Locus 5229

Sequence ID 3R_DroMel_CAF1
Location 13,679,968 – 13,680,164
Length 196
Max. P 0.989635
window8530 window8531 window8532

overview

Window 0

Location 13,679,968 – 13,680,070
Length 102
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 72.58
Mean single sequence MFE -34.18
Consensus MFE -22.64
Energy contribution -23.95
Covariance contribution 1.31
Combinations/Pair 1.30
Mean z-score -2.13
Structure conservation index 0.66
SVM decision value 2.17
SVM RNA-class probability 0.989635
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13679968 102 - 27905053
GAGAGCAAGUGACGCCACAUGCAGCUGGCCGACUUCCUGUGAUAGGAUCUACGGUCAGUCUGCUGUCACAACCAAUGGACAGUCUGUGGCGAACUAUGGACA------
.....(((((..(((((((.(((((((((((...(((((...)))))....))))))).))))((((.((.....))))))...))))))).))).))....------ ( -39.90)
>DroSec_CAF1 7287 102 - 1
GAGGACAAGUGACGCCACAUGCAGCUGGCCGACUUCCUGUGGUAGGAUCUACGGUCAGUCUGCUGUCACAGCCAAUGGACAGUCUGUGGCGAACUAUGGACA------
..(..(((((..(((((((.(((((((((((...(((((...)))))....))))))).))))((((.((.....))))))...))))))).))).))..).------ ( -43.70)
>DroSim_CAF1 7320 102 - 1
GAGGACAAGUGACGCCACAUGCAGCUGGCCGACUUCCUGUGAUAGGAUCUACGGUCAGUCUGCUGUCACAGCCAAUGGACAGUCUGUGGCGAACUAUGGACA------
..(..(((((..(((((((.(((((((((((...(((((...)))))....))))))).))))((((.((.....))))))...))))))).))).))..).------ ( -43.70)
>DroEre_CAF1 1838 81 - 1
-------------------UGCAGCUGGCCGACU--CUGUGAUAGGAUCUACGGUCAGUGUGCUGUCACAGCCAAUGGACAGUCUGUGGCGGACUAUAGACU------
-------------------.(((((((((((..(--((......)))....)))))))).)))((((.((.....))))))((((((((....)))))))).------ ( -29.40)
>DroYak_CAF1 1834 81 - 1
-------------------UGCAGCUGGCAGAGU--CUGUGAUAGGAUCUACGGUCAGUCUGCUGUCGCAACCAAUGGACAGUCUGUGGCGGACCAUAUACC------
-------------------.(((((((((..(((--((......))).))...))))).))))((((.((.....))))))((.(((((....))))).)).------ ( -24.40)
>DroAna_CAF1 6949 102 - 1
AACAACAAAGGACUCUCCCUGUAGCUGGUUGCCUUCCUGCGAUUCGAUCUAUAGUCAGCUUGCUGUCACAUCCAAUCCUGAGUCCAU------AUAUGUACGGAAGUA
.........((((((...(((((((..(((((......)))))..)..)))))).(((....)))..............))))))..------.....(((....))) ( -24.00)
>consensus
GAG_ACAAGUGACGCCACAUGCAGCUGGCCGACUUCCUGUGAUAGGAUCUACGGUCAGUCUGCUGUCACAGCCAAUGGACAGUCUGUGGCGAACUAUGGACA______
....................(((((((((((...(((((...)))))....))))))).))))((((.((.....))))))((((((((....))))))))....... (-22.64 = -23.95 +   1.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,680,070 – 13,680,164
Length 94
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 79.57
Mean single sequence MFE -24.00
Consensus MFE -11.80
Energy contribution -12.36
Covariance contribution 0.56
Combinations/Pair 1.18
Mean z-score -1.92
Structure conservation index 0.49
SVM decision value -0.01
SVM RNA-class probability 0.528961
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13680070 94 + 27905053
CACUAUGCAUCAUCCCCUUUCAGUCCCCAAAUACAUAAUGCCAUUAAGUAUGAAACUUACAGCCCAGAAGGGUUGGA------UCCUUCUGGAGCAGGAG
............(((.............................(((((.....)))))..((((((((((((...)------))))))))).)).))). ( -22.00)
>DroSec_CAF1 7389 99 + 1
