Locus 6391

Sequence ID	3R_DroMel_CAF1
Location	16,768,248 – 16,768,482
Length	234
Max. P	0.986995

overview

Window 2

Location	16,768,248 – 16,768,362
Length	114
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	85.84
Mean single sequence MFE	-41.37
Consensus MFE	-37.72
Energy contribution	-37.50
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.61
Structure conservation index	0.91
SVM decision value	0.71
SVM RNA-class probability	0.829040
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16768248 114 + 27905053
------CUUGUAAGUGCUCAUUAACAUAAGCCGCUGAUGUCGUUGCGCACAUUGUUGCCAUUCCGGUGGCUCCACGGACUUUUGUCUGCCCUUUUUGGGCGCUGGGAGUCGAGUGGCCCG
------.......((((.((...((((.((...)).))))...)).))))......(((((((....((((((..((((....))))((((.....))))....)))))))))))))... ( -40.10)
>DroSec_CAF1 1 119 + 1
UUACAGCUUGUAAGUGCUCAUUAACAUAAGCCGCUGAUGUCGUUGUGCACAUUGUUGCCAUUCCGGUGGCUCCACGGACUUUUGUCUGCCCUU-UUGGGCGCUGGGAGCCGAGUGGCCAG
((((.....))))((((.((...((((.((...)).))))...)).))))......(((((((....((((((..((((....))))((((..-..))))....)))))))))))))... ( -44.00)
>DroSim_CAF1 1 99 + 1
--------------------UUAACAUAAGCCGCUGAUGUCGUUGUGCACAUUGUUGCCAUUCCGGUGGCUCCGCGGACUUUUGUCUGCCCUU-UUGGGCGCUGGGAGCCGAGUGGCCAG
--------------------.........((((((....(((..(((((......)).)))..)))(((((((((((((....))))((((..-..))))))..)))))))))))))... ( -40.00)
>consensus
______CUUGUAAGUGCUCAUUAACAUAAGCCGCUGAUGUCGUUGUGCACAUUGUUGCCAUUCCGGUGGCUCCACGGACUUUUGUCUGCCCUU_UUGGGCGCUGGGAGCCGAGUGGCCAG
.............................(((((((((((.(.....))))))...(((.....)))((((((..((((....))))((((.....))))....)))))).))))))... (-37.72 = -37.50 +  -0.22)

alignment

secondary structure

dotplot

Window 3

Location	16,768,248 – 16,768,362
Length	114
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	85.84
Mean single sequence MFE	-34.87
Consensus MFE	-30.59
Energy contribution	-30.70
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.51
Structure conservation index	0.88
SVM decision value	0.23
SVM RNA-class probability	0.642176
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16768248 114 - 27905053
CGGGCCACUCGACUCCCAGCGCCCAAAAAGGGCAGACAAAAGUCCGUGGAGCCACCGGAAUGGCAACAAUGUGCGCAACGACAUCAGCGGCUUAUGUUAAUGAGCACUUACAAG------
(((.((((..((((.....(((((.....)))).).....)))).)))).....)))...((....)).(((((((..........)))((((((....))))))...))))..------ ( -32.20)
>DroSec_CAF1 1 119 - 1
CUGGCCACUCGGCUCCCAGCGCCCAA-AAGGGCAGACAAAAGUCCGUGGAGCCACCGGAAUGGCAACAAUGUGCACAACGACAUCAGCGGCUUAUGUUAAUGAGCACUUACAAGCUGUAA
...((((.(((((((((...((((..-..)))).(((....))).).))))))....)).))))....((((........))))((((.((((((....))))))........))))... ( -38.60)
>DroSim_CAF1 1 99 - 1
CUGGCCACUCGGCUCCCAGCGCCCAA-AAGGGCAGACAAAAGUCCGCGGAGCCACCGGAAUGGCAACAAUGUGCACAACGACAUCAGCGGCUUAUGUUAA--------------------
..((((.((.((((((..((((((..-..)))).(((....))).))))))))..((...(((((......))).)).)).....)).))))........-------------------- ( -33.80)
>consensus
CUGGCCACUCGGCUCCCAGCGCCCAA_AAGGGCAGACAAAAGUCCGUGGAGCCACCGGAAUGGCAACAAUGUGCACAACGACAUCAGCGGCUUAUGUUAAUGAGCACUUACAAG______
..((((.((.((((((..((((((.....)))).(((....))).))))))))..((...(((((......))).)).)).....)).))))............................ (-30.59 = -30.70 +   0.11)

