Locus 6290

Sequence ID 3R_DroMel_CAF1
Location 16,409,745 – 16,409,886
Length 141
Max. P 0.912634
window10258 window10259 window10260 window10261

overview

Window 8

Location 16,409,745 – 16,409,859
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 82.57
Mean single sequence MFE -39.80
Consensus MFE -28.75
Energy contribution -28.03
Covariance contribution -0.71
Combinations/Pair 1.37
Mean z-score -2.08
Structure conservation index 0.72
SVM decision value 0.51
SVM RNA-class probability 0.762271
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16409745 114 + 27905053
UGGGUGGACACAAACUCAUGGGGUCGCAUCACAUUGUUCUGAAUCAGCUCCAGGCUGCCGCCGAGCAAGCUGUCCAGCUUGAUUCCCCUCGAGGCCUUAGCCUCCGUCACCCAA
((((((.((..........((((..(((......)))...(((((.((((..(((....)))))))(((((....)))))))))).))))(((((....))))).)))))))). ( -43.10)
>DroSec_CAF1 5385 114 + 1
UGGGUGGACACAAACUCAUGGGGUCGCAUCACAUUGUUCUGAAUCAGCUCCAGCCUGCCGACGAGCAAGCUGUCCAGCUUGAUUCCCUUCGAGGCCUUGGCCUCCGUCACCCAG
((((((.((..........(((...(((......)))...(((((((((.((((.(((......))).))))...))).)))))))))..(((((....))))).)))))))). ( -41.20)
>DroSim_CAF1 5389 114 + 1
UGGGUGGACACAAACUCAUGGGGUCGCAUCACAUUGUUCUGAAUCAGCUCCAGCCUGCCGACGAGCAAGCUGUCCAGCUUGAUUCCCCUCGAGGCCUUUGCCUCCGUCACCCAG
((((((.((..........((((..(((......)))...(((((((((.((((.(((......))).))))...))).)))))).))))(((((....))))).)))))))). ( -41.80)
>DroEre_CAF1 5444 114 + 1
UGGGUGGAUACAAACUCAUGGGAUCGCAUCACAUUGUUUUGAAUCAGCUCCAAGCUGCCGACUAGCAAGCUAUCUAGCUUGAUACCAAUCGAGGCCUUGGCCUCUGUCACCCAG
(((((((...........(((.(((((.(((........)))..((((.....)))).......))(((((....)))))))).)))...(((((....)))))..))))))). ( -36.70)
>DroYak_CAF1 5448 114 + 1
UGGGUGGACACAAACUCAUGUGGUCUUAUCACAUUGUUCUGAAUCAGCUCCAACUGACCGCCUAGCAAGCUGUCCAGCUUGAUUCCAAUCGAGGCCUUGGCCUCUGUCACCCAG
((((((.(((.........((((((........(((........)))........))))))....((((((....)))))).........(((((....)))))))))))))). ( -36.99)
>DroPer_CAF1 6607 114 + 1
UGGGUGGAAACAAAGUCGUGCGGCCGCGACGCAUUGCCCUGAAUGAGCUGCAGCCUGCCGCCCAGCGUGUCAUCCAACAUAAUGCUGGACUUGUUCUCCGCCACCGUUAUCCAA
..(((((((((((.(((..(((((.((...(((..((.(.....).))))).))..))))).((((((.............)))))))))))))).))))))............ ( -39.02)
>consensus
UGGGUGGACACAAACUCAUGGGGUCGCAUCACAUUGUUCUGAAUCAGCUCCAGCCUGCCGACGAGCAAGCUGUCCAGCUUGAUUCCCAUCGAGGCCUUGGCCUCCGUCACCCAG
(((((((...........((((((....(((........)))....)))))).............((((((....)))))).........(((((....)))))..))))))). (-28.75 = -28.03 +  -0.71)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,409,745 – 16,409,859
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 82.57
Mean single sequence MFE -45.40
Consensus MFE -33.65
Energy contribution -35.02
Covariance contribution 1.37
Combinations/Pair 1.27
Mean z-score -2.34
Structure conservation index 0.74
SVM decision value 0.73
SVM RNA-class probability 0.835765
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16409745 114 - 27905053
UUGGGUGACGGAGGCUAAGGCCUCGAGGGGAAUCAAGCUGGACAGCUUGCUCGGCGGCAGCCUGGAGCUGAUUCAGAACAAUGUGAUGCGACCCCAUGAGUUUGUGUCCACCCA
