Locus 5505

Sequence ID X_DroMel_CAF1
Location 14,271,524 – 14,271,660
Length 136
Max. P 0.879836
window8932 window8933 window8934

overview

Window 2

Location 14,271,524 – 14,271,620
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.10
Mean single sequence MFE -27.14
Consensus MFE -16.64
Energy contribution -17.40
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -1.74
Structure conservation index 0.61
SVM decision value 0.91
SVM RNA-class probability 0.879836
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14271524 96 + 22224390
CCGUAGU---------------------UUUGUUGCUGC-CGUGACA-GGAGACAGCUACCGCAGCAGCUGAAAAUUCGAGCUAGUACACUGCGAGAAAA-AGAGCUGAUGCAUGCAAAU
..(((((---------------------(.(((..(...-.)..)))-(....))))))).(((.(((((.....(((..((.((....))))..)))..-..))))).)))........ ( -27.20)
>DroSec_CAF1 12119 93 + 1
CCGUAGU---------------------UUUGUUGCUGC-AGUGACA-GGAGACAGCUACCGCAGCAGCUGAAAAUUCCAGCUAGUACACUGCGAGAAAA-AAAGCAGAUGCCAGCA---
..(.(((---------------------(((((((((((-.(((.(.-(....).).))).))))))))..)))))).).(((.(((..((((.......-...)))).))).))).--- ( -29.10)
>DroSim_CAF1 16148 95 + 1
CCGUAGU---------------------UUUGUUGCUGC-AGUGACA-GGAGACAGCUACCGCAGCAGCUGAAAAUUCCAGCUAGUACACUGCGAGAAA--AAAGUAGAUGCCAACAAGA
.((((((---------------------......(((((-.(((.(.-(....).).))).)))))(((((.......))))).....)))))).....--................... ( -25.80)
>DroEre_CAF1 14546 86 + 1
CUGUAGU------------------------UUUGUUGCAAGUGGCAAGGCGACAGCUACCGCAGCAGCUGAGCACUCGAACUAGUGCACUGCGAGAAAU-AAAGG---------CAAAU
.((((((------------------------.(((((((..(((((..(....).))))).)))))))....(((((......)))))))))))......-.....---------..... ( -25.00)
>DroYak_CAF1 15211 114 + 1
CCGCAGUUCUUUUUUUUUCUUAUUUUUUUUUUUUGCUGC-AGUGACA-GGAGACAGCUACCGCAGCAGCUGAAAACUCCAACUAGUACACUGCAAAAAAAGAAAAG----CGCUACAAGC
.(((..(((((((((.....................(((-((((((.-((((.(((((........)))))....)))).....)).))))))))))))))))..)----))........ ( -28.59)
>consensus
CCGUAGU_____________________UUUGUUGCUGC_AGUGACA_GGAGACAGCUACCGCAGCAGCUGAAAAUUCCAGCUAGUACACUGCGAGAAAA_AAAGC_GAUGCCAACAAAU
.((((((...........................(((((.(((.....(....).)))...)))))(((((.......))))).....)))))).......................... (-16.64 = -17.40 +   0.76)

