Locus 7524

Sequence ID	2L_DroMel_CAF1
Location	20,876,833 – 20,876,958
Length	125
Max. P	0.927729

overview

Window 2

Location	20,876,833 – 20,876,934
Length	101
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	70.97
Mean single sequence MFE	-16.64
Consensus MFE	-9.89
Energy contribution	-11.17
Covariance contribution	1.28
Combinations/Pair	1.19
Mean z-score	-1.47
Structure conservation index	0.59
SVM decision value	0.68
SVM RNA-class probability	0.819274
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20876833 101 - 22407834
GAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA----UAAAACACACGGCGGGCAUAAU-AAA-GUAUCGAAU-----------AUAAAAAGCAACCACACUCAAC
((.(((...(((((((((.........(...)..(((((((....----......))))))))))))))))-...-)))))....-----------...................... ( -21.00)
>DroSec_CAF1 65910 101 - 1
GAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA----UAAAACACACGGCGGGCAUAAU-AAA-GUAUCGAAU-----------AUAAAAAGCGACCCCACUCAAC
((.(((...(((((((((.........(...)..(((((((....----......))))))))))))))))-...-)))))....-----------...................... ( -21.00)
>DroSim_CAF1 69858 101 - 1
GAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA----UAAAACACACGGCGGGCAUAAU-AAA-GUAUCGAAU-----------AUAAAAAGCGACCCCACUCAAC
((.(((...(((((((((.........(...)..(((((((....----......))))))))))))))))-...-)))))....-----------...................... ( -21.00)
>DroEre_CAF1 67375 114 - 1
GAAGGCAAAAUUAUGCCCAUAAUAAAAUAAACGUGCUGUGUUUAAAGUUUAAAGCACACGGCGAGCAUAAUUAAGUAUAAGGAAUAUAUAUGGAAUAUAAAAAGCGACCC----CAAU
...((((......))))..............((((((((((..............))))))).......(((..(((((.......)))))..))).......)))....----.... ( -16.74)
>DroYak_CAF1 58842 91 - 1
AAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGCUUAA----UAAAACACACGGCGGGCAAGAAUGAG-GUACCGAAUAUAUGUA----------------------UAAU
..(((((......(((((.........(...)..((((((.....----.......))))))))))).......(-....).......))))----------------------)... ( -16.00)
>DroPer_CAF1 75468 86 - 1
GAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGUUGUA----G----AGAGACAGAGAGAGGGA-----------GAAGCCAU-------------AUAAAGAGAAUCGAAUCAAU
....(((......)))...........((..((((((...----.----...))))......((..-----------....))..-------------...........))..))... (  -4.10)
>consensus
GAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA____UAAAACACACGGCGGGCAUAAU_AAA_GUAUCGAAU___________AUAAAAAGCGACCCCACUCAAC
..........((((((((...((.........))((((((................))))))))))))))................................................ ( -9.89 = -11.17 +   1.28)

