Locus 9001

Sequence ID 3R_DroMel_CAF1
Location 24,121,148 – 24,121,241
Length 93
Max. P 0.954671
window14425 window14426

overview

Window 5

Location 24,121,148 – 24,121,241
Length 93
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 80.07
Mean single sequence MFE -28.57
Consensus MFE -16.78
Energy contribution -18.48
Covariance contribution 1.70
Combinations/Pair 1.04
Mean z-score -2.93
Structure conservation index 0.59
SVM decision value 1.45
SVM RNA-class probability 0.954671
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24121148 93 + 27905053
UUCAAGCCGCCAUCGUUGCCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUGGA----------CGUCACCACCCACCCACCCAGCCACCCAA
.....(.(((((((((..((((((((((..((((........))))))))))))))))))))).----------)).)......................... ( -25.30)
>DroPse_CAF1 328130 88 + 1
-------CGCCACAGUCUGUGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGUGGACUGAGAGGGGGAGGGCGAGGCGCCCGAUCCACCCC-----C---
-------.....(((((..(((((((((..((((........)))))))))))))..)))))...(((((.(((((...)))))......))))-----)--- ( -37.60)
>DroSec_CAF1 308151 89 + 1
UUCAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUGGA----------CGUCACCACC----CACCAAGCCACCCAA
.....(((((((....))))((((((((..((((........)))))))))))).)))(((((.----------.........)----))))........... ( -28.10)
>DroSim_CAF1 308300 93 + 1
UUCAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUGGA----------CGUCACCACCCACCCACCAAGUCACCCAA
.....(((((((....))))((((((((..((((........)))))))))))).)))(((((.----------.....)))))................... ( -27.90)
>DroEre_CAF1 323644 93 + 1
UUCCAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGCUGGA----------CGUCACCACCCACCCAUCGAACCACCCAA
.(((((((((((....))))((((((((..((((........))))))))))))..).))))))----------............................. ( -24.60)
>DroYak_CAF1 322300 93 + 1
UUUAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUGGA----------CGUCACCACCCACCCACCCGACCACCCAG
.....(((((((....))))((((((((..((((........)))))))))))).)))(((((.----------.....)))))................... ( -27.90)
>consensus
UUCAAGCCGCCAUCGUUGGCGUUAUUUAUUUGCGCUCACAUAUGCAUAAAUAACGGGCGGUGGA__________CGUCACCACCCACCCACCCAGCCACCCAA
.....(((((((....))))((((((((..((((........)))))))))))).)))(((((........................)))))........... (-16.78 = -18.48 +   1.70)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,121,148 – 24,121,241
Length 93
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 80.07
Mean single sequence MFE -35.50
Consensus MFE -19.35
Energy contribution -21.76
Covariance contribution 2.41
Combinations/Pair 1.16
Mean z-score -2.85
Structure conservation index 0.55
SVM decision value 1.25
SVM RNA-class probability 0.936449
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24121148 93 - 27905053
UUGGGUGGCUGGGUGGGUGGGUGGUGACG----------UCCACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGGCAACGAUGGCGGCUUGAA
(..(((.(((((((((.(((..(....).----------.)))))))))(((((((((.....(((....))).)))))))))(....)...))).)))..). ( -40.10)
>DroPse_CAF1 328130 88 - 1
---G-----GGGGUGGAUCGGGCGCCUCGCCCUCCCCCUCUCAGUCCACGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACACAGACUGUGGCG-------
---(-----((((.(((..(((((...))))))))))))).(((((...(((((((((.....(((....))).)))))))))...))))).....------- ( -33.10)
>DroSec_CAF1 308151 89 - 1
UUGGGUGGCUUGGUG----GGUGGUGACG----------UCCACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUUGAA
(..(((.((((((((----(((((((...----------..))))))))(((((((((.....(((....))).))))))))))))).....))).)))..). ( -36.40)
>DroSim_CAF1 308300 93 - 1
UUGGGUGACUUGGUGGGUGGGUGGUGACG----------UCCACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUUGAA
..((....)).....(((((..(....).----------.)))))(((.(((((((((.....(((....))).)))))))))((((....)))))))..... ( -34.30)
>DroEre_CAF1 323644 93 - 1
UUGGGUGGUUCGAUGGGUGGGUGGUGACG----------UCCAGCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUGGAA
((.(((.(((((.(((..(((((.((...----------..)).)))))(((((((((.....(((....))).))))))))).))).)))..)).))).)). ( -31.10)
>DroYak_CAF1 322300 93 - 1
CUGGGUGGUCGGGUGGGUGGGUGGUGACG----------UCCACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUUAAA
.(((((.(((((((((.(((..(....).----------.)))))))))(((((((((.....(((....))).))))))))).........))).))))).. ( -38.00)
>consensus
UUGGGUGGCUGGGUGGGUGGGUGGUGACG__________UCCACCGCCCGUUAUUUAUGCAUAUGUGAGCGCAAAUAAAUAACGCCAACGAUGGCGGCUUGAA
((((((.(((...(((..((((((((...............))))))))(((((((((.....(((....))).))))))))).))).....))).)))))). (-19.35 = -21.76 +   2.41)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:24:33 2006