Locus 411

Sequence ID 3L_DroMel_CAF1
Location 1,195,665 – 1,195,831
Length 166
Max. P 0.854354
window602 window603 window604 window605 window606

overview

Window 2

Location 1,195,665 – 1,195,773
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.99
Mean single sequence MFE -31.65
Consensus MFE -26.42
Energy contribution -26.05
Covariance contribution -0.37
Combinations/Pair 1.13
Mean z-score -1.61
Structure conservation index 0.83
SVM decision value 0.40
SVM RNA-class probability 0.719716
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1195665 108 - 23771897
UUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGAG--------AGCUCCAACCACCUGAAACGACUUUGUCUUGGGG----CCUCCCUUUCCU
.......(((((((.......)))))))((((((((((((.((((..(((....)))((((.--------...))))............))))...))))))))----..))))...... ( -29.70)
>DroSec_CAF1 12423 107 - 1
UUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGAG--------AGCUCCAACCACCUGAAACGACUUUGUCUUGGGG----CCUCCCUUCCC-
.......(((((((.......)))))))((((((((((((.((((..(((....)))((((.--------...))))............))))...))))))))----..)))).....- ( -29.70)
>DroEre_CAF1 10133 107 - 1
UUCAUUUAUGAGUUCAUCCAUAAUUCAUGGGACCCUAAGAAGGUCACGCUGGCAAGCUGGG---------AGCUCCAAACGCCUGAAUCGACUUUGUCUUAGCGG---CCUCCCUGCCC-
.......(((((((.......)))))))((((((((((((.((((...(.(((....(((.---------....)))...))).)....))))...)))))).))---..)))).....- ( -27.50)
>DroYak_CAF1 11942 119 - 1
UUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGGGAGCUGUUGAGCUCCAACCACCUGAAACGACUUUGUCUUAGGGGCUCCCUCCUUGCCC-
.....(((((((((.......)))))))))(((.((....))))).....((((((..((((((((((((.....))))..(((((.(((....))).))))))))))))).)))))).- ( -39.70)
>consensus
UUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGAG________AGCUCCAACCACCUGAAACGACUUUGUCUUAGGG____CCUCCCUGCCC_
.......(((((((.......)))))))((((((((((((.((((..(((....)))(((((..........)))))............))))...))))))))......))))...... (-26.42 = -26.05 +  -0.37)

alignment

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secondary structure

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Window 3

Location 1,195,701 – 1,195,813
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.28
Mean single sequence MFE -35.95
Consensus MFE -28.25
Energy contribution -29.12
Covariance contribution 0.87
Combinations/Pair 1.14
Mean z-score -1.43
Structure conservation index 0.79
SVM decision value -0.03
SVM RNA-class probability 0.519291
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1195701 112 + 23771897
GGUUGGAGCU--------CUCCAGCUUGCCAGCGUGACCUUCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUGGUGAGCGAGUGGGGCGCUCAUCGGCGAGAUG
(((((((...--------.)))))))...(((((((((((....)).)))..(((((((.......)))))))......))))))(((((((((((.......)))))))))))...... ( -38.80)
>DroSec_CAF1 12458 112 + 1
GGUUGGAGCU--------CUCCAGCUUGCCAGCGUGACCUUCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUGGUGAGCGAGUGGAGCGCUCAUCGGCGAGAUG
.((((((((.--------((((((((..((((((.(((((....)).))).)(((((((.......)))))))............)))))..)))...))))).))))..))))...... ( -39.00)
>DroEre_CAF1 10169 102 + 1
GUUUGGAGCU---------CCCAGCUUGCCAGCGUGACCUUCUUAGGGUCCCAUGAAUUAUGGAUGAACUCAUAAAUGAAUGCUGGUUUGUGAGC---------GUUUGUGAGCGAGAUG
.......(((---------(.(((((((((((((((((((.....))))).......((((..(((....)))..))))))))))))....))))---------...)).))))...... ( -30.80)
>DroYak_CAF1 11981 111 + 1
GGUUGGAGCUCAACAGCUCCCCAGCUUGCCAGCGUGACCUUCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUUGUGAGC---------UCUCAUCGGGGGGAUG
(((.((((((((..((((....)))).(((((((((((((....)).)))..(((((((.......)))))))......))))))))...)))))---------))).)))......... ( -35.20)
>consensus
GGUUGGAGCU________CCCCAGCUUGCCAGCGUGACCUUCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUGGUGAGC_________GCUCAUCGGCGAGAUG
((((((((..........)))))))).(((((((((((((....)).)))..(((((((.......)))))))......))))))))(((((((((.......)))))))))........ (-28.25 = -29.12 +   0.87)

