Locus 1022

Sequence ID 3R_DroMel_CAF1
Location 3,211,503 – 3,211,671
Length 168
Max. P 0.999942
window1651 window1652 window1653 window1654 window1655 window1656

overview

Window 1

Location 3,211,503 – 3,211,594
Length 91
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 96.28
Mean single sequence MFE -30.10
Consensus MFE -27.86
Energy contribution -28.30
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -2.83
Structure conservation index 0.93
SVM decision value 4.37
SVM RNA-class probability 0.999882
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3211503 91 + 27905053
U-GCUAUUGUUGUUGUAAUCCUAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAU
.-............................((((((((........))))))))...(((((((((((......)))).....))))))).. ( -31.20)
>DroSec_CAF1 36201 91 + 1
U-GCUAUUGUUGUUGUAAUCCUAUUAAAAGGCCAGCAAUCUAGUUUUUAUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAU
(-((((..(((((((....(((......))).)))))))...........)))))..(((((((((((......)))).....))))))).. ( -28.02)
>DroSim_CAF1 37694 91 + 1
U-GCUAUUGUUGUUGUAAUCCUAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAU
.-............................((((((((........))))))))...(((((((((((......)))).....))))))).. ( -31.20)
>DroEre_CAF1 30132 92 + 1
UGGCUUUUGUUGUUGUAAUCCUAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAU
.((((((((...............))))))((((((((........)))))))).))(((((((((((......)))).....))))))).. ( -33.96)
>DroYak_CAF1 19626 90 + 1
U-GCUUUUGUUGUUGUAAUCCUAUUAAAGGGCCAGCUAUCUAGCUUUUGUUGGCACCGUCGGCUGC-GAUUUUCCAGCCUGUCAGCCGGCAU
.-..........................((((((((............)))))).))(((((((((-(...........)).)))))))).. ( -26.10)
>consensus
U_GCUAUUGUUGUUGUAAUCCUAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAU
..............................((((((((........))))))))...(((((((((((......)))).....))))))).. (-27.86 = -28.30 +   0.44)

alignment

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secondary structure

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Window 2

Location 3,211,503 – 3,211,594
Length 91
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 96.28
Mean single sequence MFE -26.82
Consensus MFE -23.70
Energy contribution -23.78
Covariance contribution 0.08
Combinations/Pair 1.11
Mean z-score -2.30
Structure conservation index 0.88
SVM decision value 2.83
SVM RNA-class probability 0.997263
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3211503 91 - 27905053
AUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUAGGAUUACAACAACAAUAGC-A
.(((((((((...(..(....)..)..)))))))))............((((..(((.((.(((......)))....)).)))...))))-. ( -28.70)
>DroSec_CAF1 36201 91 - 1
AUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAAUAAAAACUAGAUUGCUGGCCUUUUAAUAGGAUUACAACAACAAUAGC-A
.(((((((((...(..(....)..)..))))))))).(((.........((((....))))(((......)))...............))-) ( -24.40)
>DroSim_CAF1 37694 91 - 1
AUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUAGGAUUACAACAACAAUAGC-A
.(((((((((...(..(....)..)..)))))))))............((((..(((.((.(((......)))....)).)))...))))-. ( -28.70)
>DroEre_CAF1 30132 92 - 1
AUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUAGGAUUACAACAACAAAAGCCA
..((((((((...(..(....)..)..))))))))(((((((.(((........))).))))(((.....)))...............))). ( -27.80)
>DroYak_CAF1 19626 90 - 1
AUGCCGGCUGACAGGCUGGAAAAUC-GCAGCCGACGGUGCCAACAAAAGCUAGAUAGCUGGCCCUUUAAUAGGAUUACAACAACAAAAGC-A
..((((((((.(.((((((.....)-.)))))......((........))..).))))))))(((.....))).................-. ( -24.50)
>consensus
AUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUAGGAUUACAACAACAAUAGC_A
..((((((((...(..(....)..)..))))))))((.((((.(((........))).))))))............................ (-23.70 = -23.78 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,211,523 – 3,211,634
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 97.12
Mean single sequence MFE -38.52
Consensus MFE -36.70
Energy contribution -37.34
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -3.08
Structure conservation index 0.95
SVM decision value 4.71
SVM RNA-class probability 0.999942
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3211523 111 + 27905053
UAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAG
.........((((((((........))))))))...(((((((((((......)))).....))))))).((((((((((..((..........))..)))).)))))).. ( -41.40)
>DroSec_CAF1 36221 111 + 1
UAUUAAAAGGCCAGCAAUCUAGUUUUUAUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAG
.........(((((.((........)).)))))...(((((((((((......)))).....))))))).((((((((((..((..........))..)))).)))))).. ( -35.10)
>DroSim_CAF1 37714 111 + 1
UAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAG
.........((((((((........))))))))...(((((((((((......)))).....))))))).((((((((((..((..........))..)))).)))))).. ( -41.40)
>DroEre_CAF1 30153 111 + 1
UAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAG
.........((((((((........))))))))...(((((((((((......)))).....))))))).((((((((((..((..........))..)))).)))))).. ( -41.40)
>DroYak_CAF1 19646 110 + 1
UAUUAAAGGGCCAGCUAUCUAGCUUUUGUUGGCACCGUCGGCUGC-GAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGACUCGUUUCGGCGAAACAAAG
.......((((((((............)))))).))(((((((((-(...........)).)))))))).((((((((((...(..........)...)))).)))))).. ( -33.30)
>consensus
UAUUAAAAGGCCAGCAAUCUAGCUUUUGUUGGCACCGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAG
.........((((((((........))))))))...(((((((((((......)))).....))))))).((((((((((..((..........))..)))).)))))).. (-36.70 = -37.34 +   0.64)

