Locus 5376

Sequence ID	2R_DroMel_CAF1
Location	17,355,935 – 17,356,073
Length	138
Max. P	0.986512

overview

Window 3

Location	17,355,935 – 17,356,033
Length	98
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	73.88
Mean single sequence MFE	-17.84
Consensus MFE	-13.30
Energy contribution	-13.30
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.05
Structure conservation index	0.75
SVM decision value	0.79
SVM RNA-class probability	0.851221
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17355935 98 + 20766785
AUGAACAAAUAUUUUU---CA------GAAAU-AAAAAAAAA--AA---ACAACAAAAAGUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAA
...........(((((---((------(....-.........--((---((........))))......((((.(((((((.......))))).)).)).))))))))))... ( -16.00)
>DroVir_CAF1 64479 89 + 1
--UACUAAAUAUAUUUCC---------U---U-AGAAAAAAA---------AAUAAAAUAUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAA
--...........(((((---------.---.-.........---------......(((......)))((((.(((((((.......))))).)).)).))..))))).... ( -15.00)
>DroGri_CAF1 57954 97 + 1
---AGUUAAUUUAGUUUGAUGUGGUAAU---C-AAAAUUAAC---------AACAAAAAAUUAACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAA
---(((((((((..((((.(((......---.-.......))---------).))))))))))))).....((.(((((((.......))))).)).))((((.....)))). ( -21.04)
>DroEre_CAF1 70450 87 + 1
AUGAACAAACAUUUUA---U-------------AAAA-UAAA---------AACAAAAAGCUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAA
................---.-------------....-....---------........((((.((...((((.(((((((.......))))).)).)).))..)).)))).. ( -18.20)
>DroYak_CAF1 52067 80 + 1
AUGAAUAAA------A---U-------------AAAA--AAA---------AUCAAAAAGUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAA
.........------.---.-------------....--...---------........((((.((...((((.(((((((.......))))).)).)).))..)).)))).. ( -15.70)
>DroPer_CAF1 78643 99 + 1
--GAACGAAAACAUAA---GC------CG--AAAAAA-UAGAAAAAUAUUUUACAAAAAAUGUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAA
--((.(((...(((((---(.------..--..((((-((......))))))(((.....))).))))))..))).(((((.......))))).))...((((.....)))). ( -21.10)
>consensus
__GAACAAAUAUAUUA___U_____________AAAA_UAAA_________AACAAAAAAUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAA
.......................................................................((.(((((((.......))))).)).))((((.....)))). (-13.30 = -13.30 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	17,355,935 – 17,356,033
Length	98
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	73.88
Mean single sequence MFE	-19.33
Consensus MFE	-14.50
Energy contribution	-14.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.75
SVM decision value	1.46
SVM RNA-class probability	0.956116
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17355935 98 - 20766785
UUGCCUUCCAAGCAGUUGAUCCGGGUUCGAUUCCCGGCCGACGCACAAGUAAACUUUUUGUUGU---UU--UUUUUUUUU-AUUUC------UG---AAAAAUAUUUGUUCAU
.(((.......)))((((..(((((.......))))).))))(.((((((((((.....)))..---..--...((((((-(....------))---)))))))))))).).. ( -19.90)
>DroVir_CAF1 64479 89 - 1
UUGCCUUCCAAGCAGUUGAUCCGGGUUCGAUUCCCGGCCGACGCACAAGUAAAUAUUUUAUU---------UUUUUUUCU-A---A---------GGAAAUAUAUUUAGUA--
...........((.((((..(((((.......))))).))))))...(.((((((...((((---------(((((....-)---)---------))))))))))))).).-- ( -19.40)
>DroGri_CAF1 57954 97 - 1
UUGCCUUCCAAGCAGUUGAUCCGGGUUCGAUUCCCGGCCGACGCACAAGUUAAUUUUUUGUU---------GUUAAUUUU-G---AUUACCACAUCAAACUAAAUUAACU---
