Locus 3359

Sequence ID 3L_DroMel_CAF1
Location 9,826,563 – 9,826,707
Length 144
Max. P 0.998423
window5245 window5246 window5247 window5248

overview

Window 5

Location 9,826,563 – 9,826,667
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.93
Mean single sequence MFE -22.54
Consensus MFE -18.00
Energy contribution -17.12
Covariance contribution -0.88
Combinations/Pair 1.18
Mean z-score -1.62
Structure conservation index 0.80
SVM decision value 0.26
SVM RNA-class probability 0.659345
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9826563 104 + 23771897
----------------UUGAUGGGCAAUAGAGGUGACACAGCAGCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUGGGAAAUGAAUAACUUUCAUUCUUCAAUCAUUAGAAA
----------------......((((....((.((......)).))....)))).(((((((...(((((((....)))))))((..((((((.....))))))..)).))))))).... ( -22.60)
>DroSec_CAF1 120583 96 + 1
---------------------GGGGAAUAAAGGUGACACA---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCGGAAA
---------------------..........(....)..(---((......)))....((((......)))).((((((((..(((((.((((.....))))))))).)))))))).... ( -19.00)
>DroSim_CAF1 123821 116 + 1
AAGGGGAAGUUGGGGGUAGG-GGGGCAUUAAGGUGACACA---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCGGAAA
....((..((((((((..(.-.((((((((..(((.((((---.....)))).)))..)))))).(((((((....))))))).............))..)..))))))))..))..... ( -28.10)
>DroEre_CAF1 123440 100 + 1
----------------GUGG-GGGGUAUAAAGGUGACAUA---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCAGAAA
----------------....-...((((...(....)(((---((......)))))....)))).........((((((((..(((((.((((.....))))))))).)))))))).... ( -22.20)
>DroYak_CAF1 133669 100 + 1
----------------GUGG-GGGGUAUAAAGGUGACACA---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCGUCAGAAG
----------------....-...((((....(((.((((---.....)))).)))....)))).........((((((((..(((((.((((.....))))))))).)))))))).... ( -20.80)
>consensus
________________GUGG_GGGGAAUAAAGGUGACACA___GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCAGAAA
................................(((.((((........)))).)))..((((......)))).((((((((..(((((.((((.....))))))))).)))))))).... (-18.00 = -17.12 +  -0.88)

alignment

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secondary structure

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Window 6

Location 9,826,563 – 9,826,667
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.93
Mean single sequence MFE -18.17
Consensus MFE -14.18
Energy contribution -14.42
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.43
Structure conservation index 0.78
SVM decision value 1.66
SVM RNA-class probability 0.970719
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9826563 104 - 23771897
UUUCUAAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCCAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGCUGCUGUGUCACCUCUAUUGCCCAUCAA----------------
.....(((((((((.(((((((.....)))))))....((((((....))))))))).))))))((((((.......)))))).....................---------------- ( -17.00)
>DroSec_CAF1 120583 96 - 1
UUUCCGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---UGUGUCACCUUUAUUCCCC---------------------
.....((((((((.((((((((.....))))))..)).))))))))..((((......)))).((((((......))---))))...............--------------------- ( -18.10)
>DroSim_CAF1 123821 116 - 1
UUUCCGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---UGUGUCACCUUAAUGCCCC-CCUACCCCCAACUUCCCCUU
.....((((((((.((((((((.....))))))..)).))))))))..........((((.......(((((.....---))))).......))))...-.................... ( -19.24)
>DroEre_CAF1 123440 100 - 1
UUUCUGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---UAUGUCACCUUUAUACCCC-CCAC----------------
....(((((((((.((((((((.....))))))..)).))))))))).((((......)))).((((((......))---))))...............-....---------------- ( -18.40)
>DroYak_CAF1 133669 100 - 1
CUUCUGACGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---UGUGUCACCUUUAUACCCC-CCAC----------------
....((((((((((.(((((((.....)))))))....((((((....))))))))).)))...(((((......))---)))))))............-....---------------- ( -18.10)
>consensus
UUUCUGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC___UGUGUCACCUUUAUACCCC_CCAA________________
.....(((((((((.(((((((.....)))))))....((((((....))))))))).))))))...(((((........)))))................................... (-14.18 = -14.42 +   0.24)

