Locus 7163

Sequence ID 2L_DroMel_CAF1
Location 20,043,238 – 20,043,406
Length 168
Max. P 0.971695
window11437 window11438 window11439 window11440 window11441

overview

Window 7

Location 20,043,238 – 20,043,332
Length 94
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 61.54
Mean single sequence MFE -23.27
Consensus MFE -9.95
Energy contribution -10.73
Covariance contribution 0.78
Combinations/Pair 1.06
Mean z-score -1.89
Structure conservation index 0.43
SVM decision value 0.17
SVM RNA-class probability 0.618226
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20043238 94 + 22407834
----GCCAAAUAUUUUGCACAGAGCUCC----------------------UUUGACAGCAGUUCCCAUGAUAGUGCUGCCUUGAAACUACUUUCCAGCCAUAUCAUGGUUUCACUCUGUG
----.............(((((((((..----------------------......))).....((((((((..((((....((((....))))))))..))))))))......)))))) ( -24.10)
>DroSec_CAF1 225518 81 + 1
AAAUGCCAACUAUUUUGC---------------------------------------GAAGUUCCCAUGAUAGUGCUGCCUUGAAACUACUUUCCAGCCAUAUCAUGGUUACACCCUGUG
..................---------------------------------------...((..((((((((..((((....((((....))))))))..))))))))..))........ ( -18.50)
>DroYak_CAF1 219457 120 + 1
ACAAGCCAAUGAUUUCCCGAAGAGCCCCUUUGAUCCAAUUCCCAGUGACUUGGGGCCACAAGUGCCAUUAUAGUUUUACCUUGAAACUACUUUCCAGUCAUAUCAUGGUUUCAUUCUGUG
..((((((.((((....(((((.....)))))............((((((.((((((....).)))....(((((((.....)))))))....))))))))))))))))))......... ( -27.20)
>consensus
A_A_GCCAAAUAUUUUGC__AGAGC_CC______________________U__G_C_GCAGUUCCCAUGAUAGUGCUGCCUUGAAACUACUUUCCAGCCAUAUCAUGGUUUCACUCUGUG
................................................................((((((((..((((....((((....))))))))..))))))))............ ( -9.95 = -10.73 +   0.78)

alignment

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secondary structure

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Window 8

Location 20,043,262 – 20,043,368
Length 106
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 81.63
Mean single sequence MFE -27.80
Consensus MFE -17.85
Energy contribution -19.60
Covariance contribution 1.75
Combinations/Pair 1.08
Mean z-score -1.77
Structure conservation index 0.64
SVM decision value 0.19
SVM RNA-class probability 0.627721
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20043262 106 + 22407834
----------UUUGACAGCAGUUCCCAUGAUAGUGCUGCCUUGAAACUACUUUCCAGCCAUAUCAUGGUUUCACUCUGUGGCCUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUA
----------....((((.(((..((((((((..((((....((((....))))))))..))))))))....)))))))(((((((((..........)))))).)))........ ( -27.70)
>DroSec_CAF1 225536 99 + 1
-----------------GAAGUUCCCAUGAUAGUGCUGCCUUGAAACUACUUUCCAGCCAUAUCAUGGUUACACCCUGUGGCCUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUA
-----------------...((..((((((((..((((....((((....))))))))..))))))))..))....((((((((((((..........)))))).).))))).... ( -25.80)
>DroEre_CAF1 220453 116 + 1
CCCAGUGGCUUGUGGCCACAGUUCCCAUGAUAGUUUUGCCUUGAAACUACUUUCCUGCCAUAUCAUGGUUUCACUCUGCGGCAUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUA
....(((((.....))))).....((((((((.....((...((((....))))..))..))))))))...(((((((.....))))(((((......)))))))).......... ( -28.40)
>DroYak_CAF1 219497 116 + 1
CCCAGUGACUUGGGGCCACAAGUGCCAUUAUAGUUUUACCUUGAAACUACUUUCCAGUCAUAUCAUGGUUUCAUUCUGUGGCGUAGACAGACAAAUAUGUCUGGUGUUUAUAAAUA
(((((....)))))((((((((((......(((((((.....)))))))....(((.........)))...)))).)))))).....((((((....))))))............. ( -29.30)
>consensus
__________UGUGGCCACAGUUCCCAUGAUAGUGCUGCCUUGAAACUACUUUCCAGCCAUAUCAUGGUUUCACUCUGUGGCCUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUA
..............(((((((...((((((((.....((...((((....))))..))..)))))))).......))))))).....(((((......)))))............. (-17.85 = -19.60 +   1.75)

