Locus 4971

Sequence ID 2L_DroMel_CAF1
Location 14,313,657 – 14,313,794
Length 137
Max. P 0.987505
window7884 window7885 window7886

overview

Window 4

Location 14,313,657 – 14,313,757
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.48
Mean single sequence MFE -17.19
Consensus MFE -12.66
Energy contribution -12.42
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.74
SVM decision value 1.94
SVM RNA-class probability 0.983451
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14313657 100 + 22407834
CCGGCCAA--------------------ACGGCAUCAACUUCAACACCAACACCAAAACCGGCAUUAAACUGAGGCCAGUUACUGUUACAUGACACACGGUGUCAAAAUAUGAACAGUAA
..((((..--------------------..((..............))....((......))...........))))..((((((((.((((((((...)))))).....)))))))))) ( -21.54)
>DroPse_CAF1 180269 114 + 1
ACAUCCAAUAGCAACAGCAACAGCAACAUCAG------CAUCAACACCAACACCGAAACCGACCAUAAACUGAGGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAA
..........((..(((.....((.......)------)..............((....))........)))..))...((((((((.((((((((...)))))).....)))))))))) ( -16.30)
>DroWil_CAF1 218336 88 + 1
------AU--------------------AAGG---CUACAUCAACACCAACACCAUAUCC---AUAAAGCUAAAGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGCAA
------..--------------------..((---((.......................---..........)))).....(((((.((((((((...)))))).....)))))))... ( -11.01)
>DroYak_CAF1 137573 100 + 1
CCAGCCAA--------------------ACGGCAUCAACUUCAACACCAACACCAAAACCGGCAUUAAACUGAGGCCAGUUACUGUUACAUGACACACGGUGUCAAAAUAUGAACAGUAA
...(((..--------------------..)))...........................(((.((.....)).)))..((((((((.((((((((...)))))).....)))))))))) ( -20.70)
>DroAna_CAF1 150385 85 + 1
CCGGAGG-----------------------------------AACACCAACACCAAAACCGGCAAUAAACUGAGCCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAA
((((.((-----------------------------------..........))....)))).....(((((....)))))((((((.((((((((...)))))).....)))))))).. ( -17.00)
>DroPer_CAF1 185718 120 + 1
ACAUCCAAUAGCAACAGCAACAGCAACAUCAGCAUCAGCAUCAACACCAACACCGAAACCGACCAUAAACUGAGGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAA
................((..(((........((....))..............((....))........)))..))...((((((((.((((((((...)))))).....)))))))))) ( -16.60)
>consensus
CCAGCCAA____________________ACGG___CAACAUCAACACCAACACCAAAACCGGCAAUAAACUGAGGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAA
...................................................................(((((....)))))((((((.((((((((...)))))).....)))))))).. (-12.66 = -12.42 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,313,657 – 14,313,757
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.48
Mean single sequence MFE -29.17
Consensus MFE -15.36
Energy contribution -15.30
Covariance contribution -0.05
Combinations/Pair 1.13
Mean z-score -2.31
Structure conservation index 0.53
SVM decision value 2.08
SVM RNA-class probability 0.987505
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14313657 100 - 22407834
UUACUGUUCAUAUUUUGACACCGUGUGUCAUGUAACAGUAACUGGCCUCAGUUUAAUGCCGGUUUUGGUGUUGGUGUUGAAGUUGAUGCCGU--------------------UUGGCCGG
((((((((((.....((((((...)))))))).))))))))((((((.......(((((((....)))))))((((((......))))))..--------------------..)))))) ( -32.50)
>DroPse_CAF1 180269 114 - 1
UUACUGUUCAUAUUUUGACAUCAUAUGUCAUGUAACAGUAACUGGCCUCAGUUUAUGGUCGGUUUCGGUGUUGGUGUUGAUG------CUGAUGUUGCUGUUGCUGUUGCUAUUGGAUGU
.....(((((.....((((((...)))))).(((((((((((.((((.........))))(((.((((((((......))))------))))....))))))))))))))...))))).. ( -34.10)
>DroWil_CAF1 218336 88 - 1
UUGCUGUUCAUAUUUUGACAUCAUAUGUCAUGUAACAGUAACUGGCUUUAGCUUUAU---GGAUAUGGUGUUGGUGUUGAUGUAG---CCUU--------------------AU------
