Locus 8229

Sequence ID 3R_DroMel_CAF1
Location 22,063,492 – 22,063,692
Length 200
Max. P 0.999068
window13261 window13262 window13263 window13264

overview

Window 1

Location 22,063,492 – 22,063,612
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.00
Mean single sequence MFE -37.88
Consensus MFE -37.40
Energy contribution -37.44
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 0.99
SVM decision value 1.32
SVM RNA-class probability 0.941235
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22063492 120 + 27905053
UUUGAACCCAUUGAGAUCCGAGGCCAAGGGAUGUGUCGGCCGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGC
((((((..(((.((((..(..(((....((((((...(((.((((..(....)..))))))).)))))).)))..).)))).(((((((....))))))).))).))))))......... ( -38.10)
>DroSec_CAF1 55476 120 + 1
UUUGAACCCAUAGAGAUCCGAGGCCAAGGGAUGUGUCGGCCGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGC
((((((..((((((((..(..(((....((((((...(((.((((..(....)..))))))).)))))).)))..).)))))(((((((....))))))).))).))))))......... ( -39.40)
>DroSim_CAF1 48487 120 + 1
UUUGAACCCAUAGAGAUCCGAGGCCAAGGGAUGUGUCGGCCGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGC
((((((..((((((((..(..(((....((((((...(((.((((..(....)..))))))).)))))).)))..).)))))(((((((....))))))).))).))))))......... ( -39.40)
>DroEre_CAF1 50056 120 + 1
UUUGAACCCAUACAGAUCCGAGGCCAAGGGAUGUGUCGGCCGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGC
((((((..(((..........(((....((((((...(((.((((..(....)..))))))).)))))).))).........(((((((....))))))).))).))))))......... ( -35.30)
>DroYak_CAF1 57867 120 + 1
UUUGAACCCAUAGAGAUCCGAGGCCAAGGGAUGUGUCGGCCGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUUAAAUAUUGUCGC
((((((..((((((((..(..(((....((((((...(((.((((..(....)..))))))).)))))).)))..).)))))(((((((....))))))).))).))))))......... ( -37.20)
>consensus
UUUGAACCCAUAGAGAUCCGAGGCCAAGGGAUGUGUCGGCCGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGC
((((((..(((.((((..(..(((....((((((...(((.((((..(....)..))))))).)))))).)))..).)))).(((((((....))))))).))).))))))......... (-37.40 = -37.44 +   0.04)

