Locus 1729

Sequence ID	3L_DroMel_CAF1
Location	5,007,104 – 5,007,252
Length	148
Max. P	0.917863

overview

Window 5

Location	5,007,104 – 5,007,212
Length	108
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	82.10
Mean single sequence MFE	-36.45
Consensus MFE	-23.44
Energy contribution	-26.05
Covariance contribution	2.61
Combinations/Pair	1.12
Mean z-score	-1.84
Structure conservation index	0.64
SVM decision value	0.15
SVM RNA-class probability	0.609597
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5007104 108 + 23771897
GCAUAAAUUUCCGUUUCCGGCGACUGCAAAUGAGCCACAAGCGGCCACAGUCGCCCAGUUUGGGGUCAG--------UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUU
............((((((((((((((....((.(((......))))))))))((((......))))..)--------)))))).))....((((((((......)))))))).... ( -40.10)
>DroSec_CAF1 227589 108 + 1
GCAUAAAUUUCCGUUUCCGGCGACUGCAAAUGAGCCACAAGCGGCCACAGUCGCCCAGUUUGGAGUCAG--------UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUU
........(((((.((((((((((((....((.(((......)))))))))))))......))))....--------.))))).......((((((((......)))))))).... ( -38.50)
>DroSim_CAF1 247621 86 + 1
G-AUAAAUUUCG--UUCCGGCAACUGCA-AUGAU-CAC-AGCGG-CACAGUC--CCAGUUGGGU---AG--------C-CGAGCA--UUAAGCCA--ACUA---UUGUGGCCU--U
.-.........(--(((.(((..((((.-.....-...-.))))-......(--((....))).---.)--------)-))))).--....((((--.(..---..)))))..--. ( -21.00)
>DroEre_CAF1 230797 108 + 1
GCAUAAAUUUCCGUUUCCGGCGACUGCAAAUGAGCCACAAGCGGCCACAGUCGCCCAGUUUGGGGUCAG--------UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUU
............((((((((((((((....((.(((......))))))))))((((......))))..)--------)))))).))....((((((((......)))))))).... ( -40.10)
>DroYak_CAF1 236205 108 + 1
GCAUAAAUUUCCGUUUCCGGCGACUGCAAAUGAGCCACAAGCGGCCACAGUCGCCCAGUUUGGGGUCAG--------UCGGAGCACUUUAGGCCGCAGCUAAAUUUGUGGCCCUUU
............((((((((((((((....((.(((......))))))))))((((......))))..)--------)))))).))....((((((((......)))))))).... ( -39.70)
>DroAna_CAF1 238169 109 + 1
GCAUAAAUUUCCGUUUCCGGCGACUGCAAAUGAGCCACAAGCGGCC-------CCCUGUUUGGGGUCGGCUAGCUAGUAGCUACUCUCCGGGCCGCAACUAAAUUUGUGGCCCUUU
(((....((.(((....))).)).))).....(((.((.(((((((-------((((....))))..)))).))).)).))).......(((((((((......)))))))))... ( -39.30)
>consensus
GCAUAAAUUUCCGUUUCCGGCGACUGCAAAUGAGCCACAAGCGGCCACAGUCGCCCAGUUUGGGGUCAG________UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUU
........(((((.....((((((((....((.(((......))))))))))))).....))))).........................((((((((......)))))))).... (-23.44 = -26.05 +   2.61)

