Locus 1262

Sequence ID	2L_DroMel_CAF1
Location	3,343,178 – 3,343,332
Length	154
Max. P	0.995108

overview

Window 2

Location	3,343,178 – 3,343,274
Length	96
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	71.62
Mean single sequence MFE	-31.50
Consensus MFE	-17.60
Energy contribution	-18.85
Covariance contribution	1.25
Combinations/Pair	1.12
Mean z-score	-1.62
Structure conservation index	0.56
SVM decision value	0.72
SVM RNA-class probability	0.831451
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3343178 96 + 22407834
GUGG---UGGAGG--AAGGGAUGGCUUAUGCCAAACAGAGGCAGACGAUGUCGAGUCGAGACCAGUCAAGUGGCACUUGUUGCACGCCACUUGACUUCGAG
.(((---(.....--...(..((((....))))..)...(((.(((...)))..)))...))))((((((((((...........))))))))))...... ( -31.70)
>DroSec_CAF1 34003 101 + 1
GAGGUGGUGGGGGGAGCAGGGUGGCUUAUGCCAAGGAGGGGCAGACGAUGUCGAGUUGAGUCGAGUCAAGUGGCACUUGUUGCACGCCACUUGACUUCGAG
((((((((((.((.((((((((.((((.((((.......))))...(((.((((......))))))))))).)).)))))).).).)))))..)))))... ( -38.30)
>DroSim_CAF1 30088 99 + 1
GAGGUGGUGGGGG--GCAGGGUGGCUUAUGCCAAAGAGGGGCAGACGAUGUCGAGUCGAGUCGAGUCAAGUGGCACUUGUUGCACGCCACUUGACUUCGAG
.((((((((.(.(--(((((((.((((.((((.......))))...(((.((((......))))))))))).)).)))))).).))))))))......... ( -36.50)
>DroEre_CAF1 28492 82 + 1
AAU---A----------GGGGGGUCUUAUGCCAAAGAGG-GUAUGCGAAGUCG-----CGUCGAGUCAAGUGGCACUUGUUGCGCGCCACUUGACUUCGAG
...---.----------(.((..((.((((((......)-))))).))..)).-----).((((((((((((((.(.......).)))))))))).)))). ( -33.10)
>DroYak_CAF1 29367 85 + 1
GAGGUGA----------GAGGGGGUUUAUGCCAAAGAGG-GUAGACGAAGUCG-----AGUCGAGUCAAGUAGCACUUGUUGCGCGCCACUUGACUUCGAG
.......----------......((((((.((.....))-))))))(((((((-----(((.(.((...(((((....)))))..)))))))))))))... ( -25.60)
>DroAna_CAF1 36257 74 + 1
GAGG------A--------GGGAGCUGAGGUGAA--------CAACGAAGCCA-----AGUCGUGUCAAGUGGCACUUGUUGCCUGGCACUCGACUUGGAG
..(.------.--------(...((....))...--------)..)....(((-----((((((((((.(..((....))..).))))))..))))))).. ( -23.80)
>consensus
GAGG_____________GGGGGGGCUUAUGCCAAAGAGG_GCAGACGAAGUCG_____AGUCGAGUCAAGUGGCACUUGUUGCACGCCACUUGACUUCGAG
......................(((....)))............................((((((((((((((...........)))))))))).)))). (-17.60 = -18.85 +   1.25)

