Locus 5620

Sequence ID	3R_DroMel_CAF1
Location	14,814,768 – 14,814,940
Length	172
Max. P	0.914602

overview

Window 4

Location	14,814,768 – 14,814,866
Length	98
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	83.76
Mean single sequence MFE	-33.00
Consensus MFE	-20.50
Energy contribution	-23.12
Covariance contribution	2.62
Combinations/Pair	1.03
Mean z-score	-1.73
Structure conservation index	0.62
SVM decision value	-0.02
SVM RNA-class probability	0.525238
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14814768 98 - 27905053
GCAACGCAACCCGUUGCUGCCGUCGAUAUUGGCGAU--------AUGGCUGCUCUUGCCAAUCUCGAGAAGGCACGCAACAAGCAAUUCCAGGCAAGAAUCUCCUC
............(((((((((.((((.((((((((.--------..........)))))))).))))...)))).)))))..((........))............ ( -29.20)
>DroSec_CAF1 7375 106 - 1
GCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAUAUUGGGAUAUGGCUGCUGUUGCCAAUCUCGAGUAGGCACGCAACAAGCCAUUCCAGGCAAGAAUCUGCAC
.....(((....(((((((((((((....))))....(((((((.((((.......)))))))))))...)))).)))))..(((......))).......))).. ( -40.20)
>DroSim_CAF1 7405 106 - 1
GCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAUAUUGGGAUAUGGCUGCUGUUGCCAAUCUCGAGUAGGCACGCAACAAGCCAUUCCAGGCAAGAAUCUCCAC
((((((.....))))))((((((((....)))).......(((.((((((..(((((((...........)))).)))...))))))))).))))........... ( -37.60)
>DroEre_CAF1 9132 87 - 1
GCAACGCAACCCGUUGCUGCCGCCGAUAUU-----------------GCUGCUGUUGCCAU--UCGAGGAAGCACGCAACAAGCAAUUUCAGGGAAGAAUCUCCUU
((((((.....)))))).......((.(((-----------------(((..((((((..(--((...)))....)))))))))))).))(((((......))))) ( -25.00)
>consensus
GCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAU________AUGGCUGCUGUUGCCAAUCUCGAGUAGGCACGCAACAAGCAAUUCCAGGCAAGAAUCUCCAC
((((((.....))))))((((((((....))))...........((((((..((((((...(((.....)))...))))))))))))....))))........... (-20.50 = -23.12 +   2.62)

alignment

secondary structure

dotplot

Window 5

Location	14,814,796 – 14,814,904
Length	108
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	87.65
Mean single sequence MFE	-40.75
Consensus MFE	-35.66
Energy contribution	-37.73
Covariance contribution	2.06
Combinations/Pair	1.03
Mean z-score	-1.74
Structure conservation index	0.88
SVM decision value	0.77
SVM RNA-class probability	0.846266
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14814796 108 + 27905053
UGCGUGCCUUCUCGAGAUUGGCAAGAGCAGCCAU--------AUCGCCAAUAUCGACGGCAGCAACGGGUUGCGUUGCUGUUGCGUCUGGAAUCUGCAGAUUGAUUGCCGAUCGCU
(((.((((.((....))..))))...)))((...--------((((.((((..((.(((((((((((.....)))))))))))))((((.......))))...)))).)))).)). ( -37.40)
>DroSec_CAF1 7403 116 + 1
UGCGUGCCUACUCGAGAUUGGCAACAGCAGCCAUAUCCCAAUAUCGCCAAUAUCGGCGGCAGCAACGGGUUGCGUUGCUGUUGCGUCUGGAAUCUGCAGAUUGAUUGCCGAUCGCU
.((.(((....((.((((..(((((((((((.............((((......))))(((((.....)))))))))))))))))))).))....)))(((((.....))))))). ( -45.60)
>DroSim_CAF1 7433 116 + 1
UGCGUGCCUACUCGAGAUUGGCAACAGCAGCCAUAUCCCAAUAUCGCCAAUAUCGGCGGCAGCAACGGGUUGCGUUGCUGUUGCGUCUGGAAUCUGCAGAUUGAUUGCCGAUCGCU
.((.(((....((.((((..(((((((((((.............((((......))))(((((.....)))))))))))))))))))).))....)))(((((.....))))))). ( -45.60)
>DroEre_CAF1 9160 97 + 1
UGCGUGCUUCCUCGA--AUGGCAACAGCAGC-----------------AAUAUCGGCGGCAGCAACGGGUUGCGUUGCUGUUGCGUCUGGAAUCUGUAGAUUGAUUGCCGAUCGCU
(((.((((.......--..))))...)))((-----------------.......((((((((((((.....))))))))))))(((.(.((((........)))).).))).)). ( -34.40)
>consensus
UGCGUGCCUACUCGAGAUUGGCAACAGCAGCCAU________AUCGCCAAUAUCGGCGGCAGCAACGGGUUGCGUUGCUGUUGCGUCUGGAAUCUGCAGAUUGAUUGCCGAUCGCU
.((.(((....((.((((..(((((((((((.............((((......))))(((((.....)))))))))))))))))))).))....)))(((((.....))))))). (-35.66 = -37.73 +   2.06)