..(((..(((....(..(((((((((.(((((...(((...)))((....))..)))---)))))))))))..)...)))...))---)...--------------------..------ ( -20.70)
>DroYak_CAF1 137573 100 - 1
UUACUGUUCAUAUUUUGACACCGUGUGUCAUGUAACAGUAACUGGCCUCAGUUUAAUGCCGGUUUUGGUGUUGGUGUUGAAGUUGAUGCCGU--------------------UUGGCUGG
((((((((((.....((((((...)))))))).))))))))..(((.(((((((((((((..(......)..))))))))).)))).)))..--------------------........ ( -30.70)
>DroAna_CAF1 150385 85 - 1
UUACUGUUCAUAUUUUGACAUCAUAUGUCAUGUAACAGUAACUGGGCUCAGUUUAUUGCCGGUUUUGGUGUUGGUGUU-----------------------------------CCUCCGG
.(((((((((.....((((((...)))))))).)))))))((((....))))......((((....((..........-----------------------------------)).)))) ( -18.20)
>DroPer_CAF1 185718 120 - 1
UUACUGUUCAUAUUUUGACAUCAUAUGUCAUGUAACAGUAACUGGCCUCAGUUUAUGGUCGGUUUCGGUGUUGGUGUUGAUGCUGAUGCUGAUGUUGCUGUUGCUGUUGCUAUUGGAUGU
.....(((((.....((((((...)))))).(((((((((((.((((.........))))(((.(((((((..((......))..)))))))....))))))))))))))...))))).. ( -38.80)
>consensus
UUACUGUUCAUAUUUUGACAUCAUAUGUCAUGUAACAGUAACUGGCCUCAGUUUAAUGCCGGUUUUGGUGUUGGUGUUGAUGUUG___CCGU____________________UUGGCUGG
.(((((((((.....((((((...)))))))).)))))))((..((.((((.............)))).))..))............................................. (-15.36 = -15.30 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,313,677 – 14,313,794
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.73
Mean single sequence MFE -20.13
Consensus MFE -12.66
Energy contribution -12.42
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.53
Structure conservation index 0.63
SVM decision value 0.03
SVM RNA-class probability 0.549595
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14313677 117 + 22407834
UCAACACCAACACCAAAACCGGCAUUAAACUGAGGCCAGUUACUGUUACAUGACACACGGUGUCAAAAUAUGAACAGUAAUCCAAACGAUACAAAAUAUAUUUGCACAAACCGAUUA---
...................(((...........((...(((((((((.((((((((...)))))).....)))))))))))))........((((.....))))......)))....--- ( -18.50)
>DroPse_CAF1 180303 117 + 1
UCAACACCAACACCGAAACCGACCAUAAACUGAGGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAAGCCAAAUGAUACAAUAUGGGUUUCUAUGAGCCGAUUA---
..........((..((((((...((.....)).(((...((((((((.((((((((...)))))).....)))))))))))))...............))))))..)).........--- ( -22.90)
>DroWil_CAF1 218347 112 + 1
UCAACACCAACACCAUAUCC---AUAAAGCUAAAGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGCAAUCGG-AUGAUGUAAAUGAUAAAU----GAGUGGAUUUUCU
..........((((((...(---((...((.....((.(((.(((((.((((((((...)))))).....))))))).))).))-.....))..)))....))----).)))........ ( -16.80)
>DroYak_CAF1 137593 117 + 1
UCAACACCAACACCAAAACCGGCAUUAAACUGAGGCCAGUUACUGUUACAUGACACACGGUGUCAAAAUAUGAACAGUAAUCCAAACGAUACAAAAUAUAUUUGCACAAACCGAUUU---
...................(((...........((...(((((((((.((((((((...)))))).....)))))))))))))........((((.....))))......)))....--- ( -18.50)
>DroAna_CAF1 150392 112 + 1
--AACACCAACACCAAAACCGGCAAUAAACUGAGCCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAAGCCAAAAAAUU--AAAUG-GUUUUUACAAGUCCAUUC---
--..................(((....(((((....)))))((((((.((((((((...)))))).....))))))))..)))........--.((((-(...........))))).--- ( -21.20)
>DroPer_CAF1 185758 117 + 1
UCAACACCAACACCGAAACCGACCAUAAACUGAGGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAAGCCAAAUGAUACAAUAUGGGUUUCUAUGAGCCGAUUA---
..........((..((((((...((.....)).(((...((((((((.((((((((...)))))).....)))))))))))))...............))))))..)).........--- ( -22.90)
>consensus
UCAACACCAACACCAAAACCGGCAAUAAACUGAGGCCAGUUACUGUUACAUGACAUAUGAUGUCAAAAUAUGAACAGUAAGCCAAAUGAUACAAAAUAUAUUUCUACAAGCCGAUUA___
...........................(((((....)))))((((((.((((((((...)))))).....)))))))).......................................... (-12.66 = -12.42 +  -0.25)

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 11:32:18 2006