Locus 3702

Sequence ID X_DroMel_CAF1
Location 9,865,297 – 9,865,463
Length 166
Max. P 0.951274
window6059 window6060 window6061

overview

Window 9

Location 9,865,297 – 9,865,398
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.52
Mean single sequence MFE -30.75
Consensus MFE -24.13
Energy contribution -25.38
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.78
SVM decision value 1.41
SVM RNA-class probability 0.951274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9865297 101 + 22224390
UACCGGUUU-UUGGGCUAUUAAACCGCAUUGGCCUGAAAUUCCAGCAUUCCCAG----------UGCAAUCGCCUUUGGUAAUUGUAUCUGUCAGAUGCACAGAUACACGUG--------
((((((.((-(..(((((...........)))))..)))..)).((((.....)----------)))..........))))..((((((((((....).)))))))))....-------- ( -31.40)
>DroPse_CAF1 10208 120 + 1
UACCGGUUUUUUGUGCUAUUAAACCGCAUUUGCCUGAAAUUCCAGCAUUCCCAGUCGCAUCCACUGCAAUCGCUUUUGGUAACUGUAUCUGACAGAUACACAGAUACACCGGGCCACAAA
..(((((..((((((.((((..........(((.((......)))))....(((..(((.(((..((....))...)))....)))..)))...))))))))))...)))))........ ( -26.80)
>DroSec_CAF1 10070 102 + 1
UACCGGUUUUUUGGGCUAUUAAACCGCAUUGGCCUGAAAUUCCAGCAUUCCCAG----------UGCAAUCGCCUUUGGUAAUUGUAUCUGUCAGAUGCACAGAUACACGUG--------
((((((..(((..(((((...........)))))..)))..)).((((.....)----------)))..........))))..((((((((((....).)))))))))....-------- ( -33.40)
>DroYak_CAF1 9521 101 + 1
UACCGGUUU-UUGGGCUAUUAAACCGCAUUGGCCUGAAAUUCCAGCAUUCCCAG----------UGCAAUCGCUUUUGGUAAUUGUAUCUGUCAGAUGCACAGAUACACGUG--------
((((((.((-(..(((((...........)))))..)))..)).((((.....)----------)))..........))))..((((((((((....).)))))))))....-------- ( -31.40)
>consensus
UACCGGUUU_UUGGGCUAUUAAACCGCAUUGGCCUGAAAUUCCAGCAUUCCCAG__________UGCAAUCGCCUUUGGUAAUUGUAUCUGUCAGAUGCACAGAUACACGUG________
((((((..((((((((((...........))))))))))..)).(((.................)))..........))))..(((((((((.......)))))))))............ (-24.13 = -25.38 +   1.25)

alignment

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secondary structure

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Window 0

Location 9,865,366 – 9,865,463
Length 97
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 64.86
Mean single sequence MFE -20.52
Consensus MFE -9.90
Energy contribution -10.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.48
SVM decision value 0.58
SVM RNA-class probability 0.790011
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9865366 97 + 22224390
AAUUGUAUCUGUCAGAUGCACAGAUACACGUG----------CA-UCGGGAUCUGUCUUCAGUUUUAUUGCAAAAUGUGCCAUUUUUCUUUUUUAUUUUUGUUGGCUA
...((((((((((....).)))))))))..((----------((-..((((.(((....)))))))..))))......((((....................)))).. ( -21.55)
>DroPse_CAF1 10288 108 + 1
AACUGUAUCUGACAGAUACACAGAUACACCGGGCCACAAAUACACACGUGCGGUGCCUUCAACCUCAUUGCAAAAUUUGCUACAUUUUUUUUUGUAUUUUGUCUUCCU
...((((((((.........))))))))..(((..(((((((((...(((.(((.......))).))).(((.....)))............)))).)))))..))). ( -22.30)
>DroSec_CAF1 10140 77 + 1
AAUUGUAUCUGUCAGAUGCACAGAUACACGUG----------CA-UCGGGAUCUGUCUUCAGUUUUAUUGCAAAAUGUGCCAUUUUUU--------------------
...((((((((((....).)))))))))..((----------((-..((((.(((....)))))))..))))................-------------------- ( -17.70)
>consensus
AAUUGUAUCUGUCAGAUGCACAGAUACACGUG__________CA_UCGGGAUCUGUCUUCAGUUUUAUUGCAAAAUGUGCCAUUUUUUUUUUU___UUUUGU___C__
...(((((((((.......))))))))).........................................(((.....)))............................ ( -9.90 = -10.23 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,865,366 – 9,865,463
Length 97
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 64.86
Mean single sequence MFE -18.13
Consensus MFE -11.40
Energy contribution -11.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.05
Structure conservation index 0.63
SVM decision value 0.23
SVM RNA-class probability 0.642446
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9865366 97 - 22224390
UAGCCAACAAAAAUAAAAAAGAAAAAUGGCACAUUUUGCAAUAAAACUGAAGACAGAUCCCGA-UG----------CACGUGUAUCUGUGCAUCUGACAGAUACAAUU
..((((....................))))......((((......(((....))).......-))----------))..(((((((((.......)))))))))... ( -18.07)
>DroPse_CAF1 10288 108 - 1
AGGAAGACAAAAUACAAAAAAAAAUGUAGCAAAUUUUGCAAUGAGGUUGAAGGCACCGCACGUGUGUAUUUGUGGCCCGGUGUAUCUGUGUAUCUGUCAGAUACAGUU
.(((.(((....((((........))))(((.....)))......)))....((((((((((........))))...)))))).))).((((((.....))))))... ( -21.90)
>DroSec_CAF1 10140 77 - 1
--------------------AAAAAAUGGCACAUUUUGCAAUAAAACUGAAGACAGAUCCCGA-UG----------CACGUGUAUCUGUGCAUCUGACAGAUACAAUU
--------------------..((((((...))))))(((......(((....))).......-))----------)...(((((((((.......)))))))))... ( -14.42)
>consensus
__G___ACAAAA___AAAAAAAAAAAUGGCACAUUUUGCAAUAAAACUGAAGACAGAUCCCGA_UG__________CACGUGUAUCUGUGCAUCUGACAGAUACAAUU
............................(((.....))).........................................(((((((((.......)))))))))... (-11.40 = -11.73 +   0.33)

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 11:06:00 2006