Locus 9594

Sequence ID 3R_DroMel_CAF1
Location 25,341,512 – 25,341,646
Length 134
Max. P 0.988817
window15337 window15338 window15339 window15340

overview

Window 7

Location 25,341,512 – 25,341,609
Length 97
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 71.74
Mean single sequence MFE -21.75
Consensus MFE -12.03
Energy contribution -12.03
Covariance contribution 0.00
Combinations/Pair 1.33
Mean z-score -1.52
Structure conservation index 0.55
SVM decision value 0.39
SVM RNA-class probability 0.716073
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25341512 97 + 27905053
UUUUCACAUUU-UCCAUGCAUUGCUACAUCGCAAAA-UAAAUUA--------AGUAU-CUUCAGGAUGAUAAGUUUCCUGAAAUUGGCCAGGAAUCCUGGCCAGCUGC
...........-.....((.((((......))))..-.......--------.....-.(((((((.........)))))))..((((((((...))))))))))... ( -27.20)
>DroPse_CAF1 28437 96 + 1
------------UUCUUUCAAAGUCCCGACUAAAUAACAAAUUUUUACUUUCAAUAUCCAGCAGAAUGUUUGGAUCCCUCAAAAUGUAUAAGAAUGCAGUGAUGCUGC
------------(((((.((.(((....)))........................(((((((.....).)))))).........))...))))).((((.....)))) ( -11.30)
>DroSec_CAF1 26473 94 + 1
UUUUCACAUUU-UUCAUUCAUUGCCACAACGAAAAA-UAAAUUA--------GGCAU-CUUCAGGAUGAUAAGUUUCCUGAAAUUAGCCAGGAAUCCUGGCCAGC---
...........-.........((((...........-.......--------)))).-.(((((((.........)))))))....((((((...))))))....--- ( -21.27)
>DroSim_CAF1 26856 97 + 1
UUUUCACAUUU-UUCAUUCACUGCCACAACGAAAAA-UAAAUUA--------GGCAU-CUUCAGGAUGAUAAGUUUCCUGAAAUUAGCCAGGAAUCCUGGCCAGCUGC
.......((((-(((...............))))))-)......--------(((..-.(((((((.........)))))))....((((((...))))))..))).. ( -23.26)
>DroEre_CAF1 26649 98 + 1
UUUUCACAUCUCUUCAUUCACUGCCGCAACGAAAAA-UAAAUUA--------AGUCU-CAGCAGGAUGAUAGGCUUCCUGAUAUGGGCCAGGAAUCCUGGCAAGCUGC
.............((((.(.((((.(..((......-.......--------.))..-).)))))))))..(((((((......))((((((...))))))))))).. ( -23.04)
>DroYak_CAF1 29224 99 + 1
UUUUCACAUUUUUCCACUCACUGCCACAGCUGAAAAUCAAAUUA--------AGUCU-CUGCAGGAUGUUAAGUGUCCUGAUGUUGGCCAGGAAUCCUGGCAAGCGGC
....................((((..((((((.....)).....--------.....-...((((((.......))))))..))))((((((...))))))..)))). ( -24.40)
>consensus
UUUUCACAUUU_UUCAUUCACUGCCACAACGAAAAA_UAAAUUA________AGUAU_CUGCAGGAUGAUAAGUUUCCUGAAAUUGGCCAGGAAUCCUGGCAAGCUGC
......................((.....................................(((((.........)))))......(((((.....)))))..))... (-12.03 = -12.03 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 25,341,512 – 25,341,609
Length 97
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 71.74
Mean single sequence MFE -26.63
Consensus MFE -11.70
Energy contribution -11.90
Covariance contribution 0.20
Combinations/Pair 1.38
Mean z-score -2.07
Structure conservation index 0.44
SVM decision value 1.14
SVM RNA-class probability 0.921414
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25341512 97 - 27905053
GCAGCUGGCCAGGAUUCCUGGCCAAUUUCAGGAAACUUAUCAUCCUGAAG-AUACU--------UAAUUUA-UUUUGCGAUGUAGCAAUGCAUGGA-AAAUGUGAAAA
.....((((((((...)))))))).((((((((.........))))))))-.....--------.....((-((((.(.(((((....))))).))-)))))...... ( -31.00)
>DroPse_CAF1 28437 96 - 1
GCAGCAUCACUGCAUUCUUAUACAUUUUGAGGGAUCCAAACAUUCUGCUGGAUAUUGAAAGUAAAAAUUUGUUAUUUAGUCGGGACUUUGAAAGAA------------
((((.....)))).((((((.......))))))...((((..((((((((((((....((((....))))..))))))).))))).))))......------------ ( -17.00)
>DroSec_CAF1 26473 94 - 1
---GCUGGCCAGGAUUCCUGGCUAAUUUCAGGAAACUUAUCAUCCUGAAG-AUGCC--------UAAUUUA-UUUUUCGUUGUGGCAAUGAAUGAA-AAAUGUGAAAA
