Locus 6332

Sequence ID 2R_DroMel_CAF1
Location 19,846,045 – 19,846,280
Length 235
Max. P 0.859673
window10115 window10116 window10117 window10118 window10119

overview

Window 5

Location 19,846,045 – 19,846,158
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 85.62
Mean single sequence MFE -32.45
Consensus MFE -22.58
Energy contribution -24.00
Covariance contribution 1.42
Combinations/Pair 1.11
Mean z-score -1.89
Structure conservation index 0.70
SVM decision value 0.28
SVM RNA-class probability 0.667429
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19846045 113 + 20766785
UGCUCUGAUUUCCAGGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGCGAGUUUGAGAUCGGGAACGAGAACGAGAUCGAUCGGGCGAUCGAUCGAC
(((.(((.....))))))...(((......(((((...........)))))..(.(((((((((((.((((...(((....)))...)))).)))..)))))))).)...))) ( -36.10)
>DroSec_CAF1 88153 113 + 1
UGCUCUGAUUUCCAGGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGGGAGCUUGAGAUCGGGAACGGGAACGAGAUCGAUCGAGCGAUCGAUCGAC
...(((((((((..(((....)))....(((((((......................)))))))......)))))))))..((....)).((((((((....))))))))... ( -38.15)
>DroSim_CAF1 64384 113 + 1
UGCUCUGAUUUCCAGGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGCGAGUUUGAGAUCGGGAACGAGAACGAGAUCGAUCAAGCGAUCGAUCGAC
..(((.(((((.(.(((((..((....)).(((((...........))))).....))))).).))))).))).(((....)))......((((((((....))))))))... ( -34.00)
>DroEre_CAF1 89664 103 + 1
UGCUCUGAUUUCCAGGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGGCCGCG------AGAUCGAGAACGAGAUCGAGAUCGAUCG----GUCGAUCGAC
(((.(((.....))))))...(((......(((((...........)))))....((((((((((------(..((((........))))..)))..))----)))))).))) ( -32.10)
>DroYak_CAF1 87598 93 + 1
UGCUCUGAUUACCAGGCAAAAGUCAAAGCCUGGCACAAAUUAAAAAUGCCCCACAAUUGCCGAUG------UGAUCGAGAACGAGAUCGA--------------UGGAUCGAC
..(((.((((((..(((((..((....))..((((...........))))......)))))...)------)))))))).....((((..--------------..))))... ( -21.90)
>consensus
UGCUCUGAUUUCCAGGCAAAAGUCAAAGCCGGGCACAAAUUAAAAAUGCCCCACAAUUGCCCGCGAG_UUGAGAUCGGGAACGAGAACGAGAUCGAUCG_GCGAUCGAUCGAC
..(((.((((((..(((..........)))(((((...........)))))...................)))))))))..((....)).((((((((....))))))))... (-22.58 = -24.00 +   1.42)

