Locus 8226

Sequence ID	X_DroMel_CAF1
Location	20,430,318 – 20,430,485
Length	167
Max. P	0.763545

overview

Window 4

Location	20,430,318 – 20,430,430
Length	112
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	87.51
Mean single sequence MFE	-34.63
Consensus MFE	-24.77
Energy contribution	-24.30
Covariance contribution	-0.47
Combinations/Pair	1.14
Mean z-score	-3.65
Structure conservation index	0.72
SVM decision value	0.51
SVM RNA-class probability	0.763545
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20430318 112 + 22224390
AUGGCGAAGGAUGG--GCCGU----CGGGAGAUGUCAGAAAUGCGUGUGAAAAAUAAACGAGAUUUUCGCGACGCGCUUUUGAUAUUUUUGCCUGACAGAAGCCAAAUGAGAAAAUGC
.((((...((....--.))((----((((.((((((((((.((((((((((((..........))))))).))))).))))))))))....))))))....))))............. ( -39.00)
>DroVir_CAF1 18535 116 + 1
UUGAGGCAGAGUCU--GCUGUGCUACGGAGAAUGUCAGAAAUGCGUGUGAAAAAUAAACGAGAUUUUCGCAGCGCGCUUUUGAUAUUUUUGCAUGACAGAAGCCAAAUGAGAAAAUGC
....(((....(((--(..((((....(((((((((((((.((((((((((((..........)))))))).)))).)))))))))))))))))..)))).))).............. ( -38.50)
>DroPse_CAF1 18961 113 + 1
AUG-AGAAGGAAGAGGAGAGU----GGGAGAAUGUCAGAAAUGCGUGUGAAAAAUAAACGAGAUUUUCGCAACGCGCUUUUGAUAUUUUUGCAUGACAGAAGCCAAAUGAGAAAAUGC
...-....((.........((----(.(((((((((((((.((((((((((((..........))))))).))))).))))))))))))).)))........)).............. ( -31.33)
>DroGri_CAF1 16987 116 + 1
GUGAGGAAGUGUCU--GCUCUACUCCAGAGAAUGUCAGAAAUGCGUGUGAAAAAUAAACGAGAUUUUCGCAACGCGCUUUUGAUAUUUUUGCAUGACAGAAGCCAAAUGAGAAAAUGC
....((...(((((--((.........(((((((((((((.((((((((((((..........))))))).))))).)))))))))))))))).))))....)).............. ( -31.80)
>DroMoj_CAF1 27473 116 + 1
AUGAGGAAGUGUCU--GCUGUGCUACGGAGAAUGUCAGAAAUGCGUGUGAAAAAUAAACGAGAUUUUCGCAGCGCGCUUUUGAUAUUUUUGCAUGACAGAAGCCAAAUGAGAAAAUGC
....((.....(((--(..((((....(((((((((((((.((((((((((((..........)))))))).)))).)))))))))))))))))..))))..)).............. ( -35.80)
>DroPer_CAF1 19888 113 + 1
AUG-AGAAGGAAGAGGAGAGU----GGGAGAAUGUCAGAAAUGCGUGUGAAAAAUAAACGAGAUUUUCGCAACGCGCUUUUGAUAUUUUUGCAUGACAGAAGCCAAAUGAGAAAAUGC
...-....((.........((----(.(((((((((((((.((((((((((((..........))))))).))))).))))))))))))).)))........)).............. ( -31.33)
>consensus
AUGAGGAAGGAUCU__GCUGU____CGGAGAAUGUCAGAAAUGCGUGUGAAAAAUAAACGAGAUUUUCGCAACGCGCUUUUGAUAUUUUUGCAUGACAGAAGCCAAAUGAGAAAAUGC
...........................(((((((((((((.((((((((((((..........))))))).))))).)))))))))))))((((....................)))) (-24.77 = -24.30 +  -0.47)

alignment

secondary structure

dotplot

Window 5

Location	20,430,390 – 20,430,485
Length	95
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	82.30
Mean single sequence MFE	-25.08
Consensus MFE	-18.91
Energy contribution	-19.05
Covariance contribution	0.14
Combinations/Pair	1.11
Mean z-score	-1.55
Structure conservation index	0.75
SVM decision value	0.22
SVM RNA-class probability	0.640716
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20430390 95 - 22224390
CACGUC------------------CACGUC------CAUGUCCAUGUCCAUGUCAUUGGCCGGGGCAAUGCGGAAAAUCGCAUUUUCUCAUUUGGCUUCUGUCAGGCAAAAAUAUCAAA
...(((------------------...(..------(((....)))..).((.((..((((((((.((((((......)))))).))))....))))..)).)))))............ ( -22.40)
>DroVir_CAF1 18611 92 - 1
CAUUGC------------------C---GG------CAUAUCCAUGCUCAUGUCAUUGGCCGGAGCUGUGCGGAAAAUCGCAUUUUCUCAUUUGGCUUCUGUCAUGCAAAAAUAUCAAA
..((((------------------.---((------(((....))))).(((.((..((((.(((..(((((......)))))...)))....))))..)).))))))).......... ( -25.30)
>DroPse_CAF1 19034 95 - 1
CAUUGC------------------CAUUGC------CACCGCCAUGUCCAUGUCAUUGGCCGGAGCAAUGCGGAAAAUCGCAUUUUCUCAUUUGGCUUCUGUCAUGCAAAAAUAUCAAA
..((((------------------(((.((------....)).)))...(((.((..((((.(((.((((((......))))))..)))....))))..)).))))))).......... ( -23.60)
>DroGri_CAF1 17063 92 - 1
CAUUGC------------------C---GC------CAUGUUCAUGCUCAUGUCAUUGGCCGGAGCAAUGCGGAAAAUCGCAUUUUCUCAUUUGGCUUCUGUCAUGCAAAAAUAUCAAA
......------------------.---..------.(((((..(((..(((.((..((((.(((.((((((......))))))..)))....))))..)).))))))..))))).... ( -22.40)
>DroEre_CAF1 2558 119 - 1
CACGUCCACGUCCACGUUCACGUCCACAUCCACGUCCAUGUCCAUGGCCAUGUCAUUGGCCGGGGCAAUGCGGAAAAUCGCAUUUUCUCAUUUGGCUUCUGUCAGGCAAAAAUAUCAAA
.((((..(((....)))..))))..........(((..(((((.((((((......)))))))))))(((((......))))).........((((....)))))))............ ( -32.00)
>DroPer_CAF1 19961 95 - 1
CACUGC------------------CAUUGC------UACCGCCAUGUCCAUGUCAUUGGCCGGAGCAAUGCGGAAAAUCGCAUUUUCUCAUUUGGCUUCUGUCAUGCAAAAAUAUCAAA
..((((------------------.(((((------(.((((((((.......)).))).)))))))))))))......(((..........((((....)))))))............ ( -24.80)
>consensus
CACUGC__________________CA__GC______CAUGUCCAUGUCCAUGUCAUUGGCCGGAGCAAUGCGGAAAAUCGCAUUUUCUCAUUUGGCUUCUGUCAUGCAAAAAUAUCAAA
................................................((((.((..((((.(((.((((((......))))))..)))....))))..)).))))............. (-18.91 = -19.05 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:50 2006