alignment

secondary structure

dotplot

Window 6

Location	5,007,104 – 5,007,212
Length	108
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	82.10
Mean single sequence MFE	-40.48
Consensus MFE	-28.87
Energy contribution	-31.07
Covariance contribution	2.20
Combinations/Pair	1.19
Mean z-score	-2.72
Structure conservation index	0.71
SVM decision value	0.97
SVM RNA-class probability	0.892165
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5007104 108 - 23771897
AAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA--------CUGACCCCAAACUGGGCGACUGUGGCCGCUUGUGGCUCAUUUGCAGUCGCCGGAAACGGAAAUUUAUGC
...((((((((........)))))))).((((..(((..--------..............((((((((((((((....))))).....)))))))))(....)))).)))).... ( -43.30)
>DroSec_CAF1 227589 108 - 1
AAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA--------CUGACUCCAAACUGGGCGACUGUGGCCGCUUGUGGCUCAUUUGCAGUCGCCGGAAACGGAAAUUUAUGC
...((((((((........)))))))).((((..(((..--------..............((((((((((((((....))))).....)))))))))(....)))).)))).... ( -43.30)
>DroSim_CAF1 247621 86 - 1
A--AGGCCACAA---UAGU--UGGCUUAA--UGCUCG-G--------CU---ACCCAACUGG--GACUGUG-CCGCU-GUG-AUCAU-UGCAGUUGCCGGAA--CGAAAUUUAU-C
.--((((((...---....--))))))..--...(((-.--------..---.(((....))--).(((.(-(.(((-(..-(...)-..)))).)))))..--))).......-. ( -24.40)
>DroEre_CAF1 230797 108 - 1
AAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA--------CUGACCCCAAACUGGGCGACUGUGGCCGCUUGUGGCUCAUUUGCAGUCGCCGGAAACGGAAAUUUAUGC
...((((((((........)))))))).((((..(((..--------..............((((((((((((((....))))).....)))))))))(....)))).)))).... ( -43.30)
>DroYak_CAF1 236205 108 - 1
AAAGGGCCACAAAUUUAGCUGCGGCCUAAAGUGCUCCGA--------CUGACCCCAAACUGGGCGACUGUGGCCGCUUGUGGCUCAUUUGCAGUCGCCGGAAACGGAAAUUUAUGC
...(((((((((........((((((...(((((((.(.--------.((....))..).)))).)))..)))))))))))))))....(((....(((....))).......))) ( -42.50)
>DroAna_CAF1 238169 109 - 1
AAAGGGCCACAAAUUUAGUUGCGGCCCGGAGAGUAGCUACUAGCUAGCCGACCCCAAACAGGG-------GGCCGCUUGUGGCUCAUUUGCAGUCGCCGGAAACGGAAAUUUAUGC
...(((((((((........(((((.(((....((((.....)))).))).((((.....)))-------)))))))))))))))....(((....(((....))).......))) ( -46.10)
>consensus
AAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA________CUGACCCCAAACUGGGCGACUGUGGCCGCUUGUGGCUCAUUUGCAGUCGCCGGAAACGGAAAUUUAUGC
...((((((((........)))))))).......(((........................((((((((((((((....))))).....)))))))))(....))))......... (-28.87 = -31.07 +   2.20)

alignment

secondary structure

dotplot

Window 7

Location	5,007,142 – 5,007,252
Length	110
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	70.22
Mean single sequence MFE	-34.27
Consensus MFE	-20.63
Energy contribution	-21.85
Covariance contribution	1.22
Combinations/Pair	1.11
Mean z-score	-1.18
Structure conservation index	0.60
SVM decision value	0.06
SVM RNA-class probability	0.561928
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5007142 110 + 23771897
AAGCGGCCACAGUCGCCCAGUUUGGGGUCAG--------UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUUCGCGGCACGCAUUGUAAUGCCGAGAGCACUGCAAACAAAU
..(((((....)))))...(((((.((((..--------((((.(((.....((((((((......)))))))).....(((...)))..)))....))))..).))).))))).... ( -37.10)
>DroSec_CAF1 227627 110 + 1
AAGCGGCCACAGUCGCCCAGUUUGGAGUCAG--------UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUUCGCGGCACGCAUUGUAAUGCCAAGAGCACUGCAAACAAAU
..((((((.((((.((((...(((....)))--------..)).)))))...((((((((......)))))))).....).))).))).(((((.(((.....))).)))))...... ( -35.50)
>DroSim_CAF1 247654 87 + 1
-AGCGG-CACAGUC--CCAGUUGGGU---AG--------C-CGAGCA--UUAAGCCA--ACUA---UUGUGGCCU--UCGCGCCC------UUGAUGCNNNNNNNNNNNNNNNNNNNN
-..(((-(.....(--((....))).---.)--------)-)).(((--(((((...--((..---..))(((..--....))))------))))))).................... ( -20.50)
>DroEre_CAF1 230835 110 + 1
AAGCGGCCACAGUCGCCCAGUUUGGGGUCAG--------UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUUCGCGGCACGCAUUGUAAUGCCAGGAGCACUGGAAACAUAU
..((((((......((((......))))..(--------(..(((.......((((((((......)))))))))))..))))).)))..(((....((((.....))))..)))... ( -36.61)
>DroYak_CAF1 236243 110 + 1
AAGCGGCCACAGUCGCCCAGUUUGGGGUCAG--------UCGGAGCACUUUAGGCCGCAGCUAAAUUUGUGGCCCUUUCGCGGCACGCAUUGUAAUGCCAAGAGCACUGUAAACAAAA
..(((((....)))))...(((((.((((.(--------((((((.......((((((((......))))))))..))).))))..((((....)))).....).))).))))).... ( -32.70)
>DroAna_CAF1 238207 97 + 1
AAGCGGCC-------CCCUGUUUGGGGUCGGCUAGCUAGUAGCUACUCUCCGGGCCGCAACUAAAUUUGUGGCCCUUUCGCGGCACGCAUUACAAUGCCGGCCG--------------
...(((((-------((......)))))))((((((.....))))......(((((((((......)))))))))....))(((..((((....))))..))).-------------- ( -43.20)
>consensus
AAGCGGCCACAGUCGCCCAGUUUGGGGUCAG________UCGGAGCACUUUAGGCCACAGCUAAAUUUGUGGCCCUUUCGCGGCACGCAUUGUAAUGCCAAGAGCACUG_AAACAAAU
..((((((.......(((.....)))..................((......((((((((......)))))))).....))))).))).............................. (-20.63 = -21.85 +   1.22)

