Locus 1708

Sequence ID	2R_DroMel_CAF1
Location	6,458,414 – 6,458,571
Length	157
Max. P	0.999818

overview

Window 4

Location	6,458,414 – 6,458,505
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	95.38
Mean single sequence MFE	-19.54
Consensus MFE	-17.52
Energy contribution	-18.52
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.90
SVM decision value	2.68
SVM RNA-class probability	0.996329
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6458414 91 + 20766785
GAAUGGCGCCCACCCUUUUGUACCCAUACUGCCCAUCUCUCUCGGCAUUGUUCUACCCAUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCA
..((((.(..((......))..)))))..((((..........))))............(((((((.....)))))))..(((....))). ( -15.00)
>DroSec_CAF1 34048 90 + 1
GAAUGGCGCCCUCCCUUUUGUGCCCAUUCUACCCGUCUC-CUCGGCAUUGUUCUACCCGUCCCUUUCUCAUAAAGAGACUGCAGUUAUGCA
((((((.((.(........).))))))))...(((....-..))).............(((.((((.....)))).))).(((....))). ( -19.10)
>DroSim_CAF1 25410 91 + 1
GAAUGGCGCCCUCCCUUUUGUGCCCAUUCUACCCGUCUCUCUCGGCAUUGUUCUACCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCA
((((((.((.(........).))))))))...(((.......))).............((((((((.....)))))))).(((....))). ( -23.40)
>DroEre_CAF1 32368 90 + 1
GAAUGGCGCCCUC-CUUUUGUGCCCACUCUACCCAUCUCUCUCGGCAUUGUUCUACCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCA
(((((((((....-.....)))))........((.........))....)))).....((((((((.....)))))))).(((....))). ( -18.20)
>DroYak_CAF1 36010 91 + 1
GAAUGGCGCCCUCCCUUUUGUGCCCAUUCUACCCAUCUCUCUCGGCAUUGUUCUACCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCA
((((((.((.(........).))))))))...............((((....((.(..((((((((.....)))))))).).))..)))). ( -22.00)
>consensus
GAAUGGCGCCCUCCCUUUUGUGCCCAUUCUACCCAUCUCUCUCGGCAUUGUUCUACCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCA
((((((.((.(........).))))))))...............((((....((..(.((((((((.....)))))))).).))..)))). (-17.52 = -18.52 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	6,458,414 – 6,458,505
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	95.38
Mean single sequence MFE	-26.82
Consensus MFE	-25.28
Energy contribution	-24.68
Covariance contribution	-0.60
Combinations/Pair	1.20
Mean z-score	-2.40
Structure conservation index	0.94
SVM decision value	4.16
SVM RNA-class probability	0.999818
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6458414 91 - 20766785
UGCAUAACUGCAGUCUCUUUAUGAGAAAGAGAUGGGUAGAACAAUGCCGAGAGAGAUGGGCAGUAUGGGUACAAAAGGGUGGGCGCCAUUC
..((((.((((.((((((((.....))))))))..)))).....((((.(......).)))).)))).........((((((...)))))) ( -24.50)
>DroSec_CAF1 34048 90 - 1
UGCAUAACUGCAGUCUCUUUAUGAGAAAGGGACGGGUAGAACAAUGCCGAG-GAGACGGGUAGAAUGGGCACAAAAGGGAGGGCGCCAUUC
.......((((.((((((((.....))))))))..)))).....((((..(-....).))))((((((((.(........).)).)))))) ( -28.70)
>DroSim_CAF1 25410 91 - 1
UGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGACGGGUAGAAUGGGCACAAAAGGGAGGGCGCCAUUC
(((....((((.((((((((.....))))))))..)))).......(((.......))))))((((((((.(........).)).)))))) ( -26.50)
>DroEre_CAF1 32368 90 - 1
UGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGAUGGGUAGAGUGGGCACAAAAG-GAGGGCGCCAUUC
.......((((.((((((((.....))))))))..)))).....((((.(......).))))((((((((.(.....-...))).)))))) ( -27.10)
>DroYak_CAF1 36010 91 - 1
UGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGAUGGGUAGAAUGGGCACAAAAGGGAGGGCGCCAUUC
.......((((.((((((((.....))))))))..)))).....((((.(......).))))((((((((.(........).)).)))))) ( -27.30)
>consensus
UGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGAUGGGUAGAAUGGGCACAAAAGGGAGGGCGCCAUUC
.......((((.((((((((.....))))))))..)))).....((((..........))))((((((((.(........).)).)))))) (-25.28 = -24.68 +  -0.60)

