Locus 7712

Sequence ID	3L_DroMel_CAF1
Location	20,611,910 – 20,612,064
Length	154
Max. P	0.999164

overview

Window 7

Location	20,611,910 – 20,612,030
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-23.68
Consensus MFE	-23.08
Energy contribution	-23.32
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.34
Structure conservation index	0.97
SVM decision value	3.41
SVM RNA-class probability	0.999164
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20611910 120 + 23771897
UAACUGACAGAAAUCAAAGCCACACAAAACAAAUCAAAAUGCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACCGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGA
.............(((.((((...(......(((((....(((.(((((...))))))))....))))).((((((......))))))...................)...))))..))) ( -22.90)
>DroSec_CAF1 56741 120 + 1
UAACUGACAGAAAUCAAAGCCACACAAAACAAAUCAAAAUGCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGA
.............(((.((((...(......(((((....(((.(((((...))))))))....))))).(((((((....)))))))...................)...))))..))) ( -24.60)
>DroAna_CAF1 78620 120 + 1
UAACUGACAGAAAUCAAAGCCACACAAAACAAAUCAAAAUGCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGAAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGA
.............(((.((((...(...............((((.((((((((.....))))))))....))))(((....))).......................)...))))..))) ( -19.30)
>DroSim_CAF1 51615 120 + 1
UAACUGACAGAAAUCAAAGCCACACAAAACAAAUCAAAAUGCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGA
.............(((.((((...(......(((((....(((.(((((...))))))))....))))).(((((((....)))))))...................)...))))..))) ( -24.60)
>DroEre_CAF1 49317 120 + 1
UAACUGGCAGAAAUCAAAGCCACACAAAACAAAUCAAAAUGCAUGCAUAUAAUAUGCUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGA
.............(((.((((...(......(((((....(((.(((((...))))))))....))))).(((((((....)))))))...................)...))))..))) ( -27.00)
>consensus
UAACUGACAGAAAUCAAAGCCACACAAAACAAAUCAAAAUGCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGA
.............(((.((((...(......(((((....(((.(((((...))))))))....))))).(((((((....)))))))...................)...))))..))) (-23.08 = -23.32 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	20,611,910 – 20,612,030
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-28.20
Consensus MFE	-27.70
Energy contribution	-27.94
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.20
Structure conservation index	0.98
SVM decision value	3.19
SVM RNA-class probability	0.998705
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20611910 120 - 23771897
UCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCGGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGCAUUUUGAUUUGUUUUGUGUGGCUUUGAUUUCUGUCAGUUA
((((.((((.................((((..((((((......)))))).))))((((((.((((.((((.(((....)))..)))).))))))))))))))))))............. ( -28.80)
>DroSec_CAF1 56741 120 - 1
UCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGCAUUUUGAUUUGUUUUGUGUGGCUUUGAUUUCUGUCAGUUA
((((.((((.................((((..(((((((....))))))).))))((((((.((((.((((.(((....)))..)))).))))))))))))))))))............. ( -29.70)
>DroAna_CAF1 78620 120 - 1
UCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUUCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGCAUUUUGAUUUGUUUUGUGUGGCUUUGAUUUCUGUCAGUUA
((((.((((.................((((..((.((((....)))).)).))))((((((.((((.((((.(((....)))..)))).))))))))))))))))))............. ( -23.10)
>DroSim_CAF1 51615 120 - 1
UCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGCAUUUUGAUUUGUUUUGUGUGGCUUUGAUUUCUGUCAGUUA
((((.((((.................((((..(((((((....))))))).))))((((((.((((.((((.(((....)))..)))).))))))))))))))))))............. ( -29.70)
>DroEre_CAF1 49317 120 - 1
UCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAGCAUAUUAUAUGCAUGCAUUUUGAUUUGUUUUGUGUGGCUUUGAUUUCUGCCAGUUA
((((.((((.................((((..(((((((....))))))).))))((((((.((((.((((.(((....)))..)))).))))))))))))))))))............. ( -29.70)
>consensus
UCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGCAUUUUGAUUUGUUUUGUGUGGCUUUGAUUUCUGUCAGUUA
((((.((((.................((((..(((((((....))))))).))))((((((.((((.((((.(((....)))..)))).))))))))))))))))))............. (-27.70 = -27.94 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	20,611,950 – 20,612,064
