Locus 6444

Sequence ID X_DroMel_CAF1
Location 16,153,245 – 16,153,496
Length 251
Max. P 0.940185
window10517 window10518 window10519 window10520

overview

Window 7

Location 16,153,245 – 16,153,357
Length 112
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -26.76
Consensus MFE -23.12
Energy contribution -23.46
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.86
SVM decision value 0.15
SVM RNA-class probability 0.606908
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16153245 112 + 22224390
GCAAACGGGUUUACAGAACUCGCGCAUUCACACCCGAAUAUCUCUGUGUGUACACUGUACAUCUGCGCGUACAUUACCCGCAUGCACACAUGUACAUAUGCAAGCACGACAA
((...(((((((...))))))).((((.(((((..((.....)).))))).....(((((((.((.((((.(.......).)))).)).))))))).))))..))....... ( -28.40)
>DroSec_CAF1 5369 112 + 1
GCAAACGGGUUUACAGAACUCGCGCAUUCACACCCGAAUAUCUCUGUGUGUACACUGUACAUCUGCGCGUACAUUACCCGCAUGCACACAUGUACAUAUGCAUGCACGAAUA
(((..(((((..........((((((...((((..((.....)).))))((((...))))...))))))......)))))..)))...((((((....))))))........ ( -29.49)
>DroEre_CAF1 6459 99 + 1
GCAAACGGGUUUACAGAACUCGCGCAUUCACACCCGAAUAUCUCUGUGUGUACACUGUACAUCUGCGCGUACAU-ACCCGCAUACACACAUGUAUAAAUG------------
.....(((((.(((.(....)(((((...((((..((.....)).))))((((...))))...))))))))...-))))).(((((....))))).....------------ ( -22.40)
>consensus
GCAAACGGGUUUACAGAACUCGCGCAUUCACACCCGAAUAUCUCUGUGUGUACACUGUACAUCUGCGCGUACAUUACCCGCAUGCACACAUGUACAUAUGCA_GCACGA__A
(((..(((((..........((((((...((((..((.....)).))))((((...))))...))))))......)))))..)))........................... (-23.12 = -23.46 +   0.33)

alignment

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secondary structure

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Window 8

Location 16,153,245 – 16,153,357
Length 112
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 89.58
Mean single sequence MFE -38.53
Consensus MFE -33.02
Energy contribution -33.47
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.77
Structure conservation index 0.86
SVM decision value 1.24
SVM RNA-class probability 0.935309
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16153245 112 - 22224390
UUGUCGUGCUUGCAUAUGUACAUGUGUGCAUGCGGGUAAUGUACGCGCAGAUGUACAGUGUACACACAGAGAUAUUCGGGUGUGAAUGCGCGAGUUCUGUAAACCCGUUUGC
...((((((.(((((.(((((((.(((((.((((.....)))).))))).))))))))))))(((((.(((...)))..)))))...)))))).....(((((....))))) ( -40.90)
>DroSec_CAF1 5369 112 - 1
UAUUCGUGCAUGCAUAUGUACAUGUGUGCAUGCGGGUAAUGUACGCGCAGAUGUACAGUGUACACACAGAGAUAUUCGGGUGUGAAUGCGCGAGUUCUGUAAACCCGUUUGC
.((((((((((((((.(((((((.(((((.((((.....)))).))))).))))))))))).(((((.(((...)))..))))).))))))))))...(((((....))))) ( -43.90)
>DroEre_CAF1 6459 99 - 1
------------CAUUUAUACAUGUGUGUAUGCGGGU-AUGUACGCGCAGAUGUACAGUGUACACACAGAGAUAUUCGGGUGUGAAUGCGCGAGUUCUGUAAACCCGUUUGC
------------....(((((....))))).((((((-.(((((((...........))))))).(((((...(((((.((......)).))))))))))..)))))).... ( -30.80)
>consensus
U__UCGUGC_UGCAUAUGUACAUGUGUGCAUGCGGGUAAUGUACGCGCAGAUGUACAGUGUACACACAGAGAUAUUCGGGUGUGAAUGCGCGAGUUCUGUAAACCCGUUUGC
...........((((((....))))))(((.((((((..(((((((...........))))))).(((((...(((((.((......)).))))))))))..)))))).))) (-33.02 = -33.47 +   0.45)