.((((((((((((((....)))))..((((.((((..((((((((((..((.(((....))).))))))).))))).......))))....)))).........))).)))))) ( -47.10)
>DroSec_CAF1 5385 114 - 1
CUGGGUGACGGAGGCCAAGGCCUCGAAGGGAAUCAAGCUGGACAGCUUGCUCGUCGGCAGGCUGGAGCUGAUUCAGAACAAUGUGAUGCGACCCCAUGAGUUUGUGUCCACCCA
..(((((((((((((....))))).....((((((.(((...(((((((((....))))))))).))))))))).......)))(((((((.(......).)))))))))))). ( -48.30)
>DroSim_CAF1 5389 114 - 1
CUGGGUGACGGAGGCAAAGGCCUCGAGGGGAAUCAAGCUGGACAGCUUGCUCGUCGGCAGGCUGGAGCUGAUUCAGAACAAUGUGAUGCGACCCCAUGAGUUUGUGUCCACCCA
..(((((((((((((....)))))..(((((((((.(((...(((((((((....))))))))).))))))))).......((.....))..))).........))).))))). ( -48.00)
>DroEre_CAF1 5444 114 - 1
CUGGGUGACAGAGGCCAAGGCCUCGAUUGGUAUCAAGCUAGAUAGCUUGCUAGUCGGCAGCUUGGAGCUGAUUCAAAACAAUGUGAUGCGAUCCCAUGAGUUUGUAUCCACCCA
..(((((((((((((....)))))((((((...((((((....))))))))))))..((((.....))))...........)))(((((((..........)))))))))))). ( -42.20)
>DroYak_CAF1 5448 114 - 1
CUGGGUGACAGAGGCCAAGGCCUCGAUUGGAAUCAAGCUGGACAGCUUGCUAGGCGGUCAGUUGGAGCUGAUUCAGAACAAUGUGAUAAGACCACAUGAGUUUGUGUCCACCCA
..(((((((((((((....))))).....((((((.(((...(((((.(((....))).))))).))))))))).((((.(((((.......)))))..)))).))).))))). ( -44.60)
>DroPer_CAF1 6607 114 - 1
UUGGAUAACGGUGGCGGAGAACAAGUCCAGCAUUAUGUUGGAUGACACGCUGGGCGGCAGGCUGCAGCUCAUUCAGGGCAAUGCGUCGCGGCCGCACGACUUUGUUUCCACCCA
.........(((((....(((((((((((((....((((....)))).))))))).((.((((((.((.((((......)))).)).))))))))......))))))))))).. ( -42.20)
>consensus
CUGGGUGACGGAGGCCAAGGCCUCGAGGGGAAUCAAGCUGGACAGCUUGCUCGGCGGCAGGCUGGAGCUGAUUCAGAACAAUGUGAUGCGACCCCAUGAGUUUGUGUCCACCCA
.((((((((((((((....))))).....((((((.(((...(((((((((....))))))))).))))))))).......)))(((((((.(......).))))))))))))) (-33.65 = -35.02 +   1.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,409,785 – 16,409,886
Length 101
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.14
Mean single sequence MFE -29.95
Consensus MFE -16.29
Energy contribution -16.35
Covariance contribution 0.06
Combinations/Pair 1.32
Mean z-score -2.40
Structure conservation index 0.54
SVM decision value 1.00
SVM RNA-class probability 0.897062
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16409785 101 + 27905053
GAAUCAGCUCCAGGCUGCCGCCGAGCAAGCUGUCCAGCUUGAUUCCCCUCGAGGCCUUAGCCUCCGUCACCCAAAAAAAUGUGAC-GAACUUCUCCACUUCC
(((((.((((..(((....)))))))(((((....)))))))))).....(((((....)))))((((((..........)))))-)............... ( -33.50)
>DroSec_CAF1 5425 101 + 1
GAAUCAGCUCCAGCCUGCCGACGAGCAAGCUGUCCAGCUUGAUUCCCUUCGAGGCCUUGGCCUCCGUCACCCAGAAGAAGGAGAU-AGACUUCUCCACUUCC
(((((((((.((((.(((......))).))))...))).)))))).....(((((....))))).........((((..(((((.-.....))))).)))). ( -37.30)
>DroSim_CAF1 5429 101 + 1
GAAUCAGCUCCAGCCUGCCGACGAGCAAGCUGUCCAGCUUGAUUCCCCUCGAGGCCUUUGCCUCCGUCACCCAGAAGAAGGAGAU-AGACUUCUCCACUUCC
(((((((((.((((.(((......))).))))...))).)))))).....(((((....))))).........((((..(((((.-.....))))).)))). ( -35.20)
>DroEre_CAF1 5484 101 + 1
GAAUCAGCUCCAAGCUGCCGACUAGCAAGCUAUCUAGCUUGAUACCAAUCGAGGCCUUGGCCUCUGUCACCCAGAAAAACGAGAU-GAACUUCUCCACUUCC
