Locus 60

Sequence ID	4_DroMel_CAF1
Location	512,984 – 513,209
Length	225
Max. P	0.879486

overview

Window 0

Location	512,984 – 513,104
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.31
Mean single sequence MFE	-30.91
Consensus MFE	-26.59
Energy contribution	-26.52
Covariance contribution	-0.06
Combinations/Pair	1.10
Mean z-score	-1.73
Structure conservation index	0.86
SVM decision value	0.38
SVM RNA-class probability	0.713352
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 512984 120 + 1281640
UUUACUGGAGAGCGUAAUUACGAGGAGUACUCUACGCGUUCUGCGACACUUACUGCUCCCAAGCAGCCAAUUCGAAAUACAUGCAUCAACAUAUUAUUUGUGCUGGCUGCUAAUUCUCUU
.....(((.((((((((....(((.....)))..(((.....)))....)))).)))))))((((((((...((((....(((......)))....))))...))))))))......... ( -33.30)
>DroSec_CAF1 19677 120 + 1
UUAACUGGAGAGCGUAAUUACGAGGAGUACUCUACGCGUUCUGCGACACUUACUACUCCCAAGCAGCCAAUUCGAAAUACAUGCAUCAACAUAUUAUUUGUGCUGGCUGCUAAUUCUCUU
......((((((.........(.((((((.....(((.....)))........))))))).((((((((...((((....(((......)))....))))...))))))))..)))))). ( -30.02)
>DroSim_CAF1 19550 120 + 1
UUAACUGGAGAGCGUAAUUACGGGGAGUACUCUACGCGUUCUGCGACACUUACUACUCCCAAGCAGCCAAUUCGAAAUACAUGCAUCAACAUAUUAUUUGUGCUGGCUGCUAAUUCUCUU
......(((((((((....)))(((((((.....(((.....)))........))))))).((((((((...((((....(((......)))....))))...))))))))..)))))). ( -34.12)
>DroYak_CAF1 25071 120 + 1
UUUACUGGAGAGCCUAAUUACGAGAAGUACUCUAUGCGUUCUGCGACACGUACUGUUCCCAAGCAGCGAACUCGAAAUACAUGCAUCGACAUAUUAUUUCUGCUGGCUGCUGAUUCUCUU
......((((((.........(((.(((((....(((.....)))....))))).)))...((((((.(.(..((((((.(((......)))..)))))).).).))))))..)))))). ( -26.20)
>consensus
UUAACUGGAGAGCGUAAUUACGAGGAGUACUCUACGCGUUCUGCGACACUUACUACUCCCAAGCAGCCAAUUCGAAAUACAUGCAUCAACAUAUUAUUUGUGCUGGCUGCUAAUUCUCUU
......((((((.........(((.((((.....(((.....))).....)))).)))...((((((((...((((....(((......)))....))))...))))))))..)))))). (-26.59 = -26.52 +  -0.06)

