Locus 6115

Sequence ID	3L_DroMel_CAF1
Location	16,211,772 – 16,212,081
Length	309
Max. P	0.992798

overview

Window 2

Location	16,211,772 – 16,211,892
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-31.59
Consensus MFE	-26.40
Energy contribution	-27.80
Covariance contribution	1.40
Combinations/Pair	1.07
Mean z-score	-1.75
Structure conservation index	0.84
SVM decision value	1.16
SVM RNA-class probability	0.924880
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16211772 120 + 23771897
CCGACACACAGGCUGCAUAUCUAAUGAGCAUCGGAUACAGAUUCAUCUCGAGUGGCACUUGGCCCAAUAUUGCACAGCGAUUGCCAUUCUCCCACUUGAUUGUUCUCACGUAGACCGAUA
...........(((.(((.....))))))(((((.((((((..((..((((((((....((((.....(((((...))))).)))).....)))))))).)).)))...)))..))))). ( -31.20)
>DroSec_CAF1 30475 120 + 1
CCGACACACAGGCUGCAUUUCUAAUGAGCAUCGGAUACACAUCCAUCUCGAGUGGCACUUGGCCCAAUAUUGCACAGCGAUUGCCAUUCUGCCACUUGAUUGUUCUCACGUAGACCGAUA
..........((((((.........(((((..((((....))))...((((((((((..((((.....(((((...))))).))))...)))))))))).)))))....)))).)).... ( -36.42)
>DroSim_CAF1 32358 120 + 1
CCGACACACAGGCUGCAUAUCUAAUGAGCAUCGGAUACAGAUCCAUCUCGAGUGGCACUUGGCCCAAUAUUGCACAGCGAUUGCCAUUCUGCCACUUGAUUGUUCUCACGUAGACCGAUA
..........((((((.........(((((..((((....))))...((((((((((..((((.....(((((...))))).))))...)))))))))).)))))....)))).)).... ( -36.72)
>DroEre_CAF1 30040 120 + 1
CCAACACACAGGCUGCAUAUCUAAUGAGAAUCGGAUACAGAUCCAUCUCGAGUGGCACUUCACCCAAUACUGCACAGCAAUUGCCAAUCUGCCUCUUGAUUGUUCCCACGUACACCGAUA
..........((..(((.(((....((((...((((....)))).))))(((.((((.......((((..(((...)))))))......)))).)))))))))..))............. ( -22.12)
>DroYak_CAF1 67119 120 + 1
CCGACACACAGGCUGCAUAGCUAAUGAGAAUCGGAUACAGAUCCAUCUCGAGUGGCACUUCACCCAAUAUUGCACAGCAAUUGCCUAUCUGCCACUUGAUUGUUCUCACGUAGACCGAUA
..........((((((........(((((((.((((....))))...((((((((((...........(((((...)))))........))))))))))..))))))).)))).)).... ( -31.51)
>consensus
CCGACACACAGGCUGCAUAUCUAAUGAGCAUCGGAUACAGAUCCAUCUCGAGUGGCACUUGGCCCAAUAUUGCACAGCGAUUGCCAUUCUGCCACUUGAUUGUUCUCACGUAGACCGAUA
..........((((((................((((....))))...((((((((((..((((.....(((((...))))).))))...))))))))))..........)))).)).... (-26.40 = -27.80 +   1.40)

