Locus 8482

Sequence ID	X_DroMel_CAF1
Location	21,046,386 – 21,046,571
Length	185
Max. P	0.975889

overview

Window 3

Location	21,046,386 – 21,046,492
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.43
Mean single sequence MFE	-29.30
Consensus MFE	-23.92
Energy contribution	-24.80
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-1.54
Structure conservation index	0.82
SVM decision value	0.35
SVM RNA-class probability	0.699886
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21046386 106 - 22224390
GACAUUAUCAACAAGACAAAAAAGCCAGCACAACACCGCUUGGCCCAAAAGUGUUUGUCAUCCAUCCGCCUUUGUCUUCGGUG--------------ACCGGGUGAUAAAUCUGCAUUAA
.......................((((((........)).))))......(((((((((((((...((((.........))))--------------...)))))))))))..))..... ( -24.50)
>DroSec_CAF1 16771 102 - 1
GACACUAUCAACAAGACGAAAAGGCCAGCACAGCACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCGGUG--------------ACCGGGUGAUAAAUCUGCAUUAA
((((((.((........))...(((((((........)).)))))....))))))((((((----(((.....(((......)--------------)))))))))))............ ( -28.20)
>DroSim_CAF1 17294 102 - 1
GACAUUAUCAACAAGACAAAAAGGCCAGCACAGCACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCGGUG--------------ACCGGGUGAUAAAUCUGCAUUAA
......................(((((((........)).))))).....(((((((((((----(((.....(((......)--------------))))))))))))))..))..... ( -27.20)
>DroEre_CAF1 17490 99 - 1
GACAUUAUCAACAAGACAAAGAGGCCAGCUU---ACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCGGUG--------------ACCGGGUGAUAAAUCUGCAUUAA
....................(.(((((((..---...)).))))))....(((((((((((----(((.....(((......)--------------))))))))))))))..))..... ( -27.50)
>DroYak_CAF1 19282 113 - 1
GGCAUUAUCAACAAGACAAAGAAGCCAGCUC---ACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCGGUGACCGGUGACCGGUGACCGGGUGAUAAAUCUGCAUUAA
.(((((((((.((((((((((..((((((..---...)).)))).((((....))))....----....)))))))))((((.(((((...))))).))))).))))))...)))..... ( -39.10)
>consensus
GACAUUAUCAACAAGACAAAAAGGCCAGCACA_CACCGCUUGGCCCAAAAGUGUUUGUCAU____CCGCCUUUGUCUUCGGUG______________ACCGGGUGAUAAAUCUGCAUUAA
((((..........((((....(((((((........)).)))))......))))))))........((.((((((((((((.((((.....)))).)))))).))))))...))..... (-23.92 = -24.80 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	21,046,412 – 21,046,531
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.49
Mean single sequence MFE	-33.86
Consensus MFE	-29.26
Energy contribution	-29.86
Covariance contribution	0.60
Combinations/Pair	1.09
Mean z-score	-1.88
Structure conservation index	0.86
SVM decision value	1.76
SVM RNA-class probability	0.975889
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21046412 119 + 22224390
CGAAGACAAAGGCGGAUGGAUGACAAACACUUUUGGGCCAAGCGGUGUUGUGCUGGCUUUUUUGUCUUGUUGAUAAUGUCAACAAGUUUGAGGAUAAUUCCCUCCACAGA-AAAGUUAAA
......((((((.(..((.....))..).))))))((((((......))).)))((((((((((((((((((((...)))))))))...((((.......)))).)))))-))))))... ( -33.50)
>DroSec_CAF1 16797 115 + 1
CGAAGACAAAGGCGG----AUGACAAACACUUUUGGGCCAAGCGGUGCUGUGCUGGCCUUUUCGUCUUGUUGAUAGUGUCAACAAGUUUGGGGAUAAUUCCCUGCACAGA-AAAGUUAAA
((((((((((((.(.----........).))))))(((((.(((......)))))))))))))).(((((((((...)))))))))...(((((....))))).......-......... ( -35.40)
>DroSim_CAF1 17320 115 + 1
CGAAGACAAAGGCGG----AUGACAAACACUUUUGGGCCAAGCGGUGCUGUGCUGGCCUUUUUGUCUUGUUGAUAAUGUCAACAAGUUUGGGGAUAAUUCCCUGCACAGA-AAAGUUAAA
......((((((.(.----........).))))))(((((.(((......))))))))((((((((((((((((...)))))))))...(((((....)))))..)))))-))....... ( -35.40)
>DroEre_CAF1 17516 112 + 1
CGAAGACAAAGGCGG----AUGACAAACACUUUUGGGCCAAGCGGU---AAGCUGGCCUCUUUGUCUUGUUGAUAAUGUCAACAAGUUUAGGGAUAAUUCCCUGCACAGA-AAAGUAAAA
..((((((((((...----....((((....))))(((((.((...---..)))))))))))))))))((((((...))))))..((.((((((....)))))).))...-......... ( -37.60)
>DroYak_CAF1 19322 113 + 1
CGAAGACAAAGGCGG----AUGACAAACACUUUUGGGCCAAGCGGU---GAGCUGGCUUCUUUGUCUUGUUGAUAAUGCCAACCAGUUUAGGGCUAAUUCCCCGCACAAAAAAAGUCAAA
....(((...(((..----....((((....)))).)))..(((((---(((((((.....(((((.....)))))......))))))))(((.....))))))).........)))... ( -27.40)
>consensus
CGAAGACAAAGGCGG____AUGACAAACACUUUUGGGCCAAGCGGUG_UGUGCUGGCCUUUUUGUCUUGUUGAUAAUGUCAACAAGUUUGGGGAUAAUUCCCUGCACAGA_AAAGUUAAA
..((((((((((...........((((....))))(((((.((........)))))))))))))))))((((((...))))))..((.((((((....)))))).))............. (-29.26 = -29.86 +   0.60)