alignment

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secondary structure

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Window 9

Location 20,043,262 – 20,043,368
Length 106
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 81.63
Mean single sequence MFE -29.10
Consensus MFE -20.88
Energy contribution -22.12
Covariance contribution 1.25
Combinations/Pair 1.15
Mean z-score -1.87
Structure conservation index 0.72
SVM decision value 0.66
SVM RNA-class probability 0.816007
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20043262 106 - 22407834
UAUUUAUAAACACCAGACUUAUUUGUCUGUCUAGGCCACAGAGUGAAACCAUGAUAUGGCUGGAAAGUAGUUUCAAGGCAGCACUAUCAUGGGAACUGCUGUCAAA----------
.............(((((......)))))........(((((((....((((((((..((((((((....))))....))))..))))))))..))).))))....---------- ( -28.50)
>DroSec_CAF1 225536 99 - 1
UAUUUAUAAACACCAGACUUAUUUGUCUGUCUAGGCCACAGGGUGUAACCAUGAUAUGGCUGGAAAGUAGUUUCAAGGCAGCACUAUCAUGGGAACUUC-----------------
.........(((((((((......))))((....)).....)))))..((((((((..((((((((....))))....))))..)))))))).......----------------- ( -26.90)
>DroEre_CAF1 220453 116 - 1
UAUUUAUAAACACCAGACUUAUUUGUCUGUCUAUGCCGCAGAGUGAAACCAUGAUAUGGCAGGAAAGUAGUUUCAAGGCAAAACUAUCAUGGGAACUGUGGCCACAAGCCACUGGG
.............(((((......)))))......((....(((....((((((((..((..((((....))))...)).....))))))))..)))(((((.....))))).)). ( -31.40)
>DroYak_CAF1 219497 116 - 1
UAUUUAUAAACACCAGACAUAUUUGUCUGUCUACGCCACAGAAUGAAACCAUGAUAUGACUGGAAAGUAGUUUCAAGGUAAAACUAUAAUGGCACUUGUGGCCCCAAGUCACUGGG
.............((((((....)))))).....(((((((......(((.(((.((.(((....))).)).))).)))....(......)....)))))))((((......)))) ( -29.60)
>consensus
UAUUUAUAAACACCAGACUUAUUUGUCUGUCUAGGCCACAGAGUGAAACCAUGAUAUGGCUGGAAAGUAGUUUCAAGGCAAAACUAUCAUGGGAACUGCGGCCACA__________
.............(((((......))))).....(((((((.......((((((((..((..((((....))))...)).....))))))))...))))))).............. (-20.88 = -22.12 +   1.25)

