Locus 7736

Sequence ID X_DroMel_CAF1
Location 19,248,801 – 19,248,966
Length 165
Max. P 0.847788
window12692 window12693 window12694 window12695 window12696

overview

Window 2

Location 19,248,801 – 19,248,906
Length 105
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 81.34
Mean single sequence MFE -18.42
Consensus MFE -11.85
Energy contribution -11.97
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.78
Structure conservation index 0.64
SVM decision value 0.27
SVM RNA-class probability 0.660397
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19248801 105 + 22224390
CCCACUUGCCACCACCCACUUGCC-ACCA-CCCACUGCUGUUUGCUGUCUCAGCGCAAAAUGUUGCUGCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAU
.....................((.-....-......((((..........))))((((....)))).))......((((((((((.........))))))))))... ( -15.70)
>DroPse_CAF1 79100 93 + 1
--------------CCUGCCUGCCUGCCGGCCUUUCAGUGUUUGCUGGCUCAGCGCAAAACGCUGCUGCUCUAAUUAUAAUGAAACGAUUUUCAUUUCAUUUUGCAU
--------------..((((((...((((((............)))))).))).))).........(((...(((...(((((((....)))))))..)))..))). ( -21.30)
>DroSec_CAF1 35670 98 + 1
CCC-------ACCACCCACUUGCC-ACCA-CCCACUGCUGUUUGCUGUCUCAGCGCAAAAUGUUGCUGCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAU
...-------...........((.-....-......((((..........))))((((....)))).))......((((((((((.........))))))))))... ( -15.70)
>DroEre_CAF1 33081 96 + 1
GGC-------ACCACCCACUUG----CCACCCCACUGCUGUUUGCUGUCUCAGCGCAAAAUGUUGCUGCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAU
(((-------(.........))----))........((.....((((...))))((((....)))).))......((((((((((.........))))))))))... ( -19.70)
>DroYak_CAF1 34921 97 + 1
--C-------ACCACCCACUAGCU-ACCACCCCACUGCUGUUUGCUGUCUCAGCGCAAAAUGUUGCUGCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAU
--.-------..........(((.-...........((((..........))))((((....)))).))).....((((((((((.........))))))))))... ( -16.80)
>DroPer_CAF1 46192 93 + 1
--------------CCUGCCUGCCUGCCGGCCUUUCAGUGUUUGCUGGCUCAGCGCAAAACGCUGCUGCUCUAAUUAUAAUGAAACGAUUUUCAUUUCAUUUUGCAU
--------------..((((((...((((((............)))))).))).))).........(((...(((...(((((((....)))))))..)))..))). ( -21.30)
>consensus
__C_______ACCACCCACUUGCC_ACCA_CCCACUGCUGUUUGCUGUCUCAGCGCAAAAUGUUGCUGCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAU
...........................................((((...))))(((......))).........((((((((((.........))))))))))... (-11.85 = -11.97 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 19,248,801 – 19,248,906
Length 105
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 81.34
Mean single sequence MFE -27.62
Consensus MFE -17.19
Energy contribution -17.58
Covariance contribution 0.39
Combinations/Pair 1.09
Mean z-score -2.47
Structure conservation index 0.62
SVM decision value 0.78
SVM RNA-class probability 0.847788
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19248801 105 - 22224390
AUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAGCAGUGGG-UGGU-GGCAAGUGGGUGGUGGCAAGUGGG
...((((((((((..(...)..))))))))))......((.((.((..(((((((((...))))...((.((.....-)).)-))))))...)).)).))....... ( -27.10)
>DroPse_CAF1 79100 93 - 1
AUGCAAAAUGAAAUGAAAAUCGUUUCAUUAUAAUUAGAGCAGCAGCGUUUUGCGCUGAGCCAGCAAACACUGAAAGGCCGGCAGGCAGGCAGG--------------
.(((..(((((((((.....))))))))).......(.((..(((((.....))))).))).)))....(((....(((....)))...))).-------------- ( -29.60)
>DroSec_CAF1 35670 98 - 1
AUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAGCAGUGGG-UGGU-GGCAAGUGGGUGGU-------GGG