alignment

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secondary structure

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Window 2

Location 22,063,492 – 22,063,612
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.00
Mean single sequence MFE -38.86
Consensus MFE -37.98
Energy contribution -38.58
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.38
Structure conservation index 0.98
SVM decision value 3.35
SVM RNA-class probability 0.999068
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22063492 120 - 27905053
GCGACAAUAUUUGAAUCAUGUCAUGGAAUAUUCCAUGAAGAGAACUUGGCUGAAUGUUGACGGGCCACAAUCACAGCCCGGCCGACACAUCCCUUGGCCUCGGAUCUCAAUGGGUUCAAA
.........((((((((...(((((((....))))))).((((.((.(((..(.(((((.(((((..........)))))..)))))......)..)))..)).))))....)))))))) ( -40.30)
>DroSec_CAF1 55476 120 - 1
GCGACAAUAUUUGAAUCAUGUCAUGGAAUAUUCCAUGAAGAGAACUUGGCUGAAUGUUGACGGGCCACAAUCACAGCCCGGCCGACACAUCCCUUGGCCUCGGAUCUCUAUGGGUUCAAA
.........((((((((...(((((((....)))))))(((((.((.(((..(.(((((.(((((..........)))))..)))))......)..)))..)).)))))...)))))))) ( -41.00)
>DroSim_CAF1 48487 120 - 1
GCGACAAUAUUUGAAUCAUGUCAUGGAAUAUUCCAUGAAGAGAACUUGGCUGAAUGUUGACGGGCCACAAUCACAGCCCGGCCGACACAUCCCUUGGCCUCGGAUCUCUAUGGGUUCAAA
.........((((((((...(((((((....)))))))(((((.((.(((..(.(((((.(((((..........)))))..)))))......)..)))..)).)))))...)))))))) ( -41.00)
>DroEre_CAF1 50056 120 - 1
GCGACAAUAUUUGAAUCAUGUCAUGGAAUAUUCCAUGAAGAGAACUUGGCUGAAUGUUGACGGGCCACAAUCACAGCCCGGCCGACACAUCCCUUGGCCUCGGAUCUGUAUGGGUUCAAA
.........((((((((...(((((((....)))))))(.(((.((.(((..(.(((((.(((((..........)))))..)))))......)..)))..)).))).)...)))))))) ( -36.90)
>DroYak_CAF1 57867 120 - 1
GCGACAAUAUUUAAAUCAUGUCAUGGAAUAUUCCAUGAAGAGAACUUGGCUGAAUGUUGACGGGCCACAAUCACAGCCCGGCCGACACAUCCCUUGGCCUCGGAUCUCUAUGGGUUCAAA
...............((((.(((((((....)))))))(((((.((.(((..(.(((((.(((((..........)))))..)))))......)..)))..)).)))))))))....... ( -35.10)
>consensus
GCGACAAUAUUUGAAUCAUGUCAUGGAAUAUUCCAUGAAGAGAACUUGGCUGAAUGUUGACGGGCCACAAUCACAGCCCGGCCGACACAUCCCUUGGCCUCGGAUCUCUAUGGGUUCAAA
.........((((((((...(((((((....)))))))(((((.((.(((..(.(((((.(((((..........)))))..)))))......)..)))..)).)))))...)))))))) (-37.98 = -38.58 +   0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,063,532 – 22,063,652
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -37.52
Consensus MFE -35.96
Energy contribution -35.64
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -1.74
Structure conservation index 0.96
SVM decision value 1.92
SVM RNA-class probability 0.982548
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22063532 120 + 27905053
CGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAAUCUGU
(((((..(....)..))))).....((((((((.(((((...(((((((....)))))))((.((((......((((......)))).....)))).)))))))...))).))))).... ( -38.00)
>DroSec_CAF1 55516 120 + 1
CGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAUUCUGU
(((((..(....)..)))))...(((.((((((.(((((...(((((((....)))))))((.((((......((((......)))).....)))).)))))))...))).)))...))) ( -36.80)
>DroSim_CAF1 48527 120 + 1
CGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAUUCUGU
(((((..(....)..)))))...(((.((((((.(((((...(((((((....)))))))((.((((......((((......)))).....)))).)))))))...))).)))...))) ( -36.80)
>DroEre_CAF1 50096 120 + 1
CGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGACUUGAAUCUGU
(((((..(....)..)))))........(((.(((((((((.(((((((....)))))))((.((((......((((......)))).....)))).)).....)))))))))...))). ( -36.10)
>DroYak_CAF1 57907 120 + 1
CGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUUAAAUAUUGUCGCACAACAAGCAGAAAUCUUGGAGCUGGGGGCUUGAGUCUGU
(((((..(....)..))))).....((((((((.(((((...(((((((....)))))))((.(((((.....((((......))))....))))).)))))))...))).))))).... ( -39.90)
>consensus
CGGGCUGUGAUUGUGGCCCGUCAACAUUCAGCCAAGUUCUCUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAAUCUGU
(((((..(....)..)))))........(((.(((((((((.(((((((....)))))))((.((((......((((......)))).....)))).)).....)))))))))...))). (-35.96 = -35.64 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,063,572 – 22,063,692
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -29.70
Consensus MFE -29.58
Energy contribution -29.26
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -1.41
Structure conservation index 1.00
SVM decision value 1.11
SVM RNA-class probability 0.916985
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22063572 120 + 27905053
CUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAAUCUGUCCUCCCUGUAGUUGUUUAUAAAGUUUUAUUCUCCAGCUUA
..(((((((....)))))))((.((((......((((......)))).....)))).))(((((((((((........))))....(((((....)))))............))))))). ( -29.20)
>DroSec_CAF1 55556 120 + 1
CUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAUUCUGUCCUCCCUGUAGUUGUUUAUAAAGUUUUAUUCUCCAGCUUA
..(((((((....)))))))((.((((......((((......)))).....)))).))(((((((((((........))))....(((((....)))))............))))))). ( -29.20)
>DroSim_CAF1 48567 120 + 1
CUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAUUCUGUCCUCCCUGUAGUUGUUUAUAAAGUUUUAUUCUCCAGCUUA
..(((((((....)))))))((.((((......((((......)))).....)))).))(((((((((((........))))....(((((....)))))............))))))). ( -29.20)
>DroEre_CAF1 50136 120 + 1
CUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGACUUGAAUCUGUCCUCCCUGUAGUUGUUUAUAAAGUUUUAUUCUCCAGCUUA
..(((((((....)))))))((.((((......((((......)))).....)))).))(((((((((((........))))....(((((....)))))............))))))). ( -29.80)
>DroYak_CAF1 57947 120 + 1
CUUCAUGGAAUAUUCCAUGACAUGAUUUAAAUAUUGUCGCACAACAAGCAGAAAUCUUGGAGCUGGGGGCUUGAGUCUGUCCUCCCUGUAGUUGUUUAUAAAGUUUUAUUCUCCAGCUUA
..(((((((....)))))))((.(((((.....((((......))))....))))).))(((((((((((........))))....(((((....)))))............))))))). ( -31.10)
>consensus
CUUCAUGGAAUAUUCCAUGACAUGAUUCAAAUAUUGUCGCACAGCAAGCAGAAAUCUUGGAGCUGGGGGCUUGAAUCUGUCCUCCCUGUAGUUGUUUAUAAAGUUUUAUUCUCCAGCUUA
..(((((((....)))))))((.((((......((((......)))).....)))).))(((((((((((........))))....(((((....)))))............))))))). (-29.58 = -29.26 +  -0.32)

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 13:06:11 2006