Locus 4673

Sequence ID	3L_DroMel_CAF1
Location	13,215,417 – 13,215,636
Length	219
Max. P	0.986816

overview

Window 4

Location	13,215,417 – 13,215,530
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.44
Mean single sequence MFE	-36.18
Consensus MFE	-30.34
Energy contribution	-31.02
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-1.95
Structure conservation index	0.84
SVM decision value	1.68
SVM RNA-class probability	0.971578
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13215417 113 + 23771897
CUGUGAGCU-------GUGAGUUGGCGAAAAUAUUAUUUAAUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUU
..(((((..-------..((.(((((((.(((........))).)).((((.((((((......)))....))).))))))))).)).)))))....((((((......))))))..... ( -36.30)
>DroSec_CAF1 8743 113 + 1
CUGUGAGCU-------GUGAGUUGGCGAAAAUAUUAUUUAAUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUU
..(((((..-------..((.(((((((.(((........))).)).((((.((((((......)))....))).))))))))).)).)))))....((((((......))))))..... ( -36.30)
>DroSim_CAF1 13819 113 + 1
CUGUGAGCU-------GUGAGUUGGCGAAAAUAUUAUUUAAUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUU
..(((((..-------..((.(((((((.(((........))).)).((((.((((((......)))....))).))))))))).)).)))))....((((((......))))))..... ( -36.30)
>DroYak_CAF1 8681 120 + 1
CUGUGAGCUGCGAGUUGUGAGUUGGCGAAAAUAUUAUUUAAUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUU
..(((....(((((....((.(((((((.(((........))).)).((((.((((((......)))....))).))))))))).)).)))))....((((((......))))))))).. ( -41.40)
>DroAna_CAF1 97273 111 + 1
--GCCAGCU-------GUGAGCCGGCGAAAAUAUUAUUUAAUUGUCAGGCCAGGCGCUAAUUAAAGUCCGAGCCGGGUCGCGAAGUGUUUCGCCCGUUUUGGCCAUAAAGCCAAACACUU
--.......-------((((((.(((((((.((((......((((..((((.((((((......)))....))).))))))))))))))))))).)))(((((......))))).))).. ( -30.60)
>consensus
CUGUGAGCU_______GUGAGUUGGCGAAAAUAUUAUUUAAUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUU
..(((...........((((((((((((.(((........))).)).((((.((((((......)))....))).)))))))))....)))))....((((((......))))))))).. (-30.34 = -31.02 +   0.68)

