Locus 8496

Sequence ID	3L_DroMel_CAF1
Location	22,289,442 – 22,289,594
Length	152
Max. P	0.993421

overview

Window 4

Location	22,289,442 – 22,289,559
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.73
Mean single sequence MFE	-36.87
Consensus MFE	-30.49
Energy contribution	-31.49
Covariance contribution	1.00
Combinations/Pair	1.06
Mean z-score	-3.62
Structure conservation index	0.83
SVM decision value	1.37
SVM RNA-class probability	0.947334
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22289442 117 + 23771897
GUUGUUUGUUAUGGUAACGAGUGUAAAUUUCAUGGCAAAUUACCGGGAACUUUGAUAGAUUACAGGUGUAAAGCGCCUGCUAAUCAAUCGAAGCUCCCA--UGGAGAAAAAUCGAUAAA-
((.(((((((((((...............))))))))))).)).((((.(((((((.(((((((((((.....)))))).))))).))))))).))))(--(.((......)).))...- ( -40.26)
>DroSec_CAF1 47846 117 + 1
GUUGUUUGUUAUGGUAACGAGUGUAAAUUUCAUGGCAAUUUAC-GGGGACUUUGAUAGAUUACAGGUGUAAAGCGCCUGCUAAUCAAUCGAAGCUCCCA--UGGUGAAAAAUCGAUAAAA
((...(((((((((...............)))))))))...))-(((..(((((((.(((((((((((.....)))))).))))).)))))))..))).--((((.....))))...... ( -38.76)
>DroEre_CAF1 46337 118 + 1
GUUGUUUGUUAUGGUAACGAGCGUACAUUUCAUGGCAAUUUAC-GGGCACUUUGAUAGAUUACAGGUGUAAAACGCUUGCUAAUCAAUCGAAGCUGGGAGCUAGAGAAAAAUCGAUGAA-
(((((((((((...))))))))).)).((((.((((......(-.(((..((((((.(((((((((((.....)))))).))))).))))))))).)..))))))))............- ( -31.60)
>consensus
GUUGUUUGUUAUGGUAACGAGUGUAAAUUUCAUGGCAAUUUAC_GGGAACUUUGAUAGAUUACAGGUGUAAAGCGCCUGCUAAUCAAUCGAAGCUCCCA__UGGAGAAAAAUCGAUAAA_
((((.(((((((((...............)))))))))......((((.(((((((.(((((((((((.....)))))).))))).))))))).))))..............)))).... (-30.49 = -31.49 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	22,289,482 – 22,289,594
Length	112
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	82.62
Mean single sequence MFE	-39.00
Consensus MFE	-27.53
Energy contribution	-27.87
Covariance contribution	0.34
Combinations/Pair	1.15
Mean z-score	-4.38
Structure conservation index	0.71
SVM decision value	2.40
SVM RNA-class probability	0.993421
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22289482 112 + 23771897
UACCGGGAACUUUGAUAGAUUACAGGUGUAAAGCGCCUGCUAAUCAAUCGAAGCUCCCA--UGGAGAAAAAUCGAUAAA--AUAACCUUCGCUGAGCGGU----AUCACCAGCUCUCCUA
....((((.(((((((.(((((((((((.....)))))).))))).))))))).)))).--.(((((......((....--.......))((((.(.(..----..).)))))))))).. ( -40.80)
>DroSec_CAF1 47886 113 + 1
UAC-GGGGACUUUGAUAGAUUACAGGUGUAAAGCGCCUGCUAAUCAAUCGAAGCUCCCA--UGGUGAAAAAUCGAUAAAAAAAAACCUUCGCUGAGCGGU----AACACCAGCUCUCCAA
...-(((..(((((((.(((((((((((.....)))))).))))).)))))))..))).--.((((((...................))))))((((((.----....)).))))..... ( -40.61)
>DroEre_CAF1 46377 117 + 1
UAC-GGGCACUUUGAUAGAUUACAGGUGUAAAACGCUUGCUAAUCAAUCGAAGCUGGGAGCUAGAGAAAAAUCGAUGAA--AUAACCUUCGUUGAGUGGUCGGUCAACCAAAUUCUCGUA
..(-.(((..((((((.(((((((((((.....)))))).))))).))))))))).)......(((((...((((((((--......)))))))).((((......))))..)))))... ( -35.60)
>consensus
UAC_GGGAACUUUGAUAGAUUACAGGUGUAAAGCGCCUGCUAAUCAAUCGAAGCUCCCA__UGGAGAAAAAUCGAUAAA__AUAACCUUCGCUGAGCGGU____AACACCAGCUCUCCUA
....((((.(((((((.(((((((((((.....)))))).))))).))))))).))))...................................((((..............))))..... (-27.53 = -27.87 +   0.34)

alignment

secondary structure

dotplot

Window 6

Location	22,289,482 – 22,289,594
Length	112
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	82.62
Mean single sequence MFE	-33.20
Consensus MFE	-20.66
Energy contribution	-22.00
Covariance contribution	1.34
Combinations/Pair	1.06
Mean z-score	-2.17
Structure conservation index	0.62
SVM decision value	0.24
SVM RNA-class probability	0.650902
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22289482 112 - 23771897
UAGGAGAGCUGGUGAU----ACCGCUCAGCGAAGGUUAU--UUUAUCGAUUUUUCUCCA--UGGGAGCUUCGAUUGAUUAGCAGGCGCUUUACACCUGUAAUCUAUCAAAGUUCCCGGUA
..((((((((((((..----..))).))))...(((...--...)))......))))).--(((((((((.(((.(((((.((((.(.....).))))))))).))).)))))))))... ( -42.90)
>DroSec_CAF1 47886 113 - 1
UUGGAGAGCUGGUGUU----ACCGCUCAGCGAAGGUUUUUUUUUAUCGAUUUUUCACCA--UGGGAGCUUCGAUUGAUUAGCAGGCGCUUUACACCUGUAAUCUAUCAAAGUCCCC-GUA
..((.((((.((....----.))))))(((....)))...................))(--((((..(((.(((.(((((.((((.(.....).))))))))).))).)))..)))-)). ( -35.20)
>DroEre_CAF1 46377 117 - 1
UACGAGAAUUUGGUUGACCGACCACUCAACGAAGGUUAU--UUCAUCGAUUUUUCUCUAGCUCCCAGCUUCGAUUGAUUAGCAAGCGUUUUACACCUGUAAUCUAUCAAAGUGCCC-GUA
((((.(..((((((.((..........((((...((((.--((.(((((.........(((.....)))))))).)).))))...))))((((....)))))).))))))...).)-))) ( -21.50)
>consensus
UAGGAGAGCUGGUGUU____ACCGCUCAGCGAAGGUUAU__UUUAUCGAUUUUUCUCCA__UGGGAGCUUCGAUUGAUUAGCAGGCGCUUUACACCUGUAAUCUAUCAAAGUCCCC_GUA
...((((((.((.........))))))(((....)))........))...............(((.((((.(((.(((((.((((.(.....).))))))))).))).)))).))).... (-20.66 = -22.00 +   1.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:05 2006