Locus 376

Sequence ID 2L_DroMel_CAF1
Location 1,175,874 – 1,176,074
Length 200
Max. P 0.995246
window590 window591 window592 window593

overview

Window 0

Location 1,175,874 – 1,175,994
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.67
Mean single sequence MFE -46.18
Consensus MFE -38.48
Energy contribution -38.40
Covariance contribution -0.08
Combinations/Pair 1.17
Mean z-score -1.67
Structure conservation index 0.83
SVM decision value 0.94
SVM RNA-class probability 0.886201
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1175874 120 + 22407834
GCAGCGGUUGCCCUCUCGGCCAUCCAGCGCAAGCAGAAGAAGAUGAGCAGUAUCGAGACCACGAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGCAAGUGAAGGCCACAUUG
((.((.((((((.(((((((((((..((....)).......)))).)).....)))))...........((((((((....))))))))...)))))).))))..(((.....))).... ( -47.60)
>DroSec_CAF1 9288 120 + 1
GCAGCGGUUGCCCUCUCGGCCAUCCAGCGCAAGCAGAAGAAGAUGAACAGUAUCGAGACCACGAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGCAAGUGAAGGCCACAUUG
((.((.((((((.((((.........((....)).......((((.....))))))))...........((((((((....))))))))...)))))).))))..(((.....))).... ( -46.00)
>DroEre_CAF1 10280 120 + 1
GCAGCGGUUGCCCUCUCGGCCAUCCAGCGCAAGCAGAAGAAGAUGAACAGUAUCGAGACCACAAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUG
...((.((((((.((((.........((....)).......((((.....))))))))...........((((((((....))))))))...)))))).))....(((.....))).... ( -44.20)
>DroYak_CAF1 9903 120 + 1
GCAGCGGUUGCUCUCUCGGCCAUCCAGCGCAAGCAGAAGAAGAUGAGCAAUAUCGAGACCACAAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUU
((.((.(((((((((((((....)).((....))....).))).)))))))...((........))...)).))((((...((((((.....)))))).((....))...))))...... ( -46.80)
>DroAna_CAF1 9676 120 + 1
GCUGCCGUGGCUCUAUCGGCUAUCCAACGCAAGCAGAAGAAGAUGAGCAACAUCGAGACCACGAUUACAGCAGCGGCAGCAGCUGCCGCCCAAGCAGCUGCUGAGGUGAAGGCUGCCUUU
(((((((((((((..((.(((..........))).))....((((.....))))))).)))))......)))))..((((((((((.......))))))))))((((.......)))).. ( -46.30)
>consensus
GCAGCGGUUGCCCUCUCGGCCAUCCAGCGCAAGCAGAAGAAGAUGAGCAGUAUCGAGACCACGAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUG
...((.((((((.((((.........((....)).......((((.....))))))))...........((((((((....))))))))...)))))).))....(((.....))).... (-38.48 = -38.40 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,175,914 – 1,176,034
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.33
Mean single sequence MFE -50.34
Consensus MFE -40.58
Energy contribution -41.22
Covariance contribution 0.64
Combinations/Pair 1.13
Mean z-score -2.80
Structure conservation index 0.81
SVM decision value 2.56
SVM RNA-class probability 0.995246
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1175914 120 + 22407834
AGAUGAGCAGUAUCGAGACCACGAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGCAAGUGAAGGCCACAUUGGCUGCUCAGGUGGCCAGUGCGCCCAAGGGCAACGAUGGAA