alignment

secondary structure

dotplot

Window 8

Location	5,007,142 – 5,007,252
Length	110
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	70.22
Mean single sequence MFE	-36.15
Consensus MFE	-22.59
Energy contribution	-23.90
Covariance contribution	1.31
Combinations/Pair	1.21
Mean z-score	-1.53
Structure conservation index	0.62
SVM decision value	1.12
SVM RNA-class probability	0.917863
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5007142 110 - 23771897
AUUUGUUUGCAGUGCUCUCGGCAUUACAAUGCGUGCCGCGAAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA--------CUGACCCCAAACUGGGCGACUGUGGCCGCUU
......(((.(((((.....))))).))).(((.(((((....((((((((........))))))))..(((((((.(.--------.((....))..).)))).))))))))))).. ( -39.70)
>DroSec_CAF1 227627 110 - 1
AUUUGUUUGCAGUGCUCUUGGCAUUACAAUGCGUGCCGCGAAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA--------CUGACUCCAAACUGGGCGACUGUGGCCGCUU
......(((.(((((.....))))).))).(((.(((((....((((((((........))))))))..(((((((.(.--------.((....))..).)))).))))))))))).. ( -39.70)
>DroSim_CAF1 247654 87 - 1
NNNNNNNNNNNNNNNNNNNNGCAUCAA------GGGCGCGA--AGGCCACAA---UAGU--UGGCUUAA--UGCUCG-G--------CU---ACCCAACUGG--GACUGUG-CCGCU-
....................((.....------(((((...--((((((...---....--))))))..--)))))(-(--------(.---.(((....))--).....)-)))).- ( -22.90)
>DroEre_CAF1 230835 110 - 1
AUAUGUUUCCAGUGCUCCUGGCAUUACAAUGCGUGCCGCGAAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA--------CUGACCCCAAACUGGGCGACUGUGGCCGCUU
...(((..((((.....))))....)))..(((.(((((....((((((((........))))))))..(((((((.(.--------.((....))..).)))).))))))))))).. ( -38.60)
>DroYak_CAF1 236243 110 - 1
UUUUGUUUACAGUGCUCUUGGCAUUACAAUGCGUGCCGCGAAAGGGCCACAAAUUUAGCUGCGGCCUAAAGUGCUCCGA--------CUGACCCCAAACUGGGCGACUGUGGCCGCUU
..((((....(((((.....))))))))).(((.(((((....(((((.((........)).)))))..(((((((.(.--------.((....))..).)))).))))))))))).. ( -34.50)
>DroAna_CAF1 238207 97 - 1
--------------CGGCCGGCAUUGUAAUGCGUGCCGCGAAAGGGCCACAAAUUUAGUUGCGGCCCGGAGAGUAGCUACUAGCUAGCCGACCCCAAACAGGG-------GGCCGCUU
--------------.(((((((((........))))).(....)))))............(((((.(((....((((.....)))).))).((((.....)))-------)))))).. ( -41.50)
>consensus
AUUUGUUU_CAGUGCUCUUGGCAUUACAAUGCGUGCCGCGAAAGGGCCACAAAUUUAGCUGUGGCCUAAAGUGCUCCGA________CUGACCCCAAACUGGGCGACUGUGGCCGCUU
..............................(((.(((((....((((((((........)))))))).........................(((.....))).....)))))))).. (-22.59 = -23.90 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:44 2006