...((((((((((..(...)..)))))))))).......((.((.(((((.((((((...))))...((.((.....-)).)-))))))))..)).)-------).. ( -25.70)
>DroEre_CAF1 33081 96 - 1
AUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAGCAGUGGGGUGG----CAAGUGGGUGGU-------GCC
...((((((((((..(...)..))))))))))......(((.((.(((((.((((((...))))...((.(.....).)))----))))))..)).)-------)). ( -27.70)
>DroYak_CAF1 34921 97 - 1
AUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAGCAGUGGGGUGGU-AGCUAGUGGGUGGU-------G--
...((((((((((..(...)..))))))))))((((..(((((..(((((..(((((..........)))).)..)))))..-.))).))...))))-------.-- ( -26.00)
>DroPer_CAF1 46192 93 - 1
AUGCAAAAUGAAAUGAAAAUCGUUUCAUUAUAAUUAGAGCAGCAGCGUUUUGCGCUGAGCCAGCAAACACUGAAAGGCCGGCAGGCAGGCAGG--------------
.(((..(((((((((.....))))))))).......(.((..(((((.....))))).))).)))....(((....(((....)))...))).-------------- ( -29.60)
>consensus
AUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAGCAGUGGG_UGGU_GGCAAGUGGGUGGU_______G__
...(((((((((((((...)))))))))))))......((.((((....))))((((...))))....................))..................... (-17.19 = -17.58 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 19,248,836 – 19,248,935
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.57
Mean single sequence MFE -23.38
Consensus MFE -13.64
Energy contribution -14.17
Covariance contribution 0.53
Combinations/Pair 1.09
Mean z-score -2.29
Structure conservation index 0.58
SVM decision value 0.38
SVM RNA-class probability 0.713923
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19248836 99 - 22224390
-----------AAGGCAAUGCCAACGACGACAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAG----------
-----------..(((...)))..........((((....))))(((((((((..(...)..)))))))))..........((((....))))((((...))))......---------- ( -22.40)
>DroVir_CAF1 73416 102 - 1
-----------GAGGCAAAAGCAA--ACGACAACAUGAAAAUGCAAA-----AUGAAAAUCGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAGACGUCAAACA
-----------...((....))..--..(((...........(((((-----(((......(((..(.......)..))).....))))))))((((...))))........)))..... ( -17.20)
>DroPse_CAF1 79123 99 - 1
-----------ACGGCUAUGGAAGCGACGACAACAUGAAAAUGCAAAAUGAAAUGAAAAUCGUUUCAUUAUAAUUAGAGCAGCAGCGUUUUGCGCUGAGCCAGCAAACAC----------
-----------..((((......((........(((....)))...(((((((((.....))))))))).........))..(((((.....))))))))).........---------- ( -26.80)
>DroEre_CAF1 33107 110 - 1
GUGGAAGCAGCAUGGCAAUGCCAACGACGACAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAG----------
......((((.(((....((((..........((((....))))(((((((((..(...)..))))))))).....).)))....))).))))((((...))))......---------- ( -27.60)
>DroYak_CAF1 34948 95 - 1
---------------CAACGACGACGACGACAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAG----------
---------------.................((((....))))(((((((((..(...)..)))))))))..........((((....))))((((...))))......---------- ( -19.50)
>DroPer_CAF1 46215 99 - 1
-----------ACGGCUAUGGAAGCGACGACAACAUGAAAAUGCAAAAUGAAAUGAAAAUCGUUUCAUUAUAAUUAGAGCAGCAGCGUUUUGCGCUGAGCCAGCAAACAC----------
-----------..((((......((........(((....)))...(((((((((.....))))))))).........))..(((((.....))))))))).........---------- ( -26.80)
>consensus
___________AAGGCAAUGGCAACGACGACAACAUGAAAAUGCAAAAUGAAAUGAAAAUCGUUUCAUUCUAAUUAGAGCAGCAACAUUUUGCGCUGAGACAGCAAACAG__________
..............((.................(((....)))...((((((((((...)))))))))).........)).((((....))))((((...))))................ (-13.64 = -14.17 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 19,248,866 – 19,248,966
Length 100
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.52
