Locus 3291

Sequence ID 2L_DroMel_CAF1
Location 9,529,308 – 9,529,523
Length 215
Max. P 0.998959
window5226 window5227 window5228 window5229 window5230 window5231

overview

Window 6

Location 9,529,308 – 9,529,419
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 77.67
Mean single sequence MFE -24.73
Consensus MFE -15.11
Energy contribution -14.37
Covariance contribution -0.75
Combinations/Pair 1.24
Mean z-score -2.25
Structure conservation index 0.61
SVM decision value 1.43
SVM RNA-class probability 0.953227
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9529308 111 - 22407834
UCCCGCCAGAACUACCUGUUGGUUUUUCCCCAGGACUUACAAUCGGUUUCUCUUCGGGACGUCCUGUCGAGCCAUCGCUAUCACCUCCAGGUUUUCCUUUUGGAAUUUCUA
.....((((((..(((((..(((...((..((((((...(....)((..(.....)..))))))))..))((....))....)))..))))).....))))))........ ( -28.10)
>DroSec_CAF1 36820 101 - 1
UUCCGCCAGAACUACCUGCUGGUUUUCCUACAGGACUUCCAAUCGGGUUCUCUCCGGGACGUCCUUUCGAGCCAUCGCUAUCACCUCCAGGUUUUCCCUCU----------
........(((..(((((..(((........(((((.(((...((((.....))))))).)))))....(((....)))...)))..))))).))).....---------- ( -26.30)
>DroSim_CAF1 39930 92 - 1
UUCCGCCA---------GCUGGUUUUCCUCCAGGACUUCCAAUCGGGUUCUCUCCGGGACGUCCUUUCGAGCCAUCGCUAUCAGCUCCAGGUUUUCCCUCU----------
..((...(---------((((((........(((((.(((...((((.....))))))).)))))....(((....))))))))))...))..........---------- ( -24.80)
>DroYak_CAF1 44724 96 - 1
UUUCUCCAGAACUACCUGCAGGUUUUCCUCCAGGACUUCCAAUCGGGUUUUCUCCGAGUCGUCCUUUCGAUCCUUCACUAUCCCCCCCAGGAUUUC---------------
..............((((.(((....))).))))...(((..(((((.....)))))((((......))))..................)))....--------------- ( -19.70)
>consensus
UUCCGCCAGAACUACCUGCUGGUUUUCCUCCAGGACUUCCAAUCGGGUUCUCUCCGGGACGUCCUUUCGAGCCAUCGCUAUCACCUCCAGGUUUUCCCUCU__________
..(((.(((......))).))).........(((((......(((((.....)))))...)))))...(((((................)))))................. (-15.11 = -14.37 +  -0.75)

