Locus 1293

Sequence ID	X_DroMel_CAF1
Location	3,860,465 – 3,860,586
Length	121
Max. P	0.894430

overview

Window 8

Location	3,860,465 – 3,860,566
Length	101
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.23
Mean single sequence MFE	-25.52
Consensus MFE	-18.07
Energy contribution	-17.93
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.12
Structure conservation index	0.71
SVM decision value	0.29
SVM RNA-class probability	0.670483
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3860465 101 + 22224390
C---CCAUACCGUUCGUCCACU--UUUUGGCUUUUUG-GCAGACUUUGACUUCAAUGAAGGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAC
.---(((((((.((((((((..--...))(((....)-)).))).(((....))).)))))((((((((....))))))))..)))))................... ( -26.70)
>DroPse_CAF1 47634 89 + 1
CCUCCUCUGGUGUCC-UCC----------CCUG-CUGUC------CUGGCUUCAACGAAUGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAC
......(((((((..-(((----------...(-((...------..)))...........((((((((....)))))))).....))).....)))))))...... ( -23.80)
>DroSec_CAF1 43594 101 + 1
C--CCCAUUCCGUGCGUCCACU--UUUUGGCUU-UUG-GCAGACUUUGACUUCAAUGAAGGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAC
.--........(((((((....--.((((.(..-..)-.))))....))).....(((...((((((((....))))))))..(((((....))))))))...)))) ( -27.30)
>DroEre_CAF1 42442 96 + 1
C-CCCCAUUCCGUUCGACCAUU--UUUUGG--------CCAGACUUUGACUUCAAUGAAGGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAC
.-.....((((((..(.(((..--...)))--------.)..)).....((((...)))).((((((((....)))))))).....))))................. ( -25.00)
>DroYak_CAF1 38568 96 + 1
C---CCACUCCGUUCGCCCACUGGUUUUGG--------CCAGACUUUGACUUCAAUGAAGGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAC
.---....(((((....((.(((((....)--------)))).(.(((....))).)..))((((((((....))))))))...))))).................. ( -27.90)
>DroAna_CAF1 44564 98 + 1
C--CCCCUCACACAAAUAUAUU--UUUCAUUUU-UUGGCCAGACUUC----ACAAUGAAGGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAC
.--........((..((((..(--((((((...-.........((((----.....)))).((((((((....))))))))...)))))))...))))..))..... ( -22.40)
>consensus
C__CCCAUUCCGUUCGUCCACU__UUUUGGCUU_UUG_CCAGACUUUGACUUCAAUGAAGGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAC
....................................................((((.....((((((((....)))))))).((((((....))))))..))))... (-18.07 = -17.93 +  -0.14)

alignment

secondary structure

dotplot

Window 9

Location	3,860,465 – 3,860,566
Length	101
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	77.23
Mean single sequence MFE	-30.44
Consensus MFE	-20.40
Energy contribution	-20.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.67
SVM decision value	0.98
SVM RNA-class probability	0.894430
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3860465 101 - 22224390
GUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUUGAAGUCAAAGUCUGC-CAAAAAGCCAAAA--AGUGGACGAACGGUAUGG---G
...................(((((..((((((((....))))))))(((((.(((....))).(((..(-.............--.)..)))))).)))))))---. ( -30.24)
>DroPse_CAF1 47634 89 - 1
GUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCAUUCGUUGAAGCCAG------GACAG-CAGG----------GGA-GGACACCAGAGGAGG
(((((((.((((((......))))))((((((((....)))))))).....))))...((..------(....-)..)----------)..-...)))......... ( -26.40)
>DroSec_CAF1 43594 101 - 1
GUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUUGAAGUCAAAGUCUGC-CAA-AAGCCAAAA--AGUGGACGCACGGAAUGGG--G
((((.(((((((((......))))))((((((((....))))))))..........)))....(((..(-...-.........--.)..)))))))........--. ( -32.42)
>DroEre_CAF1 42442 96 - 1
GUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUUGAAGUCAAAGUCUGG--------CCAAAA--AAUGGUCGAACGGAAUGGGG-G
........((((((......))))))((((((((....))))))))(((((((((....)...((.(((--------(((...--..)))))).))..)))))))-) ( -34.30)
>DroYak_CAF1 38568 96 - 1
GUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUUGAAGUCAAAGUCUGG--------CCAAAACCAGUGGGCGAACGGAGUGG---G
........((((((......))))))((((((((....))))))))(((((......(((.....((((--------......))))..))).....))).))---. ( -31.00)
>DroAna_CAF1 44564 98 - 1
GUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUUGU----GAAGUCUGGCCAA-AAAAUGAAA--AAUAUAUUUGUGUGAGGGG--G
...(..((.(((..(((....(((((((((((((....))))))))..((((((.(----(.........)).-..)))))).--))))))))..))).))..)--. ( -28.30)
>consensus
GUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUUGAAGUCAAAGUCUGG_CAA_AAGCCAAAA__AGUGGACGAACGGAAUGGG__G
........((((((......))))))((((((((....))))))))............................................................. (-20.40 = -20.40 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	3,860,496 – 3,860,586
Length	90
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	83.38
Mean single sequence MFE	-29.11
Consensus MFE	-21.12
Energy contribution	-21.57
Covariance contribution	0.45
Combinations/Pair	1.05
Mean z-score	-2.19
Structure conservation index	0.73
SVM decision value	0.40
SVM RNA-class probability	0.720240
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3860496 90 - 22224390
CUUGGAAGUC-AACUGCUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUU-----GAAGUCAAAGUCUGC-C
(((.((..((-((.(((......)))...((((((......))))))((((((((....))))))))......))-----))..)).))).....-. ( -28.20)
>DroSec_CAF1 43625 89 - 1
CCUGGAAGGC-A-GUGCUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUU-----GAAGUCAAAGUCUGC-C
...((.((((-.-.((((.(((((.....((((((......))))))((((((((....))))))))....))))-----).)).))..)))).)-) ( -32.70)
>DroEre_CAF1 42469 88 - 1
CCUGAAAACC-A-GUCCUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUU-----GAAGUCAAAGUCUGG--
........((-(-(.(((.(((((.....((((((......))))))((((((((....))))))))....))))-----).)).....).))))-- ( -28.20)
>DroWil_CAF1 42044 93 - 1
CCUGUGUUCC-U-AGCUUACAGUACAACCGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCGUUCCUAAGGGAGAACGCAAAAGCGGG--
..((((((((-(-..((((....((....((((((......))))))((((((((....)))))))).))...)))))).)))))))........-- ( -31.20)
>DroYak_CAF1 38595 88 - 1
CCUGGAAAGC-A-AUCCUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUU-----GAAGUCAAAGUCUGG--
.(..((....-.-...((.(((((.....((((((......))))))((((((((....))))))))....))))-----).))......))..)-- ( -26.94)
>DroAna_CAF1 44595 87 - 1
CCUCGAACUCGA-AUCCUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUU-----GU----GAAGUCUGGCC
(((((....)))-.....((((((.....((((((......))))))((((((((....))))))))....))))-----))----.......)).. ( -27.40)
>consensus
CCUGGAAACC_A_AUCCUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCCUUCAUU_____GAAGUCAAAGUCUGG__
...................(((.......((((((......))))))((((((((....)))))))).((((........)))).......)))... (-21.12 = -21.57 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:55 2006