Locus 5835

Sequence ID 3L_DroMel_CAF1
Location 15,757,519 – 15,757,826
Length 307
Max. P 0.977479
window9293 window9294 window9295 window9296 window9297

overview

Window 3

Location 15,757,519 – 15,757,628
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.49
Mean single sequence MFE -29.66
Consensus MFE -13.16
Energy contribution -16.74
Covariance contribution 3.58
Combinations/Pair 1.07
Mean z-score -2.33
Structure conservation index 0.44
SVM decision value 1.79
SVM RNA-class probability 0.977479
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15757519 109 + 23771897
U------UAAAACUUAUCCUUAUCACACAACCGCAACUAAACGAUUGUAACACGAUCAGUGCUAUAAUUUAGUUGCUGACUUGGCCUUCAGCUUU-----GGGCUCAUGGGUUUGGCCUG
.------..................((.(((((((((((...(((((((.(((.....))).))))))))))))))...(.((((((........-----)))).)).)))))))..... ( -26.90)
>DroSec_CAF1 9210 109 + 1
U------UAAAACAUAUCCUUAUCACCCAACCGCAACUAAACGAUUGUAACACGAUCAGUGCUAUAAUUUAGUUGCUGACUUGGCCUUUAGCUUU-----GGUCACAUGGGUUGGGCCUG
.------..................((((((((((((((...(((((((.(((.....))).))))))))))))))(((((.(((.....)))..-----)))))....))))))).... ( -36.30)
>DroSim_CAF1 9445 109 + 1
U------UAAAACAUAUCCUUAUCACCCAACCGCAACUAAACGAUUGUAACACGAUCAGUGCUAUAAUUUAGUUGCUGACUUGGCCUUUAGCUUU-----GGGCACAUGGGUUGGGCCUG
.------..................((((((((((((((...(((((((.(((.....))).))))))))))))))...(.((((((........-----)))).)).)))))))).... ( -35.50)
>DroEre_CAF1 9333 108 + 1
U------UAU-CCUUAUCCUUAUCACCCAACGGCAACUAAACGAUUGUAACACGAUCAGUGCCAUCAUUUAGUUGCUGGCUUGGCCUUUAGCUUU-----GGGGACAUGGGUUGGGCAUG
.------...-(((.((((...((.((((((((((((((((.(((.(...(((.....)))).))).)))))))))))(((........))).))-----)))))...)))).))).... ( -35.50)
>DroAna_CAF1 3953 103 + 1
UAGCAAAUAUCAUUUAUUCUUAUCGUGAA-----AACUAAACGUUUGUAACGCGAUCAUUACUAUCGUUUAG------GCCAGGCCCUGAAAAAUACCCUCCCCAAAC-UGUUG-----G
(((((................((((((.(-----(((.....))))....))))))......(((..(((((------(......))))))..)))............-)))))-----. ( -14.10)
>consensus
U______UAAAACUUAUCCUUAUCACCCAACCGCAACUAAACGAUUGUAACACGAUCAGUGCUAUAAUUUAGUUGCUGACUUGGCCUUUAGCUUU_____GGGCACAUGGGUUGGGCCUG
.........................((((((((((((((((...(((((.(((.....))).))))))))))))))......(((.....)))................))))))).... (-13.16 = -16.74 +   3.58)