Mean single sequence MFE -21.90
Consensus MFE -14.21
Energy contribution -14.53
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.65
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19248866 100 + 22224390
GCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAUUUUCAUGUUGUCGUCGUUGGCAUUGCCUU-------------ACUGCU------UGCUACACGGAUAAAAA-GCAGCUCU
(((((...((((((((((.........))))))))))..........(((((..((((((((..((...-------------...)).------))))).))))))))..)-).)))... ( -21.80)
>DroSec_CAF1 35728 106 + 1
GCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAUUUUCAUGUUAUCGUCGUUGGCAUUGCCUU-------------ACUGCUCGCUUUUGCUACACGGAUAAAAA-GCAGCUCU
(((((...((((((((((.........))))))))))..........(((((..((((((((..((...-------------.......))...))))).))))))))..)-).)))... ( -21.20)
>DroEre_CAF1 33137 113 + 1
GCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAUUUUCAUGUUGUCGUCGUUGGCAUUGCCAUGCUGCUUCCACUUACUGCU------UGCUACACGGAUAAAAA-GCAGCUCU
((......((((((((((.........))))))))))...........(((((....)))))..))...(((((((((..........------........))).....)-)))))... ( -21.47)
>DroYak_CAF1 34978 97 + 1
GCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAUUUUCAUGUUGUCGUCGUCGUCGUUG-----------------GCUGCU------UGCUACACGGAUAAAAAGGCAGCUCU
........((((((((((.........)))))))))).........((((((.......((((((-----------------((....------.)))).)))).......))))))... ( -23.14)
>consensus
GCUCUAAUUAGAAUGAAACAAUUUUCAUUUCAUUCUACAUUUUCAUGUUGUCGUCGUUGGCAUUGCCUU_____________ACUGCU______UGCUACACGGAUAAAAA_GCAGCUCU
(((.....((((((((((.........))))))))))..........(((((..(((.(((...)))..................((........))...))))))))......)))... (-14.21 = -14.53 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 19,248,866 – 19,248,966
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.52
Mean single sequence MFE -24.85
Consensus MFE -18.27
Energy contribution -18.77
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.74
SVM decision value 0.66
SVM RNA-class probability 0.816078
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19248866 100 - 22224390
AGAGCUGC-UUUUUAUCCGUGUAGCA------AGCAGU-------------AAGGCAAUGCCAACGACGACAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGC
...(((((-((.((((....)))).)------))))))-------------..(((...)))..........((((....))))(((((((((..(...)..)))))))))......... ( -25.20)
>DroSec_CAF1 35728 106 - 1
AGAGCUGC-UUUUUAUCCGUGUAGCAAAAGCGAGCAGU-------------AAGGCAAUGCCAACGACGAUAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGC
...(((((-((..(((....)))((....)))))))))-------------..(((...)))..........((((....))))(((((((((..(...)..)))))))))......... ( -23.70)
>DroEre_CAF1 33137 113 - 1
AGAGCUGC-UUUUUAUCCGUGUAGCA------AGCAGUAAGUGGAAGCAGCAUGGCAAUGCCAACGACGACAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGC
...(((((-((((......(((....------.)))......))))))))).((((...)))).........((((....))))(((((((((..(...)..)))))))))......... ( -30.20)
>DroYak_CAF1 34978 97 - 1
AGAGCUGCCUUUUUAUCCGUGUAGCA------AGCAGC-----------------CAACGACGACGACGACAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGC
.(.(((((.((.((((....)))).)------))))))-----------------)................((((....))))(((((((((..(...)..)))))))))......... ( -20.30)
>consensus
AGAGCUGC_UUUUUAUCCGUGUAGCA______AGCAGU_____________AAGGCAAUGCCAACGACGACAACAUGAAAAUGUAGAAUGAAAUGAAAAUUGUUUCAUUCUAAUUAGAGC
...(((...........(((((.((........))..................(((...)))..........)))))......((((((((((..(...)..)))))))))).....))) (-18.27 = -18.77 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:21 2006