Locus 9153

Sequence ID 3R_DroMel_CAF1
Location 24,408,129 – 24,408,303
Length 174
Max. P 0.891311
window14644 window14645 window14646 window14647

overview

Window 4

Location 24,408,129 – 24,408,223
Length 94
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 93.75
Mean single sequence MFE -39.12
Consensus MFE -31.91
Energy contribution -31.98
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.49
Structure conservation index 0.82
SVM decision value 0.97
SVM RNA-class probability 0.891311
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24408129 94 + 27905053
UGCACUCGCUAAUUGGCAGGCCCGCUACAAAGCCGCUGCCUGUGGAGAUCGGGAUC----UAUAGCUAUAGCUACAGAAGAUUCUGCAGAGCGGCGGC
.((.((.(((....)))))))..........(((((((((((..(((.((....((----(.((((....)))).))).)))))..))).)))))))) ( -38.00)
>DroSec_CAF1 1707 94 + 1
UGCACUCGCUAAUUGGCAGGCCCGCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUC----UGUAGCUAUAGCUACAGAAGAUUCUGCAGGGCGGCGGC
(((.(..(((....)))..)...))).....(((((((((((..(((.((....((----((((((....)))))))).)))))..)).))))))))) ( -44.10)
>DroEre_CAF1 2397 94 + 1
UGCACUCGCUAAUUGGCUGGCCCGCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUC----UAUAGCUAUAGCUAGAGCAGAUUCUGCAGGGCGGCGGC
(((.((.(((....))).))...))).....(((((((((((..(((.((....((----(..(((....))))))...)))))..)).))))))))) ( -36.30)
>DroYak_CAF1 5128 98 + 1
UGCACUCGCUAAUUGGCUGGCCCGCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUCUAUCUAUAGCUAUAGCUAGAGCAGAUUCUGCAAGGCGGCGGC
(((.((.(((....))).))...))).....(((((((((((..(((.((....((((.((((....)))).))))...)))))..).)))))))))) ( -38.10)
>consensus
UGCACUCGCUAAUUGGCAGGCCCGCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUC____UAUAGCUAUAGCUACAGAAGAUUCUGCAGGGCGGCGGC
.((.((.(((....))).))...))......((((((((((...(....(((((((......((((....)))).....)))))))).)))))))))) (-31.91 = -31.98 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,408,152 – 24,408,263
Length 111
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 81.93
Mean single sequence MFE -43.10
Consensus MFE -27.25
Energy contribution -28.78
Covariance contribution 1.53
Combinations/Pair 1.15
Mean z-score -2.04
Structure conservation index 0.63
SVM decision value 0.31
SVM RNA-class probability 0.682643
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24408152 111 + 27905053
-GCUACAAAGCCGCUGCCUGUGGAGAUCGGGAUC----UAUAGCUAUAGCUACAGAAGAUUCUGCAGAGCGGCGGCUCCAUUGAAAGCCAGGCCGUGAUUCCAAUUUCUGUAGCCU
-((((((.((((((((((((..(((.((....((----(.((((....)))).))).)))))..))).))))))))).....((((....((........))..)))))))))).. ( -44.00)
>DroPse_CAF1 4700 100 + 1
UGCCACAAAGCCGCCGCUUGUG-----CGGG-----------GCCAGGGCUACAGGAGGUUCUGCAGGGCGGCGGCUCCAUUGAACGUGAGGCUGUGAUUCCAGUUCCGGUAGCUG
((((.((((((((((((((.((-----((((-----------(((..(....)....))))))))))))))))))))...))).....(..((((......))))..))))).... ( -44.70)
>DroSec_CAF1 1730 111 + 1
-GCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUC----UGUAGCUAUAGCUACAGAAGAUUCUGCAGGGCGGCGGCUCCAUUGAAAGCCAGGCCGUGAUUCCAAUUUCUAUAGCCU
-.(((...((((((((((((..(((.((....((----((((((....)))))))).)))))..)).))))))))))...)))......((((..(((........)).)..)))) ( -47.60)
>DroEre_CAF1 2420 111 + 1
-GCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUC----UAUAGCUAUAGCUAGAGCAGAUUCUGCAGGGCGGCGGCCCCAUUGAAAGCCAGGCCGUGAUUCCAAUUUCUGUAGCCU