alignment

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secondary structure

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Window 3

Location 14,271,524 – 14,271,620
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.10
Mean single sequence MFE -27.76
Consensus MFE -16.28
Energy contribution -16.48
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -1.73
Structure conservation index 0.59
SVM decision value 0.70
SVM RNA-class probability 0.826858
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14271524 96 - 22224390
AUUUGCAUGCAUCAGCUCU-UUUUCUCGCAGUGUACUAGCUCGAAUUUUCAGCUGCUGCGGUAGCUGUCUCC-UGUCACG-GCAGCAACAAA---------------------ACUACGG
...(((.((((.(((((..-.....(((.(((......))))))......))))).)))))))((((((...-......)-)))))......---------------------....... ( -25.02)
>DroSec_CAF1 12119 93 - 1
---UGCUGGCAUCUGCUUU-UUUUCUCGCAGUGUACUAGCUGGAAUUUUCAGCUGCUGCGGUAGCUGUCUCC-UGUCACU-GCAGCAACAAA---------------------ACUACGG
---..((((((.((((...-.......)))))))...(((((((...)))))))((((((((..(.......-.)..)))-)))))......---------------------....))) ( -29.10)
>DroSim_CAF1 16148 95 - 1
UCUUGUUGGCAUCUACUUU--UUUCUCGCAGUGUACUAGCUGGAAUUUUCAGCUGCUGCGGUAGCUGUCUCC-UGUCACU-GCAGCAACAAA---------------------ACUACGG
..(((((((......)...--......((((((.((.....(((.....(((((((....)))))))..)))-.))))))-))..)))))).---------------------....... ( -25.90)
>DroEre_CAF1 14546 86 - 1
AUUUG---------CCUUU-AUUUCUCGCAGUGCACUAGUUCGAGUGCUCAGCUGCUGCGGUAGCUGUCGCCUUGCCACUUGCAACAAA------------------------ACUACAG
..(((---------(....-.......))))((((..(((.((((.((.(((((((....)))))))..))))))..))))))).....------------------------....... ( -21.70)
>DroYak_CAF1 15211 114 - 1
GCUUGUAGCG----CUUUUCUUUUUUUGCAGUGUACUAGUUGGAGUUUUCAGCUGCUGCGGUAGCUGUCUCC-UGUCACU-GCAGCAAAAAAAAAAAAUAAGAAAAAAAAAGAACUGCGG
........((----(..((((((((((((((((.((.....((((....(((((((....))))))).))))-.))))))-))).....................)))))))))..))). ( -37.09)
>consensus
ACUUGCAGGCAUC_CCUUU_UUUUCUCGCAGUGUACUAGCUGGAAUUUUCAGCUGCUGCGGUAGCUGUCUCC_UGUCACU_GCAGCAACAAA_____________________ACUACGG
.........................(((((((.....((((((.....)))))))))))))..(((((.............))))).................................. (-16.28 = -16.48 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,271,542 – 14,271,660
Length 118
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 73.50
Mean single sequence MFE -26.32
Consensus MFE -19.20
Energy contribution -19.20
Covariance contribution -0.00
Combinations/Pair 1.23
Mean z-score -1.33
Structure conservation index 0.73
SVM decision value 0.25
SVM RNA-class probability 0.655042
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14271542 118 - 22224390
AACAUGGCAGCACGAUUUUAAAUCUAUAUUUUCUAUAACAAUUUGCAUGCAUCAGCUCU-UUUUCUCGCAGUGUACUAGCUCGAAUUUUCAGCUGCUGCGGUAGCUGUCUCCUGUCACG
.(((.((((((..(((.....)))...................(((.((((.(((((..-.....(((.(((......))))))......))))).)))))))))))))...))).... ( -26.62)
>DroSec_CAF1 12137 105 - 1
AACAAGGCACCACGAUUUGAAAUCUAUAUU-------------UGCUGGCAUCUGCUUU-UUUUCUCGCAGUGUACUAGCUGGAAUUUUCAGCUGCUGCGGUAGCUGUCUCCUGUCACU
.....((((.....................-------------.(((((.((((((...-.......)))).)).))))).(((.....(((((((....)))))))..)))))))... ( -26.40)
>DroSim_CAF1 16166 117 - 1
AACUUGGCACUACGAUCUGAAAUCUAUAUUCUCUAUAACAUCUUGUUGGCAUCUACUUU--UUUCUCGCAGUGUACUAGCUGGAAUUUUCAGCUGCUGCGGUAGCUGUCUCCUGUCACU
.....((((((((.....((((.............((((.....))))...........--)))).((((((.....(((((((...))))))))))))))))).)))).......... ( -25.25)
>DroYak_CAF1 15250 92 - 1
AACAAGGCAGCA--AUUC---------------------GGCUUGUAGCG----CUUUUCUUUUUUUGCAGUGUACUAGUUGGAGUUUUCAGCUGCUGCGGUAGCUGUCUCCUGUCACU
.....(((((..--...(---------------------((((.(((.((----((.............))))))).)))))(((....(((((((....))))))).))))))))... ( -27.02)
>consensus
AACAAGGCACCACGAUUUGAAAUCUAUAUU_________A_CUUGCAGGCAUCUGCUUU_UUUUCUCGCAGUGUACUAGCUGGAAUUUUCAGCUGCUGCGGUAGCUGUCUCCUGUCACU
.....((((((.................................((........)).........(((((((.....(((((((...))))))))))))))..)))))).......... (-19.20 = -19.20 +  -0.00)

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 11:49:36 2006