alignment

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secondary structure

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Window 4

Location 15,757,519 – 15,757,628
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.49
Mean single sequence MFE -31.08
Consensus MFE -18.08
Energy contribution -20.46
Covariance contribution 2.38
Combinations/Pair 1.15
Mean z-score -2.19
Structure conservation index 0.58
SVM decision value 1.72
SVM RNA-class probability 0.974024
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15757519 109 - 23771897
CAGGCCAAACCCAUGAGCCC-----AAAGCUGAAGGCCAAGUCAGCAACUAAAUUAUAGCACUGAUCGUGUUACAAUCGUUUAGUUGCGGUUGUGUGAUAAGGAUAAGUUUUA------A
..(((((......)).))).-----((((((.....((..((((((((((((((..((((((.....)))))).....)))))))))).......))))..))...)))))).------. ( -26.61)
>DroSec_CAF1 9210 109 - 1
CAGGCCCAACCCAUGUGACC-----AAAGCUAAAGGCCAAGUCAGCAACUAAAUUAUAGCACUGAUCGUGUUACAAUCGUUUAGUUGCGGUUGGGUGAUAAGGAUAUGUUUUA------A
...((((((((....((((.-----...((.....))...))))((((((((((..((((((.....)))))).....)))))))))))))))))).................------. ( -35.30)
>DroSim_CAF1 9445 109 - 1
CAGGCCCAACCCAUGUGCCC-----AAAGCUAAAGGCCAAGUCAGCAACUAAAUUAUAGCACUGAUCGUGUUACAAUCGUUUAGUUGCGGUUGGGUGAUAAGGAUAUGUUUUA------A
...((((((((..((.(((.-----.........))))).....((((((((((..((((((.....)))))).....)))))))))))))))))).................------. ( -34.60)
>DroEre_CAF1 9333 108 - 1
CAUGCCCAACCCAUGUCCCC-----AAAGCUAAAGGCCAAGCCAGCAACUAAAUGAUGGCACUGAUCGUGUUACAAUCGUUUAGUUGCCGUUGGGUGAUAAGGAUAAGG-AUA------A
....((....((.(((((((-----((.......(((...))).(((((((((((((.((((.....))))....)))))))))))))..))))).)))).))....))-...------. ( -37.30)
>DroAna_CAF1 3953 103 - 1
C-----CAACA-GUUUGGGGAGGGUAUUUUUCAGGGCCUGGC------CUAAACGAUAGUAAUGAUCGCGUUACAAACGUUUAGUU-----UUCACGAUAAGAAUAAAUGAUAUUUGCUA
.-----.....-(((((((..((((..........))))..)------))))))....((((((....))))))...((((((.((-----((......)))).)))))).......... ( -21.60)
>consensus
CAGGCCCAACCCAUGUGCCC_____AAAGCUAAAGGCCAAGUCAGCAACUAAAUUAUAGCACUGAUCGUGUUACAAUCGUUUAGUUGCGGUUGGGUGAUAAGGAUAAGUUUUA______A
...((((((((.......................(((...))).((((((((((..((((((.....)))))).....))))))))))))))))))........................ (-18.08 = -20.46 +   2.38)

alignment

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secondary structure

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Window 5

Location 15,757,593 – 15,757,706
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.54
Mean single sequence MFE -34.12
Consensus MFE -24.76
Energy contribution -25.04
Covariance contribution 0.28
Combinations/Pair 1.17
Mean z-score -2.58
Structure conservation index 0.73
SVM decision value 1.55
SVM RNA-class probability 0.963066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15757593 113 - 23771897
CCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGUAGUCCAGGCCAAACCCAUGAGCCC-----AAAGCUGAAGGCCAA
(((((--.(((((.((((.((((.......(((((((((.......)))))))))...((.((((((..........)))))))).)))).)))).))).-----...)).))))).... ( -33.20)
>DroSec_CAF1 9284 113 - 1
CCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACCGUGGCCCAGGCCCAACCCAUGUGACC-----AAAGCUAAAGGCCAA
(((((--.((((((((((.(((........(((((((((.......)))))))))...((.((((((..........))))))))..))).)))))).))-----...)).))))).... ( -35.20)
>DroSim_CAF1 9519 113 - 1
CCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGAGGCCCAGGCCCAACCCAUGUGCCC-----AAAGCUAAAGGCCAA
(((((--.((((((((((.(((........(((((((((.......)))))))))...((.((((((.((....)).))))))))..))).)))))))).-----...)).))))).... ( -39.10)
>DroEre_CAF1 9406 113 - 1
CCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGGGGCCCAUGCCCAACCCAUGUCCCC-----AAAGCUAAAGGCCAA
(((((--.(((((.((((....))))....(((((((((.......))))))))))))))...((((((......((((....)))).....))))))..-----......))))).... ( -31.80)
>DroAna_CAF1 4022 114 - 1
UCCUUUGUGCAACACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCCCUGGGCAUUUAUUUUUGCCC-----CAACA-GUUUGGGGAGGGUAUUUUUCAGGGCCUG
...((..((.((((....))))))..))..(((((((((.......)))))))))...((((((((.(..(((((...(((-----(((..-..)))))).)))))..)))))))))... ( -31.30)
>consensus
CCUUU__UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGUGGCCCAGGCCCAACCCAUGUGCCC_____AAAGCUAAAGGCCAA
(((((...(((((.((((....))))....(((((((((.......))))))))))))))(((((((..........)))))))...........................))))).... (-24.76 = -25.04 +   0.28)

