Locus 2925

Sequence ID 2L_DroMel_CAF1
Location 8,417,683 – 8,417,813
Length 130
Max. P 0.939909
window4638 window4639 window4640 window4641

overview

Window 8

Location 8,417,683 – 8,417,787
Length 104
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 79.65
Mean single sequence MFE -27.95
Consensus MFE -18.50
Energy contribution -18.70
Covariance contribution 0.20
Combinations/Pair 1.23
Mean z-score -2.41
Structure conservation index 0.66
SVM decision value 1.30
SVM RNA-class probability 0.939372
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8417683 104 + 22407834
UUUGCCAGUCGUUCA--CUGAGGACGAGCAUAUACAUAUAAUGCUUU-UUGG------UGUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGC
...(((((((((((.--....))))))((((.........))))...-))))------).(((((......)))))....--..(((.((((((((..-....)))))))).))). ( -32.00)
>DroSec_CAF1 15722 104 + 1
UUUGCCAGUCGUUCA--CUGAGGACGAGUAUAUACAUAUAAUGCUUU-UUGC------UGUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGC
.....((((.....)--)))..(((((((.............((...-..))------..(((((......)))))))))--)))...((((((((..-....))))))))..... ( -28.90)
>DroSim_CAF1 15568 104 + 1
UUUGCCAGUCGUUCA--CUGAGGACGAGUAUAUACAUAUAAUGCUCU-UUGC------UGUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGC
.....((((.((((.--....))))((((((.........)))))).-..))------))(((((......)))))....--..(((.((((((((..-....)))))))).))). ( -29.50)
>DroEre_CAF1 16052 96 + 1
UUUGCCAGUCGUUCA--CUGGGGAGGAGU--------AUAAUGCUUU-UUGC------UCUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGC
(((.(((((.....)--)))).)))((((--------(.((....))-.)))------))(((((......)))))....--..(((.((((((((..-....)))))))).))). ( -30.50)
>DroWil_CAF1 35940 109 + 1
UUU------UGUUGAUGCUGAGAAAAAAGGCAAAAAAAUAAUCUUUCGUUAUUGUUUGUCUUAUUUGUAUU-GUGAAUUUUCGUCAACGUUUGCUAAAAAAUCAAAUAAACAUUGU
...------.((((((((..(.(((.((((((((..((((((.....)))))).)))))))).))).)...-))((....))))))))(((((.............)))))..... ( -15.72)
>DroYak_CAF1 15872 96 + 1
UUUGCAAGUCGUUCA--CUGAGGACGACU--------AUAAUGCUUU-UUGC------UCUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGC
...(((((((((((.--....))))))))--------....)))...-....------..(((((......)))))....--..(((.((((((((..-....)))))))).))). ( -31.10)
>consensus
UUUGCCAGUCGUUCA__CUGAGGACGAGUAUAUACAUAUAAUGCUUU_UUGC______UCUCGCCUUUAUUGGCGAAUUU__GUCAACGUUUGCUCAA_ACUCGAGUAAACAUUGC
........((((((.......)))))).................................(((((......)))))........(((.((((((((.......)))))))).))). (-18.50 = -18.70 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,417,683 – 8,417,787
Length 104
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 79.65
Mean single sequence MFE -26.04
Consensus MFE -15.60
Energy contribution -15.85
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -2.59
Structure conservation index 0.60
SVM decision value 1.30
SVM RNA-class probability 0.939909
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8417683 104 - 22407834
GCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGACA------CCAA-AAAGCAUUAUAUGUAUAUGCUCGUCCUCAG--UGAACGACUGGCAAA
((..((((((((.(((.-.((((((.........--....(((((......)))))..------....-...((((...))))...))))))..)))))--))))))....))... ( -31.80)
