Locus 868

Sequence ID 3L_DroMel_CAF1
Location 2,611,341 – 2,611,597
Length 256
Max. P 0.773274
window1333 window1334 window1335 window1336 window1337

overview

Window 3

Location 2,611,341 – 2,611,455
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.32
Mean single sequence MFE -27.82
Consensus MFE -14.78
Energy contribution -19.38
Covariance contribution 4.60
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.53
SVM decision value -0.01
SVM RNA-class probability 0.528430
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2611341 114 + 23771897
----AAAUG--AAAUCCAUUUAUUUGGGGACUCCAAAUUCGAUGACAGCUGCAGUAAUUGGUUUCACCCAUUUUACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUAAAAUCCAC
----(((((--.....)))))((((..(((((((...................((((.(((......)))..)))).((((((((((.....)))))))))).)))))))..)))).... ( -35.30)
>DroSec_CAF1 9525 106 + 1
AGUUAAAUAAUAAAUCCAUUUAUUUGGGGACUCCAAAUUCGAUGACAGCUGCAGUAAUUGGUUUCACCCAUUU--------------AUUUAUCCACCUGUCAGCAGUUUUAAAAUCCAC
...............(((......)))(((....(((((...((((((.((.(((((.(((......))).))--------------)))....)).))))))..))))).....))).. ( -18.70)
>DroSim_CAF1 12210 106 + 1
AGUUAAAUAAUAAAUCCAUUUAUUUGGGGACUCCAAAUUCGAUGACAGCUGCAGUAAUUGGUUUCACCCAUUU--------------AUUUAUCCACCUGUCAGCAGUUUUAAAAUCCAC
...............(((......)))(((....(((((...((((((.((.(((((.(((......))).))--------------)))....)).))))))..))))).....))).. ( -18.70)
>DroEre_CAF1 9736 116 + 1
AAUGAAAUAAUAAAUCCUCAUAUUUGGGGACCCCAAAUUCGAUGACAGCUGCAGUAAUUGGUUUCACCCAUUCAACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUAAAAA----
..((((((......((((......((((((..((((......((.(....)))....))))..)).)))).......((((((((((.....))))))))))))))))))))....---- ( -33.00)
>DroYak_CAF1 13002 120 + 1
AAUGAAAUAAUAAAUCCAUGUAUUUGGGGACCCAAAAUUCGAUGACAGCUGCAGUAAUUGGUUUCACCCAUUCAACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUGAAAUCCGC
...............(((......)))(((..((((((((.............((...(((......)))....)).((((((((((.....))))))))))..))))))))...))).. ( -33.40)
>consensus
AAUGAAAUAAUAAAUCCAUUUAUUUGGGGACUCCAAAUUCGAUGACAGCUGCAGUAAUUGGUUUCACCCAUUU_ACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUAAAAUCCAC
..............(((.......((((((..((((......((.(....)))....))))..)).)))).......((((((((((.....)))))))))).))).............. (-14.78 = -19.38 +   4.60)

alignment

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secondary structure

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Window 4

Location 2,611,341 – 2,611,455
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.32
Mean single sequence MFE -30.90
Consensus MFE -17.52
Energy contribution -20.28
Covariance contribution 2.76
Combinations/Pair 1.04
Mean z-score -2.63
Structure conservation index 0.57
SVM decision value 0.54
SVM RNA-class probability 0.773274
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2611341 114 - 23771897
GUGGAUUUUAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGUAAAAUGGGUGAAACCAAUUACUGCAGCUGUCAUCGAAUUUGGAGUCCCCAAAUAAAUGGAUUU--CAUUU----
..((((((((((......((((((((((.....)))))))))).((((..(((......))).))))................))))))))))(((......)))....--.....---- ( -33.60)
>DroSec_CAF1 9525 106 - 1
GUGGAUUUUAAAACUGCUGACAGGUGGAUAAAU--------------AAAUGGGUGAAACCAAUUACUGCAGCUGUCAUCGAAUUUGGAGUCCCCAAAUAAAUGGAUUUAUUAUUUAACU
..((((((((((..((.((((((.((.(....(--------------((.(((......))).))).).)).)))))).))..))))))))))(((......)))............... ( -25.70)
>DroSim_CAF1 12210 106 - 1
GUGGAUUUUAAAACUGCUGACAGGUGGAUAAAU--------------AAAUGGGUGAAACCAAUUACUGCAGCUGUCAUCGAAUUUGGAGUCCCCAAAUAAAUGGAUUUAUUAUUUAACU
..((((((((((..((.((((((.((.(....(--------------((.(((......))).))).).)).)))))).))..))))))))))(((......)))............... ( -25.70)
>DroEre_CAF1 9736 116 - 1
----UUUUUAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGUUGAAUGGGUGAAACCAAUUACUGCAGCUGUCAUCGAAUUUGGGGUCCCCAAAUAUGAGGAUUUAUUAUUUCAUU
----..........((((((((((((((.....))))))))))(((....((((.((..((((.....................))))..))))))...))))))).............. ( -35.00)
>DroYak_CAF1 13002 120 - 1
GCGGAUUUCAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGUUGAAUGGGUGAAACCAAUUACUGCAGCUGUCAUCGAAUUUUGGGUCCCCAAAUACAUGGAUUUAUUAUUUCAUU
((((..(((((.......((((((((((.....))))))))))..)))))(((......)))....))))..............(((((....)))))...(((((........))))). ( -34.50)
>consensus
GUGGAUUUUAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGU_AAAUGGGUGAAACCAAUUACUGCAGCUGUCAUCGAAUUUGGAGUCCCCAAAUAAAUGGAUUUAUUAUUUAACU
..((((((((((.....(((((((((((.....)))))............(((......)))..........)))))).....))))))))))(((......)))............... (-17.52 = -20.28 +   2.76)

