Locus 221

Sequence ID 3L_DroMel_CAF1
Location 617,106 – 617,276
Length 170
Max. P 0.968351
window327 window328 window329 window330

overview

Window 7

Location 617,106 – 617,198
Length 92
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 85.34
Mean single sequence MFE -27.24
Consensus MFE -19.56
Energy contribution -21.08
Covariance contribution 1.52
Combinations/Pair 1.18
Mean z-score -1.63
Structure conservation index 0.72
SVM decision value 0.05
SVM RNA-class probability 0.558455
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 617106 92 + 23771897
CGUCGGCGUCUCGUAUCAUCGCUC------CAACAACAACAAAAACGGCAGCACUAUGGCAGCAGCAACCUCAAAUGCGCUCUUGCUACUGCUGCCGA
.((.((((...........)))).------..))...........((((((((...((((((.(((............))).)))))).)))))))). ( -27.00)
>DroSec_CAF1 28400 89 + 1
CGUCGGCGUCUCGUAUCAUCGCUC------CAACA---ACAAAAGCGGCAGCACUACGGCAGCAGCAACCUCAAAUGCGCUCUUGCUGCUGCUGCCGA
..(((((....((......))...------.....---.....((((((((((....((.(((.(((........))))))))))))))))))))))) ( -30.30)
>DroSim_CAF1 26790 89 + 1
CGUCGGCGUCUCGUAUCAUCGCUC------CAACA---ACAAAAGCGGCAGCACUAUGGCAGCAGCAACCUCAAAUGCGCUCUUGCUGCUGCUGCCGA
..(((((....((......))...------.....---.....((((((((((....((.(((.(((........))))))))))))))))))))))) ( -30.30)
>DroEre_CAF1 30509 77 + 1
CGCCGGCGUCCCGUAUCAUCGCU------ACAACA---ACAAAAGCGGCAGCACUGUGGCAGCAGCAACCUCAAAUGCGCUCA------------CGC
.(((((....))........(((------......---.....))))))......(((((.(((...........))))).))------------).. ( -15.40)
>DroYak_CAF1 32166 94 + 1
CGUCGGCGUCUCGUAUCAUCGCUCCACAAACAACA---ACAAAAGCGGCGGCACUGUGGCAGCAGCAACCUCGAAUGCGCUCU-GCCGCUGCUGCCGA
.((.((((...........))).).))........---.......((((((((..(((((((..(((........)))...))-))))))))))))). ( -33.20)
>consensus
CGUCGGCGUCUCGUAUCAUCGCUC______CAACA___ACAAAAGCGGCAGCACUAUGGCAGCAGCAACCUCAAAUGCGCUCUUGCUGCUGCUGCCGA
....((((...........))))......................((((((((...(((((((.(((........))))))...)))).)))))))). (-19.56 = -21.08 +   1.52)