>DroSec_CAF1 15722 104 - 1
GCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGACA------GCAA-AAAGCAUUAUAUGUAUAUACUCGUCCUCAG--UGAACGACUGGCAAA
((..((((((((.(((.-.((((.....((((..--....(((((......)))))))------))..-...((((...)))).....))))..)))))--))))))....))... ( -28.70)
>DroSim_CAF1 15568 104 - 1
GCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGACA------GCAA-AGAGCAUUAUAUGUAUAUACUCGUCCUCAG--UGAACGACUGGCAAA
((..((((((((.(((.-.((((.....((((..--....(((((......)))))))------))..-...((((...)))).....))))..)))))--))))))....))... ( -28.70)
>DroEre_CAF1 16052 96 - 1
GCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGAGA------GCAA-AAAGCAUUAU--------ACUCCUCCCCAG--UGAACGACUGGCAAA
.((((((((.((((...-.)))).))))))))..--...((((((......)))))).------((..-...)).....--------........((((--(.....))))).... ( -26.10)
>DroWil_CAF1 35940 109 - 1
ACAAUGUUUAUUUGAUUUUUUAGCAAACGUUGACGAAAAUUCAC-AAUACAAAUAAGACAAACAAUAACGAAAGAUUAUUUUUUUGCCUUUUUUCUCAGCAUCAACA------AAA
.....((((..((((....)))).))))(((((.(((((.....-.........(((.((((.((((((....).)))))..)))).))))))))))))).......------... ( -12.13)
>DroYak_CAF1 15872 96 - 1
GCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGAGA------GCAA-AAAGCAUUAU--------AGUCGUCCUCAG--UGAACGACUUGCAAA
.((((((((.((((...-.)))).))))))))..--...((((((......)))))).------....-...(((....--------((((((.(....--.).)))))))))... ( -28.80)
>consensus
GCAAUGUUUACUCGAGU_UUGAGCAAACGUUGAC__AAAUUCGCCAAUAAAGGCGACA______GCAA_AAAGCAUUAUAUGUAUAUACUCGUCCUCAG__UGAACGACUGGCAAA
.((((((((.(((((...))))).))))))))........(((((......)))))............................................................ (-15.60 = -15.85 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,417,717 – 8,417,813
Length 96
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 79.72
Mean single sequence MFE -27.65
Consensus MFE -19.39
Energy contribution -18.95
Covariance contribution -0.44
Combinations/Pair 1.33
Mean z-score -1.51
Structure conservation index 0.70
SVM decision value 0.51
SVM RNA-class probability 0.764161
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8417717 96 + 22407834
UAUAAUGCUUU-UUGG------UGUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGCAUUGCGAUACGGUGUGGAGGGACUGG---
..((((((...-(((.------.((((((......)))))...)--..))).((((((((..-....))))))))...)))))).....((((........)))).--- ( -27.40)
>DroSec_CAF1 15756 96 + 1
UAUAAUGCUUU-UUGC------UGUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGCAUUGCGAUACGGAGUGGAGGGACUGG---
.......((((-(..(------(.(((((......)))))...(--(.(((.((((((((..-....)))))))).)))))...........))..))))).....--- ( -28.40)
>DroSim_CAF1 15602 96 + 1
UAUAAUGCUCU-UUGC------UGUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGCAUUGCGAUACGGAGUGGAGGGACUGG---
.......((((-(..(------(.(((((......)))))...(--(.(((.((((((((..-....)))))))).)))))...........))..))))).....--- ( -30.90)
>DroEre_CAF1 16079 95 + 1
-AUAAUGCUUU-UUGC------UCUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGCAUUGCGAUACGGCGGGGAGGGACCGG---
-....((((..-((((------..(((((......)))))...(--(.(((.((((((((..-....)))))))).)))))..))))...))))((......))..--- ( -29.70)
