Locus 498

Sequence ID X_DroMel_CAF1
Location 1,428,399 – 1,428,557
Length 158
Max. P 0.996318
window769 window770 window771 window772 window773 window774

overview

Window 9

Location 1,428,399 – 1,428,498
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 93.16
Mean single sequence MFE -38.75
Consensus MFE -31.20
Energy contribution -32.33
Covariance contribution 1.12
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.81
SVM decision value 1.10
SVM RNA-class probability 0.915276
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1428399 99 + 22224390
ACUGGAAUCGGCUCGCCGGACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGCAUGCGUUGCAUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUC
(((((((..((((.(.....).))))(((.((((((((((((((..((((((.....))))))..)))))))...))))))))))...))))))).... ( -41.90)
>DroSec_CAF1 33173 90 + 1
ACUGGAAUCGGCUCGCCGGACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGC---------AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUC
(((((((..((((.(.....).))))(((.(((((((.(((((((.((((.....)))---------))))))))))))))))))...))))))).... ( -36.10)
>DroSim_CAF1 24717 90 + 1
ACUGGAAUCGGCUCGCCGGACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGC---------AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUC
(((((((..((((.(.....).))))(((.(((((((.(((((((.((((.....)))---------))))))))))))))))))...))))))).... ( -36.10)
>DroEre_CAF1 28398 99 + 1
ACUGGAAUCGGCUCGCCGGACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGCAUGUGUUGCAUGCGUGUGCGUGCAUCCUUUUUUCGGAUUUC
.((((((..((....))(((...((((.(((((((((.((((((((.((....)).)))))))).))))))).)).)).)).)))...))))))..... ( -40.90)
>consensus
ACUGGAAUCGGCUCGCCGGACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGC_________AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUC
.((((((..((((.(.....).))))(((.(((((((.(((((.....)))))...(((((.....)))))....))))))))))...))))))..... (-31.20 = -32.33 +   1.12)

alignment

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secondary structure

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Window 0

Location 1,428,399 – 1,428,498
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 93.16
Mean single sequence MFE -27.88
Consensus MFE -23.90
Energy contribution -25.03
Covariance contribution 1.13
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.86
SVM decision value 0.44
SVM RNA-class probability 0.736550
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1428399 99 - 22224390
GAAAACCGAAAAAAGGAUGCACGCACACGCAUGCAACGCAUGCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGUCCGGCGAGCCGAUUCCAGU
..............(((.((.(((....((((((...(((((.....))))).((....)).))))))....(((.....)))))).))....)))... ( -31.50)
>DroSec_CAF1 33173 90 - 1
GAAAACCGAAAAAAGGAUGCACGCACACGCAU---------GCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGUCCGGCGAGCCGAUUCCAGU
..............(((((((.((....((((---------(.....))))).((....)).)).))))...((((..(.....)..))))..)))... ( -25.70)
>DroSim_CAF1 24717 90 - 1
GAAAACCGAAAAAAGGAUGCACGCACACGCAU---------GCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGUCCGGCGAGCCGAUUCCAGU
..............(((((((.((....((((---------(.....))))).((....)).)).))))...((((..(.....)..))))..)))... ( -25.70)
>DroEre_CAF1 28398 99 - 1
GAAAUCCGAAAAAAGGAUGCACGCACACGCAUGCAACACAUGCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGUCCGGCGAGCCGAUUCCAGU
(.((((........(((((((.((....(((((.....)))))......((((.....)))))).)))).)))(((..(.....)..))))))).)... ( -28.60)
>consensus
GAAAACCGAAAAAAGGAUGCACGCACACGCAU_________GCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGUCCGGCGAGCCGAUUCCAGU
..............(((((((.((....(((((.....)))))......((((.....)))))).))))...((((..(.....)..))))..)))... (-23.90 = -25.03 +   1.13)

alignment

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secondary structure

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Window 1

Location 1,428,418 – 1,428,537
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -43.01
Consensus MFE -37.78
Energy contribution -38.91
Covariance contribution 1.13
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.88
SVM decision value 0.92
SVM RNA-class probability 0.882814
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1428418 119 + 22224390
ACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGCAUGCGUUGCAUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCACA
....((..(((.((((((.((....)).)))))))))((((((...))))))(((((((((..(((((((..((.....))..)).............))))))))))))))..))... ( -43.71)
>DroSec_CAF1 33192 108 + 1
ACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGC---------AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA--
....((......((((((.(((((((...))))))).))---------))))(((((((((..(((((((..((.....))..)).............))))))))))))))..)).-- ( -40.11)
>DroSim_CAF1 24736 108 + 1
ACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGC---------AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA--
....((......((((((.(((((((...))))))).))---------))))(((((((((..(((((((..((.....))..)).............))))))))))))))..)).-- ( -40.11)
>DroEre_CAF1 28417 117 + 1
ACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGCAUGUGUUGCAUGCGUGUGCGUGCAUCCUUUUUUCGGAUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA--
....((......((((((.((((((((.((....)).)))))))).))))))((((((((((((((.......))))((((.(..(......)..).))))).)))))))))..)).-- ( -48.10)
>consensus
ACUGGCCGGACUGCAUGCUGCAUGUGCUGCAUGUGUUGC_________AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA__
....((..(((.((((((.((....)).)))))))))(((((.....)))))(((((((((..(((((((..((.....))..)).............))))))))))))))..))... (-37.78 = -38.91 +   1.13)