alignment

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secondary structure

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Window 9

Location 16,153,357 – 16,153,456
Length 99
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 79.29
Mean single sequence MFE -30.35
Consensus MFE -18.77
Energy contribution -20.43
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.62
SVM decision value 1.28
SVM RNA-class probability 0.940185
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16153357 99 - 22224390
CGGCGUGGUCUGCGUA--UGUGUGG-CUCAUACCCAUACACACAUGCAGAUCAAUACACGAACAUAACCUCUAAGCGGUCACUCGCGUAU---GUCUGUAUGUUC
.(...((((((((((.--(((((((-.......)))))))...))))))))))...)..(((((((........((((....))))....---.....))))))) ( -32.33)
>DroSec_CAF1 5481 102 - 1
CGGCGUGGUCUGCGUA--UGUGUGG-CCCAUACCCAUACACACAUGCAGAUCAAUACACGAACAUAACCUCCAAGCGGUCACUCGCGUAUCGCGUCUGUAUGUUC
.(...((((((((((.--(((((((-.......)))))))...))))))))))...)..(((((((........(((((.((....))))))).....))))))) ( -33.82)
>DroEre_CAF1 6558 85 - 1
CGGCGUGCCGUGCCUGUGUGUGUGGCCCCAUACCCAUACACACAUUCAGAUCAAUACACGAACAUAACCUCCAUGCGGUCACUCG--------------------
(((.(((((((...(((((((((((........)))))))))))....(.((.......)).)...........)))).))))))-------------------- ( -24.90)
>consensus
CGGCGUGGUCUGCGUA__UGUGUGG_CCCAUACCCAUACACACAUGCAGAUCAAUACACGAACAUAACCUCCAAGCGGUCACUCGCGUAU___GUCUGUAUGUUC
.(...((((((((((...(((((((........)))))))...))))))))))...).(((.....(((.......)))...))).................... (-18.77 = -20.43 +   1.67)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,153,388 – 16,153,496
Length 108
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 88.48
Mean single sequence MFE -33.20
Consensus MFE -24.01
Energy contribution -26.57
Covariance contribution 2.56
Combinations/Pair 1.03
Mean z-score -3.43
Structure conservation index 0.72
SVM decision value 0.98
SVM RNA-class probability 0.893537
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16153388 108 - 22224390
UUUAUAUGCAUCUGUGCAUGUGUGCUAUAUAUGUACAUUCCGGCGUGGUCUGCGUA--UGUGUGG-CUCAUACCCAUACACACAUGCAGAUCAAUACACGAACAUAACCUC
....((((....(((((((((((...)))))))))))...((...((((((((((.--(((((((-.......)))))))...)))))))))).....))..))))..... ( -33.80)
>DroSec_CAF1 5515 108 - 1
UUUAUAUGCAUCUGUUCAUGUGUGCUAUAUAUGUACAUUCCGGCGUGGUCUGCGUA--UGUGUGG-CCCAUACCCAUACACACAUGCAGAUCAAUACACGAACAUAACCUC
............(((((..((((((.......))))))...(...((((((((((.--(((((((-.......)))))))...))))))))))...)..)))))....... ( -32.40)
>DroEre_CAF1 6572 109 - 1
UUUCAAUGCAUAUGCGCUUGUGUGCUAU--AAGUACAUUCCGGCGUGCCGUGCCUGUGUGUGUGGCCCCAUACCCAUACACACAUUCAGAUCAAUACACGAACAUAACCUC
.(((...((((.((((((.((((((...--..))))))...))))))..)))).(((((((((((........)))))))))))...............)))......... ( -33.40)
>consensus
UUUAUAUGCAUCUGUGCAUGUGUGCUAUAUAUGUACAUUCCGGCGUGGUCUGCGUA__UGUGUGG_CCCAUACCCAUACACACAUGCAGAUCAAUACACGAACAUAACCUC
.....((((...(((((((((((...))))))))))).....))))(((((((((...(((((((........)))))))...)))))))))................... (-24.01 = -26.57 +   2.56)

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 12:13:53 2006