroMel_CAF1
Location 21,047,366 – 21,047,636
Length 270
Max. P 0.968846
window12874 window12875 window12876 window12877 window12878 window12879

overview

Window 4

Location 21,047,366 – 21,047,486
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.53
Mean single sequence MFE -42.58
Consensus MFE -40.30
Energy contribution -41.55
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -4.17
Structure conservation index 0.95
SVM decision value 1.60
SVM RNA-class probability 0.966778
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21047366 120 + 23771897
CCAGCAUAAGCAGACAUAGAAGCGGUCCGGCGUUUUAAAACAGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAA
..(((((..((((((((.(...(((((.(...........).))))).).))))))))...(((((((.(((((.....))))).)))))))....................)))))... ( -40.80)
>DroSec_CAF1 102603 120 + 1
CCAGCAUAAGCAGACAUAGAAGCGGUCCGGCGUUUUAAAACGGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUACAACAAAAUGCUCAA
..(((((..((((((((.(...(((((((...........))))))).).))))))))...(((((((.(((((.....))))).)))))))....................)))))... ( -46.90)
>DroSim_CAF1 8855 120 + 1
CCAGCAUAAGCAGACAUAGAAGCGGUCCGGCGUUUUAAAACGGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAA
..(((((..((((((((.(...(((((((...........))))))).).))))))))...(((((((.(((((.....))))).)))))))....................)))))... ( -46.90)
>DroEre_CAF1 24650 115 + 1
CCAGCAUAAGCAGACAUAGAAACGGUCCGGCGUUUUAAAACAGACCGACAAUGUCUGUC-----AGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAA
..(((((....((((((.(...(((((.(...........).))))).).))))))(((-----((((.(((((.....))))).)))))))....................)))))... ( -35.70)
>consensus
CCAGCAUAAGCAGACAUAGAAGCGGUCCGGCGUUUUAAAACAGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAA
..(((((..((((((((.(...(((((((...........))))))).).))))))))...(((((((.(((((.....))))).)))))))....................)))))... (-40.30 = -41.55 +   1.25)

alignment

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secondary structure

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Window 5

Location 21,047,366 – 21,047,486
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.53
Mean single sequence MFE -42.50
Consensus MFE -38.72
Energy contribution -39.47
Covariance contribution 0.75
Combinations/Pair 1.03
Mean z-score -2.52
Structure conservation index 0.91
SVM decision value 1.39
SVM RNA-class probability 0.948849
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21047366 120 - 23771897
UUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCUGUUUUAAAACGCCGGACCGCUUCUAUGUCUGCUUAUGCUGG
.((((((...(((..((((.....))).(((((((.((((.......)))).))))))))..)))(((((.(.(((((((...........))))))))....)))))))))))...... ( -42.10)
>DroSec_CAF1 102603 120 - 1
UUGAGCAUUUUGUUGUAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCCGUUUUAAAACGCCGGACCGCUUCUAUGUCUGCUUAUGCUGG
...(((((...((..(.....)..))..(((((((.((((.......)))).)))))))....(((((((.(.(((((((...........))))))))....)))))))...))))).. ( -42.80)
>DroSim_CAF1 8855 120 - 1
UUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCCGUUUUAAAACGCCGGACCGCUUCUAUGUCUGCUUAUGCUGG
.((((((...(((..((((.....))).(((((((.((((.......)))).))))))))..)))(((((.(.(((((((...........))))))))....)))))))))))...... ( -44.30)
>DroEre_CAF1 24650 115 - 1
UUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACU-----GACAGACAUUGUCGGUCUGUUUUAAAACGCCGGACCGUUUCUAUGUCUGCUUAUGCUGG
...(((((...((..((((.....))))(((((((.((((.......)))).))))-----)))((((((.(.(((((((...........)))))))...).))))))))..))))).. ( -40.80)
>consensus
UUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCCGUUUUAAAACGCCGGACCGCUUCUAUGUCUGCUUAUGCUGG
...(((((.......((((.....))))(((((((.((((.......)))).)))))))....(((((((.(.(((((((...........)))))))...).)))))))...))))).. (-38.72 = -39.47 +   0.75)