>DroWil_CAF1 35970 108 + 1
AAUAAUCUUUCGUUAUUGUUUGUCUUAUUUGUAUU-GUGAAUUUUCGUCAACGUUUGCUAAAAAAUCAAAUAAACAUUGUGGGGCAGUCAAAUUCAGUCAGACUGAGAG
......((((((.....(((((.((.(((((.(((-((.....((((.(((.(((((.............))))).)))))))))))))))))..)).))))))))))) ( -16.72)
>DroYak_CAF1 15899 95 + 1
-AUAAUGCUUU-UUGC------UCUCGCCUUUAUUGGCGAAUUU--GUCAACGUUUGCUCAA-ACUCGAGUAAACAUUGCAUUGUGAAUGCGGGCGGAGGGACUGG---
-......((((-((((------(((((((......)))))....--......((((((((..-....))))))))...((((.....)))))))))))))).....--- ( -32.80)
>consensus
UAUAAUGCUUU_UUGC______UCUCGCCUUUAUUGGCGAAUUU__GUCAACGUUUGCUCAA_ACUCGAGUAAACAUUGCAUUGCGAUACGGAGUGGAGGGACUGG___
........................(((((......)))))......(((...((((((((.......))))))))(((((...)))))............)))...... (-19.39 = -18.95 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,417,717 – 8,417,813
Length 96
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 79.72
Mean single sequence MFE -21.72
Consensus MFE -15.60
Energy contribution -15.85
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -1.69
Structure conservation index 0.72
SVM decision value 0.76
SVM RNA-class probability 0.844503
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8417717 96 - 22407834
---CCAGUCCCUCCACACCGUAUCGCAAUGCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGACA------CCAA-AAAGCAUUAUA
---.....................((..((((((((((.((((...-.)))).)))))))).)--)...(((((......)))))..------....-...))...... ( -22.10)
>DroSec_CAF1 15756 96 - 1
---CCAGUCCCUCCACUCCGUAUCGCAAUGCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGACA------GCAA-AAAGCAUUAUA
---.....................((..((((((((((.((((...-.)))).)))))))).)--)...(((((......)))))..------))..-........... ( -22.10)
>DroSim_CAF1 15602 96 - 1
---CCAGUCCCUCCACUCCGUAUCGCAAUGCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGACA------GCAA-AGAGCAUUAUA
---.....................((..((((((((((.((((...-.)))).)))))))).)--)...(((((......)))))..------))..-........... ( -22.10)
>DroEre_CAF1 16079 95 - 1
---CCGGUCCCUCCCCGCCGUAUCGCAAUGCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGAGA------GCAA-AAAGCAUUAU-
---.((((........))))....((..((((((((((.((((...-.)))).)))))))).)--)..((((((......)))))).------))..-..........- ( -26.70)
>DroWil_CAF1 35970 108 - 1
CUCUCAGUCUGACUGAAUUUGACUGCCCCACAAUGUUUAUUUGAUUUUUUAGCAAACGUUGACGAAAAUUCAC-AAUACAAAUAAGACAAACAAUAACGAAAGAUUAUU
....(((((...........)))))........((((((((((.....(((((....))))).((....))..-....))))).)))))...((((((....).))))) ( -13.60)
>DroYak_CAF1 15899 95 - 1
---CCAGUCCCUCCGCCCGCAUUCACAAUGCAAUGUUUACUCGAGU-UUGAGCAAACGUUGAC--AAAUUCGCCAAUAAAGGCGAGA------GCAA-AAAGCAUUAU-
---...(((.........((((.....))))(((((((.((((...-.)))).))))))))))--...((((((......)))))).------((..-...)).....- ( -23.70)
>consensus
___CCAGUCCCUCCACACCGUAUCGCAAUGCAAUGUUUACUCGAGU_UUGAGCAAACGUUGAC__AAAUUCGCCAAUAAAGGCGACA______GCAA_AAAGCAUUAUA
..............................((((((((.(((((...))))).))))))))........(((((......)))))........................ (-15.60 = -15.85 +   0.25)

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 10:39:39 2006