alignment

secondary structure

dotplot

Window 6

Location	14,814,796 – 14,814,904
Length	108
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	87.65
Mean single sequence MFE	-38.85
Consensus MFE	-30.14
Energy contribution	-30.70
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.21
Structure conservation index	0.78
SVM decision value	1.10
SVM RNA-class probability	0.914602
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14814796 108 - 27905053
AGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGUCGAUAUUGGCGAU--------AUGGCUGCUCUUGCCAAUCUCGAGAAGGCACGCA
.(((.((((.((((........)))))).)))))...(((((((.....)))))))(((.((((.((((((((.--------..........)))))))).))))...)))..... ( -36.80)
>DroSec_CAF1 7403 116 - 1
AGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAUAUUGGGAUAUGGCUGCUGUUGCCAAUCUCGAGUAGGCACGCA
.(((((((((......((((.......)))).....((((((((.....))))))))..))))))....((....(((((((.((((.......)))))))))))....)).))). ( -43.20)
>DroSim_CAF1 7433 116 - 1
AGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAUAUUGGGAUAUGGCUGCUGUUGCCAAUCUCGAGUAGGCACGCA
.(((((((((......((((.......)))).....((((((((.....))))))))..))))))....((....(((((((.((((.......)))))))))))....)).))). ( -43.20)
>DroEre_CAF1 9160 97 - 1
AGCGAUCGGCAAUCAAUCUACAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUU-----------------GCUGCUGUUGCCAU--UCGAGGAAGCACGCA
.(((((((((....((((....))))..........((((((((.....))))))))..))))))...-----------------..((((....((..--....)).))))))). ( -32.20)
>consensus
AGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAU________AUGGCUGCUGUUGCCAAUCUCGAGUAGGCACGCA
.(((((((((......((((.......)))).....((((((((.....))))))))..))))))..................((((.......))))..............))). (-30.14 = -30.70 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	14,814,830 – 14,814,940
Length	110
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	87.61
Mean single sequence MFE	-34.06
Consensus MFE	-28.23
Energy contribution	-30.04
Covariance contribution	1.81
Combinations/Pair	1.06
Mean z-score	-1.57
Structure conservation index	0.83
SVM decision value	0.39
SVM RNA-class probability	0.718433
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14814830 110 - 27905053
UAGGCGAACGUGCAAAAAUGCGGCAUGAGCGGCCUAAGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGUCGAUAUUGGCGAU----
((((((..(((((.........)))))..).))))).(((.((((.((((........)))))).)))))..((((((((.....)))))))).(((((....)))))..---- ( -36.60)
>DroSec_CAF1 7441 114 - 1
UAGGCGAACGUGCAAAAAUGCGGCAUGAGCGGCCUAAGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAUAUUG
((((((..(((((.........)))))..).))))).(((.((((.((((........)))))).)))))..((((((((.....)))))))).(((((....)))))...... ( -39.30)
>DroSim_CAF1 7471 114 - 1
UAGGCGAACGUGCAAAAAUGCGGCAUGAGCGGCCUAAGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAUAUUG
((((((..(((((.........)))))..).))))).(((.((((.((((........)))))).)))))..((((((((.....)))))))).(((((....)))))...... ( -39.30)
>DroEre_CAF1 9189 104 - 1
UAGGCGAACGUGCAAAAAUGCGGCAUGAGCGGUCUAAGCGAUCGGCAAUCAAUCUACAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUU----------
..((((..(((((.........))))).((((((.....))))((.((((........))))))....))..((((((((.....)))))))).))))......---------- ( -33.50)
>DroYak_CAF1 8216 89 - 1
UAGGCGAACGUGCAAAAAUGCGGCAUAAGCGGCCUAAGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAAAAGCAACGCAACCCGUU-------------------------
...(((....(((......((.((....)).))....(((.((((.((((........)))))).)))))....))).)))........------------------------- ( -21.60)
>consensus
UAGGCGAACGUGCAAAAAUGCGGCAUGAGCGGCCUAAGCGAUCGGCAAUCAAUCUGCAGAUUCCAGACGCAACAGCAACGCAACCCGUUGCUGCCGCCGAUAUUGGCGAU____
((((((..(((((.........)))))..).))))).(((.((((.((((........)))))).)))))..((((((((.....)))))))).(((((....)))))...... (-28.23 = -30.04 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:34 2006