Locus 14

Sequence ID 2L_DroMel_CAF1
Location 59,255 – 59,372
Length 117
Max. P 0.970469
window21 window22 window23 window24

overview

Window 1

Location 59,255 – 59,345
Length 90
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 76.94
Mean single sequence MFE -37.05
Consensus MFE -22.40
Energy contribution -23.40
Covariance contribution 1.00
Combinations/Pair 1.17
Mean z-score -2.30
Structure conservation index 0.60
SVM decision value 1.66
SVM RNA-class probability 0.970469
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 59255 90 + 22407834
UCUUGAGACU------------CUG-GGCAAGCGCAGCCA----GCCAA--CCAAGUUUCGAAG-UCUGGCUU----UUGGGCCAAGCUUGGUCUGCGCCACGCUUGGCCCCGA
..((((((((------------.((-(....((.......----))...--)))))))))))..-........----..(((((((((.((((....)))).)))))))))... ( -36.20)
>DroSec_CAF1 32294 90 + 1
UCUUGAGACU------------CUC-GGCAAGCUCAGCCA----GCCAA--CCAAGUUUCGAAG-UCAGACUU----UUGGGCCAAGCUUGGUCUGAGCCACGCUUGGCCCCGA
..((((((((------------...-(((..((...))..----)))..--...))))))))..-........----..(((((((((.((((....)))).)))))))))... ( -34.90)
>DroSim_CAF1 34610 90 + 1
UCUUGAGACU------------CUC-GGCAAGCUCAGCCA----GCCAA--CCAAGUUUCGAAG-UCAGGCUU----UUGGGCCAAGCUUGGUCUGAGCCACGCUUGGCCCCGA
..((((((((------------...-(((..((...))..----)))..--...))))))))..-........----..(((((((((.((((....)))).)))))))))... ( -34.90)
>DroEre_CAF1 33727 102 + 1
UCUCGAGACUCGAGACUCGAGUCUC-GGCAAGCUCGGCCA----GCCAA--CCAAGUUUCGAAG-CCAGGCCU----UUGGGCCAAGCUUGGUCUGAGCCACGCUUUGCCCCGA
....((((((((.....))))))))-(((((((..(((((----(...(--((((((((.(...-.).((((.----...)))))))))))))))).)))..)).))))).... ( -47.90)
>DroYak_CAF1 32142 106 + 1
UCUCGACACUCGAGUCUCAAGUCUC-GGCAAGCUCAGCCAGCCAGCCAA--CCAUGUUUCGAAG-CCAGGCUU----UUGGGCCAAGCUUGGUCUCAGCCACGCUUAGACCCGA
..((((.((..(((.(....).)))-(((..(((.....)))..)))..--....)).))))((-(..((((.----...))))..))).(((((.(((...))).)))))... ( -32.40)
>DroPer_CAF1 43093 98 + 1
UCUCGAGACA------------CUCAAGCAAGCUCAGACA----GGCGACGCCAAGUUUCGGGCCCCAAGCUUAAGCUUGGCCCCAGCUUCGACUGAGCUGUGGUCGGCUCUUG
....(((..(------------(.((....(((((((.((----(((...(((((((((.((((.....)))))))))))))....)))).).))))))).))))...)))... ( -36.00)
>consensus
UCUCGAGACU____________CUC_GGCAAGCUCAGCCA____GCCAA__CCAAGUUUCGAAG_CCAGGCUU____UUGGGCCAAGCUUGGUCUGAGCCACGCUUGGCCCCGA
..(((((((.................(((.......))).....(.......)..))))))).................(((((((((.(((......))).)))))))))... (-22.40 = -23.40 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 59,255 – 59,345
Length 90
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 76.94
Mean single sequence MFE -40.82
Consensus MFE -19.46
Energy contribution -19.86
Covariance contribution 0.40
Combinations/Pair 1.33
Mean z-score -2.46
Structure conservation index 0.48
SVM decision value 1.29
SVM RNA-class probability 0.938497
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 59255 90 - 22407834
UCGGGGCCAAGCGUGGCGCAGACCAAGCUUGGCCCAA----AAGCCAGA-CUUCGAAACUUGG--UUGGC----UGGCUGCGCUUGCC-CAG------------AGUCUCAAGA