alignment

secondary structure

dotplot

Window 5

Location	13,215,417 – 13,215,530
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.44
Mean single sequence MFE	-36.54
Consensus MFE	-29.08
Energy contribution	-29.36
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-1.85
Structure conservation index	0.80
SVM decision value	0.81
SVM RNA-class probability	0.856164
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13215417 113 - 23771897
AAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGGCGGCCCGGCUUGGACUUUAAUUAGCGCCUGGCCUGACAAUUAAAUAAUAUUUUCGCCAACUCAC-------AGCUCACAG
.....(((((((....))))))).(((((..(((..(((((((((.(((...((......))...))).)))).((.(((........))).))))))))))..-------.)))))... ( -36.70)
>DroSec_CAF1 8743 113 - 1
AAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGGCGGCCCGGCUUGGACUUUAAUUAGCGCCUGGCCUGACAAUUAAAUAAUAUUUUCGCCAACUCAC-------AGCUCACAG
.....(((((((....))))))).(((((..(((..(((((((((.(((...((......))...))).)))).((.(((........))).))))))))))..-------.)))))... ( -36.70)
>DroSim_CAF1 13819 113 - 1
AAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGGCGGCCCGGCUUGGACUUUAAUUAGCGCCUGGCCUGACAAUUAAAUAAUAUUUUCGCCAACUCAC-------AGCUCACAG
.....(((((((....))))))).(((((..(((..(((((((((.(((...((......))...))).)))).((.(((........))).))))))))))..-------.)))))... ( -36.70)
>DroYak_CAF1 8681 120 - 1
AAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGGCGGCCCGGCUUGGACUUUAAUUAGCGCCUGGCCUGACAAUUAAAUAAUAUUUUCGCCAACUCACAACUCGCAGCUCACAG
..((((((((((....)))))))....(((((.((.(((((((((.(((...((......))...))).)))).((.(((........))).))))))).))....)))))....))).. ( -39.00)
>DroAna_CAF1 97273 111 - 1
AAGUGUUUGGCUUUAUGGCCAAAACGGGCGAAACACUUCGCGACCCGGCUCGGACUUUAAUUAGCGCCUGGCCUGACAAUUAAAUAAUAUUUUCGCCGGCUCAC-------AGCUGGC--
..((.(((((((....)))))))))(((((((....)))))...))((((.((.((......))..)).)))).....................((((((....-------.))))))-- ( -33.60)
>consensus
AAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGGCGGCCCGGCUUGGACUUUAAUUAGCGCCUGGCCUGACAAUUAAAUAAUAUUUUCGCCAACUCAC_______AGCUCACAG
..((((((((((....)))))))...((((((((.......((((.(((...((......))...))).)))).....(((....))).))))))))..................))).. (-29.08 = -29.36 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	13,215,450 – 13,215,566
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.31
Mean single sequence MFE	-32.88
Consensus MFE	-29.40
Energy contribution	-30.04
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.79
Structure conservation index	0.89
SVM decision value	2.06
SVM RNA-class probability	0.986816
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13215450 116 + 23771897
AUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAUCUGCAGCAUCUU---CAGU-CCGAUAU
.(((...((((.((((((......)))....))).))))..))).....(((..(..((((((......))))))........((((((.(....).))))))..---..).-.)))... ( -30.70)
>DroSec_CAF1 8776 113 + 1
AUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC---GAGCAUCUU---CAGU-CCGAUAU
.(((...((((.((((((......)))....))).))))..))).....(((..(..((((((......))))))........(((((((...---)))))))..---..).-.)))... ( -32.30)
>DroSim_CAF1 13852 113 + 1
AUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC---GAGCAUCUU---CAGU-CCGAUAU
.(((...((((.((((((......)))....))).))))..))).....(((..(..((((((......))))))........(((((((...---)))))))..---..).-.)))... ( -32.30)
>DroYak_CAF1 8721 113 + 1
AUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC---GACCAUCUU---CAGC-CCGAUAU
..((((.(((..((.(((......)))))..)))((((...................((((((......))))))........((((.((...---)).))))..---..))-)))))). ( -28.10)
>DroAna_CAF1 97304 116 + 1
AUUGUCAGGCCAGGCGCUAAUUAAAGUCCGAGCCGGGUCGCGAAGUGUUUCGCCCGUUUUGGCCAUAAAGCCAAACACUUAACGAUGCGGCGA---G-GCAUCUUCUCCAGCACCGAUAU
..((((.(((..((.(((......)))))..))).(((.((((((((((((((((((((((((......))))).........)))).)))))---)-))).))))....))))))))). ( -41.00)
>consensus
AUUGUCAGGCCAGGCGCUAAUUAAAGUCCAAGCCGGGCCGCCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC___GAGCAUCUU___CAGU_CCGAUAU
..((((.(((((((((((......)))....)))((((.............))))....)))))...................(((((((......)))))))............)))). (-29.40 = -30.04 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	13,215,490 – 13,215,606
Length	116
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-30.80
Consensus MFE	-27.08
Energy contribution	-28.57
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.88
SVM decision value	1.20
SVM RNA-class probability	0.930199
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13215490 116 + 23771897
CCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAUCUGCAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUUUUGCUGGCU
...........(((((.((((((......))))))........((((((.(....).)))))).((((((.((((........)))))))))).))))).(((((....)).))). ( -34.50)
>DroSec_CAF1 8816 111 + 1
CCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC---GAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUCUUGCCGG--
.((((......(((((.((((((......))))))........(((((((...---))))))).((((((.((((........)))))))))).))))).......))))....-- ( -33.72)
>DroSim_CAF1 13892 111 + 1
CCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC---GAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUUUUGCCGG--
((.........(((((.((((((......))))))........(((((((...---))))))).((((((.((((........)))))))))).)))))....((....)).))-- ( -33.30)
>DroYak_CAF1 8761 107 + 1
CCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC---GACCAUCUUCAGCCCGAUAUUUAUGUUUAUUGACUGGUGAGGCUGCUGCUUCUG------
...((((((.(......((((((......))))))........((((.((...---)).))))..(((..(((((........))))).)))).))))))..........------ ( -21.70)
>consensus
CCAAGUCUCUCGCCCAUUUUGGCCAUAAAGCCAAACACUUAACGAUGCUCCAC___GAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUUUUGCCGG__
..((((..(..(((((.((((((......))))))........(((((((......))))))).((((((.((((........)))))))))).))))).)..))))......... (-27.08 = -28.57 +   1.50)