alignment

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secondary structure

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Window 8

Location 617,124 – 617,238
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.12
Mean single sequence MFE -31.24
Consensus MFE -16.88
Energy contribution -18.40
Covariance contribution 1.52
Combinations/Pair 1.22
Mean z-score -2.50
Structure conservation index 0.54
SVM decision value 1.62
SVM RNA-class probability 0.968351
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 617124 114 + 23771897
UCGCUC------CAACAACAACAAAAACGGCAGCACUAUGGCAGCAGCAACCUCAAAUGCGCUCUUGCUACUGCUGCCGAUGCACUGCAAGAAAUGGACGCCAAAUAUGAAAUAUCCCAA
..((((------((.............((((((((...((((((.(((............))).)))))).)))))))).(((...))).....)))).))................... ( -31.10)
>DroSec_CAF1 28418 103 + 1
UCGCUC------CAACA---ACAAAAGCGGCAGCACUACGGCAGCAGCAACCUCAAAUGCGCUCUUGCUGCUGCUGCCGAUGCACUGAAAGAAACGGA--------GUGAAAUAUCCCCU
((((((------(....---......((....))....(((((((((((..(......).((....)))))))))))))................)))--------)))).......... ( -36.10)
>DroSim_CAF1 26808 103 + 1
UCGCUC------CAACA---ACAAAAGCGGCAGCACUAUGGCAGCAGCAACCUCAAAUGCGCUCUUGCUGCUGCUGCCGAUGCACUGAAAGAAACGGA--------GUGAAAUAUCCCCU
((((((------(....---.....((((((((((....((.(((.(((........))))))))))))))))))((....))............)))--------)))).......... ( -35.10)
>DroEre_CAF1 30527 99 + 1
UCGCU------ACAACA---ACAAAAGCGGCAGCACUGUGGCAGCAGCAACCUCAAAUGCGCUCA------------CGCUGCACUGAGAGAAAUGGACGCAGAACAUAAAAUAUCCCAA
.((((------......---.....))))(((((...(((((.(((...........))))).))------------)))))).(((.(.........).)))................. ( -19.10)
>DroYak_CAF1 32184 116 + 1
UCGCUCCACAAACAACA---ACAAAAGCGGCGGCACUGUGGCAGCAGCAACCUCGAAUGCGCUCU-GCCGCUGCUGCCGAUGCACUGCAAGAAAUGAACGAAGGACAUAGGAUAUCCCAA
..(.(((..........---.......((((((((..(((((((..(((........)))...))-))))))))))))).(((...))).............))))...((.....)).. ( -34.80)
>consensus
UCGCUC______CAACA___ACAAAAGCGGCAGCACUAUGGCAGCAGCAACCUCAAAUGCGCUCUUGCUGCUGCUGCCGAUGCACUGAAAGAAAUGGACG____A_AUGAAAUAUCCCAA
...........................((((((((...(((((((.(((........))))))...)))).))))))))......................................... (-16.88 = -18.40 +   1.52)

alignment

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secondary structure

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dotplot

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Window 9

Location 617,124 – 617,238
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.12
Mean single sequence MFE -39.47
Consensus MFE -24.59
Energy contribution -26.87
Covariance contribution 2.28
Combinations/Pair 1.18
Mean z-score -2.29
Structure conservation index 0.62
SVM decision value 1.48
SVM RNA-class probability 0.957490
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 617124 114 - 23771897
UUGGGAUAUUUCAUAUUUGGCGUCCAUUUCUUGCAGUGCAUCGGCAGCAGUAGCAAGAGCGCAUUUGAGGUUGCUGCUGCCAUAGUGCUGCCGUUUUUGUUGUUGUUG------GAGCGA
...((((...(((....))).)))).......((((..(...((((((((((((.(((.....)))...))))))))))))...)..))))((((((..........)------))))). ( -39.40)
>DroSec_CAF1 28418 103 - 1
AGGGGAUAUUUCAC--------UCCGUUUCUUUCAGUGCAUCGGCAGCAGCAGCAAGAGCGCAUUUGAGGUUGCUGCUGCCGUAGUGCUGCCGCUUUUGU---UGUUG------GAGCGA
.((((........)--------)))........(((..(..(((((((((((((.(((.....)))...)))))))))))))..)..))).((((((...---....)------))))). ( -44.10)
>DroSim_CAF1 26808 103 - 1
AGGGGAUAUUUCAC--------UCCGUUUCUUUCAGUGCAUCGGCAGCAGCAGCAAGAGCGCAUUUGAGGUUGCUGCUGCCAUAGUGCUGCCGCUUUUGU---UGUUG------GAGCGA
.((((........)--------)))........(((..(...((((((((((((.(((.....)))...))))))))))))...)..))).((((((...---....)------))))). ( -41.20)
>DroEre_CAF1 30527 99 - 1
UUGGGAUAUUUUAUGUUCUGCGUCCAUUUCUCUCAGUGCAGCG------------UGAGCGCAUUUGAGGUUGCUGCUGCCACAGUGCUGCCGCUUUUGU---UGUUGU------AGCGA
..(((((((...)))))))...........(((((((((.((.------------...))))).))))))(((((((.((.((((.((....))..))))---.)).))------))))) ( -30.00)
>DroYak_CAF1 32184 116 - 1
UUGGGAUAUCCUAUGUCCUUCGUUCAUUUCUUGCAGUGCAUCGGCAGCAGCGGC-AGAGCGCAUUCGAGGUUGCUGCUGCCACAGUGCCGCCGCUUUUGU---UGUUGUUUGUGGAGCGA
..(((((((...)))))))((((((.......((.(..(...((((((((((((-.(((....)))...))))))))))))...)..).))(((......---........))))))))) ( -42.64)
>consensus
UUGGGAUAUUUCAU_U____CGUCCAUUUCUUUCAGUGCAUCGGCAGCAGCAGCAAGAGCGCAUUUGAGGUUGCUGCUGCCAUAGUGCUGCCGCUUUUGU___UGUUG______GAGCGA
...((((..............))))........(((..(...((((((((((((..(((....)))...))))))))))))...)..))).(((((..................))))). (-24.59 = -26.87 +   2.28)