((.((((.(((((..((((.(((((((..((((....----..))))(.-...)....)))))--)).))----..))..))))))))-).)------------)......... ( -38.20)
>DroSec_CAF1 32294 90 - 1
UCGGGGCCAAGCGUGGCUCAGACCAAGCUUGGCCCAA----AAGUCUGA-CUUCGAAACUUGG--UUGGC----UGGCUGAGCUUGCC-GAG------------AGUCUCAAGA
...(((((((((.(((......))).)))))))))..----........-(((.((..(((((--(.(((----(.....)))).)))-)))------------..))..))). ( -38.50)
>DroSim_CAF1 34610 90 - 1
UCGGGGCCAAGCGUGGCUCAGACCAAGCUUGGCCCAA----AAGCCUGA-CUUCGAAACUUGG--UUGGC----UGGCUGAGCUUGCC-GAG------------AGUCUCAAGA
...(((((((((.(((......))).)))))))))..----........-(((.((..(((((--(.(((----(.....)))).)))-)))------------..))..))). ( -38.50)
>DroEre_CAF1 33727 102 - 1
UCGGGGCAAAGCGUGGCUCAGACCAAGCUUGGCCCAA----AGGCCUGG-CUUCGAAACUUGG--UUGGC----UGGCCGAGCUUGCC-GAGACUCGAGUCUCGAGUCUCGAGA
((..(((((.((.((((.(((.(((((((.((((...----.)))).))-).((((...))))--)))))----)))))).)))))))-((((((((.....)))))))))).. ( -49.70)
>DroYak_CAF1 32142 106 - 1
UCGGGUCUAAGCGUGGCUGAGACCAAGCUUGGCCCAA----AAGCCUGG-CUUCGAAACAUGG--UUGGCUGGCUGGCUGAGCUUGCC-GAGACUUGAGACUCGAGUGUCGAGA
((((((((.(((...))).))))((((((..(((...----.((((.((-((.........))--))))))....)))..))))))))-))..(((((.((....)).))))). ( -43.90)
>DroPer_CAF1 43093 98 - 1
CAAGAGCCGACCACAGCUCAGUCGAAGCUGGGGCCAAGCUUAAGCUUGGGGCCCGAAACUUGGCGUCGCC----UGUCUGAGCUUGCUUGAG------------UGUCUCGAGA
...((((........))))..((((.(((.((((.(((((((..(..(((((((((...)))).))).))----.)..))))))))))).))------------)...)))).. ( -36.10)
>consensus
UCGGGGCCAAGCGUGGCUCAGACCAAGCUUGGCCCAA____AAGCCUGA_CUUCGAAACUUGG__UUGGC____UGGCUGAGCUUGCC_GAG____________AGUCUCAAGA
...((((((....))))))....(((((((((((.........(((......((((...))))....))).....)))))))))))............................ (-19.46 = -19.86 +   0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 59,282 – 59,372
Length 90
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 81.62
Mean single sequence MFE -30.30
Consensus MFE -19.21
Energy contribution -21.10
Covariance contribution 1.89
Combinations/Pair 1.10
Mean z-score -2.31
Structure conservation index 0.63
SVM decision value 0.61
SVM RNA-class probability 0.798343
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 59282 90 + 22407834
----GCCAA--CCAAGUUUCGAAG-UCUGGCUU----UUGGGCCAAGCUUGGUCUGCGCCACGCUUGGCCCCGACUGUUACUUUACAUUAACAGACUGUUC---
----((((.--.(..........)-..))))..----..(((((((((.((((....)))).)))))))))...((((((........)))))).......--- ( -33.00)
>DroSec_CAF1 32321 90 + 1
----GCCAA--CCAAGUUUCGAAG-UCAGACUU----UUGGGCCAAGCUUGGUCUGAGCCACGCUUGGCCCCGACUGUUACUUUACAUUAACAGACUGUUC---
----.....--.............-.(((....----..(((((((((.((((....)))).)))))))))...((((((........)))))).)))...--- ( -30.70)
>DroSim_CAF1 34637 90 + 1
----GCCAA--CCAAGUUUCGAAG-UCAGGCUU----UUGGGCCAAGCUUGGUCUGAGCCACGCUUGGCCCCGACUGUUACUUUACAUUAACAGACUGUUC---
----(((..--.............-...)))..----..(((((((((.((((....)))).)))))))))...((((((........)))))).......--- ( -31.07)
>DroEre_CAF1 33766 90 + 1
----GCCAA--CCAAGUUUCGAAG-CCAGGCCU----UUGGGCCAAGCUUGGUCUGAGCCACGCUUUGCCCCGACUGUUACUUUACAUUAACAGACUGUUA---