alignment

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secondary structure

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Window 4

Location 3,211,523 – 3,211,634
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 97.12
Mean single sequence MFE -32.68
Consensus MFE -30.88
Energy contribution -31.28
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.94
SVM decision value 2.61
SVM RNA-class probability 0.995748
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3211523 111 - 27905053
CUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUA
...(((((((.(((......)))...)))))))(((.....(((((((((...(..(....)..)..))))))))).)))....(((((((((....)))).))))).... ( -34.10)
>DroSec_CAF1 36221 111 - 1
CUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAAUAAAAACUAGAUUGCUGGCCUUUUAAUA
.((..(((((.((...))...)))))..)).((((((.(...((((((((...(..(....)..)..))))))))(((..........))).).))))))........... ( -31.30)
>DroSim_CAF1 37714 111 - 1
CUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUA
...(((((((.(((......)))...)))))))(((.....(((((((((...(..(....)..)..))))))))).)))....(((((((((....)))).))))).... ( -34.10)
>DroEre_CAF1 30153 111 - 1
CUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUA
...(((((((.(((......)))...)))))))(((.....(((((((((...(..(....)..)..))))))))).)))....(((((((((....)))).))))).... ( -34.10)
>DroYak_CAF1 19646 110 - 1
CUUUGUUUCGCCGAAACGAGUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUC-GCAGCCGACGGUGCCAACAAAAGCUAGAUAGCUGGCCCUUUAAUA
.((((((.(((((....................(((.....)))((((((...(..(....)..)-.)))))).)))))..)))))).(((((....)))))......... ( -29.80)
>consensus
CUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCGGUGCCAACAAAAGCUAGAUUGCUGGCCUUUUAAUA
...(((((((.(((......)))...)))))))(((.....(((((((((...(..(....)..)..))))))))).)))........(((((....)))))......... (-30.88 = -31.28 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,211,558 – 3,211,671
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 97.35
Mean single sequence MFE -31.08
Consensus MFE -28.70
Energy contribution -28.74
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.63
Structure conservation index 0.92
SVM decision value 1.52
SVM RNA-class probability 0.960853
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3211558 113 + 27905053
CGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAGACUUAAAGUGCUCAUUCACCUGAUUUUGCUGGUUUUA
.(((((((((((......)))).....)))))))..(((((((((..((..........))..)))).)))))((((((......((....((....))....)).)))))). ( -32.30)
>DroSec_CAF1 36256 113 + 1
CGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAGACUUAAAGUGCUCAUUCACCUGAUUUUGCUGGUUUUA
.(((((((((((......)))).....)))))))..(((((((((..((..........))..)))).)))))((((((......((....((....))....)).)))))). ( -32.30)
>DroSim_CAF1 37749 113 + 1
CGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAGACUUAAAGUGCUCAUUCACCUGAUUUUGCUGGUUUUA
