Locus 4206

Sequence ID 3R_DroMel_CAF1
Location 11,352,538 – 11,352,695
Length 157
Max. P 0.999851
window6782 window6783 window6784 window6785

overview

Window 2

Location 11,352,538 – 11,352,655
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.05
Mean single sequence MFE -29.12
Consensus MFE -23.00
Energy contribution -23.72
Covariance contribution 0.72
Combinations/Pair 1.10
Mean z-score -2.09
Structure conservation index 0.79
SVM decision value 1.27
SVM RNA-class probability 0.938240
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11352538 117 + 27905053
-AUAUAUACACAUGCACCCCU-AUCCA-GUCCGAUACUUUCCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAU
-...........(((((....-....(-(.((((((..(((...((((((.(((((....)))))...))))))...))).))))))))(((((........)))))...)))))..... ( -30.80)
>DroSec_CAF1 100126 117 + 1
-AUAUAUGUACAUGCACCCCU-AUCCA-GUCCGAUACUUUCCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGCGCGAGAAGAUGCGCCCUCUGUGCAGAAAU
-...........(((((....-....(-(.((((((..(((...((((((.(((((....)))))...))))))...))).))))))))(((((......))))).....)))))..... ( -27.30)
>DroSim_CAF1 90893 117 + 1
-AUAUAUAUAUGUGCACCCCU-AUCCA-GUCCGAUACUUUUCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAU
-.........(.(((((....-....(-(.((((((...((((.((((((.(((((....)))))...))))))..)))).))))))))(((((........)))))...))))).)... ( -31.70)
>DroEre_CAF1 87660 119 + 1
-AUACAGACAUAUCGACCCCCUAUCCAACCCCGAUAUUUCCCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGCGCGGAAAU
-......................(((.....(((((.(((....((((((.(((((....)))))...))))))...))).)))))((.(((((........)))))...))..)))... ( -27.50)
>DroYak_CAF1 90066 119 + 1
UAUACAAAUAUAUAGACCCCC-AUCCAAGCCCAAUAUUUUCCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAU
..........((((((.....-.....((((.((((..(((...((((((.(((((....)))))...))))))...))).))))))))(((((........)))))))))))....... ( -28.30)
>consensus
_AUAUAUAUAUAUGCACCCCU_AUCCA_GUCCGAUACUUUCCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAU
............(((((.............((((((.(((....((((((.(((((....)))))...))))))...))).))))))..(((((........)))))...)))))..... (-23.00 = -23.72 +   0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,352,538 – 11,352,655
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.05
Mean single sequence MFE -32.32
Consensus MFE -23.88
Energy contribution -23.72
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.64
Structure conservation index 0.74
SVM decision value -0.05
SVM RNA-class probability 0.507111
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11352538 117 - 27905053
AUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGGAAAGUAUCGGAC-UGGAU-AGGGGUGCAUGUGUAUAUAU-
.....((((((....((((..((......((((((.(((.(((.(((((((..((((((......))))))))))))).)))..))).)).)-)))..-))..)))).)))))).....- ( -33.10)
>DroSec_CAF1 100126 117 - 1
AUUUCUGCACAGAGGGCGCAUCUUCUCGCGCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGGAAAGUAUCGGAC-UGGAU-AGGGGUGCAUGUACAUAUAU-
((..(((..(((...((((........))))..((.(((.(((.(((((((..((((((......))))))))))))).)))..))).)).)-))..)-))..))..............- ( -29.60)
>DroSim_CAF1 90893 117 - 1
AUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGAAAAGUAUCGGAC-UGGAU-AGGGGUGCACAUAUAUAUAU-
((..(((..(((.(((((........)))))..((.(((.((((.((((((..((((((......))))))))))))))))...))).)).)-))..)-))..))..............- ( -31.50)
>DroEre_CAF1 87660 119 - 1
AUUUCCGCGCAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGGGAAAUAUCGGGGUUGGAUAGGGGGUCGAUAUGUCUGUAU-
........(((((.(.((.(((((((...((((((.(((.(((.(((((((..((((((......)))))))))))))..))).)))...))))))..)))))))))...).)))))..- ( -36.50)
>DroYak_CAF1 90066 119 - 1
AUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGGAAAAUAUUGGGCUUGGAU-GGGGGUCUAUAUAUUUGUAUA
((..(((..(((.(((((........)))))..((((((.(((.(((((((..((((((......))))))))))))).)))..))))))..)))..)-))..))............... ( -30.90)
>consensus
AUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGGAAAGUAUCGGAC_UGGAU_AGGGGUGCAUAUAUAUAUAU_
((..((...((..(((((........)))))..((.(((.(((.(((((((..((((((......))))))))))))).)))..))).))...))....))..))............... (-23.88 = -23.72 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,352,575 – 11,352,695
