Locus 2950

Sequence ID 3L_DroMel_CAF1
Location 8,422,694 – 8,422,814
Length 120
Max. P 0.970446
window4613 window4614 window4615

overview

Window 3

Location 8,422,694 – 8,422,784
Length 90
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 63.25
Mean single sequence MFE -21.49
Consensus MFE -16.32
Energy contribution -15.80
Covariance contribution -0.52
Combinations/Pair 1.33
Mean z-score -1.81
Structure conservation index 0.76
SVM decision value 1.66
SVM RNA-class probability 0.970446
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8422694 90 + 23771897
-------------------UAUCACAUAUAUAAUCAGACUUAUUUCCCCCACUUUUUUUCAGUGCAUUCCCAGCUGCAUGUUGGUUUCUGCGCUAAGAAGUGCAGCUGU
-------------------..............................((((((((...((((((...(((((.....)))))....))))))))))))))....... ( -19.60)
>DroSec_CAF1 4638 69 + 1
------------------------------------UACUU----UCCCCACUUUCUGUCAGUGCAUACCCAGCUGCACGUUGGUUUCUGAGCUAAGAAGUGCAGCUGU
------------------------------------.....----....((((.......))))......(((((((((.((((((....))))))...))))))))). ( -21.40)
>DroSim_CAF1 11167 73 + 1
------------------------------------UACUUAGUCACCCCACUUUCUUUCAGUGCAUUCCCAGCUGCAUUUCGGUUUCUGAGCUAAGAAGUGCAGCUGU
------------------------------------.............((((.......))))......((((((((((((((((....))))..)))))))))))). ( -21.60)
>DroEre_CAF1 4712 109 + 1
CGAAAUAGAAUGUUCUGCAUGGCGCACUUAUUAUUCGAAUUGUUUGCCCAAACUUUUUUCAGUGCACUCCCAGCUGCAUGACGGCUUCCCAGCCAAGAAGUGCAGCUGU
.....((((....))))...((.(((((........(((..((((....))))....)))))))).))..(((((((((...((((....)))).....))))))))). ( -28.00)
>DroYak_CAF1 11276 96 + 1
-------------UCCGCAUACCACACCUAUUAUUUGACUUGUGCUCCCCAACUUUUUCCAGUGCAUUCACAGUUGCUUGAUGGUUUCCCAGCCCAGAAGUGCAGCUGU
-------------.......................((..((..((..............))..)).))((((((((((..(((.........)))..)).)))))))) ( -16.84)
>consensus
___________________U__C_CA__UAU_AU__GACUUAUUCUCCCCACUUUUUUUCAGUGCAUUCCCAGCUGCAUGUUGGUUUCUGAGCUAAGAAGUGCAGCUGU
......................................................................(((((((((...(((......))).....))))))))). (-16.32 = -15.80 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,422,694 – 8,422,784
Length 90
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 63.25
Mean single sequence MFE -23.86
Consensus MFE -13.46
Energy contribution -14.06
Covariance contribution 0.60
Combinations/Pair 1.12
Mean z-score -1.69
Structure conservation index 0.56
SVM decision value 1.04
SVM RNA-class probability 0.905228
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8422694 90 - 23771897
ACAGCUGCACUUCUUAGCGCAGAAACCAACAUGCAGCUGGGAAUGCACUGAAAAAAAGUGGGGGAAAUAAGUCUGAUUAUAUAUGUGAUA-------------------
.(((.((((.(((((((((((..........))).)))))))))))))))......(((.(((........))).)))............------------------- ( -21.40)
>DroSec_CAF1 4638 69 - 1
ACAGCUGCACUUCUUAGCUCAGAAACCAACGUGCAGCUGGGUAUGCACUGACAGAAAGUGGGGA----AAGUA------------------------------------
.(((((((((((((......))))......)))))))))....(.((((.......)))).)..----.....------------------------------------ ( -20.00)
>DroSim_CAF1 11167 73 - 1
ACAGCUGCACUUCUUAGCUCAGAAACCGAAAUGCAGCUGGGAAUGCACUGAAAGAAAGUGGGGUGACUAAGUA------------------------------------