.(((((((((((......)))).....)))))))..(((((((((..((..........))..)))).)))))((((((......((....((....))....)).)))))). ( -32.30)
>DroEre_CAF1 30188 113 + 1
CGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAGACUUAAAGUGCUCAUUCACCUGAUUUUACUGGUUUUA
.(((((((((((......)))).....)))))))..(((((((((..((..........))..)))).)))))((((((...((((.(((......)))...)))))))))). ( -32.30)
>DroYak_CAF1 19681 112 + 1
CGUCGGCUGC-GAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGACUCGUUUCGGCGAAACAAAGACUUAAAGUACUCAUUCACCUGCUUUUACUGGUUUUA
.(((((((((-(...........)).)))))))).........((((((...((((......)))).))))))((((((.((((((..........))))))....)))))). ( -26.20)
>consensus
CGCCGGCUGCUGAUUUUCCAGCCUGUCAGCCGGCAUUGUUUGCUGUUUCAUUUCGAUUCGAUUCGGCGAAACAAAGACUUAAAGUGCUCAUUCACCUGAUUUUGCUGGUUUUA
.(((((((((((......)))).....)))))))...((((..((((((...((((......)))).)))))).))))...............(((..........))).... (-28.70 = -28.74 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,211,558 – 3,211,671
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 97.35
Mean single sequence MFE -29.90
Consensus MFE -28.28
Energy contribution -28.24
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.95
SVM decision value 1.95
SVM RNA-class probability 0.983524
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3211558 113 - 27905053
UAAAACCAGCAAAAUCAGGUGAAUGAGCACUUUAAGUCUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCG
........((....(((((((((.(((.((.....)))))...))))))...(((...)))..)))....)).......((((((((...(..(....)..)..)))))))). ( -31.10)
>DroSec_CAF1 36256 113 - 1
UAAAACCAGCAAAAUCAGGUGAAUGAGCACUUUAAGUCUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCG
........((....(((((((((.(((.((.....)))))...))))))...(((...)))..)))....)).......((((((((...(..(....)..)..)))))))). ( -31.10)
>DroSim_CAF1 37749 113 - 1
UAAAACCAGCAAAAUCAGGUGAAUGAGCACUUUAAGUCUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCG
........((....(((((((((.(((.((.....)))))...))))))...(((...)))..)))....)).......((((((((...(..(....)..)..)))))))). ( -31.10)
>DroEre_CAF1 30188 113 - 1
UAAAACCAGUAAAAUCAGGUGAAUGAGCACUUUAAGUCUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCG
........((....(((((((((.(((.((.....)))))...))))))...(((...)))..)))....)).......((((((((...(..(....)..)..)))))))). ( -29.50)
>DroYak_CAF1 19681 112 - 1
UAAAACCAGUAAAAGCAGGUGAAUGAGUACUUUAAGUCUUUGUUUCGCCGAAACGAGUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUC-GCAGCCGACG
.................((((((.(((.((.....)))))...)))))).......(((.........((((...........))))...((((((.....)-.)))))))). ( -26.70)
>consensus
UAAAACCAGCAAAAUCAGGUGAAUGAGCACUUUAAGUCUUUGUUUCGCCGAAUCGAAUCGAAAUGAAACAGCAAACAAUGCCGGCUGACAGGCUGGAAAAUCAGCAGCCGGCG
........((.......((((((.(((.((.....)))))...))))))((......))...........)).......((((((((...(..(....)..)..)))))))). (-28.28 = -28.24 +  -0.04)

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 09:58:36 2006