-.(((....(((((((((((..(((.((....((----(..(((....))))))...)))))..)).)))))))))....)))......((((..(((........)).)..)))) ( -37.50)
>DroYak_CAF1 5151 115 + 1
-GCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUCUAUCUAUAGCUAUAGCUAGAGCAGAUUCUGCAAGGCGGCGGCCCCAUUGAAUGCCAGGCCGUGAUUCCAAUUUCUGUAGCCU
-(((.(((.(((((((((((..(((.((....((((.((((....)))).))))...)))))..).))))))))))....)))..))).((((..(((........)).)..)))) ( -40.10)
>DroPer_CAF1 4693 100 + 1
UGCCACAAAGCCGCCGCUUGUG-----CGGG-----------GCCAGGGCUACAGGAGGUUCUGCAGGGCGGCGGCUCCAUUGAACGUGAGGCUGUGAUUCCAGUUCCGGUAGCUG
((((.((((((((((((((.((-----((((-----------(((..(....)....))))))))))))))))))))...))).....(..((((......))))..))))).... ( -44.70)
>consensus
_GCAACAAAGCCGCUGCCUGUGGAGAUCGGGAUC____UAUAGCUAUAGCUACAGAAGAUUCUGCAGGGCGGCGGCUCCAUUGAAAGCCAGGCCGUGAUUCCAAUUUCUGUAGCCU
.((..((((((((((((((.((.....(((((((......((((....)))).....))))))))))))))))))))...)))...))..(((...((........))....))). (-27.25 = -28.78 +   1.53)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,408,152 – 24,408,263
Length 111
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 81.93
Mean single sequence MFE -40.40
Consensus MFE -24.95
Energy contribution -25.53
Covariance contribution 0.58
Combinations/Pair 1.16
Mean z-score -2.20
Structure conservation index 0.62
SVM decision value 0.37
SVM RNA-class probability 0.706838
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24408152 111 - 27905053
AGGCUACAGAAAUUGGAAUCACGGCCUGGCUUUCAAUGGAGCCGCCGCUCUGCAGAAUCUUCUGUAGCUAUAGCUAUA----GAUCCCGAUCUCCACAGGCAGCGGCUUUGUAGC-
..((((((...((((((((((.....))).))))))).(((((((.((.(((..(((((.((((((((....))))))----))....))).))..))))).)))))))))))))- ( -42.20)
>DroPse_CAF1 4700 100 - 1
CAGCUACCGGAACUGGAAUCACAGCCUCACGUUCAAUGGAGCCGCCGCCCUGCAGAACCUCCUGUAGCCCUGGC-----------CCCG-----CACAAGCGGCGGCUUUGUGGCA
..(((((((((.(((......)))..)).))......((((((((((((((((((......))))))....)))-----------...(-----(....)))))))))))))))). ( -39.60)
>DroSec_CAF1 1730 111 - 1
AGGCUAUAGAAAUUGGAAUCACGGCCUGGCUUUCAAUGGAGCCGCCGCCCUGCAGAAUCUUCUGUAGCUAUAGCUACA----GAUCCCGAUCUCCACAGGCAGCGGCUUUGUUGC-
((((..(.((........)))..))))......(((..(((((((.(((.((..(((((.((((((((....))))))----))....))).))..))))).)))))))..))).- ( -44.30)
>DroEre_CAF1 2420 111 - 1
AGGCUACAGAAAUUGGAAUCACGGCCUGGCUUUCAAUGGGGCCGCCGCCCUGCAGAAUCUGCUCUAGCUAUAGCUAUA----GAUCCCGAUCUCCACAGGCAGCGGCUUUGUUGC-
(((((...((........))..)))))......((((..((((((.(((..((((...))))..((((....)))).(----(((....)))).....))).))))))..)))).- ( -35.80)
>DroYak_CAF1 5151 115 - 1
AGGCUACAGAAAUUGGAAUCACGGCCUGGCAUUCAAUGGGGCCGCCGCCUUGCAGAAUCUGCUCUAGCUAUAGCUAUAGAUAGAUCCCGAUCUCCACAGGCAGCGGCUUUGUUGC-
(((((...((........))..)))))......((((..((((((.((((((.((((((((((.((((....)))).)).))))).....))).)).)))).))))))..)))).- ( -40.90)
>DroPer_CAF1 4693 100 - 1
CAGCUACCGGAACUGGAAUCACAGCCUCACGUUCAAUGGAGCCGCCGCCCUGCAGAACCUCCUGUAGCCCUGGC-----------CCCG-----CACAAGCGGCGGCUUUGUGGCA
..(((((((((.(((......)))..)).))......((((((((((((((((((......))))))....)))-----------...(-----(....)))))))))))))))). ( -39.60)
>consensus
AGGCUACAGAAAUUGGAAUCACGGCCUGGCUUUCAAUGGAGCCGCCGCCCUGCAGAAUCUCCUGUAGCUAUAGCUAUA____GAUCCCGAUCUCCACAGGCAGCGGCUUUGUUGC_
(((((...((........))..)))))........(..(((((((.(((.(((((......)))))((....))........................))).)))))))..).... (-24.95 = -25.53 +   0.58)