alignment

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secondary structure

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Window 6

Location 19,846,045 – 19,846,158
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 85.62
Mean single sequence MFE -36.32
Consensus MFE -25.30
Energy contribution -28.04
Covariance contribution 2.74
Combinations/Pair 1.03
Mean z-score -2.30
Structure conservation index 0.70
SVM decision value 0.82
SVM RNA-class probability 0.859673
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19846045 113 - 20766785
GUCGAUCGAUCGCCCGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCCUGGAAAUCAGAGCA
...((((((((....))))))))..(((((..(((((((........))).((((((..((.((((((.........)))))).))........))))))))))...))))). ( -41.00)
>DroSec_CAF1 88153 113 - 1
GUCGAUCGAUCGCUCGAUCGAUCUCGUUCCCGUUCCCGAUCUCAAGCUCCCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCCUGGAAAUCAGAGCA
...((((((((....))))))))......................((((((((((((..((.((((((.........)))))).))........))))))))......)))). ( -40.60)
>DroSim_CAF1 64384 113 - 1
GUCGAUCGAUCGCUUGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCCUGGAAAUCAGAGCA
...((((((((....))))))))..(((((..(((((((........))).((((((..((.((((((.........)))))).))........))))))))))...))))). ( -40.10)
>DroEre_CAF1 89664 103 - 1
GUCGAUCGAC----CGAUCGAUCUCGAUCUCGUUCUCGAUCU------CGCGGCCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCCUGGAAAUCAGAGCA
(((((((...----.))))))).........(((((.(((.(------(..((((((..((.((((((.........)))))).)).)))......)))..)).)))))))). ( -33.20)
>DroYak_CAF1 87598 93 - 1
GUCGAUCCA--------------UCGAUCUCGUUCUCGAUCA------CAUCGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCAGGCUUUGACUUUUGCCUGGUAAUCAGAGCA
(((((....--------------)))))...(((((.(((((------((........)))))...............((((((((..........)))))))).))))))). ( -26.70)
>consensus
GUCGAUCGAUCGC_CGAUCGAUCUCGUUCUCGUUCCCGAUCUCAA_CUCGCGGGCAAUUGUGGGGCAUUUUUAAUUUGUGCCCGGCUUUGACUUUUGCCUGGAAAUCAGAGCA
...((((((((....))))))))..(((((((....)))...........(((((((..((.((((((.........)))))).))........))))))).......)))). (-25.30 = -28.04 +   2.74)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,846,084 – 19,846,190
Length 106
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 87.98
Mean single sequence MFE -33.88
Consensus MFE -24.43
Energy contribution -25.44
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.72
SVM decision value 0.49
SVM RNA-class probability 0.754803
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19846084 106 - 20766785
CAUAUGAAAAUUCCACUGGCAG-------UGCAGAAGCUGUCGAUCGAUCGCCCGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAA
....((((((((((((.(((((-------(......))))))((((((((....))))))))........((((.(((........))).))))....)))))..))))))). ( -33.60)
>DroSec_CAF1 88192 106 - 1
CAUAUGAAAAUUCCACUGGCAG-------UGCAGAAGCUGUCGAUCGAUCGCUCGAUCGAUCUCGUUCCCGUUCCCGAUCUCAAGCUCCCGGGCAAUUGUGGGGCAUUUUUAA
....(((((((......(((((-------(......))))))((((((((....))))))))..(((((((((((((............)))).)).)).)))))))))))). ( -33.10)
>DroSim_CAF1 64423 106 - 1
CAUAUGAAAAUUCCACUGGCAG-------UGCAGAAGCUGUCGAUCGAUCGCUUGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAA
....((((((((((((.(((((-------(......))))))((((((((....))))))))........((((.(((........))).))))....)))))..))))))). ( -32.70)
>DroEre_CAF1 89703 103 - 1
CAUAUGAAAAUUCCACUGGCAGAAGCCAGCGCAGAAGCUGUCGAUCGAC----CGAUCGAUCUCGAUCUCGUUCUCGAUCU------CGCGGCCAAUUGUGGGGCAUUUUUAA
....((((((((((.(((((....)))))(((((..(((((.((((((.----.(((((....)))))......)))))).------.)))))...)))))))).))))))). ( -36.10)
>consensus
CAUAUGAAAAUUCCACUGGCAG_______UGCAGAAGCUGUCGAUCGAUCGCUCGAUCGAUCUCGUUCUCGUUCCCGAUCUCAAACUCGCGGGCAAUUGUGGGGCAUUUUUAA
....((((((((((((.(((((...............)))))((((((((....))))))))........(..(.(((........))).)..)....)))))..))))))). (-24.43 = -25.44 +   1.00)

