Locus 598

Sequence ID	X_DroMel_CAF1
Location	1,670,411 – 1,670,664
Length	253
Max. P	0.998696

overview

Window 6

Location	1,670,411 – 1,670,527
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.96
Mean single sequence MFE	-25.26
Consensus MFE	-24.28
Energy contribution	-24.32
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.63
Structure conservation index	0.96
SVM decision value	1.72
SVM RNA-class probability	0.974080
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1670411 116 - 22224390
UCGGUAUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGGGCCUCGUUUUUUGCCAGAGCUUACUGAACCCAACCCUU----
((((((..((((...(((((....))))).((((((....(((....((((....))))...)))....))))))..(((..........))).)))).))))))...........---- ( -24.30)
>DroSec_CAF1 4478 116 - 1
UCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGCCUCGUUUUUUGCCAGAGCUUACUGAACCCAACCCUU----
((((((..(((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))((((.((.....)).)).)).))))))...........---- ( -25.50)
>DroSim_CAF1 5330 116 - 1
UCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGCCUCGUUUUUUGCCAGAGCUUACUGAACCCAACCCUU----
((((((..(((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))((((.((.....)).)).)).))))))...........---- ( -25.50)
>DroEre_CAF1 8106 120 - 1
UCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGCCUCGUUUUUUGCCAGAGCUUACUGAACCCAACCCUUCAUC
((((((..(((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))((((.((.....)).)).)).))))))............... ( -25.50)
>DroYak_CAF1 5508 116 - 1
UCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGCCUCGUUUUUUGCCAGAGCUUACUGAACCCAACCCUU----
((((((..(((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))((((.((.....)).)).)).))))))...........---- ( -25.50)
>consensus
UCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGCCUCGUUUUUUGCCAGAGCUUACUGAACCCAACCCUU____
((((((..(((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))((((.((.....)).)).)).))))))............... (-24.28 = -24.32 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	1,670,447 – 1,670,567
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-37.08
Consensus MFE	-33.82
Energy contribution	-34.42
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.91
SVM decision value	3.19
SVM RNA-class probability	0.998696
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1670447 120 - 22224390
UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCGAAAGGUGUCGGUAUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGGGC
....(((((((((((((((......)))..((....)).))))))))).((((((((.(((((((((((.........))))))).(((....)))....)))).....))))))))))) ( -36.60)
>DroSec_CAF1 4514 120 - 1
UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCAAAAGGUGUCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGC
..(((((((((((((((((......)))))).....)))))))))))((((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))). ( -37.70)
>DroSim_CAF1 5366 120 - 1
UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCGAAAGGUGUCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGC
..(((((((((((((((((......)))))).....)))))))))))((((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))). ( -37.70)
>DroEre_CAF1 8146 118 - 1
U--UGCCGAUGCCGAUGGGCUUGGGUCCGUCCGAAAGGUGUCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGC
.--.((((((((((((((((....))))))).....)))))))))..((((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))). ( -40.80)
>DroYak_CAF1 5544 117 - 1
U--UGCCGAUGGC-AUGGGUUUGUGUCCGUCCGUAAGGUGUCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGC
.--.(((((((((-((......)))))...((....)).))))))..((((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))). ( -32.60)
>consensus
UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCGAAAGGUGUCGGUGUCGCUCAGAUUCACAGGAGUGAAACAAAUCCCUUUACUCAUAAUUCAUUAAUUUCUGUAUUUAGAUUUGAGCGC
....(((((((((((((((......)))))).....)))))))))..((((((((((.(((((((((((.........))))))).(((....)))....)))).....)))))))))). (-33.82 = -34.42 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	1,670,527 – 1,670,624
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.71
Mean single sequence MFE	-36.58
Consensus MFE	-27.90
Energy contribution	-28.18
Covariance contribution	0.28
Combinations/Pair	1.09
Mean z-score	-1.60
Structure conservation index	0.76
SVM decision value	0.14
SVM RNA-class probability	0.602403
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1670527 97 + 22224390
CACCUUUCGGACGGACACAAACCCAUCGGCAUCGGCAUGA-----GGACAA------------------CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAG
.......((.((((((((....((.(((((....)).)))-----))....------------------.......((((((.....)))))))))))))).)).((((....))))... ( -35.70)
>DroSec_CAF1 4594 97 + 1
CACCUUUUGGACGGACACAAACCCAUCGGCAUCGGCAUGA-----GGACAA------------------CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAG
..((....))((((((((....((.(((((....)).)))-----))....------------------.......((((((.....))))))))))))))....((((....))))... ( -35.30)
>DroSim_CAF1 5446 97 + 1
CACCUUUCGGACGGACACAAACCCAUCGGCAUCGGCAUGA-----GGACAA------------------CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAG
.......((.((((((((....((.(((((....)).)))-----))....------------------.......((((((.....)))))))))))))).)).((((....))))... ( -35.70)