alignment

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secondary structure

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dotplot

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Window 7

Location 24,408,185 – 24,408,303
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.51
Mean single sequence MFE -40.65
Consensus MFE -24.67
Energy contribution -24.42
Covariance contribution -0.25
Combinations/Pair 1.27
Mean z-score -2.15
Structure conservation index 0.61
SVM decision value 0.65
SVM RNA-class probability 0.810782
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24408185 118 - 27905053
AGCAGUUGUACAACAACUAUCAGCAGUAUGCCGCGGCGGCAGGCUACAGAAAUUGGAAUCACGGCCUGGCUUUCAAUGGAGCCGCCGCUCUGCAGAAUCUUCUGUAGCUAUAGCUAUA--
...(((((.....)))))...(((....(((((...)))))(((((((((....(((.((..(((..(((((......))))))))((...)).)).))))))))))))...)))...-- ( -40.50)
>DroPse_CAF1 4726 111 - 1
AGCAG---UACAACAAUUACCAGCAGUACGCGGCGGCCGCCAGCUACCGGAACUGGAAUCACAGCCUCACGUUCAAUGGAGCCGCCGCCCUGCAGAACCUCCUGUAGCCCUGGC------
.....---...........((((......((((((((..(((.....((((.(((......)))..)).)).....))).)))))))).((((((......))))))..)))).------ ( -38.50)
>DroSec_CAF1 1763 118 - 1
AGCAGUUGUACAACAACUAUCAGCAGUAUGCCGCGGCGGCAGGCUAUAGAAAUUGGAAUCACGGCCUGGCUUUCAAUGGAGCCGCCGCCCUGCAGAAUCUUCUGUAGCUAUAGCUACA--
...(((((.....)))))...((.((..(((.(.((((((((((..(.((........)))..))))(((((......)))))))))))).)))....)).))(((((....))))).-- ( -43.00)
>DroYak_CAF1 5186 120 - 1
AGCAGUUGUACAACAACUAUCAGCAGUAUGCCGCGGCGGCAGGCUACAGAAAUUGGAAUCACGGCCUGGCAUUCAAUGGGGCCGCCGCCUUGCAGAAUCUGCUCUAGCUAUAGCUAUAGA
...(((((.....)))))...(((((..(((.(((((((((((((...((........))..)))))..(((...)))..))))))))...)))....))))).((((....)))).... ( -40.40)
>DroAna_CAF1 4740 112 - 1
--------UACAACAACUACCAGCAAUAUGCAGCGGCGGCCAGCUACCGCAACUGGAAUCACAGUCUCACGUUCAACGGGGCUGCUGCCUUGCAGAACUUGCUGUAGCUGUAGCUGCAGC
--------..............((.....)).(((((...(((((((.(((((((......)))).....((((..((((((....))))))..)))).))).)))))))..)))))... ( -43.00)
>DroPer_CAF1 4719 111 - 1
AGCAG---UACAACAAUUACCAGCAGUACGCGGCGGCCGCCAGCUACCGGAACUGGAAUCACAGCCUCACGUUCAAUGGAGCCGCCGCCCUGCAGAACCUCCUGUAGCCCUGGC------
.....---...........((((......((((((((..(((.....((((.(((......)))..)).)).....))).)))))))).((((((......))))))..)))).------ ( -38.50)
>consensus
AGCAG___UACAACAACUACCAGCAGUAUGCCGCGGCGGCAAGCUACAGAAACUGGAAUCACAGCCUCACGUUCAAUGGAGCCGCCGCCCUGCAGAACCUCCUGUAGCUAUAGCUA_A__
.....................(((........((((((((............(((......)))((...........)).)))))))).((((((......)))))).....)))..... (-24.67 = -24.42 +  -0.25)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:27:47 2006