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.13
Mean single sequence MFE	-23.04
Consensus MFE	-18.24
Energy contribution	-18.64
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.79
SVM decision value	0.15
SVM RNA-class probability	0.609077
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20611950 114 + 23771897
GCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACCGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGAAAUUCUUAAUAAAGAUAAAGAUAA------AGGCUGGGCA
((((.((((((((.....))))))))....))))...((.((((.(......(((((...((......))...))..)))...((((....)))).........------.).)))))). ( -22.40)
>DroSec_CAF1 56781 120 + 1
GCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGAAAUUCUUAAUAAAGAUAAAGAUAAACAUAAAGGCUGGGCA
((..((......((((((......(((((.(((((((....)))))))..)))))...((((....(((.......)))....((((....))))....))))))))))...))...)). ( -25.70)
>DroAna_CAF1 78660 120 + 1
GCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGAAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGAAAUUCUUAAUAAAGAUACAGAUAAAGAUAAAGACUGGGCA
((((.((((((((.....))))))))....))))...((.(((............((...((......))...)).(((....((((....))))..))).............))).)). ( -19.40)
>DroSim_CAF1 51655 120 + 1
GCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGAAAUUCUUAAUAAAGAUAAAGAUAAACAUAAUGGCUGGGCA
((..((.(((..((((((......(((((.(((((((....)))))))..)))))...((((....(((.......)))....((((....))))....)))))))))))))))...)). ( -25.80)
>DroEre_CAF1 49357 106 + 1
GCAUGCAUAUAAUAUGCUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGAAAUUCUUAAUAAAGAUAAAGAUAAA------G--------
(((.(((((...))))))))....(((((.(((((((....)))))))..)))))...((((....(((.......)))....((((....))))....))))..------.-------- ( -21.90)
>consensus
GCAUGCAUAUAAUAUGUUGUUAUAUGAUUAAUGCCCUGCACAGGGCAUAAAAUCAAGAUAUCAAAACGGAGGGCUACUGAAAUUCUUAAUAAAGAUAAAGAUAAA_AUAAAGGCUGGGCA
.....((((((((.....))))))))....(((((((....)))))))..........((((....(((.......)))....((((....))))....))))................. (-18.24 = -18.64 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	20,611,950 – 20,612,064
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.13
Mean single sequence MFE	-20.86
Consensus MFE	-17.64
Energy contribution	-18.04
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.38
Structure conservation index	0.85
SVM decision value	0.38
SVM RNA-class probability	0.712931
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20611950 114 - 23771897
UGCCCAGCCU------UUAUCUUUAUCUUUAUUAAGAAUUUCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCGGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGC
(((((.....------..............(((((((...((((.(((.....)))))))..)))))))....(((.....)))))))).....(((((((.......)))))))..... ( -19.90)
>DroSec_CAF1 56781 120 - 1
UGCCCAGCCUUUAUGUUUAUCUUUAUCUUUAUUAAGAAUUUCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGC
(((........((((((................((((...((((.(((.....)))))))..))))((((..(((((((....))))))).)))).......))))))......)))... ( -22.74)
>DroAna_CAF1 78660 120 - 1
UGCCCAGUCUUUAUCUUUAUCUGUAUCUUUAUUAAGAAUUUCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUUCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGC
(((((((.......)).....(((((....(((((((...((((.(((.....)))))))..)))))))..........)))))))))).....(((((((.......)))))))..... ( -17.24)
>DroSim_CAF1 51655 120 - 1
UGCCCAGCCAUUAUGUUUAUCUUUAUCUUUAUUAAGAAUUUCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGC
(((........((((((................((((...((((.(((.....)))))))..))))((((..(((((((....))))))).)))).......))))))......)))... ( -22.74)
>DroEre_CAF1 49357 106 - 1
--------C------UUUAUCUUUAUCUUUAUUAAGAAUUUCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAGCAUAUUAUAUGCAUGC
--------.------..................((((...((((.(((.....)))))))..))))((((..(((((((....))))))).))))........(((((...))))).... ( -21.70)
>consensus
UGCCCAGCCUUUAU_UUUAUCUUUAUCUUUAUUAAGAAUUUCAGUAGCCCUCCGUUUUGAUAUCUUGAUUUUAUGCCCUGUGCAGGGCAUUAAUCAUAUAACAACAUAUUAUAUGCAUGC
..............................(((((((...((((.(((.....)))))))..)))))))...(((((((....)))))))....(((((((.......)))))))..... (-17.64 = -18.04 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:45 2006