......((.((((((......)))).)).))(((((((...((((((.....)))))).((....))...)))).(((((((..(....)..))))))).)))((..(....)..))... ( -51.10)
>DroSec_CAF1 9328 120 + 1
AGAUGAACAGUAUCGAGACCACGAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGCAAGUGAAGGCCACAUUGGCUGCUCAGGUGGCCAGUGCGCCCAAGGGCAACGAUGGAA
.((((.....))))....(((((......((.(.((((...((((((.....)))))).((....))...)))).)((((((..(....)..))))))))(((....)))..)).))).. ( -51.10)
>DroEre_CAF1 10320 120 + 1
AGAUGAACAGUAUCGAGACCACAAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUGGCUGCUCAAGUGGUCAGUGCGCCCAAGGGCAACGAUGGAA
..........(((((.((((((.......((((((((....))))))))....(.((((((.((.(((.....))).)).)))))))..)))))).....(((....)))..)))))... ( -52.60)
>DroYak_CAF1 9943 120 + 1
AGAUGAGCAAUAUCGAGACCACAAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUUGCUGCUCAGGUGGUCAGUGCGCCCAAGGGCAACGAUGGAA
..........(((((.((((((.......((((((((....))))))))....(.(((((((((.(((.....))).))))))))))..)))))).....(((....)))..)))))... ( -53.40)
>DroAna_CAF1 9716 120 + 1
AGAUGAGCAACAUCGAGACCACGAUUACAGCAGCGGCAGCAGCUGCCGCCCAAGCAGCUGCUGAGGUGAAGGCUGCCUUUGCCGCCAAGAACGUAACUGCUCCAAGAGGCAACGAUGGAA
..........(((((.....(((....((((((((((((...)))))((....)).))))))).((..((((...))))..))........)))...((((......)))).)))))... ( -43.50)
>consensus
AGAUGAGCAGUAUCGAGACCACGAUCACAGCGGCGGCCACAGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUGGCUGCUCAGGUGGUCAGUGCGCCCAAGGGCAACGAUGGAA
..........(((((..............((((((((....))))))))...(((....((....))....))).((((((((((....)))))))))).(((....)))..)))))... (-40.58 = -41.22 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,175,914 – 1,176,034
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.33
Mean single sequence MFE -47.70
Consensus MFE -41.44
Energy contribution -41.60
Covariance contribution 0.16
Combinations/Pair 1.18
Mean z-score -1.83
Structure conservation index 0.87
SVM decision value 1.38
SVM RNA-class probability 0.948102
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1175914 120 - 22407834
UUCCAUCGUUGCCCUUGGGCGCACUGGCCACCUGAGCAGCCAAUGUGGCCUUCACUUGCGCCGCUGCCUGUGCGGCAGCUGUGGCCGCCGCUGUGAUCGUGGUCUCGAUACUGCUCAUCU
....((((..(((....))).....((((((....(((((....((((((...((..(((((((.......))))).)).)))))))).)))))....)))))).))))........... ( -47.70)
>DroSec_CAF1 9328 120 - 1
UUCCAUCGUUGCCCUUGGGCGCACUGGCCACCUGAGCAGCCAAUGUGGCCUUCACUUGCGCCGCUGCCUGUGCGGCAGCUGUGGCCGCCGCUGUGAUCGUGGUCUCGAUACUGUUCAUCU
....((((..(((....))).....((((((....(((((....((((((...((..(((((((.......))))).)).)))))))).)))))....)))))).))))........... ( -47.70)
>DroEre_CAF1 10320 120 - 1
UUCCAUCGUUGCCCUUGGGCGCACUGACCACUUGAGCAGCCAAUGUGGCCUUCACUUCCGCCGCUGCCUGUGCGGCAGCUGUGGCCGCCGCUGUGAUUGUGGUCUCGAUACUGUUCAUCU
....((((..(((....))).....((((((....(((((....((((((.........((.((((((.....)))))).)))))))).)))))....)))))).))))........... ( -48.00)
>DroYak_CAF1 9943 120 - 1
UUCCAUCGUUGCCCUUGGGCGCACUGACCACCUGAGCAGCAAAUGUGGCCUUCACUUCCGCCGCUGCCUGUGCGGCAGCUGUGGCCGCCGCUGUGAUUGUGGUCUCGAUAUUGCUCAUCU