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.00
Mean single sequence MFE -30.50
Consensus MFE -29.18
Energy contribution -29.62
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.61
Structure conservation index 0.96
SVM decision value 3.95
SVM RNA-class probability 0.999721
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11352575 120 + 27905053
CCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAUUUACUUUUUAAUUUACUCAGAAAACCGAGUAAAAAGGAAA
...(((((((((((((......((.(((((.((....)).))))).)).(((((........)))))...)))))))))))..........(((((((........)))))))..))... ( -32.60)
>DroSec_CAF1 100163 120 + 1
CCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGCGCGAGAAGAUGCGCCCUCUGUGCAGAAAUUUACUUUUUAAUUUACUCAGAAAACCGAGUAAAAAGGAAA
...(((((((((((((...((.((.(((((.((....)).))))).)).(((((......))))).))..)))))))))))..........(((((((........)))))))..))... ( -29.30)
>DroSim_CAF1 90930 120 + 1
UCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAUUUACUUUUUAAUUUACUCAGAAAACCGAGUAAAAAGGAAA
...(((((((((((((......((.(((((.((....)).))))).)).(((((........)))))...)))))))))))..........(((((((........)))))))..))... ( -32.60)
>DroEre_CAF1 87699 120 + 1
CCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGCGCGGAAAUUUACUUUUUAAUUUACUCCGAAAACCGAGUAAAAAGGAAA
...(((((((((((........((.(((((.((....)).))))).)).(((((........))))).....)))))))))..........(((((((........)))))))..))... ( -30.00)
>DroYak_CAF1 90105 120 + 1
CCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAUUUACUUUUUAAUUUACUCAGAAAACCGAGCAAAAAGGAAA
...(((((((((((((......((.(((((.((....)).))))).)).(((((........)))))...)))))))))))..........(((.(((........))).)))..))... ( -28.00)
>consensus
CCACCAAUUUCUGCAUUAAAGUGCAAAUAAAUUGAUUGAAUUAUUGGCUGGGCGAGAAGAUGCGCCCUCUGUGCAGAAAUUUACUUUUUAAUUUACUCAGAAAACCGAGUAAAAAGGAAA
...(((((((((((((......((.(((((.((....)).))))).)).(((((........)))))...)))))))))))..........(((((((........)))))))..))... (-29.18 = -29.62 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,352,575 – 11,352,695
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.00
Mean single sequence MFE -33.20
Consensus MFE -31.12
Energy contribution -31.40
Covariance contribution 0.28
Combinations/Pair 1.06
Mean z-score -3.51
Structure conservation index 0.94
SVM decision value 4.25
SVM RNA-class probability 0.999851
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11352575 120 - 27905053
UUUCCUUUUUACUCGGUUUUCUGAGUAAAUUAAAAAGUAAAUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGG
...((..(((((((((....)))))))))..........((((((((((....(((((........))))).((.(((((..........))))).)).......))))))))))))... ( -34.40)
>DroSec_CAF1 100163 120 - 1
UUUCCUUUUUACUCGGUUUUCUGAGUAAAUUAAAAAGUAAAUUUCUGCACAGAGGGCGCAUCUUCUCGCGCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGG
...((..(((((((((....)))))))))..........((((((((((..((((((((........)))).((.(((((..........))))).)).))))..))))))))))))... ( -35.00)
>DroSim_CAF1 90930 120 - 1
UUUCCUUUUUACUCGGUUUUCUGAGUAAAUUAAAAAGUAAAUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGA
...((..(((((((((....)))))))))..........((((((((((....(((((........))))).((.(((((..........))))).)).......))))))))))))... ( -34.40)
>DroEre_CAF1 87699 120 - 1
UUUCCUUUUUACUCGGUUUUCGGAGUAAAUUAAAAAGUAAAUUUCCGCGCAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGG
.......(((((((.(....).)))))))...............((((.....(((((........)))))...............(((((..((((((......))))))))))))))) ( -27.80)
>DroYak_CAF1 90105 120 - 1
UUUCCUUUUUGCUCGGUUUUCUGAGUAAAUUAAAAAGUAAAUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGG
...((..(((((((((....)))))))))..........((((((((((....(((((........))))).((.(((((..........))))).)).......))))))))))))... ( -34.40)
>consensus
UUUCCUUUUUACUCGGUUUUCUGAGUAAAUUAAAAAGUAAAUUUCUGCACAGAGGGCGCAUCUUCUCGCCCAGCCAAUAAUUCAAUCAAUUUAUUUGCACUUUAAUGCAGAAAUUGGUGG
...((..(((((((((....)))))))))..........((((((((((....(((((........))))).((.(((((..........))))).)).......))))))))))))... (-31.12 = -31.40 +   0.28)

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 11:21:38 2006