Locus 6980

Sequence ID	3R_DroMel_CAF1
Location	18,411,653 – 18,411,801
Length	148
Max. P	0.998644

overview

Window 6

Location	18,411,653 – 18,411,748
Length	95
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	78.34
Mean single sequence MFE	-36.88
Consensus MFE	-19.64
Energy contribution	-20.92
Covariance contribution	1.28
Combinations/Pair	1.21
Mean z-score	-2.63
Structure conservation index	0.53
SVM decision value	1.49
SVM RNA-class probability	0.958638
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18411653 95 - 27905053
UUGGCCAGCGACUUGGCUGCGGCCAGCUGCAACUUCUGGGUGGCGGCAUUCUU-GUUGCUCUUAGCCGGCGGAGCUAUUUUCU---UCUUCUGCACACC
.((((.((((((..(..(((.((((.((.........)).)))).)))..)..-))))))....))))((((((.........---..))))))..... ( -33.60)
>DroVir_CAF1 4773 95 - 1
UUGGCCAACUGCUUGGCCGCGGCCAGCUGCAGCGUUUUCGUGGCCGCAUUUUU-GGUCACUUUGGACGCUGCAGUGGGCUUCUUUUU---CUGCACACC
..((((((....))))))(.((((.((((((((((((..(((((((......)-))))))...)))))))))))).)))).).....---......... ( -47.00)
>DroSim_CAF1 5029 95 - 1
UUGGCCAGCGACUUGGCUGCGGCCAGCUGCAGCUUCUGGGUGGCGGCAUUCUU-GUUGCUCUUGGCCGGCAGAGCUACUUUCU---UCUUCUGCACACC
.((((((((.((((((((((((....))))))))...)))).))((((.....-..))))..))))))((((((.........---..))))))..... ( -38.80)
>DroEre_CAF1 4993 95 - 1
UUGGCCAGCGAUUUGGCUGCGGCCAGCUGCAGUUUCUGGGUGGCGACAUUCUU-GCUGCUCUUCGCAGCCGGAGCUAUUUUCC---UUUUCUGCACGCC
..(((..(((....((((((((..((..(((((....(((((....)))))..-))))).))))))))))((((.....))))---.....)))..))) ( -35.90)
>DroYak_CAF1 4966 95 - 1
UUGGCCACCGACUUGGCUGCGGCCAGCUGCAGCUUCUGGGUGGCGACAUUCUU-GCUGCUUUUGGCCACCGGAGCUAUUUUCU---UUUUCUGCACGCC
..(((((......)))))((((((((..(((((....(((((....)))))..-)))))..))))))..(((((.........---..)))))...)). ( -35.50)
>DroAna_CAF1 5164 95 - 1
UUAGCCAGCUUUUUUGCUGCGGCCAGCUGCAGUUUCUGGGUGGCAUCAUUCUUAGGUGCU-UUAACUGCUGGAGCCACCUUUU---UCUUCUGGAUACC
...((((.((.....(((((((....)))))))....)).))))(((......(((((((-(((.....))))).)))))...---.......)))... ( -30.49)
>consensus
UUGGCCAGCGACUUGGCUGCGGCCAGCUGCAGCUUCUGGGUGGCGGCAUUCUU_GCUGCUCUUGGCCGCCGGAGCUAUUUUCU___UCUUCUGCACACC
...((((.(.(...((((((((....))))))))..).).)))).............(((((........)))))........................ (-19.64 = -20.92 +   1.28)

