Locus 1501

Sequence ID 3R_DroMel_CAF1
Location 4,315,978 – 4,316,278
Length 300
Max. P 0.993748
window2487 window2488 window2489 window2490 window2491 window2492 window2493

overview

Window 7

Location 4,315,978 – 4,316,082
Length 104
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.47
Mean single sequence MFE -31.35
Consensus MFE -26.72
Energy contribution -26.50
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.85
SVM decision value 0.45
SVM RNA-class probability 0.739972
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4315978 104 + 27905053
AAUACGUACAACAAAGGUGUGCGAAAGCCACUGUUGUUGUUGCCU----------------UUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUA
.....(((((((((.((((.((....)))))).))))).(((((.----------------...(((((((.................)))))))....)))))...))))......... ( -30.63)
>DroSec_CAF1 3368 116 + 1
----CGUACAACAAAGGUGUGCGAAAGCCACUGUUGUUGUUGCCUUUGCAAAGGCAAAGCUUUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUA
----.(((((((((.((((.((....)))))).))))).((((((((((....)))))((....(((((((.................)))))))..)))))))...))))......... ( -36.33)
>DroEre_CAF1 3378 100 + 1
----CGUACAACAAAGGUGUGCGAAGGCCACUGUUGUUGUUGGCU----------------UUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCGUGCGGCAGUUUGUGCUUUUAAUUA
----((.(((((((.((((.((....)))))).)))))))))((.----------------......))........(((((((.((((((...))))))...))))))).......... ( -27.10)
>consensus
____CGUACAACAAAGGUGUGCGAAAGCCACUGUUGUUGUUGCCU________________UUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUA
.......(((((((.((((.((....)))))).))))))).....................................(((((((.((((((...))))))...))))))).......... (-26.72 = -26.50 +  -0.22)

alignment

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secondary structure

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Window 8

Location 4,315,978 – 4,316,082
Length 104
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.47
Mean single sequence MFE -25.57
Consensus MFE -22.37
Energy contribution -22.70
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.87
SVM decision value 1.18
SVM RNA-class probability 0.927398
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4315978 104 - 27905053
UAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAA----------------AGGCAACAACAACAGUGGCUUUCGCACACCUUUGUUGUACGUAUU
.........((......((((((.....)).(((((...(((....)))))))).....----------------.))))(((((((..(((((....)).)))..)))))))..))... ( -25.50)
>DroSec_CAF1 3368 116 - 1
UAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAAAGCUUUGCCUUUGCAAAGGCAACAACAACAGUGGCUUUCGCACACCUUUGUUGUACG----
......(((((......(((.(((((...)))))....((((....)))).)))......)))))(((((....))))).(((((((..(((((....)).)))..)))))))...---- ( -30.60)
>DroEre_CAF1 3378 100 - 1
UAAUUAAAAGCACAAACUGCCGCACGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAA----------------AGCCAACAACAACAGUGGCCUUCGCACACCUUUGUUGUACG----
.........((......(((.(....).)))(((((...(((....)))))))).....----------------.))..(((((((..(((((....)).)))..)))))))...---- ( -20.60)
>consensus
UAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAA________________AGGCAACAACAACAGUGGCUUUCGCACACCUUUGUUGUACG____
.................((((((.....)).(((((...(((....))))))))......................))))(((((((..(((((....)).)))..)))))))....... (-22.37 = -22.70 +   0.33)