alignment

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secondary structure

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Window 6

Location 21,047,406 – 21,047,524
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.15
Mean single sequence MFE -31.01
Consensus MFE -27.30
Energy contribution -28.05
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.88
SVM decision value 1.31
SVM RNA-class probability 0.940818
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21047406 118 + 23771897
CAGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAACACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAA--
..((((((((.....)))).))))..((((.(.(((((((((..((.((....)).)).))))).)))).....((((..............)))).).))))...............-- ( -31.04)
>DroSec_CAF1 102643 120 + 1
CGGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUACAACAAAAUGCUCAACACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAACA
.((...((((.....))))..(((((((.(((((.....))))).)))))))...))...........................(((((........))))).................. ( -31.40)
>DroSim_CAF1 8895 120 + 1
CGGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAACACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAACA
.(((..((((.....))))..(((((((.(((((.....))))).)))))))...........)))..................(((((........))))).................. ( -32.60)
>DroEre_CAF1 24690 111 + 1
CAGACCGACAAUGUCUGUC-----AGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAACACCUCGCCAAAGAGCCGGCGGAAAACGAAA--UAAAA--
.....((.....(..((((-----((((.(((((.....))))).))))))))..)............................(((((........)))))....))...--.....-- ( -29.00)
>consensus
CAGACCGACAAUGUCUGUCAGGUCAGUCCGGCAGUUGAGUUGCCUGACUGACAAGCCAUCAACUCCAACAAAAUGCUCAACACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAA__
..(((.(((...))).)))..(((((((.(((((.....))))).)))))))................................(((((........))))).................. (-27.30 = -28.05 +   0.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,047,406 – 21,047,524
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.15
Mean single sequence MFE -43.25
Consensus MFE -37.10
Energy contribution -38.10
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.02
Structure conservation index 0.86
SVM decision value 1.63
SVM RNA-class probability 0.968846
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21047406 118 - 23771897
--UUUUAUGUUUUAUUUUCCGCCGGCUCUUUGGCGAGGUGUUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCUG
--..................((((...(((..((((((((.....))))))))..)))....))))..(((((((.((((.......)))).)))))))(((((((...))))))).... ( -43.40)
>DroSec_CAF1 102643 120 - 1
UGUUUUAUGUUUUAUUUUCCGCCGGCUCUUUGGCGAGGUGUUGAGCAUUUUGUUGUAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCCG
......((((((.((.(..((((((....))))))..).)).))))))......((((((((..(((((.....)))))...))))))))(((((((((.((.....))..))))))))) ( -41.50)
>DroSim_CAF1 8895 120 - 1
UGUUUUAUGUUUUAUUUUCCGCCGGCUCUUUGGCGAGGUGUUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCCG
....................((((...(((..((((((((.....))))))))..)))....))))..(((((((.((((.......)))).)))))))(((((((...))))))).... ( -43.40)
>DroEre_CAF1 24690 111 - 1
--UUUUA--UUUCGUUUUCCGCCGGCUCUUUGGCGAGGUGUUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACU-----GACAGACAUUGUCGGUCUG
--.....--...........((((((.(((..((((((((.....))))))))..)))..((((..(((((((((.((((.......)))).))))-----))))).))))))))))... ( -44.70)
>consensus
__UUUUAUGUUUUAUUUUCCGCCGGCUCUUUGGCGAGGUGUUGAGCAUUUUGUUGGAGUUGAUGGCUUGUCAGUCAGGCAACUCAACUGCCGGACUGACCUGACAGACAUUGUCGGUCCG
....................((((...(((..((((((((.....))))))))..)))....))))..(((((((.((((.......)))).)))))))..(((.(((...))).))).. (-37.10 = -38.10 +   1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,047,486 – 21,047,596