alignment

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secondary structure

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Window 5

Location 2,611,375 – 2,611,485
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 81.77
Mean single sequence MFE -27.68
Consensus MFE -12.92
Energy contribution -17.00
Covariance contribution 4.08
Combinations/Pair 1.12
Mean z-score -2.19
Structure conservation index 0.47
SVM decision value 0.03
SVM RNA-class probability 0.547352
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2611375 110 + 23771897
GAUGACAGCUGCAGUAAUUGGUUUCACCCAUUUUACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUAAAAUCCACCUCUUUGCUGCAACAUUUUCUUUCGGCUUA
.......(.((((((((..(((...............((((((((((.....)))))))))).(((.........))))))...)))))))).)................ ( -34.90)
>DroSec_CAF1 9565 96 + 1
GAUGACAGCUGCAGUAAUUGGUUUCACCCAUUU--------------AUUUAUCCACCUGUCAGCAGUUUUAAAAUCCACCUCUUUGCUGGAACAUUUUCUUUCGGCUUA
..((((((.((.(((((.(((......))).))--------------)))....)).)))))).......................(((((((.......)))))))... ( -18.60)
>DroSim_CAF1 12250 96 + 1
GAUGACAGCUGCAGUAAUUGGUUUCACCCAUUU--------------AUUUAUCCACCUGUCAGCAGUUUUAAAAUCCACCUCUUUGCUGGAGCAUUUUCUUUCGGCUUA
..((((((.((.(((((.(((......))).))--------------)))....)).)))))).......................(((((((.......)))))))... ( -18.30)
>DroEre_CAF1 9776 98 + 1
GAUGACAGCUGCAGUAAUUGGUUUCACCCAUUCAACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUAAAAA------------UGAAACAUUUUCUUUCGGGCCG
..(((.((((.........)))))))(((..((....((((((((((.....))))))))))..))((((((....------------))))))..........)))... ( -28.10)
>DroYak_CAF1 13042 110 + 1
GAUGACAGCUGCAGUAAUUGGUUUCACCCAUUCAACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUGAAAUCCGCCGCUUGGCUGGAGCAUUUUCCUUCGGCUUG
......(((((.((.((...((((((.(((..(....((((((((((.....)))))))))).(((.........)))...)..))).))))))...)).)).))))).. ( -38.50)
>consensus
GAUGACAGCUGCAGUAAUUGGUUUCACCCAUUU_ACGGACAGGUGGAAUUUAUCCACCUGUCAGGAGUUUUAAAAUCCACCUCUUUGCUGGAACAUUUUCUUUCGGCUUA
......((((.(......(((......))).......((((((((((.....)))))))))).).)))).................(((((((.......)))))))... (-12.92 = -17.00 +   4.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,611,375 – 2,611,485
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 81.77
Mean single sequence MFE -28.78
Consensus MFE -12.76
Energy contribution -16.72
Covariance contribution 3.96
Combinations/Pair 1.05
Mean z-score -2.46
Structure conservation index 0.44
SVM decision value 0.43
SVM RNA-class probability 0.732945
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2611375 110 - 23771897
UAAGCCGAAAGAAAAUGUUGCAGCAAAGAGGUGGAUUUUAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGUAAAAUGGGUGAAACCAAUUACUGCAGCUGUCAUC
..........((....(((((((.....(((.(..........).)))((((((((((.....)))))))))).......(((......)))....)))))))..))... ( -34.70)
>DroSec_CAF1 9565 96 - 1