....((((.....))))..(((...((((((....)))))).........(((((....))))).)))............((((.-.....))))....... ( -27.90)
>DroYak_CAF1 5488 101 + 1
GAAUCAGCUCCAACUGACCGCCUAGCAAGCUGUCCAGCUUGAUUCCAAUCGAGGCCUUGGCCUCUGUCACCCAGAAAAAGGAGAC-GAACUUCUCCACUUCC
(((((((((......(((.((.......)).))).))).)))))).....(((((....)))))...............(((((.-.....)))))...... ( -27.70)
>DroPer_CAF1 6647 98 + 1
GAAUGAGCUGCAGCCUGCCGCCCAGCGUGUCAUCCAACAUAAUGCUGGACUUGUUCUCCGCCACCGUUAUCCAAAACA----GAUAGGACUUAUCAACCCUC
(((..(((.((.....)).))(((((((.............)))))))..)..)))(((....(.(((......))).----)...)))............. ( -18.12)
>consensus
GAAUCAGCUCCAGCCUGCCGACGAGCAAGCUGUCCAGCUUGAUUCCCAUCGAGGCCUUGGCCUCCGUCACCCAGAAAAAGGAGAU_GAACUUCUCCACUUCC
(((((.((((............))))(((((....)))))))))).....(((((....)))))...................................... (-16.29 = -16.35 +   0.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,409,785 – 16,409,886
Length 101
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.14
Mean single sequence MFE -38.08
Consensus MFE -25.61
Energy contribution -26.45
Covariance contribution 0.84
Combinations/Pair 1.36
Mean z-score -2.01
Structure conservation index 0.67
SVM decision value 1.08
SVM RNA-class probability 0.912634
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16409785 101 - 27905053
GGAAGUGGAGAAGUUC-GUCACAUUUUUUUGGGUGACGGAGGCUAAGGCCUCGAGGGGAAUCAAGCUGGACAGCUUGCUCGGCGGCAGCCUGGAGCUGAUUC
......(((..(((((-(((((..........)))))..(((((...((((((((......((((((....))))))))))).)))))))).)))))..))) ( -35.80)
>DroSec_CAF1 5425 101 - 1
GGAAGUGGAGAAGUCU-AUCUCCUUCUUCUGGGUGACGGAGGCCAAGGCCUCGAAGGGAAUCAAGCUGGACAGCUUGCUCGUCGGCAGGCUGGAGCUGAUUC
(((((.(((((.....-.)))))..))))).(....).(((((....))))).....((((((.(((...(((((((((....))))))))).))))))))) ( -46.10)
>DroSim_CAF1 5429 101 - 1
GGAAGUGGAGAAGUCU-AUCUCCUUCUUCUGGGUGACGGAGGCAAAGGCCUCGAGGGGAAUCAAGCUGGACAGCUUGCUCGUCGGCAGGCUGGAGCUGAUUC
(((((.(((((.....-.)))))..))))).(....).(((((....))))).....((((((.(((...(((((((((....))))))))).))))))))) ( -44.60)
>DroEre_CAF1 5484 101 - 1
GGAAGUGGAGAAGUUC-AUCUCGUUUUUCUGGGUGACAGAGGCCAAGGCCUCGAUUGGUAUCAAGCUAGAUAGCUUGCUAGUCGGCAGCUUGGAGCUGAUUC
(((((..((((.....-.))))...))))).(....).(((((....)))))((((((...((((((....))))))))))))..((((.....)))).... ( -34.40)
>DroYak_CAF1 5488 101 - 1
GGAAGUGGAGAAGUUC-GUCUCCUUUUUCUGGGUGACAGAGGCCAAGGCCUCGAUUGGAAUCAAGCUGGACAGCUUGCUAGGCGGUCAGUUGGAGCUGAUUC
(((((.(((((.....-.))))).)))))..(....).(((((....))))).....((((((.(((...(((((.(((....))).))))).))))))))) ( -36.70)
>DroPer_CAF1 6647 98 - 1
GAGGGUUGAUAAGUCCUAUC----UGUUUUGGAUAACGGUGGCGGAGAACAAGUCCAGCAUUAUGUUGGAUGACACGCUGGGCGGCAGGCUGCAGCUCAUUC
..((((((...((((.((((----(.....)))))...((.((..((.....(((((((.....)))))))......))..)).)).)))).)))))).... ( -30.90)
>consensus
GGAAGUGGAGAAGUCC_AUCUCCUUUUUCUGGGUGACGGAGGCCAAGGCCUCGAGGGGAAUCAAGCUGGACAGCUUGCUCGGCGGCAGGCUGGAGCUGAUUC
(((((..((((.......))))...))))).(....).(((((....))))).....((((((.(((...(((((((((....))))))))).))))))))) (-25.61 = -26.45 +   0.84)

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 12:17:50 2006