alignment

secondary structure

dotplot

Window 3

Location	3,343,178 – 3,343,274
Length	96
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	71.62
Mean single sequence MFE	-26.93
Consensus MFE	-18.94
Energy contribution	-19.42
Covariance contribution	0.47
Combinations/Pair	1.32
Mean z-score	-3.03
Structure conservation index	0.70
SVM decision value	2.54
SVM RNA-class probability	0.995108
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3343178 96 - 22407834
CUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUGGUCUCGACUCGACAUCGUCUGCCUCUGUUUGGCAUAAGCCAUCCCUU--CCUCCA---CCAC
.....((((((((((((.........))))))))))))(((...(((........))).......(..((((....))))..)...--.....)---)).. ( -28.80)
>DroSec_CAF1 34003 101 - 1
CUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUCGACUCAACUCGACAUCGUCUGCCCCUCCUUGGCAUAAGCCACCCUGCUCCCCCCACCACCUC
.((((.(((((((((((.........)))))))))))))))........(((...)))..........((((....))))..................... ( -27.00)
>DroSim_CAF1 30088 99 - 1
CUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUCGACUCGACUCGACAUCGUCUGCCCCUCUUUGGCAUAAGCCACCCUGC--CCCCCACCACCUC
.((((.(((((((((((.........)))))))))))))))...(((........)))..........((((....))))......--............. ( -28.50)
>DroEre_CAF1 28492 82 - 1
CUCGAAGUCAAGUGGCGCGCAACAAGUGCCACUUGACUCGACG-----CGACUUCGCAUAC-CCUCUUUGGCAUAAGACCCCCC----------U---AUU
.((((.((((((((((((.......)))))))))))))))).(-----((....)))....-..((((......))))......----------.---... ( -31.70)
>DroYak_CAF1 29367 85 - 1
CUCGAAGUCAAGUGGCGCGCAACAAGUGCUACUUGACUCGACU-----CGACUUCGUCUAC-CCUCUUUGGCAUAAACCCCCUC----------UCACCUC
.((((.((((((((((((.......))))))))))))))))..-----.......(((...-.......)))............----------....... ( -25.70)
>DroAna_CAF1 36257 74 - 1
CUCCAAGUCGAGUGCCAGGCAACAAGUGCCACUUGACACGACU-----UGGCUUCGUUG--------UUCACCUCAGCUCCC--------U------CCUC
..((((((((.((....((((.....)))).....)).)))))-----)))....((((--------.......))))....--------.------.... ( -19.90)
>consensus
CUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUCGACU_____CGACAUCGUCUGC_CCUCUUUGGCAUAAGCCACCCC_____________CCUC
.((((.((((((((((((.......))))))))))))))))..............(((...........)))............................. (-18.94 = -19.42 +   0.47)