alignment

secondary structure

dotplot

Window 3

Location	20,876,862 – 20,876,958
Length	96
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	81.74
Mean single sequence MFE	-23.99
Consensus MFE	-17.15
Energy contribution	-17.35
Covariance contribution	0.20
Combinations/Pair	1.39
Mean z-score	-2.99
Structure conservation index	0.71
SVM decision value	1.19
SVM RNA-class probability	0.927729
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20876862 96 + 22407834
AC-UUU-AUUAUGCCCGCCGUGUGUUUUA----UUAAACACAGCACGUUUCUUUUAUUAUGGGCAUAAUUUUGCAUUCAAUUAAAACGGCGAGCAAAAAACC
..-...-....(((.((((((((((((..----..)))))).....................(((......)))...........)))))).)))....... ( -23.50)
>DroSec_CAF1 65939 96 + 1
AC-UUU-AUUAUGCCCGCCGUGUGUUUUA----UUAAACACAGCACGUUUCUUUUAUUAUGGGCAUAAUUUUGCAUUCAAUUAAAACGGCGAGCAAAAAACC
..-...-....(((.((((((((((((..----..)))))).....................(((......)))...........)))))).)))....... ( -23.50)
>DroSim_CAF1 69887 96 + 1
AC-UUU-AUUAUGCCCGCCGUGUGUUUUA----UUAAACACAGCACGUUUCUUUUAUUAUGGGCAUAAUUUUGCAUUCAAUUAAAACGGCGAGCAGAAAACC
..-...-....(((.((((((((((((..----..)))))).....................(((......)))...........)))))).)))....... ( -23.50)
>DroEre_CAF1 67411 100 + 1
AUACUUAAUUAUGCUCGCCGUGUGCUUUAAACUUUAAACACAGCACGUUUAUUUUAUUAUGGGCAUAAUUUUGCCUUCGAUUA-AACGGCGAGCAAAAA-CC
...........(((((((((((((((...............))))).........(((..(((((......)))))..)))..-.))))))))))....-.. ( -31.76)
>DroYak_CAF1 58860 96 + 1
AC-CUCAUUCUUGCCCGCCGUGUGUUUUA----UUAAGCACAGCACGUUUCUUUUAUUAUGGGCAUAAUUUUGCAUUUAAUUAAAACGGCGAGCAAAAA-AC
..-.......((((.((((((((((((..----..))))))..........(((.((((...(((......)))...)))).))))))))).))))...-.. ( -25.30)
>DroAna_CAF1 56958 81 + 1
-----------------UUGGCUGUUGUA----UUUAGUGCAACACGUUUCGUUUAUAAUGGGCAUAAUUUUGCAUUCAAUUUAAAUGGCUAGGAAAAAACC
-----------------((((((((((((----(...)))))))).....((((((...((.(((......)))...))...)))))))))))......... ( -16.40)
>consensus
AC_UUU_AUUAUGCCCGCCGUGUGUUUUA____UUAAACACAGCACGUUUCUUUUAUUAUGGGCAUAAUUUUGCAUUCAAUUAAAACGGCGAGCAAAAAACC
...........(((.((((((((((((........)))))).....................(((......)))...........)))))).)))....... (-17.15 = -17.35 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	20,876,862 – 20,876,958
Length	96
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	81.74
Mean single sequence MFE	-23.41
Consensus MFE	-15.84
Energy contribution	-18.32
Covariance contribution	2.47
Combinations/Pair	1.11
Mean z-score	-2.46
Structure conservation index	0.68
SVM decision value	0.82
SVM RNA-class probability	0.859220
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20876862 96 - 22407834
GGUUUUUUGCUCGCCGUUUUAAUUGAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA----UAAAACACACGGCGGGCAUAAU-AAA-GU
.......(((((((((((((.((((...(((......)))...)))).))))........(((((((..----..))))))))))))))))....-...-.. ( -24.70)
>DroSec_CAF1 65939 96 - 1
GGUUUUUUGCUCGCCGUUUUAAUUGAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA----UAAAACACACGGCGGGCAUAAU-AAA-GU
.......(((((((((((((.((((...(((......)))...)))).))))........(((((((..----..))))))))))))))))....-...-.. ( -24.70)
>DroSim_CAF1 69887 96 - 1
GGUUUUCUGCUCGCCGUUUUAAUUGAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA----UAAAACACACGGCGGGCAUAAU-AAA-GU
.......(((((((((((((.((((...(((......)))...)))).))))........(((((((..----..))))))))))))))))....-...-.. ( -24.60)
>DroEre_CAF1 67411 100 - 1
GG-UUUUUGCUCGCCGUU-UAAUCGAAGGCAAAAUUAUGCCCAUAAUAAAAUAAACGUGCUGUGUUUAAAGUUUAAAGCACACGGCGAGCAUAAUUAAGUAU
..-....((((((((((.-........((((......))))...............(((((...............)))))))))))))))........... ( -30.26)
>DroYak_CAF1 58860 96 - 1
GU-UUUUUGCUCGCCGUUUUAAUUAAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGCUUAA----UAAAACACACGGCGGGCAAGAAUGAG-GU
..-(((((((((((((((((.((((...(((......)))...))))....)))))(((.(((......----....))))))))))))))))))....-.. ( -27.10)
>DroAna_CAF1 56958 81 - 1
GGUUUUUUCCUAGCCAUUUAAAUUGAAUGCAAAAUUAUGCCCAUUAUAAACGAAACGUGUUGCACUAAA----UACAACAGCCAA-----------------
((((.((((...((.((((.....))))))....(((((.....)))))..)))).(((((......))----)))...))))..----------------- (  -9.10)
>consensus
GGUUUUUUGCUCGCCGUUUUAAUUGAAUGCAAAAUUAUGCCCAUAAUAAAAGAAACGUGCUGUGUUUAA____UAAAACACACGGCGGGCAUAAU_AAA_GU
.......((((((((((...........(((......))).....................((((((........))))))))))))))))........... (-15.84 = -18.32 +   2.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:56 2006