alignment

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secondary structure

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Window 4

Location 1,195,701 – 1,195,813
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.28
Mean single sequence MFE -29.90
Consensus MFE -21.70
Energy contribution -22.45
Covariance contribution 0.75
Combinations/Pair 1.10
Mean z-score -2.00
Structure conservation index 0.73
SVM decision value 0.80
SVM RNA-class probability 0.854354
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1195701 112 - 23771897
CAUCUCGCCGAUGAGCGCCCCACUCGCUCACCAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGAG--------AGCUCCAACC
...(((.(((.((((((.......)))))).)..(((((......(((((((((.......)))))))))(((.((....)))))..)))))......)).)--------))........ ( -30.00)
>DroSec_CAF1 12458 112 - 1
CAUCUCGCCGAUGAGCGCUCCACUCGCUCACCAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGAG--------AGCUCCAACC
............((((.(((((...(((......(((((......(((((((((.......)))))))))(((.((....)))))..)))))..))))))))--------.))))..... ( -31.20)
>DroEre_CAF1 10169 102 - 1
CAUCUCGCUCACAAAC---------GCUCACAAACCAGCAUUCAUUUAUGAGUUCAUCCAUAAUUCAUGGGACCCUAAGAAGGUCACGCUGGCAAGCUGGG---------AGCUCCAAAC
......((((.((...---------(((......(((((......(((((((((.......)))))))))((((.......))))..)))))..))))).)---------)))....... ( -25.50)
>DroYak_CAF1 11981 111 - 1
CAUCCCCCCGAUGAGA---------GCUCACAAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGGGAGCUGUUGAGCUCCAACC
((((.....)))).((---------(((((....(((((......(((((((((.......)))))))))(((.((....)))))..)))))..((((....))))..)))))))..... ( -32.90)
>consensus
CAUCUCGCCGAUGAGC_________GCUCACAAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGAAGGUCACGCUGGCAAGCUGGAG________AGCUCCAACC
...........((((((.......))))))....(((((......(((((((((.......)))))))))((((.......))))..))))).....(((((..........)))))... (-21.70 = -22.45 +   0.75)

alignment

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secondary structure

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Window 5

Location 1,195,733 – 1,195,831
Length 98
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 86.53
Mean single sequence MFE -24.55
Consensus MFE -21.02
Energy contribution -20.78
Covariance contribution -0.25
Combinations/Pair 1.23
Mean z-score -1.40
Structure conservation index 0.86
SVM decision value 0.04
SVM RNA-class probability 0.555042
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1195733 98 + 23771897
UCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUGGUGAGCGAGUGGGGCGCUCAUCGGCGAGAUGAGUUGUAGAUUCUUUUGU
....((((((..(((((((.......))))))).(((..((.((.(((((((((((.......))))))))))).))))..)))...))))))..... ( -28.80)
>DroSec_CAF1 12490 98 + 1
UCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUGGUGAGCGAGUGGAGCGCUCAUCGGCGAGAUGAGUUGUAGAUUCUUUUGU
....((((((..(((((((.......))))))).(((..((.((.(((((((((((.......))))))))))).))))..)))...))))))..... ( -28.80)
>DroEre_CAF1 10200 89 + 1
UCUUAGGGUCCCAUGAAUUAUGGAUGAACUCAUAAAUGAAUGCUGGUUUGUGAGC---------GUUUGUGAGCGAGAUGAGUUGUCGAUUCUUUUGU
....(((((((((((...)))))...(((((((..(..((((((.(....).)))---------)))..).......)))))))...))))))..... ( -21.10)
>DroYak_CAF1 12021 89 + 1
UCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUUGUGAGC---------UCUCAUCGGGGGGAUGAGUUGUCGAUUCUUUUGU
....((((((.((..(((..(((....(((((....))))).))))))..)).((---------.((((((.....))))))..)).))))))..... ( -19.50)
>consensus
UCUUAGAGUCCCAUGAAUUAUAGAUGAAUUCAUAAAUGAAUGCUGGUUGGUGAGC_________GCUCAUCGGCGAGAUGAGUUGUAGAUUCUUUUGU
....((((((..(((((((.......))))))).(((..((.((.(((((((((((.......))))))))))).))))..)))...))))))..... (-21.02 = -20.78 +  -0.25)

alignment

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secondary structure

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Window 6

Location 1,195,733 – 1,195,831
Length 98
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 86.53
Mean single sequence MFE -14.82
Consensus MFE -11.46
Energy contribution -12.28
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.77
SVM decision value 0.40
SVM RNA-class probability 0.719799
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1195733 98 - 23771897
ACAAAAGAAUCUACAACUCAUCUCGCCGAUGAGCGCCCCACUCGCUCACCAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGA
.....(((........((((((.....))))))...(((....(((........)))........(((((((.......))))))))))..))).... ( -17.70)
>DroSec_CAF1 12490 98 - 1
ACAAAAGAAUCUACAACUCAUCUCGCCGAUGAGCGCUCCACUCGCUCACCAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGA
.....(((........((((((.....))))))...(((....(((........))).......((((((((.......))))))))))).))).... ( -16.60)
>DroEre_CAF1 10200 89 - 1
ACAAAAGAAUCGACAACUCAUCUCGCUCACAAAC---------GCUCACAAACCAGCAUUCAUUUAUGAGUUCAUCCAUAAUUCAUGGGACCCUAAGA
..............(((((((...(....)....---------(((........)))........)))))))..(((((.....)))))......... (  -8.70)
>DroYak_CAF1 12021 89 - 1
ACAAAAGAAUCGACAACUCAUCCCCCCGAUGAGA---------GCUCACAAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGA
.....(((.((((...((((((.....)))))).---------(((........)))..))..(((((((((.......))))))))))).))).... ( -16.30)
>consensus
ACAAAAGAAUCGACAACUCAUCUCGCCGAUGAGC_________GCUCACAAACCAGCAUUCAUUUAUGAAUUCAUCUAUAAUUCAUGGGACUCUAAGA
......((((......((((((.....))))))..........(((........))))))).((((((((((.......))))))))))......... (-11.46 = -12.28 +   0.81)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:16 2006