Locus 9138

Sequence ID 3R_DroMel_CAF1
Location 24,383,233 – 24,383,457
Length 224
Max. P 0.953314
window14619 window14620 window14621

overview

Window 9

Location 24,383,233 – 24,383,340
Length 107
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 78.98
Mean single sequence MFE -21.21
Consensus MFE -14.75
Energy contribution -15.87
Covariance contribution 1.12
Combinations/Pair 1.20
Mean z-score -1.86
Structure conservation index 0.70
SVM decision value 0.88
SVM RNA-class probability 0.872322
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24383233 107 - 27905053
ACUCGCGGAUUAACGCUAGUGCACAUAUAUUGAAAAC-AAAAUGACACACAGUAGGCCUCGUUCCCUAUGCAAAGGACGAUUUAAGUCAUAAGCUCAGCAACAAUAUU
(((.(((......))).)))......((((((.....-.............(((((........)))))((....(((.......)))....)).......)))))). ( -17.50)
>DroSec_CAF1 205482 98 - 1
ACUCGCGGAUUAACGCUAGUGCACAUUUAUUCAAAACCAUAAUGGCACACAAAGGAAGAGGUCCUUUA----------AAUUUGAGUCAUAAGCUCAGAAACAAUAUU
....(((......)))..((((.((((.............))))))))..((((((.....)))))).----------..(((((((.....)))))))......... ( -22.52)
>DroSim_CAF1 214101 98 - 1
ACUCGCGGAUUAACGCUAGUGCACAUUUAUUAAAACCCAGAAUGGCACACAAAGGAAGAGGUCCUUUA----------AAUUUGAGUCAAAAGCUCAAAAACAAUAUU
....(((......)))..((((.(((((...........)))))))))..((((((.....)))))).----------..(((((((.....)))))))......... ( -23.60)
>consensus
ACUCGCGGAUUAACGCUAGUGCACAUUUAUUAAAAACCAAAAUGGCACACAAAGGAAGAGGUCCUUUA__________AAUUUGAGUCAUAAGCUCAGAAACAAUAUU
....(((......)))..((((.(((((...........)))))))))..((((((.....)))))).............(((((((.....)))))))......... (-14.75 = -15.87 +   1.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 24,383,340 – 24,383,457
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.20
Mean single sequence MFE -39.32
Consensus MFE -26.94
Energy contribution -27.87
Covariance contribution 0.92
Combinations/Pair 1.16
Mean z-score -3.31
Structure conservation index 0.69
SVM decision value 0.66
SVM RNA-class probability 0.815587
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24383340 117 + 27905053
AAUAAUGCCUCAA-UUUGGCAAUCUGUCAUGACUCAUGAGGCAGG-CCGCUUUUUGUUGGCUCUGUCCGAAAUGUUGAUUCAUU-UUGUUGCCAAAAGUCAUUGAGGCGGCUUAAUGCCU
......(((((((-((((((((....(((((...)))))((((((-((((.....).)))).)))))(((((((......))))-)))))))))).....))))))))(((.....))). ( -43.70)
>DroSec_CAF1 205580 117 + 1
AAUAAUGCCUCAA-UUUGGCAAUCGGUCAUGACUCAUGAGGCAGG-CCGCUUUUUGUUGGCUCUGACCGAAAUGUUGAUUCAUU-UUGUUGCCAAAAGUCAUUGAGGCGGCUUAAUGCCU
......(((((((-(((((((((.(((((.((..((.(((((...-..)))))....))..)))))))((((((......))))-)))))))))).....))))))))(((.....))). ( -43.50)
>DroSim_CAF1 214199 117 + 1
AAUAAUGCCUCAA-UUUGGCAAUCGGUCAUGAAUCAUGAGGCAGG-CCGCUUUUUGUUGGCUCUGACCGAAAUGUUGAUUCAUU-UUGUUGCCAAAAGUCAUUGAGGCGGCUUAAUGCCU
......(((((((-((((((((.(((..((((((((...((((((-((((.....).)))).))).)).......)))))))).-)))))))))).....))))))))(((.....))). ( -44.90)
>DroEre_CAF1 219773 113 + 1
-----AGCCUCCA-UUCGGCAAUCCGUCAUGACUCACGAGGCAGGAACGCUUUUUGUGGGCUCUGACCGAAAUGUUGAUUCAUU-UUGUUGCCAAAAGUCAUUGAGGCGGCUUAAUGCCU
-----.(((((..-...(((((...((((.((((((((((((......)))..))))))).))))))(((((((......))))-))))))))..((....)))))))(((.....))). ( -38.20)
>DroYak_CAF1 213304 114 + 1