alignment

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secondary structure

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Window 2

Location 1,428,418 – 1,428,537
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -38.45
Consensus MFE -36.35
Energy contribution -36.35
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.04
Structure conservation index 0.95
SVM decision value 2.68
SVM RNA-class probability 0.996318
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1428418 119 - 22224390
UGUGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAUGCAACGCAUGCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGU
((.(((((((((.(((((((.(....)...........((.....)).....))))))).)))))))((((((...(((((.....))))).((....)).))))))......)))).. ( -42.60)
>DroSec_CAF1 33192 108 - 1
--UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAU---------GCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGU
--((((((((((.(((((((.(....)...........((.....)).....))))))).)))))))))).---------((.((.(((((.((....)).)))))..))...)).... ( -36.30)
>DroSim_CAF1 24736 108 - 1
--UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAU---------GCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGU
--((((((((((.(((((((.(....)...........((.....)).....))))))).)))))))))).---------((.((.(((((.((....)).)))))..))...)).... ( -36.30)
>DroEre_CAF1 28417 117 - 1
--UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAUCCGAAAAAAGGAUGCACGCACACGCAUGCAACACAUGCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGU
--.((..((((((((((....(....)...............((((.......))))))))))))))((((((......((((.....))))((....)).))))))......)).... ( -38.60)
>consensus
__UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAU_________GCAACACAUGCAGCACAUGCAGCAUGCAGUCCGGCCAGU
..((((((((((.(((((((.(....)...........((.....)).....))))))).))))))))))..........((.((.(((((.((....)).)))))..))...)).... (-36.35 = -36.35 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,428,458 – 1,428,557
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 89.32
Mean single sequence MFE -29.84
Consensus MFE -25.63
Energy contribution -25.63
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.86
SVM decision value 0.15
SVM RNA-class probability 0.607206
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1428458 99 + 22224390
UGCGUUGCAUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCACACAAACACAACGCACUGGCAA
(((((((.....(((((((((...........(((((((((.(..(......)..).))))))).))....))))))))).....)))))))....... ( -32.76)
>DroSec_CAF1 33231 83 + 1
--------AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA--------CAACGCACUGGCAA
--------.((((((((((((..(((((((..((.....))..)).............))))))))))))))..((.--------....))....))). ( -26.81)
>DroSim_CAF1 24775 83 + 1
--------AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA--------CAACGCACUGGCAA
--------.((((((((((((..(((((((..((.....))..)).............))))))))))))))..((.--------....))....))). ( -26.81)
>DroEre_CAF1 28457 91 + 1
UGUGUUGCAUGCGUGUGCGUGCAUCCUUUUUUCGGAUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA--------CAACGCACUGGCAA
(((((((..((.((((((((((((((.......))))((((.(..(......)..).))))).))))))))).))..--------)))))))....... ( -33.00)
>consensus
________AUGCGUGUGCGUGCAUCCUUUUUUCGGUUUUCGGGGGUUGUUUUGUUCACGAGGACACGCACACACGCA________CAACGCACUGGCAA
.........((((((((((((..(((((((..((.....))..)).............))))))))))))))..((.............))....))). (-25.63 = -25.63 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,428,458 – 1,428,557
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 89.32
Mean single sequence MFE -32.00
Consensus MFE -27.45
Energy contribution -27.45
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.92
Structure conservation index 0.86
SVM decision value 2.27
SVM RNA-class probability 0.991510
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1428458 99 - 22224390
UUGCCAGUGCGUUGUGUUUGUGUGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAUGCAACGCA
.......((((((((......(((((((((((.(((((((.(....)...........((.....)).....))))))).))))))))))))))))))) ( -38.30)
>DroSec_CAF1 33231 83 - 1
UUGCCAGUGCGUUG--------UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAU--------
..((....))...(--------((((((((((.(((((((.(....)...........((.....)).....))))))).)))))))))))-------- ( -28.40)
>DroSim_CAF1 24775 83 - 1
UUGCCAGUGCGUUG--------UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAU--------
..((....))...(--------((((((((((.(((((((.(....)...........((.....)).....))))))).)))))))))))-------- ( -28.40)
>DroEre_CAF1 28457 91 - 1
UUGCCAGUGCGUUG--------UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAUCCGAAAAAAGGAUGCACGCACACGCAUGCAACACA
..((....))((((--------(..((((((((((((....(....)...............((((.......))))))))))))))))..)))))... ( -32.90)
>consensus
UUGCCAGUGCGUUG________UGCGUGUGUGCGUGUCCUCGUGAACAAAACAACCCCCGAAAACCGAAAAAAGGAUGCACGCACACGCAU________
..((....))............((((((((((.(((((((.(....)...........((.....)).....))))))).))))))))))......... (-27.45 = -27.45 +  -0.00)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:06 2006