Locus 4638

Sequence ID 3L_DroMel_CAF1
Location 13,177,503 – 13,177,686
Length 183
Max. P 0.994682
window7279 window7280 window7281 window7282 window7283

overview

Window 9

Location 13,177,503 – 13,177,594
Length 91
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 89.70
Mean single sequence MFE -28.71
Consensus MFE -26.56
Energy contribution -26.38
Covariance contribution -0.19
Combinations/Pair 1.09
Mean z-score -2.62
Structure conservation index 0.93
SVM decision value 2.50
SVM RNA-class probability 0.994682
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13177503 91 + 23771897
ACCUCCU---------GUUCCUCCUUGAGUCCUGCAGCAGGUCCUGAUUUGAGCUCCUGUUCUUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGA
...((((---------((........(((((((((((((((.........((((....))))........)))))...)).)))).))))...)))).)) ( -23.83)
>DroSec_CAF1 28943 91 + 1
UCCUCCU---------GUUCCUCCUUGAGUCCUGGAGCAGGUCCUGAUUUGAGCUCCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGA
...((((---------((........(((((..((((((((..((......))..))))))))..)))))..(((((.....)))))......)))).)) ( -29.00)
>DroEre_CAF1 32846 91 + 1
UCCCCCU---------GCUCCUCCUCGAGUCCUGGAACAGGUCCUGAUUUGAGCUCCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGA
....(((---------((........(((((..((((((((..((......))..))))))))..)))))..(((((.....)))))......)))).). ( -30.80)
>DroYak_CAF1 27994 100 + 1
UCCUGCUCCUUCUUCUUCUACUCCUUGAGUCCUGGAACAGGUCCUGAUUUGAGCUCCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGA
((((((....................(((((..((((((((..((......))..))))))))..)))))..(((((.....)))))......)))).)) ( -31.20)
>consensus
UCCUCCU_________GCUCCUCCUUGAGUCCUGGAACAGGUCCUGAUUUGAGCUCCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGA
....................(.((..(((((..((((((((..((......))..))))))))..)))))..(((((.....)))))........)).). (-26.56 = -26.38 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,177,503 – 13,177,594
Length 91
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 89.70
Mean single sequence MFE -28.25
Consensus MFE -25.15
Energy contribution -26.15
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.89
SVM decision value 0.07
SVM RNA-class probability 0.568029
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13177503 91 - 23771897
UCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAAGAACAGGAGCUCAAAUCAGGACCUGCUGCAGGACUCAAGGAGGAAC---------AGGAGGU
...((.....((((.((((((...(((.....)))...).))))).))))......))((((.(((.....(((...)))...)---------)).)))) ( -25.10)
>DroSec_CAF1 28943 91 - 1
UCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGGAGCUCAAAUCAGGACCUGCUCCAGGACUCAAGGAGGAAC---------AGGAGGA
...((....))....(((((.....))))).((((..(((.((((..((......))..)))).)))..))))...........---------....... ( -25.70)
>DroEre_CAF1 32846 91 - 1
UCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGGAGCUCAAAUCAGGACCUGUUCCAGGACUCGAGGAGGAGC---------AGGGGGA
((.((((........(((((.....))))).((((..((((((((..((......))..))))))))..)))).........))---------.)).)). ( -31.80)
>DroYak_CAF1 27994 100 - 1
UCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGGAGCUCAAAUCAGGACCUGUUCCAGGACUCAAGGAGUAGAAGAAGAAGGAGCAGGA
...((.....((((.((((((...(((.....)))...).))))).))))......)).((((((((...((((...))))..........)))))))). ( -30.42)
>consensus
UCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGGAGCUCAAAUCAGGACCUGCUCCAGGACUCAAGGAGGAAC_________AGGAGGA
...((....))....(((((.....))))).((((..((((((((..((......))..))))))))..))))........................... (-25.15 = -26.15 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,177,526 – 13,177,630