alignment

secondary structure

dotplot

Window 5

Location	21,046,412 – 21,046,531
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.49
Mean single sequence MFE	-28.62
Consensus MFE	-23.64
Energy contribution	-23.56
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-1.56
Structure conservation index	0.83
SVM decision value	0.60
SVM RNA-class probability	0.795100
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21046412 119 - 22224390
UUUAACUUU-UCUGUGGAGGGAAUUAUCCUCAAACUUGUUGACAUUAUCAACAAGACAAAAAAGCCAGCACAACACCGCUUGGCCCAAAAGUGUUUGUCAUCCAUCCGCCUUUGUCUUCG
......(((-(.(((.(((((.....)))))...((((((((.....))))))))))).))))((((((........)).)))).((((.(((..((.....))..))).))))...... ( -28.40)
>DroSec_CAF1 16797 115 - 1
UUUAACUUU-UCUGUGCAGGGAAUUAUCCCCAAACUUGUUGACACUAUCAACAAGACGAAAAGGCCAGCACAGCACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCG
.....((((-((......((((....))))....((((((((.....))))))))..))))))((((((........)).)))).((((.(((........----.))).))))...... ( -28.80)
>DroSim_CAF1 17320 115 - 1
UUUAACUUU-UCUGUGCAGGGAAUUAUCCCCAAACUUGUUGACAUUAUCAACAAGACAAAAAGGCCAGCACAGCACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCG
....(((((-(.(((...((((....))))....((((((((.....)))))))))))....(((((((........)).))))).)))))).........----............... ( -27.70)
>DroEre_CAF1 17516 112 - 1
UUUUACUUU-UCUGUGCAGGGAAUUAUCCCUAAACUUGUUGACAUUAUCAACAAGACAAAGAGGCCAGCUU---ACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCG
.........-...((..(((((....)))))..))(((((((.....)))))))(((((((.(((((((..---...)).)))))((((....))))....----....))))))).... ( -31.90)
>DroYak_CAF1 19322 113 - 1
UUUGACUUUUUUUGUGCGGGGAAUUAGCCCUAAACUGGUUGGCAUUAUCAACAAGACAAAGAAGCCAGCUC---ACCGCUUGGCCCAAAAGUGUUUGUCAU----CCGCCUUUGUCUUCG
.............((..((((......))))..))..(((((.....)))))(((((((((..((((((..---...)).)))).((((....))))....----....))))))))).. ( -26.30)
>consensus
UUUAACUUU_UCUGUGCAGGGAAUUAUCCCCAAACUUGUUGACAUUAUCAACAAGACAAAAAGGCCAGCACA_CACCGCUUGGCCCAAAAGUGUUUGUCAU____CCGCCUUUGUCUUCG
.............((...(((......)))...))..(((((.....)))))((((((((..(((((((........)).)))))((((....)))).............)))))))).. (-23.64 = -23.56 +  -0.08)