...........((.((((..(((((.......))))).))))))...(((((((((((((.(---------((((((...-.---))))..))).))))..)))))))))--- ( -22.40)
>DroEre_CAF1 70450 87 - 1
UUGCCUUCCAAGCAGUUGAUCCGGGUUCGAUUCCCGGCCGACGCACAAGUAAGCUUUUUGUU---------UUUA-UUUU-------------A---UAAAAUGUUUGUUCAU
........((((((((((..(((((.......))))).))))..(((((.......))))).---------....-....-------------.---.....))))))..... ( -18.50)
>DroYak_CAF1 52067 80 - 1
UUGCCUUCCAAGCAGUUGAUCCGGGUUCGAUUCCCGGCCGACGCACAAGUAAACUUUUUGAU---------UUU--UUUU-------------A---U------UUUAUUCAU
...........((.((((..(((((.......))))).)))))).((((.......))))..---------...--....-------------.---.------......... ( -14.90)
>DroPer_CAF1 78643 99 - 1
UUGCCUUCCAAGCAGUUGAUCCGGGUUCGAUUCCCGGCCGACGCACAAGUACAUUUUUUGUAAAAUAUUUUUCUA-UUUUUU--CG------GC---UUAUGUUUUCGUUC--
..(((......((.((((..(((((.......))))).)))))).....((((.....)))).............-......--.)------))---..............-- ( -20.90)
>consensus
UUGCCUUCCAAGCAGUUGAUCCGGGUUCGAUUCCCGGCCGACGCACAAGUAAACUUUUUGUU_________UUUA_UUUU_____________A___AAAUAUAUUUAUUC__
...........((.((((..(((((.......))))).))))))..................................................................... (-14.50 = -14.50 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	17,355,965 – 17,356,073
Length	108
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	85.97
Mean single sequence MFE	-31.57
Consensus MFE	-29.05
Energy contribution	-29.05
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.92
SVM decision value	2.04
SVM RNA-class probability	0.986512
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17355965 108 + 20766785
AA--AA---ACAACAAAAAGUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAACUAUGCUGACCAUUACACCACCGACGCCCCUUAAAAAUAG
..--((---((........))))......((((((((((((.......)))))..........(((..((((....))))..)))........)))))))............. ( -29.30)
>DroVir_CAF1 64504 104 + 1
AA---------AAUAAAAUAUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAACUAUGCUGACCAUUACACCACCGACGCCCGUUGUUUUCAA
..---------................(.((((((((((((.......)))))..........(((..((((....))))..)))........))))))).)........... ( -29.30)
>DroPse_CAF1 79534 113 + 1
GAAAAAUAUUUUACAAAAAAUGUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAACUAUGCUGACCAUUACACCACCGACGCCACUUGAAAGAUC
.....(((((((....))))))).(..((((((((((((((.......)))))..........(((..((((....))))..)))........)))))).)))..)....... ( -32.20)
>DroGri_CAF1 57987 104 + 1
AC---------AACAAAAAAUUAACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAACUAUGCUGACCAUUACACCACCGACGCCACAUGAAUAUAG
..---------.............(.(((((((((((((((.......)))))..........(((..((((....))))..)))........)))))).)))).)....... ( -31.20)
>DroSec_CAF1 71844 108 + 1
AA--AG---GAAACAAAAAAUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAACUAUGCUGACCAUUACACCACCGACGCGCCUUGAGGAGAU
..--.(---....)..........(((((((((((((((((.......)))))..........(((..((((....))))..)))........)))))))))...)))..... ( -35.20)
>DroPer_CAF1 78669 113 + 1
GAAAAAUAUUUUACAAAAAAUGUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAACUAUGCUGACCAUUACACCACCGACGCCACUUGAAAGAUC
.....(((((((....))))))).(..((((((((((((((.......)))))..........(((..((((....))))..)))........)))))).)))..)....... ( -32.20)
>consensus
AA__AA_____AACAAAAAAUUUACUUGUGCGUCGGCCGGGAAUCGAACCCGGAUCAACUGCUUGGAAGGCAACUAUGCUGACCAUUACACCACCGACGCCACUUGAAAAAAC
.............................((((((((((((.......)))))..........(((..((((....))))..)))........)))))))............. (-29.05 = -29.05 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:23 2006