Locus 804

Sequence ID	3R_DroMel_CAF1
Location	2,733,903 – 2,734,064
Length	161
Max. P	0.999586

overview

Window 1

Location	2,733,903 – 2,734,008
Length	105
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	74.81
Mean single sequence MFE	-29.12
Consensus MFE	-20.89
Energy contribution	-22.45
Covariance contribution	1.56
Combinations/Pair	1.41
Mean z-score	-2.67
Structure conservation index	0.72
SVM decision value	3.73
SVM RNA-class probability	0.999569
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2733903 105 - 27905053
ACUGCUUUAUAUUGUGUUUCCUGCUUGAUAUUAGAUCACUAAGCAAGCAG-ACGCGCAAGCAGUUCACGCAGAUCACGCAG---------ACGUUAAAAAUUUAAAAAUGUUUUU
.((((......((((((...(((((((...((((....)))).)))))))-..((....)).....)))))).....))))---------......................... ( -27.20)
>DroSec_CAF1 9842 106 - 1
ACUGCUUUAUAUUAUGUUUACUGCUUGAUAUUAGAUCACUAAGCAAGCAGUACAUGCAUGCAGCUAGAGUAGAUCGGGCAG---------ACGUUAAAAAUUUAAAAAUGUUUUU
.((((((((...(((((.(((((((((...((((....)))).)))))))))...)))))....)))))))).......((---------(((((...........))))))).. ( -28.10)
>DroSim_CAF1 10573 106 - 1
ACUGCUUUAUUUUGUACUUACUGCUUGAUAUUAGAUCACUAAGCAAGCAGUGCGUGCAAGCAGUUCGCGAAGAUCGGGCAG---------ACGUUAAGAAUUUAAAAAUGUUUUU
.(((((..(((((((((.(((((((((...((((....)))).))))))))).))))..((.....)).)))))..)))))---------......................... ( -32.50)
>DroEre_CAF1 11042 105 - 1
ACAGCUUGGUAGCGCGUUUACUGCUUGACAGUAGAUCACAUAGCAAGCAGU-GAUGCGAGCAGUUCAAGUC--------UGCUUGAUAAGACGUUUAACAUUUAAACAU-UUUUG
.((((((((..((.(((((((((((((...((.....))....))))))))-)).))).))...))))).)--------))...........(((((.....)))))..-..... ( -28.70)
>consensus
ACUGCUUUAUAUUGUGUUUACUGCUUGAUAUUAGAUCACUAAGCAAGCAGUACAUGCAAGCAGUUCAAGUAGAUCGGGCAG_________ACGUUAAAAAUUUAAAAAUGUUUUU
.((((((((..((((((.(((((((((...((((....)))).))))))))).)))))).....))))))))........................................... (-20.89 = -22.45 +   1.56)