>DroEre_CAF1 8226 113 + 1
CACCUUUCGGACGGACCCAAGCCCAUCGGCAUCGGCA--A-----CGACAACAGGACGAGCAGGACGGGCAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAG
..(((((((..(........(((....))).(((...--.-----))).....)..)))).)))..((((((((((((((((.....)))))).)))))...)))))............. ( -44.80)
>DroYak_CAF1 5624 114 + 1
CACCUUACGGACGGACACAAACCCAU-GCCAUCGGCA--ACCCAACGACAACG---AGAACAGGACGAGCAGGACGAACAGGACCAUUCUGAUGUGUCCGUGUGCCCACUUAAGUGGAAG
.......((.(((((((((...((.(-(((.(((...--.)....((....))---.......)).).))))).....(((((...))))).))))))))).)).((((....))))... ( -31.40)
>consensus
CACCUUUCGGACGGACACAAACCCAUCGGCAUCGGCAUGA_____GGACAA__________________CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAG
.......((.((((((((..........((....))........................................((((((.....)))))))))))))).)).((((....))))... (-27.90 = -28.18 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	1,670,527 – 1,670,624
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.71
Mean single sequence MFE	-40.56
Consensus MFE	-33.20
Energy contribution	-33.44
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.66
Structure conservation index	0.82
SVM decision value	0.35
SVM RNA-class probability	0.699764
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1670527 97 - 22224390
CUUCCACUUAAGUGGGCACACGGACACAGCAGGAUGGUCCUGCUCGUCCUG------------------UUGUCC-----UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCGAAAGGUG
..(((((....)))))...((((((((((((((.....)))))....((((------------------(((.(.-----((.....)).).)))))))..)))))))))((....)).. ( -39.20)
>DroSec_CAF1 4594 97 - 1
CUUCCACUUAAGUGGGCACACGGACACAGCAGGAUGGUCCUGCUCGUCCUG------------------UUGUCC-----UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCAAAAGGUG
....(((((...(((((((((((((((((((((((((......))))))))------------------))))((-----((..((....)).)).))))))))))..)))))..))))) ( -38.00)
>DroSim_CAF1 5446 97 - 1
CUUCCACUUAAGUGGGCACACGGACACAGCAGGAUGGUCCUGCUCGUCCUG------------------UUGUCC-----UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCGAAAGGUG
..(((((....)))))...((((((((((((((.....)))))....((((------------------(((.(.-----((.....)).).)))))))..)))))))))((....)).. ( -39.20)
>DroEre_CAF1 8226 113 - 1
CUUCCACUUAAGUGGGCACACGGACACAGCAGGAUGGUCCUGCUCGUCCUGCCCGUCCUGCUCGUCCUGUUGUCG-----U--UGCCGAUGCCGAUGGGCUUGGGUCCGUCCGAAAGGUG
..(((((....)))))...((((((...(((((((((......)))))))))(((....(((((((..(..((((-----.--...))))..)))))))).)))))))))((....)).. ( -46.30)
>DroYak_CAF1 5624 114 - 1
CUUCCACUUAAGUGGGCACACGGACACAUCAGAAUGGUCCUGUUCGUCCUGCUCGUCCUGUUCU---CGUUGUCGUUGGGU--UGCCGAUGGC-AUGGGUUUGUGUCCGUCCGUAAGGUG
..(((((....)))))...(((((((((.(((.((((......)))).)))...........((---(((.((((((((..--..))))))))-)))))..)))))))))((....)).. ( -40.10)
>consensus
CUUCCACUUAAGUGGGCACACGGACACAGCAGGAUGGUCCUGCUCGUCCUG__________________UUGUCC_____UCAUGCCGAUGCCGAUGGGUUUGUGUCCGUCCGAAAGGUG
..(((((....)))))...(((((((((.((((((((......)))))))).................................(((.((....)).))).)))))))))((....)).. (-33.20 = -33.44 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	1,670,567 – 1,670,664
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.73
Mean single sequence MFE	-34.16
Consensus MFE	-27.88
Energy contribution	-28.32
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.82
SVM decision value	0.58
SVM RNA-class probability	0.788763
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1670567 97 + 22224390
-----GGACAA------------------CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAGACGACAUAAAUAGUAACCAUACCUGAACGUGUGGAGGUUU
-----(.(((.------------------..(((((((((((.....)))))).))))).))).)((((....))))...................((((((......))))))...... ( -33.40)
>DroSec_CAF1 4634 97 + 1
-----GGACAA------------------CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAGACGACAUAAAUAGUAACCAUACCUGAGCGUGUGGAGGUUU
-----(.(((.------------------..(((((((((((.....)))))).))))).))).)((((....))))...................((((((......))))))...... ( -33.40)
>DroSim_CAF1 5486 97 + 1
-----GGACAA------------------CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAGACGACAUAAAUAGUAACCAUACCUGAGCGUGUGGAGGUUU
-----(.(((.------------------..(((((((((((.....)))))).))))).))).)((((....))))...................((((((......))))))...... ( -33.40)
>DroEre_CAF1 8264 115 + 1
-----CGACAACAGGACGAGCAGGACGGGCAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAGACGACAUAAAUAGUAAGCAUACCUGAGCGUGUGGAGGUUU
-----.(((....(.(((..((((..((((((((((((((((.....)))))).)))))...)))))(((...(((........)))....))).......))))..))).)....))). ( -41.80)
>DroYak_CAF1 5661 117 + 1
CCCAACGACAACG---AGAACAGGACGAGCAGGACGAACAGGACCAUUCUGAUGUGUCCGUGUGCCCACUUAAGUGGAAGACGACAUAAAUAGUAAGCAUACCUGAGCGUGUGGAGAUUU
.((((((.(....---......(((((..(((((.(........).)))))...)))))((((((((((....))))...((..........))..))))))....)))).)))...... ( -28.80)
>consensus
_____GGACAA__________________CAGGACGAGCAGGACCAUCCUGCUGUGUCCGUGUGCCCACUUAAGUGGAAGACGACAUAAAUAGUAACCAUACCUGAGCGUGUGGAGGUUU
.......((......................(((((((((((.....)))))).)))))((.(..((((....)))).).))..........))..((((((......))))))...... (-27.88 = -28.32 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:06 2006