alignment

secondary structure

dotplot

Window 6

Location	21,046,452 – 21,046,571
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.35
Mean single sequence MFE	-30.98
Consensus MFE	-14.28
Energy contribution	-15.84
Covariance contribution	1.56
Combinations/Pair	1.07
Mean z-score	-2.41
Structure conservation index	0.46
SVM decision value	0.22
SVM RNA-class probability	0.637903
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21046452 119 + 22224390
AGCGGUGUUGUGCUGGCUUUUUUGUCUUGUUGAUAAUGUCAACAAGUUUGAGGAUAAUUCCCUCCACAGA-AAAGUUAAAUCACUACACACGCUUUCGUUCUGUAAGUGAAGUGAAUAAU
((((((((.(((.(((((((((((((((((((((...)))))))))...((((.......)))).)))))-)))))))...))).)))).))))(((((((.......))).)))).... ( -38.40)
>DroSec_CAF1 16833 109 + 1
AGCGGUGCUGUGCUGGCCUUUUCGUCUUGUUGAUAGUGUCAACAAGUUUGGGGAUAAUUCCCUGCACAGA-AAAGUUAAAUC-------ACGCUUACAAUCUGUAAAAGAA---CAUAUU
((((...((((((............(((((((((...)))))))))...(((((....))))))))))).-...(......)-------.)))).....(((.....))).---...... ( -29.00)
>DroSim_CAF1 17356 109 + 1
AGCGGUGCUGUGCUGGCCUUUUUGUCUUGUUGAUAAUGUCAACAAGUUUGGGGAUAAUUCCCUGCACAGA-AAAGUUAAAUC-------ACGCUUACAAUCUGUAAGUGAA---CAUAUU
(((....((((((............(((((((((...)))))))))...(((((....))))))))))).-...))).....-------.(((((((.....)))))))..---...... ( -35.50)
>DroEre_CAF1 17552 111 + 1
AGCGGU---AAGCUGGCCUCUUUGUCUUGUUGAUAAUGUCAACAAGUUUAGGGAUAAUUCCCUGCACAGA-AAAGUAAAAUCACUAC--ACGGUUUCAUUCUGCAAAUGAA---AAUAUU
.((((.---((((((...(((.((((((((((((...)))))))))...(((((....)))))))).)))-...(((.......)))--.))))))....)))).......---...... ( -28.80)
>DroYak_CAF1 19358 112 + 1
AGCGGU---GAGCUGGCUUCUUUGUCUUGUUGAUAAUGCCAACCAGUUUAGGGCUAAUUCCCCGCACAAAAAAAGUCAAAUCACUAG--ACGGUUUCAUUUUGAAAAUGAU---AAUAUU
.(((((---(((((((.....(((((.....)))))......))))))))(((.....))))))).........(((.........)--))....(((((.....))))).---...... ( -23.20)
>consensus
AGCGGUG_UGUGCUGGCCUUUUUGUCUUGUUGAUAAUGUCAACAAGUUUGGGGAUAAUUCCCUGCACAGA_AAAGUUAAAUCACUA___ACGCUUUCAUUCUGUAAAUGAA___AAUAUU
..((((.....))))((........(((((((((...)))))))))...(((((....))))))).((((.(((((...............)))))...))))................. (-14.28 = -15.84 +   1.56)

alignment

secondary structure

dotplot

Window 7

Location	21,046,452 – 21,046,571
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.35
Mean single sequence MFE	-26.92
Consensus MFE	-15.54
Energy contribution	-14.78
Covariance contribution	-0.76
Combinations/Pair	1.24
Mean z-score	-2.08
Structure conservation index	0.58
SVM decision value	0.29
SVM RNA-class probability	0.668691
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21046452 119 - 22224390
AUUAUUCACUUCACUUACAGAACGAAAGCGUGUGUAGUGAUUUAACUUU-UCUGUGGAGGGAAUUAUCCUCAAACUUGUUGACAUUAUCAACAAGACAAAAAAGCCAGCACAACACCGCU
..........................((((.((((.(((......((((-(.(((.(((((.....)))))...((((((((.....))))))))))).)))))....))).)))))))) ( -31.90)
>DroSec_CAF1 16833 109 - 1
AAUAUG---UUCUUUUACAGAUUGUAAGCGU-------GAUUUAACUUU-UCUGUGCAGGGAAUUAUCCCCAAACUUGUUGACACUAUCAACAAGACGAAAAGGCCAGCACAGCACCGCU
......---.....((((.....))))((((-------(..........-.((((((.((((....))))....((((((((.....))))))))............)))))))).))). ( -26.50)
>DroSim_CAF1 17356 109 - 1
AAUAUG---UUCACUUACAGAUUGUAAGCGU-------GAUUUAACUUU-UCUGUGCAGGGAAUUAUCCCCAAACUUGUUGACAUUAUCAACAAGACAAAAAGGCCAGCACAGCACCGCU
......---.((((((((.....))))..))-------)).........-.((((((.((((....))))....((((((((.....))))))))............))))))....... ( -27.50)
>DroEre_CAF1 17552 111 - 1
AAUAUU---UUCAUUUGCAGAAUGAAACCGU--GUAGUGAUUUUACUUU-UCUGUGCAGGGAAUUAUCCCUAAACUUGUUGACAUUAUCAACAAGACAAAGAGGCCAGCUU---ACCGCU
.....(---(((((((...))))))))....--(..((((.((..((((-(.(((..(((((....)))))...((((((((.....))))))))))).)))))..)).))---))..). ( -26.50)
>DroYak_CAF1 19358 112 - 1
AAUAUU---AUCAUUUUCAAAAUGAAACCGU--CUAGUGAUUUGACUUUUUUUGUGCGGGGAAUUAGCCCUAAACUGGUUGGCAUUAUCAACAAGACAAAGAAGCCAGCUC---ACCGCU
......---.(((((.....)))))......--...((((.(((.(((((((.((..((((......))))...((.(((((.....))))).))))))))))).))).))---)).... ( -22.20)
>consensus
AAUAUU___UUCAUUUACAGAAUGAAAGCGU___UAGUGAUUUAACUUU_UCUGUGCAGGGAAUUAUCCCCAAACUUGUUGACAUUAUCAACAAGACAAAAAGGCCAGCACA_CACCGCU
.............................................((((...(((...(((......)))....((((((((.....)))))))))))..))))..(((........))) (-15.54 = -14.78 +  -0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:25 2006