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.50
Mean single sequence MFE -40.73
Consensus MFE -23.00
Energy contribution -24.07
Covariance contribution 1.07
Combinations/Pair 1.27
Mean z-score -2.55
Structure conservation index 0.56
SVM decision value 1.47
SVM RNA-class probability 0.956440
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13177526 104 + 23771897
UGCAGCAGGUCCUGAUUUG------AGCU------CCUGUUCUUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGACUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAA----GGAU
....(((((..((......------))..------)))))(((((..((.(((((((((((...(((.((...((((...)))).)))))....)))).))))))).)).))----))). ( -34.60)
>DroSec_CAF1 28966 108 + 1
UGGAGCAGGUCCUGAUUUG------AGCU------CCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGACUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAAGGAAGGAU
.((((((((..((......------))..------))))))))....((((((((((.....)))).((.(((((.....(((((((.......)))))))))))).))..))))))... ( -42.00)
>DroSim_CAF1 27273 108 + 1
UGGAGCUGGUCCUGAUUUG------AGCU------CCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGACUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAAGGAAGGAU
.((((((.(........).------))))------))(.((((((..((.(((((((((((...(((.((...((((...)))).)))))....)))).))))))).)).)))))).).. ( -42.00)
>DroEre_CAF1 32869 104 + 1
UGGAACAGGUCCUGAUUUG------AGCU------CCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGACUGUUGAUGCAUAUUCAGCAGGCGGGCAGAAA----GGAU
.((((((((..((......------))..------))))))))....(((.(((((.(((.((((.....)))))))((.(((((((.......))))))).))))))).))----)... ( -39.90)
>DroYak_CAF1 28026 104 + 1
UGGAACAGGUCCUGAUUUG------AGCU------CCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGACUGUUGAUGCAUAUUCAGCAGGCAGGCAGCAA----GGAU
.((((((((..((......------))..------)))))))).........(((((.....))))).(((((((.((..(((((((.......)))))))....)).))))----))). ( -42.70)
>DroMoj_CAF1 77599 102 + 1
-GCUGUUGGACUUGGUUGGGGCAGGAGCACUGGAGUCUGUUGUCUGUCCUCUAGCCUCUCUU-CUCUGUCCUCGCU-UG---GCUGUUGCAUAUUCAACAGCCGAG------------CU
-......((((..((..(((((.((((.((.(((........))))).)))).)))))....-))..))))..(((-((---(((((((......)))))))))))------------). ( -43.20)
>consensus
UGGAGCAGGUCCUGAUUUG______AGCU______CCUGUUCCUUGACUUCCUGCCUCUGACAGGCACUCCUUGCGGCGACUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAA____GGAU
.((((((((..........................))))))))....((.(((((((((((...(((.((...((((...)))).)))))....)))).))))))).))........... (-23.00 = -24.07 +   1.07)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,177,526 – 13,177,630
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.50
Mean single sequence MFE -37.62
Consensus MFE -17.33
Energy contribution -19.52
Covariance contribution 2.20
Combinations/Pair 1.13
Mean z-score -2.60
Structure conservation index 0.46
SVM decision value 0.98
SVM RNA-class probability 0.893406
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13177526 104 - 23771897
AUCC----UUUCUGCCUGCCUGCUGAAUAUGCAUCAACAGUCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAAGAACAGG------AGCU------CAAAUCAGGACCUGCUGCA
...(----(((((.(((((((.((((....((((.........((....)).))))...))))))))))).))..))))..(((.------((.(------(.......)).)).))).. ( -31.90)
>DroSec_CAF1 28966 108 - 1
AUCCUUCCUUUCUGCCUGCCUGCUGAAUAUGCAUCAACAGUCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGG------AGCU------CAAAUCAGGACCUGCUCCA