CACUAUGCAUCA-CCCCUUUCAGAUCCCAAAUACAUAAUGCCAUUAAGUAUGGAGCCUACAGCCCAGAAAGGGUUGAUUAUACUCCUUCUGGAGCAGGAG
...((((.((((-.(((((((.........((((.((((...)))).))))((.((.....)))).))))))).))))))))(((((.(....).))))) ( -25.50)
>DroSim_CAF1 7422 99 + 1
CACUAUGCAUCA-CCCCUUUUAGUUCCCAAAUACAUAAUGCCAUUAAGUAUGGAACUUACAGCCCAGAAAGGGUUGACUAUACUCCUUCUGGAGCAGGAG
............-..(((...((((((...((((.((((...)))).))))))))))....((((((((.((((.......)))).)))))).))))).. ( -24.90)
>DroEre_CAF1 1919 89 + 1
----------CA-CCCCUUUCAGUCCCCAAAUACACAAUUCCAUUAAGUAUGGAACUUACUGCCCAGAAAGGGGGGAUUAUACUCCUCCUGGAGCAGAAG
----------..-.........................((((((.....))))))(((.((((((((...((((((......)))))))))).))))))) ( -25.00)
>DroYak_CAF1 1915 88 + 1
----------CA-CCCCUUUCGGUCCCCAAAUACACGAUUUCAUUAAGUAUGGAACUGAGAGCCCAGAAAGGGGUGAUUAUACUUC-CCUGUAGCAGAUG
----------((-((((((((((...)).......((.((((((.....)))))).))........))))))))))....(((...-...)))....... ( -22.60)
>consensus
CACUAUGCAUCA_CCCCUUUCAGUCCCCAAAUACAUAAUGCCAUUAAGUAUGGAACUUACAGCCCAGAAAGGGUUGAUUAUACUCCUUCUGGAGCAGGAG
..............(((((((.((........))......((((.....)))).............))))))).........((((....))))...... (-11.80 = -12.36 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,680,070 – 13,680,164
Length 94
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 79.57
Mean single sequence MFE -29.18
Consensus MFE -19.52
Energy contribution -19.52
Covariance contribution -0.00
Combinations/Pair 1.24
Mean z-score -1.90
Structure conservation index 0.67
SVM decision value 0.76
SVM RNA-class probability 0.844039
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13680070 94 - 27905053
CUCCUGCUCCAGAAGGA------UCCAACCCUUCUGGGCUGUAAGUUUCAUACUUAAUGGCAUUAUGUAUUUGGGGACUGAAAGGGGAUGAUGCAUAGUG
..((.((.((((((((.------......))))))))))..(((((.....)))))..))(((((((((((......((....))....))))))))))) ( -30.10)
>DroSec_CAF1 7389 99 - 1
CUCCUGCUCCAGAAGGAGUAUAAUCAACCCUUUCUGGGCUGUAGGCUCCAUACUUAAUGGCAUUAUGUAUUUGGGAUCUGAAAGGGG-UGAUGCAUAGUG
..((((((((((((((.((.......)).)))))))))..)))))..((((.....))))(((((((((((.....(((....))).-.))))))))))) ( -31.70)
>DroSim_CAF1 7422 99 - 1
CUCCUGCUCCAGAAGGAGUAUAGUCAACCCUUUCUGGGCUGUAAGUUCCAUACUUAAUGGCAUUAUGUAUUUGGGAACUAAAAGGGG-UGAUGCAUAGUG
(((((((.((((((((.((.......)).))))))))))....((((((((((.((((...)))).))))...))))))...)))))-............ ( -27.90)
>DroEre_CAF1 1919 89 - 1
CUUCUGCUCCAGGAGGAGUAUAAUCCCCCCUUUCUGGGCAGUAAGUUCCAUACUUAAUGGAAUUGUGUAUUUGGGGACUGAAAGGGG-UG----------
....((((((....))))))......((((((((...(((...((((((((.....)))))))).)))....(....).))))))))-..---------- ( -31.00)
>DroYak_CAF1 1915 88 - 1
CAUCUGCUACAGG-GAAGUAUAAUCACCCCUUUCUGGGCUCUCAGUUCCAUACUUAAUGAAAUCGUGUAUUUGGGGACCGAAAGGGG-UG----------
..((((...))))-..........((((((((((.((..((((((....((((...........))))..)))))).))))))))))-))---------- ( -25.20)
>consensus
CUCCUGCUCCAGAAGGAGUAUAAUCAACCCUUUCUGGGCUGUAAGUUCCAUACUUAAUGGCAUUAUGUAUUUGGGGACUGAAAGGGG_UGAUGCAUAGUG
(((((((.((((((((.............))))))))))....((((((((((.((((...)))).))))...))))))...)))))............. (-19.52 = -19.52 +  -0.00)

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 11:49:37 2006