alignment

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secondary structure

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Window 7

Location 9,529,339 – 9,529,459
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.83
Mean single sequence MFE -39.65
Consensus MFE -25.85
Energy contribution -25.35
Covariance contribution -0.50
Combinations/Pair 1.33
Mean z-score -2.71
Structure conservation index 0.65
SVM decision value 2.09
SVM RNA-class probability 0.987695
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9529339 120 + 22407834
UAGCGAUGGCUCGACAGGACGUCCCGAAGAGAAACCGAUUGUAAGUCCUGGGGAAAAACCAACAGGUAGUUCUGGCGGGAAUGCUAAGGGAAAUGUAGGAGAAAAACCUGCAGGCUCCGC
(((((....((((.((((((.((((..((.((.((.....))...)))).))))...(((....))).)))))).))))..)))))..(((..((((((.......))))))...))).. ( -37.20)
>DroSec_CAF1 36841 120 + 1
UAGCGAUGGCUCGAAAGGACGUCCCGGAGAGAACCCGAUUGGAAGUCCUGUAGGAAAACCAGCAGGUAGUUCUGGCGGAAACGCUAAAGGAAAUACAGGAGAAAAACCUGUAGGCUCCGC
....((((..((....)).)))).(((((.....((....((((.((((((.((....)).))))).).))))((((....))))...))...((((((.......))))))..))))). ( -43.00)
>DroSim_CAF1 39951 108 + 1
UAGCGAUGGCUCGAAAGGACGUCCCGGAGAGAACCCGAUUGGAAGUCCUGGAGGAAAACCAGC---------UGGCGGAAACGCUAAAGAAAAUGCAGG---AAAACCUGUAGGCUCCGC
..(((....(((...(((((.((((((.......)))...))).))))).))).......(((---------(((((....))))........((((((---....)))))))))).))) ( -37.80)
>DroYak_CAF1 44740 120 + 1
UAGUGAAGGAUCGAAAGGACGACUCGGAGAAAACCCGAUUGGAAGUCCUGGAGGAAAACCUGCAGGUAGUUCUGGAGAAAACUCCAAAGGAAGUGCGGUAGGAAAACCUACUGGGUCCUC
......((((((...(((((...((((.......))))........((((.(((....))).))))..)))))((((....))))..........(((((((....))))))))))))). ( -40.60)
>consensus
UAGCGAUGGCUCGAAAGGACGUCCCGGAGAGAACCCGAUUGGAAGUCCUGGAGGAAAACCAGCAGGUAGUUCUGGCGGAAACGCUAAAGGAAAUGCAGGAGAAAAACCUGCAGGCUCCGC
......(((.((...(((((.((((((.......)))...))).)))))...))....)))...........(((((....)))))..(((..((((((.......))))))...))).. (-25.85 = -25.35 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,529,339 – 9,529,459
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.83
Mean single sequence MFE -34.55
Consensus MFE -21.24
Energy contribution -20.99
Covariance contribution -0.25
Combinations/Pair 1.23
Mean z-score -2.27
Structure conservation index 0.61
SVM decision value 1.00
SVM RNA-class probability 0.898648
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9529339 120 - 22407834
GCGGAGCCUGCAGGUUUUUCUCCUACAUUUCCCUUAGCAUUCCCGCCAGAACUACCUGUUGGUUUUUCCCCAGGACUUACAAUCGGUUUCUCUUCGGGACGUCCUGUCGAGCCAUCGCUA
((((((((.((((((..((((...............((......)).))))..)))))).)))))(((..((((((...(....)((..(.....)..))))))))..)))....))).. ( -31.99)
>DroSec_CAF1 36841 120 - 1
GCGGAGCCUACAGGUUUUUCUCCUGUAUUUCCUUUAGCGUUUCCGCCAGAACUACCUGCUGGUUUUCCUACAGGACUUCCAAUCGGGUUCUCUCCGGGACGUCCUUUCGAGCCAUCGCUA
..((((..((((((.......)))))).))))..(((((.....((.((......))))((((((......(((((.(((...((((.....))))))).)))))...)))))).))))) ( -35.10)
>DroSim_CAF1 39951 108 - 1
GCGGAGCCUACAGGUUUU---CCUGCAUUUUCUUUAGCGUUUCCGCCA---------GCUGGUUUUCCUCCAGGACUUCCAAUCGGGUUCUCUCCGGGACGUCCUUUCGAGCCAUCGCUA
((((((((((((((....---)))).........))).).)))))).(---------((((((((......(((((.(((...((((.....))))))).)))))...))))))..))). ( -33.10)
>DroYak_CAF1 44740 120 - 1
GAGGACCCAGUAGGUUUUCCUACCGCACUUCCUUUGGAGUUUUCUCCAGAACUACCUGCAGGUUUUCCUCCAGGACUUCCAAUCGGGUUUUCUCCGAGUCGUCCUUUCGAUCCUUCACUA
((((((((.(((((....))))).........(((((((....)))))))....((((.(((....))).))))..........))))))))...(..(((......)))..)....... ( -38.00)
>consensus
GCGGAGCCUACAGGUUUUUCUCCUGCAUUUCCUUUAGCGUUUCCGCCAGAACUACCUGCUGGUUUUCCUCCAGGACUUCCAAUCGGGUUCUCUCCGGGACGUCCUUUCGAGCCAUCGCUA
((((((((((.(((................))).))).))).))))...........(.((((((......(((((......(((((.....)))))...)))))...)))))).).... (-21.24 = -20.99 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,529,379 – 9,529,488
Length 109
Sequences 3
Columns 109
Reading direction forward
Mean pairwise identity 80.12
Mean single sequence MFE -35.20
Consensus MFE -25.85
Energy contribution -24.20
Covariance contribution -1.65
Combinations/Pair 1.36
Mean z-score -3.61
Structure conservation index 0.73
SVM decision value 3.28
SVM RNA-class probability 0.998917
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9529379 109 + 22407834