---((((((((((...)))))))).((((((((.........))))))))-..)).--------.....((-(((((((((((....)).))))))-)))))...... ( -27.60)
>DroSim_CAF1 26856 97 - 1
GCAGCUGGCCAGGAUUCCUGGCUAAUUUCAGGAAACUUAUCAUCCUGAAG-AUGCC--------UAAUUUA-UUUUUCGUUGUGGCAGUGAAUGAA-AAAUGUGAAAA
(((..((((((((...)))))))).((((((((.........))))))))-.))).--------.....((-(((((((((.........))))))-)))))...... ( -29.00)
>DroEre_CAF1 26649 98 - 1
GCAGCUUGCCAGGAUUCCUGGCCCAUAUCAGGAAGCCUAUCAUCCUGCUG-AGACU--------UAAUUUA-UUUUUCGUUGCGGCAGUGAAUGAAGAGAUGUGAAAA
.......((((((...)))))).(((((((((...))).(((((((((((-..((.--------.((....-..))..))..)))))).).))))...)))))).... ( -29.50)
>DroYak_CAF1 29224 99 - 1
GCCGCUUGCCAGGAUUCCUGGCCAACAUCAGGACACUUAACAUCCUGCAG-AGACU--------UAAUUUGAUUUUCAGCUGUGGCAGUGAGUGGAAAAAUGUGAAAA
.(((((..(((((...))))((((.((.(((((.........)))))..(-(((.(--------(.....)).))))...)))))).)..)))))............. ( -25.70)
>consensus
GCAGCUGGCCAGGAUUCCUGGCCAAUUUCAGGAAACUUAUCAUCCUGAAG_AUACU________UAAUUUA_UUUUUCGUUGUGGCAGUGAAUGAA_AAAUGUGAAAA
...(((.(((((.....)))))......(((((.........)))))....................................)))...................... (-11.70 = -11.90 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 25,341,545 – 25,341,646
Length 101
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 68.12
Mean single sequence MFE -33.50
Consensus MFE -15.55
Energy contribution -16.42
Covariance contribution 0.87
Combinations/Pair 1.30
Mean z-score -2.32
Structure conservation index 0.46
SVM decision value 2.14
SVM RNA-class probability 0.988817
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25341545 101 + 27905053
AA-UAAAUUA--------AGUAU-CUUCAGGAUGAUAAGUUUCCUGAAAUUGGCCAGGAAUCCUGGCCAGCUGCUGCUGCCUGGCAGUGGAGU-GCUGCA--AUCCCAGUGGCU
..-.......--------(((..-.(((((((.........)))))))..((((((((...)))))))))))((..(((....(((((.....-))))).--....)))..)). ( -40.30)
>DroPse_CAF1 28459 108 + 1
UAACAAAUUUUUACUUUCAAUAUCCAGCAGAAUGUUUGGAUCCCUCAAAAUGUAUAAGAAUGCAGUGAUGCUGC---UGCCCCG---UGGACCGGCUGUCGGCUCUCUCUGGAU
.....................((((((.(((.............(((...(((((....))))).))).(((((---.(((...---......))).).))))..))))))))) ( -22.50)
>DroSec_CAF1 26506 77 + 1
AA-UAAAUUA--------GGCAU-CUUCAGGAUGAUAAGUUUCCUGAAAUUAGCCAGGAAUCCUGGCCAGC-------------------------UGCA--AUCCCAGUGGCU
..-.......--------.....-.(((((((.........)))))))....((((((...)))))).(((-------------------------..(.--......)..))) ( -23.10)
>DroSim_CAF1 26889 101 + 1
AA-UAAAUUA--------GGCAU-CUUCAGGAUGAUAAGUUUCCUGAAAUUAGCCAGGAAUCCUGGCCAGCUGCUGCUUCCUUGCAGUGGAGU-GCUGCA--AUCCCAGUGGCU
..-.......--------(((..-.(((((((.........)))))))....((((((...))))))..)))((..((...(((((((.....-))))))--)....))..)). ( -36.30)
>DroEre_CAF1 26683 101 + 1
AA-UAAAUUA--------AGUCU-CAGCAGGAUGAUAGGCUUCCUGAUAUGGGCCAGGAAUCCUGGCAAGCUGCUGCUCCCCCGCAGCGGAGU-GAUGCC--GUCCCAGCUGCU
..-.......--------.....-((((.(((((.((((.((((((........)))))).)))).((..(((((((......)))))))..)-)....)--))))..)))).. ( -38.30)
>DroYak_CAF1 29258 102 + 1
AAUCAAAUUA--------AGUCU-CUGCAGGAUGUUAAGUGUCCUGAUGUUGGCCAGGAAUCCUGGCAAGCGGCUGCUGCCUCGCAGUGGAGU-GCUGCA--AGCCCAGUGGCU
..........--------((((.-(((((((((.......))))))..(((.((((((...)))))).)))((((((.(((((......))).-)).)).--))))))).)))) ( -40.50)
>consensus
AA_UAAAUUA________AGUAU_CUGCAGGAUGAUAAGUUUCCUGAAAUUGGCCAGGAAUCCUGGCAAGCUGCUGCUGCCUCGCAGUGGAGU_GCUGCA__AUCCCAGUGGCU
...................(((.....(((((.........)))))......(((((.....)))))...(((((((......)))))))......)))............... (-15.55 = -16.42 +   0.87)

