Locus 105

Sequence ID	3L_DroMel_CAF1
Location	359,363 – 359,586
Length	223
Max. P	0.999938

overview

Window 5

Location	359,363 – 359,482
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.73
Mean single sequence MFE	-38.34
Consensus MFE	-34.48
Energy contribution	-34.52
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.60
Structure conservation index	0.90
SVM decision value	1.45
SVM RNA-class probability	0.955252
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 359363 119 - 23771897
-GACAAGCAAACGUCGGCUGUGGUUUAAACCCGAAUCUGAAUCUCGGAGUCCCGUCUUCGGCACCGACUUGGAGAUUCGUAUCUCAGCCGAAAGCGUCGUCGUCUUGGCCAUAAAAAUAU
-(((..((.....(((((((.(((((......))))).(((((((.((((((((....)))....))))).)))))))......)))))))..))...)))................... ( -38.20)
>DroSec_CAF1 13513 119 - 1
-GACAAGCAAACGUCGGCUUGGGUUUAAGCCCGAAUCUGAAUCUCGGAGUCCCGUCUUCGGCACCGACUUGGAGAUUCGUAUCUCAGCCGAAAGCGUCGUCGUCUUGGCCAUAAAAAUAU
-(((..((.....(((((((((((....))))))....(((((((.((((((((....)))....))))).)))))))........)))))..))...)))................... ( -40.70)
>DroSim_CAF1 14125 119 - 1
-GACAAGCAAACGUCGGCUUGGGUUUAAGCCCGAAUCUGAAUCUCGGAGUCCCGUCUUCGGCACCGACUUGGAGAUUCGUAUCUCAGCCGAAAGCGUCGUCGUCUUGGCCAUAAAAAUAU
-(((..((.....(((((((((((....))))))....(((((((.((((((((....)))....))))).)))))))........)))))..))...)))................... ( -40.70)
>DroEre_CAF1 14832 119 - 1
ACACAAGCAAAAGUCGGCU-UGGUUUAAGCCCGAAUCUGAAUCUCGGAGUACCGUCUUCGGCACCGACUUGGAGAUUCGUAUCUCAGCCGAAAGCGUCGUCGUCGUGGCCAUAAAAAUAU
.(((.........((((((-.(((....))).((((.((((((((.((((.(.(((....).)).))))).)))))))).)).))))))))..(((....))).)))............. ( -33.60)
>DroYak_CAF1 14844 119 - 1
-CACAUGCCAACGUCGGCUUUGGUUUAAGCCCGAAUCUGAAUCUCGGAGUCCCGUCUUCGGCAACGACUUGGAGAUUCGUAUCUCAGCCGAAAGCGUCGUCGUCUUGGCCAUAAAAAUAU
-.....(((((.(.((((..((.(((..((..((((.((((((((.((((((((....)))....))))).)))))))).)).)).))..))).))..)))).))))))........... ( -38.50)
>consensus
_GACAAGCAAACGUCGGCUUUGGUUUAAGCCCGAAUCUGAAUCUCGGAGUCCCGUCUUCGGCACCGACUUGGAGAUUCGUAUCUCAGCCGAAAGCGUCGUCGUCUUGGCCAUAAAAAUAU
......((.....((((((..(((....))).((((.((((((((.((((((((....)))....))))).)))))))).)).))))))))..))((((......))))........... (-34.48 = -34.52 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	359,443 – 359,546
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.90
Mean single sequence MFE	-36.46
Consensus MFE	-26.24
Energy contribution	-26.60
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.72
SVM decision value	0.52
SVM RNA-class probability	0.766999
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 359443 103 - 23771897
CACAGGCUUGAAGCUUCGUU-UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA----------------GACAAGCAAACGUCGGCUGUGGUUUAAACCCGAAUCUGA
..(((..((((((((.((..-..)).)))))..((((((((((((.((((.....(((.((....----------------))..)))....)))))).))))))))))..)))..))). ( -31.30)
>DroSec_CAF1 13593 103 - 1
CACAGGCUUGAAGCUUCGUU-UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA----------------GACAAGCAAACGUCGGCUUGGGUUUAAGCCCGAAUCUGA
..(.((((((((.(....((-((((.((((......((((((....))))))..))))..)))))----------------).(((((........)))))).)))))))).)....... ( -33.50)
>DroSim_CAF1 14205 103 - 1
CACAGGCUUGAAGCUUCGUU-UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA----------------GACAAGCAAACGUCGGCUUGGGUUUAAGCCCGAAUCUGA
..(.((((((((.(....((-((((.((((......((((((....))))))..))))..)))))----------------).(((((........)))))).)))))))).)....... ( -33.50)
>DroEre_CAF1 14912 119 - 1
CACGGGCUUGAAGCUGCGUUUUUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAGCACAAAAACACAGAAACACAAGCAAAAGUCGGCU-UGGUUUAAGCCCGAAUCUGA
..(((((((((((((((((.....(..((((.....))))..)))))))))))(((((.....))).)).........((((.(((((........)))-)))))))))))))....... ( -44.10)
>DroYak_CAF1 14924 106 - 1
CACGGGCUUGAAGCUCCGUUUUUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAGCCU--------------CACAUGCCAACGUCGGCUUUGGUUUAAGCCCGAAUCUGA
..(((((((((((((.((.....)).))))))((..((((((.(((.(((....((((....)))).--------------.....)))..)))))))))..))..)))))))....... ( -39.90)
>consensus
CACAGGCUUGAAGCUUCGUU_UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA________________GACAAGCAAACGUCGGCUUUGGUUUAAGCCCGAAUCUGA
..((((((.((((((.(((.....(..((((.....))))..)))).)))))).)))....................................(((((((......))).))))..))). (-26.24 = -26.60 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	359,482 – 359,586