alignment

secondary structure

dotplot

Window 3

Location	16,211,852 – 16,211,972
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.64
Mean single sequence MFE	-34.58
Consensus MFE	-28.84
Energy contribution	-29.08
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.59
Structure conservation index	0.83
SVM decision value	0.81
SVM RNA-class probability	0.855308
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16211852 120 + 23771897
UUGCCAUUCUCCCACUUGAUUGUUCUCACGUAGACCGAUAUUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAGCGAUUUAAUUCGAACCA
.....................((((.(((...((((.(....).))))...))).(((((((.....(((((....))))).......((((((....))))))...))))))))))).. ( -32.70)
>DroSec_CAF1 30555 120 + 1
UUGCCAUUCUGCCACUUGAUUGUUCUCACGUAGACCGAUAUUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAACGAUUUAAUUCGAACCA
..((....((((((((((...((((.(((...((((.(....).))))...))).))))...)....(((((....))))).....))).))))))..))...(((......)))..... ( -34.30)
>DroSim_CAF1 32438 120 + 1
UUGCCAUUCUGCCACUUGAUUGUUCUCACGUAGACCGAUAUUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAACGAUUUAAUUCGAACCA
..((....((((((((((...((((.(((...((((.(....).))))...))).))))...)....(((((....))))).....))).))))))..))...(((......)))..... ( -34.30)
>DroEre_CAF1 30120 116 + 1
UUGCCAAUCUGCCUCUUGAUUGUUCCCACGUACACCGAUAUUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAU----UUGGCAGUAGCCAAAGAUUUGAUUCGGGCCA
....(((((........)))))..(((..(((((((.(....).)))....))))(((((((.((...((((..((((((.....----.))))))..))))...))))))))))))... ( -34.70)
>DroYak_CAF1 67199 116 + 1
UUGCCUAUCUGCCACUUGAUUGUUCUCACGUAGACCGAUAUUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGCGCCUGCCGCAUAU----UUGGCAGUAGCGAAAGAUUUAAUGCCAACCA
..((..((((((((((((...((((.(((...((((.(....).))))...))).)))).....))))))))((((((((.....----.))))))..))...)))).....))...... ( -36.90)
>consensus
UUGCCAUUCUGCCACUUGAUUGUUCUCACGUAGACCGAUAUUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAACGAUUUAAUUCGAACCA
..((....(((((...((...((((.(((...((((.(....).))))...))).))))...))...(((((....)))))..........)))))..)).................... (-28.84 = -29.08 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	16,211,892 – 16,212,010
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.23
Mean single sequence MFE	-37.36
Consensus MFE	-31.44
Energy contribution	-31.60
Covariance contribution	0.16
Combinations/Pair	1.13
Mean z-score	-2.24
Structure conservation index	0.84
SVM decision value	2.35
SVM RNA-class probability	0.992798
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16211892 118 + 23771897
UUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAGCGAUUUAAUUCGAACCAAAAAUAGCAGCUCGUGUUGCUCAAGGACCGA--AGGACUC
(((.((((...((.((((((((.....(((((....))))).......((((((....))))))...)))))))).)).......((((((....))))))....)))).)--))..... ( -38.40)
>DroSec_CAF1 30595 118 + 1
UUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAACGAUUUAAUUCGAACCAAAAAUAGCAGCUCGUGUUGCCCAAGGACCGA--AGGACUC
(((.((((...((.((((((((.....(((((....))))).......((((((....))))))...)))))))).))........(((((....))))).....)))).)--))..... ( -37.50)
>DroSim_CAF1 32478 118 + 1
UUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAACGAUUUAAUUCGAACCAAAAAUAGCAGCUCGUGUUGCCCAAGGAGCGA--AGGACUC
(((((......((.((((((((.....(((((....))))).......((((((....))))))...)))))))).))........(((((....))))))))))((((..--..).))) ( -36.50)
>DroEre_CAF1 30160 114 + 1
UUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAU----UUGGCAGUAGCCAAAGAUUUGAUUCGGGCCAAAAAUGGCAGCUCGUGUUGCCCAAGGACCAA--AGGACUC
....((((...((.((((((((.((...((((..((((((.....----.))))))..))))...)))))))))).)).......((((((....))))))....))))..--....... ( -41.50)
>DroYak_CAF1 67239 116 + 1
UUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGCGCCUGCCGCAUAU----UUGGCAGUAGCGAAAGAUUUAAUGCCAACCAAAAAUAGCAGCUCGUGUUGUCCAAGGACCAAAAAGGACUC
...(((((..((..(((.((.((....(((((....)))))....----((((((....(....)......)))))).........)))).)))..))(((....))).......))))) ( -32.90)
>consensus
UUUGGGUCAAAGUGCGAAUUAGCAUAAGUGGUGCCUGCCGCAUAUAAAGUUGGCAGUAGCCAACGAUUUAAUUCGAACCAAAAAUAGCAGCUCGUGUUGCCCAAGGACCGA__AGGACUC
....((((...((.((((((((.((...((((..((((((..........))))))..))))...)))))))))).))........(((((....))))).....))))........... (-31.44 = -31.60 +   0.16)