alignment

secondary structure

dotplot

Window 4

Location	3,343,203 – 3,343,297
Length	94
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	72.49
Mean single sequence MFE	-26.62
Consensus MFE	-18.92
Energy contribution	-19.28
Covariance contribution	0.36
Combinations/Pair	1.27
Mean z-score	-2.52
Structure conservation index	0.71
SVM decision value	2.47
SVM RNA-class probability	0.994359
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3343203 94 - 22407834
-----GGCCAUC-------ACCCAGCCAUCCCCC----UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUGGUCUCGACUCGACAUCGUCUGCCUCUGUUUGG
-----(((....-------.....))).....((----...((.((((((((((((.........))))))))))))(((...(((........))).)))..))...)) ( -25.90)
>DroSec_CAF1 34033 94 - 1
-----GGCCAUC-------ACCCAACCAUUCCCC----UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUCGACUCAACUCGACAUCGUCUGCCCCUCCUUGG
-----(((....-------...............----..((((.(((((((((((.........)))))))))))))))........(((...))).)))......... ( -25.80)
>DroSim_CAF1 30116 94 - 1
-----GGCCAUC-------ACCCAACAAUCCCCC----UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUCGACUCGACUCGACAUCGUCUGCCCCUCUUUGG
-----(((....-------...............----..((((.(((((((((((.........)))))))))))))))...(((........))).)))......... ( -27.30)
>DroEre_CAF1 28509 93 - 1
CCAUCGCCCAUC-------ACCCAGCCAUCCCCC----UCUCGAAGUCAAGUGGCGCGCAACAAGUGCCACUUGACUCGACG-----CGACUUCGCAUAC-CCUCUUUGG
............-------..((((.........----..((((.((((((((((((.......)))))))))))))))).(-----((....)))....-.....)))) ( -32.70)
>DroYak_CAF1 29387 79 - 1
---------------------CCAGUCAUCCCCC----UCUCGAAGUCAAGUGGCGCGCAACAAGUGCUACUUGACUCGACU-----CGACUUCGUCUAC-CCUCUUUGG
---------------------((((.........----..((((.((((((((((((.......))))))))))))))))..-----.(((...)))...-.....)))) ( -26.30)
>DroAna_CAF1 36273 92 - 1
-----CACCACCACAUCGCACACAACACUCGCACACAACCUCCAAGUCGAGUGCCAGGCAACAAGUGCCACUUGACACGACU-----UGGCUUCGUUG--------UUCA
-----............((...........))..(((((..((((((((.((....((((.....)))).....)).)))))-----)))....))))--------)... ( -21.70)
>consensus
_____GGCCAUC_______ACCCAACCAUCCCCC____UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGACUCGACU_____CGACAUCGUCUGC_CCUCUUUGG
.....................((((...............((((.((((((((((((.......)))))))))))))))).......((....))...........)))) (-18.92 = -19.28 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	3,343,237 – 3,343,332
Length	95
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	76.86
Mean single sequence MFE	-23.17
Consensus MFE	-17.05
Energy contribution	-17.00
Covariance contribution	-0.05
Combinations/Pair	1.31
Mean z-score	-1.97
Structure conservation index	0.74
SVM decision value	1.63
SVM RNA-class probability	0.968518
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3343237 95 - 22407834
AGUGGCAUCAGAUAAAUAGCACCCACCCAUCGCCU----------GGCCAUC-------ACCCAGCCAUCCCCC----UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGAC
((((((((..........((((((((.....(.((----------((.....-------..)))).).......----....(....)..)))).)))).....)))))))).... ( -23.66)
>DroSec_CAF1 34067 95 - 1
AGUGGCAUCAGAUAAAUAGCACCCACCCAUCGCCC----------GGCCAUC-------ACCCAACCAUUCCCC----UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGAC
.(((((....(((...............)))....----------.))))).-------...............----.......(((((((((((.........))))))))))) ( -22.56)
>DroSim_CAF1 30150 95 - 1
AGUGGCAUCAGAUAAAUAGCACCCACCCAUCCCCC----------GGCCAUC-------ACCCAACAAUCCCCC----UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGAC
.(((((....(((...............)))....----------.))))).-------...............----.......(((((((((((.........))))))))))) ( -21.46)
>DroEre_CAF1 28537 105 - 1
AGUGGCAUCAGAUAAAUAGCACCCACCCAUCGCCCAUCGCCCAUCGCCCAUC-------ACCCAGCCAUCCCCC----UCUCGAAGUCAAGUGGCGCGCAACAAGUGCCACUUGAC
.(((((............((...........)).....((.....)).....-------.....))))).....----.......((((((((((((.......)))))))))))) ( -27.60)
>DroYak_CAF1 29415 77 - 1
AGUGGCAUCAGAUAAAUAGCACCCAC-----------------------------------CCAGUCAUCCCCC----UCUCGAAGUCAAGUGGCGCGCAACAAGUGCUACUUGAC
.((((.................))))-----------------------------------.............----.......((((((((((((.......)))))))))))) ( -21.03)
>DroAna_CAF1 36294 105 - 1
AGUGGCAUCAGAUAAACUGUC-UACCCCACCGCAC----------CACCACCACAUCGCACACAACACUCGCACACAACCUCCAAGUCGAGUGCCAGGCAACAAGUGCCACUUGAC
((((((((.((((.....)))-)............----------............((......((((((.((...........))))))))....)).....)))))))).... ( -22.70)
>consensus
AGUGGCAUCAGAUAAAUAGCACCCACCCAUCGCCC__________GGCCAUC_______ACCCAACCAUCCCCC____UCUCGAAGUCAAGUGGCGUGCAACAAGUGCCACUUGAC
.((((.................))))...........................................................((((((((((((.......)))))))))))) (-17.05 = -17.00 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:04 2006