Locus 6584

Sequence ID 2L_DroMel_CAF1
Location 18,512,382 – 18,512,652
Length 270
Max. P 0.974136
window10504 window10505 window10506 window10507

overview

Window 4

Location 18,512,382 – 18,512,477
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 90.35
Mean single sequence MFE -27.05
Consensus MFE -22.58
Energy contribution -23.20
Covariance contribution 0.62
Combinations/Pair 1.04
Mean z-score -2.58
Structure conservation index 0.83
SVM decision value 1.70
SVM RNA-class probability 0.972830
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512382 95 + 22407834
UAAAUGUUUUUGGCUGAUUUCGAUUAGCAAUUGAGGUGCCGCCCUUACACAUAGGCAUUAUUUUCGGGCGAAGCCUCCUUUUUGAUGACAUUUAG
((((((((.((.((((((....))))))....(((((..(((((.....................)))))..)))))......)).)))))))). ( -27.80)
>DroSec_CAF1 32825 95 + 1
UAAAUGUUUUUGGCUGAUUUCGAUUAGCGAUUGAGGUGCCACCCUUACACGUAGGUUUUGUUUUCGGGCGAAGCCUCCUUUUUGAUGACAUUUAG
((((((((..((((..(((((((((...))))))))))))).........(.((((((((((....)))))))))).)........)))))))). ( -25.30)
>DroSim_CAF1 31378 95 + 1
UAAAUGUUUUUGGCUGAUUUCGAUUAGCGAUUGAGGUGCCACCCUUAAACGUAGGUUUUGUUUUCGGGCGAAGCCUCCUUUUUGAUGACAUUUAG
((((((((.((.((((((....))))))....(((((..(.(((..(((((.......)))))..))).)..)))))......)).)))))))). ( -27.70)
>DroYak_CAF1 32810 93 + 1
UAAAUGUUUCAGGCUGAUUUCAAUUAGCAAUUCAGGUGUCACCCUUAC--AUAGUCUUUAUUUUUGGGUGAAGCCUCCUUUUUGAUGACAUUUAG
((((((((((((((((((....)))))).....((((.((((((....--...............)))))).)))).....)))).)))))))). ( -27.41)
>consensus
UAAAUGUUUUUGGCUGAUUUCGAUUAGCAAUUGAGGUGCCACCCUUACACAUAGGCUUUAUUUUCGGGCGAAGCCUCCUUUUUGAUGACAUUUAG
((((((((....((((((....))))))....(((((..(((((.....................)))))..))))).........)))))))). (-22.58 = -23.20 +   0.62)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,512,382 – 18,512,477
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 90.35
Mean single sequence MFE -20.55
Consensus MFE -18.46
Energy contribution -18.15
Covariance contribution -0.31
Combinations/Pair 1.14
Mean z-score -2.21
Structure conservation index 0.90
SVM decision value 1.72
SVM RNA-class probability 0.974136
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512382 95 - 22407834
CUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAAUAAUGCCUAUGUGUAAGGGCGGCACCUCAAUUGCUAAUCGAAAUCAGCCAAAAACAUUUA
.(((((((..........((((..((((((....(((.......)))....))))))..))))....(((.((....)).))).....))))))) ( -21.50)
>DroSec_CAF1 32825 95 - 1
CUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAACAAAACCUACGUGUAAGGGUGGCACCUCAAUCGCUAAUCGAAAUCAGCCAAAAACAUUUA
.(((((((..........((((..((((((....((.........))....))))))..))))....(((.((....)).))).....))))))) ( -20.40)
>DroSim_CAF1 31378 95 - 1
CUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAACAAAACCUACGUUUAAGGGUGGCACCUCAAUCGCUAAUCGAAAUCAGCCAAAAACAUUUA
.(((((((..........((((..((((((..((((.........))))..))))))..))))....(((.((....)).))).....))))))) ( -22.00)
>DroYak_CAF1 32810 93 - 1
CUAAAUGUCAUCAAAAAGGAGGCUUCACCCAAAAAUAAAGACUAU--GUAAGGGUGACACCUGAAUUGCUAAUUGAAAUCAGCCUGAAACAUUUA
.(((((((..(((......(((..((((((....(((.....)))--....))))))..))).....(((.((....)).))).))).))))))) ( -18.30)
>consensus
CUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAACAAAACCUACGUGUAAGGGUGGCACCUCAAUCGCUAAUCGAAAUCAGCCAAAAACAUUUA
.(((((((..........((((..((((((.....................))))))..))))....(((.((....)).))).....))))))) (-18.46 = -18.15 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,512,440 – 18,512,557
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.09
Mean single sequence MFE -34.02
Consensus MFE -25.54
Energy contribution -25.34
Covariance contribution -0.20
Combinations/Pair 1.15
Mean z-score -1.63
Structure conservation index 0.75
SVM decision value 0.14
SVM RNA-class probability 0.604097
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512440 117 - 22407834