alignment

secondary structure

dotplot

Window 7

Location	18,411,677 – 18,411,785
Length	108
Sequences	3
Columns	116
Reading direction	reverse
Mean pairwise identity	67.35
Mean single sequence MFE	-39.10
Consensus MFE	-25.76
Energy contribution	-23.33
Covariance contribution	-2.42
Combinations/Pair	1.43
Mean z-score	-1.78
Structure conservation index	0.66
SVM decision value	3.17
SVM RNA-class probability	0.998644
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18411677 108 - 27905053
CUACUUGGAUUUCUUGGCCUUUCCCUUGGGCAAGGGUUUGGCCAGCGACUUGGCUGCGGCCAGCUGCAACUUCUGGGUGGCGGCAUUCUUGUUGCUCUUAGCCGGCGG--------
....((((......(((((...(((((....)))))...)))))(((((..(..(((.((((.((.........)).)))).)))..)..)))))......))))...-------- ( -42.30)
>DroWil_CAF1 12479 113 - 1
CUUCUUAAGCUUCUUUGCUGUUACUUUCUUUAGAGGCUGGGCCAACUCCUUCGCAGCAGUCAAUUUUAAUGUCUGGGUGG---CCUUCUUGUUGAUCUUAUUUGACGAGGAUUUCG
.......(((((((.................))))))).(((((...(((..(((..((......))..)))..))))))---))(((((((..(......)..)))))))..... ( -28.03)
>DroYak_CAF1 4990 108 - 1
CUACUUGGAUUUCUUGGCCUUUCCCUUGGGCAAGGGUUUGGCCACCGACUUGGCUGCGGCCAGCUGCAGCUUCUGGGUGGCGACAUUCUUGCUGCUUUUGGCCACCGG--------
.....(((......(((((.........(((((((((.(.((((((.(...((((((((....))))))))..).)))))).).)))))))))......)))))))).-------- ( -46.96)
>consensus
CUACUUGGAUUUCUUGGCCUUUCCCUUGGGCAAGGGUUUGGCCAACGACUUGGCUGCGGCCAGCUGCAACUUCUGGGUGGCG_CAUUCUUGUUGCUCUUAGCCGACGG________
.....(((......(((((...(((((....)))))...))))).....(((((....)))))..(((((....(((((....)))))..)))))......)))............ (-25.76 = -23.33 +  -2.42)

alignment

secondary structure

dotplot

Window 8

Location	18,411,708 – 18,411,801
Length	93
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	76.78
Mean single sequence MFE	-26.73
Consensus MFE	-12.07
Energy contribution	-11.85
Covariance contribution	-0.22
Combinations/Pair	1.17
Mean z-score	-2.04
Structure conservation index	0.45
SVM decision value	0.21
SVM RNA-class probability	0.635737
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18411708 93 + 27905053
CCCAGAAGUUGCAGCUGGCCGCAGCCAAGUCGCUGGCCAAACCCUUGCCCAAGGGAAAGGCCAAGAAAUCCAA---GUAGUAG-CUUAAAAUACAU-U
.....(((((((.((((((....)))...((..(((((...(((((....)))))...))))).))......)---)).))))-))).........-. ( -30.20)
>DroPse_CAF1 6268 95 + 1
CACAGAAGCUGCAGCUGGCCGCAGCCAAGACGCUGGCCAAGCCGCUGCAGAAGGUCAAGUCCAAGAAGUUGAA---GAAAUAGUCGUAAACUACAUUU
....((..(((((((.(((....((((......))))...))))))))))....))........(.((((...---((.....))...)))).).... ( -27.10)
>DroSec_CAF1 5079 93 + 1
CCCAGAAGCUGCAGCUGGCCGCAGCCAAGUCGCUGGCCAAGCCCUUGCCCAAGGGAAAGGCCAAGAAAUCCAA---GUAGUAG-CUUAAAAUACAU-U
.....(((((((.((((((....)))...((..(((((...(((((....)))))...))))).))......)---)).))))-))).........-. ( -33.70)
>DroMoj_CAF1 4261 95 + 1
CAAAGACACUGCAGCUGGCCGCAGCCAAACAACUGGCCAAGCCAUUGCAGAAGAAGAUUGGCAAAAAGCUAAA---GAAGUAGAAUUGUAGUAUAUUU
.....(((((((((.((((....((((......))))...)))))))))).......(((((.....))))).---..........)))......... ( -23.90)
>DroAna_CAF1 5219 93 + 1
CCCAGAAACUGCAGCUGGCCGCAGCAAAAAAGCUGGCUAAACCCCUGCCCAAG---AAAGCAAAGAAGUCCAAGAAGUAGUAG-UUUAAAAUGUAU-C
.....(((((((.(((((((..(((......))))))).......(((.....---...))).............))).))))-))).........-. ( -18.40)
>DroPer_CAF1 6333 95 + 1
CACAGAAGCUGCAGCUGGCCGCAGCCAAGACGCUGGCCAAGCCGCUGCAGAAGGUCAAGUCCAAGAAGUUGAA---GAAAUAGUCGUAAACUACAUUU
....((..(((((((.(((....((((......))))...))))))))))....))........(.((((...---((.....))...)))).).... ( -27.10)
>consensus
CACAGAAGCUGCAGCUGGCCGCAGCCAAGACGCUGGCCAAGCCCCUGCACAAGGGAAAGGCCAAGAAGUCCAA___GAAGUAG_CUUAAAAUACAU_U
..........((((.(((((..(((......)))))))).....)))).................................................. (-12.07 = -11.85 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:43 2006