alignment

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secondary structure

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Window 8

Location 19,846,123 – 19,846,229
Length 106
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 81.07
Mean single sequence MFE -28.78
Consensus MFE -15.04
Energy contribution -16.52
Covariance contribution 1.47
Combinations/Pair 1.04
Mean z-score -2.40
Structure conservation index 0.52
SVM decision value 0.29
SVM RNA-class probability 0.668290
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19846123 106 + 20766785
GAACGAGAACGAGAUCGAUCGGGCGAUCGAUCGACAGCUUCUGCA-------CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUA
....((((.((((.((((((((....))))))))..((....)).-------..(((((((((...))))).)).)).)))).))))...(((((((((....))))))))). ( -28.10)
>DroSec_CAF1 88231 106 + 1
GAACGGGAACGAGAUCGAUCGAGCGAUCGAUCGACAGCUUCUGCA-------CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUA
...((....)).((((((((....))))))))....((....)).-------..(((((((((...))))).)).))(((.(....))))(((((((((....))))))))). ( -28.70)
>DroSim_CAF1 64462 106 + 1
GAACGAGAACGAGAUCGAUCAAGCGAUCGAUCGACAGCUUCUGCA-------CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUA
....(((((...((((((((....))))))))......(((..(.-------......)..))))))))........(((.(....))))(((((((((....))))))))). ( -27.00)
>DroEre_CAF1 89736 109 + 1
GAACGAGAUCGAGAUCGAUCG----GUCGAUCGACAGCUUCUGCGCUGGCUUCUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGAAAAAUUACAUACUUGUAAUUUUA
....(((((((((.((((((.----...))))))..((((...(((((((....)))))))((....))....)))).)))))))))...(((((((((....))))))))). ( -40.40)
>DroYak_CAF1 87670 93 + 1
GAACGAGAUCGA--------------UGGAUCGACAG------CACUGGCCUCUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUA
....((((((((--------------((..(((....------(((((((....)))))))((....))...))).)).))))))))...(((((((((....))))))))). ( -26.70)
>DroMoj_CAF1 167937 81 + 1
--------------UCGAUC----GAUCGAUCGACAGCUUC-------------G-CUGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUA
--------------((((((----....))))))..(((.(-------------(-.((((((...)))))))))))(((.(....))))(((((((((....))))))))). ( -21.80)
>consensus
GAACGAGAACGAGAUCGAUCG___GAUCGAUCGACAGCUUCUGCA_______CUGCCAGUGGAAUUUUCAUAUGAGCGCUUGAUUUCAGCAAAAUUACAUACUUGUAAUUUUA
............((((((((....))))))))...........................((((((((((....))).....)))))))..(((((((((....))))))))). (-15.04 = -16.52 +   1.47)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,846,190 – 19,846,280
Length 90
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 85.21
Mean single sequence MFE -21.02
Consensus MFE -17.24
Energy contribution -17.13
Covariance contribution -0.11
Combinations/Pair 1.22
Mean z-score -2.36
Structure conservation index 0.82
SVM decision value 0.80
SVM RNA-class probability 0.853794
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19846190 90 + 20766785
AGCGCUUGAUUUCAGCAAAAUUACAUACU-UGUAAUUUUAAAAUGCUGCC--GAGUGCCGAGAGAGUUGAAAAGCAACAGCA-CAAAA----AAACGC
.(((((((....(((((((((((((....-)))))))).....))))).)--)))))).......((((.....))))....-.....----...... ( -22.20)
>DroPse_CAF1 91601 96 + 1
AGCGCUUGAUUUCAGCAAAAUUACAUACU-UGUAAUUUUAAAAUGCUGCCAAGAGUGCCAAGAGAGUUGAAA-CCAACAGCAACAGAAAACUAAACGA
.((((((.....(((((((((((((....-)))))))).....)))))....)))))).......((((...-.)))).................... ( -21.80)
>DroWil_CAF1 207727 88 + 1
AGCGCUUGAUUUCAGUGAAAUUACAUACUUUGUAAUUUUAAAAUGCUACC--AACUGCCGAGAGAGUUGAAG-CUCACA-------AAAAAUAAAGGA
.(((.(((.(..((.((((((((((.....))))))))))...))..).)--)).))).....((((....)-)))...-------............ ( -16.20)
>DroYak_CAF1 87724 89 + 1
AGCGCUUGAUUUCAGCAAAAUUACAUACU-UGUAAUUUUAAAAUGCUGCC--GAGUGCCGAGAGAGUUGAGCAGCAGCAGCA-CAAA-----AAACGC
.(((((.(....))))(((((((((....-)))))))))....((((((.--(...(((....).))....).)))))))).-....-----...... ( -23.10)
>DroAna_CAF1 85209 92 + 1
AGCGCUUGAUUUCAGUAAAAUUACAUACU-UGUAAUUUUAAAAUGCUACC--GAGUGCCGAGAGAGUUGAA-AGCAACAGCA-CAGAAAAA-AAACGU
.(((((((.(..((.((((((((((....-))))))))))...))..).)--)))))).......((((..-..))))....-........-...... ( -21.00)
>DroPer_CAF1 92192 96 + 1
AGCGCUUGAUUUCAGCAAAAUUACAUACU-UGUAAUUUUAAAAUGCUGCCAAGAGUGCCAAGAGAGUUGAAA-CCAACAGCAACAGAAAACUAAACGA
.((((((.....(((((((((((((....-)))))))).....)))))....)))))).......((((...-.)))).................... ( -21.80)
>consensus
AGCGCUUGAUUUCAGCAAAAUUACAUACU_UGUAAUUUUAAAAUGCUGCC__GAGUGCCGAGAGAGUUGAAA_CCAACAGCA_CAGAAAA__AAACGA
.((((((.....(((((((((((((.....)))))))).....)))))....)))))).......((((.....)))).................... (-17.24 = -17.13 +  -0.11)

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 12:08:30 2006