alignment

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secondary structure

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Window 9

Location 4,316,018 – 4,316,122
Length 104
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.75
Mean single sequence MFE -30.84
Consensus MFE -24.12
Energy contribution -24.57
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.78
SVM decision value -0.01
SVM RNA-class probability 0.528460
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4316018 104 + 27905053
UGCCU----------------UUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAAUGCCGCUGCAGCAGCAGGGAAAAAAAGAAGCG
..(((----------------...(((((.(((......)))...((((.(((((((...(((.((((..........)))).))).)))))))))))))))).)))............. ( -30.00)
>DroSec_CAF1 3404 115 + 1
UGCCUUUGCAAAGGCAAAGCUUUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAACGCCGCUGCAGCAG-----AAAAAAAGAAGGG
((((((....))))))...((((...(((((.............)))))(((.(((.(((((.(((.((..(((.....)))..))))))))))))).))).-----.......)))).. ( -31.92)
>DroEre_CAF1 3414 101 + 1
UGGCU----------------UUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCGUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAACGCCGCUGCAGCAGC---GGAAAAAAGAAGGG
....(----------------((.(((((.(((......)))...((((.(((((((...(((.((((..........)))).))).))))))))))))))))---.))).......... ( -30.60)
>consensus
UGCCU________________UUGGUUGCAUUACUUUCAUAAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAACGCCGCUGCAGCAGC___GAAAAAAAGAAGGG
........................(((((.(((......)))...((((.(((((((...(((.((((..........)))).))).))))))))))))))))................. (-24.12 = -24.57 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,316,018 – 4,316,122
Length 104
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.75
Mean single sequence MFE -28.11
Consensus MFE -24.58
Energy contribution -24.13
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.45
Structure conservation index 0.87
SVM decision value 1.53
SVM RNA-class probability 0.961647
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4316018 104 - 27905053
CGCUUCUUUUUUUCCCUGCUGCUGCAGCGGCAUUGCAUUUUAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAA----------------AGGCA
.((..(((((......((((((.(((((((((.(((.((((....))))))).....)))))).))).))).))).......)))))....))......----------------..... ( -28.32)
>DroSec_CAF1 3404 115 - 1
CCCUUCUUUUUUU-----CUGCUGCAGCGGCGUUGCAUUUUAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAAAGCUUUGCCUUUGCAAAGGCA
.............-----.(((.(((((((((((((.((((....)))))))...)).))))).))).)))(((((...(((....))))))))..........((((((....)))))) ( -30.80)
>DroEre_CAF1 3414 101 - 1
CCCUUCUUUUUUCC---GCUGCUGCAGCGGCGUUGCAUUUUAAUUAAAAGCACAAACUGCCGCACGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAA----------------AGCCA
..............---..((((((((((((((.((.((((....))))(((.....))).))))))))).))))...((((....)))).))).....----------------..... ( -25.20)
>consensus
CCCUUCUUUUUUUC___GCUGCUGCAGCGGCGUUGCAUUUUAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUUAUGAAAGUAAUGCAACCAA________________AGGCA
...................((((((((((((((.((.((((....))))(((.....))).))))))))).))))...((((....)))).))).......................... (-24.58 = -24.13 +  -0.44)

alignment

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secondary structure

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Window 1

Location 4,316,042 – 4,316,160
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.55
Mean single sequence MFE -28.97
Consensus MFE -23.90
Energy contribution -24.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.81
Structure conservation index 0.83
SVM decision value 0.91
SVM RNA-class probability 0.879981
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4316042 118 + 27905053
AAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAAUGCCGCUGCAGCAGCAGGGAAAAAAAGAAGCGAAACUACAAAAAAAAAA--AAACGGAACUGCACACAUAUU
.((((((..(((.(((.((((((.....(((((((....)))).))).))))))))).)))((((................................--........))))...)))))) ( -28.80)
>DroSec_CAF1 3444 112 + 1
AAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAACGCCGCUGCAGCAG-----AAAAAAAGAAGGGAAACUACAAGAAA-AAA--AAGCGGAACUGCACACAUAUU
.((((((..(((.(((.(((((.(((.((..(((.....)))..))))))))))))).))).-----..........((....))........-...--..(((....)))...)))))) ( -27.20)
>DroEre_CAF1 3438 117 + 1
AAAUAUGCAUGCGGCGUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAACGCCGCUGCAGCAGC---GGAAAAAAGAAGGGAAACUACAAAAAAAAAAUAAGGCGGAACUGCACACAUAUU
.....((((((...))))))(((((((.(((((((....)))).))).((((.((((....))---)).........((....))...............)))))))))))......... ( -30.90)
>consensus
AAAUAUGCAUGCGGCAUGCGGCAGUUUGUGCUUUUAAUUAAAAUGCAACGCCGCUGCAGCAGC___GAAAAAAAGAAGGGAAACUACAAAAAAAAAA__AAGCGGAACUGCACACAUAUU
.((((((..((((((.((((((.((...(((((((....)))).)))..)).)))))))).................((....)).......................))))..)))))) (-23.90 = -24.23 +   0.33)