alignment

secondary structure

dotplot

Window 4

Location	16,768,322 – 16,768,442
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.77
Mean single sequence MFE	-42.93
Consensus MFE	-38.59
Energy contribution	-38.37
Covariance contribution	-0.22
Combinations/Pair	1.02
Mean z-score	-2.25
Structure conservation index	0.90
SVM decision value	0.62
SVM RNA-class probability	0.803001
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16768322 120 + 27905053
UUUGUCUGCCCUUUUUGGGCGCUGGGAGUCGAGUGGCCCGGAGUCCGGACUUGGGGCUCUCGACUCGCGCUGAUUGUCGUAUUUAAAUUAAUUUCAAUACAACGACAAAGAGUACGAAUC
((((((.((((.....))))((.(.((((((((.(((((.((((....)))).))))))))))))).))).....((.(((((.(((....))).))))).))))))))........... ( -49.70)
>DroSec_CAF1 81 119 + 1
UUUGUCUGCCCUU-UUGGGCGCUGGGAGCCGAGUGGCCAGGAGUCCGGACUUGGGGCUCUCGACUCGCGCUGAUUGUCGUAUUUAAAUUAAUUUCAAUACAACAACAAAGAGUACGAAUC
(((((((((((..-..))))((.(.(((.((((.((((..((((....))))..)))))))).))).)))((.((((.(((((.(((....))).))))).))))))...)).))))).. ( -39.10)
>DroSim_CAF1 61 119 + 1
UUUGUCUGCCCUU-UUGGGCGCUGGGAGCCGAGUGGCCAGGAGUCCGGACUUGGGGCUCUCGACUCGCGCUGAUUGUCGUAUUUAAAUUAAUUUCAAUACAACGACAAAGAGUACGAAUC
((((((.((((..-..))))((.(.(((.((((.((((..((((....))))..)))))))).))).))).....((.(((((.(((....))).))))).))))))))........... ( -40.00)
>consensus
UUUGUCUGCCCUU_UUGGGCGCUGGGAGCCGAGUGGCCAGGAGUCCGGACUUGGGGCUCUCGACUCGCGCUGAUUGUCGUAUUUAAAUUAAUUUCAAUACAACGACAAAGAGUACGAAUC
(((((((((((.....))))((.(.(((.((((.((((..((((....))))..)))))))).))).)))((.((((.(((((.(((....))).))))).))))))...)).))))).. (-38.59 = -38.37 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	16,768,322 – 16,768,442
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.77
Mean single sequence MFE	-42.90
Consensus MFE	-41.11
Energy contribution	-40.67
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-3.65
Structure conservation index	0.96
SVM decision value	2.06
SVM RNA-class probability	0.986995
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16768322 120 - 27905053
GAUUCGUACUCUUUGUCGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUCCGGGCCACUCGACUCCCAGCGCCCAAAAAGGGCAGACAAA
............(((((((((((((.(((....))).)))))))).....((..((((((((.((((..(((....)))..))))..))))))))...))((((.....)))).))))). ( -46.20)
>DroSec_CAF1 81 119 - 1
GAUUCGUACUCUUUGUUGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUCCUGGCCACUCGGCUCCCAGCGCCCAA-AAGGGCAGACAAA
((((((..((....(((((((((((.(((....))).))))))))))).))..))))))(.(((((...(((((((....))))..))).))))).)...((((..-..))))....... ( -40.90)
>DroSim_CAF1 61 119 - 1
GAUUCGUACUCUUUGUCGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUCCUGGCCACUCGGCUCCCAGCGCCCAA-AAGGGCAGACAAA
((((((..((..(((((((....(((((.....)))))..)))))))..))..))))))(.(((((...(((((((....))))..))).))))).)...((((..-..))))....... ( -41.60)
>consensus
GAUUCGUACUCUUUGUCGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUCCUGGCCACUCGGCUCCCAGCGCCCAA_AAGGGCAGACAAA
............(((((((((((((.(((....))).)))))))).....((..((((((((.(((...(((....)))...)))..))))))))...))((((.....)))).))))). (-41.11 = -40.67 +  -0.44)

alignment

secondary structure

dotplot

Window 6

Location	16,768,362 – 16,768,482
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-32.33
Consensus MFE	-31.85
Energy contribution	-31.97
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.17
Structure conservation index	0.99
SVM decision value	1.21
SVM RNA-class probability	0.931187
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16768362 120 - 27905053
ACUUUUAUGGGCCAGUGUCUUUUGAUUCUAUAAUUUGCAUGAUUCGUACUCUUUGUCGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUC
........(((((((.(((....))).))..........(((((((..((..(((((((....(((((.....)))))..)))))))..))..))))))).).))))............. ( -30.10)
>DroSec_CAF1 120 120 - 1
ACUUUUAUGGGCCAGUGUCUUUUGAUUCUAUAAUUUGCUUGAUUCGUACUCUUUGUUGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUC
........((((.((.(((....))).))........(((((((((..((....(((((((((((.(((....))).))))))))))).))..))))))))).))))............. ( -33.10)
>DroSim_CAF1 100 120 - 1
ACUUUUAUGGGCCAGUGUCUUUUGAUUCUAUAAUUUGCUUGAUUCGUACUCUUUGUCGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUC
........((((.((.(((....))).))........(((((((((..((..(((((((....(((((.....)))))..)))))))..))..))))))))).))))............. ( -33.80)
>consensus
ACUUUUAUGGGCCAGUGUCUUUUGAUUCUAUAAUUUGCUUGAUUCGUACUCUUUGUCGUUGUAUUGAAAUUAAUUUAAAUACGACAAUCAGCGCGAGUCGAGAGCCCCAAGUCCGGACUC
........((((.((.(((....))).))........(((((((((..((..(((((((....(((((.....)))))..)))))))..))..))))))))).))))............. (-31.85 = -31.97 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:19 2006