----.....--.............-.(((....----..((((.((((.((((....)))).)))).))))...((((((........)))))).)))...--- ( -24.60)
>DroYak_CAF1 32181 97 + 1
GCCAGCCAA--CCAUGUUUCGAAG-CCAGGCUU----UUGGGCCAAGCUUGGUCUCAGCCACGCUUAGACCCGACUGUUACUUUACAAUAACAGACUGUUAUUG
..(((....--.......((((((-(..((((.----...))))..))))(((((.(((...))).))))))))((((((........)))))).)))...... ( -26.40)
>DroPer_CAF1 43121 93 + 1
----GGCGACGCCAAGUUUCGGGCCCCAAGCUUAAGCUUGGCCCCAGCUUCGACUGAGCUGUGGUCGGCUCUUGCUGUUACUUUACAGU----GCCUGUUA---
----(((((.(((((((((.((((.....))))))))))((((.((((((.....)))))).)))))))))..(((((......)))))----))).....--- ( -36.00)
>consensus
____GCCAA__CCAAGUUUCGAAG_CCAGGCUU____UUGGGCCAAGCUUGGUCUGAGCCACGCUUGGCCCCGACUGUUACUUUACAUUAACAGACUGUUA___
..........................(((..........(((((((((.(((......))).)))))))))...((((((........)))))).)))...... (-19.21 = -21.10 +   1.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 59,282 – 59,372
Length 90
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 81.62
Mean single sequence MFE -32.83
Consensus MFE -19.50
Energy contribution -21.50
Covariance contribution 2.00
Combinations/Pair 1.15
Mean z-score -2.54
Structure conservation index 0.59
SVM decision value 0.63
SVM RNA-class probability 0.805651
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 59282 90 - 22407834
---GAACAGUCUGUUAAUGUAAAGUAACAGUCGGGGCCAAGCGUGGCGCAGACCAAGCUUGGCCCAA----AAGCCAGA-CUUCGAAACUUGG--UUGGC----
---.....(.((((((........)))))).).(((((((((.(((......))).)))))))))..----..(((((.-((.........))--)))))---- ( -34.20)
>DroSec_CAF1 32321 90 - 1
---GAACAGUCUGUUAAUGUAAAGUAACAGUCGGGGCCAAGCGUGGCUCAGACCAAGCUUGGCCCAA----AAGUCUGA-CUUCGAAACUUGG--UUGGC----
---.....(.((((((........)))))).).(((((((((.(((......))).)))))))))..----....(..(-((.........))--)..).---- ( -32.10)
>DroSim_CAF1 34637 90 - 1
---GAACAGUCUGUUAAUGUAAAGUAACAGUCGGGGCCAAGCGUGGCUCAGACCAAGCUUGGCCCAA----AAGCCUGA-CUUCGAAACUUGG--UUGGC----
---.....(.((((((........)))))).).(((((((((.(((......))).)))))))))..----..(((.((-((.........))--)))))---- ( -33.90)
>DroEre_CAF1 33766 90 - 1
---UAACAGUCUGUUAAUGUAAAGUAACAGUCGGGGCAAAGCGUGGCUCAGACCAAGCUUGGCCCAA----AGGCCUGG-CUUCGAAACUUGG--UUGGC----
---((((...((((((........))))))(((((((.((((.(((......))).))))((((...----.))))..)-))))))......)--)))..---- ( -28.90)
>DroYak_CAF1 32181 97 - 1
CAAUAACAGUCUGUUAUUGUAAAGUAACAGUCGGGUCUAAGCGUGGCUGAGACCAAGCUUGGCCCAA----AAGCCUGG-CUUCGAAACAUGG--UUGGCUGGC
(((((((.....)))))))........((((((((.((((((.(((......))).)))))))))..----.((((((.-........)).))--))))))).. ( -33.40)
>DroPer_CAF1 43121 93 - 1
---UAACAGGC----ACUGUAAAGUAACAGCAAGAGCCGACCACAGCUCAGUCGAAGCUGGGGCCAAGCUUAAGCUUGGGGCCCGAAACUUGGCGUCGCC----
---.....(((----.((((......))))...(((((((...((((((....).)))))(((((.(((....)))...))))).....))))).)))))---- ( -34.50)
>consensus
___GAACAGUCUGUUAAUGUAAAGUAACAGUCGGGGCCAAGCGUGGCUCAGACCAAGCUUGGCCCAA____AAGCCUGA_CUUCGAAACUUGG__UUGGC____
........(.((((((........)))))).).(((((((((.(((......))).)))))))))........(((......((((...))))....))).... (-19.50 = -21.50 +   2.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:23:18 2006