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.11
Mean single sequence MFE	-26.96
Consensus MFE	-22.84
Energy contribution	-23.00
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.70
Structure conservation index	0.85
SVM decision value	1.18
SVM RNA-class probability	0.927595
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 359482 104 + 23771897
---------------UUUUGAGAGCCAGAAGCCGCGCGCGGCUCAAAUAAAGCUACAAA-AACGAAGCUUCAAGCCUGUGAUGAGCGCAUUAAAAUAAAUUUAAGAGCCCUCAAAAUGUU
---------------(((((((.(((....((.((.(((((((......(((((.(...-...).)))))..)))).)))....)))).(((((.....)))))).)).))))))).... ( -23.90)
>DroSec_CAF1 13632 104 + 1
---------------UUUUGAGAGCCAGAAGCCGCGCGCGGCUCAAAUAAAGCUACAAA-AACGAAGCUUCAAGCCUGUGAUGAGCGCAUUAAAAUAAAUUUAAGAGCCCUCAAAAUGUU
---------------(((((((.(((....((.((.(((((((......(((((.(...-...).)))))..)))).)))....)))).(((((.....)))))).)).))))))).... ( -23.90)
>DroSim_CAF1 14244 104 + 1
---------------UUUUGAGAGCCAGAAGCCGCGCGCGGCUCAAAUAAAGCUACAAA-AACGAAGCUUCAAGCCUGUGAUGAGCGCAUUAAAAUAAAUUUAAGAGCCCUCAAAAUGUU
---------------(((((((.(((....((.((.(((((((......(((((.(...-...).)))))..)))).)))....)))).(((((.....)))))).)).))))))).... ( -23.90)
>DroEre_CAF1 14951 120 + 1
UUCUGUGUUUUUGUGCUUUGAGAGCCAGAAGCCGCGCGCGGCUCAAAUAAAGCUACAAAAAACGCAGCUUCAAGCCCGUGAUGAGCGCAUUAAAAUAAAUUUAAGAGCCCUCAAAAUGUU
..((((((((((((((((((.(((((....((...))..)))))...)))))).)).)))))))))).........(((..((((.((.(((((.....)))))..)).))))..))).. ( -33.50)
>DroYak_CAF1 14963 106 + 1
-------------AGGCUUGAGAGCCAGAAGCCGCGCGCGGCUCAAAUAAAGCUACAAAAAACGGAGCUUCAAGCCCGUGAUGAGCGCAUUAAAAUAAAUUUAAGAGCCCUCA-AAUGUU
-------------.((((((((((((....((...))..)))))......((((.(.......).)))))))))))(((..((((.((.(((((.....)))))..)).))))-.))).. ( -29.60)
>consensus
_______________UUUUGAGAGCCAGAAGCCGCGCGCGGCUCAAAUAAAGCUACAAA_AACGAAGCUUCAAGCCUGUGAUGAGCGCAUUAAAAUAAAUUUAAGAGCCCUCAAAAUGUU
................((((((.(((....((((((((.((((......(((((.(.......).)))))..)))))))).)).))...(((((.....)))))).)).))))))..... (-22.84 = -23.00 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	359,482 – 359,586
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.11
Mean single sequence MFE	-33.38
Consensus MFE	-30.50
Energy contribution	-30.30
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-2.96
Structure conservation index	0.91
SVM decision value	4.69
SVM RNA-class probability	0.999938
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 359482 104 - 23771897
AACAUUUUGAGGGCUCUUAAAUUUAUUUUAAUGCGCUCAUCACAGGCUUGAAGCUUCGUU-UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA---------------
....((((((((((..(((((.....)))))...........(((...(((((((.((..-..)).)))))))...((((((....)))))))))))))))))))--------------- ( -31.20)
>DroSec_CAF1 13632 104 - 1
AACAUUUUGAGGGCUCUUAAAUUUAUUUUAAUGCGCUCAUCACAGGCUUGAAGCUUCGUU-UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA---------------
....((((((((((..(((((.....)))))...........(((...(((((((.((..-..)).)))))))...((((((....)))))))))))))))))))--------------- ( -31.20)
>DroSim_CAF1 14244 104 - 1
AACAUUUUGAGGGCUCUUAAAUUUAUUUUAAUGCGCUCAUCACAGGCUUGAAGCUUCGUU-UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA---------------
....((((((((((..(((((.....)))))...........(((...(((((((.((..-..)).)))))))...((((((....)))))))))))))))))))--------------- ( -31.20)
>DroEre_CAF1 14951 120 - 1
AACAUUUUGAGGGCUCUUAAAUUUAUUUUAAUGCGCUCAUCACGGGCUUGAAGCUGCGUUUUUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAGCACAAAAACACAGAA
....(((((((((((...................((((.....))))..((((((((((.....(..((((.....))))..))))))))))).)))))))))))............... ( -39.20)
>DroYak_CAF1 14963 106 - 1
AACAUU-UGAGGGCUCUUAAAUUUAUUUUAAUGCGCUCAUCACGGGCUUGAAGCUCCGUUUUUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAGCCU-------------
......-((((.((..(((((.....))))).)).))))....((((((((((((((((....((..((((.....))))..)).)))).....)))).))))))))------------- ( -34.10)
>consensus
AACAUUUUGAGGGCUCUUAAAUUUAUUUUAAUGCGCUCAUCACAGGCUUGAAGCUUCGUU_UUUGUAGCUUUAUUUGAGCCGCGCGCGGCUUCUGGCUCUCAAAA_______________
.....(((((((((..(((((.....)))))...........(((...(((((((.((.....)).)))))))...((((((....))))))))))))))))))................ (-30.50 = -30.30 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:33 2006