Locus 1671

Sequence ID 3R_DroMel_CAF1
Location 4,799,953 – 4,800,067
Length 114
Max. P 0.848300
window2758 window2759

overview

Window 8

Location 4,799,953 – 4,800,067
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.79
Mean single sequence MFE -33.18
Consensus MFE -23.35
Energy contribution -23.93
Covariance contribution 0.58
Combinations/Pair 1.07
Mean z-score -3.01
Structure conservation index 0.70
SVM decision value 0.19
SVM RNA-class probability 0.624289
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4799953 114 + 27905053
GCAACCCGUUUGC-UGUCAAUGGGAGCAAGCCAAGACAAGACGCAACUAAGCCAACCAUGACUUGGCCUGGCCCCCAAAAACAGACGCACA-CAAUGUACCCAAA----GUGGCAAAAAC
((.....((...(-(((...((((.((..((((((.((.(..((......))....).)).))))))...)).))))...))))..)).((-(..((....))..----)))))...... ( -28.50)
>DroSec_CAF1 35368 114 + 1
GCAACCCGUUUGC-UGUCAAUGGGAGCAAGCCAAGUCAAGACGCAACUAAGCCAACCAUGACUUGGCCCGGCCCCCAAAAACAGACGCACA-CAAUGUACCCAAA----GUGGCAAAAAC
((.....((...(-(((...((((.((..(((((((((.(..((......))....).)))))))))...)).))))...))))..)).((-(..((....))..----)))))...... ( -33.90)
>DroSim_CAF1 31472 114 + 1
GCAACCCGUUUGC-UGUCAAUGGGAGCAAGCCAAGUCAAGACGCAACUAAGCCAACCAUGACUUGGCCCGGCCCCCAAAAACAGACGCACA-CAAUGUACCCAAA----GUGGCAAAAAC
((.....((...(-(((...((((.((..(((((((((.(..((......))....).)))))))))...)).))))...))))..)).((-(..((....))..----)))))...... ( -33.90)
>DroEre_CAF1 36206 109 + 1
GCAACCCGUUUGC-UGUCAAUGGGAGCAAGCCAAGUCAAGACGCAACUAAGCCAACCAUGACUUGGCCCGGCCCCCAAAAACAGA--CACC-CAAAGUUCCUAAA----GUGGCCAA---
.......(..(((-(((...((((.((..(((((((((.(..((......))....).)))))))))...)).))))...)))).--))..-)...((..(....----)..))...--- ( -31.10)
>DroYak_CAF1 36491 112 + 1
GCAACCCGUUUGC-UGUCAAUGGGAGCAAGCCAAGUCAAGACGCAACUAAGCCAACCAUGACUUGGCCCGGCCCCCAAAAACAGG--CACA-CAAAGUUCCUAAA----GUGGCCAACAU
((((.....))))-(((...((((.((..(((((((((.(..((......))....).)))))))))...)).))))...)))((--(.((-(............----))))))..... ( -35.20)
>DroAna_CAF1 35134 119 + 1
CCAACCCGUUUGCCCGUCAAUGGGAUCAGGCCAAGUCAAGACGAGAC-AAUCCAACCAUGACUUGGCCUAGCCCCUCACUCUCCUCGCACAACAUAGUAGUCAAGGAGAGUUCCAAAAAA
....((((((........))))))...(((((((((((.(..((...-..))....).)))))))))))........((((((((.((((......)).))..))))))))......... ( -36.50)
>consensus
GCAACCCGUUUGC_UGUCAAUGGGAGCAAGCCAAGUCAAGACGCAACUAAGCCAACCAUGACUUGGCCCGGCCCCCAAAAACAGACGCACA_CAAAGUACCCAAA____GUGGCAAAAAC
((((.....))))..((((.((((.((..(((((((((.(..((......))....).)))))))))...)).))))...........((......))............))))...... (-23.35 = -23.93 +   0.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 4,799,953 – 4,800,067
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.79
Mean single sequence MFE -47.48
Consensus MFE -33.77
Energy contribution -34.47
Covariance contribution 0.70
Combinations/Pair 1.11
Mean z-score -3.72
Structure conservation index 0.71
SVM decision value 0.78
SVM RNA-class probability 0.848300
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4799953 114 - 27905053
GUUUUUGCCAC----UUUGGGUACAUUG-UGUGCGUCUGUUUUUGGGGGCCAGGCCAAGUCAUGGUUGGCUUAGUUGCGUCUUGUCUUGGCUUGCUCCCAUUGACA-GCAAACGGGUUGC
((((..(((((----..((....))..)-)).))(.(((((..(((((((.((((((((.((.((...((......))..)))).)))))))))))))))..))))-))))))....... ( -45.80)
>DroSec_CAF1 35368 114 - 1
GUUUUUGCCAC----UUUGGGUACAUUG-UGUGCGUCUGUUUUUGGGGGCCGGGCCAAGUCAUGGUUGGCUUAGUUGCGUCUUGACUUGGCUUGCUCCCAUUGACA-GCAAACGGGUUGC
((((..(((((----..((....))..)-)).))(.(((((..(((((((.(((((((((((.((...((......))..))))))))))))))))))))..))))-))))))....... ( -48.90)
>DroSim_CAF1 31472 114 - 1
GUUUUUGCCAC----UUUGGGUACAUUG-UGUGCGUCUGUUUUUGGGGGCCGGGCCAAGUCAUGGUUGGCUUAGUUGCGUCUUGACUUGGCUUGCUCCCAUUGACA-GCAAACGGGUUGC
((((..(((((----..((....))..)-)).))(.(((((..(((((((.(((((((((((.((...((......))..))))))))))))))))))))..))))-))))))....... ( -48.90)
>DroEre_CAF1 36206 109 - 1
---UUGGCCAC----UUUAGGAACUUUG-GGUG--UCUGUUUUUGGGGGCCGGGCCAAGUCAUGGUUGGCUUAGUUGCGUCUUGACUUGGCUUGCUCCCAUUGACA-GCAAACGGGUUGC
---....((..----....))(((((.(-..((--.(((((..(((((((.(((((((((((.((...((......))..))))))))))))))))))))..))))-)))..)))))).. ( -46.00)
>DroYak_CAF1 36491 112 - 1
AUGUUGGCCAC----UUUAGGAACUUUG-UGUG--CCUGUUUUUGGGGGCCGGGCCAAGUCAUGGUUGGCUUAGUUGCGUCUUGACUUGGCUUGCUCCCAUUGACA-GCAAACGGGUUGC
.......((..----....))(((((.(-(.((--(.((((..(((((((.(((((((((((.((...((......))..))))))))))))))))))))..))))-))).))))))).. ( -45.40)
>DroAna_CAF1 35134 119 - 1
UUUUUUGGAACUCUCCUUGACUACUAUGUUGUGCGAGGAGAGUGAGGGGCUAGGCCAAGUCAUGGUUGGAUU-GUCUCGUCUUGACUUGGCCUGAUCCCAUUGACGGGCAAACGGGUUGG
.........((((((((((.(.((......)))))))))))))..(((..((((((((((((.((..((...-..))..)).))))))))))))..))).....((......))...... ( -49.90)
>consensus
GUUUUUGCCAC____UUUGGGUACAUUG_UGUGCGUCUGUUUUUGGGGGCCGGGCCAAGUCAUGGUUGGCUUAGUUGCGUCUUGACUUGGCUUGCUCCCAUUGACA_GCAAACGGGUUGC
..............................((.....((((..(((((((.(((((((((((.((...((......))..))))))))))))))))))))..)))).....))....... (-33.77 = -34.47 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:30 2006