alignment

secondary structure

dotplot

Window 5

Location	16,211,972 – 16,212,081
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.82
Mean single sequence MFE	-29.10
Consensus MFE	-21.91
Energy contribution	-22.27
Covariance contribution	0.36
Combinations/Pair	1.12
Mean z-score	-1.92
Structure conservation index	0.75
SVM decision value	0.59
SVM RNA-class probability	0.792217
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16211972 109 - 23771897
UAAUGGCACUCGUCCUGUAAUUUCAUUUUUCAUGUAAGAC-------CAGUGGGG--AGAAAAUUUAAUGAAAUUUUCAAGAGUCCU--UCGGUCCUUGAGCAACACGAGCUGCUAUUUU
.((((((((((((..(((..(..((((..((......)).-------.))))..)--.((((((((....))))))))..(((..(.--...)..)))..)))..))))).))))))).. ( -28.60)
>DroSec_CAF1 30675 110 - 1
UAAUGGUACUCGUCCUGUAAUUUCAUUUUUCAUGUAAGAC-------CAGUGGGG-GGGUAAAUUUAAUGAAAUUUUCAAGAGUCCU--UCGGUCCUUGGGCAACACGAGCUGCUAUUUU
.((((((((((((..((((((((((((.......((...(-------(.....))-...)).....))))))))).(((((.(.((.--..)).)))))))))..))))).))))))).. ( -25.50)
>DroSim_CAF1 32558 111 - 1
UAAUGGCACUCGUCCUGUAAUUUCAUUUUUCAUGUAAGAC-------CAGUGGGGCGGGGAAAUUUAAUGAAAUUUUCAAGAGUCCU--UCGCUCCUUGGGCAACACGAGCUGCUAUUUU
.((((((((((((..(((...........((......))(-------(((.((((((((((.......(((.....)))....))).--))))))))))))))..))))).))))))).. ( -33.70)
>DroEre_CAF1 30236 108 - 1
UAAUGGCACUCGUUCUGUUAUUUCAUUUUUCAUAUAACAC-------CAGUAGG---GGAAAAUUUAAUGAAAUUUUCAAGAGUCCU--UUGGUCCUUGGGCAACACGAGCUGCCAUUUU
.((((((((((((...(((((............)))))((-------(((.(((---(((((((((....)))))))).....))))--))))).....(....)))))).))))))).. ( -28.40)
>DroYak_CAF1 67315 117 - 1
UAAUGGCACUCACUCUGUAAUUUGAUUUUUCAUGUAACACCAGUCACCAGUAGG---GGAAAAUUUAAUGAAAUUUUCAAGAGUCCUUUUUGGUCCUUGGACAACACGAGCUGCUAUUUU
.((((((((((....(((.((.(((....))).)).)))((((..(((((.(((---(((((((((....))))))))......)))).)))))..)))).......))).))))))).. ( -29.30)
>consensus
UAAUGGCACUCGUCCUGUAAUUUCAUUUUUCAUGUAAGAC_______CAGUGGGG__GGAAAAUUUAAUGAAAUUUUCAAGAGUCCU__UCGGUCCUUGGGCAACACGAGCUGCUAUUUU
.((((((((((((..((((((((((((.......................................))))))))).(((((.(.((.....)).)))))))))..))))).))))))).. (-21.91 = -22.27 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:27 2006