Locus 6394

Sequence ID	3L_DroMel_CAF1
Location	17,128,630 – 17,128,755
Length	125
Max. P	0.999081

overview

Window 9

Location	17,128,630 – 17,128,729
Length	99
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	75.17
Mean single sequence MFE	-38.90
Consensus MFE	-19.36
Energy contribution	-19.68
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-2.89
Structure conservation index	0.50
SVM decision value	3.36
SVM RNA-class probability	0.999081
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17128630 99 + 23771897
GAGUGGGCCUGGUAAUUUCUGG-----G-G-GGCGGUUGGUGUU-------UGGGAGGCACGCGCCUCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAU
.(((...((..(......)..)-----)-(-(.(.((((.((((-------(.((((((....)))))).))))).)))).)...)).)))(((((((....))))))).... ( -40.70)
>DroPse_CAF1 11737 102 + 1
GAG----ACAGUCGACUGCUGA-----GUGGGUUCGGUGGUUAUUGCAGGGUGCCAGGCACGCGCCGCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAU--
...----..........(((((-----.....(((.((.((((((.((((((((.......))))).))).)))))).)).))).)))))((((((((....)))))))).-- ( -41.80)
>DroSec_CAF1 12946 100 + 1
GAGUGGGGCUGGUAAUUUCUGG-----GGG-GGCGUUUGGUGUU-------UGGGAGGCACGCGCCUCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAU
......(((((((..(..(...-----.).-.)((((.(.((((-------(.((((((....)))))).))))).)))))...)))))))(((((((....))))))).... ( -40.30)
>DroEre_CAF1 13564 99 + 1
GAGUGGGGCUGGUAAUUUCGGG-----G-G-GCGGGGUGGUGUU-------UGGGAGGCACGCGCCUCUGGAAUGGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAU
......(((((((...(((.((-----(-(-(((.(...((.((-------...)).)).).))))))).)))((....))...)))))))(((((((....))))))).... ( -39.70)
>DroWil_CAF1 15274 90 + 1
GGGUGGGUUUUGAAGGUG----GAGGUG-G-GCCGGGU---------------AGAGGCACGCGCCUCUGAAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCGU--
((.((..(((((...(((----((((((-(-(((....---------------...))).).)))))))......))..)))))..)).))(((((((....)))))))..-- ( -32.00)
>consensus
GAGUGGGGCUGGUAAUUUCUGG_____G_G_GCCGGGUGGUGUU_______UGGGAGGCACGCGCCUCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAU
.....................................................((((((....)))))).....(((...........)))(((((((....))))))).... (-19.36 = -19.68 +   0.32)

alignment

secondary structure

dotplot

Window 0

Location	17,128,630 – 17,128,729
Length	99
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	75.17
Mean single sequence MFE	-22.26
Consensus MFE	-17.03
Energy contribution	-17.07
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-1.27
Structure conservation index	0.77
SVM decision value	0.77
SVM RNA-class probability	0.847197
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17128630 99 - 23771897
AUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGAGGCGCGUGCCUCCCA-------AACACCAACCGCC-C-C-----CCAGAAAUUACCAGGCCCACUC
...((((((........))))))(((((((((.((((........(((((....)))))...-------.....)))).(..-.-.-----.).))))))....)))...... ( -20.29)
>DroPse_CAF1 11737 102 - 1
--AUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGCGGCGCGUGCCUGGCACCCUGCAAUAACCACCGAACCCAC-----UCAGCAGUCGACUGU----CUC
--.((((((........))))))(((((...((((((......))))))((.(((....((.....))......))))).......-----)))))..........----... ( -27.20)
>DroSec_CAF1 12946 100 - 1
AUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGAGGCGCGUGCCUCCCA-------AACACCAAACGCC-CCC-----CCAGAAAUUACCAGCCCCACUC
...((((((........))))))(((((((((((((.........(((((....)))))...-------.......))))..-...-----...)))))...))))....... ( -22.71)
>DroEre_CAF1 13564 99 - 1
AUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCCAUUCCAGAGGCGCGUGCCUCCCA-------AACACCACCCCGC-C-C-----CCCGAAAUUACCAGCCCCACUC
...((((((........))))))(((((((((...((......))(((((....)))))...-------.............-.-.-----...)))))...))))....... ( -20.60)
>DroWil_CAF1 15274 90 - 1
--ACGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUUCAGAGGCGCGUGCCUCU---------------ACCCGGC-C-CACCUC----CACCUUCAAAACCCACCC
--..((((((((........(((((.(....).)))))........))))))))(((...---------------....)))-.-......----.................. ( -20.49)
>consensus
AUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGAGGCGCGUGCCUCCCA_______AACACCACCCGCC_C_C_____CCAGAAAUUACCAGCCCCACUC
...(((((((((........(((((.(....).)))))........))))))))).......................................................... (-17.03 = -17.07 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	17,128,656 – 17,128,755
Length	99
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	79.06
Mean single sequence MFE	-37.98
Consensus MFE	-21.98
Energy contribution	-23.87
Covariance contribution	1.89
Combinations/Pair	1.16
Mean z-score	-2.81
Structure conservation index	0.58
SVM decision value	1.64
SVM RNA-class probability	0.969273
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17128656 99 + 23771897
CGGUUGGUGUU-------UGGGAGGCACGCGCCUCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAUAGCUCCAAGG---AAAGUUGCUGCCAACC
.((((((((((-------(.((((((....)))))).))))((((((........((((((((((....)))))))....)))((....)---)..))))))))))))) ( -44.30)
>DroPse_CAF1 11761 92 + 1
UCGGUGGUUAUUGCAGGGUGCCAGGCACGCGCCGCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAU--AGCUCUGUGG---AG------------GC
((.((.((((((.((((((((.......))))).))).)))))).)).)).....((((((((((....)))))))).--..(((....)---))------------)) ( -35.60)
>DroSec_CAF1 12973 99 + 1
CGUUUGGUGUU-------UGGGAGGCACGCGCCUCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAUAGCUCCAAGG---AAAGUUGCUGCCAACC
...((((((((-------(.((((((....)))))).))))((((((........((((((((((....)))))))....)))((....)---)..))))))))))).. ( -38.70)
>DroEre_CAF1 13590 99 + 1
GGGGUGGUGUU-------UGGGAGGCACGCGCCUCUGGAAUGGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAUAGCUCCAAGG---AAAGUUGCUGGCGACC
..(((.(((((-------(.((((((....)))))).))))((((((........((((((((((....)))))))....)))((....)---)..)))))).)).))) ( -38.90)
>DroWil_CAF1 15301 85 + 1
CGGGU---------------AGAGGCACGCGCCUCUGAAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCGU--AGCUCCAAGCCCAAAAGA-GACG------
.((((---------------((((((....))))))...........(((.....(((((((((........))))))--))))))..))))......-....------ ( -31.80)
>DroYak_CAF1 13506 99 + 1
GGUGUGGUGUU-------UGGGAGGCACGCGCCUCUGGAAUGGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAUAGCUCCAAGG---AAAGUUGCCGACGACC
...((.(((((-------(.((((((....)))))).))))((((((........((((((((((....)))))))....)))((....)---)..)))))).)).)). ( -38.60)
>consensus
CGGGUGGUGUU_______UGGGAGGCACGCGCCUCUGGAAUAGCAACGGAAAUCAGCUGCGUGUUGAUAAGCACGCAUAUAGCUCCAAGG___AAAGUUGCUG_C_ACC
....................((((((....))))))....(((((((.(....)(((((((((((....))))))))....)))............)))))))...... (-21.98 = -23.87 +   1.89)

