Locus 532

Sequence ID	3L_DroMel_CAF1
Location	1,561,148 – 1,561,258
Length	110
Max. P	0.876705

overview

Window 3

Location	1,561,148 – 1,561,258
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.72
Mean single sequence MFE	-24.85
Consensus MFE	-16.13
Energy contribution	-16.80
Covariance contribution	0.67
Combinations/Pair	1.27
Mean z-score	-1.73
Structure conservation index	0.65
SVM decision value	0.90
SVM RNA-class probability	0.876705
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1561148 110 + 23771897
-ACCCACACAUGCAUACAGGCUUUUACUAUCCGUGUGAGCCGCAA-ACAACAAAUAAGCCGCUAUAAGAAA-AAAACGCGUAUUUUGGCGGUCCCU-------CCGCCCACUUUUUCCCC
-........((((.....(((((.(((.....))).)))))((..-..............)).........-.....)))).....(((((.....-------)))))............ ( -21.89)
>DroSec_CAF1 5585 107 + 1
-ACCCACACAUGCAUGCAGGCUUUCGCUAUCCGUGUGAGCCGCAA-ACAACAAAUAAGCCGCUAUAAAA----AAACGCGUAUUUUGGCGGCCCCU-------CCGCCCGCUUUUAGCCC
-..........((.(((.(((((.(((.....))).)))))))).-.........(((((((.......----....)))......(((((.....-------))))).))))...)).. ( -27.20)
>DroSim_CAF1 5638 111 + 1
-ACCCACACAUGCAUGCAGGCUUUCGCUAUCCGUGUGAGCCGCAA-ACAACAAAUAAGCCGCUAUAAAAAACAAAACGCGUAUUUUGGCGGCCCCU-------CCGCCCACUUUUAGCCC
-..........((.(((.(((((.(((.....))).)))))))).-...........(((((((..(((.((.......)).))))))))))....-------..))............. ( -25.70)
>DroEre_CAF1 11775 104 + 1
-ACACACACAUUCAAGCGGGCUUUCGCCAUCUGUGUGAGCCGCAA-ACAACAAAUAAGCCGCUAUGUG-----AAGCGCGUAUUUUGGCGGCCCC--------CCGCCCACUU-UCCCCC
-............(((.((((..(((((....).))))(((((..-....((((...((((((.....-----.)))).))..)))))))))...--------..)))).)))-...... ( -27.70)
>DroYak_CAF1 5752 112 + 1
-ACCCACACAUUCACGCAGGCUUUUGCCAUCUGUGUGAGCCGCAA-ACAACAAAUAAGCCGCCAUAAA-----AAACGCGUAUUUUGGCGGCCCCUUCGCCCGCCGCCCACUU-UCGCCC
-..........((((((((((....)))...)))))))((.((..-...........)).))......-----....(((......((((((..........)))))).....-.))).. ( -29.82)
>DroAna_CAF1 10681 101 + 1
CACUCAUACAUUCAUACAA------AACAUCUGUGUGAGCCGCAAAACAACAAAUAAGCCGCUUUUCUU----UUUUUUUUUUUUUGGCGGCCCA--------CUCUUUACUUUUU-ACA
..((((((((.........------......))))))))..................((((((......----.............))))))...--------.............-... ( -16.77)
>consensus
_ACCCACACAUGCAUGCAGGCUUUCGCCAUCCGUGUGAGCCGCAA_ACAACAAAUAAGCCGCUAUAAAA____AAACGCGUAUUUUGGCGGCCCCU_______CCGCCCACUUUUAGCCC
..................(((((.(((.....))).)))))................(((((((.....................)))))))............................ (-16.13 = -16.80 +   0.67)

alignment

secondary structure

dotplot

Window 4

Location	1,561,148 – 1,561,258
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-35.20
Consensus MFE	-21.48
Energy contribution	-21.54
Covariance contribution	0.06
Combinations/Pair	1.30
Mean z-score	-1.48
Structure conservation index	0.61
SVM decision value	0.20
SVM RNA-class probability	0.630894
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1561148 110 - 23771897
GGGGAAAAAGUGGGCGG-------AGGGACCGCCAAAAUACGCGUUUU-UUUCUUAUAGCGGCUUAUUUGUUGU-UUGCGGCUCACACGGAUAGUAAAAGCCUGUAUGCAUGUGUGGGU-
(..(((((.((((((((-------.....)))))......))).))))-)..)....((((((......)))))-)....(((((((((.((((.......)))).....)))))))))- ( -31.30)
>DroSec_CAF1 5585 107 - 1
GGGCUAAAAGCGGGCGG-------AGGGGCCGCCAAAAUACGCGUUU----UUUUAUAGCGGCUUAUUUGUUGU-UUGCGGCUCACACGGAUAGCGAAAGCCUGCAUGCAUGUGUGGGU-
.......((((.(((((-------.....)))))......(((....----.......))))))).((((((((-(((.(.....).))))))))))).(((..(((....)))..)))- ( -35.70)
>DroSim_CAF1 5638 111 - 1
GGGCUAAAAGUGGGCGG-------AGGGGCCGCCAAAAUACGCGUUUUGUUUUUUAUAGCGGCUUAUUUGUUGU-UUGCGGCUCACACGGAUAGCGAAAGCCUGCAUGCAUGUGUGGGU-
..((((...(((.....-------..(((((((((((((....))))))........((((((......)))))-).))))))).)))...))))....(((..(((....)))..)))- ( -34.70)
>DroEre_CAF1 11775 104 - 1
GGGGGA-AAGUGGGCGG--------GGGGCCGCCAAAAUACGCGCUU-----CACAUAGCGGCUUAUUUGUUGU-UUGCGGCUCACACAGAUGGCGAAAGCCCGCUUGAAUGUGUGUGU-
......-.....(((((--------....)))))...((((((((((-----((...((((((((..((((..(-(((.(.....).))))..))))))).))))))))).))))))))- ( -40.50)
>DroYak_CAF1 5752 112 - 1
GGGCGA-AAGUGGGCGGCGGGCGAAGGGGCCGCCAAAAUACGCGUUU-----UUUAUGGCGGCUUAUUUGUUGU-UUGCGGCUCACACAGAUGGCAAAAGCCUGCGUGAAUGUGUGGGU-
..((..-..((((((.((((((((..(((((((((.((.........-----.)).))))))))).....))))-)))).)))))).(....)))....(((..((......))..)))- ( -43.60)
>DroAna_CAF1 10681 101 - 1
UGU-AAAAAGUAAAGAG--------UGGGCCGCCAAAAAAAAAAAAA----AAGAAAAGCGGCUUAUUUGUUGUUUUGCGGCUCACACAGAUGUU------UUGUAUGAAUGUAUGAGUG
.((-((((......(((--------((((((((..............----.......)))))))))))....)))))).(((((.(((..(((.------....)))..))).))))). ( -25.40)
>consensus
GGGCAAAAAGUGGGCGG_______AGGGGCCGCCAAAAUACGCGUUU____UUUUAUAGCGGCUUAUUUGUUGU_UUGCGGCUCACACAGAUAGCGAAAGCCUGCAUGAAUGUGUGGGU_
.............((((.........(((((((.........................)))))))..........)))).(((((((((....(((......))).....))))))))). (-21.48 = -21.54 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:31 2006