alignment

secondary structure

dotplot

Window 6

Location	6,458,439 – 6,458,540
Length	101
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	88.12
Mean single sequence MFE	-28.20
Consensus MFE	-22.84
Energy contribution	-23.20
Covariance contribution	0.36
Combinations/Pair	1.12
Mean z-score	-2.16
Structure conservation index	0.81
SVM decision value	0.30
SVM RNA-class probability	0.680060
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6458439 101 - 20766785
GCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGAUGGGUAGAACAAUGCCGAGAGAGAUGGGCAGUAU
((.((....))..(((((.....-----)))))...)).((((....((((.((((((((.....))))))))..)))).....((((.(......).)))))))) ( -30.20)
>DroSec_CAF1 34073 100 - 1
GCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGGGACGGGUAGAACAAUGCCGAG-GAGACGGGUAGAAU
(((((....))..(((((.....-----))))).......)))....((((.((((((((.....))))))))..)))).....((((..(-....).)))).... ( -30.30)
>DroSim_CAF1 25435 101 - 1
GCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGACGGGUAGAAU
(((((....))..(((((.....-----))))).......)))....((((.((((((((.....)))))))).((((......))))...........))))... ( -28.40)
>DroEre_CAF1 32392 101 - 1
GCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGAUGGGUAGAGU
(((((....))..(((((.....-----))))).......)))....((((.((((((((.....))))))))..)))).((..((((.(......).))))..)) ( -29.50)
>DroYak_CAF1 36035 101 - 1
GCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGAUGGGUAGAAU
(((((....))..(((((.....-----))))).......)))....((((.((((((((.....))))))))..)))).....((((.(......).)))).... ( -28.90)
>DroAna_CAF1 35576 94 - 1
GCAGAGCAAUCAAGCGCGAAAUCUCUGCUGUGCACAGCAAUGCAUAACUGCAGUCUCCGUGUGAGACAAAAACAG---------U---GAAAGAGAAGGGACUAGU
((.((....))..))......(((((((((....))))..((((....))))(((((.....)))))........---------.---...))))).......... ( -21.90)
>consensus
GCAGAGCAAUCAAGCGCGAAAUC_____UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGGUAGAACAAUGCCGAGAGAGAUGGGUAGAAU
((((.((......)).............((((((......)))))).)))).((((((((.....)))))))).((((......)))).................. (-22.84 = -23.20 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	6,458,469 – 6,458,571
Length	102
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	92.50
Mean single sequence MFE	-27.53
Consensus MFE	-23.62
Energy contribution	-23.27
Covariance contribution	-0.36
Combinations/Pair	1.13
Mean z-score	-2.10
Structure conservation index	0.86
SVM decision value	1.13
SVM RNA-class probability	0.920546
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6458469 102 + 20766785
CCCAUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCAUUGCUGUGCACA-----GAUUUCGCGCUUGAUUGCUCUGCUUAUGCGCCUGAUGCGUUUUGUAUUUAUAUU---------
....(((((((.....))))))).(((((..(((((((...(((((((-----((....(((......)))))))....)))))..))))))).)))))........--------- ( -24.30)
>DroSec_CAF1 34102 102 + 1
CCCGUCCCUUUCUCAUAAAGAGACUGCAGUUAUGCAUUGCUGUGCACA-----GAUUUCGCGCUUGAUUGCUCUGCUUAUGCGCCUGAUGCGUUUUGUAUUUAUAUU---------
...(((.((((.....)))).)))(((((..(((((((...(((((((-----((....(((......)))))))....)))))..))))))).)))))........--------- ( -22.90)
>DroSim_CAF1 25465 102 + 1
CCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCAUUGCUGUGCACA-----GAUUUCGCGCUUGAUUGCUCUGCUUAUGCGCCUGAUGCGUUUUGUAUUUAUAUU---------
...((((((((.....))))))))(((((..(((((((...(((((((-----((....(((......)))))))....)))))..))))))).)))))........--------- ( -27.70)
>DroEre_CAF1 32422 102 + 1
CCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCAUUGCUGUGCACA-----GAUUUCGCGCUUGAUUGCUCUGCUUAUGCGCCUGAUGCGUUUUGUAUUUAUAUU---------
...((((((((.....))))))))(((((..(((((((...(((((((-----((....(((......)))))))....)))))..))))))).)))))........--------- ( -27.70)
>DroYak_CAF1 36065 102 + 1
CCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCAUUGCUGUGCACA-----GAUUUCGCGCUUGAUUGCUCUGCUUAUGCGCCUGAUGCGUUUUGUAUUUAUAUU---------
...((((((((.....))))))))(((((..(((((((...(((((((-----((....(((......)))))))....)))))..))))))).)))))........--------- ( -27.70)
>DroAna_CAF1 35595 115 + 1
-CUGUUUUUGUCUCACACGGAGACUGCAGUUAUGCAUUGCUGUGCACAGCAGAGAUUUCGCGCUUGAUUGCUCUGCUUAUGCGCCUGAUGCGUUUUGUAUUUAUAUUUGUAUAUAU
-........(((((.....)))))(((((..(((((((...(((((.(((((((...(((....)))...)))))))..)))))..))))))).)))))..(((((....))))). ( -34.90)
>consensus
CCCGUCUCUUUCUCAUAAAGAGACUGCAGUUAUGCAUUGCUGUGCACA_____GAUUUCGCGCUUGAUUGCUCUGCUUAUGCGCCUGAUGCGUUUUGUAUUUAUAUU_________
...((((((((.....))))))))(((((..(((((((...(((((.......(....)((((......))...))...)))))..))))))).)))))................. (-23.62 = -23.27 +  -0.36)