UCGUUUAGUAGUCGGGUGCUAAAAUGCCAGGCAAACACCGCCGACAGGUGGCGCAUGUCCGACAGCCAUAAAUUGGACAGCUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAAUA---
...........(((((((.......(((.(((.......)))((((..((((...(((((((..........)))))))))))..))))...........)))..))))))).....--- ( -37.30)
>DroPse_CAF1 39412 114 - 1
UCGAUUAGUGUCGAGGCGCUAAAAUGCCAAGCAAACAGGGACGACAGGUGGCGCAUGUCUGUUGGCCAUAAAUUGGAUGGCUAAAUGUCAUCAAAAAG-AGGCU-----CAAAACCAUCA
..(((((((((....)))))))...(((...(((....((.((((((..(.....)..)))))).)).....)))((((((.....))))))......-.))).-----........)). ( -32.00)
>DroSec_CAF1 32883 117 - 1
UCGAUUAGUAGCCGGGUGCUAAAAUGCCAGGCAAACACCGCCGACAGGUGGCGCAUGUCCGUCAGCCAUAAAUUGGACAGCUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAACA---
............((((((.......(((.(((.......)))((((..((((...((((((............))))))))))..))))...........)))..))))))......--- ( -35.30)
>DroSim_CAF1 31436 117 - 1
UCGAUUAGUAGCCGGGUGCUAAAAUGCCAGGCAAACACCGCCGACAGGUGGCGCAUGUCCGUCAGCCAUAAAUUGGACAGCUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAACA---
............((((((.......(((.(((.......)))((((..((((...((((((............))))))))))..))))...........)))..))))))......--- ( -35.30)
>DroYak_CAF1 32866 117 - 1
UCGAUUAGUAGCCGGGUGCUAAAAUGCCAGUCAAACACCGCCGACAGGUGGCGCAUGUCCGACAGCCAUAAAUUGGACAGCUAAAUGUCAUCAAAAAGGAGGCUUCACCCAAAAAUA---
.............(((((.......(((.........(((((....))))).((.(((((((..........)))))))))...................)))..))))).......--- ( -30.20)
>consensus
UCGAUUAGUAGCCGGGUGCUAAAAUGCCAGGCAAACACCGCCGACAGGUGGCGCAUGUCCGUCAGCCAUAAAUUGGACAGCUAAAUGUCAUCAAAAAGGAGGCUUCGCCCGAAAACA___
....((((((......))))))...(((.(((.......)))((((..((((...((((((............))))))))))..))))...........)))................. (-25.54 = -25.34 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,512,557 – 18,512,652
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.84
Mean single sequence MFE -31.38
Consensus MFE -22.54
Energy contribution -23.70
Covariance contribution 1.16
Combinations/Pair 1.25
Mean z-score -1.82
Structure conservation index 0.72
SVM decision value 0.62
SVM RNA-class probability 0.802483
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512557 95 + 22407834
AAUGUUUGGCCAAACAAUCAACGUGGCCAA-----------------------GUCAGCUUUUGUGUCUGGGCAUCGCGG-GGAUGCCCUAUCACUGAUGGUUUGCACUCGAUUUCUAA-
.....(((((((...........)))))))-----------------------((.((((...(((...(((((((....-.)))))))...)))....)))).)).............- ( -30.50)
>DroPse_CAF1 39526 119 + 1
AAUGUUUGGCCAGAUAAUUAACUUGGCCGACAAGAGAUGUACCCAAGAGAUGGGUCUGGUC-UGGGUCUGGUCGUGGCGGGGGAUGCCCUCUCGCUGAUAAGUUGCAUUCGAUUUCUAAU
(((((..((((((((......((((.....))))((((..(((((.....)))))...)))-)..))))))))..((((((((.....))))))))........)))))........... ( -37.70)
>DroSec_CAF1 33000 95 + 1
AAUGUUUGGCUAAACAAUCAACUUGGCCAA-----------------------GUCAGCUUUGGUGUCUGGGCAUCGCGG-GGAUGCCCUAUCACUGAUGGUUUGCAUUCGAUUUCUAA-
.....((((((((.........))))))))-----------------------((.(((((..(((...(((((((....-.)))))))...)))..).)))).)).............- ( -31.80)
>DroSim_CAF1 31553 95 + 1
AAUGUUUGGCCAAACAAUCAACUUGGCCAA-----------------------AUCAGCUUUUGUGUCUGGGCAUCGCGG-GGAUGCCCUAUCACUGAUGGUUUGCAUUCGAUUUCUAA-
...((((((((((.........))))))))-----------------------)).((((...(((...(((((((....-.)))))))...)))....))))................- ( -30.60)
>DroYak_CAF1 32983 94 + 1
AAUGUUUGGCCAAACAAUCAACUUCGCCAA-----------------------GUCAGCUU-UGUGUCUGGGCAUCGCGG-GGAUGCCCUAUAACUGAUGGCUUGCAUUCGAUUUCUAA-
(((((..(((((............(((.((-----------------------(....)))-.)))...(((((((....-.))))))).........))))).)))))..........- ( -26.30)
>consensus
AAUGUUUGGCCAAACAAUCAACUUGGCCAA_______________________GUCAGCUUUUGUGUCUGGGCAUCGCGG_GGAUGCCCUAUCACUGAUGGUUUGCAUUCGAUUUCUAA_
.....((((((((.........)))))))).......................((.((((...(((...(((((((......)))))))...)))....)))).)).............. (-22.54 = -23.70 +   1.16)

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 12:14:50 2006