alignment

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secondary structure

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Window 6

Location 15,757,628 – 15,757,746
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.85
Mean single sequence MFE -31.50
Consensus MFE -26.40
Energy contribution -26.64
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.47
Structure conservation index 0.84
SVM decision value 0.54
SVM RNA-class probability 0.773102
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15757628 118 - 23771897
UUUCUCCUUGGGGUCGCUUGCCAUCGACUUUGAGUUGCCUCCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGUAGUC
......((..((((((........))))))..)).(((((.....--.(((((.((((....))))....(((((((((.......))))))))))))))...)))))............ ( -31.70)
>DroSec_CAF1 9319 118 - 1
UUUCUCCUUGGGGUCGCUUGCCAUCGACUUUGAGUUGCCUCCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACCGUGGCC
......((..((((((........))))))..)).(((((.....--.(((((.((((....))))....(((((((((.......))))))))))))))...)))))............ ( -31.70)
>DroSim_CAF1 9554 118 - 1
UUUCUCCUUGGGGUCGCUUGCCAUCGACUGUGAGUUGCCUCCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGAGGCC
.....(((..((((.(((..(........)..))).))).(((..--.(((((.((((....))))....(((((((((.......))))))))))))))...)))......)..))).. ( -34.20)
>DroEre_CAF1 9441 118 - 1
UUUCUCCUUGGGGUCGCUUGGCAUCGACUUUGAGCUGCCUCCUUU--UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGGGGCC
.....(((..((((.(((..(........)..))).))).(((..--.(((((.((((....))))....(((((((((.......))))))))))))))...)))......)..))).. ( -34.10)
>DroAna_CAF1 4056 118 - 1
UUUCUCCUUGGGGUCGCUUGCCAUCGACUUGGA--CGCCUUCCUUUGUGCAACACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCCCUGGGCAUUUAUUUUUGCC
.........(((((.((((((...(((...(((--.....))).))).))))..((((....))))....(((((((((.......))))))))))).))))).((((........)))) ( -25.80)
>consensus
UUUCUCCUUGGGGUCGCUUGCCAUCGACUUUGAGUUGCCUCCUUU__UGCGGCACAUGUGUUUAUGAAUACAUAGAAAUUUUUGACAUUUUUAUGGCUGCUCUGGGCAUUUACUGUGGCC
......(((..(((((........)))))..)))..((((........(((((.((((....))))....(((((((((.......))))))))))))))...))))............. (-26.40 = -26.64 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,757,706 – 15,757,826
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.58
Mean single sequence MFE -26.39
Consensus MFE -22.20
Energy contribution -22.95
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.84
SVM decision value 0.50
SVM RNA-class probability 0.760025
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15757706 120 + 23771897
AGGCAACUCAAAGUCGAUGGCAAGCGACCCCAAGGAGAAACCCAAAACCCCAAAAACACGCCAACGCAUUUCGACCACAAAGUUGUCGAGGACACUCCGCACUUCGCUCCCCAUAUAUGU
.(((........))).((((..(((((......((((......................((....)).(((((((.((...)).)))))))...)))).....)))))..))))...... ( -27.10)
>DroSec_CAF1 9397 120 + 1
AGGCAACUCAAAGUCGAUGGCAAGCGACCCCAAGGAGAAACCCAAAACCCCAAAAACACGCCAACGCAUUUCGACCACAAAGUUGUCGAGGACACUCCGCACUUCGCUCCCCAUAUAUGU
.(((........))).((((..(((((......((((......................((....)).(((((((.((...)).)))))))...)))).....)))))..))))...... ( -27.10)
>DroSim_CAF1 9632 120 + 1
AGGCAACUCACAGUCGAUGGCAAGCGACCCCAAGGAGAAACCCAAAACCCCAAAAACACGCCAACGCAUUUCGACCACAAAGUUGUCGAGGACACUCCGCACUUCGCUCCCCAUAUAUGU
((....)).(((....((((..(((((......((((......................((....)).(((((((.((...)).)))))))...)))).....)))))..))))...))) ( -27.90)
>DroEre_CAF1 9519 117 + 1
AGGCAGCUCAAAGUCGAUGCCAAGCGACCCCAAGGAGAAACACAAAACCCCCA-AACACGCCAACGCAAUUCGACCACAAAGUUGUCGAGGACACUCCACACUUCAGUCCACAUAUAU--
.(((((((....((((((((...(((.......((.............))...-....)))....)))..))))).....)))))))..((((.............))))........-- ( -23.48)
>consensus
AGGCAACUCAAAGUCGAUGGCAAGCGACCCCAAGGAGAAACCCAAAACCCCAAAAACACGCCAACGCAUUUCGACCACAAAGUUGUCGAGGACACUCCGCACUUCGCUCCCCAUAUAUGU
.(((........))).((((..(((((......((((......................((....))..((((((.((...)).))))))....)))).....)))))..))))...... (-22.20 = -22.95 +   0.75)

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 12:01:31 2006