alignment

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secondary structure

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dotplot

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Window 0

Location 25,341,545 – 25,341,646
Length 101
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 68.12
Mean single sequence MFE -30.05
Consensus MFE -11.01
Energy contribution -11.68
Covariance contribution 0.67
Combinations/Pair 1.28
Mean z-score -1.80
Structure conservation index 0.37
SVM decision value 0.25
SVM RNA-class probability 0.654266
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25341545 101 - 27905053
AGCCACUGGGAU--UGCAGC-ACUCCACUGCCAGGCAGCAGCAGCUGGCCAGGAUUCCUGGCCAAUUUCAGGAAACUUAUCAUCCUGAAG-AUACU--------UAAUUUA-UU
(((..((((((.--((...)-).))).((((...)))))))..)))(((((((...)))))))..((((((((.........))))))))-.....--------.......-.. ( -32.50)
>DroPse_CAF1 28459 108 - 1
AUCCAGAGAGAGCCGACAGCCGGUCCA---CGGGGCA---GCAGCAUCACUGCAUUCUUAUACAUUUUGAGGGAUCCAAACAUUCUGCUGGAUAUUGAAAGUAAAAAUUUGUUA
((((((((((..(((.....)))..).---.(((...---((((.....)))).((((((.......)))))).)))......))).))))))..................... ( -25.70)
>DroSec_CAF1 26506 77 - 1
AGCCACUGGGAU--UGCA-------------------------GCUGGCCAGGAUUCCUGGCUAAUUUCAGGAAACUUAUCAUCCUGAAG-AUGCC--------UAAUUUA-UU
......((((..--....-------------------------..((((((((...)))))))).((((((((.........))))))))-...))--------)).....-.. ( -23.80)
>DroSim_CAF1 26889 101 - 1
AGCCACUGGGAU--UGCAGC-ACUCCACUGCAAGGAAGCAGCAGCUGGCCAGGAUUCCUGGCUAAUUUCAGGAAACUUAUCAUCCUGAAG-AUGCC--------UAAUUUA-UU
.((..((....(--(((((.-......))))))...))..)).((((((((((...)))))))).((((((((.........))))))))-..)).--------.......-.. ( -31.60)
>DroEre_CAF1 26683 101 - 1
AGCAGCUGGGAC--GGCAUC-ACUCCGCUGCGGGGGAGCAGCAGCUUGCCAGGAUUCCUGGCCCAUAUCAGGAAGCCUAUCAUCCUGCUG-AGACU--------UAAUUUA-UU
.(((((..(((.--(.....-.))))))))).(((...((((((..((..(((.(((((((......))))))).)))..))..))))))-...))--------)......-.. ( -37.00)
>DroYak_CAF1 29258 102 - 1
AGCCACUGGGCU--UGCAGC-ACUCCACUGCGAGGCAGCAGCCGCUUGCCAGGAUUCCUGGCCAACAUCAGGACACUUAACAUCCUGCAG-AGACU--------UAAUUUGAUU
.....(((((((--.((.((-.(((......))))).))))))....((((((...))))))......(((((.........))))))))-.....--------.......... ( -29.70)
>consensus
AGCCACUGGGAU__UGCAGC_ACUCCACUGCGAGGCAGCAGCAGCUGGCCAGGAUUCCUGGCCAAUUUCAGGAAACUUAUCAUCCUGAAG_AUACU________UAAUUUA_UU
.......((((................((((......)))).........(((.(((((((......))))))).)))....))))............................ (-11.01 = -11.68 +   0.67)

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 13:37:54 2006