alignment

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secondary structure

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Window 0

Location 20,043,292 – 20,043,406
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 94.01
Mean single sequence MFE -25.49
Consensus MFE -23.74
Energy contribution -24.24
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.93
SVM decision value 1.68
SVM RNA-class probability 0.971695
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20043292 114 + 22407834
UUGAAACUACUUUCCAGCCAUAUCAUGGUUUCACUCUGUGGCCUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUAAACCAUCAUUGCCAUAAUGGCCAUCAUCAGCCAAUGCG
.((((((((................))))))))...((((((.....(((((......)))))(.(((((....))))))......)))))).((((........))))..... ( -25.39)
>DroSec_CAF1 225559 114 + 1
UUGAAACUACUUUCCAGCCAUAUCAUGGUUACACCCUGUGGCCUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUAAACCAUCAUUGCCAUAAUGGCCAUCAUCAGCCAAUGCA
...............((((((...))))))......((((((.....(((((......)))))(.(((((....))))))......)))))).((((........))))..... ( -24.40)
>DroEre_CAF1 220493 111 + 1
UUGAAACUACUUUCCUGCCAUAUCAUGGUUUCACUCUGCGGCAUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUAAACCAUCAUUGCCAUAAUGGCCAUCAUCAGCCAAU---
.((((((((................))))))))......((((..(((((((......)))))(.(((((....)))))).))..))))....((((........))))..--- ( -24.59)
>DroYak_CAF1 219537 114 + 1
UUGAAACUACUUUCCAGUCAUAUCAUGGUUUCAUUCUGUGGCGUAGACAGACAAAUAUGUCUGGUGUUUAUAAAUAAACCAUCAUUGCCAUAAUGGCCAUCAUCAGCCAAUAUA
.((((((((................))))))))...(((((((..((((((((....))))))(.(((((....)))))).))..))))))).((((........))))..... ( -27.59)
>consensus
UUGAAACUACUUUCCAGCCAUAUCAUGGUUUCACUCUGUGGCCUAGACAGACAAAUAAGUCUGGUGUUUAUAAAUAAACCAUCAUUGCCAUAAUGGCCAUCAUCAGCCAAUGCA
.((((((((................))))))))...((((((.....(((((......)))))(.(((((....))))))......)))))).((((........))))..... (-23.74 = -24.24 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,043,292 – 20,043,406
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 94.01
Mean single sequence MFE -29.25
Consensus MFE -25.95
Energy contribution -26.07
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.89
SVM decision value 0.11
SVM RNA-class probability 0.588865
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20043292 114 - 22407834
CGCAUUGGCUGAUGAUGGCCAUUAUGGCAAUGAUGGUUUAUUUAUAAACACCAGACUUAUUUGUCUGUCUAGGCCACAGAGUGAAACCAUGAUAUGGCUGGAAAGUAGUUUCAA
.....(((((.((((.(((((((((....)))))))))...))))......(((((......)))))....))))).....(((((((((...)))(((....))).)))))). ( -29.80)
>DroSec_CAF1 225559 114 - 1
UGCAUUGGCUGAUGAUGGCCAUUAUGGCAAUGAUGGUUUAUUUAUAAACACCAGACUUAUUUGUCUGUCUAGGCCACAGGGUGUAACCAUGAUAUGGCUGGAAAGUAGUUUCAA
((((((((((.((((.(((((((((....)))))))))...))))......(((((......)))))....)))))....)))))....(((.((.(((....))).)).))). ( -31.00)
>DroEre_CAF1 220493 111 - 1
---AUUGGCUGAUGAUGGCCAUUAUGGCAAUGAUGGUUUAUUUAUAAACACCAGACUUAUUUGUCUGUCUAUGCCGCAGAGUGAAACCAUGAUAUGGCAGGAAAGUAGUUUCAA
---...(((((((((.(((((((((....)))))))))...))))......(((((......)))))(((.(((((.(..(((....)))..).))))))))...))))).... ( -26.90)
>DroYak_CAF1 219537 114 - 1
UAUAUUGGCUGAUGAUGGCCAUUAUGGCAAUGAUGGUUUAUUUAUAAACACCAGACAUAUUUGUCUGUCUACGCCACAGAAUGAAACCAUGAUAUGACUGGAAAGUAGUUUCAA
.....((((..((((.(((((((((....)))))))))...))))......((((((....)))))).....)))).....(((((((((...)))(((....))).)))))). ( -29.30)
>consensus
UGCAUUGGCUGAUGAUGGCCAUUAUGGCAAUGAUGGUUUAUUUAUAAACACCAGACUUAUUUGUCUGUCUAGGCCACAGAGUGAAACCAUGAUAUGGCUGGAAAGUAGUUUCAA
.....((((..((((.(((((((((....)))))))))...))))......(((((......))))).....)))).....(((((((((...)))(((....))).)))))). (-25.95 = -26.07 +   0.12)

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 12:29:04 2006