UAAGCCGAAAGAAAAUGUUCCAGCAAAGAGGUGGAUUUUAAAACUGCUGACAGGUGGAUAAAU--------------AAAUGGGUGAAACCAAUUACUGCAGCUGUCAUC
..((((....).......((((.(.....).))))..........)))(((((.((.(....(--------------((.(((......))).))).).)).)))))... ( -21.00)
>DroSim_CAF1 12250 96 - 1
UAAGCCGAAAGAAAAUGCUCCAGCAAAGAGGUGGAUUUUAAAACUGCUGACAGGUGGAUAAAU--------------AAAUGGGUGAAACCAAUUACUGCAGCUGUCAUC
..((((....).......((((.(.....).))))..........)))(((((.((.(....(--------------((.(((......))).))).).)).)))))... ( -20.90)
>DroEre_CAF1 9776 98 - 1
CGGCCCGAAAGAAAAUGUUUCA------------UUUUUAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGUUGAAUGGGUGAAACCAAUUACUGCAGCUGUCAUC
((((.(....).....((((((------------(((....(((....((((((((((.....)))))))))).)))....)))))))))...........))))..... ( -32.10)
>DroYak_CAF1 13042 110 - 1
CAAGCCGAAGGAAAAUGCUCCAGCCAAGCGGCGGAUUUCAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGUUGAAUGGGUGAAACCAAUUACUGCAGCUGUCAUC
......((.(((......))).....(((.((((..(((((.......((((((((((.....))))))))))..)))))(((......)))....)))).))).))... ( -35.20)
>consensus
UAAGCCGAAAGAAAAUGUUCCAGCAAAGAGGUGGAUUUUAAAACUCCUGACAGGUGGAUAAAUUCCACCUGUCCGU_AAAUGGGUGAAACCAAUUACUGCAGCUGUCAUC
..........((....(((.(((.........................((((((((((.....)))))))))).......(((......)))....))).)))..))... (-12.76 = -16.72 +   3.96)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,611,485 – 2,611,597
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.18
Mean single sequence MFE -16.78
Consensus MFE -11.45
Energy contribution -11.56
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -2.01
Structure conservation index 0.68
SVM decision value 0.19
SVM RNA-class probability 0.627817
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2611485 112 + 23771897
UAUAAAUUAAUCAAGCAAUUUAAUGCCAUUUUUUCCACCUCAUGAGCGUUGAAUUAUCCAUCAUUGAGAGUGGAAAAUCCAUU--------UGCAUUUUUUUUUUUUUUUUAGAUUUAAA
..((((((.............(((((....(((((((((((((((..((......))...))).)))).))))))))......--------.)))))...............)))))).. ( -18.99)
>DroSec_CAF1 9661 113 + 1
UAUAAUUUAAUCAAGCAAUUUAAUUCCCUUUUUUCCACCCCAAAAACGCUGAAUUAUCCAUCAUUCAGUGUGGAAAAUCCUUCACUAUGAAUGCAUUCU-------UUUUUAGAUUUAAA
...(((((((..(((.(((...((((....((((((((.........(((((((........)))))))))))))))...........))))..)))))-------)..))))))).... ( -16.66)
>DroSim_CAF1 12346 114 + 1
UAUAAUUUAAUCAAGCAAUUUAAUUCCCUUUUUUCCACCCCAAAAACGCUGAAUUAUCCAUCAUUCAGAGUGGAAAAUCCUUCACUAUGAAUGCAUUUU------UUUUUUAGAUUUAAA
..............(((.............((((((((..........((((((........)))))).))))))))...(((.....)))))).....------............... ( -14.70)
>consensus
UAUAAUUUAAUCAAGCAAUUUAAUUCCCUUUUUUCCACCCCAAAAACGCUGAAUUAUCCAUCAUUCAGAGUGGAAAAUCCUUCACUAUGAAUGCAUUUU______UUUUUUAGAUUUAAA
..............(((.............((((((((..........((((((........)))))).))))))))..............))).......................... (-11.45 = -11.56 +   0.11)

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 09:53:11 2006