alignment

secondary structure

dotplot

Window 8

Location	6,458,469 – 6,458,571
Length	102
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	92.50
Mean single sequence MFE	-25.27
Consensus MFE	-23.44
Energy contribution	-23.38
Covariance contribution	-0.05
Combinations/Pair	1.13
Mean z-score	-2.14
Structure conservation index	0.93
SVM decision value	2.78
SVM RNA-class probability	0.996993
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6458469 102 - 20766785
---------AAUAUAAAUACAAAACGCAUCAGGCGCAUAAGCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGAUGGG
---------...............(((.....))).....((((.((......))........-----((((((......)))))).)))).((((((((.....))))))))... ( -23.20)
>DroSec_CAF1 34102 102 - 1
---------AAUAUAAAUACAAAACGCAUCAGGCGCAUAAGCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGGGACGGG
---------...............(((.....))).....((((.((......))........-----((((((......)))))).)))).((((((((.....))))))))... ( -24.50)
>DroSim_CAF1 25465 102 - 1
---------AAUAUAAAUACAAAACGCAUCAGGCGCAUAAGCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGG
---------...............(((.....))).....((((.((......))........-----((((((......)))))).)))).((((((((.....))))))))... ( -25.40)
>DroEre_CAF1 32422 102 - 1
---------AAUAUAAAUACAAAACGCAUCAGGCGCAUAAGCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGG
---------...............(((.....))).....((((.((......))........-----((((((......)))))).)))).((((((((.....))))))))... ( -25.40)
>DroYak_CAF1 36065 102 - 1
---------AAUAUAAAUACAAAACGCAUCAGGCGCAUAAGCAGAGCAAUCAAGCGCGAAAUC-----UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGG
---------...............(((.....))).....((((.((......))........-----((((((......)))))).)))).((((((((.....))))))))... ( -25.40)
>DroAna_CAF1 35595 115 - 1
AUAUAUACAAAUAUAAAUACAAAACGCAUCAGGCGCAUAAGCAGAGCAAUCAAGCGCGAAAUCUCUGCUGUGCACAGCAAUGCAUAACUGCAGUCUCCGUGUGAGACAAAAACAG-
.(((((....))))).........(((((.(((((((((.((((((...((......))...))))))))))).......((((....))))))))..)))))............- ( -27.70)
>consensus
_________AAUAUAAAUACAAAACGCAUCAGGCGCAUAAGCAGAGCAAUCAAGCGCGAAAUC_____UGUGCACAGCAAUGCAUAACUGCAGUCUCUUUAUGAGAAAGAGACGGG
........................(((.....))).....((((.((......)).............((((((......)))))).)))).((((((((.....))))))))... (-23.44 = -23.38 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:22 2006