....((((..(((....))).....((((((....(((((....((((((.........((.((((((.....)))))).)))))))).)))))....)))))).))))........... ( -47.30)
>DroAna_CAF1 9716 120 - 1
UUCCAUCGUUGCCUCUUGGAGCAGUUACGUUCUUGGCGGCAAAGGCAGCCUUCACCUCAGCAGCUGCUUGGGCGGCAGCUGCUGCCGCUGCUGUAAUCGUGGUCUCGAUGUUGCUCAUCU
..(((.(((((((.((.(((((......))))).)).))))).((((((........(((((((((((.....)))))))))))..)))))).....)))))....((((.....)))). ( -47.80)
>consensus
UUCCAUCGUUGCCCUUGGGCGCACUGACCACCUGAGCAGCCAAUGUGGCCUUCACUUCCGCCGCUGCCUGUGCGGCAGCUGUGGCCGCCGCUGUGAUCGUGGUCUCGAUACUGCUCAUCU
....((((.((((....))))....((((((....(((((....((((((.........((.((((((.....)))))).)))))))).)))))....)))))).))))........... (-41.44 = -41.60 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,175,954 – 1,176,074
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.83
Mean single sequence MFE -47.64
Consensus MFE -35.52
Energy contribution -38.68
Covariance contribution 3.16
Combinations/Pair 1.22
Mean z-score -2.44
Structure conservation index 0.75
SVM decision value 1.74
SVM RNA-class probability 0.974714
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1175954 120 + 22407834
AGCUGCCGCACAGGCAGCGGCGCAAGUGAAGGCCACAUUGGCUGCUCAGGUGGCCAGUGCGCCCAAGGGCAACGAUGGAAAGAUAUACCGUAUGUCGCCACUCACUUGAGUAUGCUAGCA
.((((((.....))))))(((((((((((.(((..(((((((..(....)..))))))).)))....(((.(((((((.........)))).))).)))..)))))))....)))).... ( -51.90)
>DroSec_CAF1 9368 120 + 1
AGCUGCCGCACAGGCAGCGGCGCAAGUGAAGGCCACAUUGGCUGCUCAGGUGGCCAGUGCGCCCAAGGGCAACGAUGGAAAGAUCUACCGUAUGUCGCCACGCACUUGUGUUCUCUAGCA
.((((((.....))))))((((((((((..(((..(((((((..(....)..))))))).(((....))).(((.((((....)))).))).....)))...))))))))))........ ( -55.20)
>DroEre_CAF1 10360 120 + 1
AGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUGGCUGCUCAAGUGGUCAGUGCGCCCAAGGGCAACGAUGGAAAGAUCUACCGUAAGUGACGGCAUACUAUUGUUUGCUAGCA
.((((((.....)))))).((((.((......((((((((((..(....)..))))))).(((....))).....)))......)).))))..((...((((.((....)).)))).)). ( -46.50)
>DroYak_CAF1 9983 120 + 1
AGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUUGCUGCUCAGGUGGUCAGUGCGCCCAAGGGCAACGAUGGAAAGAUCUACCGUAAGUGGCCACAUACAUGUGUUUGCUAGCA
.(((((.(((((.(.(((((((((.(((.....))).))))))))))..(((((((.(..(((....))).(((.((((....)))).))).).))))))).....)))))..)).))). ( -47.90)
>DroAna_CAF1 9756 119 + 1
AGCUGCCGCCCAAGCAGCUGCUGAGGUGAAGGCUGCCUUUGCCGCCAAGAACGUAACUGCUCCAAGAGGCAACGAUGGAAAGGUCUACCGUAAGUAUUCG-AUAGAAGAAAAUGUUCGCA
((((((.......))))))((...((..((((...))))..)).....((((((..((..((((...(....)..)))).)).((((.((........))-.)))).....)))))))). ( -36.70)
>consensus
AGCUGCCGCACAGGCAGCGGCGGAAGUGAAGGCCACAUUGGCUGCUCAGGUGGUCAGUGCGCCCAAGGGCAACGAUGGAAAGAUCUACCGUAAGUCGCCACAUACUUGUGUUUGCUAGCA
.((((((.....))))))((((((((((..(((((((((((((((....)))))))))..(((....))).(((.((((....)))).)))..))))))...))))))))))........ (-35.52 = -38.68 +   3.16)

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 09:34:19 2006