Locus 1811

Sequence ID	3R_DroMel_CAF1
Location	5,170,796 – 5,170,962
Length	166
Max. P	0.949033

overview

Window 3

Location	5,170,796 – 5,170,902
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	95.09
Mean single sequence MFE	-26.07
Consensus MFE	-24.50
Energy contribution	-24.94
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.21
Structure conservation index	0.94
SVM decision value	0.56
SVM RNA-class probability	0.781994
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5170796 106 + 27905053
AAUUUAAUGACCGCAGCUGUUUCUUUUGGGGACAGACUGUACUGCUUCGAUUUCGAUCUUGAUUAAAUCCCAUUGAAAAUAGGCAUUUAGAAUGCACAUAUAUCGG
..(((((((...((((((((..(.....)..)))).))))......(((....)))..............))))))).....((((.....))))........... ( -22.20)
>DroSec_CAF1 9332 105 + 1
AAUGCAAUGACCGCAGCUGUUUCUUUUGGGGACAGACUGUACUGCUUCGAU-UCGAUCUUGAUUAAAUCCCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGG
...(((......((((((((..(.....)..)))).))))..)))..((((-.........((((((((((((.....))))).)))))))..........)))). ( -26.71)
>DroSim_CAF1 9337 106 + 1
AAUGCAAUGACCGCAGCUGUUUCUUUUGGGGACAGACUGUACUGCUUCGAUUUCGAUCUUGAUUAAAUCCCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGG
..((((......((((((((..(.....)..)))).))))......(((....))).....((((((((((((.....))))).))))))).)))).......... ( -27.90)
>DroEre_CAF1 9136 106 + 1
AAUUUAAUGACCGCAGCUGUUUGUUUUGGGGACAGACUGUACUGCUUCGAUUUCGAUCUUGAUUAAAUCCCAUUGUAAAUGGGCAUUUAGUAUGCACAUAUAUCGG
............((((..(((((((.....)))))))....))))..((((..........((((((((((((.....))))).)))))))..........)))). ( -25.25)
>DroYak_CAF1 9547 105 + 1
AAAUUCAUGACCGCAGCUGUUUCUUUUGGGAACAGACUGUAC-GCUUCGAGUUCGAUCUUGAUUAAAUCCCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGG
..........(((((((((((((.....))))))).))))..-((..((((......))))((((((((((((.....))))).)))))))..)).........)) ( -28.30)
>consensus
AAUUUAAUGACCGCAGCUGUUUCUUUUGGGGACAGACUGUACUGCUUCGAUUUCGAUCUUGAUUAAAUCCCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGG
..........(((((((((((((.....))))))).))))...((.(((....))).....((((((((((((.....))))).)))))))..)).........)) (-24.50 = -24.94 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	5,170,865 – 5,170,962
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	96.28
Mean single sequence MFE	-23.68
Consensus MFE	-21.20
Energy contribution	-22.00
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.90
SVM decision value	1.39
SVM RNA-class probability	0.949033
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5170865 97 + 27905053
CCAUUGAAAAUAGGCAUUUAGAAUGCACAUAUAUCGGCUUUUUUUGGGAGCACAAUUACCGCGUCCAAAUGCGGGCAUAGAUUUCAAUGUAAAUUAA
.((((((((....((((.....))))...(((..(.((....(((((..((.........))..))))).)).)..)))..))))))))........ ( -23.10)
>DroSec_CAF1 9400 97 + 1
CCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGGCUUUUUUUGGGAGCACAAUUACCGCGUCGAAAUGCGGGCAUAGAUUUCAAUGUAAAUUAA