alignment

secondary structure

dotplot

Window 8

Location	13,215,490 – 13,215,606
Length	116
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	92.22
Mean single sequence MFE	-33.00
Consensus MFE	-29.61
Energy contribution	-29.80
Covariance contribution	0.19
Combinations/Pair	1.10
Mean z-score	-1.65
Structure conservation index	0.90
SVM decision value	0.66
SVM RNA-class probability	0.813867
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13215490 116 - 23771897
AGCCAGCAAAAGCAGCAGCCCAACCAGUCAAUAAACAUAAAUAUCGGACUGAAGAUGCUGCAGAUGGAGCAUCGUUAAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGG
..(((((....))....(((((..(((((.(((........)))..)))))..((((((.(....).))))))........(((((((....))))))).)))))........))) ( -35.80)
>DroSec_CAF1 8816 111 - 1
--CCGGCAAGAGCAGCAGCCCAACCAGUCAAUAAACAUAAAUAUCGGACUGAAGAUGCUC---GUGGAGCAUCGUUAAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGG
--....((((.......(((((..(((((.(((........)))..)))))..(((((((---...)))))))........(((((((....))))))).)))))......)))). ( -35.12)
>DroSim_CAF1 13892 111 - 1
--CCGGCAAAAGCAGCAGCCCAACCAGUCAAUAAACAUAAAUAUCGGACUGAAGAUGCUC---GUGGAGCAUCGUUAAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGG
--(((((....))....(((((..(((((.(((........)))..)))))..(((((((---...)))))))........(((((((....))))))).)))))........))) ( -34.20)
>DroYak_CAF1 8761 107 - 1
------CAGAAGCAGCAGCCUCACCAGUCAAUAAACAUAAAUAUCGGGCUGAAGAUGGUC---GUGGAGCAUCGUUAAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGG
------..((.((....)).)).((((((......((((((.....((((......))))---((.((((((......)))))).))))))))(((......)))....))).))) ( -26.90)
>consensus
__CCGGCAAAAGCAGCAGCCCAACCAGUCAAUAAACAUAAAUAUCGGACUGAAGAUGCUC___GUGGAGCAUCGUUAAGUGUUUGGCUUUAUGGCCAAAAUGGGCGAGAGACUUGG
.........((((....(((((..(((((.(((........)))..)))))..(((((((......)))))))........(((((((....))))))).)))))....).))).. (-29.61 = -29.80 +   0.19)

alignment

secondary structure

dotplot

Window 9

Location	13,215,530 – 13,215,636
Length	106
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	87.73
Mean single sequence MFE	-28.17
Consensus MFE	-22.92
Energy contribution	-25.05
Covariance contribution	2.13
Combinations/Pair	1.07
Mean z-score	-1.89
Structure conservation index	0.81
SVM decision value	0.79
SVM RNA-class probability	0.852481
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13215530 106 + 23771897
AACGAUGCUCCAUCUGCAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUUUUGCUGGCUGCCAGGCUGGCAACUGACAUCAUCAUCAUC
...((((.((.....(((((((((((((((.((((........))))))))))..))).))))))..((((..(((....)))..))))..))))))......... ( -34.90)
>DroSec_CAF1 8856 95 + 1
AACGAUGCUCCAC---GAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUCUUGCCGG--------CUGGCAACUGACAUCAUCAUCAUC
...((((.((...---(((((....(((((((((......(((....)))..))))))))).)))))(((((..--------..)))))..))))))......... ( -28.50)
>DroSim_CAF1 13932 95 + 1
AACGAUGCUCCAC---GAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUUUUGCCGG--------CUGGCAACUGACAUCAUCAUCAUC
...(((((((...---)))))))..(((((.((((........)))))))))((..(..(((((((......))--------).)))).)..))............ ( -27.70)
>DroYak_CAF1 8801 91 + 1
AACGAUGCUCCAC---GACCAUCUUCAGCCCGAUAUUUAUGUUUAUUGACUGGUGAGGCUGCUGCUUCUG------------CUGGCAACUGACAUCAUCAUCAGC
...((((.((...---)).))))........(((..(.(((((..(((.(..(((((((....))))).)------------)..))))..))))).)..)))... ( -21.60)
>consensus
AACGAUGCUCCAC___GAGCAUCUUCAGUCCGAUAUUUAUGUUUAUUGACUGGUUGGGCUGCUGCUUUUGCCGG________CUGGCAACUGACAUCAUCAUCAUC
...(((((((......)))))))..(((((((((......(((....)))..))))))))).(((..((((((((......))))))))..).))........... (-22.92 = -25.05 +   2.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:22 2006