alignment

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secondary structure

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Window 0

Location 617,158 – 617,276
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.99
Mean single sequence MFE -32.46
Consensus MFE -16.42
Energy contribution -19.26
Covariance contribution 2.84
Combinations/Pair 1.17
Mean z-score -1.96
Structure conservation index 0.51
SVM decision value 0.55
SVM RNA-class probability 0.777102
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 617158 118 - 23771897
A-AAUACACGCUA-ACCAGCAAAAACUAUUAUUUCCAGCAUUGGGAUAUUUCAUAUUUGGCGUCCAUUUCUUGCAGUGCAUCGGCAGCAGUAGCAAGAGCGCAUUUGAGGUUGCUGCUGC
.-....((((((.-...))).................(((...((((...(((....))).))))......))).))).....(((((((((((.(((.....)))...))))))))))) ( -29.40)
>DroSec_CAF1 28449 110 - 1
A-AAUGCACACUA-ACCAGCAAAAACUAUUAUUUCCAGCAAGGGGAUAUUUCAC--------UCCGUUUCUUUCAGUGCAUCGGCAGCAGCAGCAAGAGCGCAUUUGAGGUUGCUGCUGC
.-.((((((....-...(((.........(((..((.....))..)))......--------...))).......))))))..(((((((((((.(((.....)))...))))))))))) ( -32.31)
>DroSim_CAF1 26839 110 - 1
A-AAUGCACACUA-ACCAGCAAAAACUAUUAUUUCCAGCAAGGGGAUAUUUCAC--------UCCGUUUCUUUCAGUGCAUCGGCAGCAGCAGCAAGAGCGCAUUUGAGGUUGCUGCUGC
.-.((((((....-...(((.........(((..((.....))..)))......--------...))).......))))))..(((((((((((.(((.....)))...))))))))))) ( -32.31)
>DroEre_CAF1 30558 108 - 1
AAAAUGUACUCUACGCUACCCAAUGCUAUUAUUUUUAGCAUUGGGAUAUUUUAUGUUCUGCGUCCAUUUCUCUCAGUGCAGCG------------UGAGCGCAUUUGAGGUUGCUGCUGC
.(((((..(((.(((((.((((((((((.......)))))))))).........((.(((.(.........).))).))))))------------))))..)))))..(((....))).. ( -35.30)
>DroYak_CAF1 32221 115 - 1
----UGUACACUUAGCUACCCAAUACUUUUAUUUUUAGCAUUGGGAUAUCCUAUGUCCUUCGUUCAUUUCUUGCAGUGCAUCGGCAGCAGCGGC-AGAGCGCAUUCGAGGUUGCUGCUGC
----(((((.....((((...((((....))))..))))...(((((((...)))))))................)))))...(((((((((((-.(((....)))...))))))))))) ( -33.00)
>consensus
A_AAUGCACACUA_ACCAGCAAAAACUAUUAUUUCCAGCAUUGGGAUAUUUCAU_U____CGUCCAUUUCUUUCAGUGCAUCGGCAGCAGCAGCAAGAGCGCAUUUGAGGUUGCUGCUGC
.....................................(((((((((........................)))))))))....(((((((((((..(((....)))...))))))))))) (-16.42 = -19.26 +   2.84)

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 09:36:44 2006