-----UGCCUCAA-UUUGGCAAUCGGUCAUGACUCACGAGGCGCAUCCGCUUUUUGUGGACUCCGACCGAAAUGUUGAUUCAUUUUUGUUGCCAAAAGUCAUUGAGGCGGCUUAAUGCCU
-----.(((((((-((((((((((((((.....((((((((.((....)).)))))))).....)))))(((((......)))))..)))))))).....))))))))(((.....))). ( -43.10)
>DroAna_CAF1 208314 103 + 1
-----UGGCUGGAUCUCGGCAAUUAGUCAUAUCGUAAGUG----------UGUUUUUUAGCUUUAACCAAAAUGUUGAUUCAUU-UUGUUGCCAAAAGUCAUUGAGGCGGCUU-AUGCCU
-----.(((........(((((.....((((.(....)))----------))...............(((((((......))))-))))))))..(((((........)))))-..))). ( -22.50)
>consensus
_____UGCCUCAA_UUUGGCAAUCGGUCAUGACUCAUGAGGCAGG_CCGCUUUUUGUUGGCUCUGACCGAAAUGUUGAUUCAUU_UUGUUGCCAAAAGUCAUUGAGGCGGCUUAAUGCCU
......(((((((.((((((((((.((((.((.(((.(((((......)))))....))).)))))).))((((......))))....)))))))).....)))))))(((.....))). (-26.94 = -27.87 +   0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 24,383,340 – 24,383,457
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.20
Mean single sequence MFE -35.55
Consensus MFE -28.57
Energy contribution -28.75
Covariance contribution 0.18
Combinations/Pair 1.22
Mean z-score -3.47
Structure conservation index 0.80
SVM decision value 1.43
SVM RNA-class probability 0.953314
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24383340 117 - 27905053
AGGCAUUAAGCCGCCUCAAUGACUUUUGGCAACAA-AAUGAAUCAACAUUUCGGACAGAGCCAACAAAAAGCGG-CCUGCCUCAUGAGUCAUGACAGAUUGCCAAA-UUGAGGCAUUAUU
.(((.....)))((((((((.....((((((((.(-((((......))))).((.(((.(((..........))-))))))(((((...)))))..).))))))))-)))))))...... ( -37.30)
>DroSec_CAF1 205580 117 - 1
AGGCAUUAAGCCGCCUCAAUGACUUUUGGCAACAA-AAUGAAUCAACAUUUCGGUCAGAGCCAACAAAAAGCGG-CCUGCCUCAUGAGUCAUGACCGAUUGCCAAA-UUGAGGCAUUAUU
.(((.....)))((((((((.....(((((((...-((((......))))(((((((..(((..........))-).((.((....)).)))))))))))))))))-)))))))...... ( -38.30)
>DroSim_CAF1 214199 117 - 1
AGGCAUUAAGCCGCCUCAAUGACUUUUGGCAACAA-AAUGAAUCAACAUUUCGGUCAGAGCCAACAAAAAGCGG-CCUGCCUCAUGAUUCAUGACCGAUUGCCAAA-UUGAGGCAUUAUU
.(((.....)))((((((((.....(((((((...-.((((((((.......((.(((.(((..........))-))))))...))))))))......))))))))-)))))))...... ( -40.90)
>DroEre_CAF1 219773 113 - 1
AGGCAUUAAGCCGCCUCAAUGACUUUUGGCAACAA-AAUGAAUCAACAUUUCGGUCAGAGCCCACAAAAAGCGUUCCUGCCUCGUGAGUCAUGACGGAUUGCCGAA-UGGAGGCU-----
.(((.....)))(((((.......((((((((...-((((......))))((.((((..((.(((.....(((....)))...))).))..)))).))))))))))-..))))).----- ( -34.50)
>DroYak_CAF1 213304 114 - 1
AGGCAUUAAGCCGCCUCAAUGACUUUUGGCAACAAAAAUGAAUCAACAUUUCGGUCGGAGUCCACAAAAAGCGGAUGCGCCUCGUGAGUCAUGACCGAUUGCCAAA-UUGAGGCA-----
.(((.....)))((((((((.....(((((((....((((......))))((((((((.((((.(.....).))))...)).(....)....))))))))))))))-))))))).----- ( -42.30)
>DroAna_CAF1 208314 103 - 1
AGGCAU-AAGCCGCCUCAAUGACUUUUGGCAACAA-AAUGAAUCAACAUUUUGGUUAAAGCUAAAAAACA----------CACUUACGAUAUGACUAAUUGCCGAGAUCCAGCCA-----
.(((..-..))).......((..((((((((((((-((((......)))))))(((..........))).----------..................)))))))))..))....----- ( -20.00)
>consensus
AGGCAUUAAGCCGCCUCAAUGACUUUUGGCAACAA_AAUGAAUCAACAUUUCGGUCAGAGCCAACAAAAAGCGG_CCUGCCUCAUGAGUCAUGACCGAUUGCCAAA_UUGAGGCA_____
.(((.....)))(((((((.....((((((((....((((......))))(((((((.............(((....)))...........))))))))))))))).)))))))...... (-28.57 = -28.75 +   0.18)

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 13:27:26 2006