alignment

secondary structure

dotplot

Window 2

Location	2,733,934 – 2,734,038
Length	104
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	77.22
Mean single sequence MFE	-28.18
Consensus MFE	-17.53
Energy contribution	-17.49
Covariance contribution	-0.04
Combinations/Pair	1.20
Mean z-score	-2.27
Structure conservation index	0.62
SVM decision value	1.77
SVM RNA-class probability	0.976603
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2733934 104 + 27905053
GAUCUGCGUGAACUGCUUGCGCGU-CUGCUUGCUUAGUGAUCUAAUAUCAAGCAGGAAACACAAUAUAAAGCAGUACAUCUAGACUGCUUUUUACUGCUUUGCUU
.....(((..(.....)..))).(-(((((((.((((....))))...))))))))..........((((((((((.....((....))...))))))))))... ( -27.90)
>DroSec_CAF1 9873 105 + 1
GAUCUACUCUAGCUGCAUGCAUGUACUGCUUGCUUAGUGAUCUAAUAUCAAGCAGUAAACAUAAUAUAAAGCAGUAUAUCUUGACUGCUUCCCACUGCUUUGCUU
..............(((.((((((((((((((.((((....))))...)))))))))...........(((((((........)))))))..)).)))..))).. ( -27.10)
>DroSim_CAF1 10604 105 + 1
GAUCUUCGCGAACUGCUUGCACGCACUGCUUGCUUAGUGAUCUAAUAUCAAGCAGUAAGUACAAAAUAAAGCAGUAUAUCUUGACUGCUUCCUACUGCUUUGCUU
.......(((((..(((((.((..((((((((.((((....))))...))))))))..)).)))....(((((((........)))))))......))))))).. ( -28.10)
>DroEre_CAF1 11077 99 + 1
----GACUUGAACUGCUCGCAUC-ACUGCUUGCUAUGUGAUCUACUGUCAAGCAGUAAACGCGCUACCAAGCUGUGUAU-UCGACUGCUUUGUACUGCUUUGUUU
----.....((((...(((.(((-((.(((((.((((((...(((((.....)))))..)))).)).))))).))).))-.)))..((........))...)))) ( -22.00)
>DroYak_CAF1 9712 104 + 1
GACCUGCUUGACCUGCUUGUAUG-ACUGCUUGCGUAUUGAUCUCGCAUUAAGCAGUAAACACGCUAUCAAGCAGGGGAUUUCGACUGCUUUGUACUGCAUUGCUU
..(((((((((...((.(((...-((((((((((.........))))...))))))..))).))..)))))))))...........((..((.....))..)).. ( -35.80)
>consensus
GAUCUACUUGAACUGCUUGCAUG_ACUGCUUGCUUAGUGAUCUAAUAUCAAGCAGUAAACACAAUAUAAAGCAGUAUAUCUCGACUGCUUUCUACUGCUUUGCUU
..............((..(((...((((((((................))))))))............(((((((........))))))).....)))...)).. (-17.53 = -17.49 +  -0.04)

alignment

secondary structure

dotplot

Window 3

Location	2,733,934 – 2,734,038
Length	104
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	77.22
Mean single sequence MFE	-32.48
Consensus MFE	-22.96
Energy contribution	-24.72
Covariance contribution	1.76
Combinations/Pair	1.32
Mean z-score	-3.39
Structure conservation index	0.71
SVM decision value	3.75
SVM RNA-class probability	0.999586
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2733934 104 - 27905053
AAGCAAAGCAGUAAAAAGCAGUCUAGAUGUACUGCUUUAUAUUGUGUUUCCUGCUUGAUAUUAGAUCACUAAGCAAGCAG-ACGCGCAAGCAGUUCACGCAGAUC
..((...((((((.(((((((((.....).)))))))).)))))).....(((((((...((((....)))).)))))))-..((....)).......))..... ( -35.40)
>DroSec_CAF1 9873 105 - 1
AAGCAAAGCAGUGGGAAGCAGUCAAGAUAUACUGCUUUAUAUUAUGUUUACUGCUUGAUAUUAGAUCACUAAGCAAGCAGUACAUGCAUGCAGCUAGAGUAGAUC
.(((...((((((.((((((((........)))))))).))))((((.(((((((((...((((....)))).)))))))))...)))))).))).......... ( -31.60)
>DroSim_CAF1 10604 105 - 1
AAGCAAAGCAGUAGGAAGCAGUCAAGAUAUACUGCUUUAUUUUGUACUUACUGCUUGAUAUUAGAUCACUAAGCAAGCAGUGCGUGCAAGCAGUUCGCGAAGAUC
..(((((((((((.....(......)...)))))))))..(((((((.(((((((((...((((....)))).))))))))).)))))))......))....... ( -35.40)
>DroEre_CAF1 11077 99 - 1
AAACAAAGCAGUACAAAGCAGUCGA-AUACACAGCUUGGUAGCGCGUUUACUGCUUGACAGUAGAUCACAUAGCAAGCAGU-GAUGCGAGCAGUUCAAGUC----
.......((..(((.((((.((...-....)).)))).))).((((((.((((((((...((.....))....))))))))-)))))).))..........---- ( -25.80)
>DroYak_CAF1 9712 104 - 1
AAGCAAUGCAGUACAAAGCAGUCGAAAUCCCCUGCUUGAUAGCGUGUUUACUGCUUAAUGCGAGAUCAAUACGCAAGCAGU-CAUACAAGCAGGUCAAGCAGGUC
......(((........)))..........((((((((((.((.(((..((((((...((((.........))))))))))-...))).))..)))))))))).. ( -34.20)
>consensus
AAGCAAAGCAGUACAAAGCAGUCAAGAUAUACUGCUUUAUAUUGUGUUUACUGCUUGAUAUUAGAUCACUAAGCAAGCAGU_CAUGCAAGCAGUUCAAGCAGAUC
.......((.....((((((((........))))))))....(((((.(((((((((...((((....)))).))))))))).))))).)).............. (-22.96 = -24.72 +   1.76)

