Locus 3446

Sequence ID 3R_DroMel_CAF1
Location 9,336,684 – 9,336,781
Length 97
Max. P 0.900333
window5532 window5533

overview

Window 2

Location 9,336,684 – 9,336,781
Length 97
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 81.50
Mean single sequence MFE -31.22
Consensus MFE -17.81
Energy contribution -18.12
Covariance contribution 0.31
Combinations/Pair 1.08
Mean z-score -1.96
Structure conservation index 0.57
SVM decision value -0.01
SVM RNA-class probability 0.528908
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9336684 97 + 27905053
UGAUUUGCCAGCUCGAACAGAGG-----AG-------CUCCACAUUUGAAUGUGAAUGUGGAACCUGUUGGGCUGUUGACUCUGCGGUUUUAAUUUGUCAGAGUGCGCU
......((((((((.(((((.(.-----..-------.(((((((((......))))))))).))))))))))))...(((((((((.......))).))))))))... ( -34.50)
>DroSec_CAF1 108975 88 + 1
UGAUUUGCCAGC------AGA--------G-------CUCCACAUUUGAAUGUGAAUGUGGAACCUGUCGGGCUGUUGACUCUGCGGUUUUAAUUUGUCAGAGUGCGCU
......(((.((------((.--------(-------.(((((((((......))))))))).)))))..))).((..(((((((((.......))).))))))..)). ( -29.90)
>DroSim_CAF1 119506 96 + 1
UGAUUUGCCAGC------AGAGGGGCACAG-------CUCCACAUUUGAAUGCGAAUGUGGAACCUGUCGGGCUGUUGACUCUGCGGUUUUAAUUUGUCAGAGUGCGCU
((((..(((.((------((((..(.((((-------(((((((((((....)))))))))).((....))))))))..)))))))))........))))......... ( -35.40)
>DroEre_CAF1 108860 95 + 1
UGAUUUGCCAGC------AGAAGGGCGGAGGGGCU--AUCCACAUUUGA------AUGUGGAACCUGUCGGACUGUUGACUCUGCGGUUUUAAUUUGUCAGAGUGCGCU
......((((((------((.....(.((.(((..--.(((((((....------))))))).))).)).).))))))(((((((((.......))).))))))))... ( -31.50)
>DroYak_CAF1 109847 97 + 1
UGAUUUGCCAGC------AGAGGGGCACUGCCUCUCCCUUCACAUUUGA------AUGUGGAACCUGUCGGGCUGUUGACUCUGCGGUUUUAAUUUGUCAGAGUGCGCU
......((((((------.(((((((...)))))))..(((((((....------))))))).((....))))))...(((((((((.......))).))))))))... ( -31.10)
>DroAna_CAF1 104937 86 + 1
UGAUUUGCUUGC------AGG--GGCA--U-------UUUAACAUUUAA------AUGUGGAACCUGUCAGGCUGUUGACUCUGCGGUUUUAAUUUGUCAGAGUGCGCU
......((((((------(((--.(((--(-------((........))------))))....)))).))))).((..(((((((((.......))).))))))..)). ( -24.90)
>consensus
UGAUUUGCCAGC______AGAGGGGCA_AG_______CUCCACAUUUGA______AUGUGGAACCUGUCGGGCUGUUGACUCUGCGGUUUUAAUUUGUCAGAGUGCGCU
......((((((..........................(((((((..........))))))).((....))))))...(((((((((.......))).))))))))... (-17.81 = -18.12 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,336,684 – 9,336,781
Length 97
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 81.50
Mean single sequence MFE -25.75
Consensus MFE -17.36
Energy contribution -17.92
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -2.68
Structure conservation index 0.67
SVM decision value 1.01
SVM RNA-class probability 0.900333
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9336684 97 - 27905053
AGCGCACUCUGACAAAUUAAAACCGCAGAGUCAACAGCCCAACAGGUUCCACAUUCACAUUCAAAUGUGGAG-------CU-----CCUCUGUUCGAGCUGGCAAAUCA
.(((.((((((.(...........))))))))..(((((.(((((((((((((((........)))))))))-------).-----...))))).).))))))...... ( -31.70)
>DroSec_CAF1 108975 88 - 1
AGCGCACUCUGACAAAUUAAAACCGCAGAGUCAACAGCCCGACAGGUUCCACAUUCACAUUCAAAUGUGGAG-------C--------UCU------GCUGGCAAAUCA
...(.((((((.(...........))))))))....(((.(.(((((((((((((........)))))))))-------)--------.))------)).)))...... ( -29.30)
>DroSim_CAF1 119506 96 - 1
AGCGCACUCUGACAAAUUAAAACCGCAGAGUCAACAGCCCGACAGGUUCCACAUUCGCAUUCAAAUGUGGAG-------CUGUGCCCCUCU------GCUGGCAAAUCA
......................((((((((...(((((((....)).((((((((........)))))))))-------))))....))))------)).))....... ( -28.80)
>DroEre_CAF1 108860 95 - 1
AGCGCACUCUGACAAAUUAAAACCGCAGAGUCAACAGUCCGACAGGUUCCACAU------UCAAAUGUGGAU--AGCCCCUCCGCCCUUCU------GCUGGCAAAUCA
.(((.((((((.(...........))))))))..((((..((.(((.(((((((------....))))))).--.((......))))))).------))))))...... ( -23.20)
>DroYak_CAF1 109847 97 - 1
AGCGCACUCUGACAAAUUAAAACCGCAGAGUCAACAGCCCGACAGGUUCCACAU------UCAAAUGUGAAGGGAGAGGCAGUGCCCCUCU------GCUGGCAAAUCA
.(((.((((((.(...........))))))))..((((((....))...(((((------....)))))...((((.(((...))).))))------))))))...... ( -25.90)
>DroAna_CAF1 104937 86 - 1
AGCGCACUCUGACAAAUUAAAACCGCAGAGUCAACAGCCUGACAGGUUCCACAU------UUAAAUGUUAAA-------A--UGCC--CCU------GCAAGCAAAUCA
...(.((((((.(...........))))))))....((.((.((((.....(((------((........))-------)--))..--)))------))).))...... ( -15.60)
>consensus
AGCGCACUCUGACAAAUUAAAACCGCAGAGUCAACAGCCCGACAGGUUCCACAU______UCAAAUGUGGAG_______CU_UGCCCCUCU______GCUGGCAAAUCA
.(((.((((((.(...........))))))))..((((((....)).(((((((..........)))))))..........................))))))...... (-17.36 = -17.92 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:15 2006