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.39
Mean single sequence MFE -29.50
Consensus MFE -20.04
Energy contribution -20.48
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -2.86
Structure conservation index 0.68
SVM decision value 0.80
SVM RNA-class probability 0.853681
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21047486 110 + 23771897
CACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAA-------CAUAAAAAGCUGGGG-AAAAACAAGAGCCACUGCAGAGACUUUCUUCGCAGACCAGCUUU--UUUCGAUGCAUCA
....(((((........)))))................-------(..((((((((((((-...........)).((((..((.....))..)))).))))))))--))..)........ ( -28.70)
>DroSec_CAF1 102723 119 + 1
CACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAACAUGCAACAUAAAAAGCUGGGG-AAAAUCAAGAGCCACUGCAGAGACUUUCCUCGCAGACCAGCUUUUUUUUCGAUGCAUCA
....(((((........))))).................(((((.(..((((((((((((-...........)).((((.(((......))))))).))))))))))....).))))).. ( -33.30)
>DroSim_CAF1 8975 118 + 1
CACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAACAUCAAACAUAAAAAGCUGGGG-AAAAACAAGAGCCACUGCAGAGACUUUCCUUGCAGACCAGCUUU-UUUUCGAUGCAUCA
....(((((........)))))................((((......((((((((((((-...........)).((((((.(.....).)))))).))))))))-))...))))..... ( -30.30)
>DroEre_CAF1 24765 107 + 1
CACCUCGCCAAAGAGCCGGCGGAAAACGAAA--UAAAA-------CACA--AAACUGUGGAAAAAACAAGAGCCACUGCAGAGACUUUCCUCGCAGACUCGCUUU--UUUCGAUGCAUCA
....(((((........))))).....((..--.....-------((((--....))))(((((((...(((...((((.(((......))))))).)))..)))--))))......)). ( -25.70)
>consensus
CACCUCGCCAAAGAGCCGGCGGAAAAUAAAACAUAAAA_______CAUAAAAAGCUGGGG_AAAAACAAGAGCCACUGCAGAGACUUUCCUCGCAGACCAGCUUU__UUUCGAUGCAUCA
....(((((........)))))............................((((((((((............)).((((.(((......))))))).))))))))............... (-20.04 = -20.48 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,047,524 – 21,047,636
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.24
Mean single sequence MFE -24.15
Consensus MFE -16.44
Energy contribution -16.88
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -2.46
Structure conservation index 0.68
SVM decision value -0.01
SVM RNA-class probability 0.529636
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21047524 112 + 23771897
-----CAUAAAAAGCUGGGG-AAAAACAAGAGCCACUGCAGAGACUUUCUUCGCAGACCAGCUUU--UUUCGAUGCAUCAUCGCAUAAUCAAAGAGUCAUAAAAACCAAUAAUCAUUAUU
-----...((((((((((((-...........)).((((..((.....))..)))).))))))))--))...((((......)))).................................. ( -24.80)
>DroSec_CAF1 102763 119 + 1
UGCAACAUAAAAAGCUGGGG-AAAAUCAAGAGCCACUGCAGAGACUUUCCUCGCAGACCAGCUUUUUUUUCGAUGCAUCAUCGCAUAAUCAAAGAGUCAUAAAAACCAAUAAUCAUUAUU
(((.....((((((((((((-...........)).((((.(((......))))))).))))))))))....((((...)))))))................................... ( -26.60)
>DroSim_CAF1 9015 118 + 1
UCAAACAUAAAAAGCUGGGG-AAAAACAAGAGCCACUGCAGAGACUUUCCUUGCAGACCAGCUUU-UUUUCGAUGCAUCAUCGCAUAAUCAAAGAGUCAUAAAAACCAAUAAUCAUUAUU
........((((((((((((-...........)).((((((.(.....).)))))).))))))))-))....((((......)))).................................. ( -23.90)
>DroEre_CAF1 24801 111 + 1
-----CACA--AAACUGUGGAAAAAACAAGAGCCACUGCAGAGACUUUCCUCGCAGACUCGCUUU--UUUCGAUGCAUCAUCGCAUAAUCAAAGAGUCAUAAAAACCAAUAAUCAUUAUU
-----....--......(((.........(((...((((.(((......))))))).)))(((((--((...((((......))))....)))))))........)))............ ( -21.30)
>consensus
_____CAUAAAAAGCUGGGG_AAAAACAAGAGCCACUGCAGAGACUUUCCUCGCAGACCAGCUUU__UUUCGAUGCAUCAUCGCAUAAUCAAAGAGUCAUAAAAACCAAUAAUCAUUAUU
..........((((((((((............)).((((.(((......))))))).)))))))).......((((......)))).................................. (-16.44 = -16.88 +   0.44)

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 13:00:16 2006