alignment

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secondary structure

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Window 2

Location 4,316,042 – 4,316,160
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.55
Mean single sequence MFE -30.13
Consensus MFE -29.00
Energy contribution -28.78
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -3.21
Structure conservation index 0.96
SVM decision value 2.42
SVM RNA-class probability 0.993748
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4316042 118 - 27905053
AAUAUGUGUGCAGUUCCGUUU--UUUUUUUUUUGUAGUUUCGCUUCUUUUUUUCCCUGCUGCUGCAGCGGCAUUGCAUUUUAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUU
(((((((((((..........--.........((((((...((..............)).))))))((((((.(((.((((....))))))).....)))))).....))))))))))). ( -31.64)
>DroSec_CAF1 3444 112 - 1
AAUAUGUGUGCAGUUCCGCUU--UUU-UUUCUUGUAGUUUCCCUUCUUUUUUU-----CUGCUGCAGCGGCGUUGCAUUUUAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUU
(((((((((((..........--...-.....((((((...............-----..))))))((((((((((.((((....)))))))...)).))))).....))))))))))). ( -29.43)
>DroEre_CAF1 3438 117 - 1
AAUAUGUGUGCAGUUCCGCCUUAUUUUUUUUUUGUAGUUUCCCUUCUUUUUUCC---GCUGCUGCAGCGGCGUUGCAUUUUAAUUAAAAGCACAAACUGCCGCACGCCGCAUGCAUAUUU
(((((((((((.((..................((((((................---...))))))((((((((((.((((....)))))))...)).)))))..)).))))))))))). ( -29.31)
>consensus
AAUAUGUGUGCAGUUCCGCUU__UUUUUUUUUUGUAGUUUCCCUUCUUUUUUUC___GCUGCUGCAGCGGCGUUGCAUUUUAAUUAAAAGCACAAACUGCCGCAUGCCGCAUGCAUAUUU
(((((((((((.....................((((((......................))))))((((((.(((.((((....))))))).....)))))).....))))))))))). (-29.00 = -28.78 +  -0.22)

alignment

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secondary structure

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Window 3

Location 4,316,160 – 4,316,278
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.62
Mean single sequence MFE -31.73
Consensus MFE -27.78
Energy contribution -27.57
Covariance contribution -0.22
Combinations/Pair 1.15
Mean z-score -1.79
Structure conservation index 0.88
SVM decision value 0.10
SVM RNA-class probability 0.584572
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4316160 118 - 27905053
CAUCGCCGCACUCUAUGUAAUUGAAAUAUCCUGUCCA--AGGAUAGCGGCAAAAGUGGAGGCGAAAAUAGAAAAUGGGCCACGAGCUCAAGGAAUUCAAUCAAUUGCAAGGCGAACUUCG
..(((((((.((((((....(((...((((((.....--))))))....)))..))))))))............(((((.....)))))....................)))))...... ( -32.90)
>DroSec_CAF1 3556 120 - 1
CAUCGUCGCACUCUACGUAAUUGAAAUAUGCUGUCCAAAAGGAUAGCGGCAGAAGUGGAGGCGAAAAUAGAAAGUGGGCCACGAGCUCAAGGAAUUCAAUCAAUUGCAAGGCGAACUUCA
..(((((((.((((((....(((.....((((((((....)))))))).)))..)))))))).......(((..(((((.....))))).....)))............)))))...... ( -35.60)
>DroEre_CAF1 3555 118 - 1
CAUCGUCGCACUCUAUGUAAUUGAAAUAUGCUGUCCA--AGGAUAAGGGCAAAAAAGGAGGCGAAUGUAGAAAAUGGGCCACAAGCUCAAGGAAUUCAAUCAAUUGCAAGGCGAACUUCA
.....((((.((...(((((((((.......(((((.--.......)))))...........((((........(((((.....)))))....))))..)))))))))))))))...... ( -26.70)
>consensus
CAUCGUCGCACUCUAUGUAAUUGAAAUAUGCUGUCCA__AGGAUAGCGGCAAAAGUGGAGGCGAAAAUAGAAAAUGGGCCACGAGCUCAAGGAAUUCAAUCAAUUGCAAGGCGAACUUCA
..(((((((.((((((....(((.......((((((....))))))...)))..))))))))............(((((.....)))))....................)))))...... (-27.78 = -27.57 +  -0.22)

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 10:12:09 2006