.(((.((((.(((((((((((..........)).))))))))))))))))..........((....)).....------------------------------------ ( -21.40)
>DroEre_CAF1 4712 109 - 1
ACAGCUGCACUUCUUGGCUGGGAAGCCGUCAUGCAGCUGGGAGUGCACUGAAAAAAGUUUGGGCAAACAAUUCGAAUAAUAAGUGCGCCAUGCAGAACAUUCUAUUUCG
.((((((((.....(((((....)))))...)))))))).(.(((((((.......(((((((.......)))))))....)))))))).................... ( -32.80)
>DroYak_CAF1 11276 96 - 1
ACAGCUGCACUUCUGGGCUGGGAAACCAUCAAGCAACUGUGAAUGCACUGGAAAAAGUUGGGGAGCACAAGUCAAAUAAUAGGUGUGGUAUGCGGA-------------
....((((((((((.((((((....)).....(((........))).........)))).)))))((((..((........))))))...))))).------------- ( -23.70)
>consensus
ACAGCUGCACUUCUUAGCUCAGAAACCAACAUGCAGCUGGGAAUGCACUGAAAAAAAGUGGGGAAAACAAGUC__AU_AUA__UG_G__A___________________
.(((.((((.(((((((((...............))))))))))))))))........................................................... (-13.46 = -14.06 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,422,715 – 8,422,814
Length 99
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 72.99
Mean single sequence MFE -26.90
Consensus MFE -14.40
Energy contribution -15.23
Covariance contribution 0.84
Combinations/Pair 1.28
Mean z-score -1.98
Structure conservation index 0.54
SVM decision value 1.33
SVM RNA-class probability 0.943164
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8422715 99 + 23771897
UAUUUCCCCCACUUUUUUUCAGUGCAUUCCCAGCUGCAUGUUGGUUUCUGCGCUAAGAAGUGCAGCUGU-------CCUGAUUUGCAGAAAAGGUCA---GCAAACAAC
.........((((((((...((((((...(((((.....)))))....))))))))))))))..((((.-------(((............))).))---))....... ( -29.90)
>DroSec_CAF1 4642 92 + 1
U----UCCCCACUUUCUGUCAGUGCAUACCCAGCUGCACGUUGGUUUCUGAGCUAAGAAGUGCAGCUGU-------CCUGAAUCGCAGAAAAAGUCA---GCAAAC---
.----.......(((((((.(...((....(((((((((.((((((....))))))...))))))))).-------..))..).)))))))......---......--- ( -26.70)
>DroSim_CAF1 11171 96 + 1
UAGUCACCCCACUUUCUUUCAGUGCAUUCCCAGCUGCAUUUCGGUUUCUGAGCUAAGAAGUGCAGCUGU-------CCUGAAUCGCAGAAAAGGUCA---GCAAAC---
..((.(((....(((((....(((.((((.((((((((((((((((....))))..)))))))))))).-------...)))))))))))).)))..---))....--- ( -27.40)
>DroEre_CAF1 4752 96 + 1
UGUUUGCCCAAACUUUUUUCAGUGCACUCCCAGCUGCAUGACGGCUUCCCAGCCAAGAAGUGCAGCUGU-------GCUGAAUCGCAGAAAAGGUCA---GCAAAC---
.((((((....((((((((...........(((((((((...((((....)))).....)))))))))(-------((......)))))))))))..---))))))--- ( -32.00)
>DroYak_CAF1 11303 96 + 1
UGUGCUCCCCAACUUUUUCCAGUGCAUUCACAGUUGCUUGAUGGUUUCCCAGCCCAGAAGUGCAGCUGU-------CCUGAAUCGCAGAAAAGGUCA---GCAAAG---
..((((.....((((((((..(((.((((((((((((((..(((.........)))..)).))))))))-------...))))))).)))))))).)---)))...--- ( -27.20)
>DroAna_CAF1 89178 95 + 1
---CUACCCUAAUCUCUCUCAGUGUA-----AGCAGGACACUCG-UCCUUAUCUAA--AAUGCAGCUAUGCAGCCUUCUGAAUCCCUGAAAAGGUCAAAUGCCAAC---
---...............((((....-----.(((((((....)-)))).......--..((((....))))))...))))...(((....)))............--- ( -18.20)
>consensus
U_UUUACCCCAAUUUCUUUCAGUGCAUUCCCAGCUGCAUGUUGGUUUCUGAGCUAAGAAGUGCAGCUGU_______CCUGAAUCGCAGAAAAGGUCA___GCAAAC___
......................(((.....(((((((((...(((......))).....))))))))).........(((.....)))............)))...... (-14.40 = -15.23 +   0.84)

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 10:45:57 2006