.(((((((((((.((((.....)))).)))...((.(((((.....))))).......((((((....)))))).....))))))))))........ ( -24.80)
>DroSim_CAF1 9406 97 + 1
CCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGGCUUUUUUUGGGAGCACAAUUACCGCGUCGAAAUGCGGGCAUAGAUUUCAAUGUAAAUUAA
.(((((((((((.((((.....)))).)))...((.(((((.....))))).......((((((....)))))).....))))))))))........ ( -24.80)
>DroEre_CAF1 9205 96 + 1
CCAUUGUAAAUGGGCAUUUAGUAUGCACAUAUAUCGGGUUU-UUUGGGAGCACAAUUACCGCGUUGAAAUGCGGGCAUAGAUAUCAAUGUAAAUUAA
.(((((...(((.((((.....)))).)))(((((..((((-.....)))).......((((((....)))))).....))))))))))........ ( -20.80)
>DroYak_CAF1 9615 96 + 1
CCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGGCUUU-UUUGGGAGCACAAUUACCGCGUUGAAAUGCGGGCAUAGAUUUCAAUGUAAAUUAA
.(((((((((((.((((.....)))).)))...((.(((((-....))))).......((((((....)))))).....))))))))))........ ( -24.90)
>consensus
CCAUUGAAAAUGGGCAUUUAGUAUGCACAUAUAUCGGCUUUUUUUGGGAGCACAAUUACCGCGUCGAAAUGCGGGCAUAGAUUUCAAUGUAAAUUAA
.(((((((((((.((((.....)))).)))...((.(((((.....))))).......((((((....)))))).....))))))))))........ (-21.20 = -22.00 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	5,170,865 – 5,170,962
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	96.28
Mean single sequence MFE	-20.50
Consensus MFE	-17.74
Energy contribution	-18.18
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.76
Structure conservation index	0.87
SVM decision value	1.32
SVM RNA-class probability	0.941684
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5170865 97 - 27905053
UUAAUUUACAUUGAAAUCUAUGCCCGCAUUUGGACGCGGUAAUUGUGCUCCCAAAAAAAGCCGAUAUAUGUGCAUUCUAAAUGCCUAUUUUCAAUGG
........((((((((.........(((((((((((((...((((.(((.........)))))))...))))...)))))))))....)))))))). ( -22.72)
>DroSec_CAF1 9400 97 - 1
UUAAUUUACAUUGAAAUCUAUGCCCGCAUUUCGACGCGGUAAUUGUGCUCCCAAAAAAAGCCGAUAUAUGUGCAUACUAAAUGCCCAUUUUCAAUGG
........((((((((.......((((........))))..((((.(((.........)))))))..(((.((((.....)))).))))))))))). ( -20.50)
>DroSim_CAF1 9406 97 - 1
UUAAUUUACAUUGAAAUCUAUGCCCGCAUUUCGACGCGGUAAUUGUGCUCCCAAAAAAAGCCGAUAUAUGUGCAUACUAAAUGCCCAUUUUCAAUGG
........((((((((.......((((........))))..((((.(((.........)))))))..(((.((((.....)))).))))))))))). ( -20.50)
>DroEre_CAF1 9205 96 - 1
UUAAUUUACAUUGAUAUCUAUGCCCGCAUUUCAACGCGGUAAUUGUGCUCCCAAA-AAACCCGAUAUAUGUGCAUACUAAAUGCCCAUUUACAAUGG
........((((((((((.....((((........))))...(((......))).-......)))))(((.((((.....)))).)))...))))). ( -17.50)
>DroYak_CAF1 9615 96 - 1
UUAAUUUACAUUGAAAUCUAUGCCCGCAUUUCAACGCGGUAAUUGUGCUCCCAAA-AAAGCCGAUAUAUGUGCAUACUAAAUGCCCAUUUUCAAUGG
........((((((((.......((((........))))..((((.(((......-..)))))))..(((.((((.....)))).))))))))))). ( -21.30)
>consensus
UUAAUUUACAUUGAAAUCUAUGCCCGCAUUUCGACGCGGUAAUUGUGCUCCCAAAAAAAGCCGAUAUAUGUGCAUACUAAAUGCCCAUUUUCAAUGG
........((((((((.......((((........))))..((((.(((.........)))))))..(((.((((.....)))).))))))))))). (-17.74 = -18.18 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:09 2006