Locus 5488

Sequence ID 2R_DroMel_CAF1
Location 17,649,015 – 17,649,255
Length 240
Max. P 0.774347
window8754 window8755

overview

Window 4

Location 17,649,015 – 17,649,135
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.11
Mean single sequence MFE -25.96
Consensus MFE -16.34
Energy contribution -18.10
Covariance contribution 1.76
Combinations/Pair 1.26
Mean z-score -1.85
Structure conservation index 0.63
SVM decision value 0.54
SVM RNA-class probability 0.774347
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17649015 120 + 20766785
GUUUACCCCAUAGACGCUAUAGUUUUCUUAACUAAACUAGACUUGAGGCACUCAAGUUUUAAUCAUGCCCAGCCCAGAUCCCUGGCAGAAUCUAAUUACAUAUUUGGAUUCUGCCACUUU
(((((.....)))))(((.((((((........))))))((((((((...))))))))............))).........(((((((((((((........))))))))))))).... ( -34.00)
>DroSec_CAF1 2652 120 + 1
GUUUACCCCAUAGAAGCUAUAGCUUUCUUAACUUAACUAGACUUGAGGCACUCAAGUUUUAAUCAUGCCCAGCCCAGAUCCCUGGCAGAGUUUAAUUAUAUAUUUGGAUUCUGGCACUUU
(((.........(((((....)))))........))).(((((((((...)))))))))......((((..(((.((....)))))(((((((((........))))))))))))).... ( -28.03)
>DroSim_CAF1 8573 109 + 1
GUUUACCCCAUAGAAGCUAUAGCUUUCUUAACUUAACUAGACUUGAGGCACUCAAGUUUUAAUCAUGCCCAGCCCA-----------GAGUUUAAUUAUAUAUUUGGAUUCUGCCACUUU
(((.........(((((....)))))........))).(((((((((...)))))))))...............((-----------((((((((........))))))))))....... ( -20.13)
>DroEre_CAF1 2730 112 + 1
U--------UUUGAAGCUAUAUCUUUAUUAGUUAAGCCGGACUUGAGGCACUCAAGUUUUAAUCAAGUCUAACCCAGAUCCAUGGCGGAGUCUAAUUACAUAUGUGUGUUCUGCCACUUU
.--------((((.(((((.........))))).....((((((((...((....)).....))))))))....))))....((((((((.(....(((....))).))))))))).... ( -23.30)
>DroYak_CAF1 13962 112 + 1
U--------UUUGAGGCUCUGACUUUUUAAGCUUAACCAGACUGGAGGCACUCAAGUUUUAAUCAUGCCCAAUCCAGAUCCCUGGCAGAGUCUAAUUACAUAUUUGUGUUGUGCCACUUU
.--------.....(((.(.(((...(((..(((..((((.(((((((((...............))))...)))))....))))..)))..)))..(((....))))))).)))..... ( -24.36)
>consensus
GUUUACCCCAUAGAAGCUAUAGCUUUCUUAACUUAACUAGACUUGAGGCACUCAAGUUUUAAUCAUGCCCAGCCCAGAUCCCUGGCAGAGUCUAAUUACAUAUUUGGAUUCUGCCACUUU
............(((((....)))))............(((((((((...))))))))).......................(((((((((((((........))))))))))))).... (-16.34 = -18.10 +   1.76)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,649,135 – 17,649,255
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.01
Mean single sequence MFE -35.80
Consensus MFE -23.70
Energy contribution -25.62
Covariance contribution 1.92
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.66
SVM decision value 0.01
SVM RNA-class probability 0.537798
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17649135 120 - 20766785
AUGUACAUGGACGGUCUUCGGGCCAUCCAGCAUUUUGUUAUUGCACCUCAUUUUGGCUGAAACAGAACGCUGGCUUAAUUGCACUAGAAAUGCCAGCAUGUGGCAAGUUAAGUAGUCUAU
......((((((((((....))))..(((((.(((((((....((((.......)).)).))))))).))))).........(((.((..(((((.....)))))..)).))).)))))) ( -37.70)
>DroSec_CAF1 2772 114 - 1
--G----GAGACGGUCUUCGGGCCAUCCAGCAUUUUGUUAUUGCACCUCACUUGAGCCGAAACAGAACGCUGGCUUUAUUGCACUAGAAAUGCCAGCAUGUGGCAUGUUAAGUAGUCUAU
--.----.((((((((....))))..(((((.(((((((.(((...(((....))).)))))))))).))))).........(((.((.((((((.....)))))).)).))).)))).. ( -38.10)
>DroSim_CAF1 8682 114 - 1
--G----GAGACGGUCUUCUUGCCAUCCAGCAUUUUGUUAUUGCACCUCAUUUGGGCCGAAACAGAACGCUGGCUUUAUUGCACCAGAAAUGCCAGCAUGUGGCAAGUUAAGUAGUCUAU
--.----.((((...((((((((((((((((.(((((((...((.((......))))...))))))).)))))......(((..((....))...))).))))))))..)))..)))).. ( -38.50)
>DroEre_CAF1 2842 108 - 1
--G------GACGGUCCUCGGGCCAUCGAGCAUUUUGUUAUUGCACUUCAUUUG----GAAACAGAACCCUGGCUAUAUUGCACUGGAAAUGCCUGCAUGCGGCAAGUUAAGUAGUCUAU
--(------(((((((....)))).....(((...(((....((......((((----....))))......)).))).)))(((.((..((((.......))))..)).))).)))).. ( -27.00)
>DroYak_CAF1 14074 112 - 1
--C------UAUGGUCUUCGGGCCAUCCAGCAUUUUGUUAUUGCACCUCAUUUGGUCCGAAACAGAACGCUGGCUAUAUUGCACUGGAAGUGGCUGCAUGUGGCAAGUUAAGUAGUCUAU
--.------.((((((....)))))).((((.(((((((.(((.(((......))).)))))))))).))))(((((((.(((((......)).))))))))))................ ( -37.70)
>consensus
__G______GACGGUCUUCGGGCCAUCCAGCAUUUUGUUAUUGCACCUCAUUUGGGCCGAAACAGAACGCUGGCUUUAUUGCACUAGAAAUGCCAGCAUGUGGCAAGUUAAGUAGUCUAU
........((((((((....))))..(((((.(((((((.(((..((......))..)))))))))).))))).........(((.((..((((.......))))..)).))).)))).. (-23.70 = -25.62 +   1.92)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:07 2006