....((((((.((.(((((((.((((....((((.........((....)).))))...))))))))))).))..))))))..((------(((.------.............))))). ( -40.34)
>DroSim_CAF1 27273 108 - 1
AUCCUUCCUUUCUGCCUGCCUGCUGAAUAUGCAUCAACAGUCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGG------AGCU------CAAAUCAGGACCAGCUCCA
....((((((.((.(((((((.((((....((((.........((....)).))))...))))))))))).))..))))))..((------((((------............)))))). ( -40.70)
>DroEre_CAF1 32869 104 - 1
AUCC----UUUCUGCCCGCCUGCUGAAUAUGCAUCAACAGUCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGG------AGCU------CAAAUCAGGACCUGUUCCA
...(----(((((((((...(((.......)))...((((.(.((....)).)...))))..).)))))))))....((((((((------..((------......))..)))))))). ( -37.40)
>DroYak_CAF1 28026 104 - 1
AUCC----UUGCUGCCUGCCUGCUGAAUAUGCAUCAACAGUCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGG------AGCU------CAAAUCAGGACCUGUUCCA
....----(((((.(((((((.((((....((((.........((....)).))))...))))))))))).)).)))((((((((------..((------......))..)))))))). ( -41.80)
>DroMoj_CAF1 77599 102 - 1
AG------------CUCGGCUGUUGAAUAUGCAACAGC---CA-AGCGAGGACAGAG-AAGAGAGGCUAGAGGACAGACAACAGACUCCAGUGCUCCUGCCCCAACCAAGUCCAACAGC-
.(------------((.((((((((......)))))))---).-)))..((((...(-..(.(.(((..(((.((.((........))..)).)))..)))))..)...))))......- ( -33.60)
>consensus
AUCC____UUUCUGCCUGCCUGCUGAAUAUGCAUCAACAGUCGCCGCAAGGAGUGCCUGUCAGAGGCAGGAAGUCAAGGAACAGG______AGCU______CAAAUCAGGACCUGCUCCA
..............(((((((.((((....((((.........((....)).))))...))))))))))).......(((.(((............................))).))). (-17.33 = -19.52 +   2.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,177,594 – 13,177,686
Length 92
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 94.12
Mean single sequence MFE -25.40
Consensus MFE -21.11
Energy contribution -20.91
Covariance contribution -0.20
Combinations/Pair 1.08
Mean z-score -1.44
Structure conservation index 0.83
SVM decision value 0.33
SVM RNA-class probability 0.689582
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13177594 92 + 23771897
CUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAA----GGAUCCUUGAGUCGAAAAUAUUACAUAAUUAUUCAGCCAAGGAGACGAAGUCCCAGCUCG-
(((((((.......)))))))((.((......----(..((((((.((.((((((........))).))).))))))))..)......)).))...- ( -23.60)
>DroSec_CAF1 29034 96 + 1
CUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAAGGAAGGAUCCUUGAGUCGAAAAUAUUACAUAAUUAUUCAGCCAAGGAGACGAAGUCCCAGCCCG-
(((((((.......)))))))...(((.....(((.(..((((((.((.((((((........))).))).))))))))..)....)))..)))..- ( -26.30)
>DroSim_CAF1 27341 96 + 1
CUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAAGGAAGGAUCCUUGAGUCGAAAAUAUUACAUAAUUAUUCAGCCAAGGAGACGAAGUCCCAGCCCG-
(((((((.......)))))))...(((.....(((.(..((((((.((.((((((........))).))).))))))))..)....)))..)))..- ( -26.30)
>DroEre_CAF1 32937 92 + 1
CUGUUGAUGCAUAUUCAGCAGGCGGGCAGAAA----GGAUCCUUGAGUCGAAAAUAUUACAUAAUUAUUCAGCCAGGGAGAGGAAGCCCCAGCUCG-
(((((((.......))))))).(((((.....----...((((((.((.((((((........))).))).))))))))..((.....)).)))))- ( -25.60)
>DroYak_CAF1 28094 93 + 1
CUGUUGAUGCAUAUUCAGCAGGCAGGCAGCAA----GGAUCCUUGAGUCGAAAAUAUUACAUAAUUAUUCAGCCAAGGAGACGAAGCCCCAGCUCGC
(((((((.......)))))))((.((..((..----(..((((((.((.((((((........))).))).))))))))..)...)).)).)).... ( -25.20)
>consensus
CUGUUGAUGCAUAUUCAGCAGGCAGGCAGAAA____GGAUCCUUGAGUCGAAAAUAUUACAUAAUUAUUCAGCCAAGGAGACGAAGUCCCAGCUCG_
(((((((.......)))))))...(((.........(..((((((.((.((((((........))).))).))))))))..).........)))... (-21.11 = -20.91 +  -0.20)

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 11:29:11 2006