GUAAGUCCUGGGGAAAAACCAACAGGUAGUUCUGGCGGGAAUGCUAAGGGAAAUGUAGGAGAAAAACCUGCAGGCUCCGCUGGAGGAACCACCAACACAAAUAUCAACA
....((..(((((.....))....(((..(((..(((((...(((........((((((.......))))))))))))))..)))..))).)))..))........... ( -30.00)
>DroSec_CAF1 36881 109 + 1
GGAAGUCCUGUAGGAAAACCAGCAGGUAGUUCUGGCGGAAACGCUAAAGGAAAUACAGGAGAAAAACCUGUAGGCUCCGCUGGAGGAACCACCAACAAAAAUAUCAACA
((((.((((((.((....)).))))).).))))((((....))))...((...((((((.......))))))((.(((......))).)).))................ ( -36.00)
>DroYak_CAF1 44780 109 + 1
GGAAGUCCUGGAGGAAAACCUGCAGGUAGUUCUGGAGAAAACUCCAAAGGAAGUGCGGUAGGAAAACCUACUGGGUCCUCUGAAGGAUCCAAGAACGUAAAUAGCAACG
((((.(((((.(((....))).)))).).))))((((....))))........(((((((((....))))))(((((((....))))))).............)))... ( -39.60)
>consensus
GGAAGUCCUGGAGGAAAACCAGCAGGUAGUUCUGGCGGAAACGCUAAAGGAAAUGCAGGAGAAAAACCUGCAGGCUCCGCUGGAGGAACCACCAACAAAAAUAUCAACA
.....((((..((((..(((....)))..))))((((....))))..))))...(((((.......))))).((.(((......))).))................... (-25.85 = -24.20 +  -1.65)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,529,379 – 9,529,488
Length 109
Sequences 3
Columns 109
Reading direction reverse
Mean pairwise identity 80.12
Mean single sequence MFE -30.23
Consensus MFE -18.23
Energy contribution -19.12
Covariance contribution 0.89
Combinations/Pair 1.12
Mean z-score -2.40
Structure conservation index 0.60
SVM decision value 0.92
SVM RNA-class probability 0.882163
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9529379 109 - 22407834
UGUUGAUAUUUGUGUUGGUGGUUCCUCCAGCGGAGCCUGCAGGUUUUUCUCCUACAUUUCCCUUAGCAUUCCCGCCAGAACUACCUGUUGGUUUUUCCCCAGGACUUAC
.(((.........(((((.(....).)))))((((((.((((((..((((...............((......)).))))..)))))).)))...)))....))).... ( -24.59)
>DroSec_CAF1 36881 109 - 1
UGUUGAUAUUUUUGUUGGUGGUUCCUCCAGCGGAGCCUACAGGUUUUUCUCCUGUAUUUCCUUUAGCGUUUCCGCCAGAACUACCUGCUGGUUUUCCUACAGGACUUCC
.(((((.......(((((.(....).)))))((((..((((((.......)))))).)))).)))))((((......))))..((((..((....))..))))...... ( -30.00)
>DroYak_CAF1 44780 109 - 1
CGUUGCUAUUUACGUUCUUGGAUCCUUCAGAGGACCCAGUAGGUUUUCCUACCGCACUUCCUUUGGAGUUUUCUCCAGAACUACCUGCAGGUUUUCCUCCAGGACUUCC
.............(((((.(((..((((((((((..(.(((((....))))).)....))))))))))..)))...)))))..((((.(((....))).))))...... ( -36.10)
>consensus
UGUUGAUAUUUAUGUUGGUGGUUCCUCCAGCGGAGCCUGCAGGUUUUUCUCCUGCAUUUCCUUUAGCGUUUCCGCCAGAACUACCUGCUGGUUUUCCUCCAGGACUUCC
...................((.((((..((..(((((.((((((..((((...............(((....))).))))..)))))).)))))..))..))))))... (-18.23 = -19.12 +   0.89)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,529,419 – 9,529,523
Length 104
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 75.12
Mean single sequence MFE -20.75
Consensus MFE -14.16
Energy contribution -14.10
Covariance contribution -0.06
Combinations/Pair 1.35
Mean z-score -2.57
Structure conservation index 0.68
SVM decision value 3.30
SVM RNA-class probability 0.998959
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9529419 104 + 22407834
AUGCUAAGGGAAAUGUAGGAGAAAAACCUGCAGGCUCCGCUGGAGGAACCACCAACACAAAUAUCAACACUAUUAAAAUACAACACAAACGCUAACUUUAGAAA-----
...((((((....((((((.......))))))((.(((......))).)).............................................))))))...----- ( -18.90)
>DroSec_CAF1 36921 109 + 1
ACGCUAAAGGAAAUACAGGAGAAAAACCUGUAGGCUCCGCUGGAGGAACCACCAACAAAAAUAUCAACAUUAUUAAAAUACAAGACAAACGCUAACUUUAAAAGUAAAC
..((....((...((((((.......))))))((.(((......))).)).))......((((.......))))................))................. ( -16.40)
>DroSim_CAF1 40022 100 + 1
ACGCUAAAGAAAAUGCAGG---AAAACCUGUAGGCUCCGCUGGAGGAACCACCAACAA-AAUAUCAACAAUAUUAAAAUACAACACAAACGCUAACUUUAGAAG-----
...((((((....((((((---....))))))((.(((......))).))........-....................................))))))...----- ( -19.30)
>DroYak_CAF1 44820 94 + 1
ACUCCAAAGGAAGUGCGGUAGGAAAACCUACUGGGUCCUCUGAAGGAUCCAAGAACGUAAAUAGCAACGAUAUUAUUAUA---------GGCUGACUUUGAAA------
....(((((....(((((((((....)))))((((((((....))))))))....))))..((((....(((....))).---------.)))).)))))...------ ( -28.40)
>consensus
ACGCUAAAGGAAAUGCAGGAGAAAAACCUGCAGGCUCCGCUGGAGGAACCACCAACAAAAAUAUCAACAAUAUUAAAAUACAACACAAACGCUAACUUUAAAAG_____
...((((((....((((((.......))))))((.(((......))).)).............................................))))))........ (-14.16 = -14.10 +  -0.06)

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 10:49:04 2006