alignment

secondary structure

dotplot

Window 2

Location	17,128,656 – 17,128,755
Length	99
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.06
Mean single sequence MFE	-29.35
Consensus MFE	-18.87
Energy contribution	-19.12
Covariance contribution	0.25
Combinations/Pair	1.11
Mean z-score	-1.59
Structure conservation index	0.64
SVM decision value	0.44
SVM RNA-class probability	0.736539
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17128656 99 - 23771897
GGUUGGCAGCAACUUU---CCUUGGAGCUAUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGAGGCGCGUGCCUCCCA-------AACACCAACCG
((((((.((((((...---....((((.....((((((........))))))......))))))))))......(((((....)))))...-------....)))))). ( -34.71)
>DroPse_CAF1 11761 92 - 1
GC------------CU---CCACAGAGCU--AUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGCGGCGCGUGCCUGGCACCCUGCAAUAACCACCGA
((------------(.---.(((..((((--..(((((........)))))))))......(((((((.....))))))).)))...)))................... ( -26.70)
>DroSec_CAF1 12973 99 - 1
GGUUGGCAGCAACUUU---CCUUGGAGCUAUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGAGGCGCGUGCCUCCCA-------AACACCAAACG
((((((.((((((...---....((((.....((((((........))))))......))))))))))......(((((....))))))))-------...)))..... ( -29.41)
>DroEre_CAF1 13590 99 - 1
GGUCGCCAGCAACUUU---CCUUGGAGCUAUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCCAUUCCAGAGGCGCGUGCCUCCCA-------AACACCACCCC
((((((((((....((---(....))).....((((((........)))))))))).........(((........)))))).))).....-------........... ( -26.40)
>DroWil_CAF1 15301 85 - 1
------CGUC-UCUUUUGGGCUUGGAGCU--ACGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUUCAGAGGCGCGUGCCUCU---------------ACCCG
------....-......(((..(((((..--.(((((((((........(((((.(....).)))))........))))))))).))))---------------)))). ( -28.29)
>DroYak_CAF1 13506 99 - 1
GGUCGUCGGCAACUUU---CCUUGGAGCUAUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCCAUUCCAGAGGCGCGUGCCUCCCA-------AACACCACACC
(((.((.((((((...---....((((.....((((((........))))))......))))))))))......(((((....)))))...-------.)))))..... ( -30.61)
>consensus
GGU_G_CAGCAACUUU___CCUUGGAGCUAUAUGCGUGCUUAUCAACACGCAGCUGAUUUCCGUUGCUAUUCCAGAGGCGCGUGCCUCCCA_______AACACCACCCG
.......................((((.....(((((((((........(((((.(....).)))))........))))))))).)))).................... (-18.87 = -19.12 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:21 2006