Locus 47

Sequence ID	3L_DroMel_CAF1
Location	175,154 – 175,354
Length	200
Max. P	0.991380

overview

Window 0

Location	175,154 – 175,274
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-38.23
Consensus MFE	-35.35
Energy contribution	-35.47
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.65
Structure conservation index	0.92
SVM decision value	0.05
SVM RNA-class probability	0.556868
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 175154 120 + 23771897
GAUGAGCUGGCGUCGUCGGUUGAUGCUGAGUCGUAUUAGUAUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACCAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGC
....(((((((...)))))))((((((((......))))))))...((((...(((((.......)))))))))((((((....))))))......((((((((((....)))))))))) ( -39.90)
>DroSec_CAF1 8860 120 + 1
GAUGAGUUGGCGUCGUCGGUUGCUGCUGAGUCGUAUUAGUAUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACCAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGC
.((((.(..(((.((.....)).)))..).))))............((((...(((((.......)))))))))((((((....))))))......((((((((((....)))))))))) ( -38.30)
>DroYak_CAF1 9075 120 + 1
GAUGAGUUGGCGUUGUCGGUUGAUGCUGCAUCGUAUUGGUAUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACAAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGC
..(.((((((((.((.((((....)))))).)))...(((((((.....(((....)))....))))))).....))))).)..............((((((((((....)))))))))) ( -36.50)
>consensus
GAUGAGUUGGCGUCGUCGGUUGAUGCUGAGUCGUAUUAGUAUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACCAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGC
.((((..((((((((.....))))))))..)))).........(((((.(((....)))...)))))(((((((.(.....).)))))))......((((((((((....)))))))))) (-35.35 = -35.47 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	175,194 – 175,314
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	99.44
Mean single sequence MFE	-40.97
Consensus MFE	-39.60
Energy contribution	-39.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.30
Structure conservation index	0.97
SVM decision value	1.20
SVM RNA-class probability	0.929603
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 175194 120 + 23771897
AUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACCAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUU
..((.(((((...(((((.......)))))))))).))......((((((((...(((((((((((....)))))))))))...((.(((......))).)).))))))))......... ( -40.70)
>DroSec_CAF1 8900 120 + 1
AUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACCAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUU
..((.(((((...(((((.......)))))))))).))......((((((((...(((((((((((....)))))))))))...((.(((......))).)).))))))))......... ( -40.70)
>DroYak_CAF1 9115 120 + 1
AUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACAAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUU
(((((.((((...(((((.......)))))))))))))).....((((((((...(((((((((((....)))))))))))...((.(((......))).)).))))))))......... ( -41.50)
>consensus
AUUGUUGAACAUUGGUAUGGAAUCAAUACCGUUCACCAUUGGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUU
.....(((((...(((((.......)))))))))).........((((((((...(((((((((((....)))))))))))...((.(((......))).)).))))))))......... (-39.60 = -39.60 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	175,194 – 175,314
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-30.30
Consensus MFE	-29.57
Energy contribution	-29.90
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.98
SVM decision value	0.94
SVM RNA-class probability	0.885945
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 175194 120 - 23771897
AACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCCAAUGGUGAACGGUAUUGAUUCCAUACCAAUGUUCAACAAU
.........(((((((.....)))((((((((((..(..(((.(((.(((....))).))).))).....(((((......))))))..))))))))...)).......))))....... ( -31.70)
>DroSec_CAF1 8900 120 - 1
AACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCCAAUGGUGAACGGUAUUGAUUCCAUACCAAUGUUCAACAAU
.........(((((((.....)))((((((((((..(..(((.(((.(((....))).))).))).....(((((......))))))..))))))))...)).......))))....... ( -31.70)
>DroYak_CAF1 9115 120 - 1
AACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCCAAUUGUGAACGGUAUUGAUUCCAUACCAAUGUUCAACAAU
.............(((.....)))((.....))((....(((.(((.(((....))).))).)))......))........((((((((((((((.......)))))...)))).))))) ( -27.50)
>consensus
AACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCCAAUGGUGAACGGUAUUGAUUCCAUACCAAUGUUCAACAAU
.........(((((((.....)))((((((((((..(..(((.(((.(((....))).))).))).....(((((......))))))..))))))))...)).......))))....... (-29.57 = -29.90 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	175,234 – 175,354
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-51.27
Consensus MFE	-48.57
Energy contribution	-48.90
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.71
Structure conservation index	0.95
SVM decision value	1.85
SVM RNA-class probability	0.979773
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 175234 120 + 23771897
GGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUUUUUACAGCUCUCAAGCUGAGCGAGGGAUCGAGCCGUUGUU
.((.(((((((....(((((((((((....))))))))))).(((((.((.(((..((((((..((((((.(((.....))).)))))).)))))))))))..))).)).))))))).)) ( -51.10)
>DroSec_CAF1 8940 120 + 1
GGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUUUUUACAGCUCUCAAGCUGAGCGAGGGAUCGAGCCGUUGUU
.((.(((((((....(((((((((((....))))))))))).(((((.((.(((..((((((..((((((.(((.....))).)))))).)))))))))))..))).)).))))))).)) ( -51.10)
>DroYak_CAF1 9155 120 + 1
GGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUUUUUACAGCUCUCAAGCUGAGCGAGAGUUCGAGCCGUUGUU
.......((((....(((((((((((....))))))))))).))))((((......((((((..((((((.(((.....))).)))))).))))))(((((....))))).))))..... ( -51.60)
>consensus
GGAGGAUGGUUAAAGGGCGCUGUAGCGUUUGCUGCAGUGCCAGGCCCGGCAUUACCGCUUGGAUAGCUGUUGAAAAAGUUUUUACAGCUCUCAAGCUGAGCGAGGGAUCGAGCCGUUGUU
.((.(((((((....(((((((((((....))))))))))).(((((.((.(((..((((((..((((((.(((.....))).)))))).)))))))))))..))).)).))))))).)) (-48.57 = -48.90 +   0.33)

alignment

secondary structure

dotplot

Window 4

Location	175,234 – 175,354
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-37.62
Consensus MFE	-37.62
Energy contribution	-37.62
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.16
Structure conservation index	1.00
SVM decision value	2.26
SVM RNA-class probability	0.991380
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 175234 120 - 23771897
AACAACGGCUCGAUCCCUCGCUCAGCUUGAGAGCUGUAAAAACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCC
......(((((.............(((((..((((((.............))))))...)))))((.....))))))).(((.(((.(((....))).))).)))............... ( -37.62)
>DroSec_CAF1 8940 120 - 1
AACAACGGCUCGAUCCCUCGCUCAGCUUGAGAGCUGUAAAAACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCC
......(((((.............(((((..((((((.............))))))...)))))((.....))))))).(((.(((.(((....))).))).)))............... ( -37.62)
>DroYak_CAF1 9155 120 - 1
AACAACGGCUCGAACUCUCGCUCAGCUUGAGAGCUGUAAAAACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCC
......(((((.............(((((..((((((.............))))))...)))))((.....))))))).(((.(((.(((....))).))).)))............... ( -37.62)
>consensus
AACAACGGCUCGAUCCCUCGCUCAGCUUGAGAGCUGUAAAAACUUUUUCAACAGCUAUCCAAGCGGUAAUGCCGGGCCUGGCACUGCAGCAAACGCUACAGCGCCCUUUAACCAUCCUCC
......(((((.............(((((..((((((.............))))))...)))))((.....))))))).(((.(((.(((....))).))).)))............... (-37.62 = -37.62 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:54 2006