alignment

secondary structure

dotplot

Window 4

Location	2,733,969 – 2,734,064
Length	95
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	72.62
Mean single sequence MFE	-24.43
Consensus MFE	-10.55
Energy contribution	-11.66
Covariance contribution	1.11
Combinations/Pair	1.12
Mean z-score	-1.91
Structure conservation index	0.43
SVM decision value	0.46
SVM RNA-class probability	0.746593
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2733969 95 - 27905053
ACUAUUACAGCGAACCUCGUGCAGCGAAGCAAAGCAGUAAAA--AGCAGUCUAGAUGUACUGCUUUAUAUUGUGUUUCCUGCUUGAUAUUAGAUCAC-
.(((.(((((((.....)))((((.(((((...((((((.((--(((((((.....).)))))))).))))))))))))))).)).)).))).....- ( -29.30)
>DroSec_CAF1 9909 95 - 1
ACUUUUACAGCGAACCUCGUGCAGCGAAGCAAAGCAGUGGGA--AGCAGUCAAGAUAUACUGCUUUAUAUUAUGUUUACUGCUUGAUAUUAGAUCAC-
.((((....(((.....))).....))))..(((((((((((--((((((........)))))))).........)))))))))(((.....)))..- ( -21.10)
>DroSim_CAF1 10640 95 - 1
ACUUUUACAGCGAACCUCGUGCUGCGAAGCAAAGCAGUAGGA--AGCAGUCAAGAUAUACUGCUUUAUUUUGUACUUACUGCUUGAUAUUAGAUCAC-
..(((..(((((.......)))))..)))..(((((((((((--((((((........))))))).........))))))))))(((.....)))..- ( -25.30)
>DroEre_CAF1 11108 94 - 1
ACUUUUACAGCGAACCUCGUGCUGCGAAACAAAGCAGUACAA--AGCAGUCGA-AUACACAGCUUGGUAGCGCGUUUACUGCUUGACAGUAGAUCAC-
.........(((.(((..(((((((........))))))).(--(((.((...-....)).)))))))..)))((((((((.....))))))))...- ( -27.90)
>DroYak_CAF1 9747 95 - 1
ACUUUUACAGCGAGCCUCGUGCUGCGAAGCAAUGCAGUACAA--AGCAGUCGAAAUCCCCUGCUUGAUAGCGUGUUUACUGCUUAAUGCGAGAUCAA-
...........((..(((((((((((......)))))))).(--((((((.(((......((((....))))..)))))))))).....))).))..- ( -26.20)
>DroPer_CAF1 28656 78 - 1
AGCUUUAAAGCGAACCUCGUUUC------CAAAGCAGUUCUUCAUGG---AGA-UAACACUGCUUC----------AACUGCUUGUCUGUUGAUCCAA
.(((((.(((((.....))))).------.))))).........(((---(..-(((((..((...----------....)).....))))).)))). ( -16.80)
>consensus
ACUUUUACAGCGAACCUCGUGCUGCGAAGCAAAGCAGUACAA__AGCAGUCGAGAUACACUGCUUUAUAUUGUGUUUACUGCUUGAUAUUAGAUCAC_
.........(((.....)))...........((((((((.....((((((........))))))............)))))))).............. (-10.55 = -11.66 +   1.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:36 2006