alignment

secondary structure

dotplot

Window 1

Location	512,984 – 513,104
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-36.23
Consensus MFE	-30.33
Energy contribution	-30.95
Covariance contribution	0.62
Combinations/Pair	1.06
Mean z-score	-2.27
Structure conservation index	0.84
SVM decision value	0.91
SVM RNA-class probability	0.879486
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 512984 120 - 1281640
AAGAGAAUUAGCAGCCAGCACAAAUAAUAUGUUGAUGCAUGUAUUUCGAAUUGGCUGCUUGGGAGCAGUAAGUGUCGCAGAACGCGUAGAGUACUCCUCGUAAUUACGCUCUCCAGUAAA
.........(((((((((..((((((.(((((....)))))))))).)..)))))))))(((((((.((((((((......))))...(((.....)))....)))))))).)))..... ( -35.90)
>DroSec_CAF1 19677 120 - 1
AAGAGAAUUAGCAGCCAGCACAAAUAAUAUGUUGAUGCAUGUAUUUCGAAUUGGCUGCUUGGGAGUAGUAAGUGUCGCAGAACGCGUAGAGUACUCCUCGUAAUUACGCUCUCCAGUUAA
..((((...(((((((((..((((((.(((((....)))))))))).)..))))))))).(((((((.(..((((......))))....).)))))))...........))))....... ( -35.70)
>DroSim_CAF1 19550 120 - 1
AAGAGAAUUAGCAGCCAGCACAAAUAAUAUGUUGAUGCAUGUAUUUCGAAUUGGCUGCUUGGGAGUAGUAAGUGUCGCAGAACGCGUAGAGUACUCCCCGUAAUUACGCUCUCCAGUUAA
..((((...(((((((((..((((((.(((((....)))))))))).)..))))))))).(((((((.(..((((......))))....).)))))))...........))))....... ( -37.90)
>DroYak_CAF1 25071 120 - 1
AAGAGAAUCAGCAGCCAGCAGAAAUAAUAUGUCGAUGCAUGUAUUUCGAGUUCGCUGCUUGGGAACAGUACGUGUCGCAGAACGCAUAGAGUACUUCUCGUAAUUAGGCUCUCCAGUAAA
..((((..(((((((.(((.((((((.(((((....)))))))))))..))).)))))).((((..(((((.(((.((.....)))))..))))))))).......)..))))....... ( -35.40)
>consensus
AAGAGAAUUAGCAGCCAGCACAAAUAAUAUGUUGAUGCAUGUAUUUCGAAUUGGCUGCUUGGGAGCAGUAAGUGUCGCAGAACGCGUAGAGUACUCCUCGUAAUUACGCUCUCCAGUAAA
..((((...(((((((((...(((((.(((((....))))))))))....))))))))).(((((((.(..((((......))))....).)))))))...........))))....... (-30.33 = -30.95 +   0.62)

alignment

secondary structure

dotplot

Window 2

Location	513,104 – 513,209
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.41
Mean single sequence MFE	-26.02
Consensus MFE	-19.54
Energy contribution	-20.47
Covariance contribution	0.94
Combinations/Pair	1.10
Mean z-score	-1.81
Structure conservation index	0.75
SVM decision value	0.58
SVM RNA-class probability	0.788378
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 513104 105 - 1281640
CAAACACUUACGUGUCUCA-------AUUCCAUCAAUUCCGUUAGCCUCAUGGAAAACCGGGGGUGAAUGGAUUUGGUG--UACAUAUA------AUGAAUUCUUAUUCUUAUUCGCAAA
...((((....))))....-------....((((((.((((((.(((((.(((....)))))))).)))))).))))))--.....(((------(.((((....))))))))....... ( -26.50)
>DroSec_CAF1 19797 99 - 1
UAAACACUUACGUGUCUCA-------AUGCUAUCAAUUGCGUUAGCCUCAUGGAAAACCGGGGGUGAAUGGAUUUGGUG--UACAUAUA------AUGAAUUCU------UAUUCGCAAA
...((((....))))....-------.(((((((((.(.((((.(((((.(((....)))))))).)))).).))))))--........------..((((...------.))))))).. ( -23.30)
>DroSim_CAF1 19670 99 - 1
UAAACACUUACGUGUCUCA-------AUGCUAUCAAUUGCGUUAGCCUCAUGGAAAACCGGGGGUGAAUGGAUUUGGUG--UACAUAUA------AUGAAUUCU------UAUUCGCAAA
...((((....))))....-------.(((((((((.(.((((.(((((.(((....)))))))).)))).).))))))--........------..((((...------.))))))).. ( -23.30)
>DroYak_CAF1 25191 113 - 1
UAAACACUUUUGUGUCUUAAUAAUUAAUGCUAUCAAUUCCGUUAGCCUUAGGGAAAACCGGGGGUGGAUGGAUUCG-UGAAUAGAUUUCGUGAAUAUGAAUUCU------UAUUCGCAAA
...((((....))))......................((((((.((((..((.....))..)))).))))))...(-((((((((.(((((....))))).)).------)))))))... ( -31.00)
>consensus
UAAACACUUACGUGUCUCA_______AUGCUAUCAAUUCCGUUAGCCUCAUGGAAAACCGGGGGUGAAUGGAUUUGGUG__UACAUAUA______AUGAAUUCU______UAUUCGCAAA
...((((....))))............(((((((((.((((((.(((((.(((....)))))))).)))))).))))))..................((((..........))))))).. (-19.54 = -20.47 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:57 2006