alignment

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secondary structure

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Window 7

Location 9,826,587 – 9,826,707
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.88
Mean single sequence MFE -28.66
Consensus MFE -24.98
Energy contribution -24.70
Covariance contribution -0.28
Combinations/Pair 1.14
Mean z-score -2.36
Structure conservation index 0.87
SVM decision value 3.10
SVM RNA-class probability 0.998423
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9826587 120 + 23771897
GCAGCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUGGGAAAUGAAUAACUUUCAUUCUUCAAUCAUUAGAAAACGUGAUCGUGAGCCGUUUGAAAUCGCAUUUCUAUAUCUU
..(((......)))(((..((((((((......(((((((..(((..((((((.....))))))..))))))))))..(((((.(..(....)))))))...))))))))..)))..... ( -27.90)
>DroSec_CAF1 120602 117 + 1
---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCGGAAAACGUGAUCGUGAGCCGUUACAAAUCGCAUUUCUAUAACUU
---((......))((((..((((((((.......(((((((..(((((.((((.....))))))))).)))))))((...(((....)))...)).......))))))))..)))).... ( -30.70)
>DroSim_CAF1 123860 117 + 1
---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCGGAAAACGUGAUCGUGAGCCGUUUCAAAUCGCAUUUCUAUAACUU
---((......))((((..((((((((.......(((((((..(((((.((((.....))))))))).)))))))((...(((....)))...)).......))))))))..)))).... ( -30.70)
>DroEre_CAF1 123463 117 + 1
---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCAGAAAACGUGUUUGUGUGCCAUUUAAAAUCGCAUUUCGAUAUGUU
---((......))(((...((((((((......((((((((..(((((.((((.....))))))))).))))))))......(..(....)..)........))))))))...))).... ( -24.90)
>DroYak_CAF1 133692 117 + 1
---GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCGUCAGAAGACGUGUAUGAGUGCCGUUGCAAAUCGCAUUUCGAUAUGUU
---((......))(((...((((((((......((((((((..(((((.((((.....))))))))).))))))))...((((.(((....)))))))....))))))))...))).... ( -29.10)
>consensus
___GCUAAUGUGCUAUAAUGAUGCGAUAAUCAAUGAUGAUUAUAGGAAAUGAAUAACUUUCAUUCUUCAAUCAUCAGAAAACGUGAUCGUGAGCCGUUUCAAAUCGCAUUUCUAUAUCUU
...((......))((((..((((((((......((((((((..(((((.((((.....))))))))).))))))))...((((.(........)))))....))))))))..)))).... (-24.98 = -24.70 +  -0.28)

alignment

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secondary structure

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Window 8

Location 9,826,587 – 9,826,707
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.88
Mean single sequence MFE -24.94
Consensus MFE -19.56
Energy contribution -20.80
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -2.04
Structure conservation index 0.78
SVM decision value 1.08
SVM RNA-class probability 0.911890
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9826587 120 - 23771897
AAGAUAUAGAAAUGCGAUUUCAAACGGCUCACGAUCACGUUUUCUAAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCCAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGCUGC
....(((((..(((((((.((((.((.....)).............(((((((..(((((((.....)))))))....)))))))..))))..)))))))..)))))((......))... ( -23.00)
>DroSec_CAF1 120602 117 - 1
AAGUUAUAGAAAUGCGAUUUGUAACGGCUCACGAUCACGUUUUCCGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---
..(((((((..(((((((...(((.((...(((....)))...))((((((((.((((((((.....))))))..)).)))))))).)))...)))))))..)))))))........--- ( -30.40)
>DroSim_CAF1 123860 117 - 1
AAGUUAUAGAAAUGCGAUUUGAAACGGCUCACGAUCACGUUUUCCGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---
..(((((((..(((((((..((((((...........))))))..((((((((.((((((((.....))))))..)).)))))))).......)))))))..)))))))........--- ( -30.20)
>DroEre_CAF1 123463 117 - 1
AACAUAUCGAAAUGCGAUUUUAAAUGGCACACAAACACGUUUUCUGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---
...........(((((((.((((.((.....))...........(((((((((.((((((((.....))))))..)).)))))))))))))..))))))).................--- ( -20.90)
>DroYak_CAF1 133692 117 - 1
AACAUAUCGAAAUGCGAUUUGCAACGGCACUCAUACACGUCUUCUGACGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC---
...........(((((((...(((.((...........(((....)))(((((.((((((((.....))))))..)).))))).)).)))...))))))).................--- ( -20.20)
>consensus
AAGAUAUAGAAAUGCGAUUUGAAACGGCUCACGAUCACGUUUUCUGAUGAUUGAAGAAUGAAAGUUAUUCAUUUCCUAUAAUCAUCAUUGAUUAUCGCAUCAUUAUAGCACAUUAGC___
....(((((..(((((((...(((((...........)))))...((((((((..(((((((.....)))))))....)))))))).......)))))))..)))))............. (-19.56 = -20.80 +   1.24)

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 10:56:08 2006